1
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Talavera RA, Prichard BE, Sommer RA, Leitao RM, Sarabia CJ, Hazir S, Paulo JA, Gygi SP, Kellogg DR. Cell growth and nutrient availability control the mitotic exit signaling network in budding yeast. J Cell Biol 2024; 223:e202305008. [PMID: 38722822 PMCID: PMC11082370 DOI: 10.1083/jcb.202305008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 01/03/2024] [Accepted: 04/04/2024] [Indexed: 05/13/2024] Open
Abstract
Cell growth is required for cell cycle progression. The amount of growth required for cell cycle progression is reduced in poor nutrients, which leads to a reduction in cell size. In budding yeast, nutrients can influence cell size by modulating the extent of bud growth, which occurs predominantly in mitosis. However, the mechanisms are unknown. Here, we used mass spectrometry to identify proteins that modulate bud growth in response to nutrient availability. This led to the discovery that nutrients regulate numerous components of the mitotic exit network (MEN), which controls exit from mitosis. A key component of the MEN undergoes gradual multisite phosphorylation during bud growth that is dependent upon bud growth and correlated with the extent of growth. Furthermore, activation of the MEN is sufficient to override a growth requirement for mitotic exit. The data suggest a model in which the MEN ensures that mitotic exit occurs only when an appropriate amount of bud growth has occurred.
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Affiliation(s)
- Rafael A. Talavera
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Beth E. Prichard
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Robert A. Sommer
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Ricardo M. Leitao
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Christopher J. Sarabia
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Semin Hazir
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Douglas R. Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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2
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Leutert M, Barente AS, Fukuda NK, Rodriguez-Mias RA, Villén J. The regulatory landscape of the yeast phosphoproteome. Nat Struct Mol Biol 2023; 30:1761-1773. [PMID: 37845410 PMCID: PMC10841839 DOI: 10.1038/s41594-023-01115-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023]
Abstract
The cellular ability to react to environmental fluctuations depends on signaling networks that are controlled by the dynamic activities of kinases and phosphatases. Here, to gain insight into these stress-responsive phosphorylation networks, we generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses in Saccharomyces cerevisiae exposed to 101 environmental and chemical perturbations. We report phosphosites on 59% of the yeast proteome, with 18% of the proteome harboring a phosphosite that is regulated within 5 min of stress exposure. We identify shared and perturbation-specific stress response programs, uncover loss of phosphorylation as an integral early event, and dissect the interconnected regulatory landscape of kinase-substrate networks, as we exemplify with target of rapamycin signaling. We further reveal functional organization principles of the stress-responsive phosphoproteome based on phosphorylation site motifs, kinase activities, subcellular localizations, shared functions and pathway intersections. This information-rich map of 25,000 regulated phosphosites advances our understanding of signaling networks.
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Affiliation(s)
- Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Anthony S Barente
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Noelle K Fukuda
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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3
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Barkova A, Adhya I, Conesa C, Asif-Laidin A, Bonnet A, Rabut E, Chagneau C, Lesage P, Acker J. A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition. Mob DNA 2022; 13:26. [PMCID: PMC9673352 DOI: 10.1186/s13100-022-00284-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Transposable elements are ubiquitous and play a fundamental role in shaping genomes during evolution. Since excessive transposition can be mutagenic, mechanisms exist in the cells to keep these mobile elements under control. Although many cellular factors regulating the mobility of the retrovirus-like transposon Ty1 in Saccharomyces cerevisiae have been identified in genetic screens, only very few of them interact physically with Ty1 integrase (IN).
Results
Here, we perform a proteomic screen to establish Ty1 IN interactome. Among the 265 potential interacting partners, we focus our study on the conserved CK2 kinase. We confirm the interaction between IN and CK2, demonstrate that IN is a substrate of CK2 in vitro and identify the modified residues. We find that Ty1 IN is phosphorylated in vivo and that these modifications are dependent in part on CK2. No significant change in Ty1 retromobility could be observed when we introduce phospho-ablative mutations that prevent IN phosphorylation by CK2 in vitro. However, the absence of CK2 holoenzyme results in a strong stimulation of Ty1 retrotransposition, characterized by an increase in Ty1 mRNA and protein levels and a high accumulation of cDNA.
Conclusion
Our study shows that Ty1 IN is phosphorylated, as observed for retroviral INs and highlights an important role of CK2 in the regulation of Ty1 retrotransposition. In addition, the proteomic approach enabled the identification of many new Ty1 IN interacting partners, whose potential role in the control of Ty1 mobility will be interesting to study.
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4
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Babu N, Bhat MY, John AE, Chatterjee A. The role of proteomics in the multiplexed analysis of gene alterations in human cancer. Expert Rev Proteomics 2021; 18:737-756. [PMID: 34602018 DOI: 10.1080/14789450.2021.1984884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Proteomics has played a pivotal role in identifying proteins perturbed in disease conditions when compared with healthy samples. Study of dysregulated proteins aids in identifying diagnostic markers and potential therapeutic targets. Cancer is an outcome of interplay of several such disarrayed proteins and molecular pathways which perturb cellular homeostasis, resulting in transformation. In this review, we discuss various facets of proteomic approaches, including tools and technological advancements, aiding in understanding differentially expressed molecules and signaling mechanisms. AREAS COVERED In this review, we have taken the approach of documenting the different methods of proteomic studies, ranging from labeling techniques, data analysis methods, and the nature of molecule detected. We summarize each technique and provide a glimpse of cancer research carried out using them, highlighting the advantages and drawbacks in comparison with others. Literature search using online resources, such as PubMed and Google Scholar were carried out for this approach. EXPERT OPINION Technological advancements in proteomics studies have come a long way from the study of two-dimensional mapping of proteins separated on gels in the early 1970s. Higher precision in molecular identification and quantification (high throughput), and greater number of samples analyzed have been the focus of researchers.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Mohd Younis Bhat
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
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5
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A global map of associations between types of protein posttranslational modifications and human genetic diseases. iScience 2021; 24:102917. [PMID: 34430807 PMCID: PMC8365368 DOI: 10.1016/j.isci.2021.102917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/27/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
There are >200 types of protein posttranslational modifications (PTMs) described in eukaryotes, each with unique proteome coverage and functions. We hypothesized that some genetic diseases may be caused by the removal of a specific type of PTMs by genomic variants and the consequent deregulation of particular functions. We collected >320,000 human PTMs representing 59 types and crossed them with >4M nonsynonymous DNA variants annotated with predicted pathogenicity and disease associations. We report >1.74M PTM-variant co-occurrences that an enrichment analysis distributed into 215 pairwise associations between 18 PTM types and 148 genetic diseases. Of them, 42% were not previously described. Removal of lysine acetylation exerts the most pronounced effect, and less studied PTM types such as S-glutathionylation or S-nitrosylation show relevance. Using pathogenicity predictions, we identified PTM sites that may produce particular diseases if prevented. Our results provide evidence of a substantial impact of PTM-specific removal on the pathogenesis of genetic diseases and phenotypes. There is an enrichment of disease-associated nsSNVs preventing certain types of PTMs We report 215 pairwise associations between 18 PTM types and 148 genetic diseases The removal of lysine acetylation exerts the most pronounced effect We report a set of PTM sites that may produce particular diseases if prevented
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Kervin TA, Wiseman BC, Overduin M. Phosphoinositide Recognition Sites Are Blocked by Metabolite Attachment. Front Cell Dev Biol 2021; 9:690461. [PMID: 34368138 PMCID: PMC8340361 DOI: 10.3389/fcell.2021.690461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022] Open
Abstract
Membrane readers take part in trafficking and signaling processes by localizing proteins to organelle surfaces and transducing molecular information. They accomplish this by engaging phosphoinositides (PIs), a class of lipid molecules which are found in different proportions in various cellular membranes. The prototypes are the PX domains, which exhibit a range of specificities for PIs. Our meta-analysis indicates that recognition of membranes by PX domains is specifically controlled by modification of lysine and arginine residues including acetylation, hydroxyisobutyrylation, glycation, malonylation, methylation and succinylation of sidechains that normally bind headgroups of phospholipids including organelle-specific PI signals. Such metabolite-modulated residues in lipid binding elements are named MET-stops here to highlight their roles as erasers of membrane reader functions. These modifications are concentrated in the membrane binding sites of half of all 49 PX domains in the human proteome and correlate with phosphoregulatory sites, as mapped using the Membrane Optimal Docking Area (MODA) algorithm. As these motifs are mutated and modified in various cancers and the responsible enzymes serve as potential drug targets, the discovery of MET-stops as a widespread inhibitory mechanism may aid in the development of diagnostics and therapeutics aimed at the readers, writers and erasers of the PI code.
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Affiliation(s)
- Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Brittany C Wiseman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Molecular and Cellular Biology, MacEwan University, Edmonton, AB, Canada.,SMALP Network, Edmonton, AB, Canada
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,SMALP Network, Edmonton, AB, Canada
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7
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Kervin TA, Overduin M. Regulation of the Phosphoinositide Code by Phosphorylation of Membrane Readers. Cells 2021; 10:cells10051205. [PMID: 34069055 PMCID: PMC8156045 DOI: 10.3390/cells10051205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 02/07/2023] Open
Abstract
The genetic code that dictates how nucleic acids are translated into proteins is well known, however, the code through which proteins recognize membranes remains mysterious. In eukaryotes, this code is mediated by hundreds of membrane readers that recognize unique phosphatidylinositol phosphates (PIPs), which demark organelles to initiate localized trafficking and signaling events. The only superfamily which specifically detects all seven PIPs are the Phox homology (PX) domains. Here, we reveal that throughout evolution, these readers are universally regulated by the phosphorylation of their PIP binding surfaces based on our analysis of existing and modelled protein structures and phosphoproteomic databases. These PIP-stops control the selective targeting of proteins to organelles and are shown to be key determinants of high-fidelity PIP recognition. The protein kinases responsible include prominent cancer targets, underscoring the critical role of regulated membrane readership.
