WO2017009253A1 - Methods and means for increasing stress tolerance and biomass in plants - Google Patents

Abstract

The invention provides methods for producing a plant with increased stress-tolerance and yield, as well as chimeric genes for use according to the methods and plant comprising such chimeric genes.

Description

Methods and means for increasing stress tolerance and biomass in plants

Field of the invention

[1 ] The present invention relates generally to the field of plant molecular biology and concerns a method for improving plant tolerance to stress conditions. More specifically, the present invention concerns a method for increasing stress tolerance and growth and for reducing ABA sensitivity, comprising increasing the expression and/or activity of a truncated H ISTONE DEACETYLASE COMPLEX 1 (HDC1 ) protein in a plant. The present invention also concerns plants having an increased expression and/or activity of such a truncated HDC1 , which plants have inter alia an increased stress tolerance, biomass, yield and reduced ABA sensitivity relative to corresponding wild-type plants. The invention also provides chimeric genes, nucleic acids and polypeptides encoding such truncated HDC1 proteins.

Background

[2] Regulation of gene transcription underpins plant development and dynamic responses to the environment. Transcription occurs in the context of chromatin, a highly condensed structure in which the DNA is wrapped around nucleosomes comprised of histone octamers comprised of histones H2A/B, H3 and H4, and further stabilised by linker histone H1 . Alteration of chromatin structure plays an important part in transcriptional regulation and is achieved through multi-protein complexes that recognize and instigate biochemical modifications of the DNA and/or the histones (Pfluger and Wagner, 2007). For example, binding of repressors to so-called co-repressors recruits histone deacetylases (HDAs) to the gene region. The HDAs in turn interact with histone binding proteins. Removal of acetyl groups from lysine residues of the core histones leads to chromatin compaction and inhibition of transcription (Kouzarides, 2007; Roudier et al., 2009). Specific recruitment at both 'ends' of the repressive protein complex generates a double lock between DNA and the nucleosome: the repressors recognize certain DNA-motifs in the gene promoters and the histone-binding proteins recognize certain histone residues and their modifications (histone 'reading'). A minimal HDAC complex therefore needs to combine at least three protein functions; repressor-binding, histone-binding and catalytic activity. Biochemical studies in yeast and in animal systems have provided evidence for large multi-protein complexes linking a co-repressor and a histone deacetylase with several histone-binding proteins and a range of associated proteins of mostly unknown functions (Yang and Seto, 2008).

[3] We recently identified the Histone Deacetylation Complex 1 (HDC1 ) protein as an important component of the plant HDAC machinery (Perrella et al., 2013). Knockout of HDC1 was found to promote histone acetylation and gene expression, and to cause a range of phenotypes, most notably hypersensitivity to abscisic acid (ABA) during germination, inhibition of leaf growth and delayed flowering (Perrella et al., 2013). Conversely, over-expression of HDC1 desensitized the plants to ABA and increased shoot biomass even in water-limited conditions. Thus, HDC1 appeared to be a rate- limiting factor of HDAC. Pulldown and BiFC assays showed that HDC1 directly interacts with the histone deacetylases HDA6 and HDA19. Both HDAs have previously been reported to function in germination (Tanaka et al., 2008; Yu et al., 201 1 ), flowering (Tanaka et al., 2008; Yu et al., 201 1 ) and ABA-mediated responses to drought or salt (Chen et al., 2010; Chen and Wu, 2010). The phenotypes of HDC1 mutants can therefore be explained by HDC1 acting through these HDAs, but the mechanism by which HDC1 controls their apparent activity remains to be elucidated.

[4] HDC1 is a ubiquitously expressed single-copy gene in Arabidopsis, and HDC1 homologs are present across the plant kingdom as single or low-copy genes. The HDC1 sequence contains no known functional or structural motifs. Sequence conservation is high in a 315-amino acid stretch within the C-terminal half of the protein, which aligns to shorter proteins in algae and fungi, including the yeast Regulator of Transcription 3 (Rxt3; see dendrogram and sequence alignment in Perrella et al., 2013). Rxt3 co-elutes with the large Rpd3 HDAC-complex in yeast but its function has remained unclear (Carrozza et al., 2005a; Carrozza et al., 2005b). Sequence analysis with JPred (Drozdetskiy et al., 2015) predicts very little secondary structure for HDC1 , particularly in the N -terminal part. Intrinsically disordered proteins often act as flexible adaptors for multiple protein interactions (Pazos et al., 2013). It is therefore possible that HDC1 enables multiple protein interactions in HDAC complexes.

[5] WO04/035798 discloses a method for altering characteristics of a plant and describes the identification of genes that are upregulated or downregulated in transgenic plants overexpressing E2Fa/DPa and the use of such sequences to alter plant characteristics.

[6] W014/1 18123 discloses methods and means for producing a plant with increased stress tolerance and yield, as well as chimeric gens for use according to the methods and plants comprising such chimeric genes.

[7] The present invention provides a contribution over the art by disclosing truncated HDC1 sequences that can be used to modulate plant stress response, ABA-sensitivity and growth.

Summary of the invention

[8] In a first embodiment, the invention provides a chimeric gene comprising the following operably linked fragments:

1 . A plant-expressible promoter (e.g. a constitutive promoter).

2. A nucleic acid encoding a functional fragment of an HDC1 protein.

3. Optionally, a 3' end region involved in transcription termination and polyadenylation functional in plants. [9] Said HDC1 protein can have at least at least 70%, at least 75%, at least 80% , at least 85%, at least 90%, at least 95%, at least 96%, at least 97% , at least 98%, at least 99% or 100% sequence identity to any one of SEQ ID SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 41. Preferably, said HDC1 protein has at least 90% sequence identity to SEQ ID NO. 6. Accordingly, said functional fragment of an HDC1 protein can have at least at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity over its entire length to the corresponding fragment of any one of SEQ ID SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 41 .

[10] A functional fragment of an HDC1 protein can correspond to a maximum of about 95% of the length of the full length protein such as about 90%, 85%, 80% , 75%, 70%, 65% , 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, or even less of the length of the full length HDC1 protein. In a specific embodiment the functional fragment can be about 35% of the length of the full length HDC1 protein.

[1 1 ] The nucleic acid encoding the functional fragment of an HDC1 protein can be codon optimized for expression in a particular target species. For example, it can be codon optimized for wheat, e.g. HDC1 can be encoded by the nucleotide sequence of SEQ ID NO. 3 and the functional fragment can hence be encoded by the corresponding fragment of SEQ ID NO.3.

[12] The functional fragment of an HDC1 protein can comprise a PF08642 motif, said PF08643 motif corresponding to amino acids 602-650 of SEQ ID NO. 6.

[13] The functional fragment of an HDC1 protein can also comprises at least one nuclear localization sequence (NLS), such as corresponding to amino acids 359-375 and 480496 of SEQ ID NO. 6, preferably at least amino acids 480496.

[14] The functional fragment of an HDC1 protein can also comprise an RXT3-like domain, said RXT3L domain corresponding to amino acids 449-764 of SEQ ID NO. 6.

[15] In one embodiment, the functional fragment of an HDC1 protein consists of an RXT3-like domain. For example, said RXT3-like domain can have an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90% , at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity to amino acids 449-764 of SEQ ID NO. 6 or to corresponding fragments in other HDC1 proteins. [16] The functional fragment of an HDC1 protein can even be shorter than the RXT3-like domain, i.e. a truncated RXT3L domain. Such a functional fragment of an RXT3L may still contain an NLS and/or a PF08642 motif.

[17] Also provided by the invention are a plant, plant part, plant organ, plant cell or seed comprising the chimeric gene as described above. This can be e.g. oilseed rape, lettuce, tobacco, cotton, corn, rice, wheat, vegetable plants, carrot, cucumber, leek, pea, melon, potato, tomato, sorghum, rye, oat, sugarcane, peanut, flax, bean, sugar beets, soya, sunflower, ornamental plants.

[18] The invention further provides a method for producing a plant, plant part, plant organ or plant cell with increased tolerance to stress conditions, or with reduced ABA sensitivity, or with increased biomass or yield or growth rate, comprising the step of expressing in said plant cell, plant part, plant organ or plant a chimeric gene as described above. Such a plant can be further crossed with another plant to obtain a progeny plant also expressing said chimeric gene.

[19] Further described are an isolated polypeptide encoding a functional fragment of an HDC1 protein as described above or an isolated nucleic acid encoding said polypeptide.

[20] The invention further describes the use of such an isolated polypeptide or of such an isolated nucleic acid sequence or of a chimeric gene as described above to produce a plant, plant part, plant organ or plant cell with increased tolerance to stress conditions, or with reduced ABA sensitivity, or with increased biomass or yield or growth rate.

Figure legends

[21 ] Figure 1 : HDC1 directly interacts with several different proteins, and the truncated RXT3L fully maintains the capacity to interact with H3-binding protein SHL1 and with H1 linker histone variants.

A: The 2-in-1 vector for ratiometric BiFC contains N- and C-terminal halves of YFP (nYFP, cYFP) and full-length RFP. B: Representative YFP signals in nuclei of tobacco epidermis cells transformed with the indicated protein pairs. Bar is 10 μίτι. C: Schematic representation of the truncation construct RXT3L representing a conserved (blue) C-terminal part of full-length HDC1. As for full-length HDC1 , GFP-fusion protein of RXT3L shows nuclear localization. Bar is 50 μίη.

D, F: YFP/RFP signal ratio determined in tobacco leaf cells after transient transformation with 2-in-1 BIFC vector containing full length HDC1 (black bars) or RXT3L (grey bars) together with other proteins. Tested interactors include histone deacetylases HDA6 and 19, Sin3-like co-repressors SNL2 and 3, Sin3-associated protein SAP18, H3-binding proteins SHL1 , ING2 and MSI1 (D), as well as H3 and H1 variants H1.1 , H1.2 and H1.3 (F). Bars are means ± SE (n > 30 cells from three independently transformed plants). Black asterisks (for full-length HDC1 ) indicate a significant (p < 0.05) difference to the signal obtained with SNL3 or H3 (negative controls). Grey asterisks (for RXT3L) indicate significant (p < 0.05) difference to the signal obtained with full-length HDC1. The two bars on the right in F are signals obtained for cells transformed with H1.2 and HDA6 or HDA19. E, G: Western blots showing in-vivo pulldown of HDC1 in nuclei- enriched protein samples from wild-type (WT) or HDC1 knockout plants (hdd-1) using GST-SHL1 (B) or GST-H1 variants (D) as bait. The upper panels show the membrane probed with HDC1 antibody (aHDC1 ). The bottom panels show the membranes re-probed with GST antibody (aGST). As labelled, lanes contain HDC1 only (Input, positive control), pull-down with GST-SHL1 or GST-H1 , and pull-down with GST alone (negative control).

[22] Figure 2: RXT3L complements germination and growth phenotypes of hdd but only partially recovers flowering and is unable to restore petiole extension.

Phenotypes for Arabidopsis thaliana wildtype (wt; black), HDC1 -knockout line (hdd-1, white), two independent lines expressing RXT3L in wt background (RXT3Lwt1 ,2) and two independent lines expressing RXT3L in hdd-1 background (RXT3L hdc1 -1 1 ,2). Significant differences (p < 0.05) for Rxt3L-expressing lines against their respective background are indicated with black asterisks for wildtype, and with white asterisks for hdd-1. A: Germination rates on agar containing different concentrations of ABA and NaCI. Bars are means ± SE of at least three plates containing 50 seeds each, hdd- 1 was significantly different from wildtype in all conditions other than control (p < 0.05). From left to right: RXT3Lwt1 , RXT3Lwt2, wt, RXT3L hdd -1 1 , RXT3L hdd -1 2, hdd -1 . B: Shoot fresh weight of plants grown in short days at the indicated days after germination. Bars are means ± SE of three plants harvested each day. hdd-1 was significantly different from wildtype from day 26 onwards (p < 0.05). Left panel from left to right: RXT3Lwt1 , RXT3Lwt2, wt. Right panel from left to right: wt, RXT3L hdd -1 1 , RXT3L hdd -1 2, hdd -1. C: Plant age and number of rosette leaves at bolting (1 cm stem length). Plants were grown in long days. Bars are means ± SE of 15 plants, hdd-1 was significantly different from wildtype for both parameters (p < 0.05). From left to right: RXT3Lwt1 , RXT3Lwt2, wt, RXT3L hdd -1 1 , RXT3L hdd -1 2, hdd -1. D: Petiole length of true rosette leaves 1 to 6. Plants were grown in short days. Bars show average petiole length of leaves from three plants ± SE. hdd-1 was significantly different from wildtype for leaves 3-6 (p < 0.05). Insert: Picture of hdd-1 and wild type plants (3-weeks old). From left to right: wt, RXT3L hdd -1 1 , RXT3L hdd - 1 2, hdc1 -1.

[23] Figure 3: Subcellular localisation of GFP-fusion protein expressed in tobacco epidermal cells.

Left: A. thaliana RXT3L, right: Saccharomyces cerevisiae RXT3. Bar = 50 μΜ.

[24] Figure 4: Interaction profiles of different HDAC complex proteins.

YFP/RFP signal ratio in tobacco leaf cells after transient transformation with protein 1 -protein 2 construct in the vector shown in Figure 1A. Bars are means ± SE (n > 30 cells from three independently transformed plants).

[25] Figure 5: HDC1 interacts with H1.2 and SHL1 in leaf tissue from A. thaliana wildtype plants.

