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.

scholarly journals Effects of an EPS Biosynthesis Gene Cluster of Paenibacillus polymyxa WLY78 on Biofilm Formation and Nitrogen Fixation under Aerobic Conditions

2021 ◽  
Vol 9 (2) ◽  
pp. 289
Author(s):  
Xiaojuan He ◽  
Qin Li ◽  
Nan Wang ◽  
Sanfeng Chen
Keyword(s):  
Extracellular Matrix ◽  
Biofilm Formation ◽  
Paenibacillus Polymyxa ◽  
Gene Clusters ◽  
Bacterial Biofilm ◽  
Biosynthesis Gene Cluster ◽  
Putative Gene ◽  
Aerobic Conditions ◽  
Biosynthesis Gene ◽  
Paenibacillus Species

Exopolysaccharides (EPS) are of high significance in bacterial biofilm formation. However, the effects of EPS cluster(s) on biofilm formation in Paenibacillus species are little known. In this study, we have shown that Paenibacillus polymyxa WLY78, a N2-fixing bacterium, can form biofilm. EPS is the major component of the extracellular matrix. The genome of P. polymyxa WLY78 contains two putative gene clusters (designated pep-1 cluster and pep-2 cluster). The pep-1 cluster is composed of 12 putative genes (pepO-lytR) co-located in a 13 kb region. The pep-2 cluster contains 17 putative genes (pepA-pepN) organized as an operon in a 20 kb region. Mutation analysis reveals that the pep-2 cluster is involved in EPS biosynthesis and biofilm formation. Disruption of the pep-2 cluster also leads to the enhancement of motility and change of the colony morphology. In contrast, disruption of the pep-1 cluster does not affect EPS synthesis or biofilm formation. More importantly, the biofilm allowed P. polymyxa WLY78 to fix nitrogen in aerobic conditions, suggesting that biofilm may provide a microaerobic environment for nitrogenase synthesis and activity.

scholarly journals Biofilm Formation in Pseudomonas aeruginosa: Fimbrial cup Gene Clusters Are Controlled by the Transcriptional Regulator MvaT

2004 ◽  
Vol 186 (9) ◽  
pp. 2880-2890 ◽  
Author(s):  
Isabelle Vallet ◽  
Stephen P. Diggle ◽  
Rachael E. Stacey ◽  
Miguel Cámara ◽  
Isabelle Ventre ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Biofilm Formation ◽  
Dna Microarrays ◽  
Transcriptional Profiling ◽  
Bacterial Pathogen ◽  
Gene Clusters ◽  
Northern Blotting ◽  
Negative Regulator ◽  
Regulatory Control ◽  
Homologous Gene

ABSTRACT Pseudomonas aeruginosa is an opportunistic bacterial pathogen which poses a major threat to long-term-hospitalized patients and individuals with cystic fibrosis. The capacity of P. aeruginosa to form biofilms is an important requirement for chronic colonization of human tissues and for persistence in implanted medical devices. Various stages of biofilm formation by this organism are mediated by extracellular appendages, such as type IV pili and flagella. Recently, we identified three P. aeruginosa gene clusters that were termed cup (chaperone-usher pathway) based on their sequence relatedness to the chaperone-usher fimbrial assembly pathway in other bacteria. The cupA gene cluster, but not the cupB or cupC cluster, is required for biofilm formation on abiotic surfaces. In this study, we identified a gene (mvaT) encoding a negative regulator of cupA expression. Such regulatory control was confirmed by several approaches, including lacZ transcriptional fusions, Northern blotting, and transcriptional profiling using DNA microarrays. MvaT also represses the expression of the cupB and cupC genes, although the extent of the regulatory effect is not as pronounced as with cupA. Consistent with this finding, mvaT mutants exhibit enhanced biofilm formation. Although the P. aeruginosa genome contains a highly homologous gene, mvaU, the repression of cupA genes is MvaT specific. Thus, MvaT appears to be an important regulatory component within a complex network that controls biofilm formation and maturation in P. aeruginosa.

scholarly journals Detection of Protozoan Hosts for Legionella pneumophila in Engineered Water Systems by Using a Biofilm Batch Test

2010 ◽  
Vol 76 (21) ◽  
pp. 7144-7153 ◽  
Author(s):  
Rinske M. Valster ◽  
Bart A. Wullings ◽  
Dick van der Kooij
Keyword(s):  
Legionella Pneumophila ◽  
Biofilm Formation ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Batch Test ◽  
Free Living ◽  
Water Types ◽  
Operational Taxonomic Units ◽  
Hartmannella Vermiformis

