Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253

AbstractThe genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: β-N-acetyl-glucosaminidases, β-1,4-glucosidases/β-xylosidases and macrolide β-glucosidases. The RmNag3 with additional β-lactamase domain clustered with the deepest rooted GH3-lineage of β-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed β-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide β-glucosidases from Actinomycetes. The β-xylosidases, RmXyl3A and RmXyl3B, and the β-glucosidases RmBgl3A and RmBgl3C clustered within the major β-glucosidases/β-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed β-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed β-1,4-glucosidase/β-xylosidase activity while RmBgl3C was active on pNP-β-Glc and β-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252T (homolog strain). The analysis showed that in the homolog strain DSM 4252TRmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.

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Consistent isomiR expression patterns and 3′ addition events in miRNA gene clusters and families implicate functional and evolutionary relationships

Molecular Biology Reports ◽

10.1007/s11033-012-1493-3 ◽

2012 ◽

Vol 39 (6) ◽

pp. 6699-6706 ◽

Cited By ~ 24

Author(s):

Li Guo ◽

Hailing Li ◽

Tingming Liang ◽

Jiafeng Lu ◽

Qi Yang ◽

...

Keyword(s):

Expression Patterns ◽

Mirna Gene ◽

Gene Clusters ◽

Evolutionary Relationships

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Multiple Transporters and Glycoside Hydrolases Are Involved in Arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium pseudocatenulatum

Applied and Environmental Microbiology ◽

10.1128/aem.01782-20 ◽

2020 ◽

Vol 86 (24) ◽

Author(s):

Yuki Saito ◽

Akira Shigehisa ◽

Yohei Watanabe ◽

Naoki Tsukuda ◽

Kaoru Moriyama-Ohara ◽

...

Keyword(s):

Abc Transporters ◽

Binding Proteins ◽

Molecular Mechanisms ◽

Bifidobacterium Longum ◽

Gene Clusters ◽

Glycoside Hydrolases ◽

Glycoside Hydrolase Family ◽

Carbohydrate Utilization ◽

Bifidobacterium Adolescentis ◽

Content Type

ABSTRACT Arabinoxylan hydrolysates (AXH) are the hydrolyzed products of the major components of the dietary fiber arabinoxylan. AXH include diverse oligosaccharides varying in xylose polymerization and side residue modifications with arabinose at the O-2 and/or O-3 position of the xylose unit. Previous studies have reported that AXH exhibit prebiotic properties on gut bifidobacteria; moreover, several adult-associated bifidobacterial species (e.g., Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum) are known to utilize AXH. In this study, we tried to elucidate the molecular mechanisms of AXH utilization by Bifidobacterium pseudocatenulatum, which is a common bifidobacterial species found in adult feces. We performed transcriptomic analysis of B. pseudocatenulatum YIT 4072T, which identified three upregulated gene clusters during AXH utilization. The gene clusters encoded three sets of ATP-binding cassette (ABC) transporters and five enzymes belonging to glycoside hydrolase family 43 (GH43). By characterizing the recombinant proteins, we found that three solute-binding proteins of ABC transporters showed either broad or narrow specificity, two arabinofuranosidases hydrolyzed either single- or double-decorated arabinoxylooligosaccharides, and three xylosidases exhibited functionally identical activity. These data collectively suggest that the transporters and glycoside hydrolases, encoded in the three gene clusters, work together to utilize AXH of different sizes and with different side residue modifications. Thus, our study sheds light on the overall picture of how these proteins collaborate for the utilization of AXH in B. pseudocatenulatum and may explain the predominance of this symbiont species in the adult human gut. IMPORTANCE Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular mechanism by which B. pseudocatenulatum, a common bifidobacterial species found in adult feces, utilizes structurally and compositionally variable AXH has yet to be extensively investigated. In this study, we identified three gene clusters (encoding five GH43 enzymes and three solute-binding proteins of ABC transporters) that were upregulated in B. pseudocatenulatum YIT 4072T during AXH utilization. By investigating their substrate specificities, we revealed how these proteins are involved in the uptake and degradation of AXH. These molecular insights may provide a better understanding of how resident bifidobacteria colonize the colon.

