Menu

Auto Tag: Bacterial

July 7, 2019

Protein O-linked glycosylation in the plant pathogen Ralstonia solanacearum.

Ralstonia solanacearum is one of the most lethal phytopathogens in the world. Due to its broad host range, it can cause wilting disease in many plant species of economic interest. In this work, we identified the O-oligosaccharyltransferase (O-OTase) responsible for protein O-glycosylation in R. solanacearum. An analysis of the glycoproteome revealed that 20 proteins, including type IV pilins are substrates of this general glycosylation system. Although multiple glycan forms were identified, the majority of the glycopeptides were modified with a pentasaccharide composed of HexNAc-(Pen)-dHex3, similar to the O antigen subunit present in the lipopolysaccharide of multiple R. solanacearum strains. Disruption of the O-OTase led to the total loss of protein glycosylation, together with a defect in biofilm formation and reduced pathogenicity towards tomato plants. Comparative proteomic analysis revealed that the loss of glycosylation is not associated with widespread proteome changes. Only the levels of a single glycoprotein, the type IV pilin, were diminished in the absence of glycosylation. In parallel, disruption of glycosylation triggered an increase in the levels of a surface lectin homologous to Pseudomonas PA-IIL. These results reveal the important role of glycosylation in the pathogenesis of R. solanacearum. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Read more
July 7, 2019

Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp. ATCC 55669 for heterologous overproduction in Escherichia coli.

As a highly valued keto-carotenoid, astaxanthin is widely used in nutritional supplements and pharmaceuticals. Therefore, the demand for biosynthetic astaxanthin and improved efficiency of astaxanthin biosynthesis has driven the investigation of metabolic engineering of native astaxanthin producers and heterologous hosts. However, microbial resources for astaxanthin are limited. In this study, we found that the a-Proteobacterium Sphingomonas sp. ATCC 55669 could produce astaxanthin naturally. We used whole-genome sequencing to identify the astaxanthin biosynthetic pathway using a combined PacBio-Illumina approach. The putative astaxanthin biosynthetic pathway in Sphingomonas sp. ATCC 55669 was predicted. For further confirmation, a high-efficiency targeted engineering carotenoid synthesis platform was constructed in E. coli for identifying the functional roles of candidate genes. All genes involved in astaxanthin biosynthesis showed discrete distributions on the chromosome. Moreover, the overexpression of exogenous E. coli idi in Sphingomonas sp. ATCC 55669 increased astaxanthin production by 5.4-fold. This study described a new astaxanthin producer and provided more biosynthesis components for bioengineering of astaxanthin in the future. © 2015 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Read more
July 7, 2019

Integrating mass spectrometry and genomics for cyanobacterial metabolite discovery.

Filamentous marine cyanobacteria produce bioactive natural products with both potential therapeutic value and capacity to be harmful to human health. Genome sequencing has revealed that cyanobacteria have the capacity to produce many more secondary metabolites than have been characterized. The biosynthetic pathways that encode cyanobacterial natural products are mostly uncharacterized, and lack of cyanobacterial genetic tools has largely prevented their heterologous expression. Hence, a combination of cutting edge and traditional techniques has been required to elucidate their secondary metabolite biosynthetic pathways. Here, we review the discovery and refined biochemical understanding of the olefin synthase and fatty acid ACP reductase/aldehyde deformylating oxygenase pathways to hydrocarbons, and the curacin A, jamaicamide A, lyngbyabellin, columbamide, and a trans-acyltransferase macrolactone pathway encoding phormidolide. We integrate into this discussion the use of genomics, mass spectrometric networking, biochemical characterization, and isolation and structure elucidation techniques.

Read more
July 7, 2019

Assembly and characterization of the MHC class I region of the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis).

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis; YFP) is the sole freshwater subspecies of N. asiaeorientalis and is now critically endangered. Major histocompatibility complex (MHC) is a family of highly polymorphic genes that play an important immunological role in antigen presentation in the vertebrates. Currently, however, little is known about MHC region in the genome of the YFP, which hampers conservation genetics and evolutionary ecology study using MHC genes. In this work, a nucleotide sequence of 774,811 bp covering the YFP MHC class I region was obtained by screening a YFP bacterial artificial chromosome (BAC) library, followed by sequencing and assembly of positive BAC clones. A total of 45 genes were successfully annotated, of which four were MHC class I genes. There are high similarities among the four YFP MHC class I genes (>94 %). Divergence in the coding region of the four YFP MHC class I genes is mainly localized to exons 2 and 3, which encode the antigen-binding sites of MHC class I genes. Additionally, comparison of the MHC structure in YFP to those of cattle, sheep, and pig showed that MHC class I genes are located in genome regions with regard to the conserved genes, and the YFP contains the fewest MHC class I genes among these species. This is the first report characterizing a cetacean MHC class I region and describing its organization, which would be valuable for further investigation of adaptation in natural populations of the YFP and other cetaceans.

Read more
July 7, 2019

Complete genome sequence of deoxynivalenol-degrading bacterium Devosia sp. strain A16.

The strain A16, capable of degrading deoxynivalenol was isolated from a wheat field and identified preliminarily as Devosia sp. Here, we present the genome sequence of the Devosia sp. A16, which has a size of 5,032,994bp, with 4913 coding sequences (CDSs). The annotated full genome sequence of the Devosia sp. A16 strain might shed light on the function of its degradation. Copyright © 2015 Elsevier B.V. All rights reserved.

Read more
July 7, 2019

Complete genome sequence of Hymenobacter sp. DG25B, a novel bacterium with gamma-radiation resistance isolated from soil in South Korea.

