MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast

English, Justin G.; Shellhammer, James P.; Malahe, Michael; McCarter, Patrick C.; Elston, Timothy C.; Dohlman, Henrik G.

doi:10.1126/scisignal.2005774

Cited by 52 publications

(77 citation statements)

References 73 publications

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“…The ratio is further prone to be misinterpreted as a phosphorylation stoichiometry, which cannot be calculated in experiments that use different antibodies to detect the phosphorylated and total protein because of differences in antibody affinity. Calculating phosphorylation stoichiometry by immunoblotting requires electrophoretic conditions that separate the phosphorylated and total forms by mobility (32). Modification stoichiometry can be critical under certain conditions (33), but there are also examples where increases in total protein have impacted signal flow (34).…”

Section: Discussionmentioning

confidence: 99%

An analysis of critical factors for quantitative immunoblotting

2015

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Immunoblotting (also known as Western blotting) combined with digital image analysis can be a reliable method for analyzing the abundance of proteins and protein modifications, but not every immunoblot-analysis combination produces an accurate result. Here, I illustrate how sample preparation, protocol implementation, detection scheme, and normalization approach profoundly affect the quantitative performance of immunoblotting. This study implemented diagnostic experiments that assess an immunoblot-analysis workflow for accuracy and precision. The results showed that ignoring such diagnostics can lead to pseudoquantitative immunoblot data that dramatically overestimate or underestimate true differences in protein abundance.

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Section: Discussionmentioning

confidence: 99%

An analysis of critical factors for quantitative immunoblotting

2015

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“…Competing for Pbs2 is one possible means of cross-inhibition between the pathways, but multiple feedbacks, both positive and negative, exist within the HOG network (Hao et al, 2007; Macia et al, 2009; Sharifian et al, 2015; English et al, 2015), and a feedback-based interaction is possible. That biochemistry can be used to measure a time-derivative on a time-scales as fast as seconds is well established (Block et al, 1983), and, in analogy with bacterial chemotaxis, we expect that upstream signalling in the fast pathway encodes a short-term memory of the level of the input to allow comparison of the current level to a value in the past.…”

Section: Discussionmentioning

confidence: 99%

Distributing tasks via multiple input pathways increases cellular survival in stress

Granados

Crane

Montaño-Gutierrez

et al. 2017

eLife

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Improving in one aspect of a task can undermine performance in another, but how such opposing demands play out in single cells and impact on fitness is mostly unknown. Here we study budding yeast in dynamic environments of hyperosmotic stress and show how the corresponding signalling network increases cellular survival both by assigning the requirements of high response speed and high response accuracy to two separate input pathways and by having these pathways interact to converge on Hog1, a p38 MAP kinase. Cells with only the less accurate, reflex-like pathway are fitter in sudden stress, whereas cells with only the slow, more accurate pathway are fitter in increasing but fluctuating stress. Our results demonstrate that cellular signalling is vulnerable to trade-offs in performance, but that these trade-offs can be mitigated by assigning the opposing tasks to different signalling subnetworks. Such division of labour could function broadly within cellular signal transduction.DOI: http://dx.doi.org/10.7554/eLife.21415.001

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“…The Ste50 IDR also represents a good candidate for evolutionary analysis because it contains a cluster of MAPK consensus phosphorylation sites (S or T, followed by a P) that contribute to signal modulation of MAPK pathways (32)(33)(34). Evolutionary turnover within clusters of phosphorylation sites in disordered regions is thought to be widespread (19,28,(35)(36)(37), and the alignment of Ste50 shows that MAPK consensus sites differ in position, spacing, and number, consistent with evolutionary turnover of these sites within the IDR (Fig.…”

Section: Significancementioning

confidence: 94%

Selection maintains signaling function of a highly diverged intrinsically disordered region

Zarin

Tsai

et al. 2017

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

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Intrinsically disordered regions (IDRs) are characterized by their lack of stable secondary or tertiary structure and comprise a large part of the eukaryotic proteome. Although these regions play a variety of signaling and regulatory roles, they appear to be rapidly evolving at the primary sequence level. To understand the functional implications of this rapid evolution, we focused on a highly diverged IDR in Saccharomyces cerevisiae that is involved in regulating multiple conserved MAPK pathways. We hypothesized that under stabilizing selection, the functional output of orthologous IDRs could be maintained, such that diverse genotypes could lead to similar function and fitness. Consistent with the stabilizing selection hypothesis, we find that diverged, orthologous IDRs can mostly recapitulate wildtype function and fitness in S. cerevisiae. We also find that the electrostatic charge of the IDR is correlated with signaling output and, using phylogenetic comparative methods, find evidence for selection maintaining this quantitative molecular trait despite underlying genotypic divergence.C urrent predictions suggest that close to 40% of all proteins in eukaryotic organisms are either entirely disordered or contain sizeable regions that are disordered, meaning they do not autonomously fold into defined secondary or tertiary structures (1, 2). These intrinsically disordered regions (IDRs) are thought to have important implications for protein function (3, 4) and are known to play regulatory roles, often through short linear motifs (SLiMs) that control protein-protein interactions, localization, degradation, and posttranslational modifications (5, 6). Although proteome-wide studies have provided in silico evidence for conservation of length (7) and composition (8) in some IDRs, reports of increased rates of insertions and deletions (9-13) and amino acid substitutions (14) in IDRs are indicative of their rapid evolution compared with ordered regions. In addition, although some SLiMs are indeed conserved in IDRs (15-17), others appear in clusters where precise position and number are not conserved (18)(19)(20). Although it is reasonable to assume that conservation of sequence in IDRs is indicative of functional conservation of SLiMs, it is more difficult to interpret the functional consequences of IDRs that are highly diverged at the sequence level: These may represent either nonfunctional sequences evolving in the absence of constraint or weakly constrained functional elements that are gained or lost in a compensatory manner [undergoing evolutionary turnover (as described in refs. 18, 21)], such that they are not conserved at the amino acid sequence level.Like IDRs, noncoding DNA often shows relatively rapid evolution and weak constraints at the sequence level (22). Interestingly, IDRs show other parallels with noncoding DNA (18,23,24). For example, nonconserved clusters of phosphorylation sites in IDRs are reminiscent of nonconserved transcription factor binding sites in enhancers. Although these enhancers and the bi...

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MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast

Cited by 52 publications

References 73 publications

An analysis of critical factors for quantitative immunoblotting

An analysis of critical factors for quantitative immunoblotting

Distributing tasks via multiple input pathways increases cellular survival in stress

Selection maintains signaling function of a highly diverged intrinsically disordered region

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