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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

Radial graph displaying the three-letter codon frequency prediction of H. hamelinensis. Expected codon frequencies are indicated in the inner circle. Squares in the outer circle are indications are overrepresented codons.
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fig1: Radial graph displaying the three-letter codon frequency prediction of H. hamelinensis. Expected codon frequencies are indicated in the inner circle. Squares in the outer circle are indications are overrepresented codons.

Mentions: The results for codon frequency indicated a bias towards high GC content in the third position (Figure 1). From the three-letter codon prediction codons, the following amino acids were observed to have high frequency: alanine (GCC, GCG, and GCA), arginine (CGA, CGC, CGG, and CGT), aspartic acid (GAC), glutamic acid (GAA, GAG), glycine (GGC, GGG, and GGT), histidine (CAC), leucine (CTC), proline (CCC, CCG), serine (TCC, TCG), threonine (ACC, ACG), and valine (GTC). Frank Wright's NC statistic for the effective number of codons used was also calculated, where the Nc output can take values from 20, in the case of extreme bias where one codon is exclusively used for each aa, to 61 when the use of alternative synonymous codons is equally likely. The Nc output value for the H. hamelinensis genome was calculated as 47.8, indicating very little bias between individual codon usage. Organisms high in GC% tend to have codons ending in C or G and this is also reflected in the H. hamelinensis genome.


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

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

Radial graph displaying the three-letter codon frequency prediction of H. hamelinensis. Expected codon frequencies are indicated in the inner circle. Squares in the outer circle are indications are overrepresented codons.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig1: Radial graph displaying the three-letter codon frequency prediction of H. hamelinensis. Expected codon frequencies are indicated in the inner circle. Squares in the outer circle are indications are overrepresented codons.
Mentions: The results for codon frequency indicated a bias towards high GC content in the third position (Figure 1). From the three-letter codon prediction codons, the following amino acids were observed to have high frequency: alanine (GCC, GCG, and GCA), arginine (CGA, CGC, CGG, and CGT), aspartic acid (GAC), glutamic acid (GAA, GAG), glycine (GGC, GGG, and GGT), histidine (CAC), leucine (CTC), proline (CCC, CCG), serine (TCC, TCG), threonine (ACC, ACG), and valine (GTC). Frank Wright's NC statistic for the effective number of codons used was also calculated, where the Nc output can take values from 20, in the case of extreme bias where one codon is exclusively used for each aa, to 61 when the use of alternative synonymous codons is equally likely. The Nc output value for the H. hamelinensis genome was calculated as 47.8, indicating very little bias between individual codon usage. Organisms high in GC% tend to have codons ending in C or G and this is also reflected in the H. hamelinensis genome.

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