Magali Remaud-Simeon

Homopolysaccharides from lactic acid bacteria

Abstract In addition to heteropolysaccharides of complex structure, lactic bacteria produce a variety of homopolysaccharides containing only either d -fructose or d -glucose. These fructans and glucans have a common feature in being synthesized by extracellular transglycosylases (glycansucrases) using sucrose as glycosyl donor. The energy of the osidic bond of sucrose enables the efficient transfer of a d -fructosyl or d -glucosyl residue via the formation of a covalent glycosyl-enzyme intermediate. In addition to the synthesis of high molecular weight homopolysaccharides, glycansucrases generally catalyse the synthesis of low molecular weight oligosaccharides or glycoconjugates when efficient acceptors, like maltose, are added to the reaction medium. While the enzymatic synthesis of fructans (levan and inulin) is poorly documented at the molecular level, the field of Streptococcus and Leuconostoc glucansucrases (glucosyltransferases and dextransucrases) has been well studied, both at the mechanistic and gene structure levels. The nutritional applications of the corresponding polysaccharides and oligosaccharides account for this increasing interest.

Amylosucrase from Neisseria polysaccharea: novel catalytic properties.

Amylosucrase is a glucosyltransferase that synthesises an insoluble α‐glucan from sucrose. The catalytic properties of the highly purified amylosucrase from Neisseria polysaccharea were characterised. Contrary to previously published results, it was demonstrated that in the presence of sucrose alone, several reactions are catalysed, in addition to polymer synthesis: sucrose hydrolysis, maltose and maltotriose synthesis by successive transfers of the glucosyl moiety of sucrose onto the released glucose, and finally turanose and trehalulose synthesis – these two sucrose isomers being obtained by glucosyl transfer onto fructose. The effect of initial sucrose concentration on initial activity demonstrated a non‐Michaelian profile never previously described.

Characterization of Leuconostoc mesenteroides NRRL B-512F dextransucrase (DSRS) and identification of amino-acid residues playing a key role in enzyme activity

Dextransucrase (DSRS) from Leuconostoc mesenteroides NRRL B-512F is a glucosyltransferase that catalyzes the synthesis of soluble dextran from sucrose or oligosaccharides when acceptor molecules, like maltose, are present. The L. mesenteroides NRRL B-512F dextransucrase-encoding gene (dsrS) was amplified by the polymerase chain reaction and cloned in an overexpression plasmid. The characteristics of DSRS were found to be similar to the characteristics of the extracellular dextransucrase produced by L. mesenteroides NRRL B-512F. The enzyme also exhibited a high homology with other glucosyltransferases. In order to identify critical amino acid residues, the DSRS sequence was aligned with glucosyltransferase sequences and four amino acid residues were selected for site- directed mutagenesis experiments: aspartic acid 511, aspartic acid 513, aspartic acid 551 and histidine 661. Asp-511, Asp-513 and Asp-551 were independently replaced with asparagine and His-661 with arginine. Mutation at Asp-511 and Asp-551 completely suppressed dextran and oligosaccharide synthesis activities, showing that at least two carboxyl groups (Asp-511 and Asp-551) are essential for the catalysis process. However, glucan-binding properties were retained, showing that DSRS has a two-domain structure like other glucosyltransferases. Mutations at Asp-513 and His-661 resulted in greatly reduced dextransucrase activity. According to amino acid sequence alignments of glucosyltransferases, α-amylases or cyclodextrin glucanotransferases, His-661 may have a hydrogen-bonding function.

Glucansucrases: molecular engineering and oligosaccharide synthesis

Due to their informative role in biological systems, the potential development of oligosaccharide utilization is very important. Today, their industrial application is increasing rapidly especially for their capability of specific stimulation of beneficial bacteria. Future development will require the access to specific oligosaccharides synthesized via processes compatible with technical and economical industrial constraints. In this context, glucansucrases are attractive tools allowing the production of different glucooligosaccharides (GOS) from simple substrates such as sucrose and maltose. These bacterial enzymes are responsible for the synthesis of glucan polymers. They can also synthesize oligomers when an acceptor molecule is introduced into the medium. A large variety of glucosidic bonds are formed corresponding to variable regiospecificities dependent on the enzyme origin. More than 30 glucansucrase-encoding genes have been cloned and sequenced. Many data were provided from studies on the structure/function relationship on these sucrose-converting glucosyltransferases (GTF). Sequence alignment analysis allowed identification of essential amino acids and clearly showed analogies with enzymes from the large α-amylase family. It is now possible to list some determinants possibly involved in the glucansucrase specificity, but many additional investigations and data, especially about the three-dimensional structure, will be necessary for the rational design of specific enzymatic tools for GOS synthesis.

