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Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event. Mol Biol Evol 2023; 40:msad246. [PMID: 37979156 PMCID: PMC10699747 DOI: 10.1093/molbev/msad246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
Whole-genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in Saccharomyces cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post-WGD. In S. cerevisiae, HRR25 encodes the casein kinase 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post-WGD and non-WGD species, and have nonconserved cellular localization, consistent with their ongoing loss of function. The analysis in Naumovozyma castellii shows that the noncomplementing ohnolog is expressed at a lower level and has become nonessential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.
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Affiliation(s)
- Daniel Evans-Yamamoto
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Gourav Saha
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani K K Birla Goa Campus, South Goa, India
| | - Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
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Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560513. [PMID: 37873368 PMCID: PMC10592909 DOI: 10.1101/2023.10.02.560513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Whole genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in S. cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post WGD. In S. cerevisiae, HRR25 encodes the casein kinase (CK) 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post and non-WGD species, and have non-conserved cellular localization, consistent with their ongoing loss of function. The analysis in N. castelli shows that the non-complementing ohnolog is expressed at a lower level and has become non-essential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.
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Affiliation(s)
- Daniel Evans-Yamamoto
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Gourav Saha
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani K K Birla Goa campus, Zuarinagar, South Goa, Goa, India
- Current address: Department of Bioengineering, University of California, CA 90095, United States
| | - Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Current address: Département de Biochimie, Université de Sherbrooke, Québec, J1K 0A5, Canada
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
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Kempen RP, Dabas P, Ansari AZ. The Phantom Mark: Enigmatic roles of phospho-Threonine 4 modification of the C-terminal domain of RNA polymerase II. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1771. [PMID: 36606410 PMCID: PMC10323045 DOI: 10.1002/wrna.1771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/04/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023]
Abstract
The largest subunit of RNA polymerase II (Pol II) has an unusual carboxyl-terminal domain (CTD). This domain is composed of a tandemly repeating heptapeptide, Y1 S2 P3 T4 S5 P6 S7 , that has multiple roles in regulating Pol II function and processing newly synthesized RNA. Transient phosphorylation of Ser2 and Ser5 of the YS2 PTS5 PS repeat have well-defined roles in recruiting different protein complexes and coordinating sequential steps in gene transcription. As such, these phospho-marks encipher a molecular recognition code, colloquially termed the CTD code. In contrast, the contribution of phospho-Threonine 4 (pThr4/pT4) to the CTD code remains opaque and contentious. Fuelling the debate on the relevance of this mark to gene expression are the findings that replacing Thr4 with a valine or alanine has varied impact on cellular function in different species and independent proteomic analyses disagree on the relative abundance of pThr4 marks. Yet, substitution with negatively charged residues is lethal and even benign mutations selectively disrupt synthesis and 3' processing of distinct sets of coding and non-coding transcripts. Suggestive of non-canonical roles, pThr4 marked Pol II regulates distinct gene classes in a species- and signal-responsive manner. Hinting at undiscovered roles of this elusive mark, multiple signal-responsive kinases phosphorylate Thr4 at target genes. Here, we focus on this under-explored residue and postulate that the pThr4 mark is superimposed on the canonical CTD code to selectively regulate expression of targeted genes without perturbing genome-wide transcriptional processes. This article is categorized under: RNA Processing > 3' End Processing RNA Processing > Processing of Small RNAs RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Ryan P Kempen
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Preeti Dabas
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Aseem Z Ansari
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Holland CL, Weis MF, England CJ, Berry AM, Hall PD, Lewis LK. Deficiency in homologous recombination is associated with changes in cell cycling and morphology in Saccharomyces cerevisiae. Exp Cell Res 2023:113701. [PMID: 37393982 DOI: 10.1016/j.yexcr.2023.113701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
Exposure of eukaryotic cells to ionizing radiation or clastogenic chemicals leads to formation of DNA double-strand breaks (DSBs). These lesions are also generated internally by chemicals and enzymes, in the absence of exogenous agents, though the sources and consequences of such endogenously generated DSBs remain poorly understood. In the current study, we have investigated the impact of reduced recombinational repair of endogenous DSBs on stress responses, cell morphology and other physical properties of S. cerevisiae (budding yeast) cells. Use of phase contrast and DAPI-based fluorescence microscopy combined with FACS analysis confirmed that recombination-deficient rad52 cell cultures exhibit chronically high levels of G2 phase cells. Cell cycle phase transit times during G1, S and M were similar in WT and rad52 cells, but the length of G2 phase was increased by three-fold in the mutants. rad52 cells were larger than WT in all phases of the cycle and displayed other quantifiable changes in physical characteristics. The high G2 cell phenotype was abolished when DNA damage checkpoint genes, but not spindle assembly checkpoint genes, were co-inactivated with RAD52. Several other RAD52 group mutants (rad51, rad54, rad55, rad57 and rad59) also exhibited the high G2 cell phenotype. The results indicate that recombination deficiency leads to accumulation of unrepaired DSBs during normal mitotic growth that activate a major stress response and produce distinct changes in cellular physiology and morphology.
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Affiliation(s)
- Cory L Holland
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Monica F Weis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Corbin J England
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Armand M Berry
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Paige D Hall
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - L Kevin Lewis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA.
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Raj K, Rishi P, Shukla G, Rudramurhty SM, Mongad DS, Kaur A. Possible Contribution of Alternative Transcript Isoforms in Mature Biofilm Growth Phase of Candida glabrata. Indian J Microbiol 2022; 62:583-601. [PMID: 36458226 PMCID: PMC9705674 DOI: 10.1007/s12088-022-01036-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/04/2022] [Indexed: 11/05/2022] Open
Abstract
Expression of genome-wide alternative transcript isoforms and differential transcript isoform usage in different biological conditions (isoform switching) are responsible for the varied proteomic functional diversity in higher eukaryotic organisms. However, these mechanisms have not been studied in Candida glabrata, which is a potent eukaryotic opportunistic pathogen. Biofilm formation is an important virulence factor of C. glabrata that withstands antifungal drug stress and overcomes the host-immune response. Here, we present the genome-wide differential transcript isoform expression (DTE) and differential transcript isoform usage (DTU) in a mature biofilm growth phase of C. glabrata (clinical isolate; NCCPF 100,037) using the RNA sequencing approach. The DTE analysis generated 7837 transcript isoforms from the C. glabrata genome (5293 genes in total), and revealed that transcript isoforms generated from 292 genes showed significant DTU in the mature biofilm cells. Gene ontology, pathway analysis and protein-protein interactions of significant transcript isoforms, further substantiated that their specific expression and differential usage is required for transitioning the planktonic cells to biofilm in C. glabrata. The present study reported the possible role of expression of alternative transcript isoforms and differential transcript isoform usage in the mature biofilms of C. glabrata. The observation derived from the study may prove to be beneficial for making future antifungal therapeutic strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-022-01036-7.
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Affiliation(s)
- Khem Raj
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
| | - Praveen Rishi
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
| | - Geeta Shukla
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
| | - Shivaprakash M. Rudramurhty
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Dattatray S. Mongad
- National Centre for Microbial Resource, National Centre for Cell Sciences (NCCS), Pune, India
| | - Amrita Kaur
- Department of Microbiology, Basic Medical Sciences Block I, South Campus, Panjab University, Sector-25, Chandigarh, 160014 India
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Stage-Specific Genetic Interaction between FgYCK1 and FgBNI4 during Vegetative Growth and Conidiation in Fusarium graminearum. Int J Mol Sci 2022; 23:ijms23169106. [PMID: 36012372 PMCID: PMC9408904 DOI: 10.3390/ijms23169106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
CK1 casein kinases are well conserved in filamentous fungi. However, their functions are not well characterized in plant pathogens. In Fusarium graminearum, deletion of FgYCK1 caused severe growth defects and loss of conidiation, fertility, and pathogenicity. Interestingly, the Fgyck1 mutant was not stable and often produced fast-growing spontaneous suppressors. Suppressor mutations were frequently identified in the FgBNI4 gene by sequencing analyses. Deletion of the entire FgBNI4 or disruptions of its conserved C-terminal region could suppress the defects of Fgyck1 in hyphal growth and conidiation, indicating the genetic relationship between FgYCK1 and FgBNI4. Furthermore, the Fgyck1 mutant showed defects in polarized growth, cell wall integrity, internalization of FgRho1 and vacuole fusion, which were all partially suppressed by deletion of FgBNI4. Overall, our results indicate a stage-specific functional relationship between FgYCK1 and FgBNI4, possibly via FgRho1 signaling for regulating polarized hyphal growth and cell wall integrity.
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CK1 Is a Druggable Regulator of Microtubule Dynamics and Microtubule-Associated Processes. Cancers (Basel) 2022; 14:cancers14051345. [PMID: 35267653 PMCID: PMC8909099 DOI: 10.3390/cancers14051345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 02/05/2023] Open
Abstract
Protein kinases of the Casein Kinase 1 family play a vital role in the regulation of numerous cellular processes. Apart from functions associated with regulation of proliferation, differentiation, or apoptosis, localization of several Casein Kinase 1 isoforms to the centrosome and microtubule asters also implicates regulatory functions in microtubule dynamic processes. Being localized to the spindle apparatus during mitosis Casein Kinase 1 directly modulates microtubule dynamics by phosphorylation of tubulin isoforms. Additionally, site-specific phosphorylation of microtubule-associated proteins can be related to the maintenance of genomic stability but also microtubule stabilization/destabilization, e.g., by hyper-phosphorylation of microtubule-associated protein 1A and RITA1. Consequently, approaches interfering with Casein Kinase 1-mediated microtubule-specific functions might be exploited as therapeutic strategies for the treatment of cancer. Currently pursued strategies include the development of Casein Kinase 1 isoform-specific small molecule inhibitors and therapeutically useful peptides specifically inhibiting kinase-substrate interactions.
