Novel Exopolysaccharides Produced byLactococcus lactissubsp.lactis, and the Diversity ofepsEGenes in the Exopolysaccharide Biosynthesis Gene Clusters

2013 ◽  
Vol 77 (10) ◽  
pp. 2013-2018 ◽  
Author(s):  
Chise SUZUKI ◽  
Miho KOBAYASHI ◽  
Hiromi KIMOTO-NIRA
Keyword(s):  
Gene Clusters ◽  
Biosynthesis Gene ◽  
Exopolysaccharide Biosynthesis

scholarly journals A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes

2019 ◽  
Vol 7 (10) ◽  
pp. 444 ◽  
Author(s):  
Dipti Deo ◽  
Dimple Davray ◽  
Ram Kulkarni
Keyword(s):  
Biofilm Formation ◽  
Gene Clusters ◽  
High Variability ◽  
Protein Families ◽  
Free Living ◽  
Biosynthesis Gene ◽  
Exopolysaccharide Biosynthesis ◽  
Pharmaceutical Industries ◽  
Living Group ◽  
Core Genes

Production of exopolysaccharides (EPS) is one of the unique features of Lactobacillus genus. EPS not only have many physiological roles such as in stress tolerance, quorum sensing and biofilm formation, but also have numerous applications in the food and pharmaceutical industries. In this study, we identified and compared EPS biosynthesis gene clusters in 106 sequenced Lactobacillus genomes representing 27 species. Of the 146 identified clusters, only 41 showed the typical generic organization of genes as reported earlier. Hierarchical clustering showed highly varied nature of the clusters in terms of the gene composition; nonetheless, habitat-wise grouping was observed for the gene clusters from host-adapted and nomadic strains. Of the core genes required for EPS biosynthesis, epsA, B, C, D and E showed higher conservation, whereas gt, wzx and wzy showed high variability in terms of the number and composition of the protein families. Analysis of the distribution pattern of the protein families indicated a higher proportion of mutually exclusive families in clusters from host-adapted and nomadic strains, whereas those from the free-living group had very few unique families. Taken together, this analysis highlights high variability in the EPS gene clusters amongst Lactobacillus with some of their properties correlated to the habitats.

An atlas of bacterial secondary metabolite biosynthesis gene clusters

2021 ◽  
Author(s):  
Bin Wei ◽  
Ao‐Qi Du ◽  
Zhen‐Yi Zhou ◽  
Cong Lai ◽  
Wen‐Chao Yu ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Gene Clusters ◽  
Biosynthesis Gene ◽  
Secondary Metabolite Biosynthesis

An alginate-like exopolysaccharide biosynthesis gene cluster involved in biofilm aerial structure formation by Pseudomonas alkylphenolia

2014 ◽  
Vol 98 (9) ◽  
pp. 4137-4148 ◽  
Author(s):  
Kyoung Lee ◽  
Eun Jin Lim ◽  
Keun Soo Kim ◽  
Shir-Ly Huang ◽  
Yaligara Veeranagouda ◽  
...  
Keyword(s):  
Structure Formation ◽  
Gene Cluster ◽  
Biosynthesis Gene Cluster ◽  
Biosynthesis Gene ◽  
Exopolysaccharide Biosynthesis

Differential expression of silent polyketide biosynthesis gene clusters in chemostat cultures of Aspergillus nidulans

2012 ◽  
Vol 160 (1-2) ◽  
pp. 64-71 ◽  
Author(s):  
Anindita Sarkar ◽  
Alexander N. Funk ◽  
Kirstin Scherlach ◽  
Fabian Horn ◽  
Volker Schroeckh ◽  
...  
Keyword(s):  
Differential Expression ◽  
Aspergillus Nidulans ◽  
Gene Clusters ◽  
Polyketide Biosynthesis ◽  
Chemostat Cultures ◽  
Biosynthesis Gene

scholarly journals Additional Og-Typing PCR Techniques Targeting Escherichia coli-Novel and Shigella-Unique O-Antigen Biosynthesis Gene Clusters

2020 ◽  
Vol 58 (11) ◽  
Author(s):  
Atsushi Iguchi ◽  
Hironobu Nishii ◽  
Kazuko Seto ◽  
Jiro Mitobe ◽  
Kenichi Lee ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Strong Association ◽  
Gene Clusters ◽  
Epidemiological Studies ◽  
Content Type ◽  
E Coli ◽  
O Antigen ◽  
Wide Range ◽  
Biosynthesis Gene ◽  
Almost All

ABSTRACT The O-serogrouping of pathogenic Escherichia coli is a standard method for subtyping strains for epidemiological studies and controls. O-serogroup diversification shows a strong association with the genetic diversity in some O-antigen biosynthesis gene clusters. Through genomic studies, in addition to the types of O-antigen biosynthesis gene clusters (Og-types) from conventional O-serogroup strains, a number of novel Og-types have been found in E. coli isolates. To assist outbreak investigations and surveillance of pathogenic E. coli at inspection institutes, in previous studies, we developed PCR methods that could determine almost all conventional O-serogroups and some novel Og-types. However, there are still many Og-types that may not be determined by simple genetic methods such as PCR. Thus, in the present study, we aimed to develop an additional Og-typing PCR system. Based on the novel Og-types, including OgN32, OgN33, and OgN34, presented in this study, we designed an additional 24 PCR primer pairs targeting 14 novel and 2 diversified E. coli Og-types and 8 Shigella-unique Og-types. Subsequently, we developed 5 new multiplex PCR sets consisting of 33 primers, including the aforementioned 24 primers and 9 primers reported in previous studies. The accuracy and specificity of the PCR system was validated using approximately 260 E. coli and Shigella O-serogroup and Og-type reference strains. The Og-typing PCR system reported here can determine a wide range of Og-types of E. coli and may help epidemiological studies, in addition to the surveillance of pathogenic E. coli.