Relative intensities of HDC1 and GST bands in Western blots of pulldown assays of HDC1 in nuclei-enriched protein samples from wild-type (WT) or HDC1 knockout plants (hdd-1) using GST-SHL1 (A) or GST-H1 variants (B) as baits. Bands intensities were quantified using Image G. Bars are means of at least three independent pulldown experiments. Significant differences of band ratios obtained with a given bait compared to those obtained with GST alone as a bait are indicated with asterisks. *: p<0.05, (*): p = 0.06.

[26] Figure 6: Truncated versions of H1.2 and SHL1 are not sufficient for binding HDC1.

Western blots showing pulldown of HDC1 in nuclei-enriched protein samples from leaves of wildtype A. thaliana plants. The following GST-fusions were used as baits (from left to right): full-length H1.2 ([positive control), N-terminal (N-ter) part of H1.2, globular domain (GD) of H1.2, C-terminal (C-ter) part of H1 .2, full-length SHL1 (positive control), bromo- adjacent homology (BAH) domain of SHL1 , and GST alone (negative control). The upper panel shows the membrane probed with HDC1 antibody (aHDC1). The bottom panel shows the membranes re-probed with GST antibody (aGST).

[27] Figure 7: HDC1 interacts with H1 .2 and SHL1 in leaf tissue from A. thaliana wildtype plants subjected to salt stress.

Western blots showing pulldown of HDC1 in nuclei-enriched protein samples from A. thaliana wildtype (WT) or HDC1 knockout plants {hdd-1) after salt treatment (150 mM NaCI for 24h) using GST-H1.2, GST-SHL1 and GST alone as bait. The upper panel shows the membrane probed with HDC1 antibody (aHDC1 ). The bottom panel shows the membranes re-probed with GST antibody (aGST). As labelled, lane contains HDC1 only (Input, positive control), pull-down with GST- HI .2 or GST-SHL1 , and pull-down with GST alone (negative control).

[28] Figure 8: Reciprocal pulldown of Rxt3L/SHL1 and Rxt3L/H1.2.

A: Western blots of recombinant H1 .2-His and His-SHL1 after pulldown with recombinant GST-RXT3L (second lanes). The first lanes contain positive controls (recombinant H1.2-His and His-SHL1), and the last lanes contain a negative control (pull down with GST alone). The upper panel shows the membrane probed with histidine antibody (aHis). The bottom panels show the membrane re-probed with GST antibody (aGST). B: Western blots of recombinant His-RXT3L after pulldown with recombinant GST-H 1 .2 (second lane) and GST-SHL1 (third lane). The first lane contains a positive control (recombinant His-RXT3L) and the last lane contains a negative control (pull down with GST alone). The upper panel shows the membrane probed with histidine antibody (aHis). The bottom panels show the membrane re-probed with GST antibody (aGST).

[29] Figure 9: Transcript levels of the RXT3-like part of HDC1 in two overexpressing lines (wildtype background 1 and 2), wild type control, two complementation lines (hdd-1 background 1 and 2) and hdc1 -1 control, depicted from left to right. Note that the fragment is not only amplified from the Rxt3L transgene but also from full-length HDC1 in wildtype background (black line) and from an out-of-frame partial mRNA in the hdd-1 plants (dotted line).

[30] Figure 10: Visual summary of protein interactions assayed in this study. [31 ] Figure 1 1 : Multiple sequence alignment of HDC1 sequences (SEQ ID NOs) indicating the RXT3L domain (underlined), the 2 NLSs (bold) and the PF08642 motif (grey).

[32] Figure 12: Primer sequences used for genotyping and cloning.

Detailed description

[33] Histone deacetylation (HDAC) is an important process in the transcriptional regulation that underpins plant development and responses to the environment. Histone deacetylase complex (HDC) 1 from Arabidopsis thaliana was previously identified as a rate-limiting factor of HDAC, which regulates a number of downstream processes in a quantitative manner, including germination, vegetative growth and flowering (W014/118123; Perrella at al., 2013 both incorporated by reference in its entirety). The N-terminal half of HDC1 is specific to plants and shows a high degree of sequence variability, while the more conserved C-terminal half is similar to Rxt3 proteins in algae and fungi. HDC1/Rxt3 proteins do not contain any known functional domains in their sequence and their molecular role is unknown. Here we determined the ability of several putative members of plant HDAC complexes to directly interact with HDC1 and with each other. We show that HDC1 and the histone-binding protein SHL1 provide a potential hub for interactions between deacetylases, histone, histone-binding proteins and co-repressor associated proteins. It was found that a truncated, Rxt3- like version of HDC1 loses some protein binding capacity and developmental functions, but surprisingly maintains the ability to interact with SHL1 and physiological functions, for example plants overexpressing this truncated protein when overexpressed retained the stress tolerance, biomass increase and ABA-insensitivity phenotype of the full length protein.

[34] Thus in a first embodiment, the invention provides a chimeric gene comprising the following operably linked fragments:

i. A plant-expressible promoter

ii. A nucleic acid encoding a functional fragment of an HDC1 protein

iii. Optionally, a 3' end region involved in transcription termination and polyadenylation functional in plants

[35] Unless indicated otherwise, the embodiments described below for the chimeric gene disclosed herein are also applicable to respective embodiments of other aspects disclosed herein.

As used herein "an HDC1 protein" is a ubiquitously expressed nuclear proteins of about 900 amino acids of which homologues are present across the plant kingdom, and of which the C-terminal half share sequence identity to the Rxt3- type proteins in green algae, protozoa and fungi, such as the 294-aa yeast protein Rxt3 (SEQ ID NO 4). HDC1 has furthermore been shown to be required for histone de-acetylation and to interact with various histone deacetylases (HDACs). Overexpression of HDC1 leads to increased stress tolerance, biomass and ABA insensitivity (Perrella et al., 2013, W014/1 18123). HDC1 has the ability to directly interact with several different types of proteins, including histone deacetylases, histone-binding proteins and associated proteins of unknown function. Particular strong interaction was found with the H3-binding protein SHL1 , which itself showed a capacity to interact with multiple other proteins. Neither HDC1 nor SHL1 directly interacted with the co-repressor SNL3, which only made close contact with HDA19. The interaction profile suggests that HDC1 associates with the 'histone-binding end' of the complex (Figure 10).

[36] In addition, HDC1 has the capacity to bind H 1 . H 1 is positioned at the edge of nucleosomes, binds to both the nucleosome core and the linker DNA, and correlates with more condensed, less accessible and transcriptionally silent DNA (Ascenzi and Gantt, 1999a). In Arabidopsis thaliana H 1 is encoded by three genes (Ascenzi and Gantt, 1999a; Wierzbicki and Jerzmanowski, 2005). H 1.1 and H 1 .2 share 85% identity at the DNA level in the nuclear domain, indicating they might be result of gene duplication. H1 .3 is more divergent and it is induced by low light and drought (Ascenzi and Gantt, 1999b; Rutowicz et al., 2015). At the phenotypic level, triple knock-out/down of the H 1 genes leads to developmental abnormalities with a reduction of plant size, delayed flowering and embryo lethality (Jerzmanowski et al., 2000). Arabidopsis H i s have been found to directly interact with the DNA glycosylase DEMETER which regulates genomic imprinting by demethylating MEDEA promoter in the endosperm (Rea et al., 2012). Furthermore, loss of H1 alters DNA methylation patterns with different effects on euchromatin and heterochromatin (Wierzbicki and Jerzmanowski, 2005; Zemach et al., 2013).). The exact role of H 1 in DNA modification remains to be elucidated but it has been proposed that it restricts the access of the DNA methyltransferase to the nucleosome (Zemach et al., 2013). The block imposed by H 1 proteins, mainly within long transposable elements, was overcome by the Swi/Snf chromatin remodeller Decrease of DNA Methylation (DDM) 1 , and it was suggested that DDM1 facilitates access of DNA- methylases by removing H 1 from the DNA.

[37] Based on the above, an interaction between HDC1 and H 1 could be functionally interpreted in two ways. In the first hypothesis, HDC1 establishes a physical link between HDAC complexes and H 1 thereby enhancing chromatin condensation and repression of the target genes. In the second hypothesis, HDC1 removes H1 , similar to DDM, thereby facilitating access of HDAs to the core histone tails. Both functions would benefit from a flexible structure of HDC1 .

[38] HDC1 proteins include for example the plant HDC1 proteins as represented by SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, and SEQ ID NO. 41 . This also includes functional variants thereof, e.g. proteins having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96% , at least 97%, at least 98%, or at least 99% sequence identity to any of the amino acid sequences cited above that encode a functional HDC1 protein. [39] HDC1 proteins as described above can be can be encoded by the nucleic acid sequences of any one of SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9, SEQ ID NO. 1 1 , SEQ ID NO. 13, SEQ ID NO. 15, SEQ ID NO. 17, SEQ ID NO. 19, SEQ ID NO. 21 , SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 27, SEQ ID NO. 29, SEQ ID NO. 31 , SEQ ID NO. 33, SEQ ID NO. 35, SEQ ID NO. 37, SEQ ID NO. 39. or by nucleic acid sequences having at least 70%, at least 75%, at least 80%, at least 85% , at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to any of the amino acid sequences cited, or by degenerate coding sequences.

[40] The "sequence identity" of two related nucleotide or amino acid sequences, expressed as a percentage, refers to the number of positions in the two optimally aligned sequences which have identical residues (x100) divided by the number of positions compared. A gap, i.e., a position in an alignment where a residue is present in one sequence but not in the other, is regarded as a position with non-identical residues. The "optimal alignment" of two sequences is found by aligning the two sequences over the entire length according to the Needleman and Wunsch global alignment algorithm (Needleman and Wunsch, 1970, J Mol Biol 48(3):443-53) in The European Molecular Biology Open Software Suite (EMBOSS, Rice et al. , 2000, Trends in Genetics 16(6): 276—277; see e.g. http://www.ebi.ac.uk/emboss/align/index.html) using default settings (gap opening penalty = 10 (for nucleotides) / 10 (for proteins) and gap extension penalty = 0.5 (for nucleotides) / 0.5 (for proteins)). For nucleotides the default scoring matrix used is EDNAFULL and for proteins the default scoring matrix is EBLOSUM62.

[41 ] Based on the available sequences as disclosed herein, the skilled person can isolate further HDC1 sequences. Homologous nucleotide sequence encoding further HDC1 proteins may be identified and isolated by hybridization under stringent conditions using as probes identified nucleotide sequences.

[42] "High stringency conditions" can be provided, for example, by hybridization at 65°C in an aqueous solution containing 6x SSC (20x SSC contains 3.0 M NaCI, 0.3 M Na-citrate, pH 7.0), 5x Denhardt's (100X Denhardt's contains 2% Ficoll, 2% Polyvinyl pyrollidone, 2% Bovine Serum Albumin), 0.5% sodium dodecyl sulphate (SDS), and 20 μg/ml denaturated carrier DNA (single-stranded fish sperm DNA, with an average length of 120 - 3000 nucleotides) as non- specific competitor. Following hybridization, high stringency washing may be done in several steps, with a final wash (about 30 min) at the hybridization temperature in 0.2-0.1 χ SSC, 0.1 % SDS.

[43] "Moderate stringency conditions" refers to conditions equivalent to hybridization in the above described solution but at about 60-62°C. Moderate stringency washing may be done at the hybridization temperature in 1 x SSC, 0.1 % SDS.

[44] "Low stringency" refers to conditions equivalent to hybridization in the above described solution at about 50- 52°C. Low stringency washing may be done at the hybridization temperature in 2x SSC, 0.1 % SDS. See also Sambrook et al. (1989) and Sambrook and Russell (2001 ). [45] Other sequences encoding HDC1 proteins may also be obtained by DNA amplification using oligonucleotides specific for genes encoding HDC1 as primers, such as but not limited to oligonucleotides comprising or consisting of about 20 to about 50 consecutive nucleotides from the known nucleotide sequences or their complement.

[46] Further HDC1 sequences may also be identified based on sequence comparisons with known sequences (e.g. based on percentages sequence identity over the entire sequence or over specific domains), for example using bioinformatics tools such a blast algorithm or by orthology inference e.g. using the OMA ("Orthologous MAtrix") browser.

[47] As used herein "a functional fragment of an HDC1 protein", relates to a truncated version of the full length HDC1 protein as described above, such as the full length proteins represented by any one of SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, and SEQ ID NO. 41. These full length HDC1 proteins are also referred to as "wild type" HDC! proteins, i.e. HDC1 proteins as they are typically found in nature. A "a functional fragment of an HDC1 protein" is thus shorter than the full length (i.e. wild type) protein, for example one or more amino acids at the N-terminal end and/or the C-terminal end have been deleted, but it retains most functionalities of the full length (wild type) protein. For example, a functional fragment of an HDC1 protein is a truncated HDC1 protein that when expressed in a plant, plant part, plant organ or plant cell retains the ability to increase tolerance to stress conditions and/or the ability to increase biomass, yield or growth rate, and/or the ability to reduce ABA sensitivity of said plant, plant part, plant organ or plant cell. A functional fragment of an HDC1 protein can also be a truncated HDC1 protein that retains the ability to interact with the histone binding protein SHL1. It can also be a truncated HDC1 protein that retains the ability to decrease acetylation level of histone H3K9/14. It can also be a truncated HDC1 protein that retains the ability to interact with the histone H1 variants. It can also be a truncated HDC1 protein that retains the ability to interact with MSI1. It can also be a a truncated HDC1 protein that retains a combination or all of these abilities. The ability of such a truncated HDC1 protein to achieve any of such effects can be performed as described further below. To facilitate expression, such a truncated HDC1 sequence can be preceded by a methionine.

