Limits...
Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.

Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT - PLoS Genet. (2014)

Bottom Line: We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain.The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation.Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

View Article: PubMed Central - PubMed

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

ABSTRACT
Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

Show MeSH

Related in: MedlinePlus

Rarefaction analysis of sampled haloarchaeal protein space.A rarefaction curve of protein diversity was created for the 80 haloarchaea included in this study using three alternative methods to define protein families: COG number (green), TRIBE-MCL clusters removing singletons (red), and TRIBE-MCL clusters without removing singletons (blue). The COG database is expected to represent an under-estimate of the true diversity. Similarly, using TRIBE-MCL clusters with all singleton genes excluded underestimates true diversity. The true diversity of the set is likely located between the blue and red curves.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4230888&req=5

pgen-1004784-g003: Rarefaction analysis of sampled haloarchaeal protein space.A rarefaction curve of protein diversity was created for the 80 haloarchaea included in this study using three alternative methods to define protein families: COG number (green), TRIBE-MCL clusters removing singletons (red), and TRIBE-MCL clusters without removing singletons (blue). The COG database is expected to represent an under-estimate of the true diversity. Similarly, using TRIBE-MCL clusters with all singleton genes excluded underestimates true diversity. The true diversity of the set is likely located between the blue and red curves.

Mentions: To estimate the fraction of haloarchaeal phylogenetic diversity represented by this set of 80 haloarchaea, we performed rarefaction analysis, plotting the number of unique protein families against the number of randomly drawn genomes (Figure 3). Accurately grouping proteins into families is a non-trivial problem that has sparked the development of a large number of protein clustering algorithms [23]. As there is no experimental data for the vast majority of haloarchaeal proteins, clustering must rely on computational sequence similarity metrics. We therefore selected three methods to define protein families and generated rarefaction curves for each. The methods were as follows: (1) COG orthology groups [24], (2) in-house homology clusters defined using the clustering algorithm TRIBE-MCL [16] (see Materials and Methods, Dataset S2, Figures S1 & S2)), and (3) TRIBE-MCL defined homology clusters excluding those with only a single member (singletons).


Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.

Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT - PLoS Genet. (2014)

Rarefaction analysis of sampled haloarchaeal protein space.A rarefaction curve of protein diversity was created for the 80 haloarchaea included in this study using three alternative methods to define protein families: COG number (green), TRIBE-MCL clusters removing singletons (red), and TRIBE-MCL clusters without removing singletons (blue). The COG database is expected to represent an under-estimate of the true diversity. Similarly, using TRIBE-MCL clusters with all singleton genes excluded underestimates true diversity. The true diversity of the set is likely located between the blue and red curves.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230888&req=5

pgen-1004784-g003: Rarefaction analysis of sampled haloarchaeal protein space.A rarefaction curve of protein diversity was created for the 80 haloarchaea included in this study using three alternative methods to define protein families: COG number (green), TRIBE-MCL clusters removing singletons (red), and TRIBE-MCL clusters without removing singletons (blue). The COG database is expected to represent an under-estimate of the true diversity. Similarly, using TRIBE-MCL clusters with all singleton genes excluded underestimates true diversity. The true diversity of the set is likely located between the blue and red curves.
Mentions: To estimate the fraction of haloarchaeal phylogenetic diversity represented by this set of 80 haloarchaea, we performed rarefaction analysis, plotting the number of unique protein families against the number of randomly drawn genomes (Figure 3). Accurately grouping proteins into families is a non-trivial problem that has sparked the development of a large number of protein clustering algorithms [23]. As there is no experimental data for the vast majority of haloarchaeal proteins, clustering must rely on computational sequence similarity metrics. We therefore selected three methods to define protein families and generated rarefaction curves for each. The methods were as follows: (1) COG orthology groups [24], (2) in-house homology clusters defined using the clustering algorithm TRIBE-MCL [16] (see Materials and Methods, Dataset S2, Figures S1 & S2)), and (3) TRIBE-MCL defined homology clusters excluding those with only a single member (singletons).

Bottom Line: We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain.The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation.Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

View Article: PubMed Central - PubMed

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

ABSTRACT
Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. To improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersaline environments and routinely experience drastic changes in environmental salinity) and analyzed these new genomes in combination with those from 21 previously sequenced haloarchaeal isolates. We propose a generalized model for haloarchaeal management of cytoplasmic osmolarity in response to osmotic shifts, where potassium accumulation and sodium expulsion during osmotic upshock are accomplished via secondary transport using the proton gradient as an energy source, and potassium loss during downshock is via a combination of secondary transport and non-specific ion loss through mechanosensitive channels. We also propose new mechanisms for magnesium and chloride accumulation. We describe the expansion and differentiation of haloarchaeal general transcription factor families, including two novel expansions of the TATA-binding protein family, and discuss their potential for enabling rapid adaptation to environmental fluxes. We challenge a recent high-profile proposal regarding the evolutionary origins of the haloarchaea by showing that inclusion of additional genomes significantly reduces support for a proposed large-scale horizontal gene transfer into the ancestral haloarchaeon from the bacterial domain. The combination of broad (17 genera) and deep (≥5 species in four genera) sampling of a phenotypically unified clade has enabled us to uncover both highly conserved and specialized features of osmoadaptation. Finally, we demonstrate the broad utility of such datasets, for metagenomics, improvements to automated gene annotation and investigations of evolutionary processes.

Show MeSH
Related in: MedlinePlus