Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases

Adesioye, Fiyinfoluwa A.; Makhalanyane, Thulani P.; Biely, Peter; Cowan, Don A.

doi:10.1016/j.enzmictec.2016.07.001

Cited by 59 publications

(39 citation statements)

References 161 publications

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“…For instance, members of the CE1, CE4, CE5, and CE7 families of archaeal, bacterial, and eukaryotic origin have been characterized as possessing the Ser-His-Asp catalytic triad, as well as the GXSXG (Gly-Xaa-Ser-Xaa-Gly) conserved motif. CE2 and CE3 family members possess the Gly-Asp-Ser-(Leu) (GDS( L )) motif, rather than the GXSXG conserved motif with the Ser-His catalytic diad and Ser-His-Asp catalytic triad, respectively [61]. CE16 family members also possess the GDS( L ) catalytic motif and Ser-Gly-Asn-His (SGNH) catalytic residues.…”

Section: Resultsmentioning

confidence: 99%

Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

Park

Jeong

Kong

2018

IJMS

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Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.

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Section: Resultsmentioning

confidence: 99%

Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

Park

Jeong

Kong

2018

IJMS

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“…For detailed information regarding such a process and the involved procedures, the readers are referred to other recently published in-depth reviews [9,155,156,157]. …”

Section: Strategies and Methodologiesmentioning

confidence: 99%

Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins

Zhu

Hassan

Lepp

et al. 2017

Toxins

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Mycotoxins, the secondary metabolites of mycotoxigenic fungi, have been found in almost all agricultural commodities worldwide, causing enormous economic losses in livestock production and severe human health problems. Compared to traditional physical adsorption and chemical reactions, interest in biological detoxification methods that are environmentally sound, safe and highly efficient has seen a significant increase in recent years. However, researchers in this field have been facing tremendous unexpected challenges and are eager to find solutions. This review summarizes and assesses the research strategies and methodologies in each phase of the development of microbiological solutions for mycotoxin mitigation. These include screening of functional microbial consortia from natural samples, isolation and identification of single colonies with biotransformation activity, investigation of the physiological characteristics of isolated strains, identification and assessment of the toxicities of biotransformation products, purification of functional enzymes and the application of mycotoxin decontamination to feed/food production. A full understanding and appropriate application of this tool box should be helpful towards the development of novel microbiological solutions on mycotoxin detoxification.

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“…The interest in extremophiles has boosted metagenomics studies of extreme environments [12][13][14][15][16], and, more recently, remarkable examples of the discovery of novel extremozymes for industrial applications from sequence-based screenings have been reported [17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments

et al. 2019

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The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy), to discover hyperthermophilic carbohydrate‐active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here, we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T = 85 °C and pH 5.5; T = 92 °C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in silico analysis led to 14 934 and 17 652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarchaeota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~ 2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β‐mannanase/β‐1,3‐glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+‐dependent GH109 with a previously unreported β‐N‐acetylglucosaminide/β‐glucoside specificity. Databases The sequencing reads are available in the NCBI Sequence Read Archive (SRA) database under the accession numbers SRR7545549 (Pool1) and SRR7545550 (Pool2). The sequences of GH5_Pool2 and GH109_Pool2 are available in GenBank database under the accession numbers MK869723 and MK86972, respectively. The environmental data relative to Pool1 and Pool2 (NCBI BioProject PRJNA481947) are available in the Biosamples database under the accession numbers SAMN09692669 (Pool1) and SAMN09692670 (Pool2).

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Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases

Cited by 59 publications

References 161 publications

Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins

Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments

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