scholarly journals Metagenomic DNA Library: Exploration of Novel Genes Encoding Glycoside Hydrolases

2018 ◽  
Vol 7 (4.7) ◽  
pp. 472
Author(s):  
Maris Kurniawati ◽  
Sudiyono . ◽  
Purkan . ◽  
Sri Sumarsih ◽  
Afaf Baktir
Keyword(s):  
Sequence Analysis ◽  
Metagenomic Library ◽  
Glycoside Hydrolases ◽  
Metagenomic Dna ◽  
Novel Genes ◽  
Dna Library ◽  
Genes Expression ◽  
Product Identification ◽  
Genes Encoding ◽  
Metagenomic Approach

Metagenomic is a potential approach to explore novel genes from a reservoir of genes. Metagenomic cDNA library as part of metagenomic approach be able to explore abundant quantity of microbiota genes. Metagenomic library collection was screened by functional and sequence analysis. Functional analysis can be done through induction genes expression substrat. Positive clones can be screened by expression of interest genes. Data of sequence analysis is very important in the process of product identification.  

scholarly journals Detection of a Novel, and Likely Ancestral, Tn916-Like Element from a Human Saliva Metagenomic Library

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 548
Author(s):  
Liam J. Reynolds ◽  
Muna F. Anjum ◽  
Adam P. Roberts
Keyword(s):  
Resistance Genes ◽  
Metagenomic Library ◽  
Tetracycline Resistance ◽  
Human Saliva ◽  
Fusion Event ◽  
Tetracycline Resistance Genes ◽  
Antimicrobial Resistance Genes ◽  
Genes Encoding ◽  
Gene Fusion Event ◽  
Metagenomic Approach

Tn916 is a conjugative transposon (CTn) and the first reported and most well characterised of the Tn916/Tn1545 family of CTns. Tn916-like elements have a characteristic modular structure and different members of this family have been identified based on similarities and variations in these modules. In addition to carrying genes encoding proteins required for their conjugation, Tn916-like elements also carry accessory, antimicrobial resistance genes; most commonly the tetracycline resistance gene, tet(M). Our study aimed to identify and characterise tetracycline resistance genes from the human saliva metagenome using a functional metagenomic approach. We identified a tetracycline-resistant clone, TT31, the sequencing of which revealed it to encode both tet(M) and tet(L). Comparison of the TT31 sequence with the accessory, regulation, and recombination modules of other Tn916-like elements indicated that a partial Tn916-like element encoding a truncated orf9 was cloned in TT31. Analysis indicated that a previous insertion within the truncated orf9 created the full length orf9 found in most Tn916-like transposons; demonstrating that orf9 is, in fact, the result of a gene fusion event. Thus, we hypothesise that the Tn916-like element cloned in TT31 likely represents an ancestral Tn916.

scholarly journals Tetracycline Resistome of the Organic Pig Gut

2009 ◽  
Vol 75 (6) ◽  
pp. 1717-1722 ◽  
Author(s):  
Katarzyna A. Kazimierczak ◽  
Karen P. Scott ◽  
Denise Kelly ◽  
Rustam I. Aminov
Keyword(s):  
Resistance Genes ◽  
Metagenomic Library ◽  
Antibiotic Resistance Genes ◽  
Artificial Chromosome ◽  
Mobile Genetic Elements ◽  
Structure Characteristic ◽  
Genetic Elements ◽  
Genes Encoding ◽  
Flanking Regions ◽  
Metagenomic Approach

ABSTRACT The occurrence of genes conferring resistance to tetracyclines in the organic pig gut was assessed through the metagenomic approach. Of 9,000 bacterial artificial chromosome clones analyzed, 10 were identified as carrying the known tet(C), tet(W), and tet(40) genes, as well as novel genes encoding resistance to the tetracyclines minocycline and doxycycline. The latter are different from the known tet genes and are homologous to genes encoding UDP-glucose 4-epimerases, with the domain structure characteristic for these enzymes. The majority of the resistance genes were associated with putative mobile genetic elements. The sequence of a novel 9.7-kb plasmid carrying tet(W) and tet(40) was also identified. Conserved flanking regions identified around the tet(W) and tet(40) genes in our metagenomic library may play a role in genetic exchange of these genes. This is the first report describing the occurrence of tet(40) outside the human intestine. The maintenance of antibiotic resistance genes in apparently antibiotic-free animals is probably due to their presence on mobile genetic elements, the fitness cost of which for the cell is ameliorated during the previous antibiotic selection.

Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatán underground water

Gene ◽  
2016 ◽  
Vol 593 (1) ◽  
pp. 154-161 ◽  
Author(s):  
Max M. Apolinar–Hernández ◽  
Yuri J. Peña–Ramírez ◽  
Ernesto Pérez-Rueda ◽  
Blondy B. Canto-Canché ◽  
César De los Santos-Briones ◽  
...  
Keyword(s):  
In Silico ◽  
Metagenomic Library ◽  
Underground Water ◽  
Functional Screening ◽  
Novel Genes ◽  
Genes Encoding ◽  
In Silico Characterization

scholarly journals Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

scholarly journals Variation of gonococcal lipooligosaccharide structure is due to alterations in poly-G tracts in lgt genes encoding glycosyl transferases.

1996 ◽  
Vol 183 (1) ◽  
pp. 323-327 ◽  
Author(s):  
Q L Yang ◽  
E C Gotschlich
Keyword(s):  
Sequence Analysis ◽  
Neisseria Gonorrhoeae ◽  
Experimental Evidence ◽  
High Frequency ◽  
Genetic Mechanism ◽  
Frequency Variation ◽  
Alpha Chain ◽  
Glycosyl Transferases ◽  
Genes Encoding

The lipooligosaccharide (LOS) expressed by gonococci spontaneously varies its structure at high frequency, but the underlying genetic mechanism has not been described. We have previously reported that the genes encoding the glycosyl transferases responsible for the biosynthesis of the variable alpha chain of the LOS of Neisseria gonorrhoeae are located in a locus containing five genes, lgtA, lgtB, lgtC, lgtD, and lgtE. Sequence analysis showed that lgtA, lgtC, and lgtD contained poly-G tracts within the coding frames, leading to the hypothesis that shifts in the number of guanosine residues in the poly-G tracts might be responsible for the high frequency variation in structure of gonococcal LOS. We now provide experimental evidence confirming this hypothesis.

scholarly journals Complete Genome Sequence of the Polysaccharide-Degrading Rumen Bacterium Pseudobutyrivibrio xylanivorans MA3014

2020 ◽  
Author(s):  
Nikola Palevich ◽  
Paul H. Maclean ◽  
William J. Kelly ◽  
Sinead C. Leahy ◽  
Jasna Rakonjac ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacterial Species ◽  
Glycoside Hydrolases ◽  
Rumen Bacterium ◽  
Protein Coding ◽  
Plant Polysaccharides ◽  
Plant Matter ◽  
Genes Encoding

AbstractRuminants are essential for maintaining the global population and managing greenhouse gas emissions. In the rumen, bacterial species belonging to the genera rumen Butyrivibrio and Pseudobutyrivibrio constitute the core bacterial rumen microbiome and are important degraders of plant-derived complex polysaccharides. Pseudobutyrivibrio xylanivorans MA3014 was selected for genome sequencing in order to examine its ability to breakdown and utilize plant polysaccharides. The complete genome sequence of MA3014 is 3.58 Mb, consists of three replicons (a chromosome, chromid and plasmid), has an overall G+C content of 39.6% and encodes 3,265 putative protein-coding genes (PCGs). Comparative pan-genomics of all cultivated and currently available P. xylanivorans genomes has revealed highly open genomes and a strong correlation of orthologous genes within this species of rumen bacteria. MA3014 is metabolically versatile and capable of utilizing a range of simple mono-or oligosaccharides to complex plant polysaccharides such as pectins, mannans, starch and hemicelluloses for growth, with lactate, butyrate and formate as the principal fermentation end-products. The genes encoding these metabolic pathways have been identified and MA3014 is predicted to encode an extensive repertoire of Carbohydrate-Active enZYmes (CAZymes) with 80 Glycoside Hydrolases (GHs), 28 Carbohydrate Esterases (CEs) and 51 Glycosyl Transferases (GTs), that suggest its role as an initiator of primary solubilization of plant matter in the rumen.

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