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8
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Šoštarić N, van Noort V. Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions. PLoS Comput Biol 2021; 17:e1008988. [PMID: 33979327 PMCID: PMC8143416 DOI: 10.1371/journal.pcbi.1008988] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 05/24/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond. Proteins are a diverse set of biological molecules responsible for numerous functions within cells, such as obtaining energy from food or transport of small molecules, and many processes rely on interactions of specific proteins. Moreover, a single protein may acquire different roles depending on cellular requirements and as a response to changes in the environment. A commonly used way to quickly change protein’s function or activity is by introducing small chemical modifications on specific locations within the protein. These modifications can cause the protein to interact in a more or less stable way with other proteins. We have previously developed a computational pipeline for predicting the effect of modifications on interactions of proteins, and in this work we apply it to all yeast proteins with known structures. We find differences in effects on the binding for different types of modifications. Importantly, we demonstrate that the modifications far from the interaction interface also significantly contribute to binding due to their impact on protein’s shape, which is often neglected by other methods. This work contributes to our understanding of the modulation of protein interactions in yeast due to modifications, while our widely applicable method will allow similar investigations in other organisms.
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Affiliation(s)
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Leuven, Belgium
- Leiden University, Institute of Biology Leiden, Leiden, The Netherlands
- * E-mail:
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9
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Lin S, Wang C, Zhou J, Shi Y, Ruan C, Tu Y, Yao L, Peng D, Xue Y. EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. Brief Bioinform 2020; 22:298-307. [PMID: 32008039 DOI: 10.1093/bib/bbz169] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
As an important post-translational modification (PTM), protein phosphorylation is involved in the regulation of almost all of biological processes in eukaryotes. Due to the rapid progress in mass spectrometry-based phosphoproteomics, a large number of phosphorylation sites (p-sites) have been characterized but remain to be curated. Here, we briefly summarized the current progresses in the development of data resources for the collection, curation, integration and annotation of p-sites in eukaryotic proteins. Also, we designed the eukaryotic phosphorylation site database (EPSD), which contained 1 616 804 experimentally identified p-sites in 209 326 phosphoproteins from 68 eukaryotic species. In EPSD, we not only collected 1 451 629 newly identified p-sites from high-throughput (HTP) phosphoproteomic studies, but also integrated known p-sites from 13 additional databases. Moreover, we carefully annotated the phosphoproteins and p-sites of eight model organisms by integrating the knowledge from 100 additional resources that covered 15 aspects, including phosphorylation regulator, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, protein expression/proteomics and subcellular localization. We anticipate that the EPSD can serve as a useful resource for further analysis of eukaryotic phosphorylation. With a data volume of 14.1 GB, EPSD is free for all users at http://epsd.biocuckoo.cn/.
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Affiliation(s)
| | | | - Jiaqi Zhou
- Huazhong University of Science and Technology
| | - Ying Shi
- Huazhong University of Science and Technology
| | - Chen Ruan
- Huazhong University of Science and Technology
| | - Yiran Tu
- Huazhong University of Science and Technology
| | - Lan Yao
- Huazhong University of Science and Technology
| | - Di Peng
- Huazhong University of Science and Technology
| | - Yu Xue
- Huazhong University of Science and Technology
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10
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Janschitz M, Romanov N, Varnavides G, Hollenstein DM, Gérecová G, Ammerer G, Hartl M, Reiter W. Novel interconnections of HOG signaling revealed by combined use of two proteomic software packages. Cell Commun Signal 2019; 17:66. [PMID: 31208443 PMCID: PMC6572760 DOI: 10.1186/s12964-019-0381-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
Modern quantitative mass spectrometry (MS)-based proteomics enables researchers to unravel signaling networks by monitoring proteome-wide cellular responses to different stimuli. MS-based analysis of signaling systems usually requires an integration of multiple quantitative MS experiments, which remains challenging, given that the overlap between these datasets is not necessarily comprehensive. In a previous study we analyzed the impact of the yeast mitogen-activated protein kinase (MAPK) Hog1 on the hyperosmotic stress-affected phosphorylome. Using a combination of a series of hyperosmotic stress and kinase inhibition experiments, we identified a broad range of direct and indirect substrates of the MAPK. Here we re-evaluate this extensive MS dataset and demonstrate that a combined analysis based on two software packages, MaxQuant and Proteome Discoverer, increases the coverage of Hog1-target proteins by 30%. Using protein-protein proximity assays we show that the majority of new targets gained by this analysis are indeed Hog1-interactors. Additionally, kinetic profiles indicate differential trends of Hog1-dependent versus Hog1-independent phosphorylation sites. Our findings highlight a previously unrecognized interconnection between Hog1 signaling and the RAM signaling network, as well as sphingolipid homeostasis.
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Affiliation(s)
- Marion Janschitz
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
- Children’s Cancer Research Institute, St. Anna Kinderspital, Vienna, Austria
| | - Natalie Romanov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Current Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gina Varnavides
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
| | | | - Gabriela Gérecová
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
| | - Gustav Ammerer
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
| | - Markus Hartl
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Wolfgang Reiter
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
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11
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Phospho-peptide binding domains in S. cerevisiae model organism. Biochimie 2019; 163:117-127. [PMID: 31194995 DOI: 10.1016/j.biochi.2019.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
Abstract
Protein phosphorylation is one of the main mechanisms by which signals are transmitted in eukaryotic cells, and it plays a crucial regulatory role in almost all cellular processes. In yeast, more than half of the proteins are phosphorylated in at least one site, and over 20,000 phosphopeptides have been experimentally verified. However, the functional consequences of these phosphorylation events for most of the identified phosphosites are unknown. A family of protein interaction domains selectively recognises phosphorylated motifs to recruit regulatory proteins and activate signalling pathways. Nine classes of dedicated modules are coded by the yeast genome: 14-3-3, FHA, WD40, BRCT, WW, PBD, and SH2. The recognition specificity relies on a few residues on the target protein and has coevolved with kinase specificity. In the present study, we review the current knowledge concerning yeast phospho-binding domains and their networks. We emphasise the relevance of both positive and negative amino acid selection to orchestrate the highly regulated outcomes of inter- and intra-molecular interactions. Finally, we hypothesise that only a small fraction of yeast phosphorylation events leads to the creation of a docking site on the target molecule, while many have a direct effect on the protein or, as has been proposed, have no function at all.
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12
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Pascovici D, Wu JX, McKay MJ, Joseph C, Noor Z, Kamath K, Wu Y, Ranganathan S, Gupta V, Mirzaei M. Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. Int J Mol Sci 2018; 20:E16. [PMID: 30577541 PMCID: PMC6337699 DOI: 10.3390/ijms20010016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023] Open
Abstract
Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra-many of which likely harbour PTMs-through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation.
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Affiliation(s)
- Dana Pascovici
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Jemma X Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Chitra Joseph
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Zainab Noor
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Karthik Kamath
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yunqi Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
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13
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Šoštarić N, O'Reilly FJ, Giansanti P, Heck AJR, Gavin AC, van Noort V. Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes. Mol Cell Proteomics 2018; 17:2387-2401. [PMID: 30181345 DOI: 10.1074/mcp.ra118.000892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/27/2018] [Indexed: 01/18/2023] Open
Abstract
Protein post-translational modifications (PTMs) have an indispensable role in living cells as they expand chemical diversity of the proteome, providing a fine regulatory layer that can govern protein-protein interactions in changing environmental conditions. Here we investigated the effects of acetylation and phosphorylation on the stability of subunit interactions in purified Saccharomyces cerevisiae complexes, namely exosome, RNA polymerase II and proteasome. We propose a computational framework that consists of conformational sampling of the complexes by molecular dynamics simulations, followed by Gibbs energy calculation by MM/GBSA. After benchmarking against published tools such as FoldX and Mechismo, we could apply the framework for the first time on large protein assemblies with the aim of predicting the effects of PTMs located on interfaces of subunits on binding stability. We discovered that acetylation predominantly contributes to subunits' interactions in a locally stabilizing manner, while phosphorylation shows the opposite effect. Even though the local binding contributions of PTMs may be predictable to an extent, the long range effects and overall impact on subunits' binding were only captured because of our dynamical approach. Employing the developed, widely applicable workflow on other large systems will shed more light on the roles of PTMs in protein complex formation.
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Affiliation(s)
- Nikolina Šoštarić
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium
| | - Francis J O'Reilly
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Technical University of Berlin, Berlin, Germany
| | - Piero Giansanti
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium; Leiden University, Institute of Biology Leiden, Leiden, The Netherlands.
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14
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Apel AR, Hoban K, Chuartzman S, Tonikian R, Sidhu S, Schuldiner M, Wendland B, Prosser D. Syp1 regulates the clathrin-mediated and clathrin-independent endocytosis of multiple cargo proteins through a novel sorting motif. Mol Biol Cell 2017; 28:2434-2448. [PMID: 28701344 PMCID: PMC5576906 DOI: 10.1091/mbc.e15-10-0731] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 06/21/2017] [Accepted: 06/27/2017] [Indexed: 12/14/2022] Open
Abstract
Internalization of proteins from the plasma membrane (PM) allows for cell-surface composition regulation, signaling of network modulation, and nutrient uptake. Clathrin-mediated endocytosis (CME) is a major internalization route for PM proteins. During CME, endocytic adaptor proteins bind cargoes at the cell surface and link them to the PM and clathrin coat. Muniscins are a conserved family of endocytic adaptors, including Syp1 in budding yeast and its mammalian orthologue, FCHo1. These adaptors bind cargo via a C-terminal μ-homology domain (μHD); however, few cargoes exhibiting muniscin-dependent endocytosis have been identified, and the sorting sequence recognized by the µHD is unknown. To reveal Syp1 cargo-sorting motifs, we performed a phage display screen and used biochemical methods to demonstrate that the Syp1 µHD binds DxY motifs in the previously identified Syp1 cargo Mid2 and the v-SNARE Snc1. We also executed an unbiased visual screen, which identified the peptide transporter Ptr2 and the ammonium permease Mep3 as Syp1 cargoes containing DxY motifs. Finally, we determined that, in addition to regulating cargo entry through CME, Syp1 can promote internalization of Ptr2 through a recently identified clathrin-independent endocytic pathway that requires the Rho1 GTPase. These findings elucidate the mechanism of Syp1 cargo recognition and its role in trafficking.