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Regulation of Pkc1 Hyper-Phosphorylation by Genotoxic Stress. J Fungi (Basel) 2021; 7:jof7100874. [PMID: 34682295 PMCID: PMC8541566 DOI: 10.3390/jof7100874] [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: 09/11/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 01/02/2023] Open
Abstract
The cell wall integrity (CWI) signaling pathway is best known for its roles in cell wall biogenesis. However, it is also thought to participate in the response to genotoxic stress. The stress-activated protein kinase Mpk1 (Slt2, is activated by DNA damaging agents through an intracellular mechanism that does not involve the activation of upstream components of the CWI pathway. Additional observations suggest that protein kinase C (Pkc1), the top kinase in the CWI signaling cascade, also has a role in the response to genotoxic stress that is independent of its recognized function in the activation of Mpk1. Pkc1 undergoes hyper-phosphorylation specifically in response to genotoxic stress; we have found that this requires the DNA damage checkpoint kinases Mec1 (Mitosis Entry Checkpoint) and Tel1 (TELomere maintenance), but not their effector kinases. We demonstrate that the casein kinase 1 (CK1) ortholog, Hrr25 (HO and Radiation Repair), previously implicated in the DNA damage transcriptional response, associates with Pkc1 under conditions of genotoxic stress. We also found that the induced association of Hrr25 with Pkc1 requires Mec1 and Tel1, and that Hrr25 catalytic activity is required for Pkc1-hyperphosphorylation, thereby delineating a pathway from the checkpoint kinases to Pkc1. We used SILAC mass spectrometry to identify three residues within Pkc1 the phosphorylation of which was stimulated by genotoxic stress. We mutated these residues as well as a collection of 13 phosphorylation sites within the regulatory domain of Pkc1 that fit the consensus for CK1 sites. Mutation of the 13 Pkc1 phosphorylation sites blocked hyper-phosphorylation and diminished RNR3 (RiboNucleotide Reductase) basal expression and induction by genotoxic stress, suggesting that Pkc1 plays a role in the DNA damage transcriptional response.
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Fulcher LJ, Sapkota GP. Functions and regulation of the serine/threonine protein kinase CK1 family: moving beyond promiscuity. Biochem J 2020; 477:4603-4621. [PMID: 33306089 PMCID: PMC7733671 DOI: 10.1042/bcj20200506] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022]
Abstract
Regarded as constitutively active enzymes, known to participate in many, diverse biological processes, the intracellular regulation bestowed on the CK1 family of serine/threonine protein kinases is critically important, yet poorly understood. Here, we provide an overview of the known CK1-dependent cellular functions and review the emerging roles of CK1-regulating proteins in these processes. We go on to discuss the advances, limitations and pitfalls that CK1 researchers encounter when attempting to define relationships between CK1 isoforms and their substrates, and the challenges associated with ascertaining the correct physiological CK1 isoform for the substrate of interest. With increasing interest in CK1 isoforms as therapeutic targets, methods of selectively inhibiting CK1 isoform-specific processes is warranted, yet challenging to achieve given their participation in such a vast plethora of signalling pathways. Here, we discuss how one might shut down CK1-specific processes, without impacting other aspects of CK1 biology.
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Affiliation(s)
- Luke J. Fulcher
- Department of Biochemistry, University of Oxford, Oxford, U.K
| | - Gopal P. Sapkota
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, U.K
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10
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Murakami-Sekimata A, Sekimata M, Sato N, Hayasaka Y, Nakano A. Deletion of PIN4 Suppresses the Protein Transport Defects Caused by sec12-4 Mutation in Saccharomyces cerevisiae. Microb Physiol 2020; 30:25-35. [PMID: 32958726 DOI: 10.1159/000509633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/24/2020] [Indexed: 11/19/2022]
Abstract
Newly synthesized secretory proteins are released into the lumen of the endoplasmic reticulum (ER). The secretory proteins are surrounded by coat protein complex II (COPII) vesicles, and transported from the ER and reach their destinations through the Golgi apparatus. Sec12p is a guanine nucleotide exchange factor for Sar1p, which initiates COPII vesicle budding from the ER. The activation of Sar1p by Sec12p and the subsequent COPII coat assembly have been well characterized, but the events that take place upstream of Sec12p remain unclear. In this study, we isolated the novel extragenic suppressor of sec12-4, PIN4/MDT1, a cell cycle checkpoint target. A yeast two-hybrid screening was used to identify Pin4/Mdt1p as a binding partner of the casein kinase I isoform Hrr25p, which we have previously identified as a modulator of Sec12p function. Deletion of PIN4 suppressed both defects of temperature-sensitive growth and the partial protein transport observed in sec12-4 mutants. The results of this study suggest that Pin4p provides novel aspects of Sec12p modulations.
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Affiliation(s)
- Akiko Murakami-Sekimata
- Division of Theoretical Nursing and Genetics, Graduate School of Medical Science, Yamagata University Faculty of Medicine, Yamagata, Japan,
| | - Masayuki Sekimata
- Radioisotope Research Center, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Natsumi Sato
- Division of Theoretical Nursing and Genetics, Graduate School of Medical Science, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Yuto Hayasaka
- Division of Theoretical Nursing and Genetics, Graduate School of Medical Science, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, Wako, Japan
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11
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Bhondeley M, Liu Z. Mitochondrial Biogenesis Is Positively Regulated by Casein Kinase I Hrr25 Through Phosphorylation of Puf3 in Saccharomyces cerevisiae. Genetics 2020; 215:463-482. [PMID: 32317286 PMCID: PMC7268985 DOI: 10.1534/genetics.120.303191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/20/2020] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial biogenesis requires coordinated expression of genes encoding mitochondrial proteins, which in Saccharomyces cerevisiae is achieved in part via post-transcriptional control by the Pumilio RNA-binding domain protein Puf3 Puf3 binds to the 3'-UTR of many messenger RNAs (mRNAs) that encode mitochondrial proteins, regulating their turnover, translation, and/or mitochondrial targeting. Puf3 hyperphosphorylation correlates with increased mitochondrial biogenesis; however, the kinase responsible for Puf3 phosphorylation is unclear. Here, we show that the casein kinase I protein Hrr25 negatively regulates Puf3 by mediating its phosphorylation. An hrr25 mutation results in reduced phosphorylation of Puf3 in vivo and a puf3 deletion mutation reverses growth defects of hrr25 mutant cells grown on medium with a nonfermentable carbon source. We show that Hrr25 directly phosphorylates Puf3, and that the interaction between Puf3 and Hrr25 is mediated through the N-terminal domain of Puf3 and the kinase domain of Hrr25 We further found that an hrr25 mutation reduces GFP expression from GFP reporter constructs carrying the 3'-UTR of Puf3 targets. Downregulation of GFP expression due to an hrr25 mutation can be reversed either by puf3Δ or by mutations to the Puf3-binding sites in the 3'-UTR of the GFP reporter constructs. Together, our data indicate that Hrr25 is a positive regulator of mitochondrial biogenesis by phosphorylating Puf3 and inhibiting its function in downregulating target mRNAs encoding mitochondrial proteins.
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Affiliation(s)
- Manika Bhondeley
- Department of Biological Sciences, University of New Orleans, Louisiana 70148
| | - Zhengchang Liu
- Department of Biological Sciences, University of New Orleans, Louisiana 70148
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12
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Abstract
The coordinated activities of many protein kinases, acting on multiple protein substrates, ensures the error-free progression through mitosis of eukaryotic cells. Enormous research effort has thus been devoted to studying the roles and regulation of these mitotic kinases, and to the identification of their physiological substrates. Central for the timely deployment of specific protein kinases to their appropriate substrates during the cell division cycle are the many anchoring proteins, which serve critical regulatory roles. Through direct association, anchoring proteins are capable of modulating the catalytic activity and/or sub-cellular distribution of the mitotic kinases they associate with. The key roles of some anchoring proteins in cell division are well-established, whilst others are still being unearthed. Here, we review the current knowledge on anchoring proteins for some mitotic kinases, and highlight how targeting anchoring proteins for inhibition, instead of the mitotic kinases themselves, could be advantageous for disrupting the cell division cycle.
