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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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Haloarchaeal osmoadaptation.(A) Generalized model for osmoadaptation in the haloarchaea. During osmotic upshock, potassium is imported through Trk H+/K+ symporters and Na+ is expelled using a combination of NhaC H+/Na+ antiporters and/or YrbG Ca2+/Na+ antiporters. During osmotic downshock, excess potassium is removed through a combination of Kef H+/K+ antiporters and the non-specific mechanosensitive channel MscS. (B) Ion transport strategies not generally encoded by the haloarchaea. Sodium export and potassium import using ABC transporters (NatABC and KdpABC) may be less energetically efficient than secondary transport systems. Use of Ktr K+/Na+ symporters for potassium uptake would result in over-accumulation of sodium. (C) Compatible solute transport systems. Na+/proline symporters (OpuE and MM_2305) are ubiquitous in the haloarchaea. Glycine betaine uptake is mediated by OpuD through symport with sodium or, rarely, through the ABC transporter OpuC. The ectoine/sodium symporter EctP is also widespread. For transport systems with multiple substrates, a representative compound is shown. (D) Magnesium uptake is mediated by primary active transport (MgtA/B) or, rarely, by facilitated diffusion (MgtE/CorA). (E) Potassium accumulation is possible in all 80 haloarchaea via both secondary active transport (Tribe63) and facilitated diffusion (Tribe105). Some species also possess ATP-dependent potassium transporters (Cog3639/PhnD). Numbers in parenthesis represent the number of haloarchaeal species possessing the transporter gene. BR – bacteriorhodopsin, HR – halorhodopsin, GB – glycine betaine, Pro - proline, Ect – ectoine. Kef, Ktr and Trk each represent a class of transporters, rather than a single homolog. Tribe63 and Tribe105 refer to protein families defined in this study.
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pgen-1004784-g004: Haloarchaeal osmoadaptation.(A) Generalized model for osmoadaptation in the haloarchaea. During osmotic upshock, potassium is imported through Trk H+/K+ symporters and Na+ is expelled using a combination of NhaC H+/Na+ antiporters and/or YrbG Ca2+/Na+ antiporters. During osmotic downshock, excess potassium is removed through a combination of Kef H+/K+ antiporters and the non-specific mechanosensitive channel MscS. (B) Ion transport strategies not generally encoded by the haloarchaea. Sodium export and potassium import using ABC transporters (NatABC and KdpABC) may be less energetically efficient than secondary transport systems. Use of Ktr K+/Na+ symporters for potassium uptake would result in over-accumulation of sodium. (C) Compatible solute transport systems. Na+/proline symporters (OpuE and MM_2305) are ubiquitous in the haloarchaea. Glycine betaine uptake is mediated by OpuD through symport with sodium or, rarely, through the ABC transporter OpuC. The ectoine/sodium symporter EctP is also widespread. For transport systems with multiple substrates, a representative compound is shown. (D) Magnesium uptake is mediated by primary active transport (MgtA/B) or, rarely, by facilitated diffusion (MgtE/CorA). (E) Potassium accumulation is possible in all 80 haloarchaea via both secondary active transport (Tribe63) and facilitated diffusion (Tribe105). Some species also possess ATP-dependent potassium transporters (Cog3639/PhnD). Numbers in parenthesis represent the number of haloarchaeal species possessing the transporter gene. BR – bacteriorhodopsin, HR – halorhodopsin, GB – glycine betaine, Pro - proline, Ect – ectoine. Kef, Ktr and Trk each represent a class of transporters, rather than a single homolog. Tribe63 and Tribe105 refer to protein families defined in this study.

Mentions: Due to the dynamic nature of hypersaline environments, the haloarchaea possess a range of ion transporters for accommodating fluctuating salinity levels. We investigated the phylogenetic distribution of a number of ion transporter genes potentially involved in osmoadaptation to hyper-osmotic or hypo-osmotic shock, as well as compatible solute import and biosynthesis genes (Figure S5). This analysis enabled us to propose a generalized haloarchaeal strategy for dynamic osmoadaptation (Figure 4A).