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Affiliation(s)
| | - Kyle Hoban
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Silvia Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Raffi Tonikian
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Sachdev Sidhu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Beverly Wendland
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Derek Prosser
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
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15
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Guerreiro JF, Mira NP, Santos AXS, Riezman H, Sá-Correia I. Membrane Phosphoproteomics of Yeast Early Response to Acetic Acid: Role of Hrk1 Kinase and Lipid Biosynthetic Pathways, in Particular Sphingolipids. Front Microbiol 2017; 8:1302. [PMID: 28747907 PMCID: PMC5506226 DOI: 10.3389/fmicb.2017.01302] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/28/2017] [Indexed: 01/02/2023] Open
Abstract
Saccharomyces cerevisiae response and tolerance to acetic acid is critical in industrial biotechnology and in acidic food and beverages preservation. The HRK1 gene, encoding a protein kinase of unknown function belonging to the “Npr1-family” of kinases known to be involved in the regulation of plasma membrane transporters, is an important determinant of acetic acid tolerance. This study was performed to identify the alterations occurring in yeast membrane phosphoproteome profile during the adaptive early response to acetic acid stress (following 1 h of exposure to a sub-lethal inhibitory concentration; 50 mM at pH 4.0) and the effect of HRK1 expression on the phosphoproteome. Results from mass spectrometry analysis following the prefractionation and specific enrichment of phosphorylated peptides using TiO2 beads highlight the contribution of processes related with translation, protein folding and processing, transport, and cellular homeostasis in yeast response to acetic acid stress, with particular relevance for changes in phosphorylation of transport-related proteins, found to be highly dependent on the Hrk1 kinase. Twenty different phosphoproteins known to be involved in lipid and sterol metabolism were found to be differently phosphorylated in response to acetic acid stress, including several phosphopeptides that had not previously been described as being phosphorylated. The suggested occurrence of cellular lipid composition remodeling during the short term yeast response to acetic acid was confirmed: Hrk1 kinase-independent reduction in phytoceramide levels and a reduction in phosphatidylcholine and phosphatidylinositol levels under acetic acid stress in the more susceptible hrk1Δ strain were revealed by a lipidomic analysis.
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Affiliation(s)
- Joana F Guerreiro
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
| | - Nuno P Mira
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
| | - Aline X S Santos
- Department of Biochemistry, University of GenevaGeneva, Switzerland
| | - Howard Riezman
- Department of Biochemistry, University of GenevaGeneva, Switzerland
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
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16
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Vlastaridis P, Kyriakidou P, Chaliotis A, Van de Peer Y, Oliver SG, Amoutzias GD. Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes. Gigascience 2017; 6:1-11. [PMID: 28327990 PMCID: PMC5466708 DOI: 10.1093/gigascience/giw015] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/20/2016] [Indexed: 12/03/2022] Open
Abstract
Background Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and p-sites for four eukaryotes (human, mouse, Arabidopsis, and yeast). Results In all, 187 HTP phosphoproteomic datasets were filtered, compiled, and studied along with two low-throughput (LTP) compendia. Estimates of the number of phosphoproteins and p-sites were inferred by two methods: Capture-Recapture, and fitting the saturation curve of cumulative redundant vs. cumulative non-redundant phosphoproteins/p-sites. Estimates were also adjusted for different levels of noise within the individual datasets and other confounding factors. We estimate that in total, 13 000, 11 000, and 3000 phosphoproteins and 230 000, 156 000, and 40 000 p-sites exist in human, mouse, and yeast, respectively, whereas estimates for Arabidopsis were not as reliable. Conclusions Most of the phosphoproteins have been discovered for human, mouse, and yeast, while the dataset for Arabidopsis is still far from complete. The datasets for p-sites are not as close to saturation as those for phosphoproteins. Integration of the LTP data suggests that current HTP phosphoproteomics appears to be capable of capturing 70 % to 95 % of total phosphoproteins, but only 40 % to 60 % of total p-sites.
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Affiliation(s)
- Panayotis Vlastaridis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, 41500, Greece
| | - Pelagia Kyriakidou
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, 41500, Greece
| | - Anargyros Chaliotis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, 41500, Greece
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Technologiepark 927, B-9052 Ghent, Belgium.,Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Stephen G Oliver
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Grigoris D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larisa, 41500, Greece
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17
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Cui TZ, Peterson TA, Burd CG. A CDC25 family protein phosphatase gates cargo recognition by the Vps26 retromer subunit. eLife 2017; 6. [PMID: 28362258 PMCID: PMC5409824 DOI: 10.7554/elife.24126] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/30/2017] [Indexed: 01/14/2023] Open
Abstract
We describe a regulatory mechanism that controls the activity of retromer, an evolutionarily conserved sorting device that orchestrates cargo export from the endosome. A spontaneously arising mutation that activates the yeast (Saccharomyces cerevisiae) CDC25 family phosphatase, Mih1, results in accelerated turnover of a subset of endocytosed plasma membrane proteins due to deficient sorting into a retromer-mediated recycling pathway. Mih1 directly modulates the phosphorylation state of the Vps26 retromer subunit; mutations engineered to mimic these states modulate the binding affinities of Vps26 for a retromer cargo, resulting in corresponding changes in cargo sorting at the endosome. The results suggest that a phosphorylation-based gating mechanism controls cargo selection by yeast retromer, and they establish a functional precedent for CDC25 protein phosphatases that lies outside of their canonical role in regulating cell cycle progression.
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Affiliation(s)
- Tie-Zhong Cui
- Department of Cell Biology, Yale School of Medicine, New Haven, United States
| | - Tabitha A Peterson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Christopher G Burd
- Department of Cell Biology, Yale School of Medicine, New Haven, United States
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18
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Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast. BMC SYSTEMS BIOLOGY 2017; 11:38. [PMID: 28298210 PMCID: PMC5353956 DOI: 10.1186/s12918-017-0418-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/08/2017] [Indexed: 11/10/2022]
Abstract
Background Kinases and phosphatases (KP) form complex self-regulating networks essential for cellular signal processing. In spite of having a wealth of data about interactions among KPs and their substrates, we have very limited models of the structures of the directed networks they form and consequently our ability to formulate hypotheses about how their structure determines the flow of information in these networks is restricted. Results We assembled and studied the largest bona fide kinase-phosphatase network (KP-Net) known to date for the yeast Saccharomyces cerevisiae. Application of the vertex sort (VS) algorithm on the KP-Net allowed us to elucidate its hierarchical structure in which nodes are sorted into top, core and bottom layers, forming a bow tie structure with a strongly connected core layer. Surprisingly, phosphatases tend to sort into the top layer, implying they are less regulated by phosphorylation than kinases. Superposition of the widest range of KP biological properties over the KP-Net hierarchy shows that core layer KPs: (i), receive the largest number of inputs; (ii), form bottlenecks implicated in multiple pathways and in decision-making; (iii), and are among the most regulated KPs both temporally and spatially. Moreover, top layer KPs are more abundant and less noisy than those in the bottom layer. Finally, we showed that the VS algorithm depends on node degrees without biasing the biological results of the sorted network. The VS algorithm is available as an R package (https://cran.r-project.org/web/packages/VertexSort/index.html). Conclusions The KP-Net model we propose possesses a bow tie hierarchical structure in which the top layer appears to ensure highest fidelity and the core layer appears to mediate signal integration and cell state-dependent signal interpretation. Our model of the yeast KP-Net provides both functional insight into its organization as we understand today and a framework for future investigation of information processing in yeast and eukaryotes in general. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0418-0) contains supplementary material, which is available to authorized users.
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19
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Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library. G3-GENES GENOMES GENETICS 2017; 7:911-921. [PMID: 28122947 PMCID: PMC5345721 DOI: 10.1534/g3.116.038471] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Kinases and transcription factors (TFs) are key modulators of important signaling pathways and their activities underlie the proper function of many basic cellular processes such as cell division, differentiation, and development. Changes in kinase and TF dosage are often associated with disease, yet a systematic assessment of the cellular phenotypes caused by the combined perturbation of kinases and TFs has not been undertaken. We used a reverse-genetics approach to study the phenotypic consequences of kinase and TF overexpression (OE) in the budding yeast, Saccharomyces cerevisiae. We constructed a collection of strains expressing stably integrated inducible alleles of kinases and TFs and used a variety of assays to characterize the phenotypes caused by TF and kinase OE. We used the Synthetic Genetic Array (SGA) method to examine dosage-dependent genetic interactions (GIs) between 239 gain-of-function (OE) alleles of TFs and six loss-of-function (LOF) and seven OE kinase alleles, the former identifying Synthetic Dosage Lethal (SDL) interactions and the latter testing a GI we call Double Dosage Lethality (DDL). We identified and confirmed 94 GIs between 65 OE alleles of TFs and 9 kinase alleles. Follow-up experiments validated regulatory relationships between genetically interacting pairs (Cdc28–Stb1 and Pho85–Pdr1), suggesting that GI studies involving OE alleles of regulatory proteins will be a rich source of new functional information.
