Proteomics of osmoregulatory responses in threespine stickleback gills

Mapping Intimacies ◽

10.1101/2020.03.11.987834 ◽

2020 ◽

Author(s):

Johnathon Li ◽

Dietmar Kültz

Keyword(s):

Stress Response ◽

Ion Transport ◽

Stress Responses ◽

Intracellular Signaling ◽

Protein Abundance ◽

General Stress Response ◽

Environmental Salinity ◽

Kegg Pathways ◽

General Stress ◽

Mesocosm Experiments

AbstractThe gill proteome of threespine sticklebacks (Gasterosteus aculeatus) differs greatly in populations that inhabit diverse environments characterized by different temperature, salinity, food availability, parasites, and other parameters. To assess the contribution of a specific environmental parameter to such differences it is necessary to isolate its effects from those of other parameters. In this study the effect of environmental salinity on the gill proteome of G. aculeatus was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by LC/MSMS data-independent acquisition (DIA) and Skyline. Relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with DIA quantitative proteomics. General stress responses were distinguished from osmoregulatory protein abundance changes by their consistent occurrence during both hypo- and hyper-osmotic salinity stress in six separate mesocosm experiments. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress, then it was considered an osmoregulatory protein. In contrast, if protein abundance was consistently increased irrespective of whether salinity was increased or decreased, then it was considered a general stress response protein. KEGG pathway analysis revealed that the salivary secretion, inositol phosphate metabolism, valine, leucine and isoleucine degradation, citrate cycle, oxidative phosphorylation, and corresponding endocrine and extracellular signaling pathways contain most of the osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to KEGG pathways that represent proteostasis, immunity, and related intracellular signaling processes. General stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and associated intracellular signaling KEGG pathways. These results demonstrate that G. aculeatus responds to salinity changes by adjusting osmoregulatory mechanisms that are distinct from transient general stress responses to control compatible osmolyte synthesis, transepithelial ion transport, and oxidative energy metabolism. Furthermore, this study establishes salinity as a key factor for causing the regulation of numerous proteins and KEGG pathways with established functions in proteostasis, immunity, and tissue remodeling. We conclude that the corresponding osmoregulatory gill proteins and KEGG pathways represent molecular phenotypes that promote transepithelial ion transport, cellular osmoregulation, and gill epithelial remodeling to adjust gill function to environmental salinity.

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Proteomics of Osmoregulatory Responses in Threespine Stickleback Gills

Integrative and Comparative Biology ◽

10.1093/icb/icaa042 ◽

2020 ◽

Vol 60 (2) ◽

pp. 304-317 ◽

Cited By ~ 1

Author(s):

Johnathon Li ◽

Dietmar Kültz

Keyword(s):

Ion Transport ◽

Salinity Stress ◽

Stress Responses ◽

Intracellular Signaling ◽

Inositol Phosphate ◽

Protein Abundance ◽

Environmental Salinity ◽

Kegg Pathways ◽

Oxidative Energy Metabolism ◽

Mesocosm Experiments

Synopsis The gill proteome of threespine sticklebacks (Gasterosteus aculeatus) differs greatly in populations that inhabit diverse environments characterized by different temperature, salinity, food availability, parasites, and other parameters. To assess the contribution of a specific environmental parameter to such differences it is necessary to isolate its effects from those of other parameters. In this study the effect of environmental salinity on the gill proteome of G. aculeatus was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by Liquid chromatography/Tandem mass spectrometry data-independent acquisition (DIA) and Skyline. Relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with DIA quantitative proteomics. Non-directional stress responses were distinguished from osmoregulatory protein abundance changes by their consistent occurrence during both hypo- and hyper-osmotic salinity stress in six separate mesocosm experiments. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress, then it was considered an osmoregulatory protein. In contrast, if protein abundance was consistently increased irrespective of whether salinity was increased or decreased, then it was considered a non-directional response protein. KEGG pathway analysis revealed that the salivary secretion, inositol phosphate metabolism, valine, leucine, and isoleucine degradation, citrate cycle, oxidative phosphorylation, and corresponding endocrine and extracellular signaling pathways contain most of the osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to KEGG pathways that represent proteostasis, immunity, and related intracellular signaling processes. Non-directional stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and associated intracellular signaling KEGG pathways. These results demonstrate that G. aculeatus responds to salinity changes by adjusting osmoregulatory mechanisms that are distinct from transient non-directional stress responses to control compatible osmolyte synthesis, transepithelial ion transport, and oxidative energy metabolism. Furthermore, this study establishes salinity as a key factor for causing the regulation of numerous proteins and KEGG pathways with established functions in proteostasis, immunity, and tissue remodeling. We conclude that the corresponding osmoregulatory gill proteins and KEGG pathways represent molecular phenotypes that promote transepithelial ion transport, cellular osmoregulation, and gill epithelial remodeling to adjust gill function to environmental salinity.