A Gram-negative, rod-shaped, non-motile, gamma and UV radiation resistant bacterium Hymenobacter radioresistens DG25B was isolated from a soil sample collected in South Korea. The complete genome sequence of H. radioresistens DG25B consists of one circular chromosome (3,874,646bp). The bacterium was isolated from gamma ray irradiated soil and contains the genomic features of enzymes involved in the nucleotide excision repair (NER) pathway that protect the damaged DNA. The genome also contains other genes involved in the efficient removal of double-strand breaks (DSB) caused by the ionizing radiations. Copyright © 2015 Elsevier B.V. All rights reserved.

Read more
July 7, 2019

Complete genome sequence of the Variibacter gotjawalensis GJW-30(T) from soil of lava forest, Gotjawal.

Variibacter gotjawalensis GJW-30(T) is a gram-negative, strictly aerobic bacterium to form pleomorphic. Here we present the 4.5-Mb genome sequence of the type strain of V. gotjawalensis GJW-30(T), which consists a chromosome for the total 4,586,237bp with a G+C content of 62.2mol%. This is the first report of the full genome sequence of a species of the novel genus Variibacter isolated from Gotjawal, a unique area in Jeju, Republic of Korea. Copyright © 2015 Elsevier B.V. All rights reserved.

Read more
July 7, 2019

Complete genome of Pseudoalteromonas phenolica KCTC 12086(T) (= O-BC30(T)), a marine bacterium producing polybrominated aromatic compounds.

Pseudoalteromonas phenolica is a Gram-negative, rod-shaped, flagellated, aerobic, antibiotic-producing bacterium that was isolated from seawater off Ogasawara Island, Japan. Here, we report the complete genome of P. phenolica KCTC 12086(T) (= O-BC30(T)), which consists of 4,868,993 bp (G+C content of 40.6%) with two chromosomes, 4168 protein-coding genes, 113 tRNAs and 9 rRNA operons. In addition, several genes related to phenolic anti-methicillin-resistant Staphylococcus aureus substances were detected in the genome suggesting that biosynthesis of industrially important polybrominated aromatic compounds could be better understood with the availability of genome data of P. phenolica. Copyright © 2015 Elsevier B.V. All rights reserved.

Read more
July 7, 2019

hybridSPAdes: an algorithm for hybrid assembly of short and long reads.

Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost.We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads.hybridSPAdes is implemented in C++?as a part of SPAdes genome assembler and is publicly available at http://bioinf.spbau.ru/en/spades CONTACT: d.antipov@spbu.ruSupplementary information: supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Read more
July 7, 2019

The complete chloroplast genome of Gentiana straminea (Gentianaceae), an endemic species to the Sino-Himalayan subregion.

Endemic to the Sino-Himalayan subregion, the medicinal alpine plant Gentiana straminea is a threatened species. The genetic and molecular data about it is deficient. Here we report the complete chloroplast (cp) genome sequence of G. straminea, as the first sequenced member of the family Gentianaceae. The cp genome is 148,991bp in length, including a large single copy (LSC) region of 81,240bp, a small single copy (SSC) region of 17,085bp and a pair of inverted repeats (IRs) of 25,333bp. It contains 112 unique genes, including 78 protein-coding genes, 30 tRNAs and 4 rRNAs. The rps16 gene lacks exon2 between trnK-UUU and trnQ-UUG, which is the first rps16 pseudogene found in the nonparasitic plants of Asterids clade. Sequence analysis revealed the presence of 13 forward repeats, 13 palindrome repeats and 39 simple sequence repeats (SSRs). An entire cp genome comparison study of G. straminea and four other species in Gentianales was carried out. Phylogenetic analyses using maximum likelihood (ML) and maximum parsimony (MP) were performed based on 69 protein-coding genes from 36 species of Asterids. The results strongly supported the position of Gentianaceae as one member of the order Gentianales. The complete chloroplast genome sequence will provide intragenic information for its conservation and contribute to research on the genetic and phylogenetic analyses of Gentianales and Asterids. Copyright © 2015 Elsevier B.V. All rights reserved.

Read more
July 7, 2019

Complete genome sequence of an aromatic compound degrader Arthrobacter sp. YC-RL1.

Arthrobacter sp. YC-RL1, isolated from a petroleum-contaminated soil, is capable of degrading and utilizing a wide range of aromatic compounds for growth. Here we report the complete genome sequence of strain YC-RL1, which may facilitate the investigation of environmental bioremediation and provide new gene resources for biotechnology and gene engineering. Copyright © 2015 Elsevier B.V. All rights reserved.

Read more
July 7, 2019

Complete genome sequence of Celeribacter marinus IMCC12053(T), the host strain of marine bacteriophage P12053L.

Isolated from coastal seawater from Yellow Sea of Korea, Celeribacter marinus IMCC12053 was used as the host bacterium for bacteriophage P12053L. Here we report the complete genome sequence of strain IMCC12053 for further study of the marine bacteriophage P12053L functional genes. Single molecule real-time technology (PacBio RSII) was used for the single circular chromosome that is 3,096,705 base pairs in length and the GC content is 56.24%. It contains 3155 ORFs with 45 tRNAs and 6 rRNAs genes. N(6)-methyladenosine patterns were also investigated for 32 unmethylated genes and intergenic regions that covered many regulators and phage genes as well as ribosomal RNA genes and tRNA genes. Cryptic N(4)-methylcytosine pattern was investigated to speculate GpC methylase activity throughout the genome. Comparative genomics with other Celeribacter genomes were carried out for polyaromatic hydrocarbon degradation, but there were no aromatic ring oxygenases in IMCC12053 when compared to Celeribacter indicus P73. Copyright © 2015 Elsevier B.V. All rights reserved.

Read more

Subscribe for blog updates:

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.