Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae
Abstract
Background: Geobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with energy conservation and growth (i.e., organohalide respiration). Strain SZ also reduces U(VI) to U(IV) and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae. Results: Sequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs) and cytosines (Cs) among the four bases within the genome), and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC), with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. Amore »
- Authors:
-
- Georgia Inst. of Technology, Atlanta, GA (United States). School of Biology
- Univ. of Toronto, ON (Canada). Dept. of Cell and Systems Biology
- Georgia Inst. of Technology, Atlanta, GA (United States). School of Civil and Environmental Engineering
- Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology
- Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
- Univ. of Toronto, ON (Canada). Dept. of Chemical Engineering and Applied Chemistry
- Georgia Inst. of Technology, Atlanta, GA (United States). School of Biology; Georgia Inst. of Technology, Atlanta, GA (United States). School of Civil and Environmental Engineering
- Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1626415
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genomics
- Additional Journal Information:
- Journal Volume: 13; Journal Issue: 1; Journal ID: ISSN 1471-2164
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity
Citation Formats
Wagner, Darlene D., Hug, Laura A., Hatt, Janet K., Spitzmiller, Melissa R., Padilla-Crespo, Elizabeth, Ritalahti, Kirsti M., Edwards, Elizabeth A., Konstantinidis, Konstantinos T., and Löffler, Frank E. Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae. United States: N. p., 2012.
Web. doi:10.1186/1471-2164-13-200.
Wagner, Darlene D., Hug, Laura A., Hatt, Janet K., Spitzmiller, Melissa R., Padilla-Crespo, Elizabeth, Ritalahti, Kirsti M., Edwards, Elizabeth A., Konstantinidis, Konstantinos T., & Löffler, Frank E. Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae. United States. https://doi.org/10.1186/1471-2164-13-200
Wagner, Darlene D., Hug, Laura A., Hatt, Janet K., Spitzmiller, Melissa R., Padilla-Crespo, Elizabeth, Ritalahti, Kirsti M., Edwards, Elizabeth A., Konstantinidis, Konstantinos T., and Löffler, Frank E. Tue .
"Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae". United States. https://doi.org/10.1186/1471-2164-13-200. https://www.osti.gov/servlets/purl/1626415.
@article{osti_1626415,
title = {Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae},
author = {Wagner, Darlene D. and Hug, Laura A. and Hatt, Janet K. and Spitzmiller, Melissa R. and Padilla-Crespo, Elizabeth and Ritalahti, Kirsti M. and Edwards, Elizabeth A. and Konstantinidis, Konstantinos T. and Löffler, Frank E.},
abstractNote = {Background: Geobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with energy conservation and growth (i.e., organohalide respiration). Strain SZ also reduces U(VI) to U(IV) and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae. Results: Sequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs) and cytosines (Cs) among the four bases within the genome), and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC), with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. A plasmid with 99% sequence identity to pSZ77 was subsequently detected in the PCE-dechlorinating G. lovleyi strain KB-1 present in the PCE-to-ethene-dechlorinating consortium KB-1. Additional PCE-to-cis-DCE dechlorinating G. lovleyi strains obtained from the PCE-contaminated Fort Lewis, WA, site did not carry a plasmid indicating that pSZ77 is not a requirement (marker) for PCE respiration within this species. Chromosomal genomic islands found within the G. lovleyi strain SZ genome encode two reductive dehalogenase (RDase) homologs and a putative conjugative pilus system. Despite the loss of many c-type cytochrome and oxidative-stress-responsive genes, strain SZ retained the majority of Geobacter core metabolic capabilities, including U(VI) respiration. Conclusions: Gene acquisitions have expanded strain SZ’s respiratory capabilities to include PCE and TCE as electron acceptors. Respiratory processes core to the Geobacter genus, such as metal reduction, were retained despite a substantially reduced number of c-type cytochrome genes. pSZ77 is stably maintained within its host strains SZ and KB-1, likely because the replicon carries essential genes including genes involved in cobalamin biosynthesis and possibly corrinoid transport. Lateral acquisition of the plasmid replicon and the RDase genomic island represent unique genome features of the PCE-respiring G. lovleyi strains SZ and KB-1, and at least the latter signifies adaptation to PCE contamination.},
doi = {10.1186/1471-2164-13-200},
journal = {BMC Genomics},
number = 1,
volume = 13,
place = {United States},
year = {Tue May 22 00:00:00 EDT 2012},
month = {Tue May 22 00:00:00 EDT 2012}
}
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