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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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Sliding-window G+C content analysis.Representative G+C content plots for (A) Haloferax mediterranei, (B) Halorubrum litoreum, (C) Haloarcula argentinensis, and (D) Natrialba aegyptia. Each of these four species is a representative from the four most populous genera in the set, which collectively contain 66% of the organisms in the study. Black line represents calculated G+C percent for each 100 bp window. Contig boundaries are represented as vertical red lines, contig mean G+C as horizontal blue lines, and genome mean G+C as a horizontal green line. The horizontal axis displays the number of 20 bp steps taken along the genome. For all G+C plots see Data Dryad package [67].
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pgen-1004784-g007: Sliding-window G+C content analysis.Representative G+C content plots for (A) Haloferax mediterranei, (B) Halorubrum litoreum, (C) Haloarcula argentinensis, and (D) Natrialba aegyptia. Each of these four species is a representative from the four most populous genera in the set, which collectively contain 66% of the organisms in the study. Black line represents calculated G+C percent for each 100 bp window. Contig boundaries are represented as vertical red lines, contig mean G+C as horizontal blue lines, and genome mean G+C as a horizontal green line. The horizontal axis displays the number of 20 bp steps taken along the genome. For all G+C plots see Data Dryad package [67].

Mentions: Regardless of the mechanism for its maintenance, genome-wide G+C bias offers a method for identification of candidates for horizontal gene transfer from organisms with G+C content differing from the recipient species, as horizontally transferred genes are often A+T shifted relative to the host genome [71]. We examined the G+C content of the 80 haloarchaeal genomes, using a sliding 100 bp window, and conducted change-point analysis to extract regions with local G+C content differing from the genome average. It is important to note here that haloarchaeal plasmids, including minichromosomes and megaplasmids, are known to have decreased G+C content compared with primary replicons (“chromosomes”) [63]. As the mechanisms for maintaining decreased G+C content in smaller replicons are unknown, and in order to accommodate draft genomes where the identity of the primary replicons are unknown, we have chosen to be replicon size neutral. Some regions of the genome are also expected to have low local G+C content due to selective pressure for maintaining a higher A+T percentage (eg. origin of replication sites). In addition, we have been neutral as to the direction of divergence from genome-wide G+C average, in order to allow detection of regions of unusually high as well as unusually low G+C (Figure 7, Figure S8, Datasets S6 & S7).


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)

Sliding-window G+C content analysis.Representative G+C content plots for (A) Haloferax mediterranei, (B) Halorubrum litoreum, (C) Haloarcula argentinensis, and (D) Natrialba aegyptia. Each of these four species is a representative from the four most populous genera in the set, which collectively contain 66% of the organisms in the study. Black line represents calculated G+C percent for each 100 bp window. Contig boundaries are represented as vertical red lines, contig mean G+C as horizontal blue lines, and genome mean G+C as a horizontal green line. The horizontal axis displays the number of 20 bp steps taken along the genome. For all G+C plots see Data Dryad package [67].
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004784-g007: Sliding-window G+C content analysis.Representative G+C content plots for (A) Haloferax mediterranei, (B) Halorubrum litoreum, (C) Haloarcula argentinensis, and (D) Natrialba aegyptia. Each of these four species is a representative from the four most populous genera in the set, which collectively contain 66% of the organisms in the study. Black line represents calculated G+C percent for each 100 bp window. Contig boundaries are represented as vertical red lines, contig mean G+C as horizontal blue lines, and genome mean G+C as a horizontal green line. The horizontal axis displays the number of 20 bp steps taken along the genome. For all G+C plots see Data Dryad package [67].
Mentions: Regardless of the mechanism for its maintenance, genome-wide G+C bias offers a method for identification of candidates for horizontal gene transfer from organisms with G+C content differing from the recipient species, as horizontally transferred genes are often A+T shifted relative to the host genome [71]. We examined the G+C content of the 80 haloarchaeal genomes, using a sliding 100 bp window, and conducted change-point analysis to extract regions with local G+C content differing from the genome average. It is important to note here that haloarchaeal plasmids, including minichromosomes and megaplasmids, are known to have decreased G+C content compared with primary replicons (“chromosomes”) [63]. As the mechanisms for maintaining decreased G+C content in smaller replicons are unknown, and in order to accommodate draft genomes where the identity of the primary replicons are unknown, we have chosen to be replicon size neutral. Some regions of the genome are also expected to have low local G+C content due to selective pressure for maintaining a higher A+T percentage (eg. origin of replication sites). In addition, we have been neutral as to the direction of divergence from genome-wide G+C average, in order to allow detection of regions of unusually high as well as unusually low G+C (Figure 7, Figure S8, Datasets S6 & S7).

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