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A common molecular signature unifies the chitosanases belonging to families 46 and 80 of glycoside hydrolases

Canadian Journal of Microbiology ◽

10.1139/w00-080 ◽

2000 ◽

Vol 46 (10) ◽

pp. 952-955 ◽

Cited By ~ 3

Author(s):

Hugo Tremblay ◽

Josée Blanchard ◽

Ryszard Brzezinski

Keyword(s):

Amino Acids ◽

Sequence Similarity ◽

Glycosyl Hydrolase ◽

3D Structure ◽

Glycoside Hydrolases ◽

Site Directed Mutagenesis ◽

Molecular Signature ◽

Directed Mutagenesis ◽

Protein Motif ◽

Streptomyces Sp

The 3D structure-oriented alignment of the primary sequences of fourteen chitosanases, mainly of bacterial origin and belonging to families 46 and 80 of glycoside hydrolases, resulted in the identification of the following pattern common to all these enzymes: E-[DNQ]-x(8,17)-Y-x(7)-D-x-[RD]-[GP]-x-[TS]-x(3)-[AIVFLY]-G-x(5,11)-D. This pattern is proposed as the molecular signature of the chitosanases from families 46 and 80. It includes several amino acids essential for enzyme activity and (or) stability as shown by site-directed mutagenesis studies on the chitosanase from Streptomyces sp. N174. In particular, it includes two carboxylic residues directly involved in catalysis. We suggest that there is a continuum of sequence similarity between all the analyzed chitosanases, and that all these enzymes should probably be classified in one family.Key words: chitosanase, glycosyl hydrolase, protein motif.

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Revealing Mammalian Evolutionary Relationships by Comparative Analysis of Gene Clusters

Genome Biology and Evolution ◽

10.1093/gbe/evs032 ◽

2012 ◽

Vol 4 (4) ◽

pp. 586-601 ◽

Cited By ~ 7

Author(s):

Giltae Song ◽

Cathy Riemer ◽

Benjamin Dickins ◽

Hie Lim Kim ◽

Louxin Zhang ◽

...

Keyword(s):

Comparative Analysis ◽

Gene Clusters ◽

Evolutionary Relationships

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A pair of esterases from a commensal gut bacterium remove acetylations from all positions on complex β-mannans

10.1101/788067 ◽

2019 ◽

Cited By ~ 1

Author(s):

Leszek Michalak ◽

Sabina Leanti La Rosa ◽

Shaun Allan Leivers ◽

Lars Jordhøy Lindstad ◽

Åsmund Røhr Kjendseth ◽

...

Keyword(s):

Cell Wall ◽

Plant Cell ◽

Active Site ◽

Plant Cell Wall ◽

3D Structure ◽

Domain Architecture ◽

Catalytic Triad ◽

Glycoside Hydrolases ◽

Time Resolved ◽

Mannose Residue

Abstractβ-Mannans and xylans are important components of the plant cell wall and they are acetylated to be protected from degradation by glycoside hydrolases. β-Mannans are widely present in human and animal diets as fiber from leguminous plants and as thickeners and stabilizers in processed foods. There are many fully characterized acetylxylan esterases (AcXEs), however, the enzymes deacetylating mannans are less understood. Here we present two carbohydrate esterases, RiCE2 and RiCEX, from the Firmicute Roseburia intestinalis, which together deacetylate complex galactoglucomannan (GGM). The 3D-structure of RiCEX with a mannopentaose in the active site shows that the CBM35 domain of RiCEX forms a confined complex, where the axially oriented C2-hydroxyl of a mannose residue points towards the Ser41 of the catalytic triad. Cavities on the RiCEX surface may accept galactosylations at the C6 positions of mannose adjacent to the mannose residue being deacetylated (subsite −1 and +1). In depth characterization of the two enzymes using time-resolved NMR, HPLC and mass spectrometry demonstrates that they work in a complementary manner. RiCEX exclusively removes the axially oriented 2-O-acetylations on any mannose residue in an oligosaccharide, including double acetylated mannoses, while the RiCE2 is active on 3-O-, 4-O- and 6-O-acetylations. Activity of RiCE2 is dependent on RiCEX removing 2-O-acetylations from double acetylated mannose. Furthermore, transacetylation of oligosaccharides with the 2-O specific RiCEX provided new insight to how temperature and pH affects acetyl migration on mannooligosaccharides.Significance statementAcetylations are an important feature of hemicellulose, altering the physical properties of the plant cell wall, and limiting enzyme accessibility. Removal of acetyl groups from beta-mannan is a key step towards efficient utilization of mannans as a carbon source for gut microbiota and in biorefineries. We present detailed insight into mannan deacetylation by two highly substrate-specific acetyl-mannan esterases (AcMEs) from a prevalent gut commensal Firmicute, which cooperatively deacetylate complex galactoglucomannan. The 3D structure of RiCEX with mannopentaose in the active site has a unique two-domain architecture including a CBM35 and an SGNH superfamily hydrolytic domain. Discovery of mannan specific esterases improves the understanding of an important step in dietary fiber utilization by gut commensal Firmicutes.

