Juge N

References (10)

Title : Ascertaining the biochemical function of an essential pectin methylesterase in the gut microbe Bacteroides thetaiotaomicron - Duan_2020_J.Biol.Chem_295_18625
Author(s) : Duan CJ , Basl A , Liberato MV , Gray J , Nepogodiev SA , Field RA , Juge N , Ndeh D
Ref : Journal of Biological Chemistry , 295 :18625 , 2020
Abstract : Pectins are a major dietary nutrient source for the human gut microbiota (HGM). The prominent gut microbe Bacteroides thetaiotaomicron was recently shown to encode the founding member (BT1017) of a new family of pectin methylesterases (PMEs) essential for the metabolism of the complex pectin rhamnogalacturonan-II (RG-II). However, biochemical and structural knowledge of this family is lacking. Here, we showed that BT1017 is critical for the metabolism of an RG-II-derived oligosaccharide deltaBT1017oligoB generated by a BT1017 deletion mutant (deltaBT1017) during growth on carbohydrate extract from apple juice. Structural analyses of deltaBT1017oligoB using a combination of enzymatic, mass spectrometric and nuclear magnetic resonance approaches revealed that it is a bi-methylated nona-oligosaccharide GlcA-beta1,4-(2-O-Me-Xyl-alpha1,3)-Fuc-alpha1,4-(GalA-beta1,3)-Rha-alpha1,3-Api-beta1,2-(Araf-alpha1,3)-(GalA-alpha1,4)-GalA containing components of the RG-II backbone and its side chains. We showed that the catalytic module of BT1017 adopts an alpha/beta (alpha/beta) hydrolase fold, consisting of a central twisted 10-stranded beta-sheet sandwiched by several alpha-helices. This constitutes a new fold for PMEs, which are predominantly right-handed beta-helical proteins. Bioinformatics analyses revealed that the family is dominated by sequences from the prominent genera of the HGM, including Bacteroides and Prevotella Our results not only highlight the critical role played by this family of enzymes in pectin metabolism but provide new insights into the molecular basis of the adaptation of B. thetaiotaomicron to the human gut.
ESTHER : Duan_2020_J.Biol.Chem_295_18625
PubMedSearch : Duan_2020_J.Biol.Chem_295_18625
PubMedID: 33097594
Gene_locus related to this paper: bactn-q8a900

Title : The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract - Wegmann_2015_BMC.Genomics_16_1023
Author(s) : Wegmann U , Mackenzie DA , Zheng J , Goesmann A , Roos S , Swarbreck D , Walter J , Crossman LC , Juge N
Ref : BMC Genomics , 16 :1023 , 2015
Abstract : BACKGROUND: Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown.
RESULTS: To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity.
CONCLUSIONS: This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations.
ESTHER : Wegmann_2015_BMC.Genomics_16_1023
PubMedSearch : Wegmann_2015_BMC.Genomics_16_1023
PubMedID: 26626322
Gene_locus related to this paper: lacre-a0a0s4nmr3

Title : Draft Genome Sequence of a Novel Lactobacillus salivarius Strain Isolated from Piglet - Mackenzie_2014_Genome.Announc_2_e01231
Author(s) : Mackenzie DA , McLay K , Roos S , Walter J , Swarbreck D , Drou N , Crossman LC , Juge N
Ref : Genome Announc , 2 : , 2014
Abstract : Lactobacillus salivarius is part of the vertebrate indigenous microbiota of the gastrointestinal tract, oral cavity, and milk. The properties associated with some L. salivarius strains have led to their use as probiotics. Here we describe the draft genome of the pig isolate L. salivarius cp400, providing insights into host-niche specialization.
ESTHER : Mackenzie_2014_Genome.Announc_2_e01231
PubMedSearch : Mackenzie_2014_Genome.Announc_2_e01231
PubMedID: 24526652