[48] A fragment or a truncation can be a deletion of at least 1 amino acids, e.g. at least 5 amino acids, at least 10 amino acids, at least 20 amino acids, at least 30 amino acids, at least 40 amino acids, at least 50 amino acids, at least 75 amino acids, at least 100 amino acids, at least 150 amino acids, at least 200 amino acids, at least 250 amino acids, at least 300 amino acids, at least 350 amino acids, at least 400 amino acids, at least 450 amino acids, at least 500 amino acids, at least 500 amino acids, at least 550 amino acids, at least 600 amino acids, at least 650 amino acids, at least 700 amino acids, at least 750 amino acids or even more with respect to the full length HDC1 protein. The deletion can be on the N-terminal end or on the C-terminal end or both. Preferably, such a deletion is on the N-terminal end or the deletion on the N-terminal end is larger than on the C-terminal end. [49] Thus, in terms of length "a functional fragment of an HDC1 protein" can be a fragment of or a truncated HCD1 protein of about 900, about 800, about 700, about 500, about 400, about 300, about 250, about 200 amino acids, about 150 amino acids in length or even less. In terms of percentage, "a functional fragment of an H DC1 protein" can be a fragment corresponding to about 95%, 90% , 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, or even less of the length of the full lengt HDC1 protein.

[50] Referring to the above cited amino acid sequences, "a functional fragment of an HDC1 protein" can be a truncated HDC1 protein that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity over its length (which is shorter than the full length protein) to the corresponding part of the sequence of the full length protein, such as to the corresponding fragment of any one of SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, and SEQ ID NO. 41 , as can be determined by alignment. For example, "a functional fragment of an HDC1 protein" can have at least 70%, at least 75% , at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity over a continuous 95%, 90%, 80%, 70%, 60% 50%, 40%, 30%, 25%, 20% or even less of the full length HDC1 protein sequence.

[51 ] In one embodiment, the functional fragment of the HDC1 protein comprises the conserved PF08642 motif. In the Arabidopsis thaliana HDC1 of SEQ ID NO. 6, amino acids 602-650 represent the PF08642 motif. Corresponding domains in other HDC1 sequences can be identified by determining the optimal alignment with SEQ ID NO. 6 (see e.g. figure 1 1 ).

[52] In one embodiment, the functional fragment of the HDC1 protein comprises at least one nuclear localization sequence (NLS). In the Arabidopsis thaliana HDC1 of SEQ ID NO. 6, contains 2 NLSs, i.e. amino acids 359-375 and 480496, of which at least the first was shown to be sufficient for nuclear localization. Preferably, the functional fragment of the HDC1 protein thus comprises an NLS corresponding to amino acids 480496 of SEQ ID NO. 6. Corresponding domains in other HDC1 sequences can be identified by determining the optimal alignment with SEQ ID NO. 6 (see e.g. figure 1 1 ). These include for example SEQ ID NO. 8 from amino acid 478 to 494, SEQ ID NO. 10 from amino acid 377 to 393, SEQ ID NO. 12 from amino acid 383 to 401 , SEQ ID NO. 14 from amino acid 374 to 390, SEQ ID NO. 18 from amino acid 373 to 389, SEQ ID NO. 20 from amino acid 362 to 379, SEQ ID NO. 22 from amino acid 362 to 379, SEQ ID NO. 24 from amino acid 358 to 373, SEQ ID NO. 26 from amino acid 364 to 379, SEQ ID NO. 28 from amino acid 365 to 380, SEQ ID NO. 30 from amino acid 372 to 388, SEQ ID NO. 32 from amino acid 367 to 383, SEQ ID NO. 34 from amino acid 373 to 389, SEQ ID NO. 36 from amino acid 365 to 381 , SEQ ID NO. 38 from amino acid 367 to 382, SEQ ID NO. 40 from amino acid 370 to 386, SEQ ID NO. 41 from amino acid 362 to 379. [53] In a further embodiment, the functional fragment of an HDC1 protein comprises an RXT3-like (RXT3L) domain, i.e. the domain of the HDC1 protein corresponding to the yeast RXT3 protein. In the Arabidopsis thaliana HDC1 of SEQ ID NO. 6, amino acids 449-764 represent the RXT3L) domain. Corresponding domains in other HDC1 sequences can be identified by determining the optimal alignment with SEQ ID NO. 6 (see e.g. Figure 1 1 ). These include for example amino SEQ ID NO. 8 from amino acid 447 to 764, SEQ ID NO. 10 from amino acid 346 to 662, SEQ ID NO. 12 from amino acid 354 to 672, SEQ ID NO. 14 from amino acid 343 to 654, SEQ ID NO. 18 from amino acid 342 to 662, SEQ ID NO. 20 from amino acid 334 to 644, SEQ ID NO. 22 from amino acid 334 to 644, SEQ ID NO. 24 from amino acid 330 to 639, SEQ ID NO. 26 from amino acid 335 to 644, SEQ ID NO. 28 from amino acid 335 to 645, SEQ ID NO. 30 from amino acid 341 to 659, SEQ ID NO. 32 from amino acid 336 to 652, SEQ ID NO. 34 from amino acid 342 to 660, SEQ ID NO. 36 from amino acid 338 to 655, SEQ ID NO. 38 from amino acid 337 to 647, SEQ ID NO. 40 from amino acid 339 to 654, SEQ ID NO. 41 from amino acid 334 to 644. This also includes functional variants thereof, e.g. RXT3L domains having at least 70%, at least 75%, at least 80% , at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to any of the amino acid sequence fragments cited above.

[54] In an even further embodiment, the functional fragment of an HDC1 protein consists of an RXTL3 domain, corresponding to amino acids 449-764 of the full length HDC1 protein of SEQ ID NO. 6 or any of the corresponding fragments and functional variants thereof as described above. Again, to facilitate expression, such a sequence can be preceded by a methionine as was for example done in the amino acid sequence of SEQ ID NO. 2.

[55] The functional fragment of an HDC1 protein can even be smaller than the RXT3L domain, such as a functional fragment of an RXT3L domain, i.e. a truncated RXT3L domain wherein one or more amino acids have been deleted at the N-terminal and/or C-terminal end of the RXT3L domain. For example, a functional fragment of an RXT3L domain is a truncated RXT3L domain that when expressed in a plant, plant part, plant organ or plant cell retains the ability to increase tolerance to stress conditions and/or the ability to increase biomass, yield or growth rate, and/or the ability to reduce ABA sensitivity of said plant, plant part, plant organ or plant cell. A functional fragment of an RXT3L domain can also be a truncated HDC1 protein that retains the ability to interact with the histone binding protein SHL1 . It can also be a truncated RXT3L domain that retains the ability to decrease acetylation level of histone H3K9/14. It can also be a truncated RXT3L domain that retains the ability to interact with the histone H 1 variants. It can also be a truncated RXT3L domain that retains the ability to interact with MSI1 . It can also be a truncated RXT3L domain that retains a combination or all of these abilities. Preferably, such a truncated RXT3L domain comprises an NLS or a PF08642 motif as described above, or both. This includes truncated RXT3L domains having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity over their entire length to any of the corresponding fragments of the RXT3L amino acid sequence fragments cited above.

[56] A chimeric gene, as used herein, refers to a gene that is made up of heterologous elements that are operably linked to enable expression of the gene, whereby that combination is not normally found in nature, i.e. it is non-naturally occurring. As such, the term "heterologous" refers to the relationship between two or more nucleic acid or protein sequences that are derived from different sources. For example, a promoter is heterologous with respect to an operably linked nucleic acid sequence, such as a coding sequence, if such a combination is not normally found in nature. In addition, a particular sequence may be "heterologous" with respect to a cell or organism into which it is inserted (i.e. does not naturally occur in that particular cell or organism).

[57] The expression "operably linked" means that said elements of the chimeric gene are linked to one another in such a way that their function is coordinated and allows expression of the coding sequence, i.e. they are functionally linked. By way of example, a promoter is functionally linked to another nucleotide sequence when it is capable of ensuring transcription and ultimately expression of said other nucleotide sequence. Two proteins encoding nucleotide sequences, e.g. a transit peptide encoding nucleic acid sequence and a nucleic acid sequence encoding an HDC1 , are functionally or operably linked to each other if they are connected in such a way that a fusion protein of first and second protein or polypeptide can be formed.

[58] As the skilled person will be well aware, various promoters may be used to promote the transcription of the nucleic acid of the invention. Such promoters include for example constitutive promoters, inducible promoters (e.g. stress-inducible promoters, drought-inducible promoters, hormone-inducible promoters, chemical-inducible promoters, etc.), tissue-specific promoters, developmental^ regulated promoters and the like.

[59] Thus, a plant expressible promoter can be a constitutive promoter, i.e. a promoter capable of directing high levels of expression in most cell types (in a spatio-temporal independent manner). Examples of plant expressible constitutive promoters include promoters of bacterial origin, such as the octopine synthase (OCS) and nopaline synthase (NOS) promoters from Agrobacterium, but also promoters of viral origin, such as that of the cauliflower mosaic virus (CaMV) 35S transcript (Hapster et al., 1988, Mol. Gen. Genet. 212: 182-190) or 19S RNAs genes (Odell et al., 1985, Nature. 6;313(6005):810-2; U.S. Pat. No. 5,352,605; WO 84/02913; Benfey et al., 1989, EMBO J. 8:2195-2202), the enhanced 2x35S promoter (Kay at al., 1987, Science 236: 1299-1302; Datla et al. (1993), Plant Sci 94:139-149) promoters of the cassava vein mosaic virus (CsVMV; WO 97/48819, US 7,053,205), 2xCsVMV (WO2004/053135) the circovirus (AU 689 31 1 ) promoter, the sugarcane bacilliform badnavirus (ScBV) promoter (Samac et al., 2004, Transgenic Res. 13(4):349-61 ), the figwort mosaic virus (FMV) promoter (Sanger et al., 1990, Plant Mol Biol. 14(3):433- 43), the subterranean clover virus promoter No 4 or No 7 (WO 96/06932) and the enhanced 35S promoter as described in US 5,164,316, US 5,196,525, US 5,322,938, US 5,359,142 and US 5,424,200. Among the promoters of plant origin, mention will be made of the promoters of the plant ribulose-biscarboxylase/oxygenase (Rubisco) small subunit promoter (US 4,962,028; W099/25842) from zea mays and sunflower, the promoter of the Arabidopsis thaliana histone H4 gene (Chaboute et al., 1987), the ubiquitin promoters (Holtorf et al., 1995, Plant Mol. Biol. 29:637-649, US 5,510,474) of Maize, Rice and sugarcane, the Rice actin 1 promoter (Act-1 , US 5,641 ,876), the histone promoters as described in EP 0 507 698 A1 , the Maize alcohol dehydrogenase 1 promoter (Adh-1 ) (from http://www.patentlens.net/daisy/promoters/242.html)). Also the small subunit promoter from Chrysanthemum may be used if that use is combined with the use of the respective terminator (Outchkourov et al., Planta, 216: 1003-1012, 2003).

[60] A variety of plant gene promoters that regulate gene expression in response to environmental, hormonal, chemical, developmental signals, and in a tissue-active manner can be used for expression of a sequence in plants. Choice of a promoter is based largely on the phenotype of interest and is determined by such factors as tissue (e.g., seed, fruit, root, pollen, vascular tissue, flower, carpel, etc.), inducibility (e.g., in response to wounding, heat, cold, drought, light, pathogens, etc.), timing, developmental stage, and the like.

[61 ] Additional promoters that can be used to practice this invention are those that elicit expression in response to stresses, such as the RD29 promoters that are activated in response to drought, low temperature, salt stress, or exposure to ABA (Yamaguchi-Shinozaki et al., 2004, Plant Cell, Vol. 6, 251 -264; WO12/101 1 18), but also promoters that are induced in response to heat (e.g., see Ainley et al. (1993) Plant Mol. Biol. 22: 13-23), light (e.g., the pea rbcS-3A promoter, Kuhlemeier et al. (1989) Plant Cell 1 : 471478, and the maize rbcS promoter, Schaffher and Sheen (1991 ) Plant Cell 3: 997-1012); wounding (e.g., wunl, Siebertz et al. (1989) Plant Cell 1 : 961 -968); pathogens (such as the PR-I promoter described in Buchel et al. (1999) Plant Mol. Biol. 40: 387-396, and the PDF 1.2 promoter described in Manners et al. (1998) Plant Mol. Biol. 38: 1071 -1080), and chemicals such as methyl jasmonate or salicylic acid (e.g., see Gatz (1997) Annu. Rev. Plant Physiol. Plant Mol. Biol. 48: 89-108). In addition, the timing of the expression can be controlled by using promoters such as those acting at senescence (e.g., see Gan and Amasino (1995) Science 270: 1986-1988); or late seed development (e.g., see Odell et al. (1994) Plant Physiol. 106: 447458).

[62] Use may also be made of salt-inducible promoters such as the salt-inducible NHX1 promoter of rice landrace Pokkali (PKN) (Jahan et al., 6^th International Rice Genetics symposium, 2009, poster abstract P4-37), the salt inducible promoter of the vacuolar ^-pyrophosphatase from Thellungiella halophila (TsVP1 ) (Sun et al., BMC Plant Biology 2010, 10:90), the salt-inducible promoter of the Citrus sinensis gene encoding phospholipid hydroperoxide isoform gpxl (Avsian-Kretchmer et al., Plant Physiology July 2004 vol. 135, p1685-1696).

