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Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.

Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT - PLoS ONE (2012)

Bottom Line: Comparisons of protein-coding gene compliments revealed large-scale differences in COG functional group enrichment between these genera.Analysis of genes encoding machinery for DNA metabolism reveals genera-specific expansions of the general transcription factor TATA binding protein as well as a history of extensive duplication and horizontal transfer of the proliferating cell nuclear antigen.Insights gained from this study emphasize the importance of haloarchaea for investigation of archaeal biology.

View Article: PubMed Central - PubMed

Affiliation: Microbiology Graduate Group, University of California Davis, Davis, California, United States of America.

ABSTRACT
We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ∼20×coverage and assembled to an average of 50 contigs (range 5 scaffolds-168 contigs). Comparisons of protein-coding gene compliments revealed large-scale differences in COG functional group enrichment between these genera. Analysis of genes encoding machinery for DNA metabolism reveals genera-specific expansions of the general transcription factor TATA binding protein as well as a history of extensive duplication and horizontal transfer of the proliferating cell nuclear antigen. Insights gained from this study emphasize the importance of haloarchaea for investigation of archaeal biology.

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Phylogeny of haloarchaeal opsins.A maximum likelihood tree of the four previously described haloarchaeal opsin families along with the newly described sensory rhodopsin 3, with bootstrap support values above 0.50 shown for 500 bootstrap iterations. Sensory rhodopsin - SR, halorhodopsin - HR, bacteriorhodopsin - BR.
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pone-0041389-g006: Phylogeny of haloarchaeal opsins.A maximum likelihood tree of the four previously described haloarchaeal opsin families along with the newly described sensory rhodopsin 3, with bootstrap support values above 0.50 shown for 500 bootstrap iterations. Sensory rhodopsin - SR, halorhodopsin - HR, bacteriorhodopsin - BR.

Mentions: We performed a genomic screen to identify opsin homologs in the twenty-one currently sequenced haloarchaeal genomes. One or more opsins were found in fourteen of the twenty-one genomes, with most species lacking at least one of the four canonical opsin classes. In fact, only Halobacterium and Haloarcula species were found to possess at least one homolog each of bacteriorhodopsin, halorhodopsin, and sensory rhodopsins 1 and 2. Phylogenetic analysis of opsin sequences obtained from the genomic screen revealed divergent sensory rhodopsins in three species of Haloarcula – Har. californiae, Har. sinaiiensis, and the previously sequenced Har. marismortui (rrnAC0559) (Figure 6). The absence of a sensory rhodopsin 3 homolog in Har. vallismortis suggests that this gene arose or was introduced into the Haloarcula clade after divergence of Har. vallismortis from the other three sequenced members of this genus. Alternatively, this gene may be undetected in Har. vallismortis due to the relatively high number of contigs in the assembly for this organism. In addition, our screen has revealed homologs of the previously discovered bacteriorhodopsin variant in Har. sinaiiensis and Har. vallismortis in addition to those known in Haloquadratum walsbyi (YP_656801) and Har. marismortui (YP_136594). The lack of annotation for this gene in Har. californiae may be due to the high number of contigs in this assembly. We have also identified, for the first time, an opsin belonging to a member of the Haloferax genus, which has previously been found to lack these proteins [44]. Our screen identified a canonical bacteriorhodopsin in the genome of Haloferax mucosum, but not in the other Haloferax species included in this study.


Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.

Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT - PLoS ONE (2012)

Phylogeny of haloarchaeal opsins.A maximum likelihood tree of the four previously described haloarchaeal opsin families along with the newly described sensory rhodopsin 3, with bootstrap support values above 0.50 shown for 500 bootstrap iterations. Sensory rhodopsin - SR, halorhodopsin - HR, bacteriorhodopsin - BR.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3404096&req=5

pone-0041389-g006: Phylogeny of haloarchaeal opsins.A maximum likelihood tree of the four previously described haloarchaeal opsin families along with the newly described sensory rhodopsin 3, with bootstrap support values above 0.50 shown for 500 bootstrap iterations. Sensory rhodopsin - SR, halorhodopsin - HR, bacteriorhodopsin - BR.
Mentions: We performed a genomic screen to identify opsin homologs in the twenty-one currently sequenced haloarchaeal genomes. One or more opsins were found in fourteen of the twenty-one genomes, with most species lacking at least one of the four canonical opsin classes. In fact, only Halobacterium and Haloarcula species were found to possess at least one homolog each of bacteriorhodopsin, halorhodopsin, and sensory rhodopsins 1 and 2. Phylogenetic analysis of opsin sequences obtained from the genomic screen revealed divergent sensory rhodopsins in three species of Haloarcula – Har. californiae, Har. sinaiiensis, and the previously sequenced Har. marismortui (rrnAC0559) (Figure 6). The absence of a sensory rhodopsin 3 homolog in Har. vallismortis suggests that this gene arose or was introduced into the Haloarcula clade after divergence of Har. vallismortis from the other three sequenced members of this genus. Alternatively, this gene may be undetected in Har. vallismortis due to the relatively high number of contigs in the assembly for this organism. In addition, our screen has revealed homologs of the previously discovered bacteriorhodopsin variant in Har. sinaiiensis and Har. vallismortis in addition to those known in Haloquadratum walsbyi (YP_656801) and Har. marismortui (YP_136594). The lack of annotation for this gene in Har. californiae may be due to the high number of contigs in this assembly. We have also identified, for the first time, an opsin belonging to a member of the Haloferax genus, which has previously been found to lack these proteins [44]. Our screen identified a canonical bacteriorhodopsin in the genome of Haloferax mucosum, but not in the other Haloferax species included in this study.

Bottom Line: Comparisons of protein-coding gene compliments revealed large-scale differences in COG functional group enrichment between these genera.Analysis of genes encoding machinery for DNA metabolism reveals genera-specific expansions of the general transcription factor TATA binding protein as well as a history of extensive duplication and horizontal transfer of the proliferating cell nuclear antigen.Insights gained from this study emphasize the importance of haloarchaea for investigation of archaeal biology.

View Article: PubMed Central - PubMed

Affiliation: Microbiology Graduate Group, University of California Davis, Davis, California, United States of America.

ABSTRACT
We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ∼20×coverage and assembled to an average of 50 contigs (range 5 scaffolds-168 contigs). Comparisons of protein-coding gene compliments revealed large-scale differences in COG functional group enrichment between these genera. Analysis of genes encoding machinery for DNA metabolism reveals genera-specific expansions of the general transcription factor TATA binding protein as well as a history of extensive duplication and horizontal transfer of the proliferating cell nuclear antigen. Insights gained from this study emphasize the importance of haloarchaea for investigation of archaeal biology.

Show MeSH