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Affiliation(s)
- Luke J Fulcher
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - Gopal P Sapkota
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
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13
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He F, Zhang R, Zhao J, Qi T, Kang Z, Guo J. Host-Induced Silencing of Fusarium graminearum Genes Enhances the Resistance of Brachypodium distachyon to Fusarium Head Blight. FRONTIERS IN PLANT SCIENCE 2019; 10:1362. [PMID: 31737001 PMCID: PMC6831556 DOI: 10.3389/fpls.2019.01362] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/03/2019] [Indexed: 05/30/2023]
Abstract
Fusarium head blight (FHB) caused by Fusarium pathogens are devastating diseases worldwide. Host-induced gene silencing (HIGS) which involves host expression of double-stranded RNA (dsRNA)-generating constructs directed against genes in the pathogen has been a potential strategy for the ecological sound control of FHB. In this study, we constructed transgenic Brachypodium distachyon lines carrying RNA interference (RNAi) cassettes to target two essential protein kinase genes Fg00677 and Fg08731, and cytochrome P450 lanosterol C14-α-demethylase (CYP51) encoding genes (CYP51A, CYP51B, and CYP51C) of Fusarium graminearum, respectively. Northern blotting confirmed the presence of short interfering RNAs (siRNA) derived from Fg00677, Fg08731, and CYP51 in transgenic B. distachyon plants, and the transcript levels of the corresponding genes were down-regulated in the F. graminearum colonizing B. distachyon spikes. All the corresponding independent, Fg00677-RNAi, Fg08731-RNAi, and CYP51-RNAi transgenic T2 lines exhibited strong resistance to F. graminearum, suggesting that silencing molecules produced by transgenic plants inhibited the corresponding gene function by down-regulating its expression, thereby reducing pathogenicity. Our results indicate that Fg00677 and Fg08731 are effective targets for HIGS and can be applied to construct transgenic HIGS materials to enhance FHB resistance in wheat and other cereal crops.
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14
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Xu P, Ianes C, Gärtner F, Liu C, Burster T, Bakulev V, Rachidi N, Knippschild U, Bischof J. Structure, regulation, and (patho-)physiological functions of the stress-induced protein kinase CK1 delta (CSNK1D). Gene 2019; 715:144005. [PMID: 31376410 DOI: 10.1016/j.gene.2019.144005] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 12/11/2022]
Abstract
Members of the highly conserved pleiotropic CK1 family of serine/threonine-specific kinases are tightly regulated in the cell and play crucial regulatory roles in multiple cellular processes from protozoa to human. Since their dysregulation as well as mutations within their coding regions contribute to the development of various different pathologies, including cancer and neurodegenerative diseases, they have become interesting new drug targets within the last decade. However, to develop optimized CK1 isoform-specific therapeutics in personalized therapy concepts, a detailed knowledge of the regulation and functions of the different CK1 isoforms, their various splice variants and orthologs is mandatory. In this review we will focus on the stress-induced CK1 isoform delta (CK1δ), thereby addressing its regulation, physiological functions, the consequences of its deregulation for the development and progression of diseases, and its potential as therapeutic drug target.
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Affiliation(s)
- Pengfei Xu
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Chiara Ianes
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Fabian Gärtner
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Congxing Liu
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Timo Burster
- Department of Biology, School of Science and Technology, Nazarbayev University, 53 Kabanbay Batyr Ave, Nur-Sultan 020000, Kazakhstan.
| | - Vasiliy Bakulev
- Ural Federal University named after the first President of Russia B. N. Eltsin, Technology for Organic Synthesis Laboratory, 19 Mirastr., 620002 Ekaterinburg, Russia.
| | - Najma Rachidi
- Unité de Parasitologie Moléculaire et Signalisation, Department of Parasites and Insect Vectors, Institut Pasteur and INSERM U1201, 25-28 Rue du Dr Roux, 75015 Paris, France.
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Joachim Bischof
- Department of General and Visceral Surgery, Surgery Center, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
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15
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It is all about the process(ing): P-body granules and the regulation of signal transduction. Curr Genet 2019; 66:73-77. [PMID: 31317215 DOI: 10.1007/s00294-019-01016-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022]
Abstract
The eukaryotic cell is subdivided into distinct functional domains by the presence of both membrane-bound and membraneless organelles. The latter include cytoplasmic granules, like the Processing-body (P-body), that are induced in response to stress and contain specific sets of mRNAs and proteins. Although P-bodies have been evolutionarily conserved, we do not yet understand the full extent of their biological functions in the cell. Early studies suggested that these structures might be sites of mRNA decay as the first protein constituents identified were enzymes involved in mRNA processing. However, more recent work indicates that this is not likely to be the primary function of these granules and has even suggested that P-bodies are sites of long-term mRNA storage. Interestingly, P-bodies and other ribonucleoprotein granules have been found to also contain a variety of signaling molecules, including protein kinases and phosphatases key to the normal control of cell growth and survival. Therefore, P-bodies could have a role in the modulation of cell signaling during particular types of stress. This review discusses both the general implications of such a proposal and one particular example that illustrates how the granule recruitment of a protein kinase can impact overall cell physiology.
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16
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Nemec CM, Singh AK, Ali A, Tseng SC, Syal K, Ringelberg KJ, Ho YH, Hintermair C, Ahmad MF, Kar RK, Gasch AP, Akhtar MS, Eick D, Ansari AZ. Noncanonical CTD kinases regulate RNA polymerase II in a gene-class-specific manner. Nat Chem Biol 2018; 15:123-131. [PMID: 30598543 PMCID: PMC6339578 DOI: 10.1038/s41589-018-0194-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/09/2018] [Indexed: 11/09/2022]
Abstract
Phosphorylation of the carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) governs stage-specific interactions with different cellular machines. The CTD consists of Y1S2P3T4S5P6S7 heptad repeats, and sequential phosphorylations of Ser7, Ser5 and Ser2 occur universally across Pol II-transcribed genes. Phosphorylation of Thr4, however, appears to selectively modulate transcription of specific classes of genes. Here, we identify 10 new Thr4 kinases from different kinase structural groups. Irreversible chemical inhibition of the most active Thr4 kinase, Hrr25, reveals a novel role for this kinase in transcription termination of specific class of noncoding snoRNA genes. Genome-wide profiles of Hrr25 reveal a selective enrichment at 3ʹ regions of noncoding genes that display termination defects. Importantly, phospho-Thr4 marks placed by Hrr25 are recognized by Rtt103, a key component of the termination machinery. Our results suggest that these uncommon CTD kinases selectively place phospho-Thr4 marks to regulate expression of targeted genes.
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Affiliation(s)
- Corey M Nemec
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Amit K Singh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India
| | - Asfa Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sandra C Tseng
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kirtimaan Syal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Yi-Hsuan Ho
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Corinna Hintermair
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Mohammad Faiz Ahmad
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Rajesh Kumar Kar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Md Sohail Akhtar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India.,Academy of Scientific and Innovative Research, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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17
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P-Body Localization of the Hrr25/Casein Kinase 1 Protein Kinase Is Required for the Completion of Meiosis. Mol Cell Biol 2018; 38:MCB.00678-17. [PMID: 29915153 DOI: 10.1128/mcb.00678-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 06/12/2018] [Indexed: 11/20/2022] Open
Abstract
P-bodies are liquid droplet-like compartments that lack a limiting membrane and are present in many eukaryotic cells. These structures contain specific sets of proteins and mRNAs at concentrations higher than that in the surrounding environment. Although highly conserved, the normal physiological roles of these ribonucleoprotein (RNP) granules remain poorly defined. Here, we report that P-bodies are required for the efficient completion of meiosis in the budding yeast Saccharomyces cerevisiae P-bodies were found to be present during all phases of the meiotic program and to provide protection for the Hrr25/CK1 protein kinase, a key regulator of this developmental process. A failure to associate with these RNP granules resulted in diminished levels of Hrr25 and an ensuing inability to complete meiosis. This work therefore identifies a novel function for these RNP granules and indicates how protein recruitment to these structures can have a significant impact on eukaryotic cell biology.
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18
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Scaiola A, Peña C, Weisser M, Böhringer D, Leibundgut M, Klingauf-Nerurkar P, Gerhardy S, Panse VG, Ban N. Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit. EMBO J 2018; 37:embj.201798499. [PMID: 29459436 DOI: 10.15252/embj.201798499] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/18/2017] [Accepted: 01/10/2018] [Indexed: 11/09/2022] Open
Abstract
Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation.
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Affiliation(s)
- Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Cohue Peña
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Melanie Weisser
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Daniel Böhringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Purnima Klingauf-Nerurkar
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Stefan Gerhardy
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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19
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Monastyrskyi A, Nilchan N, Quereda V, Noguchi Y, Ruiz C, Grant W, Cameron M, Duckett D, Roush W. Development of dual casein kinase 1δ/1ε (CK1δ/ε) inhibitors for treatment of breast cancer. Bioorg Med Chem 2017; 26:590-602. [PMID: 29289448 DOI: 10.1016/j.bmc.2017.12.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/09/2017] [Accepted: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Casein kinase 1δ/ε have been identified as promising therapeutic target for oncology application, including breast and brain cancer. Here, we described our continued efforts in optimization of a lead series of purine scaffold inhibitors that led to identification of two new CK1δ/ε inhibitors 17 and 28 displaying low nanomolar values in antiproliferative assays against the human MDA-MB-231 triple negative breast cancer cell line and have physical, in vitro and in vivo pharmacokinetic properties suitable for use in proof of principle animal xenograft studies against human cancers.
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Affiliation(s)
- Andrii Monastyrskyi
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Napon Nilchan
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Victor Quereda
- Department of Molecular Medicine, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yoshihiko Noguchi
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Claudia Ruiz
- Department of Molecular Medicine, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Wayne Grant
- Department of Molecular Medicine, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Michael Cameron
- Department of Molecular Medicine, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Derek Duckett
- Department of Molecular Medicine, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - William Roush
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States.
