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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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Enzymes of interest in biotechnology and novel metabolism.Gene counts of enzymes discussed in the text superimposed on rpoB′′ phylogeny. Methylaspartate ammonia-lyase (EC 4.3.1.2) – MA ammonia-lyase, methylaspartate mutase (EC 5.4.99.1) – MA mutase, succinyl-CoA:mesaconate CoA-transferase – SM-CoA transferase, polyhydroxyalkanoate synthase – PHA synthase, CRISPR associated sequences – CAS. Blue leaf labels indicate genomes sequenced in this study, black leaf labels indicate previously sequenced genomes. CRISPR and CAS data is represented as binary presence/ absence with abundance information provided in Table 3. MA mutase S subunit is also shown as binary although some species have two homologs of this gene, as only one homolog is present at the methylaspartate cycle locus.
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pone-0041389-g005: Enzymes of interest in biotechnology and novel metabolism.Gene counts of enzymes discussed in the text superimposed on rpoB′′ phylogeny. Methylaspartate ammonia-lyase (EC 4.3.1.2) – MA ammonia-lyase, methylaspartate mutase (EC 5.4.99.1) – MA mutase, succinyl-CoA:mesaconate CoA-transferase – SM-CoA transferase, polyhydroxyalkanoate synthase – PHA synthase, CRISPR associated sequences – CAS. Blue leaf labels indicate genomes sequenced in this study, black leaf labels indicate previously sequenced genomes. CRISPR and CAS data is represented as binary presence/ absence with abundance information provided in Table 3. MA mutase S subunit is also shown as binary although some species have two homologs of this gene, as only one homolog is present at the methylaspartate cycle locus.

Mentions: Current biofuel production processes depend upon the use of cellulases, which are abundantly distributed in nature. However, the strong ionic liquids increasingly used in biomass pretreatment are inhibitory to many cellulases [11]. The adaptation of haloarchaeal enzymes to high salt concentrations is thought to also confer added structural stability in organic solvents [11], making these organisms ideal candidates for discovery of cellulases useful for biofuels production. This potential was recently confirmed with the discovery of a halotolerant and thermostable cellulase in the haloarchaeon Halorhabdus utahensis (Hu-CBH1) [11]. Our search of haloarchaeal genomes revealed eleven cellulases distributed broadly across the haloarchaea, with Haloarcula species, however, notably lacking these enzymes (Figure 5).


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)

Enzymes of interest in biotechnology and novel metabolism.Gene counts of enzymes discussed in the text superimposed on rpoB′′ phylogeny. Methylaspartate ammonia-lyase (EC 4.3.1.2) – MA ammonia-lyase, methylaspartate mutase (EC 5.4.99.1) – MA mutase, succinyl-CoA:mesaconate CoA-transferase – SM-CoA transferase, polyhydroxyalkanoate synthase – PHA synthase, CRISPR associated sequences – CAS. Blue leaf labels indicate genomes sequenced in this study, black leaf labels indicate previously sequenced genomes. CRISPR and CAS data is represented as binary presence/ absence with abundance information provided in Table 3. MA mutase S subunit is also shown as binary although some species have two homologs of this gene, as only one homolog is present at the methylaspartate cycle locus.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3404096&req=5

pone-0041389-g005: Enzymes of interest in biotechnology and novel metabolism.Gene counts of enzymes discussed in the text superimposed on rpoB′′ phylogeny. Methylaspartate ammonia-lyase (EC 4.3.1.2) – MA ammonia-lyase, methylaspartate mutase (EC 5.4.99.1) – MA mutase, succinyl-CoA:mesaconate CoA-transferase – SM-CoA transferase, polyhydroxyalkanoate synthase – PHA synthase, CRISPR associated sequences – CAS. Blue leaf labels indicate genomes sequenced in this study, black leaf labels indicate previously sequenced genomes. CRISPR and CAS data is represented as binary presence/ absence with abundance information provided in Table 3. MA mutase S subunit is also shown as binary although some species have two homologs of this gene, as only one homolog is present at the methylaspartate cycle locus.
Mentions: Current biofuel production processes depend upon the use of cellulases, which are abundantly distributed in nature. However, the strong ionic liquids increasingly used in biomass pretreatment are inhibitory to many cellulases [11]. The adaptation of haloarchaeal enzymes to high salt concentrations is thought to also confer added structural stability in organic solvents [11], making these organisms ideal candidates for discovery of cellulases useful for biofuels production. This potential was recently confirmed with the discovery of a halotolerant and thermostable cellulase in the haloarchaeon Halorhabdus utahensis (Hu-CBH1) [11]. Our search of haloarchaeal genomes revealed eleven cellulases distributed broadly across the haloarchaea, with Haloarcula species, however, notably lacking these enzymes (Figure 5).

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
Related in: MedlinePlus