Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp. Strain JS614

Coleman, Nicholas V.; Wilson, N. L.; Barry, Kerrie; Brettin, Thomas; Bruce, David; Copeland, Alex; Dalin, Eileen; Detter, John C.; Rio, Tijana Glavina del; Goodwin, Lynne; Hammon, Nancy; Han, Shunsheng; Hauser, Loren; Israni, Sanjay; Kim, Edwin; Kyrpides, Nikos C.; Land, Miriam; Lapidus, Alla; Larimer, Frank W.; Lucas, Susan; Pitluck, Sam; Richardson, Paul M.; Schmutz, Jeremy; Tapia, Roxanne; Thompson, Sue; Tice, Hope; Spain, Jim C.; Gossett, James G.; Mattes, Timothy E.

doi:10.1128/jb.05109-11

Cited by 17 publications

(10 citation statements)

References 31 publications

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“…In addition, Nocardioides sp. strain JS614 also contains a complete set of chemotaxis proteins, even though the organism has been described as being nonmotile (48). Additionally, a number of nonmotile actinobacteria contain relatively high numbers of chemotaxis-related STPs, e.g., 21 in Sanguibacter keddieii DSM 10542.…”

Section: Resultsmentioning

confidence: 99%

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

et al. 2015

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Signal transduction is an essential process that allows bacteria to sense their complex and ever-changing environment and adapt accordingly. Three distinct major types of signal-transducing proteins (STPs) can be distinguished: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function factors (ECFs). Since Actinobacteria are particularly rich in STPs, we comprehensively investigated the abundance and diversity of STPs encoded in 119 actinobacterial genomes, based on the data stored in the Microbial Signal Transduction (MiST) database. Overall, we observed an approximately linear correlation between the genome size and the total number of encoded STPs. About half of all membrane-anchored 1CSs are protein kinases. For both 1CSs and 2CSs, a detailed analysis of the domain architectures identified novel proteins that are found only in actinobacterial genomes. Many actinobacterial genomes are particularly enriched for ECFs. As a result of this study, almost 500 previously unclassified ECFs could be classified into 18 new ECF groups. This comprehensive survey demonstrates that actinobacterial genomes encode previously unknown STPs, which may represent new mechanisms of signal transduction and regulation. This information not only expands our knowledge of the diversity of bacterial signal transduction but also provides clear and testable hypotheses about their mechanisms, which can serve as starting points for experimental studies. IMPORTANCEIn the wake of the genomic era, with its enormous increase in the amount of available sequence information, the challenge has now shifted toward making sense and use of this treasure chest. Such analyses are a prerequisite to provide meaningful information that can help guide subsequent experimental efforts, such as mechanistic studies on novel signaling strategies. This work provides a comprehensive analysis of signal transduction proteins from 119 actinobacterial genomes. We identify, classify, and describe numerous novel and conserved signaling devices. Hence, our work serves as an important resource for any researcher interested in signal transduction of this important bacterial phylum, which contains organisms of ecological, biotechnological, and medical relevance. Bacterial survival critically depends on the ability to swiftly respond to environmental changes. To efficiently monitor the surrounding environment, microbial genomes encode numerous and highly diverse proteins that can sense a given extracellular stimulus, transmit the signal to the cytoplasm, and elicit a proper response. These signal-transducing proteins (STPs) can be divided into three major groups: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function factors (ECFs). The vast majority of STPs in bacteria are 1CSs. These systems are composed of a single protein that contains an input domain, which senses the stimulus, and an output domain, which elicits the response by binding nucleic acids, modifying proteins, or performing an enzymati...

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Section: Resultsmentioning

confidence: 99%

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

et al. 2015

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“…strain JS614 [67]) are incorrectly annotated as MetE genes in GenBank. Examples of inaccurate annotation are compiled and presented in Table S10 in the supplemental material.…”

Section: Discussionmentioning

confidence: 99%

Epoxyalkane:Coenzyme M Transferase Gene Diversity and Distribution in Groundwater Samples from Chlorinated-Ethene-Contaminated Sites

