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Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes.

Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides N - PLoS ONE (2011)

Bottom Line: Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature.These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism.Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.

View Article: PubMed Central - PubMed

Affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America. IJAnderson@lbl.gov

ABSTRACT

Background: The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis.

Methodology/principal findings: We report here the comparative analysis of five newly sequenced haloarchaeal genomes with five previously published ones. Whole genome trees based on protein sequences provide strong support for deep relationships between the ten organisms. Using a soft clustering approach, we identified 887 protein clusters present in all halophiles. Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature. Four of the halophiles were isolated from water, and four were isolated from soil or sediment. Although there are few habitat-specific clusters, the soil/sediment halophiles tend to have greater capacity for polysaccharide degradation, siderophore synthesis, and cell wall modification. Halorhabdus utahensis and Haloterrigena turkmenica encode over forty glycosyl hydrolases each, and may be capable of breaking down naturally occurring complex carbohydrates. H. utahensis is specialized for growth on carbohydrates and has few amino acid degradation pathways. It uses the non-oxidative pentose phosphate pathway instead of the oxidative pathway, giving it more flexibility in the metabolism of pentoses.

Conclusions: These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism. Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.

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Secreted protease distribution in haloarchaeal genomes.A heat map shows the distribution of MEROPS protease families, and the tree shows the results of hierarchical clustering.
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pone-0020237-g002: Secreted protease distribution in haloarchaeal genomes.A heat map shows the distribution of MEROPS protease families, and the tree shows the results of hierarchical clustering.

Mentions: Since the halophiles have numerous transporters for amino acids and peptides, we analyzed the distribution of secreted proteases within their genomes. Only secreted proteases were considered because these are likely to be involved in the utilization of proteins as a nutrient source, while intracellular and integral membrane proteases are involved in a variety of cellular processes. We included proteases that have signal peptides as well as proteins that are likely to be attached to the membrane with the protease domain outside the cell. Signal peptidases (family S26) were excluded from the analysis since they have a specific cellular function. The numbers of secreted proteases in the genomes ranged from 3 to 11. Hierarchical clustering (Figure 2) shows that the halophiles fall into two groups with respect to protease distribution. The main feature separating these groups appears to be the presence or absence of secreted members of protease family S8, which includes subtilisin as well as halolysins from halophilic archaea. The organisms having secreted S8 proteases do not correspond to a habitat-specific or phylogenetic group. The presence of at least three secreted proteases in each genome suggests that all of the halophiles may be capable of degradation of extracellular proteins.


Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes.

Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides N - PLoS ONE (2011)

Secreted protease distribution in haloarchaeal genomes.A heat map shows the distribution of MEROPS protease families, and the tree shows the results of hierarchical clustering.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102087&req=5

pone-0020237-g002: Secreted protease distribution in haloarchaeal genomes.A heat map shows the distribution of MEROPS protease families, and the tree shows the results of hierarchical clustering.
Mentions: Since the halophiles have numerous transporters for amino acids and peptides, we analyzed the distribution of secreted proteases within their genomes. Only secreted proteases were considered because these are likely to be involved in the utilization of proteins as a nutrient source, while intracellular and integral membrane proteases are involved in a variety of cellular processes. We included proteases that have signal peptides as well as proteins that are likely to be attached to the membrane with the protease domain outside the cell. Signal peptidases (family S26) were excluded from the analysis since they have a specific cellular function. The numbers of secreted proteases in the genomes ranged from 3 to 11. Hierarchical clustering (Figure 2) shows that the halophiles fall into two groups with respect to protease distribution. The main feature separating these groups appears to be the presence or absence of secreted members of protease family S8, which includes subtilisin as well as halolysins from halophilic archaea. The organisms having secreted S8 proteases do not correspond to a habitat-specific or phylogenetic group. The presence of at least three secreted proteases in each genome suggests that all of the halophiles may be capable of degradation of extracellular proteins.

Bottom Line: Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature.These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism.Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.

View Article: PubMed Central - PubMed

Affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America. IJAnderson@lbl.gov

ABSTRACT

Background: The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis.

Methodology/principal findings: We report here the comparative analysis of five newly sequenced haloarchaeal genomes with five previously published ones. Whole genome trees based on protein sequences provide strong support for deep relationships between the ten organisms. Using a soft clustering approach, we identified 887 protein clusters present in all halophiles. Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature. Four of the halophiles were isolated from water, and four were isolated from soil or sediment. Although there are few habitat-specific clusters, the soil/sediment halophiles tend to have greater capacity for polysaccharide degradation, siderophore synthesis, and cell wall modification. Halorhabdus utahensis and Haloterrigena turkmenica encode over forty glycosyl hydrolases each, and may be capable of breaking down naturally occurring complex carbohydrates. H. utahensis is specialized for growth on carbohydrates and has few amino acid degradation pathways. It uses the non-oxidative pentose phosphate pathway instead of the oxidative pathway, giving it more flexibility in the metabolism of pentoses.

Conclusions: These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism. Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.

Show MeSH
Related in: MedlinePlus