scholarly journals Probe-mining of endo-1,4-beta-xylanase from goats-rumen bacterial metagenomic DNA data

2021 ◽  
Vol 19 (3) ◽  
pp. 519-528
Author(s):  
Dao Trong Khoa ◽  
Do Thi Huyen ◽  
Truong Nam Hai
Keyword(s):  
Glycoside Hydrolase ◽  
Xylanase Activity ◽  
Experimental Studies ◽  
Open Reading Frames ◽  
Kegg Database ◽  
Metagenomic Dna ◽  
Maximum Score ◽  
Online Databases ◽  
Cazy Database ◽  
Reading Frames

Endo-1,4-beta-xylanases (xylanases) are classified into 9 glycoside hydrolase families, GH5, 8, 10, 11, 30, 43, 51, 98, and 141 based on the CAZy database. The probe sequences representing the enzymes were constructed from published sequences of actual experimental studies with xylan decomposition activity. From online databases, we found one sequence belonging to the GH5 family, 6 sequences belonging to the GH8 family and 5 sequences belonging to the GH30 family exhibiting xylanase activity. Thus specific probes for xylanase GH8 and GH30 families were designed with the length of 351 and 425 amino acids respectively. The reference values for the probe of the GH8 family were defined as the sequences with maximum score greater than 168, the lowest coverage was 84%, the lowest similarity was 36%; for the probe GH30, the maximum score was greater than 316, the coverage was greater than 98%, the similarity was greater than 41%. Using the built probes, including the probe of the two GH10 and GH11 families, we found 41 xylanase-encoding sequences from the metagenomic DNA data of bacteria in Vietnamese goats’rumen. Of the 41 exploited sequences, 19 were identical to the BGI company's annotation result based on KEGG database, whereas there were 16 sequences that are not annotated by the BGI company. Total 28 of 41 exploited sequences were complete open reading frames, of which the predicted ternary structure was highly similar to the published structures of xylanase.

scholarly journals Functional-Genomics-Based Identification and Characterization of Open Reading Frames Encoding α-Glucoside-Processing Enzymes in the Hyperthermophilic Archaeon Pyrococcus furiosus

2007 ◽  
Vol 74 (4) ◽  
pp. 1281-1283 ◽  
Author(s):  
Donald A. Comfort ◽  
Chung-Jung Chou ◽  
Shannon B. Conners ◽  
Amy L. VanFossen ◽  
Robert M. Kelly
Keyword(s):  
Glycoside Hydrolase ◽  
Bioinformatics Analysis ◽  
Pyrococcus Furiosus ◽  
Transcriptional Response ◽  
Open Reading Frames ◽  
Processing Enzymes ◽  
Response Information ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT Bioinformatics analysis and transcriptional response information for Pyrococcus furiosus grown on α-glucans led to the identification of a novel isomaltase (PF0132) representing a new glycoside hydrolase (GH) family, a novel GH57 β-amylase (PF0870), and an extracellular starch-binding protein (1,141 amino acids; PF1109-PF1110), in addition to several other putative α-glucan-processing enzymes.

scholarly journals MINTIA: a metagenomic INserT integrated assembly and annotation tool

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11885
Author(s):  
Philippe Bardou ◽  
Sandrine Laguerre ◽  
Sarah Maman Haddad ◽  
Sabrina Legoueix Rodriguez ◽  
Elisabeth Laville ◽  
...  
Keyword(s):  
Software Package ◽  
Bacterial Species ◽  
Open Reading Frames ◽  
Functional Metagenomics ◽  
Metagenomic Dna ◽  
Metagenomic Sequence ◽  
Uncultured Bacteria ◽  
Activity Screening ◽  
User Friendly ◽  
Reading Frames