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)

Haloarchaeal osmoadaptation.(A) Generalized model for osmoadaptation in the haloarchaea. During osmotic upshock, potassium is imported through Trk H+/K+ symporters and Na+ is expelled using a combination of NhaC H+/Na+ antiporters and/or YrbG Ca2+/Na+ antiporters. During osmotic downshock, excess potassium is removed through a combination of Kef H+/K+ antiporters and the non-specific mechanosensitive channel MscS. (B) Ion transport strategies not generally encoded by the haloarchaea. Sodium export and potassium import using ABC transporters (NatABC and KdpABC) may be less energetically efficient than secondary transport systems. Use of Ktr K+/Na+ symporters for potassium uptake would result in over-accumulation of sodium. (C) Compatible solute transport systems. Na+/proline symporters (OpuE and MM_2305) are ubiquitous in the haloarchaea. Glycine betaine uptake is mediated by OpuD through symport with sodium or, rarely, through the ABC transporter OpuC. The ectoine/sodium symporter EctP is also widespread. For transport systems with multiple substrates, a representative compound is shown. (D) Magnesium uptake is mediated by primary active transport (MgtA/B) or, rarely, by facilitated diffusion (MgtE/CorA). (E) Potassium accumulation is possible in all 80 haloarchaea via both secondary active transport (Tribe63) and facilitated diffusion (Tribe105). Some species also possess ATP-dependent potassium transporters (Cog3639/PhnD). Numbers in parenthesis represent the number of haloarchaeal species possessing the transporter gene. BR – bacteriorhodopsin, HR – halorhodopsin, GB – glycine betaine, Pro - proline, Ect – ectoine. Kef, Ktr and Trk each represent a class of transporters, rather than a single homolog. Tribe63 and Tribe105 refer to protein families defined in this study.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004784-g004: Haloarchaeal osmoadaptation.(A) Generalized model for osmoadaptation in the haloarchaea. During osmotic upshock, potassium is imported through Trk H+/K+ symporters and Na+ is expelled using a combination of NhaC H+/Na+ antiporters and/or YrbG Ca2+/Na+ antiporters. During osmotic downshock, excess potassium is removed through a combination of Kef H+/K+ antiporters and the non-specific mechanosensitive channel MscS. (B) Ion transport strategies not generally encoded by the haloarchaea. Sodium export and potassium import using ABC transporters (NatABC and KdpABC) may be less energetically efficient than secondary transport systems. Use of Ktr K+/Na+ symporters for potassium uptake would result in over-accumulation of sodium. (C) Compatible solute transport systems. Na+/proline symporters (OpuE and MM_2305) are ubiquitous in the haloarchaea. Glycine betaine uptake is mediated by OpuD through symport with sodium or, rarely, through the ABC transporter OpuC. The ectoine/sodium symporter EctP is also widespread. For transport systems with multiple substrates, a representative compound is shown. (D) Magnesium uptake is mediated by primary active transport (MgtA/B) or, rarely, by facilitated diffusion (MgtE/CorA). (E) Potassium accumulation is possible in all 80 haloarchaea via both secondary active transport (Tribe63) and facilitated diffusion (Tribe105). Some species also possess ATP-dependent potassium transporters (Cog3639/PhnD). Numbers in parenthesis represent the number of haloarchaeal species possessing the transporter gene. BR – bacteriorhodopsin, HR – halorhodopsin, GB – glycine betaine, Pro - proline, Ect – ectoine. Kef, Ktr and Trk each represent a class of transporters, rather than a single homolog. Tribe63 and Tribe105 refer to protein families defined in this study.
Mentions: Due to the dynamic nature of hypersaline environments, the haloarchaea possess a range of ion transporters for accommodating fluctuating salinity levels. We investigated the phylogenetic distribution of a number of ion transporter genes potentially involved in osmoadaptation to hyper-osmotic or hypo-osmotic shock, as well as compatible solute import and biosynthesis genes (Figure S5). This analysis enabled us to propose a generalized haloarchaeal strategy for dynamic osmoadaptation (Figure 4A).

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