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20
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Casein Kinase I Isoform Hrr25 Is a Negative Regulator of Haa1 in the Weak Acid Stress Response Pathway in Saccharomyces cerevisiae. Appl Environ Microbiol 2017; 83:AEM.00672-17. [PMID: 28432100 DOI: 10.1128/aem.00672-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/15/2017] [Indexed: 11/20/2022] Open
Abstract
Haa1 is a transcription factor that adapts Saccharomyces cerevisiae cells to weak organic acid stresses by activating the expression of various genes. Many of these genes encode membrane proteins, such as TPO2 and YRO2 How Haa1 is activated by weak acids is not clear. Here, we show that casein kinase I isoform Hrr25 is an important negative regulator of Haa1. Haa1 is known to be multiply phosphorylated. We found that mutations in HRR25 lead to reduced Haa1 phosphorylation and increased expression of Haa1 target genes and that Hrr25 interacts with Haa1. The other three casein kinase I isoforms, Yck1, Yck2, and Yck3, do not seem to play critical roles in Haa1 regulation. Hrr25 has a 200-residue C-terminal region, including a proline- and glutamine-rich domain. Our data suggest that the C-terminal region of Hrr25 is required for normal inhibition of expression of Haa1 target genes TPO2 and YRO2 and is important for cell growth but is not required for cell morphogenesis. We propose that Hrr25 is an important regulator of cellular adaptation to weak acid stress by inhibiting Haa1 through phosphorylation.IMPORTANCE Our study has revealed the casein kinase I protein Hrr25 to be a negative regulator of Haa1, a transcription factor mediating the cellular response to stresses caused by weak acids. Many studies have focused on the target genes of Haa1 and their roles in weak acid stress responses, but little has been reported on the regulatory mechanism of Haa1. Weak acids, such as acetic acid, have long been used for food preservation by slowing down the growth of fungal species, including S. cerevisiae In the biofuel industry, acetic acid in the lignocellulosic hydrolysates limits the production of ethanol, which is undesirable. By understanding how Haa1 is regulated, we can make advances in the field of food sciences to better preserve food and engineer acetic acid-resistant strains that will increase productivity in the biofuel industry.
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21
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Greer YE, Gao B, Yang Y, Nussenzweig A, Rubin JS. Lack of Casein Kinase 1 Delta Promotes Genomic Instability - The Accumulation of DNA Damage and Down-Regulation of Checkpoint Kinase 1. PLoS One 2017; 12:e0170903. [PMID: 28125685 PMCID: PMC5268481 DOI: 10.1371/journal.pone.0170903] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/12/2017] [Indexed: 12/18/2022] Open
Abstract
Casein kinase 1 delta (CK1δ) is a conserved serine/threonine protein kinase that regulates diverse cellular processes. Mice lacking CK1δ have a perinatal lethal phenotype and typically weigh 30% less than their wild type littermates. However, the causes of death and small size are unknown. We observed cells with abnormally large nuclei in tissue from Csnk1d null embryos, and multiple centrosomes in mouse embryo fibroblasts (MEFs) deficient in CK1δ (MEFCsnk1d null). Results from γ-H2AX staining and the comet assay demonstrated significant DNA damage in MEFCsnk1d null cells. These cells often contain micronuclei, an indicator of genomic instability. Similarly, abrogation of CK1δ expression in control MEFs stimulated micronuclei formation after doxorubicin treatment, suggesting that CK1δ loss increases vulnerability to genotoxic stress. Cellular levels of total and activated checkpoint kinase 1 (Chk1), which functions in the DNA damage response and mitotic checkpoints, and its downstream effector, Cdc2/CDK1 kinase, were often decreased in MEFCsnk1d null cells as well as in control MEFs transfected with CK1δ siRNA. Hydroxyurea-induced Chk1 activation, as measured by Ser345 phosphorylation, and nuclear localization also were impaired in MEF cells following siRNA knockdown of CK1δ. Similar results were observed in the MCF7 human breast cancer cell line. The decreases in phosphorylated Chk1 were rescued by concomitant expression of siRNA-resistant CK1δ. Experiments with cycloheximide demonstrated that the stability of Chk1 protein was diminished in cells subjected to CK1δ knockdown. Together, these findings suggest that CK1δ contributes to the efficient repair of DNA damage and the proper functioning of mitotic checkpoints by maintaining appropriate levels of Chk1.
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Affiliation(s)
- Yoshimi Endo Greer
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, Bethesda, Maryland, United States of America
- Women’s Malignancies Branch, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail: (YEG); (JSR)
| | - Bo Gao
- Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Yingzi Yang
- Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jeffrey S. Rubin
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail: (YEG); (JSR)
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22
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Abstract
Clathrin-mediated endocytosis is an essential cellular process that involves the concerted assembly and disassembly of many different proteins at the plasma membrane. In yeast, live-cell imaging has shown that the spatiotemporal dynamics of these proteins is highly stereotypical. Recent work has focused on determining how the timing and functions of endocytic proteins are regulated. In this Cell Science at a Glance article and accompanying poster, we review our current knowledge of the timeline of endocytic site maturation and discuss recent works focusing on how phosphorylation, ubiquitylation and lipids regulate various aspects of the process.
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Affiliation(s)
- Rebecca Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Yidi Sun
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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23
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Ye Q, Ur SN, Su TY, Corbett KD. Structure of the Saccharomyces cerevisiae Hrr25:Mam1 monopolin subcomplex reveals a novel kinase regulator. EMBO J 2016; 35:2139-2151. [PMID: 27491543 DOI: 10.15252/embj.201694082] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/20/2016] [Indexed: 11/09/2022] Open
Abstract
In budding yeast, the monopolin complex mediates sister kinetochore cross-linking and co-orientation in meiosis I. The CK1δ kinase Hrr25 is critical for sister kinetochore co-orientation, but its roles are not well understood. Here, we present the structures of Hrr25 and its complex with the monopolin subunit Mam1. Hrr25 possesses a "central domain" that packs tightly against the kinase C-lobe, adjacent to the binding site for Mam1. Together, the Hrr25 central domain and Mam1 form a novel, contiguous embellishment to the Hrr25 kinase domain that affects Hrr25 conformational dynamics and enzyme kinetics. Mam1 binds a hydrophobic surface on the Hrr25 N-lobe that is conserved in CK1δ-family kinases, suggesting a role for this surface in recruitment and/or regulation of these enzymes throughout eukaryotes. Finally, using purified proteins, we find that Hrr25 phosphorylates the kinetochore receptor for monopolin, Dsn1. Together with our new structural insights into the fully assembled monopolin complex, this finding suggests that tightly localized Hrr25 activity modulates monopolin complex-kinetochore interactions through phosphorylation of both kinetochore and monopolin complex components.
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Affiliation(s)
- Qiaozhen Ye
- Ludwig Institute for Cancer Research, San Diego Branch, San Diego, La Jolla, CA, USA
| | - Sarah N Ur
- Ludwig Institute for Cancer Research, San Diego Branch, San Diego, La Jolla, CA, USA
| | - Tiffany Y Su
- Ludwig Institute for Cancer Research, San Diego Branch, San Diego, La Jolla, CA, USA
| | - Kevin D Corbett
- Ludwig Institute for Cancer Research, San Diego Branch, San Diego, La Jolla, CA, USA Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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24
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The Activity-Dependent Regulation of Protein Kinase Stability by the Localization to P-Bodies. Genetics 2016; 203:1191-202. [PMID: 27182950 DOI: 10.1534/genetics.116.187419] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/02/2016] [Indexed: 12/21/2022] Open
Abstract
The eukaryotic cytoplasm contains a variety of ribonucleoprotein (RNP) granules in addition to the better-understood membrane-bound organelles. These granules form in response to specific stress conditions and contain a number of signaling molecules important for the control of cell growth and survival. However, relatively little is known about the mechanisms responsible for, and the ultimate consequences of, this protein localization. Here, we show that the Hrr25/CK1δ protein kinase is recruited to cytoplasmic processing bodies (P-bodies) in an evolutionarily conserved manner. This recruitment requires Hrr25 kinase activity and the Dcp2 decapping enzyme, a core constituent of these RNP granules. Interestingly, the data indicate that this localization sequesters active Hrr25 away from the remainder of the cytoplasm and thereby shields this enzyme from the degradation machinery during these periods of stress. Altogether, this work illustrates how the presence within an RNP granule can alter the ultimate fate of the localized protein.
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25
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Hegedus DD, Gerbrandt K, Coutu C. The eukaryotic protein kinase superfamily of the necrotrophic fungal plant pathogen, Sclerotinia sclerotiorum. MOLECULAR PLANT PATHOLOGY 2016; 17:634-647. [PMID: 26395470 PMCID: PMC6638376 DOI: 10.1111/mpp.12321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Protein kinases have been implicated in the regulation of many processes that guide pathogen development throughout the course of infection. A survey of the Sclerotinia sclerotiorum genome for genes encoding proteins containing the highly conserved eukaryotic protein kinase (ePK) domain, the largest protein kinase superfamily, revealed 92 S. sclerotiorum ePKs. This review examines the composition of the S. sclerotiorum ePKs based on conserved motifs within the ePK domain family, and relates this to orthologues found in other filamentous fungi and yeasts. The ePKs are also discussed in terms of their proposed role(s) in aspects of host pathogenesis, including the coordination of mycelial growth/development and deployment of pathogenicity determinants in response to environmental stimuli, nutrients and stress.
