Limits...
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.

Show MeSH

Related in: MedlinePlus

Radial phylogenetic tree comparison between H. hamelinensis and the bacterial and archaeal lineage within IMG/ER database. Genomes of Archaea, Bacteria, and Eukaryota are displayed clockwise on the circular plot. The bar charts in between the circular plot and phylogenetic dendrograms are percentage representations of positive hits of genes between H. hamelinensis and respective genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4325475&req=5

fig2: Radial phylogenetic tree comparison between H. hamelinensis and the bacterial and archaeal lineage within IMG/ER database. Genomes of Archaea, Bacteria, and Eukaryota are displayed clockwise on the circular plot. The bar charts in between the circular plot and phylogenetic dendrograms are percentage representations of positive hits of genes between H. hamelinensis and respective genomes.

Mentions: A radial phylogenetic tree comparison between H. hamelinensis and other bacteria and Archaea (Figure 2) also indicate potential evolutionary relationships and/or potential HGT that may have occurred. To further examine the importance of potential horizontal gene transfer to the H. hamelinensis genome, a gene-independent analysis of potential HGT using interpolated variable motif scores calculated from the program Alien Hunter was performed. Several putative regions were considered likely to have been acquired by HGT (data not shown).


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

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

Radial phylogenetic tree comparison between H. hamelinensis and the bacterial and archaeal lineage within IMG/ER database. Genomes of Archaea, Bacteria, and Eukaryota are displayed clockwise on the circular plot. The bar charts in between the circular plot and phylogenetic dendrograms are percentage representations of positive hits of genes between H. hamelinensis and respective genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Radial phylogenetic tree comparison between H. hamelinensis and the bacterial and archaeal lineage within IMG/ER database. Genomes of Archaea, Bacteria, and Eukaryota are displayed clockwise on the circular plot. The bar charts in between the circular plot and phylogenetic dendrograms are percentage representations of positive hits of genes between H. hamelinensis and respective genomes.
Mentions: A radial phylogenetic tree comparison between H. hamelinensis and other bacteria and Archaea (Figure 2) also indicate potential evolutionary relationships and/or potential HGT that may have occurred. To further examine the importance of potential horizontal gene transfer to the H. hamelinensis genome, a gene-independent analysis of potential HGT using interpolated variable motif scores calculated from the program Alien Hunter was performed. Several putative regions were considered likely to have been acquired by HGT (data not shown).

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