High-resolution yeast phenomics resolves different physiological features in the saline response

Warringer, Jonas; Ericson, Elke; Fernandez, Luciano; Nerman, Olle; Blomberg, Anders

doi:10.1073/pnas.2435976100

Cited by 213 publications

(241 citation statements)

References 30 publications

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“…18. A list of putatively essential genes was obtained from The Saccharomyces Genome Database (www.yeastgenome.org) and was added to both dispensability data sets.…”

Section: Methodsmentioning

confidence: 99%

Functional genomic analysis of the rates of protein evolution

Wall

Hirsh²,

Fraser³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

259

256

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The evolutionary rates of proteins vary over several orders of magnitude. Recent work suggests that analysis of large data sets of evolutionary rates in conjunction with the results from high-throughput functional genomic experiments can identify the factors that cause proteins to evolve at such dramatically different rates. To this end, we estimated the evolutionary rates of >3,000 proteins in four species of the yeast genus Saccharomyces and investigated their relationship with levels of expression and protein dispensability. Each protein's dispensability was estimated by the growth rate of mutants deficient for the protein. Our analyses of these improved evolutionary and functional genomic data sets yield three main results. First, dispensability and expression have independent, significant effects on the rate of protein evolution. Second, measurements of expression levels in the laboratory can be used to filter data sets of dispensability estimates, removing variates that are unlikely to reflect real biological effects. Third, structural equation models show that although we may reasonably infer that dispensability and expression have significant effects on protein evolutionary rate, we cannot yet accurately estimate the relative strengths of these effects

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“…18. A list of putatively essential genes was obtained from The Saccharomyces Genome Database (www.yeastgenome.org) and was added to both dispensability data sets.…”

Section: Methodsmentioning

confidence: 99%

Functional genomic analysis of the rates of protein evolution

Wall

Hirsh²,

Fraser³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

259

256

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“…NaCl tolerance is a complex trait involving several pathways (Warringer et al, 2003;Dhar et al, 2011). This study provides an example of selection of NaCl tolerance trait through experimental evolution.…”

Section: Discussionmentioning

confidence: 99%

“…This study provides an example of selection of NaCl tolerance trait through experimental evolution. Three main physiological components of NaCl stress response, including adaptation time to NaCl stress, growth rate and efficiency of growth in NaCl stress (Warringer et al, 2003), have been improved in conversion ensure that sufficient energy is produced for cellular activities. In addition, decreased expression of flagellar assembly genes resulting in decreased cell motility allows more energy available for osmoprotection.…”

Section: Discussionmentioning

confidence: 99%

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

Zhou

Baidoo

et al. 2013

The ISME Journal

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Desulfovibrio vulgaris Hildenborough strains with significantly increased tolerance to NaCl were obtained via experimental evolution. A NaCl-evolved strain, ES9-11, isolated from a population cultured for 1200 generations in medium amended with 100 mM NaCl, showed better tolerance to NaCl than a control strain, EC3-10, cultured for 1200 generations in parallel but without NaCl amendment in medium. To understand the NaCl adaptation mechanism in ES9-11, we analyzed the transcriptional, metabolite and phospholipid fatty acid (PLFA) profiles of strain ES9-11 with 0, 100-or 250 mM-added NaCl in medium compared with the ancestral strain and EC3-10 as controls. In all the culture conditions, increased expressions of genes involved in amino-acid synthesis and transport, energy production, cation efflux and decreased expression of flagellar assembly genes were detected in ES9-11. Consistently, increased abundances of organic solutes and decreased cell motility were observed in ES9-11. Glutamate appears to be the most important osmoprotectant in D. vulgaris under NaCl stress, whereas, other organic solutes such as glutamine, glycine and glycine betaine might contribute to NaCl tolerance under low NaCl concentration only. Unsaturation indices of PLFA significantly increased in ES9-11. Branched unsaturated PLFAs i17:1 x9c, a17:1 x9c and branched saturated i15:0 might have important roles in maintaining proper membrane fluidity under NaCl stress. Taken together, these data suggest that the accumulation of osmolytes, increased membrane fluidity, decreased cell motility and possibly an increased exclusion of Na þ contribute to increased NaCl tolerance in NaCl-evolved D. vulgaris.

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“…changes in genome size, gene expression and regulation, mutation rate) and the developmental phenotypic plasticity in key traits responsible for changes in fitness that underlie the demographic recovery associated with ER. High throughput and real-time sequencing techniques coupled to new approaches in phenomics [55] are now making this goal a possibility. -Tests of quantitative theoretical predictions using models tailored to the empirical system.…”

Section: Concluding Thoughts and Future Stepsmentioning

confidence: 99%

Evolutionary rescue: an emerging focus at the intersection between ecology and evolution

Gonzalez

Ronce

Ferrière

et al. 2013

Phil. Trans. R. Soc. B

338

343

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There is concern that the rate of environmental change is now exceeding the capacity of many populations to adapt. Mitigation of biodiversity loss requires science that integrates both ecological and evolutionary responses of populations and communities to rapid environmental change, and can identify the conditions that allow the recovery of declining populations. This special issue focuses on evolutionary rescue (ER), the idea that evolution might occur sufficiently fast to arrest population decline and allow population recovery before extinction ensues. ER emphasizes a shift to a perspective on evolutionary dynamics that focuses on short time-scales, genetic variants of large effects and absolute rather than relative fitness. The contributions in this issue reflect the state of field; the articles address the latest conceptual developments, and report novel theoretical and experimental results. The examples in this issue demonstrate that this burgeoning area of research can inform problems of direct practical concern, such as the conservation of biodiversity, adaptation to climate change and the emergence of infectious disease. The continued development of research on ER will be necessary if we are to understand the extent to which anthropogenic global change will reduce the Earth's biodiversity.

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High-resolution yeast phenomics resolves different physiological features in the saline response

Cited by 213 publications

References 30 publications

Functional genomic analysis of the rates of protein evolution

Functional genomic analysis of the rates of protein evolution

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

Evolutionary rescue: an emerging focus at the intersection between ecology and evolution

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