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Affiliation(s)
- Dwayne D Hegedus
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A9
| | - Kelsey Gerbrandt
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
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26
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Wang J, Davis S, Menon S, Zhang J, Ding J, Cervantes S, Miller E, Jiang Y, Ferro-Novick S. Ypt1/Rab1 regulates Hrr25/CK1δ kinase activity in ER-Golgi traffic and macroautophagy. J Cell Biol 2016. [PMID: 26195667 PMCID: PMC4508898 DOI: 10.1083/jcb.201408075] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Ypt1 directly recruits the kinase Hrr25 to COPII vesicles to activate it in two different pathways: ER to Golgi and the catabolic macroautophagy pathway induced in response to cell stress. ER-derived COPII-coated vesicles are conventionally targeted to the Golgi. However, during cell stress these vesicles also become a membrane source for autophagosomes, distinct organelles that target cellular components for degradation. How the itinerary of COPII vesicles is coordinated on these pathways remains unknown. Phosphorylation of the COPII coat by casein kinase 1 (CK1), Hrr25, contributes to the directional delivery of ER-derived vesicles to the Golgi. CK1 family members are thought to be constitutively active kinases that are regulated through their subcellular localization. Instead, we show here that the Rab GTPase Ypt1/Rab1 binds and activates Hrr25/CK1δ to spatially regulate its kinase activity. Consistent with a role for COPII vesicles and Hrr25 in membrane traffic and autophagosome biogenesis, hrr25 mutants were defective in ER–Golgi traffic and macroautophagy. These studies are likely to serve as a paradigm for how CK1 kinases act in membrane traffic.
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Affiliation(s)
- Juan Wang
- Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093
| | - Saralin Davis
- Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093
| | - Shekar Menon
- Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093
| | - Jinzhong Zhang
- Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093
| | - Jingzhen Ding
- Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093
| | - Serena Cervantes
- Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093
| | - Elizabeth Miller
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Yu Jiang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093
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27
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Abstract
Calcium is an essential cation for a cell. This cation participates in the regulation of numerous processes in either prokaryotes or eukaryotes, from bacteria to humans. Saccharomyces cerevisiae has served as a model organism to understand calcium homeostasis and calcium-dependent signaling in fungi. In this chapter it will be reviewed known and predicted transport mechanisms that mediate calcium homeostasis in the yeast. How and when calcium enters the cell, how and where it is stored, when is reutilized, and finally secreted to the environment to close the cycle. As a second messenger, maintenance of a controlled free intracellular calcium concentration is important for mediating transcriptional regulation. Many environmental stimuli modify the concentration of cytoplasmic free calcium generating the "calcium signal". This is sensed and transduced through the calmodulin/calcineurin pathway to a transcription factor, named calcineurin-responsive zinc finger, CRZ, also known as "crazy", to mediate transcriptional regulation of a large number of genes of diverse pathways including a negative feedback regulation of the calcium homeostasis system.
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Affiliation(s)
- Eduardo A Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040, Madrid, Spain.
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28
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Peng Y, Moritz M, Han X, Giddings TH, Lyon A, Kollman J, Winey M, Yates J, Agard DA, Drubin DG, Barnes G. Interaction of CK1δ with γTuSC ensures proper microtubule assembly and spindle positioning. Mol Biol Cell 2015; 26:2505-18. [PMID: 25971801 PMCID: PMC4571304 DOI: 10.1091/mbc.e14-12-1627] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 05/04/2015] [Indexed: 01/09/2023] Open
Abstract
Casein kinase 1δ (CK1δ) family members associate with microtubule-organizing centers from yeast to humans. Budding yeast CK1δ, Hrr25, directly phosphorylated γTuSC proteins in vivo and in vitro, and this phosphorylation promoted δTuSC integrity and activity in biochemical assays. Casein kinase 1δ (CK1δ) family members associate with microtubule-organizing centers (MTOCs) from yeast to humans, but their mitotic roles and targets have yet to be identified. We show here that budding yeast CK1δ, Hrr25, is a γ-tubulin small complex (γTuSC) binding factor. Moreover, Hrr25's association with γTuSC depends on its kinase activity and its noncatalytic central domain. Loss of Hrr25 kinase activity resulted in assembly of unusually long cytoplasmic microtubules and defects in spindle positioning, consistent with roles in regulation of γTuSC-mediated microtubule nucleation and the Kar9 spindle-positioning pathway, respectively. Hrr25 directly phosphorylated γTuSC proteins in vivo and in vitro, and this phosphorylation promoted γTuSC integrity and activity. Because CK1δ and γTuSC are highly conserved and present at MTOCs in diverse eukaryotes, similar regulatory mechanisms are expected to apply generally in eukaryotes.
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Affiliation(s)
- Yutian Peng
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Michelle Moritz
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158
| | - Xuemei Han
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - Thomas H Giddings
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309
| | - Andrew Lyon
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158
| | - Justin Kollman
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158
| | - Mark Winey
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309
| | - John Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - David A Agard
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Georjana Barnes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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29
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Ghalei H, Schaub FX, Doherty JR, Noguchi Y, Roush WR, Cleveland JL, Stroupe ME, Karbstein K. Hrr25/CK1δ-directed release of Ltv1 from pre-40S ribosomes is necessary for ribosome assembly and cell growth. J Cell Biol 2015; 208:745-59. [PMID: 25778921 PMCID: PMC4362465 DOI: 10.1083/jcb.201409056] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 02/02/2015] [Indexed: 11/25/2022] Open
Abstract
Casein kinase 1δ/ε (CK1δ/ε) and their yeast homologue Hrr25 are essential for cell growth. Further, CK1δ is overexpressed in several malignancies, and CK1δ inhibitors have shown promise in several preclinical animal studies. However, the substrates of Hrr25 and CK1δ/ε that are necessary for cell growth and survival are unknown. We show that Hrr25 is essential for ribosome assembly, where it phosphorylates the assembly factor Ltv1, which causes its release from nascent 40S subunits and allows subunit maturation. Hrr25 inactivation or expression of a nonphosphorylatable Ltv1 variant blocked Ltv1 release in vitro and in vivo, and prevented entry into the translation-like quality control cycle. Conversely, phosphomimetic Ltv1 variants rescued viability after Hrr25 depletion. Finally, Ltv1 knockdown in human breast cancer cells impaired apoptosis induced by CK1δ/ε inhibitors, establishing that the antiproliferative activity of these inhibitors is due, at least in part, to disruption of ribosome assembly. These findings validate the ribosome assembly pathway as a novel target for the development of anticancer therapeutics.
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Affiliation(s)
- Homa Ghalei
- Department of Cancer Biology and Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
| | - Franz X Schaub
- Department of Cancer Biology and Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458 Department of Tumor Biology, Moffitt Cancer and Research Institute, Tampa, FL 33612
| | - Joanne R Doherty
- Department of Cancer Biology and Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
| | - Yoshihiko Noguchi
- Department of Cancer Biology and Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
| | - William R Roush
- Department of Cancer Biology and Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
| | - John L Cleveland
- Department of Cancer Biology and Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458 Department of Tumor Biology, Moffitt Cancer and Research Institute, Tampa, FL 33612
| | - M Elizabeth Stroupe
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306 Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Katrin Karbstein
- Department of Cancer Biology and Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
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30
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Tanaka C, Tan LJ, Mochida K, Kirisako H, Koizumi M, Asai E, Sakoh-Nakatogawa M, Ohsumi Y, Nakatogawa H. Hrr25 triggers selective autophagy-related pathways by phosphorylating receptor proteins. ACTA ACUST UNITED AC 2014; 207:91-105. [PMID: 25287303 PMCID: PMC4195827 DOI: 10.1083/jcb.201402128] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The budding yeast kinase Hrr25 regulates two selective autophagy–related pathways by phosphorylating degradation target receptors and thereby promoting their interaction with Atg11 and the formation of autophagosomal membrane. In selective autophagy, degradation targets are specifically recognized, sequestered by the autophagosome, and transported into the lysosome or vacuole. Previous studies delineated the molecular basis by which the autophagy machinery recognizes those targets, but the regulation of this process is still poorly understood. In this paper, we find that the highly conserved multifunctional kinase Hrr25 regulates two distinct selective autophagy–related pathways in Saccharomyces cerevisiae. Hrr25 is responsible for the phosphorylation of two receptor proteins: Atg19, which recognizes the assembly of vacuolar enzymes in the cytoplasm-to-vacuole targeting pathway, and Atg36, which recognizes superfluous peroxisomes in pexophagy. Hrr25-mediated phosphorylation enhances the interactions of these receptors with the common adaptor Atg11, which recruits the core autophagy-related proteins that mediate the formation of the autophagosomal membrane. Thus, this study introduces regulation of selective autophagy as a new role of Hrr25 and, together with other recent studies, reveals that different selective autophagy–related pathways are regulated by a uniform mechanism: phosphoregulation of the receptor–adaptor interaction.
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Affiliation(s)
- Chikara Tanaka
- Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Li-Jing Tan
- Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Keisuke Mochida
- Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Hiromi Kirisako
- Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Michiko Koizumi
- Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Eri Asai
- Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Machiko Sakoh-Nakatogawa
- Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Yoshinori Ohsumi
- Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Hitoshi Nakatogawa
- Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan Frontier Research Center and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
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31
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Mochida K, Ohsumi Y, Nakatogawa H. Hrr25 phosphorylates the autophagic receptor Atg34 to promote vacuolar transport of α-mannosidase under nitrogen starvation conditions. FEBS Lett 2014; 588:3862-9. [PMID: 25281559 DOI: 10.1016/j.febslet.2014.09.032] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 01/08/2023]
Abstract
In Saccharomyces cerevisiae, under nitrogen-starvation conditions, the α-mannosidase Ams1 is recognized by the autophagic receptor Atg34 and transported into the vacuole, where it functions as an active enzyme. In this study, we identified Hrr25 as the kinase that phosphorylates Atg34 under these conditions. Hrr25-mediated phosphorylation does not affect the interaction of Atg34 with Ams1, but instead promotes Atg34 binding to the adaptor protein Atg11, which recruits the autophagy machinery to the Ams1-Atg34 complex, resulting in activation of the vacuolar transport of Ams1. Our findings reveal the regulatory mechanism of a biosynthetic pathway mediated by the autophagy machinery.
