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

Abstract

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