[63] In alternative embodiments, tissue-specific and/or developmental stage-specific promoters are used, e.g., promoter that can promote transcription only within a certain time frame of developmental stage within that tissue. See, e.g., Blazquez (1998) Plant Cell 10:791 -800, characterizing the Arabidopsis LEAFY gene promoter. See also Cardon (1997) Plant J 12:367-77, describing the transcription factor SPL3, which recognizes a conserved sequence motif in the promoter region of the A. thaliana floral meristem identity gene API; and Mandel (1995) Plant Molecular Biology, Vol. 29, pp 995-1004, describing the meristem promoter elF4. Tissue specific promoters which are active throughout the life cycle of a particular tissue can be used. In one aspect, the nucleic acids of the invention are operably linked to a promoter active primarily only in cotton fiber cells, in one aspect, the nucleic acids of the invention are operably linked to a promoter active primarily during the stages of cotton fiber cell elongation, e.g., as described by Rinehart (1996) supra. The nucleic acids can be operably linked to the Fbl2A gene promoter to be preferentially expressed in cotton fiber cells (Ibid). See also, John (1997) Proc. Natl. Acad. Sci. USA 89:5769-5773; John, et al., U.S. Patent Nos. 5,608,148 and 5,602,321 , describing cotton fiber-specific promoters and methods for the construction of transgenic cotton plants. Root- specific promoters may also be used to express the nucleic acids of the invention. Examples of root-specific promoters include the promoter from the alcohol dehydrogenase gene (DeLisle (1990) Int. Rev. Cytol. 123:39-60) and promoters such as those disclosed in U.S. Pat. Nos. 5,618,988, 5,837,848 and 5,905,186. Other promoters that can be used to express the nucleic acids of the invention include, e.g., ovule-specific, embryo-specific, endosperm-specific, integument- specific, seed coat-specific promoters, or some combination thereof; a leaf-specific promoter (see, e.g., Busk (1997) Plant J. 1 1 :1285 1295, describing a leaf-specific promoter in maize); the ORF 13 promoter from Agrobacterium rhizogenes (which exhibits high activity in roots, see, e.g., Hansen (1997) supra); a maize pollen specific promoter (see, e.g., Guerrero (1990) Mol. Gen. Genet. 224: 161 168); a tomato promoter active during fruit ripening, senescence and abscission of leaves, a guard-cell preferential promoter e.g. as described in PCT/EP12/065608, and, to a lesser extent, of flowers can be used (see, e.g., Blume (1997) Plant J. 12:731 746); a pistil-specific promoter from the potato SK2 gene (see, e.g., Ficker (1997) Plant Mol. Biol. 35:425 431 ); the Blec4 gene from pea, which is active in epidermal tissue of vegetative and floral shoot apices of transgenic alfalfa making it a useful tool to target the expression of foreign genes to the epidermal layer of actively growing shoots or fibers; the ovule-specific BELI gene (see, e.g., Reiser (1995) Cell 83:735-742, GenBank No. U39944); and/or, the promoter in Klee, U.S. Patent No. 5,589,583, describing a plant promoter region is capable of conferring high levels of transcription in meristematic tissue and/or rapidly dividing cells. Further tissue specific promoters that may be used according to the invention include: seed-specific promoters (such as the napin, phaseolin or DC3 promoter described in U .S. Pat. No. 5,773,697), fruit-specific promoters that are active during fruit ripening (such as the dru 1 promoter (U.S. Pat. No. 5,783,393), or the 2AI 1 promoter (e.g., see U.S. Pat. No. 4,943,674) and the tomato polygalacturonase promoter (e.g., see Bird et al. (1988) Plant Mol. Biol. 1 1 : 651 -662), flower- specific promoters (e.g., see Kaiser et al. (1995) Plant Mol. Biol. 28: 231 -243), pollen-active promoters such as PTA29, PTA26 and PTAI 3 (e.g., see U.S. Pat. No. 5,792,929) and as described in e.g. Baerson et al. (1994 Plant Mol. Biol. 26: 1947-1959), promoters active in vascular tissue (e.g., see Ringli and Keller (1998) Plant Mol. Biol. 37: 977-988), carpels (e.g., see Ohl et al. (1990) Plant Cell 2:), pollen and ovules (e.g., see Baerson et al. (1993) Plant Mol. Biol. 22: 255- 267). In alternative embodiments, plant promoters which are inducible upon exposure to plant hormones, such as auxins, are used to express the nucleic acids used to practice the invention. For example, the invention can use the auxin- response elements El promoter fragment (AuxREs) in the soybean {Glycine max L.) (Liu (1997) Plant Physiol. 1 15:397- 407); the auxin-responsive Arabidopsis GST6 promoter (also responsive to salicylic acid and hydrogen peroxide) (Chen (1996) Plant J. 10: 955-966); the auxin-inducible parC promoter from tobacco (Sakai (1996) 37:906-913); a plant biotin response element (Streit (1997) Mol. Plant Microbe Interact. 10:933-937); and, the promoter responsive to the stress hormone abscisic acid (ABA) (Sheen (1996) Science 274:1900-1902). Further hormone inducible promoters that may be used include auxin-inducible promoters (such as that described in van der Kop et al. (1999) Plant Mol. Biol. 39: 979-990 or Baumann et al., (1999) Plant Cell 11 : 323-334), cytokinin-inducible promoter (e.g., see Guevara-Garcia (1998) Plant Mol. Biol. 38: 743-753), promoters responsive to gibberellin (e.g., see Shi et al. (1998) Plant Mol. Biol. 38: 1053-1060, Willmott et al. (1998) Plant Molec. Biol. 38: 817-825) and the like.

[64] In alternative embodiments, nucleic acids used to practice the invention can also be operably linked to plant promoters which are inducible upon exposure to chemicals reagents which can be applied to the plant, such as herbicides or antibiotics. For example, the maize ln2-2 promoter, activated by benzenesulfonamide herbicide safeners, can be used (De Veylder (1997) Plant Cell Physiol. 38:568-577); application of different herbicide safeners induces distinct gene expression patterns, including expression in the root, hydathodes, and the shoot apical meristem. Coding sequence can be under the control of, e.g., a tetracycline-inducible promoter, e.g. , as described with transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase gene (Masgrau (1997) Plant J. 11 :465 73); or, a salicylic acid-responsive element (Stange (1997) Plant J. 11 :1315-1324). Using chemically- {e.g. , hormone- or pesticide- ) induced promoters, i.e., promoter responsive to a chemical which can be applied to the transgenic plant in the field, expression of a polypeptide of the invention can be induced at a particular stage of development of the plant. Use may also be made of the estrogen-inducible expression system as described in US patent 6,784,340 and Zuo et al. (2000, Plant J. 24: 265-273) to drive the expression of the nucleic acids used to practice the invention.

[65] In alternative embodiments, the a promoter may be used whose host range is limited to target plant species, such as corn, rice, barley, wheat, potato or other crops, inducible at any stage of development of the crop.

[66] In alternative embodiments, a tissue-specific plant promoter may drive expression of operably linked sequences in specific target tissues. In alternative embodiments, a tissue-specific promoter that drives expression preferentially in the target tissue or cell type, but may also lead to some expression in other tissues as well, is used.

[67] In alternative embodiments, use may be made of promoter elements as e.g. described on http://arabidopsis.med.ohio-state.edu/AtcisDB/bindingsites.html., which in combination should result in a functional promoter.

[68] According to the invention, the chimeric gene may also comprise, in combination with the promoter, other regulatory sequences, which are located between the promoter and the coding sequence, such as transcription activators ("enhancers"), for instance the translation activator of the tobacco mosaic virus (TMV) described in Application WO 87/07644, or of the tobacco etch virus (TEV) described by Carrington & Freed 1990, J. Virol. 64: 1590-1597, for example.

[69] Other regulatory sequences that enhance the expression of the operably linked nucleic acid may also be located within the chimeric gene. One example of such regulatory sequences are introns. Introns are intervening sequences present in the pre-mRNA but absent in the mature RNA following excision by a precise splicing mechanism. The ability of natural introns to enhance gene expression, a process referred to as intron-mediated enhancement (IME), has been known in various organisms, including mammals, insects, nematodes and plants (WO 07/098042, p1 1 -12). IME is generally described as a posttranscriptional mechanism leading to increased gene expression by stabilization of the transcript. The intron is required to be positioned between the promoter and the coding sequence in the normal orientation. However, some introns have also been described to affect translation, to function as promoters or as position and orientation independent transcriptional enhancers (Chaubet-Gigot et al., 2001 , Plant Mol Biol. 45(1 ):17-30, p27-28).

[70] Examples of genes containing such introns include the 5' introns from the rice actin 1 gene (see US5641876), the rice actin 2 gene, the maize sucrose synthase gene (Clancy and Hannah, 2002, Plant Physiol. 130(2):918-29), the maize alcohol dehydrogenase-1 (Adh-1 ) and Bronze-1 genes (Callis et al. 1987 Genes Dev. 1 (10): 1 183-200; Mascarenhas et al. 1990, Plant Mol Biol. 15(6):913-20), the maize heat shock protein 70 gene (see US5593874), the maize shrunken 1 gene, the light sensitive 1 gene of Solanum tuberosum, and the heat shock protein 70 gene of Petunia hybrida (see US 5659122), the replacement histone H3 gene from alfalfa (Keleman et al. 2002 Transgenic Res. 1 1 (1 ):69- 72) and either replacement histone H3 (histone H3.3-like) gene of Arabidopsis thaliana (Chaubet-Gigot et al., 2001 , Plant Mol Biol. 45(1 ):17-30).

[71 ] Other suitable regulatory sequences include 5' UTRs. As used herein, a 5'UTR, also referred to as leader sequence, is a particular region of a messenger RNA (mRNA) located between the transcription start site and the start codon of the coding region. It is involved in mRNA stability and translation efficiency. For example, the 5' untranslated leader of a petunia chlorophyll a/b binding protein gene downstream of the 35S transcription start site can be utilized to augment steady-state levels of reporter gene expression (Harpster et al., 1988, Mol Gen Genet. 212(1 ):182-90). WO95/006742 describes the use of 5' non-translated leader sequences derived from genes coding for heat shock proteins to increase transgene expression.

[72] The chimeric gene may also comprise a 3' end region, i.e. a transcription termination or polyadenylation sequence, operable in plant cells. As a transcription termination or polyadenylation sequence, use may be made of any corresponding sequence of bacterial origin, such as for example the nos terminator of Agrobacterium tumefaciens, of viral origin, such as for example the CaMV 35S terminator, or of plant origin, such as for example a histone terminator as described in published Patent Application EP 0 633 317 A1. The polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The 3' end sequence to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.

[73] In a further embodiment, the coding region can be optimized for expression in the target organism, which may include adapting the codon usage, CG content, and elimination of unwanted nucleotide sequences (e.g. premature polyadenylation signals, cryptic intron splice sites, ATTTA pentamers, CCAAT box sequences, sequences that effect pre-mRNA splicing by secondary RNA structure formation such as long CG or AT stretches). An example of a wheat codon optimized HCD1 coding region is provided in SEQ ID NO. 3.

[74] Also provided are polypeptides and nucleic acids encoding the functional fragments of HDC1 proteins as decribed above, e.g. fragments of any one of SEQ ID NOs 6-41 , or fragments of sequences having at least 70%, at least 75%, at least 80%, at least 85% , at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity to the corresponding fragment of any of the amino acid sequences cited above and encoding functional fragments of HDC1 proteins.

[75] The invention further provides plants, plant cells, organs, seeds or tissues comprising a chimeric gene according to the invention. These include for example transgenic plants, plant cells, organs, seeds or tissues, comprising and expressing the nucleic acids used to practice this invention resulting in the expression of a functional fragment of an HDC1 protein; for example, the invention provides plants, e.g., transgenic plants, plant cells, organs, seeds or tissues that show improved growth under (mild or moderate) stress conditions such as limiting water conditions; thus, the invention provides stress-tolerant, and particularly drought-tolerant plants, plant cells, organs, seeds or tissues (e.g., crops). The invention also provides plants, e.g., transgenic plants, plant cells, organs, seeds or tissues that show improved growth under control conditions; thus, the invention provides plants, plant cells, organs, seeds or tissues (e.g., crops) with increased biomass and/or yield and/or growth rate. The invention further provides plants, e.g., transgenic plants, plant cells, organs, seeds or tissues that show improved growth under limiting water conditions; thus, the invention provides drought-tolerant plants, plant cells, organs, seeds or tissues (e.g., crops).

[76] The plant, plant part, plant organs and plant cell of the invention comprising a nucleic acid used to practice this invention (e.g., a transfected, infected or transformed cell) can be dicotyledonous (a dicot) or monocotyledonous (a monocot). Examples of monocots comprising a nucleic acid of this invention, e.g., as monocot transgenic plants of the invention, are grasses, such as meadow grass (blue grass, Poa), forage grass such as festuca, lolium, temperate grass, such as Agrostis, and cereals, e.g., wheat, oats, rye, barley, rice, sorghum, and maize (com). Examples of dicots comprising a nucleic acid of this invention, e.g., as dicot transgenic plants of the invention, are cotton, tobacco, legumes, such as lupins, potato, sugar beet, pea, bean and soybean, and cruciferous plants (family Brassicaceae), such as cauliflower, rape seed, and the closely related model organism Arabidopsis thaliana. Thus, plant or plant cell comprising a nucleic acid of this invention, including the transgenic plants and seeds of the invention, include a broad range of plants, including, but not limited to, species from the genera Anacardium, Arachis, Asparagus, Atropa, Avena, Brassica, Citrus, Citrullus, Capsicum, Carthamus, Cocos, Cojfea, Cucumis, Cucurbita, Daucus, Elaeis, Fragaria, Glycine, Gossypium, Helianthus, Heterocallis, Hordeum, Hyoscyamus, Lactuca, Linum, Lolium, Lupinus, Lycopersicon, Malus, Manihot, Majorana, Medicago, Nicotiana, Olea, Oryza, Panieum, Pannisetum, Persea, Phaseolus, Pistachia, Pisum, Pyrus, Prunus, Raphanus, Ricinus, Secale, Senecio, Sinapis, Solarium, Sorghum, Theobromus, Trigonella, Triticum, Vicia, Vitis, Vigna, and Zea. [77] The invention furthermore provides propagating material created from the plant of plants cells of the invention. The creation of propagating material relates to any means know in the art to produce further plants, plant parts or seeds and includes inter alia vegetative reproduction methods (e.g. air or ground layering, division, (bud) grafting, micropropagation, stolons or runners, storage organs such as bulbs, corms, tubers and rhizomes, striking or cutting, twin- scaling), sexual reproduction (crossing with another plant) and asexual reproduction (e.g. apomixis, somatic hybridization).