The earth harbors trillions of bacterial species adapted to very diverse ecosystems thanks to specific metabolic function acquisition. Most of the genes responsible for these functions belong to uncultured bacteria and are still to be discovered. Functional metagenomics based on activity screening is a classical way to retrieve these genes from microbiomes. This approach is based on the insertion of large metagenomic DNA fragments into a vector and transformation of a host to express heterologous genes. Metagenomic libraries are then screened for activities of interest, and the metagenomic DNA inserts of active clones are extracted to be sequenced and analysed to identify genes that are responsible for the detected activity. Hundreds of metagenomics sequences found using this strategy have already been published in public databases. Here we present the MINTIA software package enabling biologists to easily generate and analyze large metagenomic sequence sets, retrieved after activity-based screening. It filters reads, performs assembly, removes cloning vector, annotates open reading frames and generates user friendly reports as well as files ready for submission to international sequence repositories. The software package can be downloaded from https://github.com/Bios4Biol/MINTIA.

scholarly journals Unravelling the ORFan Puzzle

2003 ◽  
Vol 4 (4) ◽  
pp. 432-441 ◽  
Author(s):  
Naomi Siew ◽  
Daniel Fischer
Keyword(s):  
Sequence Similarity ◽  
Experimental Studies ◽  
Open Reading Frames ◽  
Bioinformatics Tools ◽  
Reading Frames

ORFans are open reading frames (ORFs) with no detectable sequence similarity to any other sequence in the databases. Each newly sequenced genome contains a significant number of ORFans. Therefore, ORFans entail interesting evolutionary puzzles. However, little can be learned about them using bioinformatics tools, and their study seems to have been underemphasized. Here we present some of the questions that the existence of so many ORFans have raised and review some of the studies aimed at understanding ORFans, their functions and their origins. These works have demonstrated that ORFans are an untapped source of research, requiring further computational and experimental studies.

scholarly journals Prediction of cellulolytic and hemicellulolytic bacterial diversity in the gut of Coptotermes gestroi in the Southern Vietnam

2020 ◽  
Vol 17 (3) ◽  
pp. 537-544
Author(s):  
Nguyen Thi Thao ◽  
Do Thi Huyen ◽  
Truong Nam Hai
Keyword(s):  
Bacterial Species ◽  
Abundant Species ◽  
Open Reading Frames ◽  
Metagenomic Dna ◽  
Free Living ◽  
Southern Vietnam ◽  
Degrading Bacteria ◽  
Coptotermes Gestroi ◽  
Reading Frames ◽  
Living Bacteria

In lower termite such as Coptotermes gestroi, cellulose and hemicellulose are hydrolysed by cellulases and hemicellulases secreted from bacteria, archaea, protozoa and fungy in the hindgut. In which, majority of the enzymes are contributed by protozoa. From the metagenomic DNA data (125,423 open reading frames -ORFs) of free-living bacteria in the gut of C. gestroi harvested in Southern Vietnam and by MEGA 4.0 software, 100.340 ORFs were classified into 1,368 species, 628 genera, 217 families, 97 orders, 41 classes and 22 phyla (Do et al., 2014). Among these, 2,131 ORFs (2,12%) belong to 24 bacterial species (account 1,75% bacterial species), 11 families, 9 orders, 8 classes and 5 phyla were predicted have ability to produce cellulases; 679 ORFs belong to 18 bacterial species 8 families, 6 orders, 5 classes, 4 phyla were predicted have ability to produce hemicellulase. Majority of cellulase producers were species which of Firmicutes (15/24 species), accumulated in class Clostridia, order Clostridiales. The most abundant cellulase producer was Pseudomonas fluorescens (1,258 ORFs) of order Pseudomonadaceae. Out of the 18 hemicellulase producers, the most abundant species was Clostridium thermocellum (113 ORFs) in the phylum Firmicutes, followed by 3 species belonging to the phylum Bacteroidetes. The species predicted to produce both cellulase, hemicellulase were C. thermocellum, Ruminococcusns flavefaciens and Bacillus subtilis. Our study provides  a data of gut cellulose and hemicellulose - degrading bacteria composition of C. gestroi

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