ABSTRACT Legionella pneumophila proliferates in aquatic habitats within free-living protozoa, 17 species of which have been identified as hosts by using in vitro experiments. The present study aimed at identifying protozoan hosts for L. pneumophila by using a biofilm batch test (BBT). Samples (600 ml) collected from 21 engineered freshwater systems, with added polyethylene cylinders to promote biofilm formation, were inoculated with L. pneumophila and subsequently incubated at 37°C for 20 days. Growth of L. pneumophila was observed in 16 of 18 water types when the host protozoan Hartmannella vermiformis was added. Twelve of the tested water types supported growth of L. pneumophila or indigenous Legionella anisa without added H. vermiformis. In 12 of 19 BBT flasks H. vermiformis was indicated as a host, based on the ratio between maximum concentrations of L. pneumophila and H. vermiformis, determined with quantitative PCR (Q-PCR), and the composition of clone libraries of partial 18S rRNA gene fragments. Analyses of 609 eukaryotic clones from the BBTs revealed that 68 operational taxonomic units (OTUs) showed the highest similarity to free-living protozoa. Forty percent of the sequences clustering with protozoa showed ≥99.5% similarity to H. vermiformis. None of the other protozoa serving as hosts in in vitro studies were detected in the BBTs. In several tests with growth of L. pneumophila, the protozoa Diphylleia rotans, Echinamoeba thermarum, and Neoparamoeba sp. were identified as candidate hosts. In vitro studies are needed to confirm their role as hosts for L. pneumophila. Unidentified protozoa were implicated as hosts for uncultured Legionella spp. grown in BBT flasks at 15°C.

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

scholarly journals Disruption of c-di-GMP signaling networks unlocks cryptic expression of secondary metabolites during biofilm growth in Burkholderia pseudomallei

2021 ◽  
Author(s):  
Grace I Borlee ◽  
Mihnea R. Mangalea ◽  
Kevin H. Martin ◽  
Brooke A. Plumley ◽  
Samuel J. Golon ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Biofilm Formation ◽  
Burkholderia Pseudomallei ◽  
Gene Clusters ◽  
Etiologic Agent ◽  
Regulatory Control ◽  
Colony Morphology ◽  
Secretion Systems ◽  
Biofilm Growth ◽  
Conditional Expression

The regulation and production of secondary metabolites during biofilm growth of Burkholderia spp. is not well understood. To learn more about the crucial role and regulatory control of cryptic molecules produced during biofilm growth, we disrupted c-di-GMP signaling in Burkholderia pseudomallei, a soil-borne bacterial saprophyte and the etiologic agent of melioidosis. Our approach to these studies combined transcriptional profiling with genetic deletions that targeted key c-di-GMP regulatory components to characterize responses to changes in temperature. Mutational analyses and conditional expression studies of c-di-GMP genes demonstrates their contribution to phenotypes such as biofilm formation, colony morphology, motility, and expression of secondary metabolite biosynthesis when grown as a biofilm at different temperatures. RNA-seq analysis was performed at varying temperatures in a ΔII2523 mutant background that is responsive to temperature alterations resulting in hypo- and hyper- biofilm forming phenotypes. Differential regulation of genes was observed for polysaccharide biosynthesis, secretion systems, and nonribosomal peptide and polyketide synthase (NRPS/PKS) clusters in response to temperature changes. Deletion mutations of biosynthetic gene clusters (BGCs) clusters 2, 11, 14 (syrbactin), and 15 (malleipeptin) in wild-type and ΔII2523 backgrounds also reveals the contribution of these BGCs to biofilm formation and colony morphology in addition to inhibition of Bacillus subtilis and Rhizoctonia solani. Our findings suggest that II2523 impacts the regulation of genes that contribute to biofilm formation and competition. Characterization of cryptic BGCs under differing environmental conditions will allow for a better understanding of the role of secondary metabolites in the context of biofilm formation and microbe-microbe interactions.

scholarly journals Bichir external gills arise via heterochronic shift that accelerates hyoid arch development

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jan Stundl ◽  
Anna Pospisilova ◽  
David Jandzik ◽  
Peter Fabian ◽  
Barbora Dobiasova ◽  
...  
Keyword(s):  
Pharyngeal Arch ◽  
Developmental Sequence ◽  
Free Living ◽  
Pharyngeal Arches ◽  
Hyoid Arch ◽  
Early Appearance ◽  
Evolutionary Changes ◽  
Insight Into ◽  
Living Group ◽  
Early Larvae

In most vertebrates, pharyngeal arches form in a stereotypic anterior-to-posterior progression. To gain insight into the mechanisms underlying evolutionary changes in pharyngeal arch development, here we investigate embryos and larvae of bichirs. Bichirs represent the earliest diverged living group of ray-finned fishes, and possess intriguing traits otherwise typical for lobe-finned fishes such as ventral paired lungs and larval external gills. In bichir embryos, we find that the anteroposterior way of formation of cranial segments is modified by the unique acceleration of the entire hyoid arch segment, with earlier and orchestrated development of the endodermal, mesodermal, and neural crest tissues. This major heterochronic shift in the anteroposterior developmental sequence enables early appearance of the external gills that represent key breathing organs of bichir free-living embryos and early larvae. Bichirs thus stay as unique models for understanding developmental mechanisms facilitating increased breathing capacity.

scholarly journals Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

2021 ◽  
Vol 9 (8) ◽  
pp. 1761
Author(s):  
Gaurav Agarwal ◽  
Ronald D. Gitaitis ◽  
Bhabesh Dutta
Keyword(s):  
Gene Transfer ◽  
Core Genome ◽  
Foxtail Millet ◽  
Gene Clusters ◽  
Evaluation Study ◽  
Full Spectrum ◽  
Pan Genome ◽  
Pantoea Stewartii ◽  
Comparative Phylogenetic Analysis ◽  
Core Genes

Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.

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