[78] In particular embodiments the plant cell described herein is a non-propagating plant cell or a plant cell that cannot be regenerated into a plant or a plant cell that cannot maintain its life by synthesizing carbohydrate and protein from the inorganics, such as water, carbon dioxide, and inorganic salt, through photosynthesis.

[79] Further provided is the use of the plant as described above, to produce seed comprising the chimeric gene according to the invention, as qwell as the use of plant as described above to produce a population of plants with increased tolerance to stress conditions, or with reduced ABA sensitivity, or with increased biomass or yield or growth rate.

[80] In a further embodiment, the invention provides a method for producing a plant, plant part, plant organ or plant cell with increased tolerance to stress conditions, or with reduced ABA sensitivity, or with increased biomass or yield or growth rate, comprising the step of expressing in said plant cell, plant part, plant organ or plant a chimeric gene as described above. Thus, the invention provides a method for increasing the tolerance of a plant, plant part, plant organ or plant cell to stress conditions, or for reducing ABA sensitivity of a plant, plant part, plant organ or plant cell; or for increasing biomass or yield or growth rate of a plant, plant organ or plant part; comprising the step of expressing in said comprising the step of expressing in said plant cell, plant part, plant organ or plant a chimeric gene as described above.

[81 ] A gene, e.g. the chimeric gene of the invention, is said to be expressed when it leads to the formation of an expression product. An expression product denotes an intermediate or end product arising from the transcription and optionally translation of the nucleic acid, DNA or RNA, coding for such product, e. g. the second nucleic acid described herein. During the transcription process, a DNA sequence under control of regulatory regions, particularly the promoter, is transcribed into an RNA molecule. An RNA molecule may either itself form an expression product or be an intermediate product when it is capable of being translated into a peptide or protein. A gene is said to encode an RNA molecule as expression product when the RNA as the end product of the expression of the gene is, e. g., capable of interacting with another nucleic acid or protein. Examples of RNA expression products include inhibitory RNA such as e. g. sense RNA (co-suppression), antisense RNA, ribozymes, miRNA or siRNA, mRNA, rRNA and tRNA. A gene is said to encode a protein as expression product when the end product of the expression of the gene is a protein or peptide. [82] Expression of a transcript (e.g. an mRNA) of a protein can be measured according to various methods known in the art such as (quantitative) RT-PCR, northern blotting, microarray analysis, western blotting, ELISA and the like.

[83] Increased expression, as used herein, refers to increase in expression level of at least 2%, or at least 5%, or at least 10%, or at least 15%, or at least 20%, or at least 25%, or at least 30%, or at least 40%, or at least 50% or even more. Said increase is an increase with respect to the expression in control plants.

[84] Stress conditions, as used herein, refers e.g. to stress imposed by the application of chemical compounds (e.g., herbicides, fungicides, insecticides, plant growth regulators, adjuvants, fertilizers), exposure to abiotic stress (e.g., drought, waterlogging, submergence, high light conditions, high UV radiation, increased hydrogen peroxide levels, extreme (high or low) temperatures, ozone and other atmospheric pollutants, soil salinity or heavy metals, hypoxia, anoxia, osmotic stress, oxidative stress, low nutrient levels such as nitrogen or phosphor etc.) or biotic stress (e.g., pathogen or pest infection including infection by fungi, viruses, bacteria, insects, nematodes, mycoplasms and mycoplasma like organisms, etc.). Stress may also be imposed by hormones such as ABA or compound influencing hormone activity.

[85] Drought, salinity, extreme temperatures, high light stress and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755- 1767) describes a particularly high degree of "cross talk" between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signalling pathways and cellular responses, such as the production of stress proteins, up- regulation of anti-oxidants, accumulation of compatible solutes and growth arrest.

[86] Applying the teaching of the present invention, when expressing a chimeric gene of the invention an increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stress conditions compared to control plants. The term "non-stress" conditions as used herein are those environmental conditions that allow optimal growth of plants.

[87] A "control plant" as used herein is generally a plant of the same species which does not contain a chimeric gene according to the invention.

[88] Various methods are available in the art to measure the tolerance of plants, plant parts, plant cells or seeds to various stresses, some of which are described in the examples here below. Increased stress tolerance will usually be apparent from the general appearance of the plants and may be measured e.g., by increased biomass production, continued vegetative growth under adverse conditions or higher seed yield. Stress tolerant plants have a broader growth spectrum, i.e. they are able to withstand a broader range of climatological and other abiotic changes, without yield penalty, as compared to control plants. Biochemically, stress tolerance may be apparent as the higher NAD+-NADH /ATP content and lower production of reactive oxygen species of stress tolerant plants compared to control plants under stress condition. Stress tolerance may also be apparent as the higher chlorophyll content, higher germination rates, higher photosynthesis and lower chlorophyll fluorescence under stress conditions in stress tolerant plants compared to control plants under the same conditions.

[89] It will be clear that it is also not required that the plant be grown continuously under the adverse conditions for the stress tolerance to become apparent. Usually, the difference in stress tolerance between a plant or plant cell produced according to the invention and a control plant or plant cell will become apparent even when only a relatively short period of adverse conditions is encountered during growth.

[90] Yield or biomass, as used herein, refers to seed number/weight, fruit number/weight, fresh weight, dry weight, leaf number/area, plant height, branching, boll number/size, fiber length, seed oil content, seed protein content, seed carbohydrate content. An increased growth rate as used herein refers to a period of increased growth or allocation to one or more of these cells or tissues that comprise the aforementioned plant organs.

[91 ] An increase in biomass or yield or growth can be an increase of at least 2%, or at least 5%, or at least 10%, or at least 15%, or at least 20%, or at least 25%, or at least 30%, or at least 40% , or at least 50%. Said increase is an increase with respect to biomass or yield or growth of control plants.

[92] Abscisic acid (ABA) is a phytohormone which functions in many plant developmental processes, including seed dormancy. Furthermore, ABA mediates stress responses in plants in reaction to water stress, high-salt stress, cold stress (Mansfield 1987, p. 41 1-430. In: P.J. Davies (ed.). Plant hormones and their role in plant growth and development. Martinus Nijhoff Publishers, Dordrecht; Yamaguchi-Shinozaki 1993, Plant Physiol. 101 , 1 1 19-1 120; Yamaguchi-Shinozaki 1994, Plant Cell 6, 251 -264) and plant pathogens (Seo and Koshiba, 2002, Trends Plant Sci. 7, 41-48). ABA is a sesquiterpenoid (15-carbon) which is partially produced via the mevalonic pathway in chloroplasts and other plastids. It is synthesized partially in the chloroplasts and accordingly, biosynthesis primarily occurs in the leaves. The production of ABA is increased by stresses such as water loss and freezing temperatures. It is believed that biosynthesis occurs indirectly through the production of carotenoids. Physiological responses known to be associated with abscisic acid include stimulation of the closure of stomata, inhibition of seedling or shoot growth, induction of storage protein synthesis in seeds and inhibition of the effect of gibberellins on stimulating de novo synthesis of a-amylase. Basic ABA levels may differ considerably from plant to plant. For example, the basal concentration of ABA in non-stressed Arabidopsis leaves is 2 to 3 ng/g fresh weight (Lopez-Carbonell and Jauregui, 2005). Under water-stress conditions, the ABA concentration reaches 10 to 21 ng/g fresh weight. [93] ABA sensitivity can be measured e.g. as described herein below. ABA sensitivity can also be measured by measurement of stomatal aperture (Zhang et al. 2009, EurAsia J BioSci 3, 10-16), measurement of ion current s (Armstrong et al 1995, PNAS 92:95204; Marten et al. 2007, Plant Physiol. Vol. 143, 28037) or measurement of ABA- dependent gene expression by microarrays, RNA-sequencing, RT-PCR or RNA gel blotting (Hoth et al. 2002, Journal of Cell Science 1 15, 48914900).

[94] Decrease in ABA sensitivity can be a decrease of at least 2%, or at least 5%, or at least 10%, or at least 15%, or at least 20% , or at least 25%, or at least 30%, or at least 40%, or at least 50%. Said decrease is a decrease with respect to ABA sensitivity of control plants.

[95] Thus, a plant made according to the invention expressing a functional fragment of an HDC1 protein can have at least one of the following phenotypes when compared to control plants, especially under adverse conditions, such as water limiting conditions, but alos under control conditions, including but not limited to: increased overall plant yield, increased root mass, increased root length, increased leaf size, increased ear size, increased seed size, increased endosperm size, improved standability, alterations in the relative size of embryos and endosperms leading to changes in the relative levels of protein, oil and/or starch in the seeds, altered floral development, changes in leaf number, altered leaf surface, altered vasculature, altered internodes, alterations in leaf senescence, absence of tassels, absence of functional pollen bearing tassels, or increased plant size when compared to a non-modified plant under normal growth conditions or under adverse conditions, such as water limiting conditions.

[96] Polypeptides, nucleic acids and chimeric genes used to practice the invention can be expressed by introduction of such nucleic acids (encoding such polypeptides), chimeric genes into a plant cell by any means. For example, nucleic acids or chimeric genes (expression constructs) can be introduced into the genome of a desired plant host, or, the nucleic acids or chimeric genes can be episomes.

[97] "Introducing" in connection with the present application relates to the placing of genetic information in a plant cell or plant by artificial means, such as transformation. This can be effected by any method known in the art for introducing RNA or DNA into plant cells, tissues, protoplasts or whole plants. In addition to artificial introduction as described above, "introducing" also comprises introgressing genes as defined further below.

[98] Transformation means introducing a nucleotide sequence into a plant in a manner to cause stable or transient expression of the sequence. Transformation and regeneration of both monocotyledonous and dicotyledonous plant cells is now routine, and the selection of the most appropriate transformation technique will be determined by the practitioner. The choice of method will vary with the type of plant to be transformed; those skilled in the art will recognize the suitability of particular methods for given plant types. Suitable methods can include, but are not limited to: electroporation of plant protoplasts; liposome-mediated transformation; polyethylene glycol (PEG) mediated transformation; transformation using viruses; micro-injection of plant cells; micro-projectile bombardment of plant cells; vacuum infiltration; and Agrobacterium- mediated transformation.

[99] In alternative embodiments, the invention uses Agrobacterium tumefaciens mediated transformation. Also other bacteria capable of transferring nucleic acid molecules into plant cells may be used, such as certain soil bacteria of the order of the Rhizobiales, e.g. Rhizobiaceae (e.g. Rhizobium spp., Sinorhizobium spp., Agrobacterium spp); Phyllobacteriaceae (e.g. Mesorhizobium spp., Phyllobacterium spp.); Brucellaceae (e.g. Ochrobactrum spp.); Bradyrhizobiaceae (e.g. Bradyrhizobium spp.), and Xanthobacteraceae (e.g. Azorhizobium spp.), Agrobacterium spp., Rhizobium spp., Sinorhizobium spp., Mesorhizobium spp., Phyllobacterium spp. Ochrobactrum spp. and Bradyrhizobium spp., examples of which include Ochrobactrum sp., Rhizobium sp., Mesorhizobium loti, Sinorhizobium meliloti. Examples of Rhizobia include R. leguminosarum bv, trifolii, R. leguminosarum bv,phaseoli and Rhizobium leguminosarum, bv, viciae (US Patent 7,888,552). Other bacteria that can be employed to carry out the invention which are capable of transforming plants cells and induce the incorporation of foreign DNA into the plant genome are bacteria of the genera Azobacter (aerobic), Closterium (strictly anaerobic), Klebsiella (optionally aerobic), and Rhodospirillum (anaerobic, photosynthetically active). Transfer of a Ti plasmid was also found to confer tumor inducing ability on several Rhizobiaceae members such as Rhizobium trifolii, Rhizobium leguminosarum and Phyllobacterium myrsinacearum, while Rhizobium sp. NGR234, Sinorhizobium meliloti and Mesorhizobium loti could indeed be modified to mediate gene transfer to a number of diverse plants (Broothaerts et al., 2005, Nature, 433:629-633).

[100] In alternative embodiments, making transgenic plants or seeds comprises incorporating sequences used to practice the invention and, in one aspect (optionally), marker genes into a target expression construct (e.g., a plasmid), along with positioning of the promoter and the terminator sequences. This can involve transferring the modified gene into the plant through a suitable method. For example, a construct may be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts, or the constructs can be introduced directly to plant tissue using ballistic methods, such as DNA particle bombardment. For example, see, e.g., Christou (1997) Plant Mol. Biol. 35:197-203; Pawlowski (1996) Mol. Biotechnol. 6:17-30; Klein (1987) Nature 327:70-73; Takumi (1997) Genes Genet. Syst. 72:63-69, discussing use of particle bombardment to introduce transgenes into wheat; and Adam (1997) supra, for use of particle bombardment to introduce YACs into plant cells. For example, Rinehart (1997) supra, used particle bombardment to generate transgenic cotton plants. Apparatus for accelerating particles is described U.S. Pat. No. 5,015,580; and, the commercially available BioRad (Biolistics) PDS-2000 particle acceleration instrument; see also, John, U.S. Patent No. 5,608,148; and Ellis, U.S. Patent No. 5, 681 ,730, describing particle-mediated transformation of gymnosperms.