scholarly journals Wide Distribution of O157-Antigen Biosynthesis Gene Clusters in Escherichia coli

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e23250 ◽  
Author(s):  
Atsushi Iguchi ◽  
Hiroki Shirai ◽  
Kazuko Seto ◽  
Tadasuke Ooka ◽  
Yoshitoshi Ogura ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gene Clusters ◽  
Wide Distribution ◽  
Biosynthesis Gene

scholarly journals Identification of Two Aflatrem Biosynthesis Gene Loci in Aspergillus flavus and Metabolic Engineering of Penicillium paxilli To Elucidate Their Function

2009 ◽  
Vol 75 (23) ◽  
pp. 7469-7481 ◽  
Author(s):  
Matthew J. Nicholson ◽  
Albert Koulman ◽  
Brendon J. Monahan ◽  
Beth L. Pritchard ◽  
Gary A. Payne ◽  
...  
Keyword(s):  
Aspergillus Flavus ◽  
Sequence Data ◽  
Soil Fungus ◽  
Gene Clusters ◽  
Deletion Mutants ◽  
Wild Type ◽  
Functional Homolog ◽  
Biosynthesis Gene ◽  
Penicillium Paxilli ◽  
Diterpene Biosynthesis

ABSTRACT Aflatrem is a potent tremorgenic toxin produced by the soil fungus Aspergillus flavus, and a member of a structurally diverse group of fungal secondary metabolites known as indole-diterpenes. Gene clusters for indole-diterpene biosynthesis have recently been described in several species of filamentous fungi. A search of Aspergillus complete genome sequence data identified putative aflatrem gene clusters in the genomes of A. flavus and Aspergillus oryzae. In both species the genes for aflatrem biosynthesis cluster at two discrete loci; the first, ATM1, is telomere proximal on chromosome 5 and contains a cluster of three genes, atmG, atmC, and atmM, and the second, ATM2, is telomere distal on chromosome 7 and contains five genes, atmD, atmQ, atmB, atmA, and atmP. Reverse transcriptase PCR in A. flavus demonstrated that aflatrem biosynthesis transcript levels increased with the onset of aflatrem production. Transfer of atmP and atmQ into Penicillium paxilli paxP and paxQ deletion mutants, known to accumulate paxilline intermediates paspaline and 13-desoxypaxilline, respectively, showed that AtmP is a functional homolog of PaxP and that AtmQ utilizes 13-desoxypaxilline as a substrate to synthesize aflatrem pathway-specific intermediates, paspalicine and paspalinine. We propose a scheme for aflatrem biosynthesis in A. flavus based on these reconstitution experiments in P. paxilli and identification of putative intermediates in wild-type cultures of A. flavus.

Glyco-recoded Escherichia coli: Recombineering-based genome editing of native polysaccharide biosynthesis gene clusters

2019 ◽  
Vol 53 ◽  
pp. 59-68 ◽  
Author(s):  
Laura E. Yates ◽  
Aravind Natarajan ◽  
Mingji Li ◽  
Margaret E. Hale ◽  
Dominic C. Mills ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Editing ◽  
Gene Clusters ◽  
Polysaccharide Biosynthesis ◽  
Biosynthesis Gene

scholarly journals Mechanism of Antibacterial Activity of Bacillus amyloliquefaciens C-1 Lipopeptide toward Anaerobic Clostridium difficile

2020 ◽  
Vol 2020 ◽  
pp. 1-12 ◽  
Author(s):  
Jia Lv ◽  
Rong Da ◽  
Yue Cheng ◽  
Xiaohong Tuo ◽  
Jie Wei ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Clostridium Difficile ◽  
Bacillus Amyloliquefaciens ◽  
Gene Clusters ◽  
Systematic Research ◽  
Attractive Alternative ◽  
Antimicrobial Compound ◽  
Genome Resequencing ◽  
Biosynthesis Gene

Probiotics may offer an attractive alternative for standard antibiotic therapy to treat Clostridium difficile infections (CDI). In this study, the antibacterial mechanism in vitro of newly isolated B. amyloliquefaciens C-1 against C. difficile was investigated. The lipopeptides surfactin, iturin, and fengycin produced by C-1 strongly inhibited C. difficile growth and viability. Systematic research of the bacteriostatic mechanism showed that the C-1 lipopeptides damage the integrity of the C. difficile cell wall and cell membrane. In addition, the lipopeptide binds to C. difficile genomic DNA, leading to cell death. Genome resequencing revealed many important antimicrobial compound-encoding clusters, including six nonribosomal peptides (surfactins (srfABCD), iturins (ituABCD), fengycins (fenABCDE), bacillibactin (bmyABC), teichuronic, and bacilysin) and three polyketides (bacillaene (baeEDLMNJRS), difficidin (difABCDEFGHIJ), and macrolactin (mlnABCDEFGHI)). In addition, there were other beneficial genes, such as phospholipase and seven siderophore biosynthesis gene clusters, which may contribute synergistically to the antibacterial activity of B. amyloliquefaciens C-1. We suggest that proper application of antimicrobial peptides may be effective in C. difficile control.

Capsular exopolysaccharide biosynthesis gene of Propionibacterium freudenreichii subsp. shermanii

2008 ◽  
Vol 125 (3) ◽  
pp. 252-258 ◽  
Author(s):  
Stéphanie-Marie Deutsch ◽  
Hélène Falentin ◽  
Marguerite Dols-Lafargue ◽  
Gisèle LaPointe ◽  
Denis Roy
Keyword(s):  
Propionibacterium Freudenreichii ◽  
Biosynthesis Gene ◽  
Exopolysaccharide Biosynthesis
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