Using OrthoMCL to Assign Proteins to OrthoMCL‐DB Groups or to Cluster Proteomes Into New Ortholog Groups

Fischer, Steven H.; Brunk, Brian P.; Chen, Feng; Gao, Xin; Harb, Omar S.; Iodice, John; Shanmugam, Dhanasekaran; Roos, David S.; Stoeckert, Christian J.

doi:10.1002/0471250953.bi0612s35

Cited by 392 publications

(354 citation statements)

References 9 publications

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“…Predicted genes and their translated protein sequences of KP35 (accession #LRXK000000000) were compared with the reference genome ATCC 43816 KPPR1, NJST258-1, and NJST258-2 (7,33), and clustered into OGs by using the OrthoMCL software (48). The protein sequences of the 2 reference genomes were calculated based on the NCBI annotations.…”

Section: Comparative Genomic Analyses and Gene Ortholog Analysismentioning

confidence: 99%

Acquired resistance to innate immune clearance promotes Klebsiella pneumoniae ST258 pulmonary infection

et al. 2016

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Section: Comparative Genomic Analyses and Gene Ortholog Analysismentioning

confidence: 99%

Acquired resistance to innate immune clearance promotes Klebsiella pneumoniae ST258 pulmonary infection

et al. 2016

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“…Complete and draft genomes with VfcB BLASTP hits were retrieved from the NCBI genome database. Ortholog group prediction was determined with orthoMCL (21). The resulting 62 single-copy gene ortholog clusters were obtained and individually aligned at the protein level with mafft-linsi (22) and then back-translated with backtranseq (23) and realigned at the nucleotide level with mafft-FFT-NS-i.…”

Section: Methodsmentioning

confidence: 99%

Characterization of the Vibrio fischeri Fatty Acid Chemoreceptors, VfcB and VfcB2

Nikolakakis

Monfils

Moriano‐Gutierrez

et al. 2016

Appl Environ Microbiol

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Bacteria use a wide variety of methyl-accepting chemotaxis proteins (MCPs) to mediate their attraction to or repulsion from different chemical signals in their environment. The bioluminescent marine bacterium Vibrio fischeri is the monospecific symbiont of the Hawaiian bobtail squid, Euprymna scolopes, and encodes a large repertoire of MCPs that are hypothesized to be used during different parts of its complex, multistage lifestyle. Here, we report the initial characterization of two such MCPs from V. fischeri that are responsible for mediating migration toward short-and medium-chain aliphatic (or fatty) acids. These receptors appear to be distributed among only members of the family Vibrionaceae and are likely descended from a receptor that has been lost by the majority of the members of this family. While chemotaxis greatly enhances the efficiency of host colonization by V. fischeri, fatty acids do not appear to be used as a chemical cue during this stage of the symbiosis. This study presents an example of straight-chain fatty acid chemoattraction and contributes to the growing body of characterized MCP-ligand interactions. F lagellar motility in bacteria is a complex, tightly regulated process. Through alternating cycles of swimming and tumbling, a bacterium is able to navigate its environment, either to move away from unfavorable conditions or to migrate toward a more favorable habitat (e.g., toward nutrient sources) (1, 2). This directed motility is termed chemotaxis and is mediated by the CheAY twocomponent signal transduction pathway. These proteins alter the relative time for which the flagellum rotates counterclockwise (CCW) or clockwise (CW) and, in turn, how much time the bacterium spends swimming or tumbling, respectively. This change in rotational direction is determined by the phosphorylation state of CheY, which is mediated primarily by membrane-bound receptors known as methyl-accepting chemotaxis proteins (MCPs). MCPs are ligand-binding sensory proteins and are generally embedded in the inner membrane with their ligand-binding domain (LBD) extended into the periplasm and their signaling domains present in the cytosol. Upon ligand binding, the MCP undergoes a conformational change that allows methylation of the signaling domain, thereby permitting a sensory signal to be transmitted across the inner membrane.Chemotaxis and MCPs have been most thoroughly studied in Escherichia coli, which encodes three to five distinct MCPs shown to be involved in the sensing of compounds such as amino acids, peptides, sugars, and electron acceptors (3-8). However, as the number of sequenced bacterial genomes grows, it has become apparent that many other bacteria contain much larger repertoires of MCPs (1). For example, the genome of Pseudomonas aeruginosa encodes 24 MCPs, that of Vibrio cholerae encodes 44, and that of Magnetospirillum magnetotacticum encodes the largest known set of 61 MCPs. Despite these large numbers of receptors, the number of known ligands is surprisingly small. Previous work has shown little ...

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“…Briefly OrthoMCL (20) was used to identify orthologs across 88 eukaryotic genomes, 16 archaeal genomes, and 34 bacterial genomes to create clusters that are made available in OrthoMCL-DB (version 5) (21). Genes from all fungal genomes in FungiDB are mapped into OrthoMCL-DB ortholog clusters by protein similarity (22). Mercator (23) was used to construct a synteny map of the homologous regions.…”

Section: Methodsmentioning

confidence: 99%

Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus

et al. 2014

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cCryptococcus, a major cause of disseminated infections in immunocompromised patients, kills over 600,000 people per year worldwide. Genes involved in the virulence of the meningitis-causing fungus are being characterized at an increasing rate, and to date, at least 648 Cryptococcus gene names have been published. However, these data are scattered throughout the literature and are challenging to find. Furthermore, conflicts in locus identification exist, so that named genes have been subsequently published under new names or names associated with one locus have been used for another locus. To avoid these conflicts and to provide a central source of Cryptococcus gene information, we have collected all published Cryptococcus gene names from the scientific literature and associated them with standard Cryptococcus locus identifiers and have incorporated them into FungiDB (www.fungidb.org). FungiDB is a panfungal genome database that collects gene information and functional data and provides search tools for 61 species of fungi and oomycetes. We applied these published names to a manually curated ortholog set of all Cryptococcus species currently in FungiDB, including Cryptococcus neoformans var. neoformans strains JEC21 and B-3501A, C. neoformans var. grubii strain H99, and Cryptococcus gattii strains R265 and WM276, and have written brief descriptions of their functions. We also compiled a protocol for gene naming that summarizes guidelines proposed by members of the Cryptococcus research community. The centralization of genomic and literature-based information for Cryptococcus at FungiDB will help researchers communicate about genes of interest, such as those related to virulence, and will further facilitate research on the pathogen.

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Using OrthoMCL to Assign Proteins to OrthoMCL‐DB Groups or to Cluster Proteomes Into New Ortholog Groups

Cited by 392 publications

References 9 publications

Acquired resistance to innate immune clearance promotes Klebsiella pneumoniae ST258 pulmonary infection

Acquired resistance to innate immune clearance promotes Klebsiella pneumoniae ST258 pulmonary infection

Characterization of the Vibrio fischeri Fatty Acid Chemoreceptors, VfcB and VfcB2

Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus

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