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PhyR Is Involved in the General Stress Response of Methylobacterium extorquens AM1

Journal of Bacteriology ◽

10.1128/jb.01483-07 ◽

2007 ◽

Vol 190 (3) ◽

pp. 1027-1035 ◽

Cited By ~ 69

Author(s):

Benjamin Gourion ◽

Anne Francez-Charlot ◽

Julia A. Vorholt

Keyword(s):

Stress Response ◽

Heat Shock ◽

Stress Responses ◽

Target Genes ◽

Stress Proteins ◽

Plant Colonization ◽

Methylobacterium Extorquens ◽

General Stress Response ◽

Amino Terminal ◽

General Stress

ABSTRACTPhyR represents a novel alphaproteobacterial family of response regulators having a structure consisting of two domains; a predicted amino-terminal extracytoplasmic function (ECF) sigma factor-like domain and a carboxy-terminal receiver domain. PhyR was first described inMethylobacterium extorquensAM1, in which it has been shown to be essential for plant colonization, probably due to its suggested involvement in the regulation of a number of stress proteins. Here we investigated the PhyR regulon using microarray technology. We found that the PhyR regulon is rather large and that most of the 246 targets are under positive control. Mapping of transcriptional start sites revealed candidate promoters for PhyR-mediated regulation. One of these promoters, an ECF-type promoter, was identified upstream of one-third of the target genes by in silico analysis. Among the PhyR targets are genes predicted to be involved in multiple stress responses, includingkatE,osmC,htrA,dnaK,gloA,dps, anduvrA. The induction of these genes is consistent with our phenotypic analyses which revealed that PhyR is involved in resistance to heat shock and desiccation, as well as oxidative, UV, ethanol, and osmotic stresses, inM. extorquensAM1. The finding that PhyR is involved in the general stress response was further substantiated by the finding that carbon starvation induces protection against heat shock and that this protection is at least in part dependent on PhyR.

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Global Transcriptional Response of Bacillus subtilis to Heat Shock

Journal of Bacteriology ◽

10.1128/jb.183.24.7318-7328.2001 ◽

2001 ◽

Vol 183 (24) ◽

pp. 7318-7328 ◽

Cited By ~ 187

Author(s):

John D. Helmann ◽

Ming Fang Winston Wu ◽

Phil A. Kobel ◽

Francisco-Javier Gamo ◽

Michael Wilson ◽

...

Keyword(s):

Bacillus Subtilis ◽

Stress Response ◽

Heat Shock ◽

Dna Sequences ◽

Stress Responses ◽

Transcriptional Response ◽

Transcriptional Responses ◽

General Stress Response ◽

General Stress ◽

Induced Genes

ABSTRACT In response to heat stress, Bacillus subtilisactivates the transcription of well over 100 different genes. Many of these genes are members of a general stress response regulon controlled by the secondary sigma factor, ςB, while others are under control of the HrcA or CtsR heat shock regulators. We have used DNA microarrays to monitor the global transcriptional response to heat shock. We find strong induction of known ςB-dependent genes with a characteristic rapid induction followed by a return to near prestimulus levels. The HrcA and CtsR regulons are also induced, but with somewhat slower kinetics. Analysis of DNA sequences proximal to newly identified heat-induced genes leads us to propose ∼70 additional members of the ςB regulon. We have also identified numerous heat-induced genes that are not members of known heat shock regulons. Notably, we observe very strong induction of arginine biosynthesis and transport operons. Induction of several genes was confirmed by quantitative reverse transcriptase PCR. In addition, the transcriptional responses measured by microarray hybridization compare favorably with the numerous previous studies of heat shock in this organism. Since many different conditions elicit both specific and general stress responses, knowledge of the heat-induced general stress response reported here will be helpful for interpreting future microarray studies of other stress responses.