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Affiliation(s)
- Keisuke Mochida
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Japan
| | | | - Hitoshi Nakatogawa
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Japan; Frontier Research Center, Tokyo Institute of Technology, Japan.
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32
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Pfaffenwimmer T, Reiter W, Brach T, Nogellova V, Papinski D, Schuschnig M, Abert C, Ammerer G, Martens S, Kraft C. Hrr25 kinase promotes selective autophagy by phosphorylating the cargo receptor Atg19. EMBO Rep 2014; 15:862-70. [PMID: 24968893 PMCID: PMC4197043 DOI: 10.15252/embr.201438932] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/30/2014] [Accepted: 06/10/2014] [Indexed: 01/08/2023] Open
Abstract
Autophagy is the major pathway for the delivery of cytoplasmic material to the vacuole or lysosome. Selective autophagy is mediated by cargo receptors, which link the cargo to the scaffold protein Atg11 and to Atg8 family proteins on the forming autophagosomal membrane. We show that the essential kinase Hrr25 activates the cargo receptor Atg19 by phosphorylation, which is required to link cargo to the Atg11 scaffold, allowing selective autophagy to proceed. We also find that the Atg34 cargo receptor is regulated in a similar manner, suggesting a conserved mechanism.
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Affiliation(s)
| | - Wolfgang Reiter
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Thorsten Brach
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | | | - Daniel Papinski
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | | | - Christine Abert
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Gustav Ammerer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Sascha Martens
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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33
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Bibian M, Rahaim RJ, Choi JY, Noguchi Y, Schürer S, Chen W, Nakanishi S, Licht K, Rosenberg LH, Li L, Feng Y, Cameron MD, Duckett DR, Cleveland JL, Roush WR. Development of highly selective casein kinase 1δ/1ε (CK1δ/ε) inhibitors with potent antiproliferative properties. Bioorg Med Chem Lett 2013; 23:4374-80. [PMID: 23787102 PMCID: PMC3783656 DOI: 10.1016/j.bmcl.2013.05.075] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 05/20/2013] [Accepted: 05/21/2013] [Indexed: 12/11/2022]
Abstract
The development of a series of potent and highly selective casein kinase 1δ/ε (CK1δ/ε) inhibitors is described. Starting from a purine scaffold inhibitor (SR-653234) identified by high throughput screening, we developed a series of potent and highly kinase selective inhibitors, including SR-2890 and SR-3029, which have IC₅₀ ≤ 50 nM versus CK1δ. The two lead compounds have ≤100 nM EC50 values in MTT assays against the human A375 melanoma cell line and have physical, in vitro and in vivo PK properties suitable for use in proof of principle animal xenograft studies against human cancer cell lines.
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Affiliation(s)
- Mathieu Bibian
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Ronald J. Rahaim
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Jun Yong Choi
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yoshihiko Noguchi
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Stephan Schürer
- Department of Molecular and Cellular Pharmacology and Center for Computational Science, University of Miami, 1120 NW 14th St., Miami, FL 33136, United States
| | - Weimin Chen
- Department of Molecular Therapeutics, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Shima Nakanishi
- Department of Cancer Biology, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Konstantin Licht
- Department of Cancer Biology, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Laura H. Rosenberg
- Department of Molecular Therapeutics, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Lin Li
- Department of Molecular Therapeutics, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yangbo Feng
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Michael D. Cameron
- Department of Molecular Therapeutics, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Derek R. Duckett
- Department of Molecular Therapeutics, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - John L. Cleveland
- Department of Cancer Biology, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
| | - William R. Roush
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, United States
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34
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Apostolaki A, Harispe L, Calcagno-Pizarelli AM, Vangelatos I, Sophianopoulou V, Arst HN, Peñalva MA, Amillis S, Scazzocchio C. Aspergillus nidulans CkiA is an essential casein kinase I required for delivery of amino acid transporters to the plasma membrane. Mol Microbiol 2012; 84:530-49. [PMID: 22489878 PMCID: PMC3491690 DOI: 10.1111/j.1365-2958.2012.08042.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Type I casein kinases are highly conserved among Eukaryotes. Of the two Aspergillus nidulans casein kinases I, CkiA is related to the δ/ε mammalian kinases and to Saccharomyces cerevisiæ Hrr25p. CkiA is essential. Three recessive ckiA mutations leading to single residue substitutions, and downregulation using a repressible promoter, result in partial loss-of-function, which leads to a pleiotropic defect in amino acid utilization and resistance to toxic amino acid analogues. These phenotypes correlate with miss-routing of the YAT plasma membrane transporters AgtA (glutamate) and PrnB (proline) to the vacuole under conditions that, in the wild type, result in their delivery to the plasma membrane. Miss-routing to the vacuole and subsequent transporter degradation results in a major deficiency in the uptake of the corresponding amino acids that underlies the inability of the mutant strains to catabolize them. Our findings may have important implications for understanding how CkiA, Hrr25p and other fungal orthologues regulate the directionality of transport at the ER-Golgi interface.
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Affiliation(s)
- Angeliki Apostolaki
- Institut de Génétique et Microbiologie, Université Paris-Sud (XI), UMR 8621 CNRS 91450 Orsay, France
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35
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Oeljeklaus S, Reinartz BS, Wolf J, Wiese S, Tonillo J, Podwojski K, Kuhlmann K, Stephan C, Meyer HE, Schliebs W, Brocard C, Erdmann R, Warscheid B. Identification of Core Components and Transient Interactors of the Peroxisomal Importomer by Dual-Track Stable Isotope Labeling with Amino Acids in Cell Culture Analysis. J Proteome Res 2012; 11:2567-80. [DOI: 10.1021/pr3000333] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Silke Oeljeklaus
- Faculty of Biology and BIOSS
Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Benedikt S. Reinartz
- Medizinisches Proteom-Center,
Zentrum für klinische Forschung, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum,
Germany
| | - Janina Wolf
- Institute of Physiological
Chemistry,
Department of Systems Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Sebastian Wiese
- Faculty of Biology and BIOSS
Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Jason Tonillo
- Medizinisches Proteom-Center,
Zentrum für klinische Forschung, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum,
Germany
| | - Katharina Podwojski
- Medizinisches Proteom-Center,
Zentrum für klinische Forschung, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum,
Germany
| | - Katja Kuhlmann
- Medizinisches Proteom-Center,
Zentrum für klinische Forschung, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum,
Germany
| | - Christian Stephan
- Medizinisches Proteom-Center,
Zentrum für klinische Forschung, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum,
Germany
| | - Helmut E. Meyer
- Medizinisches Proteom-Center,
Zentrum für klinische Forschung, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum,
Germany
| | - Wolfgang Schliebs
- Institute of Physiological
Chemistry,
Department of Systems Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Cécile Brocard
- University of Vienna, Center of Molecular Biology, Department of Biochemistry and Cell
Biology, Max F. Perutz Laboratories, Dr. Bohrgasse 9, 1030 Vienna,
Austria
| | - Ralf Erdmann
- Institute of Physiological
Chemistry,
Department of Systems Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology and BIOSS
Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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36
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Hirner H, Günes C, Bischof J, Wolff S, Grothey A, Kühl M, Oswald F, Wegwitz F, Bösl MR, Trauzold A, Henne-Bruns D, Peifer C, Leithäuser F, Deppert W, Knippschild U. Impaired CK1 delta activity attenuates SV40-induced cellular transformation in vitro and mouse mammary carcinogenesis in vivo. PLoS One 2012; 7:e29709. [PMID: 22235331 PMCID: PMC3250488 DOI: 10.1371/journal.pone.0029709] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 12/01/2011] [Indexed: 02/05/2023] Open
Abstract
Simian virus 40 (SV40) is a powerful tool to study cellular transformation in vitro, as well as tumor development and progression in vivo. Various cellular kinases, among them members of the CK1 family, play an important role in modulating the transforming activity of SV40, including the transforming activity of T-Ag, the major transforming protein of SV40, itself. Here we characterized the effects of mutant CK1δ variants with impaired kinase activity on SV40-induced cell transformation in vitro, and on SV40-induced mammary carcinogenesis in vivo in a transgenic/bi-transgenic mouse model. CK1δ mutants exhibited a reduced kinase activity compared to wtCK1δ in in vitro kinase assays. Molecular modeling studies suggested that mutation N172D, located within the substrate binding region, is mainly responsible for impaired mutCK1δ activity. When stably over-expressed in maximal transformed SV-52 cells, CK1δ mutants induced reversion to a minimal transformed phenotype by dominant-negative interference with endogenous wtCK1δ. To characterize the effects of CK1δ on SV40-induced mammary carcinogenesis, we generated transgenic mice expressing mutant CK1δ under the control of the whey acidic protein (WAP) gene promoter, and crossed them with SV40 transgenic WAP-T-antigen (WAP-T) mice. Both WAP-T mice as well as WAP-mutCK1δ/WAP-T bi-transgenic mice developed breast cancer. However, tumor incidence was lower and life span was significantly longer in WAP-mutCK1δ/WAP-T bi-transgenic animals. The reduced CK1δ activity did not affect early lesion formation during tumorigenesis, suggesting that impaired CK1δ activity reduces the probability for outgrowth of in situ carcinomas to invasive carcinomas. The different tumorigenic potential of SV40 in WAP-T and WAP-mutCK1δ/WAP-T tumors was also reflected by a significantly different expression of various genes known to be involved in tumor progression, specifically of those involved in wnt-signaling and DNA repair. Our data show that inactivating mutations in CK1δ impair SV40-induced cellular transformation in vitro and mouse mammary carcinogenesis in vivo.