[101 ] In alternative embodiments, protoplasts can be immobilized and injected with nucleic acids, e.g., an expression construct. Although plant regeneration from protoplasts is not easy with cereals, plant regeneration is possible in legumes using somatic embryogenesis from protoplast derived callus. Organized tissues can be transformed with naked DNA using gene gun technique, where DNA is coated on tungsten microprojectiles, shot 1/100th the size of cells, which carry the DNA deep into cells and organelles. Transformed tissue is then induced to regenerate, usually by somatic embryogenesis. This technique has been successful in several cereal species including maize and rice.

[102] In alternative embodiments, a third step can involve selection and regeneration of whole plants capable of transmitting the incorporated target gene to the next generation. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker that has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans et al., Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, pp. 124-176, MacMillilan Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21 -73, CRC Press, Boca Raton, 1985. Regeneration can also be obtained from plant callus, explants, organs, or parts thereof. Such regeneration techniques are described generally in Klee (1987) Ann. Rev. of Plant Phys. 38:467486. To obtain whole plants from transgenic tissues such as immature embryos, they can be grown under controlled environmental conditions in a series of media containing nutrients and hormones, a process known as tissue culture. Once whole plants are generated and produce seed, evaluation of the progeny begins.

[103] Viral transformation (transduction) may also be used for transient or stable expression of a gene, depending on the nature of the virus genome. The desired genetic material is packaged into a suitable plant virus and the modified virus is allowed to infect the plant. The progeny of the infected plants is virus free and also free of the inserted gene. Suitable methods for viral transformation are described or further detailed e. g. in WO 90/12107, WO 03/052108 or WO 2005/098004.

[104] In alternative embodiments, after the chimeric gene is stably incorporated in transgenic plants, it can be introduced into other plants by sexual crossing or introgression. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed. Since transgenic expression of the nucleic acids of the invention leads to phenotypic changes, plants comprising the recombinant nucleic acids of the invention can be sexually crossed with a second plant to obtain a final product. Thus, the seed of the invention can be derived from a cross between two transgenic plants of the invention, or a cross between a plant of the invention and another plant. The desired effects (e.g., expression of the polypeptides of the invention to produce a plant in which flowering behavior is altered) can be enhanced when both parental plants express the polypeptides, e.g., a truncated HDC1 gene of the invention. The desired effects can be passed to future plant generations by standard propagation means.

[105] Successful examples of the modification of plant characteristics by transformation with cloned sequences which serve to illustrate the current knowledge in this field of technology, and include for example: U.S. Pat. Nos. 5,571 ,706; 5,677,175; 5,510,471 ; 5,750,386; 5,597,945; 5,589,615; 5,750,871 ; 5,268,526; 5,780,708; 5,538,880; 5,773,269; 5,736,369 and 5,619,042.

[106] In alternative embodiments, following transformation, plants are selected using a dominant selectable marker incorporated into the transformation vector. Such a marker can confer antibiotic or herbicide resistance on the transformed plants, and selection of transformants can be accomplished by exposing the plants to appropriate concentrations of the antibiotic or herbicide.

[107] In alternative embodiments, after transformed plants are selected and grown to maturity, those plants showing a modified trait are identified. The modified trait can be any of those traits described above. In alternative embodiments, to confirm that the modified trait is due to changes in expression levels or activity of the transgenic polypeptide or nucleic acid can be determined by analyzing mRNA expression using Northern blots, RT-PCR or microarrays, or protein expression using immunoblots or Western blots or gel shift assays.

[108] "Introgressing" means the integration of a gene in a plant's genome by natural means, i.e. by crossing a plant comprising the chimeric gene described herein with a plant not comprising said chimeric gene. The offspring can be selected for those comprising the chimeric gene.

[109] The chimeric genes, nucleic acids and polypeptides used to practice this invention can be expressed in or inserted in any plant cell, organ, seed or tissue, including differentiated and undifferentiated tissues or plants, including but not limited to roots, stems, shoots, cotyledons, epicotyl, hypocotyl, leaves, pollen, seeds, tumor tissue and various forms of cells in culture such as single cells, protoplast, embryos, and callus tissue. The plant tissue may be in plants or in organ, tissue or cell culture.

[1 10] A nucleic acid or polynucleotide, as used herein, can be DNA or RNA, single- or double-stranded. Nucleic acids can be synthesized chemically or produced by biological expression in vitro or even in vivo. Nucleic acids can be chemically synthesized using appropriately protected ribonucleoside phosphoramidites and a conventional DNA/RNA synthesizer. Suppliers of RNA synthesis reagents are Proligo (Hamburg, Germany), Dharmacon Research (Lafayette, CO, USA), Pierce Chemical (part of Perbio Science, Rockford, IL , USA), Glen Research (Sterling, VA, USA), ChemGenes (Ashland, MA, USA), and Cruachem (Glasgow, UK). In connection with the chimeric gene of the present disclosure, DNA includes cDNA and genomic DNA.

[1 1 1 ] The terms "protein" or "polypeptide" as used herein describe a group of molecules consisting of more than 30 amino acids, whereas the term "peptide" describes molecules consisting of up to 30 amino acids. Proteins and peptides may further form dimers, trimers and higher oligomers, i.e. consisting of more than one (poly)peptide molecule. Protein or peptide molecules forming such dimers, trimers etc. may be identical or non-identical. The corresponding higher order structures are, consequently, termed homo- or heterodimers, homo- or heterotrimers etc. The terms "protein" and "peptide" also refer to naturally modified proteins or peptides wherein the modification is effected e.g. by glycosylation, acetylation, phosphorylation and the like. Such modifications are well known in the art.

[1 12] As used herein "comprising" is to be interpreted as specifying the presence of the stated features, integers, steps or components as referred to, but does not preclude the presence or addition of one or more features, integers, steps or components, or groups thereof. Thus, e.g., a nucleic acid or protein comprising a sequence of nucleotides or amino acids, may comprise more nucleotides or amino acids than the actually cited ones, i.e., be embedded in a larger nucleic acid or protein. A chimeric gene comprising a nucleic acid which is functionally or structurally defined, may comprise additional DNA regions etc.

[1 13] Unless stated otherwise in the Examples, all recombinant DNA techniques are carried out according to standard protocols as described in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, NY and in Volumes 1 and 2 of Ausubel et al. (1994) Current Protocols in Molecular Biology, Current Protocols, USA. Standard materials and methods for plant molecular work are described in Plant Molecular Biology Labfax (1993) by R.D.D. Cray, jointly published by BIOS Scientific Publications Ltd (UK) and Blackwell Scientific Publications, UK. Other references for standard molecular biology techniques include Sambrook and Russell (2001 ) Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, NY, Volumes I and II of Brown (1998) Molecular Biology LabFax, Second Edition, Academic Press (U K). Standard materials and methods for polymerase chain reactions can be found in Dieffenbach and Dveksler (1995) PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, and in McPherson at al. (2000) PCR - Basics: From Background to Bench, First Edition, Springer Verlag, Germany.

[1 14] All patents, patent applications, and publications or public disclosures (including publications on internet) referred to or cited herein are incorporated by reference in their entirety.

[1 15] The sequence listing contained in the file named "BCS15-2007-WO1_ST25.txt", which is 641 kilobytes (size as measured in Microsoft Windows®), contains 61 sequences SEQ ID NO: 1 through SEQ ID NO:61 , is filed herewith by electronic submission and is incorporated by reference herein.

[1 16] The invention will be further described with reference to the examples described herein; however, it is to be understood that the invention is not limited to such examples.

Sequence listing

[1 17] SEQ ID NO. 1 : overexpression vector 2x35S-RXT3L

[1 18] SEQ ID NO. 2: amino acid sequence RXT3L encoded by SEQ ID NO. 1 [1 19] SEQ ID NO. 3: Nucleotide sequence of HDC1 from Arabidopsis thaliana codon wheat

[120] SEQ ID NO. 4: Amino acid sequence Saccharomyces cerevisiae Rxt3

[121 ] SEQ ID NO. 5: Nucleotide sequence of HDC1 from Arabidopsis thaliana

[122] SEQ ID NO. 6: Amino acid sequence of HDC1 from Arabidopsis thaliana

[123] SEQ ID NO. 7: f Nucleotide sequence of HDC1 from Arabidopsis lyrata

[124] SEQ ID NO. 8: Amino acid sequence of HDC1 from Arabidopsis lyrata

[125] SEQ ID NO. 9: f Nucleotide sequence of HDC1 from Populus trichocarpa

[126] SEQ ID NO. 10: Amino acid sequence of HDC1 from Populus trichocarpa

[127] SEQ ID NO. 1 1 : Nucleotide sequence of HDC1 from Medicago truncatula

[128] SEQ ID NO. 12: Amino acid sequence of HDC1 from Medicago truncatula

[129] SEQ ID NO. 13: Nucleotide sequence of HDC1 from Vitis vinifera

[130] SEQ ID NO. 14: Amino acid sequence of HDC1 from Vitis vinifera

[131 ] SEQ ID NO. 15: Nucleotide sequence of HDC1 from Ricinus communis

[132] SEQ ID NO. 16: Amino acid sequence of HDC1 from Ricinus communis

[133] SEQ ID NO. 17: Nucleotide sequence of HDC1 from Oryza sativa

[134] SEQ ID NO. 18: Amino acid sequence of HDC1 from Oryza sativa

[135] SEQ ID NO. 19: Nucleotide sequence of HDC1 from Oryza sativa

[136] SEQ ID NO. 20: Amino acid sequence of HDC1 from Oryza sativa

[137] SEQ ID NO. 21 : Nucleotide sequence of HDC1 from Brachypodium distachyon

[138] SEQ ID NO. 22: Amino acid sequence of HDC1 from Brachypodium distachyon

[139] SEQ ID NO. 23: Nucleotide sequence of HDC1 from Sorghum bicolor

[140] SEQ ID NO. 24: Amino acid sequence of HDC1 from Sorghum bicolor

[141 ] SEQ ID NO. 25: Nucleotide sequence of HDC1 from Sorghum bicolor

[142] SEQ ID NO. 26: : Amino acid sequence of HDC1 from Sorghum bicolor

[143] SEQ ID NO. 27: : Nucleotide sequence of HDC1 from Zea mays

[144] SEQ ID NO. 28: : Amino acid sequence of HDC1 from Zea mays

[145] SEQ ID NO. 29: : Nucleotide sequence of HDC1 from Glycine max

[146] SEQ ID NO. 30: : Amino acid sequence of HDC1 from Glycine max

[147] SEQ ID NO. 31 : : Nucleotide sequence of HDC1 from Glycine max

[148] SEQ ID NO. 32: : Amino acid sequence of HDC1 from Glycine max

[149] SEQ ID NO. 33: : Nucleotide sequence of HDC1 from Glycine max

[150] SEQ ID NO. 34: : Amino acid sequence of HDC1 from Glycine max

[151 ] SEQ ID NO. 35: : Nucleotide sequence of HDC1 from Glycine max

[152] SEQ ID NO. 36: : Amino acid sequence of HDC1 from Glycine max [153] SEQ ID NO. 37: Nucleotide sequence of HDC1 from Triticum aestivum

[154] SEQ ID NO. 38: Amino acid sequence of HDC1 from Triticum aestivum

[155] SEQ ID NO. 39: Nucleotide sequence of HDC1 from Solanum lycopersicum

[156] SEQ ID NO. 40: Amino acid sequence of HDC1 from Solanum lycopersicum

[157] SEQ ID NO. 41 : Amino acid sequence of HDC1 from Oryza sativa

[158] SEQ ID NO. 42: Nucleotide sequence of expression vector encoding GFP-HDC1

[159] SEQ ID NO. 43: Nucleotide sequence of expression vector encoding GFP-RXTL

[160] SEQ ID NO. 44: Nucleotide sequence of expression vector encoding GFP-ScRXT3

[161 ] SEQ ID NO. 45: Nucleotide sequence of 2-in-1 vectorfor HDCI and SHL.1

[162] SEQ ID NO. 46: Nucleotide sequence of 2-in-1 vector for RXT3L and SHL1

[163] SEQ ID NO. 47: Nucleotide sequence of 2-in-1 vectorfor HDCI and Histone H1.1

[164] SEQ ID NO. 48: Nucleotide sequence of 2-in-1 vectorfor HDCI and Histone H1.2

[165] SEQ ID NO. 49: Nucleotide sequence of 2-in-1 vectorfor HDCI and Histone H1.3

[166] SEQ ID NO. 50: Nucleotide sequence of 2-in-1 vectorfor HDCI and MSI1

[167] SEQ ID NO. 51 : Nucleotide sequence of 2-in-1 vector for RXT3L and Histone H1.1

[168] SEQ ID NO. 52: Nucleotide sequence of 2-in-1 vector for RXT3L and Histone H1.2

[169] SEQ ID NO. 53: Nucleotide sequence of 2-in-1 vector for RXT3L and Histone H1.3

[170] SEQ ID NO. 54: Nucleotide sequence of 2-in-1 vector for RXT3L and MSI1

[171 ] SEQ ID NO. 55: Nucleotide sequence of expression vector encoding GST- full-length H1.1

[172] SEQ ID NO. 56: Nucleotide sequence of expression vector encoding GST- full-length H1.2

[173] SEQ ID NO. 57: Nucleotide sequence of expression vector encoding GST- full-length H1.3

[174] SEQ ID NO. 58: Nucleotide sequence of expression vector encoding GST-SHL1

[175] SEQ ID NO. 59: Nucleotide sequence of expression vector encoding HIS-H1 .2

[176] SEQ ID NO. 60: Nucleotide sequence of expression vector encoding HIS-SHL1

[177] SEQ ID NO. 61 : Nucleotide sequence of expression vector encoding HIS-RXT3L

Examples

Example 1 : Experimental procedures Plant materials, growth conditions and treatments

[178] All transgenic lines were generated in Arabidopsis thaliana Col-0 background. hdc1-1 and HDC1 - overexpressing lines have been characterised before (Perrella et al. 2013). Homozygous RXT3L-expressing lines were generated from the progeny of wild-type and hdc1-1 plants transformed with RXT3L part under the control of 35S promoters (see cloning procedures). Plants were grown and treated in controlled growth rooms at a temperature of 22°C and a light intensity of 150 pmol PAR. Plants were grown either in long days (16-h light) or in short days (10-h light) as indicated in text and figure legends. Germination, growth and flowering assays were carried out as described before (Perrella et al. 2013). Petiole and leaf blade length were measured by Image J.