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General Stress Response Regulator RpoS in Adaptive Mutation and Amplification in Escherichia coli

Genetics ◽

10.1093/genetics/166.2.669 ◽

2004 ◽

Vol 166 (2) ◽

pp. 669-680 ◽

Cited By ~ 2

Author(s):

Mary-Jane Lombardo ◽

Ildiko Aponyi ◽

Susan M Rosenberg

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Stationary Phase ◽

Point Mutation ◽

Stress Responses ◽

Genome Rearrangement ◽

Adaptive Mutation ◽

Induced Mutations ◽

General Stress Response ◽

General Stress

Abstract Microbial cells under growth-limiting stress can generate mutations by mechanisms distinct from those in rapidly growing cells. These mechanisms might be specific stress responses that increase mutation rates, potentially altering rates of evolution, or might reflect non-stress-specific processes in rare growing cells. In an Escherichia coli model system, both frameshift reversion mutations and gene amplifications occur as apparent starvation-induced mutations. Whereas frameshift reversion (“point mutation”) requires recombination proteins, the SOS response, and error-prone DNA polymerase IV (DinB), amplification requires neither SOS nor pol IV. We report that both point mutation and amplification require the stationary-phase and general stress response transcription factor RpoS (σS). Growth-dependent mutation does not. Alternative interpretations are excluded. The results imply, first, that point mutation and amplification are stress responses that occur in differentiated stationary-phase (not rare growing) cells and, second, that transient genetic instability, producing both point mutation and genome rearrangement, may be a previously unrecognized component of the RpoS-dependent general stress response.

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An Extracytoplasmic Function Sigma Factor Acts as a General Stress Response Regulator in Sinorhizobium meliloti

Journal of Bacteriology ◽

10.1128/jb.00175-07 ◽

2007 ◽

Vol 189 (11) ◽

pp. 4204-4216 ◽

Cited By ~ 96

Author(s):

Laurent Sauviac ◽

Heinui Philippe ◽

Kounthéa Phok ◽

Claude Bruand

Keyword(s):

Stress Response ◽

Stationary Phase ◽

Stress Responses ◽

Sigma Factor ◽

Sinorhizobium Meliloti ◽

In Planta ◽

General Stress Response ◽

Stress Response Genes ◽

General Stress

ABSTRACT Sinorhizobium meliloti genes transcriptionally up-regulated after heat stress, as well as upon entry into stationary phase, were identified by microarray analyses. Sixty stress response genes were thus found to be up-regulated under both conditions. One of them, rpoE2 (smc01506), encodes a putative extracytoplasmic function (ECF) sigma factor. We showed that this sigma factor controls its own transcription and is activated by various stress conditions, including heat and salt, as well as entry into stationary phase after either carbon or nitrogen starvation. We also present evidence that the product of the gene cotranscribed with rpoE2 negatively regulates RpoE2 activity, and we therefore propose that it plays the function of anti-sigma factor. By combining transcriptomic, bioinformatic, and quantitative reverse transcription-PCR analyses, we identified 44 RpoE2-controlled genes and predicted the number of RpoE2 targets to be higher. Strikingly, more than one-third of the 60 stress response genes identified in this study are RpoE2 targets. Interestingly, two genes encoding proteins with known functions in stress responses, namely, katC and rpoH2, as well as a second ECF-encoding gene, rpoE5, were found to be RpoE2 regulated. Altogether, these data suggest that RpoE2 is a major global regulator of the general stress response in S. meliloti. Despite these observations, and although this sigma factor is well conserved among alphaproteobacteria, no in vitro nor in planta phenotypic difference from the wild-type strain could be detected for rpoE2 mutants. This therefore suggests that other important actors in the general stress response have still to be identified in S. meliloti.

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Stress-induced Gene Expression inCandida albicans: Absence of a General Stress Response

Molecular Biology of the Cell ◽

10.1091/mbc.e02-08-0546 ◽

2003 ◽

Vol 14 (4) ◽

pp. 1460-1467 ◽

Cited By ~ 197

Author(s):

Brice Enjalbert ◽

André Nantel ◽

Malcolm Whiteway

Keyword(s):

Stress Response ◽

Stress Responses ◽

Fungal Pathogen ◽

Transcriptional Profiling ◽

Mild Stress ◽

General Stress Response ◽

General Stress ◽

Oxidative Stresses ◽

Common Response ◽

Incandida Albicans

We used transcriptional profiling to investigate the response of the fungal pathogen Candida albicans to temperature and osmotic and oxidative stresses under conditions that permitted >60% survival of the challenged cells. Each stress generated the transient induction of a specific set of genes including classic markers observed in the stress responses of other organisms. We noted that the classical hallmarks of the general stress response observed inSaccharomyces cerevisiae are absent from C. albicans; no C. albicans genes were significantly induced in a common response to the three stresses. This observation is supported by our inability to detect stress cross-protection in C. albicans. Similarly, in C. albicans there is essentially no induction of carbohydrate reserves like glycogen and trehalose in response to a mild stress, unlike the situation in S. cerevisiae. Thus C. albicans lacks the strong general stress response exhibited byS. cerevisiae.

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