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20
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Kanshin E, Giguère S, Jing C, Tyers M, Thibault P. Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates. Mol Cell Proteomics 2017; 16:786-798. [PMID: 28265048 DOI: 10.1074/mcp.m116.066233] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/13/2017] [Indexed: 12/12/2022] Open
Abstract
Mass spectrometry allows quantification of tens of thousands of phosphorylation sites from minute amounts of cellular material. Despite this wealth of information, our understanding of phosphorylation-based signaling is limited, in part because it is not possible to deconvolute substrate phosphorylation that is directly mediated by a particular kinase versus phosphorylation that is mediated by downstream kinases. Here, we describe a framework for assignment of direct in vivo kinase substrates using a combination of selective chemical inhibition, quantitative phosphoproteomics, and machine learning techniques. Our workflow allows classification of phosphorylation events following inhibition of an analog-sensitive kinase into kinase-independent effects of the inhibitor, direct effects on cognate substrates, and indirect effects mediated by downstream kinases or phosphatases. We applied this method to identify many direct targets of Cdc28 and Snf1 kinases in the budding yeast Saccharomyces cerevisiae Global phosphoproteome analysis of acute time-series demonstrated that dephosphorylation of direct kinase substrates occurs more rapidly compared with indirect substrates, both after inhibitor treatment and under a physiological nutrient shift in wt cells. Mutagenesis experiments revealed a high proportion of functionally relevant phosphorylation sites on Snf1 targets. For example, Snf1 itself was inhibited through autophosphorylation on Ser391 and new phosphosites were discovered that modulate the activity of the Reg1 regulatory subunit of the Glc7 phosphatase and the Gal83 β-subunit of SNF1 complex. This methodology applies to any kinase for which a functional analog sensitive version can be constructed to facilitate the dissection of the global phosphorylation network.
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Affiliation(s)
- Evgeny Kanshin
- From the ‡Institute for Research in Immunology and Cancer
| | | | - Cheng Jing
- From the ‡Institute for Research in Immunology and Cancer
| | - Mike Tyers
- From the ‡Institute for Research in Immunology and Cancer, .,§Department of Medicine
| | - Pierre Thibault
- From the ‡Institute for Research in Immunology and Cancer, .,¶Department of Chemistry, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, Québec, H3C 3J7, Canada
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21
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Abstract
Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecular machinery required to introduce these modifications into tRNA posttranscriptionally and discuss how posttranslational regulation may affect the activity of the modifying enzymes. We highlight the activity of anticodon specific RNases that target U34 containing tRNA. Finally, we discuss how defects in wobble uridine modifications lead to phenotypes in different species. Importantly, this review will mainly focus on the cytoplasmic tRNAs of eukaryotes. A recent review has extensively covered their bacterial and mitochondrial counterparts.1
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Affiliation(s)
- Raffael Schaffrath
- a Institut für Biologie, FG Mikrobiologie , Universität Kassel , Germany
| | - Sebastian A Leidel
- b Max Planck Institute for Molecular Biomedicine , Germany.,c Cells-in-Motion Cluster of Excellence , University of Münster , Münster , Germany.,d Medical Faculty , University of Münster , Albert-Schweitzer-Campus 1, Münster , Germany
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22
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Schummer A, Fischer S, Oeljeklaus S, Warscheid B. Study of Peroxisomal Protein Phosphorylation by Functional Proteomics. Methods Mol Biol 2017; 1595:267-289. [PMID: 28409471 DOI: 10.1007/978-1-4939-6937-1_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Reversible protein phosphorylation is a frequently occurring posttranslational modification mediated by protein kinases and phosphatases that plays an essential role in the regulation of a large number of cellular processes. Evidence is accumulating that protein phosphorylation is also an important mechanism governing processes associated with peroxisome biology. For an improved and detailed understanding of these processes and their regulation it is therefore crucial to study phosphorylation of peroxisome-associated proteins and to determine the phosphorylated amino acid(s). To place peroxisome-related processes into a larger, cellular context, it is further required to identify the kinases and phosphatases catalyzing phosphorylation and dephosphorylation events in peroxisomal proteins. We here provide a strategy for the targeted analysis of peroxisomal phosphoproteins of Saccharomyces cerevisiae combining affinity purification of epitope-tagged peroxisomal proteins with Phos-tag SDS-PAGE and high-resolution mass spectrometry (MS) for the identification and precise localization of in vivo phosphosites. Furthermore, we describe a protocol for an MS-based in vitro kinase assay using recombinant peroxisomal proteins and a selected kinase facilitating the site-resolved analysis of kinase-substrate relationships.
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Affiliation(s)
- Andreas Schummer
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Sven Fischer
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
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23
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Korkuć P, Walther D. Towards understanding the crosstalk between protein post-translational modifications: Homo- and heterotypic PTM pair distances on protein surfaces are not random. Proteins 2016; 85:78-92. [DOI: 10.1002/prot.25200] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/29/2016] [Accepted: 10/20/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Paula Korkuć
- Max Planck Institute for Molecular Plant Physiology; Am Mühlenberg 1 Potsdam-Golm 14476 Germany
| | - Dirk Walther
- Max Planck Institute for Molecular Plant Physiology; Am Mühlenberg 1 Potsdam-Golm 14476 Germany
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24
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Patrick R, Horin C, Kobe B, Cao KAL, Bodén M. Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1599-608. [PMID: 27507704 DOI: 10.1016/j.bbapap.2016.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/08/2016] [Accepted: 08/03/2016] [Indexed: 01/17/2023]
Abstract
Identifying kinase substrates and the specific phosphorylation sites they regulate is an important factor in understanding protein function regulation and signalling pathways. Computational prediction of kinase targets - assigning kinases to putative substrates, and selecting from protein sequence the sites that kinases can phosphorylate - requires the consideration of both the cellular context that kinases operate in, as well as their binding affinity. This consideration enables investigation of how phosphorylation influences a range of biological processes. We report here a novel probabilistic model for classifying kinase-specific phosphorylation sites from sequence across three model organisms: human, mouse and yeast. The model incorporates position-specific amino acid frequencies, and counts of co-occurring amino acids from kinase binding sites. We show how this model can be seamlessly integrated with protein interactions and cell-cycle abundance profiles. When evaluating the prediction accuracy of our method, PhosphoPICK, on an independent hold-out set of kinase-specific phosphorylation sites, it achieved an average specificity of 97%, with 32% sensitivity. We compared PhosphoPICK's ability, through cross-validation, to predict kinase-specific phosphorylation sites with alternative methods, and show that at high levels of specificity PhosphoPICK obtains greater sensitivity for most comparisons made. We investigated the relationship between kinase-specific phosphorylation sites and nuclear localisation signals. We show that kinases PKA, Akt1 and AurB have an over-representation of predicted binding sites at particular positions downstream from predicted nuclear localisation signals, demonstrating an important role for these kinases in regulating the nuclear import of proteins. PhosphoPICK is freely available as a web-service at http://bioinf.scmb.uq.edu.au/phosphopick.
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Affiliation(s)
- Ralph Patrick
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Australia.
| | - Coralie Horin
- Polytech Nice-Sophia, Université Nice Sophia-Antipolis, Nice 06103, France
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia 4072, Australia
| | - Kim-Anh Lê Cao
- The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia 4072, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia
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25
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The yeast Hsp70 homolog Ssb: a chaperone for general de novo protein folding and a nanny for specific intrinsically disordered protein domains. Curr Genet 2016; 63:9-13. [PMID: 27230907 PMCID: PMC5274638 DOI: 10.1007/s00294-016-0610-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 12/17/2022]
Abstract
Activation of the heterotrimeric kinase SNF1 via phosphorylation of a specific residue within the α subunit is essential for the release from glucose repression in the yeast Saccharomyces cerevisiae. When glucose is available, SNF1 is maintained in the dephosphorylated, inactive state by the phosphatase Glc7-Reg1. Recent findings suggest that Bmh and Ssb combine their unique client-binding properties to interact with the regulatory region of the SNF1 α subunit and by that stabilize a conformation of SNF1, which is accessible for Glc7-Reg1-dependent dephosphorylation. Together, the 14-3-3 protein Bmh and the Hsp70 homolog Ssb comprise a novel chaperone module, which is required to maintain proper glucose repression in the yeast S. cerevisiae.
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26
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Ullah S, Lin S, Xu Y, Deng W, Ma L, Zhang Y, Liu Z, Xue Y. dbPAF: an integrative database of protein phosphorylation in animals and fungi. Sci Rep 2016; 6:23534. [PMID: 27010073 PMCID: PMC4806352 DOI: 10.1038/srep23534] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/08/2016] [Indexed: 12/26/2022] Open
Abstract
Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.
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Affiliation(s)
- Shahid Ullah
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaofeng Lin
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yang Xu
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wankun Deng
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lili Ma
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ying Zhang
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zexian Liu
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu Xue
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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27
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Swaney DL, Villén J. Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry. Cold Spring Harb Protoc 2016; 2016:pdb.top077743. [PMID: 26933252 DOI: 10.1101/pdb.top077743] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The addition of posttranslational modifications (PTMs) to proteins is an influential mechanism to temporally control protein function and ultimately regulate entire cellular processes. Most PTMs are present at low stoichiometry and abundance, which limits their detection when analyzing whole cell lysates. PTM purification methods are thus required to comprehensively characterize the presence and dynamics of PTMs using mass spectrometry-based proteomics approaches. Here we describe several of the most influential PTMs and discuss the fundamentals of proteomics experiments and PTM purification methods.
