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Distinctive gene and protein characteristics of extremely piezophilic Colwellia
- Source :
- BMC Genomics, BMC genomics, vol 21, iss 1, BMC Genomics, Vol 21, Iss 1, Pp 1-18 (2020)
- Publication Year :
- 2020
- Publisher :
- Springer Science and Business Media LLC, 2020.
-
Abstract
- Background The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low concentrations of organic matter. While these conditions likely select for distinct genomic characteristics within prokaryotes, the attributes facilitating adaptation to the deep ocean are relatively unexplored. In this study, we compared the genomes of seven strains within the genus Colwellia, including some of the most piezophilic microbes known, to identify genomic features that enable life in the deep sea. Results Significant differences were found to exist between piezophilic and non-piezophilic strains of Colwellia. Piezophilic Colwellia have a more basic and hydrophobic proteome. The piezophilic abyssal and hadal isolates have more genes involved in replication/recombination/repair, cell wall/membrane biogenesis, and cell motility. The characteristics of respiration, pilus generation, and membrane fluidity adjustment vary between the strains, with operons for a nuo dehydrogenase and a tad pilus only present in the piezophiles. In contrast, the piezosensitive members are unique in having the capacity for dissimilatory nitrite and TMAO reduction. A number of genes exist only within deep-sea adapted species, such as those encoding d-alanine-d-alanine ligase for peptidoglycan formation, alanine dehydrogenase for NADH/NAD+ homeostasis, and a SAM methyltransferase for tRNA modification. Many of these piezophile-specific genes are in variable regions of the genome near genomic islands, transposases, and toxin-antitoxin systems. Conclusions We identified a number of adaptations that may facilitate deep-sea radiation in members of the genus Colwellia, as well as in other piezophilic bacteria. An enrichment in more basic and hydrophobic amino acids could help piezophiles stabilize and limit water intrusion into proteins as a result of high pressure. Variations in genes associated with the membrane, including those involved in unsaturated fatty acid production and respiration, indicate that membrane-based adaptations are critical for coping with high pressure. The presence of many piezophile-specific genes near genomic islands highlights that adaptation to the deep ocean may be facilitated by horizontal gene transfer through transposases or other mobile elements. Some of these genes are amenable to further study in genetically tractable piezophilic and piezotolerant deep-sea microorganisms.
- Subjects :
- Proteome
Operon
Hydrostatic pressure
Transposases
Genome
Medical and Health Sciences
Genomic island
Peptide Synthases
Phylogeny
Genetics
0303 health sciences
Alteromonadaceae
Piezophile
Bacterial
Biological Sciences
Adaptation, Physiological
Deep sea
Colwellia
Horizontal gene transfer
Research Article
Biotechnology
TRNA modification
lcsh:QH426-470
Bioinformatics
Membrane Fluidity
lcsh:Biotechnology
Physiological
Cell Respiration
Biology
Methylamines
Trench
03 medical and health sciences
Bacterial Proteins
lcsh:TP248.13-248.65
Information and Computing Sciences
Hydrostatic Pressure
14. Life underwater
Adaptation
Gene
Nitrites
Unsaturated fatty acid
030304 developmental biology
030306 microbiology
Human Genome
lcsh:Genetics
Alanine Dehydrogenase
Membrane biogenesis
Genome, Bacterial
Extreme Environments
Hadal
Subjects
Details
- ISSN :
- 14712164
- Volume :
- 21
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....cf0c06bffcd53d2ee84efb3a0c1e429c