WO2022096829A1

WO2022096829A1 - Use of a specific neolectin for detecting microorganisms

Info

Publication number: WO2022096829A1
Application number: PCT/FR2021/051944
Authority: WO
Inventors: Richard Daniellou; Pierre LAFITE; Mateja SENICAR; Benoît Roubinet; Ludovic LANDEMARRE
Original assignee: Centre National De La Recherche Scientifique (Cnrs); Universite D'orleans; Glycodiag
Priority date: 2020-11-06
Filing date: 2021-11-04
Publication date: 2022-05-12
Also published as: FR3116062A1

Abstract

The present invention relates to the use of a neolectin for detecting the presence of a microorganism or microorganisms in a sample, said microorganism or microorganisms having on their surface at least one hexofuranoside polysaccharide unit, characterized in that said neolectin is derived from a hydrolase specific for a hexofuranoside polysaccharide unit, the hydrolytic activity of which has been reduced.

Description

USE OF A SPECIFIC NEOLECTIN TO DETECT MICROORGANISMS

FIELD OF THE INVENTION

The present invention relates to the use of a specific neolectin for detecting the presence of microorganisms in a sample, said microorganisms having on their surface at least one osidic unit of the hexofuranoside type.

STATE OF THE ART

Glycans are molecules involved in many biological phenomena, and more particularly in cellular communication and molecular recognition, thanks to their saccharide parts. Due to their great structural diversity, many combinations can be obtained by combining several monosaccharide units.

The number of possible combinations is even higher if we consider the natural ability of osidic units to cyclize in two forms: the pyranose form, comprising a heterocycle with 6 atoms: 5 carbon and one oxygen, which is thermodynamically favored , and the furanose form, comprising a 5-atom heterocycle, consisting of 4 carbon atoms and one oxygen atom.

Pentoses, osidic units made up of 5 carbon atoms, exist in one of two forms, pyranose or furanose. We can cite as examples: ribose: ribofuranose is the form present in the nucleic acids of all organisms; in water, the predominant form is B-D-ribopyranose; xylose, a sugar present in plants and wood: the xylopyranose form is predominant in the polysaccharides (pectin, etc.) of plants; in water, the predominant form is B-D-xylofuranose.

As regards the hexoses of molecular formula CÔHIZOÔ, these saccharide units can also exist in both forms. For example, beta-galactose exists in the form D-galactofuranose (I, Gal), and in the form D-galactopyranose (II, Galp), as presented in the expanded formulas (I) and (II) below. below:

Formula (I) Formula (II)

However, in mammalian cells, hexoses are exclusively present in the pyranose form: they are called hexopyranosides.

While hexofuranosides are completely absent from mammalian cells, their presence has been observed in certain polysaccharides extracted from microorganisms, in particular pathogenic microorganisms such as Mycobacterium, Trypanosoma, Leishmania and Aspergillus (Peltier et al., 2008).

This specific presence of certain oses, and therefore of the glycoproteins comprising them, could be used to detect, in biological samples, the presence of microorganisms presenting said glycoproteins at their surface. Since hexofuranosides are absent from mammalian cells, these would thus become distinguishable from other cells present in a complex sample.

However, to date, no detection method of this type has been described, for lack of an adequate molecular tool allowing such specific detection of hexofuranosides.

Sugar recognition proteins are called lectins. Due to their specificity for glycans presented on the surface of cells, lectins can serve as a molecular probe to specifically detect certain cells.

Recently, the notion of "neolectins", synthetic lectins produced for a specific purpose, in particular to recognize certain sugars, has been developed. These neolectins can be synthesized de novo, or be derived, by point mutations, from glycosidases or natural lectins (Arnaud et al., 2013).

To date, few natural lectins capable of recognizing oses in furanose form (such as D-galactofuranose, D-arabinofuranose) have been identified.

In humans, two lectins have been identified, intelectin (Tsuji et al., 2001) and DC-SIGN (Chiodo et al., 2013), which recognize D-galactofuranose with low specificity.

However, these two lectins are not exclusively specific to furanose forms: the DC-SIGN lectin is expressed on the surface of dendritic cells, and interacts with D-galactofuranose; this interaction induces a pro-inflammatory immune system response. However, DC-SIGN also interacts with numerous other oses, in particular with D-mannopyranose, with the D-galactopyranose Galp form, as well as with glucoside 6; human intelectin (or Omentin) recognizes D-galactofuranose (B-Galf) and therefore the glycans comprising it, but also other glycans which include the following osidic units: D-phospho-glycerol (Gro-P) units , heptoses, D-glycero-D-talo-oct-2-ulosonic acid (KO) and 3-deoxy-D-manno-oct-2-ulosonic acid (KDO) (Wesener et al., 2015).

US Patent 10,082,506 describes a method for detecting microorganisms based on this ability of human intelectin to bind to these glycans, exclusively expressed by microorganisms. However, it is not a specific detection method for furanose forms.

International application WO 2018/208977 describes another method for detecting D-galactofuranose in a biological sample, based on the use of an antibody specific for D-galactofuranose, after inhibition of the intelectin / D-galactofuranose binding.

However, it is difficult to produce antibodies against sugar units, which are by nature very weakly immunogenic. The use of antibodies to detect sugars is therefore not preferred.

On the other hand, lectins are suitable tools for the detection of sugar units.

However, to date, there is no method using a lectin, making it possible to detect only and specifically the presence of a hexofuranose in a biological sample.

