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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.

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Ribosomal subunit isoelectric points.Structural mappings of the large and small ribosomal subunits, showing protein monomers with predicted low (red) and high (blue) pI. Subunits are oriented according to (A) complex formation, (B) cytoplasmic view of each subunit, and (C) internal view of each subunit. Subunits exposed to the cytoplasm tend to be acidified (red subunits, visible in B), while subunits buried within the ribosome tend to have an alkaline isoelectric point (blue subunits, visible in C). Structural models used were those for Thermus thermophilus (1FKA) [97] and Haloarcula marismortui (1QVG) [96].
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pgen-1004784-g006: Ribosomal subunit isoelectric points.Structural mappings of the large and small ribosomal subunits, showing protein monomers with predicted low (red) and high (blue) pI. Subunits are oriented according to (A) complex formation, (B) cytoplasmic view of each subunit, and (C) internal view of each subunit. Subunits exposed to the cytoplasm tend to be acidified (red subunits, visible in B), while subunits buried within the ribosome tend to have an alkaline isoelectric point (blue subunits, visible in C). Structural models used were those for Thermus thermophilus (1FKA) [97] and Haloarcula marismortui (1QVG) [96].

Mentions: Certain haloarchaeal proteins were not acidified, including many ribosomal subunits, membrane proteins, and DNA-binding proteins (Table S5). Potential reasons for non-acidification include 1) shielding from the hypersaline cytoplasm (eg. internal ribosome subunits, membrane proteins), and 2) presence of a selective force against acidification (eg. DNA-binding proteins). Structural mapping of the ribosome demonstrates that subunits exposed to the hypersaline cytosol tend to be acidified, while shielded internal subunits have high pI (Figure 6). Large regions of transporters and other membrane–associated proteins are likewise shielded from the saline cytoplasm by the cell membrane, mitigating selective pressure to acidify. DNA-binding proteins must retain positively charged residues to interact efficiently with negatively charged DNA, and so also tend not to acidify (shown for the general transcription factor TATA-binding protein (TBP), Figure S6, and ribosome elongation factor α-1, Figure S7). A large number (11,087) of non-acidified proteins were unannotated. Based on functional consistency we identified among other high pI proteins, we propose these proteins as candidates for exploratory research seeking novel DNA-binding or membrane associated proteins such as transcription factors, transporters, and chemotaxis/sensory receptors.


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)

Ribosomal subunit isoelectric points.Structural mappings of the large and small ribosomal subunits, showing protein monomers with predicted low (red) and high (blue) pI. Subunits are oriented according to (A) complex formation, (B) cytoplasmic view of each subunit, and (C) internal view of each subunit. Subunits exposed to the cytoplasm tend to be acidified (red subunits, visible in B), while subunits buried within the ribosome tend to have an alkaline isoelectric point (blue subunits, visible in C). Structural models used were those for Thermus thermophilus (1FKA) [97] and Haloarcula marismortui (1QVG) [96].
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004784-g006: Ribosomal subunit isoelectric points.Structural mappings of the large and small ribosomal subunits, showing protein monomers with predicted low (red) and high (blue) pI. Subunits are oriented according to (A) complex formation, (B) cytoplasmic view of each subunit, and (C) internal view of each subunit. Subunits exposed to the cytoplasm tend to be acidified (red subunits, visible in B), while subunits buried within the ribosome tend to have an alkaline isoelectric point (blue subunits, visible in C). Structural models used were those for Thermus thermophilus (1FKA) [97] and Haloarcula marismortui (1QVG) [96].
Mentions: Certain haloarchaeal proteins were not acidified, including many ribosomal subunits, membrane proteins, and DNA-binding proteins (Table S5). Potential reasons for non-acidification include 1) shielding from the hypersaline cytoplasm (eg. internal ribosome subunits, membrane proteins), and 2) presence of a selective force against acidification (eg. DNA-binding proteins). Structural mapping of the ribosome demonstrates that subunits exposed to the hypersaline cytosol tend to be acidified, while shielded internal subunits have high pI (Figure 6). Large regions of transporters and other membrane–associated proteins are likewise shielded from the saline cytoplasm by the cell membrane, mitigating selective pressure to acidify. DNA-binding proteins must retain positively charged residues to interact efficiently with negatively charged DNA, and so also tend not to acidify (shown for the general transcription factor TATA-binding protein (TBP), Figure S6, and ribosome elongation factor α-1, Figure S7). A large number (11,087) of non-acidified proteins were unannotated. Based on functional consistency we identified among other high pI proteins, we propose these proteins as candidates for exploratory research seeking novel DNA-binding or membrane associated proteins such as transcription factors, transporters, and chemotaxis/sensory receptors.

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