49
views
0
recommends
+1 Recommend
2 collections
    1
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Sucrose 6 F-phosphate phosphorylase: a novel insight in the human gut microbiome

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The human gut microbiome plays an essential role in maintaining human health including in degradation of dietary fibres and carbohydrates further used as nutrients by both the host and the gut bacteria. Previously, we identified a polysaccharide utilization loci (PUL) involved in sucrose and raffinose family oligosaccharide (RFO) metabolism from one of the most common Firmicutes present in individuals, Ruminococcus gnavus E1. One of the enzymes encoded by this PUL was annotated as a putative sucrose phosphate phosphorylase ( RgSPP). In the present study, we have in-depth characterized the heterologously expressed RgSPP as sucrose 6 F-phosphate phosphorylase (SPP), expanding our knowledge of the glycoside hydrolase GH13_18 subfamily. Specifically, the enzymatic characterization showed a selective activity on sucrose 6 F-phosphate (S6 FP) acting both in phosphorolysis releasing alpha- d-glucose-1-phosphate (G1P) and alpha- d-fructose-6-phosphate (F6P), and in reverse phosphorolysis from G1P and F6P to S6 FP. Interestingly, such a SPP activity had never been observed in gut bacteria before. In addition, a phylogenetic and synteny analysis showed a clustering and a strictly conserved PUL organization specific to gut bacteria. However, a wide prevalence and abundance study with a human metagenomic library showed a correlation between SPP activity and the geographical origin of the individuals and, thus, most likely linked to diet. Rgspp gene overexpression has been observed in mice fed with a high-fat diet suggesting, as observed for humans, that intestine lipid and carbohydrate microbial metabolisms are intertwined. Finally, based on the genomic environment analysis, in vitro and in vivo studies, results provide new insights into the gut microbiota catabolism of sucrose, RFOs and S6 FP.

          Related collections

          Most cited references 45

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

          Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM.

            Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism. In silico analyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus- and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.

              The human gut microbiome is a complex ecosystem composed mainly of uncultured bacteria. It plays an essential role in the catabolism of dietary fibers, the part of plant material in our diet that is not metabolized in the upper digestive tract, because the human genome does not encode adequate carbohydrate active enzymes (CAZymes). We describe a multi-step functionally based approach to guide the in-depth pyrosequencing of specific regions of the human gut metagenome encoding the CAZymes involved in dietary fiber breakdown. High-throughput functional screens were first applied to a library covering 5.4 × 10(9) bp of metagenomic DNA, allowing the isolation of 310 clones showing beta-glucanase, hemicellulase, galactanase, amylase, or pectinase activities. Based on the results of refined secondary screens, sequencing efforts were reduced to 0.84 Mb of nonredundant metagenomic DNA, corresponding to 26 clones that were particularly efficient for the degradation of raw plant polysaccharides. Seventy-three CAZymes from 35 different families were discovered. This corresponds to a fivefold target-gene enrichment compared to random sequencing of the human gut metagenome. Thirty-three of these CAZy encoding genes are highly homologous to prevalent genes found in the gut microbiome of at least 20 individuals for whose metagenomic data are available. Moreover, 18 multigenic clusters encoding complementary enzyme activities for plant cell wall degradation were also identified. Gene taxonomic assignment is consistent with horizontal gene transfer events in dominant gut species and provides new insights into the human gut functional trophic chain.
                Bookmark

                Author and article information

                Journal
                Microb Genom
                Microb Genom
                mgen
                mgen
                Microbial Genomics
                Microbiology Society
                2057-5858
                April 2019
                26 March 2019
                26 March 2019
                : 5
                : 4
                Affiliations
                [ 1]Aix Marseille Univ, CNRS, Centrale Marseille, iSm2 , Marseille, France
                [ 2]LISBP, CNRS, INRA, INSAT, Université de Toulouse , F-31400 Toulouse, France
                [ 3]INRA, Aix-Marseille Université, UMR1163, Biodiversité et Biotechnologie Fongiques, PolyTech , F-13009, Marseille, France
                [ 4]Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université , F-13288 Marseille, France
                [ 5]Department of Biological Sciences, King Abdulaziz University , 23218 Jeddah, Saudi Arabia
                [ ]Present address: LISBP, CNRS, INRA, INSAT, Université de Toulouse, F-31400 Toulouse, France.
                Author notes
                *Correspondence: Mickael Lafond, mickael.lafond@ 123456univ-amu.fr
                [†]

                These authors contributed equally to this work.

                Article
                mgen000253
                10.1099/mgen.0.000253
                6521584
                30913025
                © 2019 The Authors

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Product
                Funding
                Funded by: H2020 European Research Council
                Award ID: MSCA-IF-2015 707457
                Categories
                Research Article
                Microbe-niche Interactions: Mutualism, Commensalism and Parasitism
                Custom metadata
                0

                Comments

                Comment on this article