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Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation

Jing Zhao, Y. Deng, D. Manno and Jalal Hawari

Article (2010)

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Cite this document: Zhao, J., Deng, Y., Manno, D. & Hawari, J. (2010). Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation. PLoS One, 5(2), e9109. doi:10.1371/journal.pone.0009109
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Shewanella halifaxensis and Shewanella sediminis were among a few aquatic gamma-proteobacteria that were psychrophiles and the first anaerobic bacteria that degraded hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Although many mesophilic or psychrophilic strains of Shewanella and gamma-proteobacteria were sequenced for their genomes, the genomic evolution pathways for temperature adaptation were poorly understood. On the other hand, the genes responsible for anaerobic RDX mineralization pathways remain unknown. To determine the unique genomic properties of bacteria responsible for both cold-adaptation and RDX degradation, the genomes of S. halifaxensis and S. sediminis were sequenced and compared with 108 other gamma-proteobacteria including Shewanella that differ in temperature and Na+ requirements, as well as RDX degradation capability. Results showed that for coping with marine environments their genomes had extensively exchanged with deep sea bacterial genomes. Many genes for Na+-dependent nutrient transporters were recruited to use the high Na+ content as an energy source. For coping with low temperatures, these two strains as well as other psychrophilic strains of Shewanella and gamma-proteobacteria were found to decrease their genome G+C content and proteome alanine, proline and arginine content (p-value <0.01) to increase protein structural flexibility. Compared to poorer RDX-degrading strains, S. halifaxensis and S. sediminis have more number of genes for cytochromes and other enzymes related to RDX metabolic pathways. Experimentally, one cytochrome was found induced in S. halifaxensis by RDX when the chemical was the sole terminal electron acceptor. The isolated protein degraded RDX by mono-denitration and was identified as a multiheme 52 kDa cytochrome using a proteomic approach. The present analyses provided the first insight into divergent genomic evolution of bacterial strains for adaptation to the specific cold marine conditions and to the degradation of the pollutant RDX. The present study also provided the first evidence for the involvement of a specific c-type cytochrome in anaerobic RDX metabolism.

Uncontrolled Keywords

Bacterial Proteins/genetics/metabolism; Biodegradation, Environmental; Chromosome Mapping; Cold Temperature; DNA, Bacterial/chemistry/genetics; DNA, Circular/chemistry/genetics; *Evolution, Molecular; Gammaproteobacteria/classification/genetics; Genome, Bacterial/*genetics; Genomics; Marine Biology; Molecular Structure; Phylogeny; Proteomics; RNA, Ribosomal, 16S/genetics; Seawater/microbiology; Sequence Analysis, DNA; Shewanella/classification/*genetics/metabolism; Species Specificity; Triazines/chemistry/*metabolism

Open Access document in PolyPublie
Subjects: 5000 Génétique > 5000 Génétique
5200 Microbiologie > 5201 Bactériologie
Department: Département des génies civil, géologique et des mines
Funders: US Department of Energy's Office of Science, Biological and Environmental Research Program, University of California, Lawrence Berkeley National Laborator, Lawrence Livermore National Laboratory, Los Alamos National Laboratory, Office of Naval Research, Defense Research and Development Canada, Canada, US SERDP
Grant number: DE-AC02-05CH11231, DE-AC52-07NA27344, DE-AC02-06NA25396, 0180 051115, N000140610251, ER1609
Date Deposited: 05 Apr 2022 15:24
Last Modified: 06 Apr 2022 01:20
PolyPublie URL: https://publications.polymtl.ca/5192/
Document issued by the official publisher
Journal Title: PLoS One (vol. 5, no. 2)
Publisher: PLOS
Official URL: https://doi.org/10.1371/journal.pone.0009109


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