Comparative Genomics and CAZyme Genome Repertoires of Marine  Zobellia amurskyensis  KMM 3526 T  and  Zobellia laminariae  KMM 3676 T

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Abstract

We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526 ^Т and 5.16 Mb for Z. laminariae KMM 3676 ^Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.

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Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

Anthony Levasseur, Elodie Drula, Vincent Lombard … (2013)

Background Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category. Results Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name “Auxiliary Activities” in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). Conclusions The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.

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Environmental and Gut Bacteroidetes: The Food Connection

François Thomas, Jan-Hendrik Hehemann, Etienne Rebuffet … (2011)

Members of the diverse bacterial phylum Bacteroidetes have colonized virtually all types of habitats on Earth. They are among the major members of the microbiota of animals, especially in the gastrointestinal tract, can act as pathogens and are frequently found in soils, oceans and freshwater. In these contrasting ecological niches, Bacteroidetes are increasingly regarded as specialists for the degradation of high molecular weight organic matter, i.e., proteins and carbohydrates. This review presents the current knowledge on the role and mechanisms of polysaccharide degradation by Bacteroidetes in their respective habitats. The recent sequencing of Bacteroidetes genomes confirms the presence of numerous carbohydrate-active enzymes covering a large spectrum of substrates from plant, algal, and animal origin. Comparative genomics reveal specific Polysaccharide Utilization Loci shared between distantly related members of the phylum, either in environmental or gut-associated species. Moreover, Bacteroidetes genomes appear to be highly plastic and frequently reorganized through genetic rearrangements, gene duplications and lateral gene transfers (LGT), a feature that could have driven their adaptation to distinct ecological niches. Evidence is accumulating that the nature of the diet shapes the composition of the intestinal microbiota. We address the potential links between gut and environmental bacteria through food consumption. LGT can provide gut bacteria with original sets of utensils to degrade otherwise refractory substrates found in the diet. A more complete understanding of the genetic gateways between food-associated environmental species and intestinal microbial communities sheds new light on the origin and evolution of Bacteroidetes as animals’ symbionts. It also raises the question as to how the consumption of increasingly hygienic and processed food deprives our microbiota from useful environmental genes and possibly affects our health.

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Computational methods for Gene Orthology inference.

Maxim Wolf, Eugene V. Koonin, Arcady R Mushegian … (2011)

Accurate inference of orthologous genes is a pre-requisite for most comparative genomics studies, and is also important for functional annotation of new genomes. Identification of orthologous gene sets typically involves phylogenetic tree analysis, heuristic algorithms based on sequence conservation, synteny analysis, or some combination of these approaches. The most direct tree-based methods typically rely on the comparison of an individual gene tree with a species tree. Once the two trees are accurately constructed, orthologs are straightforwardly identified by the definition of orthology as those homologs that are related by speciation, rather than gene duplication, at their most recent point of origin. Although ideal for the purpose of orthology identification in principle, phylogenetic trees are computationally expensive to construct for large numbers of genes and genomes, and they often contain errors, especially at large evolutionary distances. Moreover, in many organisms, in particular prokaryotes and viruses, evolution does not appear to have followed a simple 'tree-like' mode, which makes conventional tree reconciliation inapplicable. Other, heuristic methods identify probable orthologs as the closest homologous pairs or groups of genes in a set of organisms. These approaches are faster and easier to automate than tree-based methods, with efficient implementations provided by graph-theoretical algorithms enabling comparisons of thousands of genomes. Comparisons of these two approaches show that, despite conceptual differences, they produce similar sets of orthologs, especially at short evolutionary distances. Synteny also can aid in identification of orthologs. Often, tree-based, sequence similarity- and synteny-based approaches can be combined into flexible hybrid methods.

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Journal

Journal ID (nlm-ta): Mar Drugs

Journal ID (iso-abbrev): Mar Drugs

Journal ID (publisher-id): marinedrugs

Title: Marine Drugs

Publisher: MDPI

ISSN (Electronic): 1660-3397

Publication date (Electronic): 24 November 2019

Publication date Collection: December 2019

Volume: 17

Issue: 12

Electronic Location Identifier: 661

Affiliations

[1 ]G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, Vladivostok 690022, Russia; chernysheva.nadezhda@ 123456gmail.com (N.C.); belyjane@ 123456gmail.com (E.B.); oined2012@ 123456gmail.com (O.N.)

[2 ]Far Eastern Federal University, 8 Sukhanova St., Vladivostok 690090, Russia; stenkova@ 123456gmail.com (A.S.); golovkin.io.1996@ 123456gmail.com (I.G.)

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[* ]Correspondence: issaeva@ 123456gmail.com ; Tel.: +7-914-702-0915

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Marina Isaeva https://orcid.org/0000-0002-2395-0485

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Publisher ID: marinedrugs-17-00661

DOI: 10.3390/md17120661

PMC ID: 6950322

PubMed ID: 31771309

SO-VID: 0e9fcc08-c6e1-4413-b944-d66810007708

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Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526 ^T and Zobellia laminariae KMM 3676 ^T

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Arabidopsis genomics

Most cited references 49

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

Environmental and Gut Bacteroidetes: The Food Connection

Computational methods for Gene Orthology inference.

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