The inventors of the present invention have generated for the first time a neolectin having excellent specificity for hexofuranoses. The present application describes certain forms of this neolectin specific for an saccharide unit of hexofuranoside type, and also the use of this neolectin for detecting the presence of microorganism(s) expressing said hexofuranoses in a sample.

DISCLOSURE OF THE INVENTION

The present invention relates to the use of a neolectin for detecting the presence of microorganism(s) in a sample, the said microorganism(s) having on their surface at least one osidic unit of the hexofuranoside type, characterized in that said neolectin is derived from a specific hydrolase of a hexofuranoside type osidic unit whose hydrolytic activity has been reduced.

More specifically, said neolectin specifically recognizing a hexofuranoside consists of a specific hydrolase of said hexofuranoside whose catalytic site has been modified to reduce the hydrolytic activity of said enzyme.

More particularly, said neolectin may consist of galactofuranosidase from JHA 19 Streptomyces sp., the hydrolytic activity of which has been reduced relative to its original natural activity.

The present invention also relates to a method for detecting the presence of microorganism(s) in a sample, the said microorganism(s) having on their surface at least one osidic unit of the hexofuranoside type.

The present invention also relates to a detection kit for identifying the presence of microorganisms having on their surface at least one osidic unit of the hexofuranoside type, comprising the following elements: at least one neolectin as described above, or a nucleic acid encoding said neolectin; reagents suitable for the detection of said neolectin.

The present invention also relates to a neolectin as defined above, in particular a neolectin coupled to a marker and/or to a molecular tag.

DESCRIPTION OF FIGURES

[Fig. 1] represents the kinetic characterization of three neolectins of the present invention, derived from the same hydrolase, whose hydrolytic activity (k _ca t) is reduced, capable of specific recognition of Gal (KM of the same order of magnitude as that of the original hydrolase). The relative hydrolysis activity as a function of pH is shown in the lower right graph, for the original hydrolase (WT, in gray) and for the neolectin E464Q (in black).

[Fig. 2A] represents the interaction profile of the BSÀ-Gal/ fluorescent probe with the DC-SIGN lectin as a function of the amount of DC-SIGN bound in the wells. The dotted curve with triangles represents the fluorescence measured when the ManBSλ probe is used. The same experiment is also carried out in the presence of a compound antagonistic to DC-SIGN binding: GalNac-BSÀ.

[Fig. 2B] represents the interaction profile of the probes BSλ-Galf (top), BSλ-Fuc and BSλ-α-Gal (bottom) with Intelectin. The intelectin/BSÀ-Galf interaction is measured as a function the amount of intelectin bound in the wells of the plate. With the other probes, the Intelectin is fixed in the wells at an amount of 2000 ng/well.

[Fig. 2C] represents the interaction profile of the BSA-Galf probe with the neolectin according to the invention, as a function of the quantity of neolectin fixed in the wells.

[Fig. 3A] represents the expanded chemical structures of the galactofuranosides tested as competitors of the BSA-Galf/Neolectin interaction, the results of this competition experiment being shown in Figure 3B.

[Fig. 3B] represents a test for inhibition of the BSA-Galf/Neolectin interaction with the galactofuranosides presented in FIG. 3A: GalfN3 (b-D-Galf N3), Galf-Thiolyl (Tolyl b-D-Galf), PNP-bGalf (pNP b-D- Galf), PNP-bGalp (pNP b-D-Galp) and PNP-aAraF.

[Fig. 4A] represents the detection of the Neolectin/Aspergillus interaction by direct recognition, or [Fig. 4B] by competition with the BSA-Galf.

[Fig. 5] represents the residual hydrolytic activity of the neolectin E464Q (SEQ ID No. 4) as a function of temperature, and demonstrates its thermostability.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to the use of a neolectin for detecting the presence of microorganism(s) in a sample, the said microorganism(s) having on their surface at least one osidic unit of the hexofuranoside type, characterized in that said neolectin is derived from a hydrolase specific for an osidic unit of the hexofuranoside type, the hydrolytic activity of which has been reduced.

The term "lectin" refers to a protein capable of interacting specifically with sugars or glycoproteins comprising sugar units. Lectins are involved in various biological processes, particularly at the level of recognition between cells, by binding with membrane glycoproteins.

Within the meaning of the invention, the term “neolectin” designates a non-natural lectin, synthesized de novo or, more often, obtained from a natural lectin which has been modified in a directed manner to present specific characteristics. This notion of neolectin is notably presented in the article (Arnaud et al., 2013). Thus, the term "neolectin" refers to a synthetic lectin.

Within the meaning of the invention, the terms "hexofuranose" and "hexofuranoside", used interchangeably in the present application, denote free sugar units ("ose") or glycosylated units in the anomeric position ("oside") cyclized in the form "furanose » that is to say comprising a cycle made up of 5 atoms, 4 of carbon and one of oxygen. An example is in particular D-galactofuranose (Gai ), furanose form of galactose, the structural formula of which is presented in formula (I).

By "hydrolytic enzyme" or "hydrolase", used interchangeably in the application, is meant an enzyme having an activity of hydrolysis of molecules according to the general reaction:

RR' + H ₂ O R-OH + R'-H

More specifically, the hydrolase considered within the meaning of the invention is a glycosidase, classified in group EC 3.2.1.x.

Within the meaning of the invention, “a hydrolase specific for an osidic unit of the hexofuranoside type” designates an enzyme whose substrate is a hexofuranoside. This hydrolase therefore has a catalytic site, consisting of a "pocket" for fixing said hexofuranoside, where the hydrolysis reaction presented in equation 1 takes place.