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MESH Headings
- Animals
- Antigens, Viral, Tumor/immunology
- Casein Kinase Idelta/chemistry
- Casein Kinase Idelta/genetics
- Casein Kinase Idelta/metabolism
- Cell Line
- Cell Line, Tumor
- Cell Transformation, Viral/genetics
- Disease Progression
- Female
- Gene Expression Regulation
- Male
- Mammary Glands, Animal/metabolism
- Mammary Glands, Animal/pathology
- Mammary Glands, Animal/virology
- Mammary Neoplasms, Experimental/enzymology
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/pathology
- Mammary Neoplasms, Experimental/virology
- Mice
- Mice, Inbred BALB C
- Mice, Transgenic
- Milk Proteins/genetics
- Models, Molecular
- Mutation
- Phenotype
- Phosphorylation
- Promoter Regions, Genetic/genetics
- Protein Structure, Tertiary
- Simian virus 40/immunology
- Simian virus 40/physiology
- Survival Analysis
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Affiliation(s)
- Heidrun Hirner
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | - Cagatay Günes
- Institute of Molecular Medicine and Max-Planck-Research Group on Stem Cell Aging, University of Ulm, Ulm, Germany
| | - Joachim Bischof
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | - Sonja Wolff
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | - Arnhild Grothey
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | - Marion Kühl
- Department of Tumor Virology, Heinrich-Pette-Institute, Leibniz-Center for Experimental Virology, Hamburg, Germany
| | - Franz Oswald
- Department of Internal Medicine I, University of Ulm, Ulm, Germany
| | - Florian Wegwitz
- Department of Tumor Virology, Heinrich-Pette-Institute, Leibniz-Center for Experimental Virology, Hamburg, Germany
| | - Michael R. Bösl
- Max Planck Institute of Neurobiology Transgenic Mouse Models, Max Planck Institute, Martinsried, Germany
| | - Anna Trauzold
- Division of Molecular Oncology, Institute for Experimental Cancer Research, CCCNorth, UK S-H, Kiel, Germany
| | - Doris Henne-Bruns
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | | | | | - Wolfgang Deppert
- Department of Tumor Virology, Heinrich-Pette-Institute, Leibniz-Center for Experimental Virology, Hamburg, Germany
| | - Uwe Knippschild
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
- * E-mail:
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37
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Ben-Nissan G, Yang Y, Lee JY. Partitioning of casein kinase 1-like 6 to late endosome-like vesicles. PROTOPLASMA 2010; 240:45-56. [PMID: 19941015 DOI: 10.1007/s00709-009-0087-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 10/29/2009] [Indexed: 05/28/2023]
Abstract
Members of the casein kinase 1 family are highly conserved protein Ser/Thr kinases found in all eukaryotes. They are involved in various cellular, physiological, and developmental processes, but the role of this family of kinase in plants is not well known. By localization studies employing fluorescent live cell imaging and biochemical membrane fractionation, here we showed that Arabidopsis casein kinase-like 6 (CKL6) localizes to motile vesicle-like structures that cofractionate with prevacuolar markers. They were found both in the cytoplasm and at the cell periphery and were motile within the cell. Apparently, this motility was dependent on actin filaments and CKL6-positive vesicles partially colocalized with a late endosomal compartment. However, CKL6-positive structures were not sensitive to brefeldin A nor wortmannin treatment, suggesting that they may belong to a novel compartment. Association of CKL6-positive structures with the cell periphery at the cellular junctions was detected after separation of the protoplasts by plasmolysis. Collectively, these data led us to propose that CKL6 is associated with late endosomal-like compartments that are not fully characterized and may play a role in cellular processes important for regulating components in membrane trafficking.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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38
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Forebrain overexpression of CK1delta leads to down-regulation of dopamine receptors and altered locomotor activity reminiscent of ADHD. Proc Natl Acad Sci U S A 2010; 107:4401-6. [PMID: 20145109 DOI: 10.1073/pnas.0915173107] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dopamine neurotransmission controls motor and perseverative behavior, is mediated by protein phosphorylation, and may be perturbed in disorders of attention and hyperactivity. To assess the role of casein kinase I (CK1) in the regulation of dopamine signaling, we generated a genetically modified mouse line that overexpresses CK1delta (CK1delta OE) specifically in the forebrain. Overexpression was confirmed both at the mRNA and at the protein levels. Under basal conditions, CK1delta OE mice exhibited horizontal and vertical hyperactivity, reduced anxiety, and nesting behavior deficiencies. The CK1delta OE mice also presented paradoxical responses to dopamine receptor stimulation, showing hypoactivity following injection of d-amphetamine or methylphenidate, indicating that CK1 activity has a profound effect on dopamine signaling in vivo. Interestingly, CK1delta overexpression led to significantly reduced D1R and D2R dopamine receptor levels. All together, under basal conditions and in response to drug stimulation, the behavioral phenotype of CK1delta OE mice is reminiscent of the symptoms and drug responses observed in attention-deficit/hyperactivity disorder and therefore the CK1delta OE mice appear to be a model for this disorder.
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39
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Abstract
Ribosome assembly is required for cell growth in all organisms. Classic in vitro work in bacteria has led to a detailed understanding of the biophysical, thermodynamic, and structural basis for the ordered and correct assembly of ribosomal proteins on ribosomal RNA. Furthermore, it has enabled reconstitution of active subunits from ribosomal RNA and proteins in vitro. Nevertheless, recent work has shown that eukaryotic ribosome assembly requires a large macromolecular machinery in vivo. Many of these assembly factors such as ATPases, GTPases, and kinases hydrolyze nucleotide triphosphates. Because these enzymes are likely regulatory proteins, much work to date has focused on understanding their role in the assembly process. Here, we review these factors, as well as other sources of energy, and their roles in the ribosome assembly process. In addition, we propose roles of energy-releasing enzymes in the assembly process, to explain why energy is used for a process that occurs largely spontaneously in bacteria. Finally, we use literature data to suggest testable models for how these enzymes could be used as targets for regulation of ribosome assembly.
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Affiliation(s)
- Bethany S Strunk
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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40
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Mehlgarten C, Jablonowski D, Breunig KD, Stark MJR, Schaffrath R. Elongator function depends on antagonistic regulation by casein kinase Hrr25 and protein phosphatase Sit4. Mol Microbiol 2009; 73:869-81. [PMID: 19656297 DOI: 10.1111/j.1365-2958.2009.06811.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In yeast, the role for the Elongator complex in tRNA anticodon modification is affected by phosphorylation of Elongator subunit Elp1. Thus, hyperphosphorylation of Elp1 due to inactivation of protein phosphatase Sit4 correlates with Elongator-minus phenotypes including resistance towards zymocin, a tRNase cleaving anticodons of Elongator-dependent tRNAs. Here we show that zymocin resistance of casein kinase hrr25 mutants associates with hypophosphorylation of Elp1 and that nonsense suppression by the Elongator-dependent SUP4 tRNA is abolished in hrr25 or sit4 mutants. Thus changes that perturb the evenly balanced ratio between hyper- and hypophosphorylated Elp1 forms present in wild-type cells lead to Elongator inactivation. Antagonistic roles for Hrr25 and Sit4 in Elongator function are further supported by our data that Sit4 inactivation is capable of restoring both zymocin sensitivity and normal ratios between the two Elp1 forms in hrr25 mutants. Hrr25 binds to Elongator in a fashion dependent on Elongator partner Kti12. Like sit4 mutants, overexpression of Kti12 triggers Elp1 hyperphosphorylation. Intriguingly, this effect of Kti12 is blocked by hrr25 mutations, which also show enhanced binding of Kti12 to Elongator. Collectively, our data suggest that rather than directly targeting Elp1, the Hrr25 kinase indirectly affects Elp1 phosphorylation states through control of Sit4-dependent dephosphorylation of Elp1.