Title : The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri - Frese_2011_PLoS.Genet_7_e1001314
Author(s) : Frese SA , Benson AK , Tannock GW , Loach DM , Kim J , Zhang M , Oh PL , Heng NC , Patil PB , Juge N , Mackenzie DA , Pearson BM , Lapidus A , Dalin E , Tice H , Goltsman E , Land M , Hauser L , Ivanova N , Kyrpides NC , Walter J
Ref : PLoS Genet , 7 :e1001314 , 2011
Abstract : Recent research has provided mechanistic insight into the important contributions of the gut microbiota to vertebrate biology, but questions remain about the evolutionary processes that have shaped this symbiosis. In the present study, we showed in experiments with gnotobiotic mice that the evolution of Lactobacillus reuteri with rodents resulted in the emergence of host specialization. To identify genomic events marking adaptations to the murine host, we compared the genome of the rodent isolate L. reuteri 100-23 with that of the human isolate L. reuteri F275, and we identified hundreds of genes that were specific to each strain. In order to differentiate true host-specific genome content from strain-level differences, comparative genome hybridizations were performed to query 57 L. reuteri strains originating from six different vertebrate hosts in combination with genome sequence comparisons of nine strains encompassing five phylogenetic lineages of the species. This approach revealed that rodent strains, although showing a high degree of genomic plasticity, possessed a specific genome inventory that was rare or absent in strains from other vertebrate hosts. The distinct genome content of L. reuteri lineages reflected the niche characteristics in the gastrointestinal tracts of their respective hosts, and inactivation of seven out of eight representative rodent-specific genes in L. reuteri 100-23 resulted in impaired ecological performance in the gut of mice. The comparative genomic analyses suggested fundamentally different trends of genome evolution in rodent and human L. reuteri populations, with the former possessing a large and adaptable pan-genome while the latter being subjected to a process of reductive evolution. In conclusion, this study provided experimental evidence and a molecular basis for the evolution of host specificity in a vertebrate gut symbiont, and it identified genomic events that have shaped this process.
ESTHER : Frese_2011_PLoS.Genet_7_e1001314
PubMedSearch : Frese_2011_PLoS.Genet_7_e1001314
PubMedID: 21379339
Gene_locus related to this paper: lacre-b3xl60 , lacrj-b2g622 , lacre-a0a0s4nmr3

Title : Genome sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608 - Heavens_2011_J.Bacteriol_193_4015
Author(s) : Heavens D , Tailford LE , Crossman L , Jeffers F , Mackenzie DA , Caccamo M , Juge N
Ref : Journal of Bacteriology , 193 :4015 , 2011
Abstract : Lactobacillus reuteri, inhabiting the gastrointestinal tracts of a range of vertebrates, is a true symbiont with effects established as beneficial to the host. Here we describe the draft genome of L. reuteri ATCC 53608, isolated from a pig. The genome sequence provides important insights into the evolutionary changes underlying host specialization.
ESTHER : Heavens_2011_J.Bacteriol_193_4015
PubMedSearch : Heavens_2011_J.Bacteriol_193_4015
PubMedID: 21622738
Gene_locus related to this paper: lacga-q047a5 , lacrj-b2g622