This hydrolase is also qualified, in the present application, as “initial enzyme” or “original enzyme” or “original hydrolase” or even “enzyme before modification”.

The neolectin defined in the invention is derived from said specific hydrolase, that is to say that it was obtained by modifications introduced into the peptide sequence of this original hydrolase.

The expression "reducing the hydrolytic activity of an enzyme" refers to one or more modifications of the peptide sequence of an enzyme, making it possible to reduce or even completely eliminate its catalytic activity.

The expression "hydrolase whose hydrolytic activity has been reduced" designates a hydrolase whose peptide sequence has been modified to reduce or even completely eliminate its enzymatic activity, in particular by modifying its primary sequence.

The reduction in hydrolytic activity can be quantified using the catalytic constant kcat of the enzyme.

The relationship between an enzyme and its substrate can be qualified according to several parameters, and in particular according to two constants: the catalytic constant kc _a t and the Michaelis constant KM.

The catalytic constant kcat represents the maximum number of molecules of substrate transformed per unit of time and per molecule of enzyme; this value is expressed in sec ¹ or min ¹ , that is to say in the number of substrate molecules transformed (in the present case, hydrolyzed according to equation 1 ) in one second or one minute.

According to the invention, the expression "reducing the hydrolytic activity of an enzyme" means reducing the kcat value of this enzyme, for example reducing its kcat value by at least 50%, 60%, 70%, 80%, or 90% of its initial value, or even completely eliminating the activity, i.e. a reduction of 100% of the initial value of kc _at t. A reduction of at least 50% from the initial kcat value means that the kcat value of the hydrolase before any modification has been halved. As shown in the examples, modified hydrolases were obtained with kcat values divided by 80 times or even by 2000 times compared to the initial value of the original enzyme.

According to the invention, a hydrolase whose hydrolytic activity has been reduced is in particular a hydrolase whose kcat value is equal to or less than 10% of the kcat value of the original hydrolase, the two values being measured in equivalent conditions (of pH, temperature, reaction medium, incubation period, etc.), well known to those skilled in the art. This hydrolase is designated in the present application by the terms “modified hydrolase” or “neolectin”.

In particular, a hydrolase whose hydrolytic activity has been reduced has a kcat value equal to or less than 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1 % of the value of k _ca t of the original hydrolase, measured under equivalent conditions.

This reduction or elimination of the hydrolytic activity of an enzyme is carried out without significantly modifying the value of the Michaelis constant of the enzyme considered.

The Michaelis constant, designated by the abbreviation KM, is a value expressed in mole/litre, which corresponds to the value of the substrate concentration for which the enzymatic reaction rate is equal to half the maximum rate Vmax; this constant is related to the dissociation constant (K<j) of the enzyme for its substrate, a value which represents the strength of the interaction between the two, but is generally not strictly equal to it. Indeed, the constant KM also depends on the value of kcat, according to the following equation:

KM = (kcat + k-i) / ki where ki represents the rate of formation of the enzyme-substrate complex and k-i the rate of the reverse reaction of dissociation of the enzyme and the substrate.

The higher the KM, the higher the concentration of substrate required for significant activity of the enzyme. This reflects a low affinity of the enzyme for its substrate.

The lower the KM, the more the maximum enzymatic activity is reached for a low level of substrate concentration. The affinity of the enzyme for the substrate is strong. This is often the case for selective and/or very active enzymes.

In the present case of a modified hydrolase having a catalytic activity represented by the reduced or even very reduced kcat value, the value of the KM is impacted by this value of kcat very weak, but without this affecting the true affinity of the modified enzyme for its substrate.

Preferably, the KM value of the neolectin will be of the same order of magnitude as the initial KM value of the enzyme before modification, the two KM values being measured under equivalent conditions (pH, temperature, reaction medium, duration of incubation...) which can be chosen by the person skilled in the art on the basis of his general knowledge.

The KM value of the neolectin will preferably be about 50%, 60%, 70%, 80%, 90% or 95% of the KM value of the original hydrolase.

D-galactofuranose and specific hydrolase

Hexoses, monosaccharides comprising 6 carbons, all have the same molecular formula CÔHIZOÔ. They all have a carbonyl group: either an aldehyde function in position 1 (aldohexoses); or a ketone function in position 2 (mainly), 3, 4 or 5 (ketohexoses or dihydroxyketone).

We can cite as examples of hexose: glucose, galactose, fucose and mannose, which are naturally present in nature.

Of these hexoses, few have been identified as adopting a furanose-like structure; thus, among the hexofuranoses, D-galactofuranose is the predominant compound.

According to a preferred implementation, the present invention relates to a neolectin specifically recognizing D-galactofuranose (Gai).

Recently, a galactofuranosidase was identified in JHÀ19 Streptomyces sp. (Matsunaga et al., 2015). After purification of this enzyme, it was shown that it exclusively hydrolyses the substrate D-galactofuranose (Senicar et al., 2019). This article reports the use of 21 different monosaccharides tested as a substrate for the enzyme; the results obtained demonstrate that only D-galactofuranose is hydrolyzed, even analogs of Gal such as Ara/ (arabinofuranose) or Rib/ (ribofuranose) are not hydrolyzed by this enzyme.

Furthermore, the kinetic characteristics of this enzyme have been determined: the constant of Michaelis KM with the substrate Gal/ is equal to 250 pM; the catalytic constancy kc _a t is 213 min ¹ . According to a particular implementation, the neolectin of the invention consists of galactofuranosidase from JHA 19 Streptomyces sp., whose catalytic activity has been reduced, and more specifically whose catalytic site has been modified.