Plant transformation

[179] Plasmids were inserted by heat shock into Agrobacterium tumefaciens strain GV3101 pMP90 (Koncz and Schell, 1986). Agrobacterium-mediated transformation of Arabidopsis was performed by the floral dip method (Clough and Bent, 1998). Transient transformation of Nicotiana benthamiana was achieved by leaf infiltration (Geelen et al., 2002). For ratiometric BiFC assays and co-localization studies, each construct was co-expressed with p19 protein of tomato bushy stunt virus, encoding for a suppressor of gene silencing (Voinnet et al., 2003).

Confocal Microscopy

[180] Fluorescence in tobacco epidermal cells was assessed 2 d after infiltration using a CLSM-510-META-UV confocal microscope (Zeiss). For single protein localization, GFP fluorescence was excited at 488 nm with light from an argon laser and collected after passage through an NFT545 dichroic mirror with a 505-nmlong-pass filter. RFP fluorescence was excited at 543 nm with light from a helium neon laser and was collected after passage through an NFT545 dichroic mirror and a 560- to 615-nm band-pass filter. YFP fluorescence was excited at 514 nm with light from an argon laser and collected using lambda mode between 520 and 550 nm. Co-localization plane and line scans were evaluated using Zeiss LSM510AIM software (v3.2).

Pull-Down Assays

[181 ] Protein pulldown were performed as previously described (Perrella et al, 2013). In short, histidine (His)-fused proteins, GST-fused proteins and GST were expressed in Escherichia coli BL21 cells. After induction with 0.5mM mM isopropyl b-D-1 -thiogalactopyranoside, cells were harvested and sonicated in lysis buffer. GST-proteins were affinity- purified using Glutathione-Sepharose resin (GE Healthcare) according to the manufacturer's instructions. His-fused proteins were purified using Nickel-NTA resin (Sigma). For pulldowns purified proteins were bound to Glutathione- Sepharose resin and applied to a microcolumn. Nuclei enriched plant lysates were incubated overnight at 4C. For in vitro pulldowns purified proteins bound to Glutathione-Sepharose resin were incubated with His-fused proteins for 4 hours at 4C. After several washes, pulled-down proteins were eluted in Laemmli buffer. For Western blots, the protein samples were boiled, loaded onto SDS-PAGE gel and transferred to nitrocellulose membrane (GE life sciences). Incubation with aHDC, aGST (GE Healthcare) or aHis (Cell Signalling Technology) was overnight at dilutions of 1 :4000, 1 :5000 or 1 :2000, respectively. Secondary antibody conjugated with horseradish peroxidase was applied for at least 1 hour at room temperature. Finally the membrane was covered with ECL Dura HRP reagent (Thermo Fisher Scientific) and the proteins were detected using a chemi-luminescence imaging platform (Fusion FX, Peqlab). Band intensities were quantified using Image J software.

Data analysis

[182] Data were collated and analysed in Excel spreadsheets. Means were calculated across replicates and relevant comparisons were tested using Student t-test. Which comparisons were tested, the numbers of replicates and the p- values are indicated in the figure legends.

Accession numbers

[183] Sequence data for genes used in this study can be found in the GenBank/EMBL libraries and in The Arabidopsis Information Resource or in the Saccharomyces Genome database under the following accession numbers: AT5G08450 (HDC1 ); AT5G631 10 (HDA6); AT4G38130 (HDA19); AT2G45640 (SAP18); AT5G15020 (SNL2); AT1 G24190 (SNL3); AT4G39100 (SHL1 ), AT1 G54390 (ING2); AT1 G09200 (H3.1); AT4G40030 (H3.3); AT1 G06760 (H1.1), AT2G30620 (H1.2); AT2G18050 (H1.3) AT5G58230 (MSI1 ); YDL076C (ScRXT3).

Example 2: HDC1 directly interacts with histone-binding protein and associated proteins

[184] Based on the homology search of proteins co-eluting with Rxt3 in yeast complexes and on reported phenotypes and protein interactions in plants (Tables 1 and 2), we selected a subset of A. thaliana proteins as candidate interactors with HDC1 : the histone-binding proteins SHL1 , ING2 and MSI1 (Mussig et al., 2000; Mussig and Altmann, 2003; Lee et al., 2009; Lopez-Gonzalez et al., 2014; Mehdi et al., 2015), the Sin3-like (SNL) co-repressors SNL2 and SNL3 (Song et al., 2005; Wang et al., 2013), and the Sin3-associated protein SAP 18 (Song and Galbraith, 2006). We also included the histone deacetylases (HDA6 , HDA19; (Chen and Wu, 2010)), H3 variants (H3.1., H3.3; (Jacob et al., 2014)) and H1 variants (H1.1 , H1.2 and H1.3; (Ascenzi and Gantt, 1999a)) in the interaction assays.

[185] The ability of protein pairs to directly interact with each other was investigated using Bimolecular Fluorescence Complementation (BiFC, Figure 1 ). The proteins were fused to N- or C-terminal halves of Yellow Fluorescent Protein (YFP) and transiently co-expressed in tobacco leaves. We used a ratiometric assay (Grefen and Blatt, 2012) expressing the two fusion proteins and a full-length Red Fluorescent Protein (RFP) from the same vector (2-in-1 vector, Figure 1A). In total, 37 pairwise interactions were assayed in almost a thousand cells. The RFP signal quantifies transgene expression in each cell, and the ratio between YFP and RFP signals allows normalisation and hence direct comparison of interactions between different cells for statistical analysis. In all positive cases the complemented YFP signal was observed inside the nuclei (Figure 1 B). [186] To assess whether the Rxt3-like part of the protein is required and sufficient for some or all of the interactions we generated a truncated version of HDC1 spanning amino acids 449 to 764 (Rxt3-like; RXT3L, Figure 1 C), approximately a third of the full-length protein. Expression of GFP-fusion proteins in tobacco leaves showed that full- length HDC1 and RXT3L were exclusively located in the nuclei. Sequence analysis with PSORT (Nakai and Kanehisa, 1992) highlighted two different putative nuclear retention signals in HDC1 (KR KELKHREWGD RDKDR starting at aa 358, and KR RERDGDSEAE RAEKR starting at aa 479). Only the latter was present in RXT3L suggesting that it is sufficient for nuclear localisation. Yeast ScRXT3 contains neither of the motifs and GFP-ScRXT3 was not retained in the nuclei (Figure 3), suggesting that the 479 motif is necessary for nuclear retention in plant cells.

[187] Figure 1 D shows the interaction profile of HDC1 based on YFP/RFP ratios obtained from cells co-expressing HDC1 with candidate interactors. Signals were measured in at least 10 cells from three independently transformed plants. Figure 4 shows the respective interaction profiles for SHL1 , ING2, MSI1 , SAP18, HDA6 and HDA19. The following observations confirmed the validity of the approach. Firstly, for each protein a significant complementation signal was detected with at least one other protein confirming that all fusion proteins were properly expressed. Secondly, the complementation signal was always observed inside the nuclei, confirming correct targeting of the fusion proteins. Thirdly, the interaction profiles differed between the proteins tested, confirming specificity of the interactions.

[188] As we have previously reported, HDC1 can directly interact with the deacetylases HDA6 and HDA19. No direct interaction was found for HDC1 with the co-repressors SNL3 or SNL2 but a strong YFP-complementation signal was recorded when HDC1 was co-expressed with SAP18. SAP18 also failed to directly interact with SNL3 or SNL2 (Figure 4). However, SNL2, SNL3 and SAP18 all produced a signal with HDA19 confirming correct expression/folding of the fusion proteins.

[189] HDC1 showed interaction with the histone-binding proteins SHL1 and ING2, but not with H3 itself. As expected, SHL1 and ING2 both produced YFP signals with H3 (Figure 4). They also showed very strong interaction with each other. In addition, SHL1 produced YFP signals when co-expressed with the HDAs or with SAP18. BiFC also showed direct interaction between HDCI and the H3-binding protein MSI 1 .

[190] HDA19 displayed the broadest interaction profile (Figure 4 ). The strongest signal was obtained with HDC1 . Complementation signals with SNL3, SNL2 and SAP18 were weaker than with HDC1 and SHL1 , but significantly higher than the signals produced by SNL3 with H DC1 or other proteins. Despite previous reports showing pull-down of MSI1 with HDA19 we did not record a BiFC signal for these two proteins, suggesting that their interaction is indirect potentially via HDC1. HDA6 had a more selective interaction profile. It strongly interacted with HDC1 and SHL1 but failed to produce BiFC signals with the other proteins tested (Figure 4).

[191 ] In summary, the BiFC study identified HDC1 and SHL1 as a potentially important interaction hub in HDAC complexes. To confirm native HDC1 -SHL1 assembly we carried out in in-vivo pulldown assays with protein extracts from A thaliana leaves using SHL1 as bait. As shown in Figure 1 E, SHL1 -GST (but not GST alone, 1 ^st negative control) pulled down native HDC1 (detected with HDC1 -antibody) in protein extracts from wildtype plants, but not from hdc1-1 knockout plants (2^nd negative control). Statistically significant SHL1 -HDC1 interaction was confirmed in three independent pulldown experiments (Figure 5). HDC1 was not recovered in pulldown assays using a truncated version of SHL1 (amino acids (aa) 21 -137) spanning the histone-binding bromo-adjacent homology (BAH) domain (- Figure 6). Thus the BAH domain is not involved or not sufficient for the interaction of SHL1 with HDC1. Motivated by our previous finding that HDC1 -mediated growth enhancement was maintained under salt stress (Perrella et al, 2013) we also tested interaction between SHL1 and HDC1 in leaf tissue collected from plants subjected to salt (150 mM NaCI for 24 h). Using full-length SHL1 as a bait HDC1 was successfully pulled-down from salt-treated wildtype plants but not from salt-treated hdc1-1 plants (- Figure 7).

Example 3: Truncation of HDC1 protein to the yeast RXT3-like core weakens most interactions but does not impact on binding of SHU or H1

[192] A 315- aa stretch in the C-terminal half of the 918-aa long HDC1 protein aligns to the shorter Rxt3-like proteins in algae and fungi (Perrella et al., 2013). This part of the protein is also more conserved within higher plants than the rest of the protein, and it contains a highly conserved motif of unknown function (PF08642, 602-650 aa in HDC1 ). To assess whether the Rxt3-like part of the protein is required and sufficient for some or all of the interactions within the plant protein complex we carried out ratiometric BiFC assays and compared the YFP/RFP ratios obtained with RXT3L (blue bars in Fig. 1 D and Fig. 1 F) with those obtained for full-length HDC1 (black bars). The complementation signals obtained for RXT3L with HDA6, HDA19, ING2, MSI1 or SAP18 were significantly lower than those obtained for full-length HDC1 , although still significantly larger than the ones obtained for each protein with SNL3 (Fig. 1 D). Thus the truncated protein maintains some affinity for these partners but the interaction is considerably weakened. Strikingly, the truncated RXT3L protein fully retained the ability to directly interact with SHL1 , generating a similarly high YFP/RFP signal as full-length HDC1. RXT3L also fully retained the ability to interact with the H1 variants (Fig. 1 F). The strong signals obtained with SHL1 and H1 also proved that lower signals with the other proteins were not due to weak expression of the RXT3L-YFP fusion protein. The ability of Rxt3L to bind SHL1 and H1 was further confirmed in reciprocal in-vitro pull-down experiments, using each of the proteins as bait (Figure 8).

Example 4: Truncation of HDC1 protein to the yeast RXT3-like core weakens most interactions but does not impact on binding of SHU or H1

RXT3L partially restores HDC1 functions in plant growth and development

[193] We have previously reported that knockout or overexpression of HDC1 causes a range of phenotypes during plant germination, vegetative growth and flowering (Perrella et al., 2013). To assess the ability of the RXT3L part of the protein to mediate downstream effects of H DC 1 -dependent histone deacetylation we expressed RXT3L in the HDC1 - knockout line hdc1-1 and in wildtype plants under the control of the 35S promoter. Two homozygous lines from each background were used for the experiments. qPCR analysis with primers in the RXT3L domain (- Figure 9) confirmed the presence of RXT3L transcript in the overexpressing and complemented lines.