Title : Structure-based mutagenesis of Penicillium griseofulvum xylanase using computational design - Andre-Leroux_2008_Proteins_72_1298
Author(s) : Andre-Leroux G , Berrin JG , Georis J , Arnaut F , Juge N
Ref : Proteins , 72 :1298 , 2008
Abstract : Penicillium griseofulvum xylanase (PgXynA) belongs to family 11 glycoside hydrolase. It exhibits unique amino acid features but its three-dimensional structure is not known. Based upon the X-ray structure of Penicillium funiculosum xylanase (PfXynC), we generated a three-dimensional model of PgXynA by homology modeling. The native structure of PgXynA displayed the overall beta-jelly roll folding common to family 11 xylanases with two large beta-pleated sheets and a single alpha-helix that form a structure resembling a partially closed right hand. Although many features of PgXynA were very similar to previously described enzymes from this family, crucial differences were observed in the loop forming the "thumb" and at the edge of the binding cleft. The robustness of the xylanase was challenged by extensive in silico-based mutagenesis analysis targeting mutations retaining stereochemical and energetical control of the protein folding. On the basis of structural alignments, modeled three-dimensional structure, in silico mutations and docking analysis, we targeted several positions for the replacement of amino acids by site-directed mutagenesis to change substrate and inhibitor specificity, alter pH profile and improve overall catalytic activity. We demonstrated the crucial role played by Ser44(PgXynA) and Ser129(PgXynA), two residues unique to PgXynA, in conferring distinct specificity to P. griseofulvum xylanase. We showed that the pH optimum of PgXynA could be shifted by -1 to +0.5 units by mutating Ser44(PgXynA) to Asp and Asn, respectively. The S44D and S44N mutants showed only slight alteration in K(m) and V(max) whereas a S44A mutant lost both pH-dependence profile and activity. We were able to produce PgXynA S129G mutants with acquired sensitivity to the Xylanase Inhibitor Protein, XIP-I. The replacement of Gln121(PgXynA), located at the start of the thumb, into an Arg residue resulted in an enzyme that possessed a higher catalytic activity.
ESTHER : Andre-Leroux_2008_Proteins_72_1298
PubMedSearch : Andre-Leroux_2008_Proteins_72_1298
PubMedID: 18384043

Title : Probing the determinants of substrate specificity of a feruloyl esterase, AnFaeA, from Aspergillus niger - Faulds_2005_Febs.J_272_4362
Author(s) : Faulds CB , Molina R , Gonzalez R , Husband F , Juge N , Sanz-Aparicio J , Hermoso JA
Ref : Febs J , 272 :4362 , 2005
Abstract : Feruloyl esterases hydrolyse phenolic groups involved in the cross-linking of arabinoxylan to other polymeric structures. This is important for opening the cell wall structure making material more accessible to glycoside hydrolases. Here we describe the crystal structure of inactive S133A mutant of type-A feruloyl esterase from Aspergillus niger (AnFaeA) in complex with a feruloylated trisaccharide substrate. Only the ferulic acid moiety of the substrate is visible in the electron density map, showing interactions through its OH and OCH(3) groups with the hydroxyl groups of Tyr80. The importance of aromatic and polar residues in the activity of AnFaeA was also evaluated using site-directed mutagenesis. Four mutant proteins were heterologously expressed in Pichia pastoris, and their kinetic properties determined against methyl esters of ferulic, sinapic, caffeic and p-coumaric acid. The k(cat) of Y80S, Y80V, W260S and W260V was drastically reduced compared to that of the wild-type enzyme. However, the replacement of Tyr80 and Trp260 with smaller residues broadened the substrate specificity of the enzyme, allowing the hydrolysis of methyl caffeate. The role of Tyr80 and Trp260 in AnFaeA are discussed in light of the three-dimensional structure.
ESTHER : Faulds_2005_Febs.J_272_4362
PubMedSearch : Faulds_2005_Febs.J_272_4362
PubMedID: 16128806
Gene_locus related to this paper: aspni-FAEA