The sequence of this galactofuranosidase, before modification of the catalytic site, is presented in SEQ ID NO. 1 .

According to another particular implementation, the neolectin of the invention consists of a galactofuranosidase having a peptide sequence exhibiting at least 80%, or 85%, or 90%, or 95%, or 98%, or 99% identity of sequence with the peptide sequence SEQ ID NO. 1.

Hydrolase Catalytic Site Modifications

All the means known to those skilled in the art for reducing the hydrolytic activity of a hydrolase can be implemented to obtain the neolectin defined in the present application.

For example, the hydrolytic activity of a hydrolase can be reduced by directed or random mutagenesis, or by directed evolution techniques.

In the case where the reduction of the hydrolytic activity of the hydrolase is carried out by site-directed mutagenesis, the point mutations introduced may concern all the portions of the protein. In particular, mutations may be introduced at the periphery of the catalytic site, or even in portions remote from the catalytic site, said mutations making it possible to reduce the activity of the catalytic site by the structural modifications induced.

According to a particular implementation, the hydrolytic activity of the original specific hydrolase has been reduced by modifying the catalytic site of said hydrolase, i.e. of at least one residue of said catalytic site.

The catalytic site, also called active site, refers to a three-dimensional structure within the enzyme, which has the shape of a cavity also called "pocket". The molecules on which the enzyme acts bind in the active site of the enzyme by forming interactions with the surface of the cavity of the active site. Certain amino acids forming the cavity of the active site can participate in the hydrolysis reaction: these amino acids are called catalytic residues.

Those skilled in the art know multiple means of modifying the catalytic site of an enzyme whose peptide sequence and enzymatic activity are known.

With regard to glycosidases, the reaction mechanisms taking place in the catalytic site have been described (Àti et al., 2017). In particular, it has been shown that the reaction hydrolysis involves residues of glutamic acid (E) or aspartic acid (D), whose side chains are negatively charged.

In the context of the present invention, the neolectin is derived from a hydrolase whose catalytic site has been modified so as to reduce its catalytic activity, and therefore the kcat value, while maintaining a significant affinity for the substrate, c ie a KM value of the same order of magnitude as the KM value of the original hydrolase, all these constants being measured independently but under equivalent or even similar experimental conditions in order to be able to be compared.

According to one implementation of the invention, at least one residue of the catalytic site of the hydrolase has been replaced by another residue. "At least one residue" means that one, two, three or even four or more residues of the catalytic site can be replaced.

In particular, a residue of glutamic acid (E) and/or an aspartic acid residue (D), located in the catalytic site of the enzyme, is replaced by another residue whose side chain is not charged. negatively.

This residue E or D may in particular be replaced: by a residue whose side chain can be charged according to the local pH: serine (S), threonine (T), asparagine (N), glutamine (Q); or else by a residue chosen from alanine (A), glycine (G), proline (P) or cysteine (C).

According to a preferred implementation of the invention, the catalytic site of the original hydrolase has been modified by replacing at least one glutamic acid residue (E). More specifically, this glutamic acid residue may be replaced by a serine, a cysteine or a glutamine, preferably by a cysteine or a glutamine. In the case of galactofuranosidase from JHA 19 Streptomyces sp., this glutamic acid residue may in particular be that located at position 464, and/or at position 573. In particular, residue E464 will be replaced by a serine, a cysteine or a glutamine.

According to another implementation of the invention, the catalytic site of the original hydrolase has been modified by the replacement of at least one residue of aspartic acid (D). More specifically, this aspartic acid residue may be replaced by a serine, a cysteine or a glutamine, preferably by a cysteine or a glutamine.

As shown in Example 1, the following residue replacements of galactofuranosidase from JHA 19 Streptomyces sp. have been tested:

E464S is the replacement of glutamic acid at position 464 with a serine;

E464C is the replacement of glutamic acid at position 464 with a cysteine; E464Q the replacement of glutamic acid at position 464 with a glutamine.

The kinetic characteristics (Michaelis constant KM and catalytic constant kc _a t) of each modified hydrolase were determined and are presented in Table 1 below:

[Table 1 ]

Among these modified enzymes, with the aim of obtaining a neolectin specifically recognizing D-galactofuranose but possessing a reduced hydrolysis activity, the choice falls on proteins presenting both a KM (constant linked to the affinity for substrate) of the same order of magnitude as that of the original enzyme, and a kcat reduced to less than 10% of the kcat value of the original hydrolase.

In the present case, the galactofuranosidases with the point mutations E464S, E464C and E464Q show these characteristics of kcat and KM.

Thus, according to a particular implementation of the invention, the neolectin is a protein having a peptide sequence chosen from the following: SEQ ID No. 2, SEQ ID No. 3, and SEQ ID No. 4. More specifically, the neolectin according to the invention is a protein having the peptide sequence SEQ ID No. 4.

Other modifications of the catalytic site of a hydrolase can be envisaged and are included in the present invention, such as for example the total elimination (without replacement) of a residue of the catalytic site, in particular of a residue of glutamic acid or of aspartic acid.

These modifications will be made by genetic engineering, by modifying the nucleic acid coding for the peptide sequence of the enzyme in question.

