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Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses.

Gudhka RK, Neilan BA, Burns BP - Archaea (2015)

Bottom Line: Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented.The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair.Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.

ABSTRACT
Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

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Related in: MedlinePlus

Schematic representation of some of the putative adaptive traits present in H. hamelinensis. The traits identified pregenome is indicated on the left, and those elucidated postgenome in the present study are indicated on the right.
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fig3: Schematic representation of some of the putative adaptive traits present in H. hamelinensis. The traits identified pregenome is indicated on the left, and those elucidated postgenome in the present study are indicated on the right.

Mentions: This study reports the detailed genome analyses of H. hamelinensis, a novel archaeon, first isolated from modern stromatolites. Early studies carried out indicated the putative presence of three distinct and unique glycine-betaine transporters BetI, BetII, and BetIII (unpublished data) and the presence of a bacterial-like nucleotide excision repair (NER) system, containing UvrA, UvrB, and UvrC genes, as well as a photolyase [12, 13] in the H. hamelinensis genome. Postgenome analysis presented here revealed a range of other potential stress response mechanisms, and Figure 3 summarises some of the key adaptive responses identified through analyses in the current study. It also highlights the advantages of high-throughput sequencing and comparative genomics to build on pregenome sequencing work. In addition to DNA repair mechanisms and osmotic response, there were selective putative genes for heavy metal resistance such as arsenic. A recent study has suggested there may be a link between salinity and heavy metal uptake in some haloarchaea [50], and further work at the transcript and growth level may help elucidate the importance of these mechanisms in H. hamelinensis.


Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses.

Gudhka RK, Neilan BA, Burns BP - Archaea (2015)

Schematic representation of some of the putative adaptive traits present in H. hamelinensis. The traits identified pregenome is indicated on the left, and those elucidated postgenome in the present study are indicated on the right.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4325475&req=5

fig3: Schematic representation of some of the putative adaptive traits present in H. hamelinensis. The traits identified pregenome is indicated on the left, and those elucidated postgenome in the present study are indicated on the right.
Mentions: This study reports the detailed genome analyses of H. hamelinensis, a novel archaeon, first isolated from modern stromatolites. Early studies carried out indicated the putative presence of three distinct and unique glycine-betaine transporters BetI, BetII, and BetIII (unpublished data) and the presence of a bacterial-like nucleotide excision repair (NER) system, containing UvrA, UvrB, and UvrC genes, as well as a photolyase [12, 13] in the H. hamelinensis genome. Postgenome analysis presented here revealed a range of other potential stress response mechanisms, and Figure 3 summarises some of the key adaptive responses identified through analyses in the current study. It also highlights the advantages of high-throughput sequencing and comparative genomics to build on pregenome sequencing work. In addition to DNA repair mechanisms and osmotic response, there were selective putative genes for heavy metal resistance such as arsenic. A recent study has suggested there may be a link between salinity and heavy metal uptake in some haloarchaea [50], and further work at the transcript and growth level may help elucidate the importance of these mechanisms in H. hamelinensis.

Bottom Line: Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented.The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair.Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.

ABSTRACT
Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

Show MeSH
Related in: MedlinePlus