[194] Figure 2 shows that the truncated protein was able to carry out functions of full-length HDC1 in germination and growth but was less effective in replacing HDC1 in other functions such as flowering and petiole length. Figure 2A shows that overexpression of RXT3L decreased the ABA- and NaCI-sensitivity of germinating seeds both in wildtype background and in hdd-1 background thus mimicking full-length HDC1 (Perrella et al., 2013). RXT3L also reproduced the growth enhancement reported for full-length HDC1 ; over-expression of RXT3L caused enhanced shoot fresh weight both in wildtype and in hdd-1 background (Fig. 2B). We have shown before that enhanced biomass is due to larger leaf size, not to changes in the plastochron (Perrella et al., 2013).

[195] RXT3L only partially complemented the delayed flowering phenotype of hdd-1; plant age and number of leaves at bolting were significantly lower than in hdd-1 but still significantly higher than in wildtype (Fig. 2C). Another phenotype of hdd-1 is compact rosette appearance due to shortened petioles (see inserts in Fig. 2D). Petiole length can be rescued by expression of full-length HDC1 (Perrella et al., 2013) but was not restored by expression of RXT3L in hdd-1 (Fig. 2D). Thus, plants expressing RXT3L in hdd-1 background were larger than the knockout plants (growth effect) but bulkier than H DC 1 -complemented or wildtype plants due to short petioles.

[196] Table 1 : Proteins in the S. cereviasae Rpd3L histone deacetylation complex and A. thaliana homologs

Gene Full name Function within the yeast complex¹ Homologs in Selected

Arabidopsis² homolog(s)

Rpd3 Reduced Potassium Histone deacetylase, required for 12 HDA6,

Dependency 3 gene repression HDA19

Sin3 Switch independent 3 Co-repressor, required for gene 20 SNL2

repression SNL3

Ume1 Unscheduled meiotic gene Unknown. Not required for gene None

expression 1 repression.

Sap30 Sin3-associated protein Unknown. Not required for gene None

repression.

Pho23 Phosphate metabolism 23 Histone binding. Required for 8 ING2

complex integrity. Linked to complex

via Rxt2. Not required for HDAC

activity or gene repression.

Cti6 CYC8-TU P-i n te ra cti ng Histone binding. Not required for 9 SHL1

protein 6 gene repression.

Sds3 Suppressor of defective Unknown. Required for complex None

silencing 3 integrity. Not required for gene

repression. Required for HDAC

activity.

Dep1 Deregulated expression of Unknown. Required for complex None phospholipid biosynthesis 1 integrity, HDAC activity and gene

repression

Rxt2 Regulator of transcription 2 Unknown. Not required for HDAC None

activity or gene repression, Links

Pho23 and Rxt3 to complex. Not

required for HDAC activity or gene

repression,

Rxt3 Regulator of transcription 3 Unknown. Required for complex 1 HDC1 integrity. Linked to complex via Rxt2.

Not required for HDAC activity or

gene repression,

^■"Summarised from (Carrozza et al., 2005a) ²E-value < 0.05 and coverage of at least 8%)

[197] Table 2: Information on selected candidates for interaction with HDC1

Lopez-Gonzalez et al., 2014

²(Mussig et al., 2000; Mussig and Altmann, 2003)

³Lee et al., 2009

⁴Wang et al., 2013

⁵Song et al., 2005

⁶Song and Galbraith 2006

⁷Mehdi et al., 2015

⁸Plant homodomain-linked zinc finger domain (histone binding)

9Bromo-adjacent homology motif (histone binding)

0Paired amphipathic helix domain (DNA binding)

1 HDA-interaction domain (protein interaction)

2Histone binding domain RBBP4, N-terminal

1³WD40 repeat Example 5: HDC 1 overexpression in wheat: Materials and methods Cloning Procedures

[198] The wheat codon-optimized RXT3L fragment (nt 1345-2293- of SEQ ID NO 3 preceded by the methionine codon ATG) is ligated between the maize ubiquitin-1 promoter PubiZm and a nos terminator in a vector contains in addition a P35S:bar selectable marker cassette, essentially as described in W014/118123. The ligation reaction product is used to transform MC1061 bacterial cells. Antibiotic marker-resistant colonies are isolated and verified by restriction digest analysis and sequencing.

[199] The plant transformation vector contains two expression cassettes; the selectable marker cassette has the 35S promoter driving the Bar gene and the RXT3L cassette has the maize ubiquitin-1 promoter driving the codon optimized A. thaliana RXT3L coding sequence.

Plant Transformation

[200] Plasmids are inserted by heat shock into Agrobacterium tumefaciens strain AGL1 (Lazo et al. 1991). Agrobacterium-mediated transformation of Triticum aestivum immature embryos is performed using a modification of the Rothamsted method (Wu et al. 2003:_Factors influencing successful Agrobacterium-mediated genetic transformation of wheat. Plant Cell Reports, 21, 659-668). Plants are selected using media containing PPT and regenerated plantlets are transferred to the greenhouse to obtain multiple events. Single copy events are confirmed by Southern Blot analysis.

Example 6: Effect of RXT3L overexpression in wheat on biomass

Plant material and growth conditions

[201 ] To evaluate the response of wheat (Triticum aestivum) containing the RXT3L gene under drought and control conditions, several independent events of the variety Fielder transformed using Agrobacterium tumefaciens with a single copy of the RXT3L gene combined with the bar gene as a selectable marker are used.

[202] 120 seeds of each event and 30 seeds of the wild type variety Fielder are sown in zip lock bags and put in a fridge at 4°C and a 12h light regime. After 8 days, the seeds are sown in square 9cm pots and put in a growth chamber with a 16h light regime (app. 250 par), with a day temperature of 20-22 °C and a night temperature of 14-16°C.

Selection of plant material

[203] At 1 -2 leaf stage, the plants for each event are sampled for cRT-PCR of bar and taqman for presence/absence of the RXTL3 gene. For each event, homozygous plants are selected to be used for the experiment. Treatment

[204] All plants are treated identically to normal watering until 19 days after sowing, when two treatments are imposed. Normal watering ("control") maintains the optimal watering, whilst a restricted watering regime to impose drought stress ("drought"). Soil Water Capacity (SWC) and Soil Retention Capacity (SRC) of the used soil are determined at the start of the experiment. These data are used to determine the target weights of the pots for each treatment. The pots with normal watering are kept at 50% SRC, the pots used in the restricted watering regime are kept at 40% SRC. All pots are weighed on daily basis and if needed, water is added until the target weight is reached. The plants are ordered in a randomized block design with 5 repetitions for each homozygous event and the wild type variety Fielder as control.

Sampling for fresh weight determination

[205] After 14 days of treatment, 33 days after sowing, all plants are harvested to determine fresh weight. Data analysis

[206] All data is recorded using Excel. Data is analyzed using the statistical programming language R. To determine the effects between the homozygous genotypes and the wild type control, a two way ANOVA is used.

Results

[207] Whilst no expression of HDC1 is detected in wild type control or azygous plants, a strong overexpression RXT3L can be detected in transformed events containing the chimeric gene. In the biomass experiment, transformed plants performed better under drought, as well as under control conditions. For those events, there is an increase in biomass (fresh weight) under drought conditions in comparison to the wild type control. The events show an increase in biomass (fresh weight) under control conditions in comparison to the wild type control.

Example 7: Effect of HDC1 overexpression in wheat on yield

Plant material and growth conditions

[208] To evaluate the response of wheat (Triticum aestivum) containing the RXT3L gene under control conditions, several independent events of the variety Fielder transformed using Agrobacterium tumefaciens with a single copy of the RXT3L gene combined with the bar gene as a selectable marker are used. Integrity of the construct is confirmed using left border/right border analysis with PCR, all events with a border that is not intact are excluded from the experiment.

[209] 50 seeds of each event and 30 seeds of the wild type variety Fielder are sown in zip lock bags and put in a fridge at 4°C and a 12h light regime. After 8 days, the seeds are sown in square 9cm pots and are put in a greenhouse compartment with a 16h light regime (app. 250 par), with a day temperature of 20-22 °C and a night temperature of 14- 16°C. After selection, the plants are transplanted in 17cm pots, and are watered with drip irrigation. The plants are grown until full maturity.

Selection of plant material

[210] At 1 -2 leaf stage, the plants are sampled for cRT-PCR of bar and taqman for presence/absence of the RXT3L genes. Of each line, 3 homozygous plants are selected to be grown under normal watering conditions ("control").

Yield traits observations

[21 1 ] The following traits are analyzed during the seed production:

Number of tillers and number of heads

Number of seeds per plant

Yield in gram per plant

Data analysis

[212] All data are recorded using Excel. Data are analyzed using the statistical programming language R. To determine the effects between the homozygous genotypes and the wild types, a two way ANOVA is used.

Results

[213] Whilst no expression of HDC1 is detected in wildtype control or azygous plants, a strong overexpression of RXT3L was detected in transformed events containing the chimeric gene. The events show an increase in comparison to the wild type control in the number of heads. These events show an increase in yield (gram) in comparison to the wild type control.

Example 8: RXT3L overexpression in crop plants

[214] HDC1 overexpression constructs are transformed into crop plants other than wheat according to standard methods known in the art and overexpression is confirmed by RT-PCR, Northern or western blotting. Biomass (of vegetative tissue and seeds) of plants overexpressing HDC1 grown under various stress conditions as described above (e.g. water limiting conditions, salt stress, osmotic stress) or grown under non-stress condition are compared to wt plants grown under the same conditions. An increased biomass is observed in RXT3L -overexpression plants compared to wt, both under stress and under non-stress conditions.

[215] Seeds of the above plants overexpressing RXT3L are subjected to ABA, osmotic stress and/or histone deacetylase inhibitors, and germination was compared to seeds of control plants as described above. Germination of the HDC1 overexpressing seeds was less inhibited by the above treatment compared to wt seeds. [216] Also, seed yield and plant height of RXT3L overexpressing crop plants is compared to that of wt plants. Overexpressing plants display an increased seed yield and increased plant height as compared to wt plants.

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Claims

Claims

1 . A chimeric gene comprising the following operably linked fragments:

i. A plant-expressible promoter

ii. A nucleic acid encoding a functional fragment of an HDC1 protein

iii. Optionally, a 3' end region involved in transcription termination and polyadenylation functional in plants

2. The chimeric gene of claim 1 , wherein said functional fragment of an HDC1 protein has at least 90% sequence identity over its entire length to the corresponding fragment of any one of SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10, SEQ ID NO. 12, SEQ ID NO. 14, SEQ ID NO. 16, SEQ ID NO. 18, SEQ ID NO. 20, SEQ ID NO. 22, SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 28, SEQ ID NO. 30, SEQ ID NO. 32, SEQ ID NO. 34, SEQ ID NO. 36, SEQ ID NO. 38, SEQ ID NO. 40, SEQ ID NO. 41 .

3. The chimeric gene of claim 1 or 2, wherein said functional fragment of an HDC1 protein corresponds to about 95% of the full length HDC1 protein.

4. The chimeric gene of any one of claims 1 -3, wherein said functional fragment of an HDC1 protein corresponds to about 35% of the full length HDC1 protein.

5. The chimeric gene of any one of claims 1 -4, wherein said functional fragment of said HDC1 protein is encoded by a fragment of the nucleotide sequence of SEQ ID NO. 3.

6. The chimeric gene of any one of claims 1 -5, wherein said functional fragment of an HDC1 protein comprises a PF08642 motif.

7. The chimeric gene of any one of claims 1 -6, wherein said functional fragment of an HDC1 protein comprises at least one nuclear localization sequence (NLS).

8. The chimeric gene of any one of claims 1 -7, wherein said functional fragment of an HDC1 protein comprises an RXT3-like domain.

9. The chimeric gene of any one of claims 1 -8, wherein said functional fragment of an HDC1 protein consists of an RXT3-like domain.

10. The chimeric gene of claims 1 -8, wherein said RXT3-like domain has an amino acid sequence having at least 90% sequence identity to amino acids 449-764 of SEQ ID NO. 6.

1 1 . The chimeric gene of any one of claims 1 -6, wherein said functional fragment of an HDC1 protein is a functional fragment of an RXT3-like domain, preferably comprising an NLS and/or a PF08642 motif.

12. A plant, plant part, plant organ, plant cell or seed comprising the chimeric gene of any one of claims 1 -1 1 .

13. The plant, plant part, plant organ, plant cell or seed of claim 12, which is oilseed rape, lettuce, tobacco, cotton, corn, rice, wheat, vegetable plants, carrot, cucumber, leek, pea, melon, potato, tomato, sorghum, rye, oat, sugarcane, peanut, flax, bean, sugar beets, soya, sunflower, ornamental plants.

14. A method for producing a plant, plant part, plant organ or plant cell with increased tolerance to stress conditions, or with reduced ABA sensitivity, or with increased biomass or yield or growth rate, comprising the step of expressing in said plant cell, plant part, plant organ or plant a chimeric gene as described in any one of claims 1 -1 1 .

15. The method of claim 13, comprising the further step of crossing said plant with another plant to obtain a progeny plant also expressing said chimeric gene.

16. An isolated polypeptide encoding a functional fragment of an HDC1 protein as described in any one of claims 1 -1 1 .

17. An isolated nucleic acid encoding the polypeptide of claim 16.

18. Use of an isolated polypeptide of claim 16, an isolated nucleic acid sequence of claim 17 or a chimeric gene of any one of claims 1 -1 1 to produce a plant, plant part, plant organ or plant cell with increased tolerance to stress conditions, or with reduced ABA sensitivity, or with increased biomass or yield or growth rate.