Advantageously, the neolectin defined above retains the original properties of the hydrolase from which it is derived. For example, the hydrolase from JHA 19 Streptomyces sp., a thermophilic microorganism, is originally thermostable. Advantageously, the neolectin derived from this hydrolase is particularly thermostable, as presented in the experimental part of the application. The present invention also relates to the use of a neolectin coupled to at least one protein having another function, for example to an enzyme or to a cytotoxic protein. Such a protein construct is referred to as a “multifunctional neolectin”. This multifunctional neolectin comprises at least two covalently or non-covalently bonded monomers, one of which is the neolectin according to the invention.

The present invention also relates to the use of a multimeric neolectin consisting of at least two neolectins, including at least one neolectin as defined above.

Each monomer is made up of a peptide chain comprising a site that specifically recognizes a particular osidic unit.

Monomeric proteins include dimers (which consist of two subunits), trimers (three subunits), tetramers (four subunits), etc.

According to one implementation, a multimeric neolectin comprises at least two, three or four monomers, all consisting of a neolectin as defined above, and therefore contains at least two, three or four identical active sites.

According to another implementation, the multimeric neolectin used comprises a single monomer consisting of a neolectin as defined above, coupled to one or more other monomers consisting of other lectins, each having a recognition site having a specificity different and therefore recognizing other saccharide units than D-galactofuranose.

For example, the multimeric neolectin used will comprise a monomer specific for a furanose entity, and another monomer specific for a pyranose entity. By thus modulating the specificity of a multimeric neolectin, it will be possible to create neolectins capable of recognizing with great specificity a particular microorganism, having an original signature of osidic entities expressed on the surface.

According to a particular implementation, the neolectin used can be coupled to a marker and/or to a molecular tag.

This coupling may be covalent or non-covalent, and will preferably be a covalent coupling. This coupling will be carried out by genetic engineering, by associating the nucleic acids encoding on the one hand the neolectin as defined, and on the other hand the marker or/and the molecular tag.

The marker can be a biotin (recognized by streptavidin), or a colored or fluorescent marker, such as for example a fluorescent protein (GFP, RFP, CFP, YFP). A molecular tag may in particular be chosen from among the "tags" well known to those skilled in the art, added by genetic modification: poly-histidine tags (5 or 6 histidines), FLAG tag (DYKDDDK), HA tag (YPYDVPDYA), glutatione -S-transferase, Calmodulin Binding Peptide (26 amino acid tag), etc.

The neolectin used according to the invention is coupled either to a marker, or to a molecular tag, or to a marker and a molecular tag.

Neolectin

The present invention also relates to a neolectin as defined above.

According to a particular implementation, the neolectin according to the invention is coupled to a marker and/or to a molecular tag.

This coupling may be covalent or non-covalent, and will preferably be a covalent coupling. This coupling will be carried out by genetic engineering, by associating the nucleic acids encoding on the one hand the neolectin according to the invention, and on the other hand the marker or/and the molecular tag.

The marker can be a biotin (recognized by streptavidin), or a colored or fluorescent marker, such as for example a fluorescent protein (GFP, RFP, CFP, YFP).

A molecular tag may in particular be chosen from the "tags" well known to those skilled in the art, added by genetic modification: poly-histidine tags (5 or 6 histidines), FLAG tag (DYKDDDK), HA tag (YPYDVPDYA), glutatione -S-transferase, Calmodulin Binding Peptide (26 amino acid tag), etc.

The neolectin according to the invention is coupled either to a marker, or to a molecular tag, or to a marker and a molecular tag.

Method for detecting microorganisms

The present invention also relates to a method for detecting the presence of microorganism(s) in a sample, the said microorganism(s) having on their surface at least one osidic unit of the hexofuranoside type, comprising the following steps: bringing the sample into contact with at least one neolectin coupled to a marker and/or to a molecular tag, detection of the marker and/or of the molecular tag, characterized in that when the said marker and/or molecular tag is detected, then the presence of at least one microorganism exhibiting at its surface at least one osidic unit of hexofuranoside type is established. In other words, the present invention relates to a method for detecting the presence of microorganism(s) in a sample, the said microorganism(s) having on their surface at least one osidic unit of the hexofuranoside type, comprising a step of bringing the neolectin into contact as described above with the sample, and a step of detecting the interactions of this neolectin with osidic units present in the sample.

The contacting step could for example be carried out in the wells of a plate suitable for such tests. Advantageously, the neolectin used is immobilized on the plate and each sample tested is placed in different wells of the plate.

The conditions of this contacting step will be easily determined by those skilled in the art, in particular as regards the incubation period, the agitation and the temperature. The conditions presented in Example 4 may in particular be used (incubation for 2 h at 37° C. with gentle agitation).

By “microorganism”, we mean in the sense of the invention any microscopic living being, that is to say invisible to the naked eye. This term refers in particular to bacteria, viruses, parasites and microscopic fungi.

More particularly, the present invention relates to the use of a neolectin as described above, or of the method according to the invention, for detecting the presence of microorganism(s) chosen from bacteria and microscopic and/or unicellular parasites .

The sugar units detected on the surface of said microorganisms are generally incorporated into glycoconjugates (glycoproteins, glycolipids, proteo- and glycosaminoglycans) or oligo-/polysaccharides, present on the surface of certain microorganisms present in the sample.

In the context of this use, the neolectin is coupled to a marker and/or to a molecular tag.

In particular, this use and this method are particularly suitable for detecting microorganisms belonging to one of the following species: Leishmania, Mycobacterium, Trypanosoma cruzi, Aspergillus, Reni bacterium salmoninarum, Actinobacillus, Pleuropneumoniae, Yersinia pestis, Lachnoanaerobaculum saburreum and Cryphonectria parasitica.