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Affiliation(s)
- Danielle L Swaney
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
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28
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Oeljeklaus S, Schummer A, Mastalski T, Platta HW, Warscheid B. Regulation of peroxisome dynamics by phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1027-37. [PMID: 26775584 DOI: 10.1016/j.bbamcr.2015.12.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/22/2015] [Accepted: 12/24/2015] [Indexed: 12/31/2022]
Abstract
Peroxisomes are highly dynamic organelles that can rapidly change in size, abundance, and protein content in response to alterations in nutritional and other environmental conditions. These dynamic changes in peroxisome features, referred to as peroxisome dynamics, rely on the coordinated action of several processes of peroxisome biogenesis. Revealing the regulatory mechanisms of peroxisome dynamics is an emerging theme in cell biology. These mechanisms are inevitably linked to and synchronized with the biogenesis and degradation of peroxisomes. To date, the key players and basic principles of virtually all steps in the peroxisomal life cycle are known, but regulatory mechanisms remained largely elusive. A number of recent studies put the spotlight on reversible protein phosphorylation for the control of peroxisome dynamics and highlighted peroxisomes as hubs for cellular signal integration and regulation. Here, we will present and discuss the results of several studies performed using yeast and mammalian cells that convey a sense of the impact protein phosphorylation may have on the modulation of peroxisome dynamics by regulating peroxisomal matrix and membrane protein import, proliferation, inheritance, and degradation. We further put forward the idea to make use of current data on phosphorylation sites of peroxisomal and peroxisome-associated proteins reported in advanced large-scale phosphoproteomic studies.
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Affiliation(s)
- Silke Oeljeklaus
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Schummer
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Mastalski
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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Knutsen JHJ, Rødland GE, Bøe CA, Håland TW, Sunnerhagen P, Grallert B, Boye E. Stress-induced inhibition of translation independently of eIF2α phosphorylation. J Cell Sci 2015; 128:4420-7. [PMID: 26493332 PMCID: PMC4712817 DOI: 10.1242/jcs.176545] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/28/2015] [Indexed: 01/21/2023] Open
Abstract
Exposure of fission yeast cells to ultraviolet (UV) light leads to inhibition of translation and phosphorylation of the eukaryotic initiation factor-2α (eIF2α). This phosphorylation is a common response to stress in all eukaryotes. It leads to inhibition of translation at the initiation stage and is thought to be the main reason why stressed cells dramatically reduce protein synthesis. Phosphorylation of eIF2α has been taken as a readout for downregulation of translation, but the role of eIF2α phosphorylation in the downregulation of general translation has not been much investigated. We show here that UV-induced global inhibition of translation in fission yeast cells is independent of eIF2α phosphorylation and the eIF2α kinase general control nonderepressible-2 protein (Gcn2). Also, in budding yeast and mammalian cells, the UV-induced translational depression is largely independent of GCN2 and eIF2α phosphorylation. Furthermore, exposure of fission yeast cells to oxidative stress generated by hydrogen peroxide induced an inhibition of translation that is also independent of Gcn2 and of eIF2α phosphorylation. Our findings show that stress-induced translational inhibition occurs through an unknown mechanism that is likely to be conserved through evolution. Summary: In contrast to textbook knowledge, the phosphorylation of translation initiation factor eIF2α is not required for UV-induced inhibition of protein synthesis, which we show in three different cell types.
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Affiliation(s)
| | - Gro Elise Rødland
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Cathrine Arnason Bøe
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Tine Weise Håland
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Per Sunnerhagen
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Erik Boye
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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Kanshin E, Kubiniok P, Thattikota Y, D'Amours D, Thibault P. Phosphoproteome dynamics of Saccharomyces cerevisiae under heat shock and cold stress. Mol Syst Biol 2015; 11:813. [PMID: 26040289 PMCID: PMC4501848 DOI: 10.15252/msb.20156170] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ability of cells and organisms to survive and function through changes in temperature evolved from their specific adaptations to nonoptimal growth conditions. Responses to elevated temperatures have been studied in yeast and other model organisms using transcriptome profiling and provided valuable biological insights on molecular mechanisms involved in stress tolerance and adaptation to adverse environment. In contrast, little is known about rapid signaling events associated with changes in temperature. To gain a better understanding of global changes in protein phosphorylation in response to heat and cold, we developed a high temporal resolution phosphoproteomics protocol to study cell signaling in Saccharomyces cerevisiae. The method allowed for quantitative analysis of phosphodynamics on 2,777 phosphosites from 1,228 proteins. The correlation of kinetic profiles between kinases and their substrates provided a predictive tool to identify new putative substrates for kinases such as Cdc28 and PKA. Cell cycle analyses revealed that the increased phosphorylation of Cdc28 at its inhibitory site Y19 during heat shock is an adaptive response that delays cell cycle progression under stress conditions. The cellular responses to heat and cold were associated with extensive changes in phosphorylation on proteins implicated in transcription, protein folding and degradation, cell cycle regulation and morphogenesis.
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Affiliation(s)
- Evgeny Kanshin
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Peter Kubiniok
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada Department of Chemistry, Université de Montréal, Montréal, QC, Canada
| | - Yogitha Thattikota
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Damien D'Amours
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada Department of Chemistry, Université de Montréal, Montréal, QC, Canada Department of Biochemistry, Université de Montréal, Montréal, QC, Canada
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31
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Lee J, Moir RD, Willis IM. Differential Phosphorylation of RNA Polymerase III and the Initiation Factor TFIIIB in Saccharomyces cerevisiae. PLoS One 2015; 10:e0127225. [PMID: 25970584 PMCID: PMC4430316 DOI: 10.1371/journal.pone.0127225] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
The production of ribosomes and tRNAs for protein synthesis has a high energetic cost and is under tight transcriptional control to ensure that the level of RNA synthesis is balanced with nutrient availability and the prevailing environmental conditions. In the RNA polymerase (pol) III system in yeast, nutrients and stress affect transcription through a bifurcated signaling pathway in which protein kinase A (PKA) and TORC1 activity directly or indirectly, through downstream kinases, alter the phosphorylation state and function of the Maf1 repressor and Rpc53, a TFIIF-like subunit of the polymerase. However, numerous lines of evidence suggest greater complexity in the regulatory network including the phosphoregulation of other pol III components. To address this issue, we systematically examined all 17 subunits of pol III along with the three subunits of the initiation factor TFIIIB for evidence of differential phosphorylation in response to inhibition of TORC1. A relatively high stoichiometry of phosphorylation was observed for several of these proteins and the Rpc82 subunit of the polymerase and the Bdp1 subunit of TFIIIB were found to be differentially phosphorylated. Bdp1 is phosphorylated on four major sites during exponential growth and the protein is variably dephosphorylated under conditions that inhibit tRNA gene transcription. PKA, the TORC1-regulated kinase Sch9 and protein kinase CK2 are all implicated in the phosphorylation of Bdp1. Alanine substitutions at the four phosphosites cause hyper-repression of transcription indicating that phosphorylation of Bdp1 opposes Maf1-mediated repression. The new findings suggest an integrated regulatory model for signaling events controlling pol III transcription.
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Affiliation(s)
- Jaehoon Lee
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Robyn D. Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (RDM); (IMW)
| | - Ian M. Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (RDM); (IMW)
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Peng Y, Grassart A, Lu R, Wong CCL, Yates J, Barnes G, Drubin DG. Casein kinase 1 promotes initiation of clathrin-mediated endocytosis. Dev Cell 2015; 32:231-40. [PMID: 25625208 DOI: 10.1016/j.devcel.2014.11.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 06/11/2014] [Accepted: 11/10/2014] [Indexed: 12/22/2022]
Abstract
In budding yeast, over 60 proteins functioning in at least five modules are recruited to endocytic sites with predictable order and timing. However, how sites of clathrin-mediated endocytosis are initiated and stabilized is not well understood. Here, the casein kinase 1 (CK1) Hrr25 is shown to be an endocytic protein and to be among the earliest proteins to appear at endocytic sites. Hrr25 absence or overexpression decreases or increases the rate of endocytic site initiation, respectively. Ede1, an early endocytic Eps15-like protein important for endocytic initiation, is an Hrr25 target and is required for Hrr25 recruitment to endocytic sites. Hrr25 phosphorylation of Ede1 is required for Hrr25-Ede1 interaction and promotes efficient initiation of endocytic sites. These observations indicate that Hrr25 kinase and Ede1 cooperate to initiate and stabilize endocytic sites. Analysis of the mammalian homologs CK1δ/ε suggests a conserved role for these protein kinases in endocytic site initiation and stabilization.
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Affiliation(s)
- Yutian Peng
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexandre Grassart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rebecca Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Catherine C L Wong
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Georjana Barnes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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33
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Piya G, Mueller EN, Haas HK, Ghospurkar PL, Wilson TM, Jensen JL, Colbert CL, Haring SJ. Characterization of the interaction between Rfa1 and Rad24 in Saccharomyces cerevisiae. PLoS One 2015; 10:e0116512. [PMID: 25719602 PMCID: PMC4342240 DOI: 10.1371/journal.pone.0116512] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/10/2014] [Indexed: 11/22/2022] Open
Abstract
Maintaining the integrity of the genome requires the high fidelity duplication of the genome and the ability of the cell to recognize and repair DNA lesions. The heterotrimeric single stranded DNA (ssDNA) binding complex Replication Protein A (RPA) is central to multiple DNA processes, which are coordinated by RPA through its ssDNA binding function and through multiple protein-protein interactions. Many RPA interacting proteins have been reported through large genetic and physical screens; however, the number of interactions that have been further characterized is limited. To gain a better understanding of how RPA functions in DNA replication, repair, and cell cycle regulation and to identify other potential functions of RPA, a yeast two hybrid screen was performed using the yeast 70 kDa subunit, Replication Factor A1 (Rfa1), as a bait protein. Analysis of 136 interaction candidates resulted in the identification of 37 potential interacting partners, including the cell cycle regulatory protein and DNA damage clamp loader Rad24. The Rfa1-Rad24 interaction is not dependent on ssDNA binding. However, this interaction appears affected by DNA damage. The regions of both Rfa1 and Rad24 important for this interaction were identified, and the region of Rad24 identified is distinct from the region reported to be important for its interaction with Rfc2 5. This suggests that Rad24-Rfc2-5 (Rad24-RFC) recruitment to DNA damage substrates by RPA occurs, at least partially, through an interaction between the N terminus of Rfa1 and the C terminus of Rad24. The predicted structure and location of the Rad24 C-terminus is consistent with a model in which RPA interacts with a damage substrate, loads Rad24-RFC at the 5’ junction, and then releases the Rad24-RFC complex to allow for proper loading and function of the DNA damage clamp.