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Data mining and machine learning methods for chromosome conformation data analysis

10.32469/10355/70076 ◽

2019 ◽

Author(s):

◽

Oluwatosin Oluwadare

Keyword(s):

Data Analysis ◽

Human Genome ◽

Structure Prediction ◽

Learning Algorithm ◽

3D Structure ◽

Three Dimensional ◽

Gene Clusters ◽

Research Field ◽

Chromosome Conformation ◽

Graphical Tool

Sixteen years after the sequencing of the human genome, the Human Genome Project (HGP), and 17 years after the introduction of Chromosome Conformation Capture (3C) technologies, three-dimensional (3-D) inference and big data remains problematic in the field of genomics, and specifically, in the field of 3C data analysis. Three-dimensional inference involves the reconstruction of a genome's 3D structure or, in some cases, ensemble of structures from contact interaction frequencies extracted from a variant of the 3C technology called the Hi-C technology. Further questions remain about chromosome topology and structure; enhancer-promoter interactions; location of genes, gene clusters, and transcription factors; the relationship between gene expression and epigenetics; and chromosome visualization at a higher scale, among others. In this dissertation, four major contributions are described, first, 3DMax, a tool for chromosome and genome 3-D structure prediction from H-C data using optimization algorithm, second, GSDB, a comprehensive and common repository that contains 3D structures for Hi-C datasets from novel 3D structure reconstruction tools developed over the years, third, ClusterTAD, a method for topological associated domains (TAD) extraction from Hi-C data using unsupervised learning algorithm. Finally, we introduce a tool called, GenomeFlow, a comprehensive graphical tool to facilitate the entire process of modeling and analysis of 3D genome organization. It is worth noting that GenomeFlow and GSDB are the first of their kind in the 3D chromosome and genome research field. All the methods are available as software tools that are freely available to the scientific community.

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Alterations in chromosome spatial compartmentalization classify prostate cancer progression

10.1101/2021.04.15.440056 ◽

2021 ◽

Author(s):

Rebeca San Martin ◽

Priyojit Das ◽

Renata Dos Reis Marques ◽

Yang Xu ◽

Rachel Patton McCord

Keyword(s):

Prostate Cancer ◽

Cancer Progression ◽

3D Structure ◽

Gene Clusters ◽

Metastatic Potential ◽

Chromosome 21 ◽

Prostate Cancer Progression ◽

Normal Epithelium ◽

Chromosome Conformation ◽

Cancer Aggressiveness

Prostate cancer aggressiveness and metastatic potential are influenced by gene expression, genomic aberrations, and cellular morphology. These processes are in turn dependent in part on the 3D structure of chromosomes, packaged inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, ranging from normal epithelium to bone metastasis. Here, we describe how chromatin compartmentalization identity (A- open vs. B-closed) changes with progression: specifically, we find that 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches could prelude transcription activation and are accompanied by changes in the structure, size, and boundaries of the topologically associating domains (TADs). Further, compartmentalization changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation: one of the main drivers of prostate cancer.  These results suggest that discrete, 3D genome structure changes play a deleterious role in prostate cancer progression. 

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Gene–Phenotype Associations Involving Human-Residential Bifidobacteria (HRB) Reveal Significant Species- and Strain-Specificity in Carbohydrate Catabolism

Microorganisms ◽

10.3390/microorganisms9050883 ◽

2021 ◽

Vol 9 (5) ◽

pp. 883

Author(s):

Shijie Liu ◽

Zhifeng Fang ◽

Hongchao Wang ◽

Qixiao Zhai ◽

Feng Hang ◽

...

Keyword(s):

Bacterial Species ◽

Carbon Sources ◽

Gene Clusters ◽

Glycoside Hydrolases ◽

Strain Specificity ◽

Carbohydrate Utilization ◽

Bifidobacterium Species ◽

Large Gene ◽

Wide Range ◽

Almost All

Bifidobacteria are among the first colonizers of the human gastrointestinal tract. Different bacterial species use different mechanisms for utilization of various carbon sources in order to establish themselves in the complex microbial ecosystem of the gut. However, these mechanisms still need to be explored. Here, a large gene–phenotype correlation analysis was carried out to explore the metabolic and genetic diversity of bifidobacterial carbohydrate utilization abilities. In this study, we used 21 different carbohydrates to determine the growth phenotypes, the distribution of glycoside hydrolases (GHs), and gene clusters related to the utilization of multiple carbon sources in six human-residential Bifidobacterium species. Five carbohydrates significantly stimulated growth of almost all strains, while the remaining sugars exhibited species- and strain-specificity. Correspondingly, different Bifidobacterium species also had specific GHs involved in fermentation of plant or host glycans. Moreover, we analyzed several carbohydrate utilization gene clusters, such as 2-fucosyllactose (2′FL), sialic acid (SA), and fructooligosaccharide (FOS). In summary, by using 217 bifidobacterial strains and a wide range of growth substrates, our research revealed inter- and intra-species differences in bifidobacterial in terms of carbohydrate utilization. The findings of this study are useful for the process of developing prebiotics for optimum growth of probiotics, especially Bifidobacterium species.

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