Liu

Mattes

2016

Appl Environ Microbiol

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Epoxyalkane:coenzyme M transferase (EaCoMT) plays a critical role in the aerobic biodegradation and assimilation of alkenes, including ethene, propene, and the toxic chloroethene vinyl chloride (VC). To improve our understanding of the diversity and distribution of EaCoMT genes in the environment, novel EaCoMT-specific terminal-restriction fragment length polymorphism (T-RFLP) and nested-PCR methods were developed and applied to groundwater samples from six different contaminated sites. T-RFLP analysis revealed 192 different EaCoMT T-RFs. Using clone libraries, we retrieved 139 EaCoMT gene sequences from these samples. Phylogenetic analysis revealed that a majority of the sequences (78.4%) grouped with EaCoMT genes found in VC-and ethene-assimilating Mycobacterium strains and Nocardioides sp. strain JS614. The four most-abundant T-RFs were also matched with EaCoMT clone sequences related to Mycobacterium and Nocardioides strains. The remaining EaCoMT sequences clustered within two emergent EaCoMT gene subgroups represented by sequences found in propene-assimilating Gordonia rubripertincta strain B-276 and Xanthobacter autotrophicus strain Py2. EaCoMT gene abundance was positively correlated with VC and ethene concentrations at the sites studied. IMPORTANCEThe EaCoMT gene plays a critical role in assimilation of short-chain alkenes, such as ethene, VC, and propene. An improved understanding of EaCoMT gene diversity and distribution is significant to the field of bioremediation in several ways. The expansion of the EaCoMT gene database and identification of incorrectly annotated EaCoMT genes currently in the database will facilitate improved design of environmental molecular diagnostic tools and high-throughput sequencing approaches for future bioremediation studies. Our results further suggest that potentially significant aerobic VC degraders in the environment are not well represented in pure culture. Future research should aim to isolate and characterize aerobic VC-degrading bacteria from these underrepresented groups. Short-chain alkenes (e.g., ethene, propene, and butenes) are common hydrocarbons in the environment, primarily encountered as fossil fuel components or products of living organisms or generated by the chemical industry (1). For instance, ethene is generated by both plants (2) and bacteria (3).Chlorinated alkenes (e.g., vinyl chloride [VC]) are also naturally occurring, albeit at very low levels (4). VC is produced industrially as a monomer for polyvinyl chloride plastics. However, most environmental VC is generated by incomplete anaerobic dechlorination of the widely used solvents tetrachloroethene (PCE) and trichloroethene (TCE) in groundwater, where ethene can also be generated as a complete dechlorination product (1). PCE, TCE, and VC are common groundwater contaminants (5), and sites contaminated with chloroethenes are widely distributed across the United States (6) and elsewhere (1, 7). VC is of particular concern as a known human carcinogen (8).In aerobic bacteria that utilize short...

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“…HTCC2649, sequence accession AAMN00000000 [133] Microbacterium testaceum StLB037, sequence accession AP012052 [134] Mycobacterium bovis BCG, sequence accession later [135] Nocardioides sp. JS614, sequence accession CP000509, CP000508 [136] Saccharopolyspora spinosa NRRL 18395, sequence accession AEYC00000000 [137] Streptomyces griseoaurantiacus, sequence accession AEYX01000000 [138] Streptomyces griseus XyelbKG-1, sequence accession ADFC00000000 [139] Streptomyces sp. PP-C42, sequence accession AEWS01000000 [140] Verrucosispora maris AB-18-032, sequence accession CP002638, CP002639 [141] Phylum Chlamydiae Chlamydia pecorum E58, sequence accession CP002608 [142] Chlamydia psittaci 6BC, sequence accession CP002586 (chromosome), CP002587 (plasmid) [143] Chlamydia psittaci Cal10, sequence accession AEZD00000000 [143] Chlamydophila psittaci RD1, sequence accession FQ482149 (chromosome) FQ482150 (plasmid) [144] Standards in Genomic Sciences…”

Section: Phylum Tenericutesmentioning

confidence: 99%

Genome sequences published outside of Standards in Genomic Sciences, January – June 2011

Nelson

2011

Stand. Genomic Sci.

122

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Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp. Strain JS614

Cited by 17 publications

References 31 publications

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

Epoxyalkane:Coenzyme M Transferase Gene Diversity and Distribution in Groundwater Samples from Chlorinated-Ethene-Contaminated Sites

Genome sequences published outside of Standards in Genomic Sciences, January – June 2011

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