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Affiliation(s)
- Gunjan Piya
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Erica N. Mueller
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Heather K. Haas
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Padmaja L. Ghospurkar
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Timothy M. Wilson
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Jaime L. Jensen
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Christopher L. Colbert
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
- Interdisciplinary Program in Cellular and Molecular Biology, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Stuart J. Haring
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
- Interdisciplinary Program in Cellular and Molecular Biology, North Dakota State University, Fargo, ND, 58108, United States of America
- * E-mail:
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34
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The DNA damage response and checkpoint adaptation in Saccharomyces cerevisiae: distinct roles for the replication protein A2 (Rfa2) N-terminus. Genetics 2015; 199:711-27. [PMID: 25595672 PMCID: PMC4349066 DOI: 10.1534/genetics.114.173211] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In response to DNA damage, two general but fundamental processes occur in the cell: (1) a DNA lesion is recognized and repaired, and (2) concomitantly, the cell halts the cell cycle to provide a window of opportunity for repair to occur. An essential factor for a proper DNA-damage response is the heterotrimeric protein complex Replication Protein A (RPA). Of particular interest is hyperphosphorylation of the 32-kDa subunit, called RPA2, on its serine/threonine-rich amino (N) terminus following DNA damage in human cells. The unstructured N-terminus is often referred to as the phosphorylation domain and is conserved among eukaryotic RPA2 subunits, including Rfa2 in Saccharomyces cerevisiae. An aspartic acid/alanine-scanning and genetic interaction approach was utilized to delineate the importance of this domain in budding yeast. It was determined that the Rfa2 N-terminus is important for a proper DNA-damage response in yeast, although its phosphorylation is not required. Subregions of the Rfa2 N-terminus important for the DNA-damage response were also identified. Finally, an Rfa2 N-terminal hyperphosphorylation-mimetic mutant behaves similarly to another Rfa1 mutant (rfa1-t11) with respect to genetic interactions, DNA-damage sensitivity, and checkpoint adaptation. Our data indicate that post-translational modification of the Rfa2 N-terminus is not required for cells to deal with "repairable" DNA damage; however, post-translational modification of this domain might influence whether cells proceed into M-phase in the continued presence of unrepaired DNA lesions as a "last-resort" mechanism for cell survival.
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Torii M, Arighi CN, Li G, Wang Q, Wu CH, Vijay-Shanker K. RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:17-29. [PMID: 26357075 PMCID: PMC4568560 DOI: 10.1109/tcbb.2014.2372765] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We introduce RLIMS-P version 2.0, an enhanced rule-based information extraction (IE) system for mining kinase, substrate, and phosphorylation site information from scientific literature. Consisting of natural language processing and IE modules, the system has integrated several new features, including the capability of processing full-text articles and generalizability towards different post-translational modifications (PTMs). To evaluate the system, sets of abstracts and full-text articles, containing a variety of textual expressions, were annotated. On the abstract corpus, the system achieved F-scores of 0.91, 0.92, and 0.95 for kinases, substrates, and sites, respectively. The corresponding scores on the full-text corpus were 0.88, 0.91, and 0.92. It was additionally evaluated on the corpus of the 2013 BioNLP-ST GE task, and achieved an F-score of 0.87 for the phosphorylation core task, improving upon the results previously reported on the corpus. Full-scale processing of all abstracts in MEDLINE and all articles in PubMed Central Open Access Subset has demonstrated scalability for mining rich information in literature, enabling its adoption for biocuration and for knowledge discovery. The new system is generalizable and it will be adapted to tackle other major PTM types. RLIMS-P 2.0 online system is available online (http://proteininformationresource.org/rlimsp/) and the developed corpora are available from iProLINK (http://proteininformationresource.org/iprolink/).
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Affiliation(s)
- Manabu Torii
- Medical Informatics Group, Kaiser Permanente Southern California, 11975 El Camino Real, San Diego, CA 92130
| | - Cecilia N. Arighi
- Center for Bioinformatics & Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711
| | - Gang Li
- Center for Bioinformatics & Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 1971
| | - Qinghua Wang
- Center for Bioinformatics & Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711
| | - Cathy H. Wu
- Center for Bioinformatics & Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711
| | - K. Vijay-Shanker
- Department of Computer and Information Sciences, University of Delaware, 101 Smith Hall, Newark, DE 19716
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Trost B, Napper S, Kusalik A. Case study: using sequence homology to identify putative phosphorylation sites in an evolutionarily distant species (honeybee). Brief Bioinform 2014; 16:820-9. [PMID: 25380664 DOI: 10.1093/bib/bbu040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Indexed: 01/27/2023] Open
Abstract
The majority of scientific resources are devoted to studying a relatively small number of model species, meaning that the ability to translate knowledge across species is of considerable importance. Obtaining species-specific knowledge enables targeted investigations of the biology and pathobiology of a particular species, and facilitates comparative analyses. Phosphorylation is the most widespread posttranslational modification in eukaryotes, and although many phosphorylation sites have been experimentally identified for some species, little or no data are available for others. Using the honeybee as a test organism, this case study illustrates the process of using protein sequence homology to identify putative phosphorylation sites in a species of interest using experimentally determined sites from other species. A number of issues associated with this process are examined and discussed. Several databases of experimentally determined phosphorylation sites exist; however, it can be difficult for the nonspecialist to ascertain how their contents compare. Thus, this case study assesses the content and comparability of several phosphorylation site databases. Additional issues examined include the efficacy of homology-based phosphorylation site prediction, the impact of the level of evolutionary relatedness between species in making these predictions, the ability to translate knowledge of phosphorylation sites across large evolutionary distances and the criteria that should be used in selecting probable phosphorylation sites in the species of interest. Although focusing on phosphorylation, the issues discussed here also apply to the homology-based cross-species prediction of other posttranslational modifications, as well as to sequence motifs in general.
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37
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Hulsman M, Dimitrakopoulos C, de Ridder J. Scale-space measures for graph topology link protein network architecture to function. ACTA ACUST UNITED AC 2014; 30:i237-45. [PMID: 24931989 PMCID: PMC4058939 DOI: 10.1093/bioinformatics/btu283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Motivation: The network architecture of physical protein interactions is an important determinant for the molecular functions that are carried out within each cell. To study this relation, the network architecture can be characterized by graph topological characteristics such as shortest paths and network hubs. These characteristics have an important shortcoming: they do not take into account that interactions occur across different scales. This is important because some cellular functions may involve a single direct protein interaction (small scale), whereas others require more and/or indirect interactions, such as protein complexes (medium scale) and interactions between large modules of proteins (large scale). Results: In this work, we derive generalized scale-aware versions of known graph topological measures based on diffusion kernels. We apply these to characterize the topology of networks across all scales simultaneously, generating a so-called graph topological scale-space. The comprehensive physical interaction network in yeast is used to show that scale-space based measures consistently give superior performance when distinguishing protein functional categories and three major types of functional interactions—genetic interaction, co-expression and perturbation interactions. Moreover, we demonstrate that graph topological scale spaces capture biologically meaningful features that provide new insights into the link between function and protein network architecture. Availability and implementation: MatlabTM code to calculate the scale-aware topological measures (STMs) is available at http://bioinformatics.tudelft.nl/TSSA Contact:j.deridder@tudelft.nl Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marc Hulsman
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2628CD Delft, The Netherlands
| | - Christos Dimitrakopoulos
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2628CD Delft, The Netherlands
| | - Jeroen de Ridder
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2628CD Delft, The Netherlands
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Eleutherio E, Panek A, De Mesquita JF, Trevisol E, Magalhães R. Revisiting yeast trehalose metabolism. Curr Genet 2014; 61:263-74. [DOI: 10.1007/s00294-014-0450-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/21/2014] [Accepted: 08/26/2014] [Indexed: 12/16/2022]
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39
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Torii M, Li G, Li Z, Oughtred R, Diella F, Celen I, Arighi CN, Huang H, Vijay-Shanker K, Wu CH. RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau081. [PMID: 25122463 PMCID: PMC4131691 DOI: 10.1093/database/bau081] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein phosphorylation is central to the regulation of most aspects of cell function. Given its importance, it has been the subject of active research as well as the focus of curation in several biological databases. We have developed Rule-based Literature Mining System for protein Phosphorylation (RLIMS-P), an online text-mining tool to help curators identify biomedical research articles relevant to protein phosphorylation. The tool presents information on protein kinases, substrates and phosphorylation sites automatically extracted from the biomedical literature. The utility of the RLIMS-P Web site has been evaluated by curators from Phospho.ELM, PhosphoGRID/BioGrid and Protein Ontology as part of the BioCreative IV user interactive task (IAT). The system achieved F-scores of 0.76, 0.88 and 0.92 for the extraction of kinase, substrate and phosphorylation sites, respectively, and a precision of 0.88 in the retrieval of relevant phosphorylation literature. The system also received highly favorable feedback from the curators in a user survey. Based on the curators’ suggestions, the Web site has been enhanced to improve its usability. In the RLIMS-P Web site, phosphorylation information can be retrieved by PubMed IDs or keywords, with an option for selecting targeted species. The result page displays a sortable table with phosphorylation information. The text evidence page displays the abstract with color-coded entity mentions and includes links to UniProtKB entries via normalization, i.e. the linking of entity mentions to database identifiers, facilitated by the GenNorm tool and by the links to the bibliography in UniProt. Log in and editing capabilities are offered to any user interested in contributing to the validation of RLIMS-P results. Retrieved phosphorylation information can also be downloaded in CSV format and the text evidence in the BioC format. RLIMS-P is freely available. Database URL:http://www.proteininformationresource.org/rlimsp/
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Affiliation(s)
- Manabu Torii
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Gang Li
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Zhiwen Li
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Rose Oughtred
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Francesca Diella
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Irem Celen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Cecilia N Arighi
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - K Vijay-Shanker
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
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Garrey SM, Katolik A, Prekeris M, Li X, York K, Bernards S, Fields S, Zhao R, Damha MJ, Hesselberth JR. A homolog of lariat-debranching enzyme modulates turnover of branched RNA. RNA (NEW YORK, N.Y.) 2014; 20:1337-48. [PMID: 24919400 PMCID: PMC4105757 DOI: 10.1261/rna.044602.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Turnover of the branched RNA intermediates and products of pre-mRNA splicing is mediated by the lariat-debranching enzyme Dbr1. We characterized a homolog of Dbr1 from Saccharomyces cerevisiae, Drn1/Ygr093w, that has a pseudo-metallophosphodiesterase domain with primary sequence homology to Dbr1 but lacks essential active site residues found in Dbr1. Whereas loss of Dbr1 results in lariat-introns failing broadly to turnover, loss of Drn1 causes low levels of lariat-intron accumulation. Conserved residues in the Drn1 C-terminal CwfJ domains, which are not present in Dbr1, are required for efficient intron turnover. Drn1 interacts with Dbr1, components of the Nineteen Complex, U2 snRNA, branched intermediates, and products of splicing. Drn1 enhances debranching catalyzed by Dbr1 in vitro, but does so without significantly improving the affinity of Dbr1 for branched RNA. Splicing carried out in in vitro extracts in the absence of Drn1 results in an accumulation of branched splicing intermediates and products released from the spliceosome, likely due to less active debranching, as well as the promiscuous release of cleaved 5'-exon. Drn1 enhances Dbr1-mediated turnover of lariat-intermediates and lariat-intron products, indicating that branched RNA turnover is regulated at multiple steps during splicing.
