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The Journal of Biological Chemistry Jul 2021Pentatricopeptide repeat (PPR) proteins are a large family of proteins that act primarily at different posttranscriptional steps of organellar gene expression. We have...
Pentatricopeptide repeat (PPR) proteins are a large family of proteins that act primarily at different posttranscriptional steps of organellar gene expression. We have previously found that the Schizosaccharomyces pombe PPR protein mpal10 interacts with mitochondrial translational activator Mpa1, and both are essential for mitochondrial protein synthesis. However, it is unclear how these two proteins function in mitochondrial protein synthesis in S. pombe. In this study, we further investigated the role of Ppr10 and Mpa1 in mitochondrial protein synthesis. Mitochondrial translational initiation requires two initiation factors, Mti2 and Mti3, which bind to the small subunit of the mitochondrial ribosome (mt-SSU) during the formation of the mitochondrial translational initiation complex. Using sucrose gradient sedimentation analysis, we found that disruption of ppr10, mpa1, or the PPR motifs in Ppr10 impairs the association of Mti2 and Mti3 with the mt-SSU, suggesting that both Ppr10 and Mpa1 may be required for the interaction of Mti2 and Mti3 with the mt-SSU during the assembly of mitochondrial translational initiation complex. Loss of Ppr10 perturbs the association of mitochondrially encoded cytochrome b (cob1) and cytochrome c oxidase subunit 1 (cox1) mRNAs with assembled mitochondrial ribosomes. Proteomic analysis revealed that a fraction of Ppr10 and Mpa1 copurified with a subset of mitoribosomal proteins. The PPR motifs of Ppr10 are necessary for its interaction with Mpa1 and that disruption of these PPR motifs impairs mitochondrial protein synthesis. Our results suggest that Ppr10 and Mpa1 function together to mediate mitochondrial translational initiation.
Topics: Binding Sites; Carrier Proteins; Eukaryotic Initiation Factors; Mitochondria; Mitochondrial Proteins; Mitochondrial Ribosomes; Peptide Chain Initiation, Translational; Protein Binding; RNA, Messenger; RNA-Binding Proteins; Schizosaccharomyces; Schizosaccharomyces pombe Proteins
PubMed: 34119521
DOI: 10.1016/j.jbc.2021.100869 -
Life Science Alliance Oct 2022Yeast use the G-protein-coupled receptor signaling pathway to detect and track the mating pheromone. The G-protein-coupled receptor pathway is inhibited by the regulator...
Yeast use the G-protein-coupled receptor signaling pathway to detect and track the mating pheromone. The G-protein-coupled receptor pathway is inhibited by the regulator of G-protein signaling (RGS) Sst2 which induces Gα GTPase activity and inactivation of downstream signaling. G-protein signaling activates the MAPK Fus3, which phosphorylates the RGS; however, the role of this modification is unknown. We found that pheromone-induced RGS phosphorylation peaks early; the phospho-state of RGS controls its localization and influences MAPK spatial distribution. Surprisingly, phosphorylation of the RGS promotes completion of cytokinesis before pheromone-induced growth. Completion of cytokinesis in the presence of pheromone is promoted by the kelch-repeat protein, Kel1 and antagonized by the formin Bni1. We found that RGS complexes with Kel1 and prefers the unphosphorylatable RGS mutant. We also found overexpression of unphosphorylatable RGS exacerbates cytokinetic defects, whereas they are rescued by overexpression of Kel1. These data lead us to a model where Kel1 promotes completion of cytokinesis before pheromone-induced polarity but is inhibited by unphosphorylated RGS binding.
Topics: Cytokinesis; GTP-Binding Proteins; GTPase-Activating Proteins; Microfilament Proteins; Mitogen-Activated Protein Kinases; Pheromones; Phosphorylation; RGS Proteins; Receptors, G-Protein-Coupled; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 35985794
DOI: 10.26508/lsa.202101245 -
The Journal of Physical Chemistry... Jul 2021The presence of metamorphism in the protein's native state is not yet fully understood. To shed light on this issue, we present an assessment, in terms of the amide...