Biodiversity of exopolysaccharides produced from sucrose by sourdough lactic acid bacteria.

The distribution and diversity of natural exopolysaccharides (EPS) produced from sucrose by thirty heterofermentative lactic acid bacteria strains from French traditional sourdoughs was investigated. The EPS production was found to be related to glucansucrase and fructansucrase extracellular activities. Depending on the strain, soluble and/or cell-associated glycansucrases were secreted. Structural characterization of the polymers by 1H and 13C NMR spectroscopy analysis further demonstrated a high diversity of EPS structures. Notably, we detected strains that synthesize glucans showing amazing variations in the amount of alpha-(1-->2), alpha-(1-->3) and alpha-(1-->6) linkages. The representation of Leuconostoc strains which produce putative alternan polymers and alpha-(1-->2) branched polymers was particularly high. The existence of glucan- and fructansucrase encoding genes was also confirmed by PCR detection. Sourdough was thus demonstrated to be a very attractive biotope for the isolation of lactic acid bacteria producing novel polymers which could find interesting applications such as texturing agent or prebiotics.

Geometric algorithms for the conformational analysis of long protein loops

The efficient filtering of unfeasible conformations would considerably benefit the exploration of the conformational space when searching for minimum energy structures or during molecular simulation. The most important conditions for filtering are the maintenance of molecular chain integrity and the avoidance of steric clashes. These conditions can be seen as geometric constraints on a molecular model. In this article, we discuss how techniques issued from recent research in robotics can be applied to this filtering. Two complementary techniques are presented: one for conformational sampling and another for computing conformational changes satisfying such geometric constraints. The main interest of the proposed techniques is their application to the structural analysis of long protein loops. First experimental results demonstrate the efficacy of the approach for studying the mobility of loop 7 in amylosucrase from Neisseria polysaccharea. The supposed motions of this 17‐residue loop would play an important role in the activity of this enzyme.

Cloning and sequencing of a gene coding for a novel dextransucrase from Leuconostoc mesenteroides NRRL B-1299 synthesizing only α(1–6) and α(1–3) linkages

Abstract The coding region for a Leuconostoc mesenteroides NRRL B-1299 dextransucrase gene ( dsrA ) was isolated and sequenced. Using a pair of primers designed on the basis of two highly conserved amino-acid (aa) sequences in L. mesenteroides NRRL B-512F dextransucrase and streptococcal glucosyltransferases (GTFs), a fragment of dsrA was amplified by the polymerase chain reaction (PCR). This PCR product was used as an hybridization probe to isolate a 1.8-kb fragment identified as the central region of dsrA . Cleavage by Sac I of this fragment allowed two probes to be obtained to isolate the 5′ and the 3′ ends of dsrA . The nucleotide sequence of the dsrA gene was determined and found to consist of an open reading frame (ORF) of 4870 base pairs (bp) coding for a 1290-aa protein with an M r of 145 590. The aa sequence exhibited a high similarity with other GTFs. The two domains previously described in GTFs are conserved in DSRA: an N-terminal conserved domain and a C-terminal domain composed of a series of repeats. Surprisingly, the expected signal peptide was not detected. The entire gene was reconstructed and the activity of DSRA was investigated. The dextran produced appeared to be composed of 85% α(1–6) and 15% α(1–3) linkages and the oligosaccharides synthesized in the presence of maltose were mainly composed of α(1–6) linkages. This enzyme is a novel dextransucrase from L. mesenteroides NRRL B-1299 producing no α(1–2) linkages and is the first glucosyltransferase having no signal peptide described.