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Affiliation(s)
- Stephen M Garrey
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Mantas Prekeris
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Kerri York
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Sarah Bernards
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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41
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Zhao Q, Xie Y, Zheng Y, Jiang S, Liu W, Mu W, Liu Z, Zhao Y, Xue Y, Ren J. GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. Nucleic Acids Res 2014; 42:W325-30. [PMID: 24880689 PMCID: PMC4086084 DOI: 10.1093/nar/gku383] [Citation(s) in RCA: 349] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/10/2014] [Accepted: 04/21/2014] [Indexed: 12/20/2022] Open
Abstract
Small ubiquitin-like modifiers (SUMOs) regulate a variety of cellular processes through two distinct mechanisms, including covalent sumoylation and non-covalent SUMO interaction. The complexity of SUMO regulations has greatly hampered the large-scale identification of SUMO substrates or interaction partners on a proteome-wide level. In this work, we developed a new tool called GPS-SUMO for the prediction of both sumoylation sites and SUMO-interaction motifs (SIMs) in proteins. To obtain an accurate performance, a new generation group-based prediction system (GPS) algorithm integrated with Particle Swarm Optimization approach was applied. By critical evaluation and comparison, GPS-SUMO was demonstrated to be substantially superior against other existing tools and methods. With the help of GPS-SUMO, it is now possible to further investigate the relationship between sumoylation and SUMO interaction processes. A web service of GPS-SUMO was implemented in PHP+JavaScript and freely available at http://sumosp.biocuckoo.org.
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Affiliation(s)
- Qi Zhao
- State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China
| | - Yubin Xie
- State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China
| | - Yueyuan Zheng
- State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China
| | - Shuai Jiang
- State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenzhong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China
| | - Weiping Mu
- State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China
| | - Zexian Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yong Zhao
- State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu Xue
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jian Ren
- State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China
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42
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Huang KY, Wu HY, Chen YJ, Lu CT, Su MG, Hsieh YC, Tsai CM, Lin KI, Huang HD, Lee TY, Chen YJ. RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. Database (Oxford) 2014; 2014:bau034. [PMID: 24771658 PMCID: PMC3999940 DOI: 10.1093/database/bau034] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/27/2014] [Accepted: 03/30/2014] [Indexed: 11/13/2022]
Abstract
Protein phosphorylation catalyzed by kinases plays crucial roles in regulating a variety of intracellular processes. Owing to an increasing number of in vivo phosphorylation sites that have been identified by mass spectrometry (MS)-based proteomics, the RegPhos, available online at http://csb.cse.yzu.edu.tw/RegPhos2/, was developed to explore protein phosphorylation networks in human. In this update, we not only enhance the data content in human but also investigate kinase-substrate phosphorylation networks in mouse and rat. The experimentally validated phosphorylation sites as well as their catalytic kinases were extracted from public resources, and MS/MS phosphopeptides were manually curated from research articles. RegPhos 2.0 aims to provide a more comprehensive view of intracellular signaling networks by integrating the information of metabolic pathways and protein-protein interactions. A case study shows that analyzing the phosphoproteome profile of time-dependent cell activation obtained from Liquid chromatography-mass spectrometry (LC-MS/MS) analysis, the RegPhos deciphered not only the consistent scheme in B cell receptor (BCR) signaling pathway but also novel regulatory molecules that may involve in it. With an attempt to help users efficiently identify the candidate biomarkers in cancers, 30 microarray experiments, including 39 cancerous versus normal cells, were analyzed for detecting cancer-specific expressed genes coding for kinases and their substrates. Furthermore, this update features an improved web interface to facilitate convenient access to the exploration of phosphorylation networks for a group of genes/proteins. Database URL: http://csb.cse.yzu.edu.tw/RegPhos2/
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Affiliation(s)
- Kai-Yao Huang
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Hsin-Yi Wu
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Yi-Ju Chen
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Cheng-Tsung Lu
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Min-Gang Su
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Yun-Chung Hsieh
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Chih-Ming Tsai
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Kuo-I Lin
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Hsien-Da Huang
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Tzong-Yi Lee
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Yu-Ju Chen
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan, Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
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Nuclear localization of Haa1, which is linked to its phosphorylation status, mediates lactic acid tolerance in Saccharomyces cerevisiae. Appl Environ Microbiol 2014; 80:3488-95. [PMID: 24682296 DOI: 10.1128/aem.04241-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Improvement of the lactic acid resistance of the yeast Saccharomyces cerevisiae is important for the application of the yeast in industrial production of lactic acid from renewable resources. However, we still do not know the precise mechanisms of the lactic acid adaptation response in yeast and, consequently, lack effective approaches for improving its lactic acid tolerance. To enhance our understanding of the adaptation response, we screened for S. cerevisiae genes that confer enhanced lactic acid resistance when present in multiple copies and identified the transcriptional factor Haa1 as conferring resistance to toxic levels of lactic acid when overexpressed. The enhanced tolerance probably results from increased expression of its target genes. When cells that expressed Haa1 only from the endogenous promoter were exposed to lactic acid stress, the main subcellular localization of Haa1 changed from the cytoplasm to the nucleus within 5 min. This nuclear accumulation induced upregulation of the Haa1 target genes YGP1, GPG1, and SPI1, while the degree of Haa1 phosphorylation observed under lactic acid-free conditions decreased. Disruption of the exportin gene MSN5 led to accumulation of Haa1 in the nucleus even when no lactic acid was present. Since Msn5 was reported to interact with Haa1 and preferentially exports phosphorylated cargo proteins, our results suggest that regulation of the subcellular localization of Haa1, together with alteration of its phosphorylation status, mediates the adaptation to lactic acid stress in yeast.
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Phosphorylation of Sli15 by Ipl1 is important for proper CPC localization and chromosome stability in Saccharomyces cerevisiae. PLoS One 2014; 9:e89399. [PMID: 24558497 PMCID: PMC3928436 DOI: 10.1371/journal.pone.0089399] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/19/2014] [Indexed: 12/29/2022] Open
Abstract
The chromosomal passenger complex (CPC) is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/Ipl1 in association with its activator (INCENP/Sli15) and two additional proteins (Survivin/Bir1 and Borealin/Nbl1). Here we have identified multiple sites of CPC autophosphorylation on yeast Sli15 that are located within its central microtubule-binding domain and examined the functional significance of their phosphorylation by Ipl1 through mutation of these sites, either to non-phosphorylatable alanine (sli15-20A) or to acidic residues to mimic constitutive phosphorylation (sli15-20D). Both mutant sli15 alleles confer chromosome instability, but this is mediated neither by changes in the capacity of Sli15 to activate Ipl1 kinase nor by decreased efficiency of chromosome biorientation, a key process in cell division that requires CPC function. Instead, we find that mimicking constitutive phosphorylation of Sli15 on the Ipl1 phosphorylation sites causes delocalization of the CPC in metaphase, whereas blocking phosphorylation of Sli15 on the Ipl1 sites drives excessive localization of Sli15 to the mitotic spindle in pre-anaphase cells. Consistent with these results, direct interaction of Sli15 with microtubules in vitro is greatly reduced either following phosphorylation by Ipl1 or when constitutive phosphorylation at the Ipl1-dependent phosphorylation sites is mimicked by aspartate or glutamate substitutions. Furthermore, we find that mimicking Ipl1 phosphorylation of Sli15 interferes with the ‘tension checkpoint’ – the CPC-dependent mechanism through which cells activate the spindle assembly checkpoint to delay anaphase in the absence of tension on kinetochore-microtubule attachments. Ipl1-dependent phosphorylation of Sli15 therefore inhibits its association with microtubules both in vivo and in vitro and may negatively regulate the tension checkpoint mechanism.
