OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

Xu, Limei; Dong, Zhaobin; Lü, Fang; Luo, Yongjiang; Wei, Zhaoyuan; Guo, Hailong; Zhang, Guoqing; Gu, Yong; Coleman‐Derr, Devin; Xia, Qingyou; Wang, Yi

doi:10.1093/nar/gkz333

Cited by 738 publications

(576 citation statements)

References 34 publications

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“…To investigate if orthologous genes are enriched with high GFP scoring sequences, we ranked, the genes of E. coli, K. oxytoca, and E. asburiae in three distinct lists, according to the score obtained for codon positions 3-5. The top 500 genes with higher scores of each list of each bacteria (1500 genes in total per analysis) were evaluated in OrthoVenn2 sever, which computes the orthologous gene clusters among multiple species 31 . The number of orthologous genes found was 351 (23%), a number 5.3 fold higher than the scramble list ( Figure 7E, compare the first hatched bar with the first red bar).…”

Section: Evolutionary Conservation Of the Short Translational Rampmentioning

confidence: 99%

From reporters to endogenous genes: the impact of the first five codons on translation efficiency in Escherichia coli

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et al. 2019

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Translation initiation is a critical step in the regulation of protein synthesis, and it is subjected to different control mechanisms, such as 5' UTR secondary structure and initiation codon context, that can influence the rates at which initiation and consequentially translation occurs. For some genes, translation elongation also affects the protein synthesis rate. Recently, it was proposed that the identity of codons three to five, called short translational ramp, have a strong influence on translation elongation and protein expression. By the use of a GFP library where nearly all combinations of nucleotides at these positions were created, it was demonstrated that some of nucleotides combinations increased GFP expression up to four orders of magnitude by enhancing their translation efficiency (TE). While it is clear that the short ramp can influence protein expression levels of artificial constructs, its impact on physiological proteins is still unknown. In this work, we aimed to investigate the relevance of the short translational ramp on a physiological context. Through bioinformatics analysis, we identified the nucleotide combinations from the GFP library on Escherichia coli genes and examined their correlation with TE. We observed that E. coli genes were enriched with nucleotide compositions that enhanced protein expression on the GFP library, but, surprisingly, it seems to affect the TE only marginally.Nevertheless, our data indicate that different enterobacteria present similar nucleotide composition enrichment as E. coli, suggesting an evolutionary pressure towards the conservation of the short translational ramp.

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Section: Evolutionary Conservation Of the Short Translational Rampmentioning

confidence: 99%

From reporters to endogenous genes: the impact of the first five codons on translation efficiency in Escherichia coli

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“…Virulence factors were predicted using the VFanalyzer tool available at the Virulence Factors Database [51]. OrthoVenn2 [52] was used to cluster predicted proteins to orthologous groups. Web-based tools PHASTER [53], CRISPR-Cas++ [54], and GView [55] were employed to find mobile genetic elements and dissimilar regions between analyzed genomes.…”

Section: Whole Genome Sequencing and Bioinformatic Analysesmentioning

confidence: 99%

Characterization of Staphylococcus intermedius Group Isolates Associated with Animals from Antarctica and Emended Description of Staphylococcus delphini

et al. 2020

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Members of the genus Staphylococcus are widespread in nature and occupy a variety of niches, however, staphylococcal colonization of animals in the Antarctic environment has not been adequately studied. Here, we describe the first isolation and characterization of two Staphylococcus intermedius group (SIG) members, Staphylococcus delphini and Staphylococcus pseudintermedius, in Antarctic wildlife. Staphylococcus delphini were found exclusively in Adélie penguins. The report of S. pseudintermedius from Weddell seals confirmed its occurrence in all families of the suborder Caniformia. Partial RNA polymerase beta-subunit (rpoB) gene sequencing, repetitive PCR fingerprinting with the (GTG)5 primer, and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry gave consistent identification results and proved to be suitable for identifying SIG members. Comparative genomics of S. delphini isolates revealed variable genomic elements, including new prophages, a novel phage-inducible chromosomal island, and numerous putative virulence factors. Surface and extracellular protein distribution were compared between genomes and showed strain-specific profiles. The pathogenic potential of S. delphini was enhanced by a novel type of exfoliative toxin, trypsin-like serine protease cluster, and enterotoxin C. Detailed analysis of phenotypic characteristics performed on six Antarctic isolates of S. delphini and eight reference strains from different animal sources enabled us to emend the species description of S. delphini.

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“…The genome sequence of L. suebicus LCV1 has been deposited at the NCBI archive with the corresponding BioProject ID PRJNA578870. Common and unique coding sequences in the two strains, with L. suebicus DSM5007 annotated with Prokka (Seemann, 2014), were identified with OrthoVenn2 (Xu et al, 2019).…”

Section: Genome Annotation and Analysismentioning

confidence: 99%

A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway

et al. 2020

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D-galacturonate, a key constituent of pectin, is a ubiquitous monomer in plant biomass. Anaerobic, fermentative conversion of D-galacturonate is therefore relevant in natural environments as well as in microbial processes for microbial conversion of pectincontaining agricultural residues. In currently known microorganisms that anaerobically ferment D-galacturonate, its catabolism occurs via the galacturonate-isomerase pathway. Redox-cofactor balancing in this pathway strongly constrains the possible range of products generated from anaerobic D-galacturonate fermentation, resulting in acetate as the predominant organic fermentation product. To explore metabolic diversity of microbial D-galacturonate fermentation, anaerobic enrichment cultures were performed at pH 4. Anaerobic batch and chemostat cultures of a dominant Lactobacillus suebicus strain isolated from these enrichment cultures produced near-equimolar amounts of lactate and acetate from D-galacturonate. A combination of whole-genome sequence analysis, quantitative proteomics, enzyme activity assays in cell extracts, and in vitro product identification demonstrated that D-galacturonate metabolism in L. suebicus occurs via a novel pathway. In this pathway, mannonate generated by the initial reactions of the canonical isomerase pathway is converted to 6-phosphogluconate by two novel biochemical reactions, catalyzed by a mannonate kinase and a 6-phosphomannonate 2-epimerase. Further catabolism of 6-phosphogluconate then proceeds via known reactions of the phosphoketolase pathway. In contrast to the classical isomerase pathway for D-galacturonate catabolism, the novel pathway enables redox-cofactor-neutral conversion of D-galacturonate to ribulose-5-phosphate. While further research is required to identify the structural genes encoding the key enzymes for the novel pathway, its redox-cofactor coupling is highly interesting for metabolic engineering of microbial cell factories for conversion of pectin-containing feedstocks into added-value fermentation products such as ethanol or lactate. This study illustrates the potential of microbial enrichment cultivation to identify novel pathways for the conversion of environmentally and industrially relevant compounds.

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OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species

Cited by 738 publications

References 34 publications

From reporters to endogenous genes: the impact of the first five codons on translation efficiency in Escherichia coli

From reporters to endogenous genes: the impact of the first five codons on translation efficiency in Escherichia coli

Characterization of Staphylococcus intermedius Group Isolates Associated with Animals from Antarctica and Emended Description of Staphylococcus delphini

A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway

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