The presence of metamorphism in the protein's native state is not yet fully understood. To shed light on this issue, we present an assessment, in terms of the amide hydrogen exchange protection factor, that aims to determine the possible existence of structural fluctuations in the native-state consistent with both the upper-bound marginal stability of proteins and the presence of metamorphism. The preliminary results enable us to conclude that the native-state metamorphism is, indeed, more probable than previously thought.
Topics: Amides; Protein Stability; Proteins
PubMed: 34192878
DOI: 10.1021/acs.jpclett.1c01831 -
FEMS Yeast Research Nov 2017Ecl1 family genes are conserved among yeast, in which their overexpression extends chronological lifespan. Ecl1 family genes were first identified in the fission yeast... (Review)
Review
Ecl1 family genes are conserved among yeast, in which their overexpression extends chronological lifespan. Ecl1 family genes were first identified in the fission yeast Schizosaccharomyces pombe; at the time, they were considered noncoding RNA owing to their short coding sequence of fewer than 300 base pairs. Schizosaccharomyces pombe carries three Ecl1 family genes, ecl1+, ecl2+ and ecl3+, whereas Saccharomyces cerevisiae has one, ECL1. Their overexpression extends chronological lifespan, increases oxidative stress resistance and induces sexual development in fission yeast. A recent study indicated that Ecl1 family genes play a significant role in responding to environmental zinc or sulfur depletion. In this review, we focus on Ecl1 family genes in fission yeast and describe the relationship between nutritional depletion and cellular output, as the latter depends on Ecl1 family genes. Furthermore, we present the roles and functions of Ecl1 family genes characterized to date.
Topics: Fungal Proteins; Gene Expression Regulation, Fungal; Multigene Family; Nuclear Proteins; Oxidative Stress; Saccharomyces cerevisiae Proteins; Schizosaccharomyces pombe Proteins; Signal Transduction; Yeasts
PubMed: 28934413
DOI: 10.1093/femsyr/fox066 -
Current Opinion in Genetics &... Oct 2019Fungi are found in diverse ecological niches as primary decomposers, mutualists, or parasites of plants and animals. Although animals and fungi share a common ancestor,... (Review)
Review
Fungi are found in diverse ecological niches as primary decomposers, mutualists, or parasites of plants and animals. Although animals and fungi share a common ancestor, fungi dramatically diversified their life cycle, cell biology, and metabolism as they evolved and colonized new niches. This review focuses on a family of fungal transcription factors (Swi4/Mbp1, APSES, Xbp1, Bqt4) derived from the lateral gene transfer of a KilA-N domain commonly found in prokaryotic and eukaryotic DNA viruses. These virus-derived fungal regulators play central roles in cell cycle, morphogenesis, sexual differentiation, and quiescence. We consider the possible origins of KilA-N and how this viral DNA binding domain came to be intimately associated with fungal processes.
Topics: DNA-Binding Proteins; Evolution, Molecular; Fungi; Gene Transfer, Horizontal; Membrane Proteins; Nuclear Proteins; Phylogeny; Protein Conformation; Protein Domains; Repressor Proteins; Saccharomyces cerevisiae Proteins; Schizosaccharomyces pombe Proteins; Transcription Factors; Viral Regulatory and Accessory Proteins
PubMed: 31600629
DOI: 10.1016/j.gde.2019.08.004 -
BMC Genomics Sep 2018The protein energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting between structures with varying energies. Reconstructing a...
BACKGROUND
The protein energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting between structures with varying energies. Reconstructing a protein's energy landscape holds the key to characterizing a protein's equilibrium conformational dynamics and its relationship to function. Many pathogenic mutations in protein sequences alter the equilibrium dynamics that regulates molecular interactions and thus protein function. In principle, reconstructing energy landscapes of a protein's healthy and diseased variants is a central step to understanding how mutations impact dynamics, biological mechanisms, and function.