This use and this process can be carried out on any type of sample, in particular biological samples.

According to a particular implementation of the invention, the sample analyzed will be chosen from the following list: a biological fluid (blood, lymph, tears, respiratory secretions, urine, cerebrospinal fluid) or a sample of tissue from a living organism, human or animal (obtained by biopsy), a sample taken from consumer products such as food or hygiene products, a sample taken from technical products such as laboratory reagents and industrial reagents, a sample taken from stagnant water (marshes, ponds) or flowing water, for example river water, sea water, and water flowing in pipes, and a sample taken from any type of surface (floor, work surfaces, reactor walls).

According to a particular implementation, the sample analyzed comes from a human organism, and the use of the neolectin or the process makes it possible to detect the presence of pathogenic microorganisms in this sample. Neolectin is thus used in a method for diagnosing microbial infections.

Detection kit

According to another aspect, the present invention relates to a detection kit for identifying the presence of microorganisms having on their surface at least one osidic unit of the hexofuranoside type, comprising the following elements: at least one neolectin according to the invention, preferably a neolectin coupled to a marker and/or to a molecular tag, or a nucleic acid encoding said neolectin; reagents suitable for the detection of said neolectin.

This kit may also include an explanatory note, and/or equipment, suitable for carrying out the method for detecting microorganisms described above.

Preferably, the neolectin will be coupled to a colored or fluorescent marker, and the kit will comprise the appropriate reagents for the detection of this colored or fluorescent marker.

According to a particular implementation, the kit comprises an expression vector, consisting of nucleic acid, coding for a neolectin according to the invention; this expression vector will be introduced into host cells, in particular bacterial cells, to allow the expression of the neolectin. Advantageously, the kit then comprises reagents allowing the introduction of the expression vector into host cells. EXAMPLES

Example 1. Generation of a neolectin from a hydrolase

An enzyme with excellent enzymatic activity has been modified to suppress its hydrolytic activity and retain only its recognition properties to make it a synthetic lectin specific for D-galactofuranose called neolectin.

The following neolectins have been characterized:

E464S is the replacement of glutamic acid at position 464 with a serine;

E464C is the replacement of glutamic acid at position 464 with a cysteine;

E464Q is the replacement of glutamic acid at position 464 with a glutamine.

The kinetic characteristics (Michaelis constant KM and catalytic constant kc _a t) were determined and are presented in Figure 1 and in the following table 2:

[Table 2]

The sequence of galactofuranosidase WT (wild) from JHA 19 Streptomyces sp., 786 amino acids in length, is as follows (SEQ ID NO.1); residue E464 is underlined:

MRRVPÀGRQRFÀWLRRRÀRWÀTTÀLÀVFÀLAÀGTÀLTÀTGSÀTAÀPRÀWTPKPSPMTTPWTDQVPVDN PLPEYPRPQLTRPDWÀNLNGIWDFÀVTSÀNÀGQPÀTFPEQIRVPFVÀESÀLSGIQRKITQNDKLWYKRTFT

VPSNWNGRRVQLNFGÀSDWRTTVWVNGRQÀGÀVHSGGYDÀFSYDVTDLLTÀGTNTLWSVWDPTETGT QÀVG KQRI RDVÀPH PGGG I LYTÀÀSG IWQTVWLEPTAAÀHVTRLDLVPDPÀNSRLKVTVRGÀG ISG HQÀR VTVSTGGTTVGTÀTGPVGTEFTVPVPNPRLWTPEDPFLYDVRÀDPLSGGTTVDSVGSYTGMRTIÀLÀSVG G HQRPVLNG KFVFQTGTLDQG YWPDG I YTÀPTDAÀLRH DLQKH KDLG FNMVRKH I KVEPQRWFYWÀDR

LGLLVWQDMPNMERTPDAAÀRTQWEÀEYDRIIDQHRSSPSLVLWVNQNEGWGQYDQÀRLÀDKVKÀYDPT RLVDNMSGVNCCGÀVDGGNGDWDHHVYVGPGTTVPSÀTRAÀVLGEFGGLGFKVÀGHEWYPGGGFSYE DQPDLÀH LN N RFVG Ll DÀI REVRMPRG LSÀSVYTEITDVEN EVNG LLTYDRQWKVDEÀRVRAÀN RÀLI DÀS RGTTÀPLTLPVDQYRSLRVTTPGYTDRFMRHKDGAÀFTEWNÀGSDSLLKNDÀTWRIVPGLÀNGTCYSFES RNYPGQYLRHREYRVYKEAGSGDLYRADATFCPVRGADGGVRLSAYNFPEQYLRHYDAELWLATPGGTH TWDNAALFTQDTTWAVEAPWAP

In the examples of the present application, the peptide sequence used comprises a histidine tag and therefore has the peptide sequence SEQ ID NO. 5, with a length of 822 amino acids, presented below, the underlined characters being the residues of the histidine tag as well as the residue E464:

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSMRRVPAGRQRFAWLRRRARWATTALAVFALAA GTALTATGSATAAPRAWTPKPSPMTTPWTDQVPVDNPLPEYPRPQLTRPDWANLNGIWDFAVTSANAGQ PATFPEQIRVPFVAESALSGIQRKITQNDKLWYKRTFTVPSNWNGRRVQLNFGASDWRTTVWVNGRQAGA VHSGGYDAFSYDVTDLLTAGTNTLWSVWDPTETGTQAVGKQRIRDVAPHPGGGILYTAASGIWQTVWLE PTAAAHVTRLDLVPDPANSRLKVTVRGAGISGHQARVTVSTGGTTVGTATGPVGTEFTVPVPNPRLWTPE DPFLYDVRADPLSGGTTVDSVGSYTGMRTIALASVGGHQRPVLNGKFVFQTGTLDQGYWPDGIYTAPTDA ALRH DLQKH KDLG FNMVRKH I KVEPQRWFYWADRLG LLVWQDMPNMERTPDAAARTQWEAEYDRI I DQH RSSPSLVLWVNQNEGWGQYDQARLADKVKAYDPTRLVDNMSGVNCCGAVDGGNGDWDHHVYVGPGT TVPSATRAAVLGEFGGLGFKVAGHEWYPGGGFSYEDQPDLAHLNNRFVGLIDAI REVRMPRG LSASVYTEI TDVENEVNGLLTYDRQWKVDEARVRAANRALIDASRGTTAPLTLPVDQYRSLRVTTPGYTDRFMRHKDG AAFTEWNAGSDSLLKNDATWRIVPGLANGTCYSFESRNYPGQYLRHREYRVYKEAGSGDLYRADATFCPV RGADGGVRLSAYNFPEQYLRHYDAELWLATPGGTHTWDNAALFTQDTTWAVEAPWAP

The following examples use the neolectin “ _E464Q ” which exhibits a k cat constant of approximately 1% of the k cat value of the original hydrolase.

The hydrolytic activity of this neolectin E464Q (SEQ ID No. 4) was measured as a function of pH and is presented at the bottom right of Figure 1. The rate of 100% is representative of the best activity obtained.

Example 2. Binding characteristics of this neolectin to Gal, in comparison with those of the lectins DC-SIGN and intelectin-1.

A fluorescent probe presenting multiple D-galactofuranose entities was used for these studies, it is called BSA-Galf. DC-SIGN is not able to recognize the D-galactofuranose entity (carried by this probe), contrary to what has been published (Figure 2A). Indeed, DC-SIGN is not able to move the probe: there is therefore no fluorescence intensity measured.

The second lectin that has been reported in the literature to interact with D-galactofuranose is lntelectin-1 (or Omentin or Intelectin). The results obtained are presented in Figure 2B, and show that the interaction of the lectin with the BSÀ-Galf probe is well detected and is specific for this sugar (no interaction with the BSÀ-Fuc and BSÀ-aGal probes).

The results presented in Figure 2C show that the neolectin according to the invention interacts with the BSλ-Galf probe (Figure 2C).

Based on these results, the IC50 for the Galf probe (which represents the amount of inhibitor needed to achieve 50% inhibition of enzyme/substrate binding, which is therefore another constant related to affinity) neolectins tested was determined:

16 nM for inlectin-1;

24 nM for the neolectin tested, i.e. an IC50 of the same order of magnitude as that determined under similar conditions for intelectin-1.

Example 3. Specificity of D-D-galactofuranose binding of neolectin

Inhibition tests were also carried out on neolectin with the following monosaccharides: PNP-BGalf, PNPBDGalp, PNPaLÀraf, GalfN3, GalfTolyl (inhibitor Galf), whose chemical structures are presented in Figure 3A.

The experimental protocol for performing inhibition tests on neolectin was described in the article (Landemarre et al., 2013). The neolectin is first immobilized at the bottom of a 96-well plate. The interaction profiles of each compound were determined by an indirect method based on the inhibition by the compound of the interaction between the neolectin and the NeoGalf neoglycoprotein specific for the latter. Briefly, a mixture of neoglycoproteins (fixed concentration) and corresponding compounds (range of concentrations) prepared in PBS supplemented with CaCl2 (1 mM) and MgCl2 (0.5 mM) is added to each well (50 µL each) in triplicate and incubated for two hours at room temperature. After washing with PBS buffer, the streptavidin-DTAF conjugate is added (50 μl) and incubated for 30 min. The plate is then washed again with PBS. Finally, 100 μl of PBS were added for reading the fluorescent plate carried out with a fluorescence reader (λex=485 nm, λem=530 nm, Fluostar OPTIAAλ, BMG LABTECH, France). Signal intensity is inversely correlated to the ability of the compound to be recognized by lectin and expressed as percentage inhibition by comparison with the corresponding tracer alone (Neoglycoprotein).

Figure 3B shows the results obtained. No inhibition takes place in the case of the following oses: PNPBDGalp, PNPaLAraf, which demonstrates the specificity of the neolectin of the invention for D-galactofuranose. The neolectin tested recognizes neither D-galactopyranose nor arabinose, which are the 2 structurally closest sugars. Only GalfN3 and Galf-Tolyle are recognized.

Example 4. Use of neolectin to detect microorganisms in a biological sample

A first conclusive and encouraging test was carried out with Aspergillus niger, by demonstrating the direct interaction between the neolectin and the microorganism (Figure 4A) or by inhibiting this interaction by BSA-Galf (Figure 4B).

The neolectin is first immobilized at the bottom of a 96-well plate. A bacterial culture of Aspergillus niger is carried out following the requirements specific to this microbial type. After centrifugation and counting, the microbial pellet is taken up in PBS and labeled with carboxyfluorescein diacetate succinimidylester (CFDA-SE, Sigma-Aldrich, St. Louis, MO, USA) for 1 hour at 37° C. Then the bacterial suspension is centrifuged and washed twice using PBS buffer. The labeled bacteria are added to each well of the microplate immobilized with the neolectin and incubated for 2 h at 37° C. with gentle shaking. After washing with PBS, the fluorescence intensity is measured using a microplate reader (λex=485 nm, λem=530 nm, Fluostar OPTIMA, BMG LABTECH, France). In parallel, a calibration curve is produced with the solution of labeled bacteria to determine the number of bacteria remaining in interaction with the neolectin.