Combinatorial engineering to enhance amylosucrase performance: construction, selection, and screening of variant libraries for increased activity

Amylosucrase is a glucosyltransferase belonging to family 13 of glycoside hydrolases and catalyses the formation of an amylose‐type polymer from sucrose. Its potential use as an industrial tool for the synthesis or the modification of polysaccharides, however, is limited by its low catalytic efficiency on sucrose alone, its low stability, and its side reactions resulting in sucrose isomer formation. Therefore, combinatorial engineering of the enzyme through random mutagenesis, gene shuffling, and selective screening (directed evolution) was started, in order to generate more efficient variants of the enzyme. A convenient zero background expression cloning strategy was developed. Mutant gene libraries were generated by error‐prone polymerase chain reaction (PCR), using Taq polymerase with unbalanced dNTPs or Mutazyme™, followed by recombination of the PCR products by DNA shuffling. A selection method was developed to allow only the growth of amylosucrase active clones on solid mineral medium containing sucrose as the sole carbon source. Automated protocols were designed to screen amylosucrase activity from mini‐cultures using dinitrosalicylic acid staining of reducing sugars and iodine staining of amylose‐like polymer. A pilot experiment using the described mutagenesis, selection, and screening methods yielded two variants with significantly increased activity (five‐fold under the screening conditions). Sequence analysis of these variants revealed mutations in amino acid residues which would not be considered for rational design of improved amylosucrase variants. A method for the characterisation of amylosucrase action on sucrose, consisting of accurate measurement of glucose and fructose concentrations, was introduced. This allows discrimination between hydrolysis and transglucosylation, enabling a more detailed comparison between wild‐type and mutant enzymes.

In vitro fermentation of linear and alpha-1,2-branched dextrans by the human fecal microbiota

ABSTRACT The role of structure and molecular weight in fermentation selectivity in linear α-1,6 dextrans and dextrans with α-1,2 branching was investigated. Fermentation by gut bacteria was determined in anaerobic, pH-controlled fecal batch cultures after 36 h. Inulin (1%, wt/vol), which is a known prebiotic, was used as a control. Samples were obtained at 0, 10, 24, and 36 h of fermentation for bacterial enumeration by fluorescent in situ hybridization and short-chain fatty acid analyses. The gas production of the substrate fermentation was investigated in non-pH-controlled, fecal batch culture tubes after 36 h. Linear and branched 1-kDa dextrans produced significant increases in Bifidobacterium populations. The degree of α-1,2 branching did not influence the Bifidobacterium populations; however, α-1,2 branching increased the dietary fiber content, implying a decrease in digestibility. Other measured bacteria were unaffected by the test substrates except for the Bacteroides-Prevotella group, the growth levels of which were increased on inulin and 6- and 70-kDa dextrans, and the Faecalibacterium prausnitzii group, the growth levels of which were decreased on inulin and 1-kDa dextrans. A considerable increase in short-chain fatty acid concentration was measured following the fermentation of all dextrans and inulin. Gas production rates were similar among all dextrans tested but were significantly slower than that for inulin. The linear 1-kDa dextran produced lower total gas and shorter time to attain maximal gas production compared to those of the 70-kDa dextran (branched) and inulin. These findings indicate that dextrans induce a selective effect on the gut flora, short-chain fatty acids, and gas production depending on their length.

Towards a novel explanation of Pseudomonas cepacia lipase enantioselectivity via molecular modelling of the enantiomer trajectory into the active site

Abstract In the transesterification reaction between ( RS )-2-bromophenyl acetic acid ethyl ester and 1-octanol in n -octane, Pseudomonas cepacia lipase enantioselectivity towards the ( R )-isomer is 57. Two strategies are described to investigate the structural basis involved in this enzyme enantioselectivity. Molecular modelling of the tetrahedral intermediate mimicking the transition state enables the identification of two potentially productive substrate-binding modes for each enantiomer. However, the conformations obtained with the faster and slower-reacting enantiomers have equivalent potential energies and most of them possess the hydrogen bonds essential for catalysis. On this basis, it is not possible to distinguish the diastereomeric complexes. The second approach is original and consists in a simple but robust protocol of pseudomolecular dynamics simulations under constraints to map the probable trajectory of the enantiomers in the active site. Enzyme/substrate interaction energy is always found to be lower for the faster-reacting enantiomer, which satisfactorily corroborates the experimental results. Energy differences are attributed to specific interactions of these substrates with a network of hydrophobic residues lining the access path. Furthermore, mechanistic details suggest that the pivoting side chains of the hydrophobic residues act in a concerted step–tooth gear motion whose basic role is to select and guide the substrates towards the active site. With this type of lipase, such dynamic features could be the key explanation of this as yet unexplored enantiorecognition. For the slower-reacting enantiomer, it appears that the concerted motion of the side chains is perturbed when the substrate passes through a bottleneck formed by Val266 and Leu17. The enantioselectivity of mutant Val266Leu with a more bulky side chain at this position supports our assumption: by narrowing the bottleneck, the enantioselectivity was considerably enhanced as much as up to 200.