Title : The crystal structure of feruloyl esterase A from Aspergillus niger suggests evolutive functional convergence in feruloyl esterase family - Hermoso_2004_J.Mol.Biol_338_495
Author(s) : Hermoso JA , Sanz-Aparicio J , Molina R , Juge N , Gonzalez R , Faulds CB
Ref : Journal of Molecular Biology , 338 :495 , 2004
Abstract : As a component of the array of enzymes produced by micro-organisms to deconstruct plant cell walls, feruloyl esterases hydrolyze phenolic groups involved in the cross-linking of arabinoxylan to other polymeric structures. This is important for opening the cell wall structure, making material more accessible to glycosyl hydrolases. Here, we describe the first crystal structure of the non-modular type-A feruloyl esterase from Aspergillus niger (AnFaeA) solved at 2.5A resolution. AnFaeA displays an alpha/beta hydrolase fold similar to that found in fungal lipases and different from that reported for other feruloyl esterases. Crystallographic and site-directed mutagenesis studies allow us to identify the catalytic triad (Ser133-His247-Asp194) that forms the catalytic machinery of this enzyme. The active-site cavity is confined by a lid (residues 68-80), on the analogy of lipases, and by a loop (residues 226-244) that confers plasticity to the substrate-binding site. The lid presents a high ratio of polar residues, which in addition to a unique N-glycosylation site stabilises the lid in an open conformation, conferring the esterase character to this enzyme. A putative model for bound 5,5'-diferulic acid-linked arabinoxylan has been built, pointing to the more relevant residues involved in substrate recognition. Comparison with structurally related lipases reveals that subtle amino acid and conformational changes within a highly conserved protein fold may produce protein variants endowed with new enzymatic properties, while comparison with functionally related proteins points to a functional convergence after evolutionary divergence within the feruloyl esterases family.
ESTHER : Hermoso_2004_J.Mol.Biol_338_495
PubMedSearch : Hermoso_2004_J.Mol.Biol_338_495
PubMedID: 15081808
Gene_locus related to this paper: aspni-FAEA

Title : Structural properties of porcine intestine acylpeptide hydrolase - Durand_2003_J.Protein.Chem_22_183
Author(s) : Durand A , Villard C , Giardina T , Perrier J , Juge N , Puigserver A
Ref : J Protein Chem , 22 :183 , 2003
Abstract : The acylpeptide hydrolase of porcine intestinal mucosa (pi-APH) is a serine peptidase belonging to the prolyl oligopeptidase family. The enzyme catalyzes the release of N-terminal acylamino acids, especially acetylamino acids, from acetylpeptides. pi-APH is an homotetramer of approximately 300 kDa. We report the loss of the native tetrameric structure of pi-APH upon citraconylation and the process was reversed at acidic pH, indicating that the subunits were noncovalently bound. Determination of free cysteines in combination with peptide mapping suggested the involvement of all cysteines in disulfide bridges. Two structural domains were identified based on the three-dimensional model of pi-APH monomer: a beta-propeller fold in the N-terminal sequence (113-455) and an alpha/beta hydrolase fold corresponding to the C-terminal catalytic domain (469-732). Preferential cleavage sites for limited proteolysis with trypsin occurred within the beta-propeller domain, in agreement with the three-dimensional model. The putative role of this domain in the specificity mechanism of APH enzymes is also discussed.
ESTHER : Durand_2003_J.Protein.Chem_22_183
PubMedSearch : Durand_2003_J.Protein.Chem_22_183
PubMedID: 12760423
Gene_locus related to this paper: pig-acph

Title : High-level production of recombinant Aspergillus niger cinnamoyl esterase (FAEA) in the methylotrophic yeast Pichia pastoris - Juge_2001_FEMS.Yeast.Res_1_127
Author(s) : Juge N , Williamson G , Puigserver A , Cummings NJ , Connerton IF , Faulds CB
Ref : FEMS Yeast Res , 1 :127 , 2001
Abstract : The cDNA encoding Aspergillus niger cinnamoyl esterase (FAEA) with its native signal sequence was isolated by reverse transcriptase-polymerase chain reaction, sequenced, and expressed in Pichia pastoris. Secretion yields up to 300 mg l(-1) were obtained in buffered medium. The recombinant FAEA was purified to homogeneity using a one-step purification protocol and found to be identical to the native enzyme with respect to size, pI, immunoreactivity and N-terminal sequence. Specific activity, pH and temperature optimum, and kinetic parameters were also found similar to the native esterase. FAEA is thus the first fungal esterase efficiently produced using a heterologous system.
ESTHER : Juge_2001_FEMS.Yeast.Res_1_127
PubMedSearch : Juge_2001_FEMS.Yeast.Res_1_127
PubMedID: 12702357