Example 5. Other characteristics of the neolectins used according to the invention

Neolectins exhibit thermostability up to 60-70°C, which is an advantage for the study of complex biological fluids.

It will be noted that in particular, the endogenous lectins of the intelectin-1 type are not thermostable. REFERENCES

US 10,082,506

WO 2018/208977

WO 2015/132699

Peltier, P., Euzen, R., Daniellou, R., Nugier-Chauvin, C., & Ferrières, V. (2008). Recent knowledge and innovations related to hexofuranosides: structure, synthesis and applications. Carbohydrate research, 343(12), 1897-1923.

Arnaud, J., Audfray, A., & Imberty, A. (2013). Binding sugars: from natural lectins to synthetic receptors and engineered neolectins. Chemical Society reviews, 42(11), 4798-4813.

Tsuji, S., Uehori, J., Matsumoto, M., Suzuki, Y., Matsuhisa, A., Toyoshima, K., & Seya, T. (2001). Human intellect is a novel soluble lectin that recognizes galactofuranose in carbohydrate chains of bacterial cell wall. The Journal of biological chemistry, 276(26), 23456-23463.

Chiodo, F., Marradi, M., Tefsen, B., Snippe, H., van Die, I., & Penadés, S. (2013). High sensitive detection of carbohydrate binding proteins in an ELISA-solid phase assay based on multivalent glyconanoparticles. PloS one, 8(8), e73027.

Wesener, D.A., Wangkanont, K., McBride, R., Song, X., Kraft, M.B., Hodges, H.L, Zarling, L.C., Splain, R.A., Smith, D.F., Cummings, R.D., Paulson, J.C., Forest , K.T., & Kiessling,

L.L. (2015). Recognition of microbial glycans by human intelectin-1. Nature structural & molecular biology, 22(8), 603-610.

Matsunaga, E., Higuchi, Y., Mori, K., Yairo, N., Oka, T., Shinozuka, S., Tashiro, K., Izumi,

M., Kuhara, S., & Takegawa, K. (2015). Identification and Characterization of a Novel Galactofuranose-Specific B-D-Galactofuranosidase from Streptomyces Species. PloSone, 10(9), e0137230.

Senicar, M., Legentil, L., Ferrières, V., Eliseeva, S. V., Petoud, S., Takegawa, K., Lafite, P., & Daniellou, R. (2019). Galactofuranosidase from JHA 19 Streptomyces sp.: subcloning and biochemical characterization. Carbohydrate research, 480, 35-41.

Ati, J., Lafite, P., a Daniellou, R. (2017). Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides. Beilstein journal of organic chemistry, 13, 1857-1865.

Landemarre, L., a Duverger, E. (2013). Lectin glycoprofiling of recombinant therapeutic interleukin-7. Methods in molecular biology (Clifton, N.J.), 988, 221-226.

Claims

1. Use of a neolectin to detect the presence of microorganism(s) in a sample, said microorganism(s) having on their surface at least one osidic unit of hexofuranoside type, characterized in that said neolectin is derived from a specific hydrolase of a hexofuranoside type osidic unit whose hydrolytic activity has been reduced.

2. Use according to claim 1, characterized in that the hydrolytic activity of the specific hydrolase has been reduced by modifying the catalytic site of said hydrolase.

3. Use according to claim 2, characterized in that at least one residue of the catalytic site of the specific hydrolase has been replaced by another residue.

4. Use according to one of claims 1 to 3, characterized in that the hydrolase specific for an osidic unit of the hexofuranoside type is a hydrolase specifically recognizing D-galactofuranose.

5. Use according to one of claims 1 to 4, characterized in that the neolectin is derived from the galactofuranosidase of JHA 19 Streptomyces sp., the hydrolytic activity of which has been reduced.

6. Use according to one of claims 1 to 5, characterized in that the neolectin used is a neolectin coupled to a marker and/or to a molecular tag.

7. Use according to one of claims 1 to 6, wherein said detected microorganisms belong to one of the following species: Leishmania, Mycobacterium, Trypanosoma cruzi, Aspergillus, Renibacterium salmoninarum, Actinobacillus, Pleuropneumoniae, Yersinia pestis, Lachnoanaerobaculum saburreum and Cryphonectria parasitica.

8. Use according to one of claims 1 to 7, in which the sample is chosen from: a biological fluid (blood, lymph, tears, respiratory secretions, urine, cerebrospinal fluid) or a tissue sample from a living organism, human or animal,

- a sample taken from consumer products such as food or hygiene products,

- a sample taken from technical products such as laboratory reagents and industrial reagents,

- a sample taken from stagnant water (marshes, ponds) or flowing water, for example river water, sea water, and water flowing in pipes, and

- a sample taken from any type of surface (floor, work surfaces, reactor walls).

9. Detection kit for the implementation of a use according to claims 1 to 8, comprising the following elements: at least one neolectin as defined in one of claims 1 to 6, preferably according to claim 6, or a nucleic acid encoding said neolectin; and reagents suitable for the detection of said neolectin.

10. Neolectin as defined according to one of claims 1 to 6, coupled to a marker and/or to a molecular tag.