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Lee J, Reiter W, Dohnal I, Gregori C, Beese-Sims S, Kuchler K, Ammerer G, Levin DE. MAPK Hog1 closes the S. cerevisiae glycerol channel Fps1 by phosphorylating and displacing its positive regulators. Genes Dev 2014; 27:2590-601. [PMID: 24298058 PMCID: PMC3861672 DOI: 10.1101/gad.229310.113] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The yeast aquagylceroporin Fps1 is a key regulator of glycerol transport in response to changes in extracellular osmolarity. Here, Lee et al. delineate how the MAPK Hog1 and glycerol channel regulators Rgc1/2 control Fps1 channel activity. The authors show that Rgc2 maintains Fps1 in an open channel state via split pleckstrin homology domains within both proteins. Hog1 induces Fbs1 channel closure by binding Fps1 and phosphorylating the activating subunit Rgc2. This study reveals a new aspect of spatial control mechanisms used by MAPKs to regulate their targets. The aquaglyceroprin Fps1 is responsible for glycerol transport in yeast in response to changes in extracellular osmolarity. Control of Fps1 channel activity in response to hyperosmotic shock involves a redundant pair of regulators, Rgc1 (regulator of the glycerol channel 1) and Rgc2, and the MAPK Hog1 (high-osmolarity glycerol response 1). However, the mechanism by which these factors influence channel activity is unknown. We show that Rgc2 maintains Fps1 in the open channel state in the absence of osmotic stress by binding to its C-terminal cytoplasmic domain. This interaction involves a tripartite pleckstrin homology (PH) domain within Rgc2 and a partial PH domain within Fps1. Activation of Hog1 in response to hyperosmotic shock induces the rapid eviction of Rgc2 from Fps1 and consequent channel closure. Hog1 was recruited to the N-terminal cytoplasmic domain of Fps1, which it uses as a platform from which to multiply phosphorylate Rgc2. Thus, these results reveal the mechanism by which Hog1 regulates Fps1 in response to hyperosmotic shock.
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Affiliation(s)
- Jongmin Lee
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts 02118, USA
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Hönscher C, Ungermann C. A close-up view of membrane contact sites between the endoplasmic reticulum and the endolysosomal system: from yeast to man. Crit Rev Biochem Mol Biol 2014; 49:262-8. [PMID: 24382115 DOI: 10.3109/10409238.2013.875512] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Maintenance of organelle identity is crucial for the functionality of eukaryotic cells. Hence, transfer reactions between different compartments must be highly efficient and tightly regulated at the same time. Membrane contact sites (MCSs) represent an important route for inter-organelle transport and communication independent of vesicular trafficking. Due to extensive research, the mechanistic understanding of these sites increases constantly. However, how the formation and the versatile functions of MCSs are regulated is mainly unclear. Within this review, we focus on one well-known MCS, the nucleus-vacuole junction in yeast and discuss its analogy to endoplasmic reticulum-late endosome contacts in metazoan. Formation of the junction in yeast requires Vac8, a protein that is involved in various cellular processes at the yeast vacuole and a target of multiple posttranslational modifications. We discuss the possibility that dual functionality of proteins involved in contact formation is a common principle to coordinate inter-organelle transfer with organellar biogenesis.
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Affiliation(s)
- Carina Hönscher
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück , Osnabrück , Germany
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47
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Trevisol ETV, Panek AD, De Mesquita JF, Eleutherio ECA. Regulation of the yeast trehalose-synthase complex by cyclic AMP-dependent phosphorylation. Biochim Biophys Acta Gen Subj 2013; 1840:1646-50. [PMID: 24380875 DOI: 10.1016/j.bbagen.2013.12.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/28/2013] [Accepted: 12/09/2013] [Indexed: 01/21/2023]
Abstract
BACKGROUND Trehalose is an important protectant in several microorganisms. In Saccharomyces cerevisiae, it is synthesized by a large complex comprising the enzymes Tps1 and Tps2 and the subunits Tps3 and Tsl1, showing an intricate metabolic control. METHODS To investigate how the trehalose biosynthesis pathway is regulated, we analyzed Tps1 and Tps2 activities as well as trehalose and trehalose-6-phosphate (T6P) contents by mass spectrometry. RESULTS Tsl1 deficiency totally abolished the increase in Tps1 activity and accumulation of trehalose in response to a heat stress, whereas absence of Tps3 only reduced Tps1 activity and trehalose synthesis. In extracts of heat stressed cells, Tps1 was inhibited by T6P and by ATP. Mg(2+) in the presence of cAMP. In contrast, cAMP-dependent phosphorylation did not inhibit Tps1 in tps3 cells, which accumulated a higher proportion of T6P after stress. Tps2 activity was not induced in a tps3 mutant. CONCLUSION Taken together these results suggest that Tsl1 is a decisive subunit for activity of the TPS complex since in its absence no trehalose synthesis occurred. On the other hand, Tps3 seems to be an activator of Tps2. To perform this task, Tps3 must be non-phosphorylated. To readily stop trehalose synthesis during stress recovery, Tps3 must be phosphorylated by cAMP-dependent protein kinase, decreasing Tps2 activity and, consequently, increasing the concentration of T6P which would inhibit Tps1. GENERAL SIGNIFICANCE A better understanding of TPS complex regulation is essential for understanding how yeast deals with stress situations and how it is able to recover when the stress is over.
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Affiliation(s)
- Eduardo T V Trevisol
- Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro, Brazil.
| | - Anita D Panek
- Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro, Brazil
| | - Joelma F De Mesquita
- Department of Genetics and Molecular Biology, Bioinformatics and Computational Biology Group, Federal University of Rio de Janeiro State, Brazil
| | - Elis C A Eleutherio
- Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro, Brazil.
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Chu D, Kazana E, Bellanger N, Singh T, Tuite MF, von der Haar T. Translation elongation can control translation initiation on eukaryotic mRNAs. EMBO J 2013; 33:21-34. [PMID: 24357599 DOI: 10.1002/embj.201385651] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Synonymous codons encode the same amino acid, but differ in other biophysical properties. The evolutionary selection of codons whose properties are optimal for a cell generates the phenomenon of codon bias. Although recent studies have shown strong effects of codon usage changes on protein expression levels and cellular physiology, no translational control mechanism is known that links codon usage to protein expression levels. Here, we demonstrate a novel translational control mechanism that responds to the speed of ribosome movement immediately after the start codon. High initiation rates are only possible if start codons are liberated sufficiently fast, thus accounting for the observation that fast codons are overrepresented in highly expressed proteins. In contrast, slow codons lead to slow liberation of the start codon by initiating ribosomes, thereby interfering with efficient translation initiation. Codon usage thus evolved as a means to optimise translation on individual mRNAs, as well as global optimisation of ribosome availability.
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Affiliation(s)
- Dominique Chu
- School of Computing, University of Kent, Canterbury, UK
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Lin CH, Tsai ZTY, Wang D. Role of antisense RNAs in evolution of yeast regulatory complexity. Genomics 2013; 102:484-90. [PMID: 24200499 DOI: 10.1016/j.ygeno.2013.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/01/2013] [Accepted: 10/26/2013] [Indexed: 01/01/2023]
Abstract
Antisense RNAs (asRNAs) are known to regulate gene expression. However, a genome-wide mechanism of asRNA regulation is unclear, and there is no good explanation why partial asRNAs are not functional. To explore its regulatory role, we investigated asRNAs using an evolutionary approach, as genome-wide experimental data are limited. We found that the percentage of genes coupling with asRNAs in Saccharomyces cerevisiae is negatively associated with regulatory complexity and evolutionary age. Nevertheless, asRNAs evolve more slowly when their sense genes are under more complex regulation. Older genes coupling with asRNAs are more likely to demonstrate inverse expression, reflecting the role of these asRNAs as repressors. Our analyses provide novel evidence, suggesting a minor contribution of asRNAs in developing regulatory complexity. Although our results support the leaky hypothesis for asRNA transcription, our evidence also suggests that partial asRNAs may have evolved as repressors. Our study deepens the understanding of asRNA regulatory evolution.
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Affiliation(s)
- Chih-Hsu Lin
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan.
| | - Zing Tsung-Yeh Tsai
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan; Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.
| | - Daryi Wang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan.
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Bhandari D, Zhang J, Menon S, Lord C, Chen S, Helm JR, Thorsen K, Corbett KD, Hay JC, Ferro-Novick S. Sit4p/PP6 regulates ER-to-Golgi traffic by controlling the dephosphorylation of COPII coat subunits. Mol Biol Cell 2013; 24:2727-38. [PMID: 23864707 PMCID: PMC3756924 DOI: 10.1091/mbc.e13-02-0114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Previous studies show that the COPII coat is phosphorylated. The phosphorylated coat, however, cannot rebind to the ER to initiate a new round of vesicle budding. The present study shows that Sit4p/PP6, a Ser/Thr phosphatase, dephosphorylates the COPII coat. Consistent with a role in coat recycling, Sit4p/PP6 regulates ER-to-Golgi traffic. Traffic from the endoplasmic reticulum (ER) to the Golgi complex is initiated when the activated form of the GTPase Sar1p recruits the Sec23p-Sec24p complex to ER membranes. The Sec23p-Sec24p complex, which forms the inner shell of the COPII coat, sorts cargo into ER-derived vesicles. The coat inner shell recruits the Sec13p-Sec31p complex, leading to coat polymerization and vesicle budding. Recent studies revealed that the Sec23p subunit sequentially interacts with three different binding partners to direct a COPII vesicle to the Golgi. One of these binding partners is the serine/threonine kinase Hrr25p. Hrr25p phosphorylates the COPII coat, driving the membrane-bound pool into the cytosol. The phosphorylated coat cannot rebind to the ER to initiate a new round of vesicle budding unless it is dephosphorylated. Here we screen all known protein phosphatases in yeast to identify one whose loss of function alters the cellular distribution of COPII coat subunits. This screen identifies the PP2A-like phosphatase Sit4p as a regulator of COPII coat dephosphorylation. Hyperphosphorylated coat subunits accumulate in the sit4Δ mutant in vivo. In vitro, Sit4p dephosphorylates COPII coat subunits. Consistent with a role in coat recycling, Sit4p and its mammalian orthologue, PP6, regulate traffic from the ER to the Golgi complex.
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Affiliation(s)
- Deepali Bhandari
- Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093, USA
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