RESULTS
Recent computational advances are yielding detailed, sample-based representations of protein energy landscapes. In this paper, we propose and describe two novel methods that leverage computed, sample-based representations of landscapes to reconstruct them and extract from them informative local structures that reveal the underlying organization of an energy landscape. Such structures constitute landscape features that, as we demonstrate here, can be utilized to detect alterations of landscapes upon mutation.
CONCLUSIONS
The proposed methods detect altered protein energy landscape features in response to sequence mutations. By doing so, the methods allow formulating hypotheses on the impact of mutations on specific biological activities of a protein. This work demonstrates that the availability of energy landscapes of healthy and diseased variants of a protein opens up new avenues to harness the quantitative information embedded in landscapes to summarize mechanisms via which mutations alter protein dynamics to percolate to dysfunction.
Topics: Algorithms; Computational Biology; Humans; Models, Molecular; Mutation; Protein Conformation; Proteins; Thermodynamics
PubMed: 30255791
DOI: 10.1186/s12864-018-5024-z -
Handbook of Experimental Pharmacology 2017Nitric oxide (NO) raises the intracellular 3',5'-cyclic guanosine monophosphate (cGMP) level through the activation of soluble guanylate cyclase and, in the presence of... (Review)
Review
Nitric oxide (NO) raises the intracellular 3',5'-cyclic guanosine monophosphate (cGMP) level through the activation of soluble guanylate cyclase and, in the presence of reactive oxygen species (ROS), reacts with biomolecules to produce nitrated cGMP derivatives. 8-Nitro-cGMP was the first endogenous cGMP derivative discovered in mammalian cells (2007) and was later found in plant cells. Among the six nitrogen atoms in this molecule, the one in the nitro group (NO) comes from NO. This chapter asserts that this newly found cGMP is undoubtedly one of the major physiological cNMPs. Multiple studies suggest that its intracellular abundance might exceed that of unmodified cGMP. The characteristic chemical feature of 8-nitro-cGMP is its ability to modify proteinous cysteine residues via a stable sulfide bond. In this posttranslational modification, the nitro group is detached from the guanine base. This modification, termed "protein S-guanylation," is known to regulate the physiological functions of several important proteins. Furthermore, 8-nitro-cGMP participates in the regulation of autophagy. For example, in antibacterial autophagy (xenophagy), S-guanylation accumulates around invading bacterial cells and functions as a "tag" for subsequent clearance of the organism via ubiquitin modifications. This finding suggests the existence of a system for recognizing the cGMP structure on proteins. Autophagy induction by 8-nitro-cGMP is mechanistically distinct from the well-described starvation-induced autophagy and is independent of the action of mTOR, the master regulator of canonical autophagy.
Topics: Animals; Autophagy; Cell Proliferation; Cellular Senescence; Cyclic GMP; Cyclic GMP-Dependent Protein Kinases; Humans; Molecular Structure; Protein Processing, Post-Translational; Second Messenger Systems
PubMed: 28213625
DOI: 10.1007/164_2016_5000 -
MSystems Dec 2022A protein's function depends on functional residues that determine its binding specificity or its catalytic activity, but these residues are typically not considered...
A protein's function depends on functional residues that determine its binding specificity or its catalytic activity, but these residues are typically not considered when annotating a protein's function. To help biologists investigate the functional residues of proteins, we developed two interactive web-based tools, SitesBLAST and Sites on a Tree. Given a protein sequence, SitesBLAST finds homologs that have known functional residues and shows whether the functional residues are conserved. Sites on a Tree shows how functional residues vary across a protein family by showing them on a phylogenetic tree. These tools are available at http://papers.genomics.lbl.gov/sites. For most microbes of interest, a genome sequence is available, but the function of its proteins is not known. Instead, proteins' functions are predicted from their similarity to other protein sequences. Within a protein's sequence, a few key residues are most important for function, such as catalyzing a chemical reaction or determining what it binds. But most function prediction tools do not take these key residues into account. We developed interactive tools for identifying functional residues in a protein sequence by comparing it to proteins with known functional residues. Our tools also make it easy to compare key residues across many similar proteins. This should help biologists check if a protein's function is predicted correctly, or to predict if groups of similar proteins have conserved functions.
Topics: Phylogeny; Computational Biology; Proteins; Amino Acid Sequence; Data Interpretation, Statistical
PubMed: 36374048
DOI: 10.1128/msystems.00705-22 -
PloS One 2023Ste5 is a prototype of scaffold proteins that regulate activation of mitogen-activated protein kinase (MAPK) cascades in all eukaryotes. Ste5 associates with many...
Ste5 is a prototype of scaffold proteins that regulate activation of mitogen-activated protein kinase (MAPK) cascades in all eukaryotes. Ste5 associates with many proteins including Gβγ (Ste4), Ste11 MAPKKK, Ste7 MAPKK, Fus3 and Kss1 MAPKs, Bem1, Cdc24. Here we show that Ste5 also associates with heat shock protein 70 chaperone (Hsp70) Ssa1 and that Ssa1 and its ortholog Ssa2 are together important for Ste5 function and efficient mating responses. The majority of purified overexpressed Ste5 associates with Ssa1. Loss of Ssa1 and Ssa2 has deleterious effects on Ste5 abundance, integrity, and localization particularly when Ste5 is expressed at native levels. The status of Ssa1 and Ssa2 influences Ste5 electrophoresis mobility and formation of high molecular weight species thought to be phosphorylated, ubiquitinylated and aggregated and lower molecular weight fragments. A Ste5 VWA domain mutant with greater propensity to form punctate foci has reduced predicted propensity to bind Ssa1 near the mutation sites and forms more punctate foci when Ssa1 Is overexpressed, supporting a dynamic protein quality control relationship between Ste5 and Ssa1. Loss of Ssa1 and Ssa2 reduces activation of Fus3 and Kss1 MAPKs and FUS1 gene expression and impairs mating shmoo morphogenesis. Surprisingly, ssa1, ssa2, ssa3 and ssa4 single, double and triple mutants can still mate, suggesting compensatory mechanisms exist for folding. Additional analysis suggests Ssa1 is the major Hsp70 chaperone for the mating and invasive growth pathways and reveals several Hsp70-Hsp90 chaperone-network proteins required for mating morphogenesis.
Topics: Adaptor Proteins, Signal Transducing; HSP70 Heat-Shock Proteins; MAP Kinase Kinase Kinases; Mitogen-Activated Protein Kinases; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 37851593
DOI: 10.1371/journal.pone.0289339 -
International Journal of Molecular... May 2023Prions are transmissible self-perpetuating protein isoforms associated with diseases and heritable traits. Yeast prions and non-transmissible protein aggregates...
Prions are transmissible self-perpetuating protein isoforms associated with diseases and heritable traits. Yeast prions and non-transmissible protein aggregates (mnemons) are frequently based on cross-β ordered fibrous aggregates (amyloids). The formation and propagation of yeast prions are controlled by chaperone machinery. Ribosome-associated chaperone Hsp70-Ssb is known (and confirmed here) to modulate formation and propagation of the prion form of the Sup35 protein []. Our new data show that both formation and mitotic transmission of the stress-inducible prion form of the Lsb2 protein ([]) are also significantly increased in the absence of Ssb. Notably, heat stress leads to a massive accumulation of [] cells in the absence of Ssb, implicating Ssb as a major downregulator of the []-dependent memory of stress. Moreover, the aggregated form of Gγ subunit Ste18, [], behaving as a non-heritable mnemon in the wild-type strain, is generated more efficiently and becomes heritable in the absence of Ssb. Lack of Ssb also facilitates mitotic transmission, while lack of the Ssb cochaperone Hsp40-Zuo1 facilitates both spontaneous formation and mitotic transmission of the Ure2 prion, []. These results demonstrate that Ssb is a general modulator of cytosolic amyloid aggregation, whose effect is not restricted only to [].
Topics: Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Molecular Chaperones; HSP70 Heat-Shock Proteins; Prions; Glutathione Peroxidase; GTP-Binding Protein gamma Subunits; Peptide Termination Factors
PubMed: 37240005
DOI: 10.3390/ijms24108660