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Affiliation(s)
- Constance Mehlgarten
- Institut für Biologie, Genetik, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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41
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Huang B, Lu J, Byström AS. A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2008; 14:2183-94. [PMID: 18755837 PMCID: PMC2553728 DOI: 10.1261/rna.1184108] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We recently showed that the gamma-subunit of Kluyveromyces lactis killer toxin (gamma-toxin) is a tRNA endonuclease that cleaves tRNA(mcm5s2UUC Glu), tRNA(mcm5s2UUU Lys), and tRNA(mcm5s2UUG Gln) 3' of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U). The 5-methoxycarbonylmethyl (mcm(5)) side chain was important for efficient cleavage by gamma-toxin, and defects in mcm(5) side-chain synthesis correlated with resistance to gamma-toxin. Based on this correlation, a genome-wide screen was performed to identify gene products involved in the formation of the mcm(5) side chain. From a collection of 4826 homozygous diploid Saccharomyces cerevisiae strains, each with one nonessential gene deleted, 63 mutants resistant to Kluyveromyces lactis killer toxin were identified. Among these, eight were earlier identified to have a defect in formation of the mcm(5) side chain. Analysis of the remaining mutants and other known gamma-toxin resistant mutants revealed that sit4, kti14, and KTI5 mutants also have a defect in the formation of mcm(5). A mutant lacking two of the Sit4-associated proteins, Sap185 and Sap190, displays the same modification defect as a sit4-null mutant. Interestingly, several mutants were found to be defective in the synthesis of the 2-thio (s(2)) group of the mcm(5)s(2)U nucleoside. In addition to earlier described mutants, formation of the s(2) group was also abolished in urm1, uba4, and ncs2 mutants and decreased in the yor251c mutant. Like the absence of the mcm(5) side chain, the lack of the s(2) group renders tRNA(mcm5s2UUC Glu) less sensitive to gamma-toxin, reinforcing the importance of the wobble nucleoside mcm(5)s(2)U for tRNA cleavage by gamma-toxin.
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Affiliation(s)
- Bo Huang
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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42
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Ray P, Basu U, Ray A, Majumdar R, Deng H, Maitra U. The Saccharomyces cerevisiae 60 S ribosome biogenesis factor Tif6p is regulated by Hrr25p-mediated phosphorylation. J Biol Chem 2008; 283:9681-91. [PMID: 18256024 DOI: 10.1074/jbc.m710294200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The biosynthesis of 60 S ribosomal subunits in Saccharomyces cerevisiae requires Tif6p, the yeast homologue of mammalian eIF6. This protein is necessary for the formation of 60 S ribosomal subunits because it is essential for the processing of 35 S pre-rRNA to the mature 25 S and 5.8 S rRNAs. In the present work, using molecular genetic and biochemical analyses, we show that Hrr25p, an isoform of yeast casein kinase I, phosphorylates Tif6p both in vitro and in vivo. Tryptic phosphopeptide mapping of in vitro phosphorylated Tif6p by Hrr25p and (32)P-labeled Tif6p isolated from yeast cells followed by mass spectrometric analysis revealed that phosphorylation occurred on a single tryptic peptide at Ser-174. Sucrose gradient fractionation and coimmunoprecipitation experiments demonstrate that a small but significant fraction of Hrr25p is bound to 66 S preribosomal particles that also contain bound Tif6p. Depletion of Hrr25p from a conditional yeast mutant that fails to phosphorylate Tif6p was unable to process pre-rRNAs efficiently, resulting in significant reduction in the formation of 25 S rRNA. These results along with our previous observations that phosphorylatable Ser-174 is required for yeast cell growth and viability, suggest that Hrr25p-mediated phosphorylation of Tif6p plays a critical role in the biogenesis of 60 S ribosomal subunits in yeast cells.
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Affiliation(s)
- Partha Ray
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
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43
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Lusk CP, Waller DD, Makhnevych T, Dienemann A, Whiteway M, Thomas DY, Wozniak RW. Nup53p is a target of two mitotic kinases, Cdk1p and Hrr25p. Traffic 2007; 8:647-60. [PMID: 17461799 DOI: 10.1111/j.1600-0854.2007.00559.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear pore complexes (NPCs) form channels across the nuclear envelope and provide the sole sites of molecular exchange between the cytoplasm and nucleoplasm. The NPC is a target of a number of post-translational modifications, including phosphorylation, yet the functions of these modifications are ill defined. Here, we have investigated the mitotic specific phosphorylation of a yeast nucleoporin Nup53p. Two kinases were identified that phosphorylate Nup53p: the mitotic kinase Cdk1p/Cdc2p/Cdc28p and the casein kinase Hrr25p. Hrr25p was identified by screening 119 yeast kinases for their ability to phosphorylate Nup53p in vitro. Conditional alleles of Hrr25p support the conclusion that Hrr25p phosphorylates Nup53p in vivo. We further demonstrated using solution binding and affinity purification assays, that Hrr25p directly binds Nup53p in an interaction that is destabilized by the phosphorylation of Nup53p. Consistent with this observation, we observed that Hrr25p moves between distinct locations in the cell during the cell cycle including the nucleus, the cortex of the emerging bud and the spindle pole bodies. Cdk1p also contributes to Nup53p phosphorylation as specific inhibition of Cdk1p or mutation of Cdk1p consensus sites partially blocked its phosphorylation. The ability of nup53 alleles containing Cdk1p site mutations to complement synthetic defects of nup53 Delta nup170 Delta strains is linked to a function for Nup53p in the spindle assembly checkpoint.
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Affiliation(s)
- C Patrick Lusk
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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44
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Petronczki M, Matos J, Mori S, Gregan J, Bogdanova A, Schwickart M, Mechtler K, Shirahige K, Zachariae W, Nasmyth K. Monopolar attachment of sister kinetochores at meiosis I requires casein kinase 1. Cell 2006; 126:1049-64. [PMID: 16990132 DOI: 10.1016/j.cell.2006.07.029] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 05/16/2006] [Accepted: 07/17/2006] [Indexed: 11/26/2022]
Abstract
In meiosis, a single round of DNA replication is followed by two consecutive rounds of chromosome segregation, called meiosis I and II. Disjunction of maternal from paternal centromeres during meiosis I depends on the attachment of sister kinetochores to microtubules emanating from the same pole. In budding yeast, monopolar attachment requires recruitment to kinetochores of the monopolin complex. How monopolin promotes monopolar attachment was unclear, as its subunits are poorly conserved and lack similarities to proteins with known functions. We show here that the monopolin subunit Mam1 binds tightly to Hrr25, a highly conserved casein kinase 1 delta/epsilon (CK1delta/epsilon), and recruits it to meiosis I centromeres. Hrr25 kinase activity and Mam1 binding are both essential for monopolar attachment. Since CK1delta/epsilon activity is important for accurate chromosome segregation during meiosis I also in fission yeast, phosphorylation of kinetochore proteins by CK1delta/epsilon might be an evolutionary conserved process required for monopolar attachment.
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Affiliation(s)
- Mark Petronczki
- Research Institute of Molecular Pathology, Dr. Bohrgasse 7, A-1030 Vienna, Austria
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45
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Guan J, Li H, Rogulja A, Axelrod JD, Cadigan KM. The Drosophila casein kinase Iepsilon/delta Discs overgrown promotes cell survival via activation of DIAP1 expression. Dev Biol 2006; 303:16-28. [PMID: 17134692 PMCID: PMC2892850 DOI: 10.1016/j.ydbio.2006.10.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 10/17/2006] [Accepted: 10/18/2006] [Indexed: 01/07/2023]
Abstract
The proper number of cells in developing tissues is achieved by coordinating cell division with apoptosis. In Drosophila, the adult wing is derived from wing imaginal discs, which undergo a period of growth and proliferation during larval stages without much programmed cell death. In this report, we demonstrate that the Drosophila casein kinase Iepsilon/delta, known as Discs overgrown (Dco), is required for maintaining this low level of apoptosis. Expression of dco can suppress the apoptotic activity of Head involution defective (Hid) in the developing eye. Loss of dco in the wing disc results in a dramatic reduction in expression of the caspase inhibitor DIAP1 and a concomitant activation of caspases. The regulation of DIAP1 by Dco occurs by a post-transcriptional mechanism that is independent of hid. Mutant clones of dco are considerably smaller than controls even when apoptosis is inhibited, suggesting that Dco promotes cell division/growth in addition to its role in cell survival. The dco phenotype cannot be explained by defects Wingless (Wg) signaling. We propose that Dco coordinates tissue size by stimulating cell division/growth and blocking apoptosis via activation of DIAP1 expression.
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Affiliation(s)
- Ju Guan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Natural Science Building, Ann Arbor MI 48109-1048, USA
| | - Hui Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Natural Science Building, Ann Arbor MI 48109-1048, USA
| | - Ana Rogulja
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Natural Science Building, Ann Arbor MI 48109-1048, USA
| | - Jeff D. Axelrod
- Department of Pathology, Stanford University School of Medicine, Stanford CA 94305
| | - Ken M. Cadigan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Natural Science Building, Ann Arbor MI 48109-1048, USA
- Corresponding author. Fax: +1 734 647-0884. Email address: (K. Cadigan)
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46
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Blanco S, Klimcakova L, Vega FM, Lazo PA. The subcellular localization of vaccinia-related kinase-2 (VRK2) isoforms determines their different effect on p53 stability in tumour cell lines. FEBS J 2006; 273:2487-504. [PMID: 16704422 DOI: 10.1111/j.1742-4658.2006.05256.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
VRK is a new kinase family of unknown function. Endogenous human vacinia-related kinase 2 (VRK2) protein is present in both the nucleus and the cytosol, which is a consequence of alternative splicing of two VRK2 messages coding for proteins of 508 and 397 amino acids, respectively. VRK2A has a C-terminal hydrophobic region that anchors the protein to membranes in the endoplasmic reticulum (ER) and mitochondria, and it colocalizes with calreticulin, calnexin and mitotracker; whereas VRK2B is detected in both the cytoplasm and the nucleus. VRK2A is expressed in all cell types, whereas VRK2B is expressed in cell lines in which VRK1 is cytoplasmic. Both VRK2 isoforms have an identical catalytic N-terminal domain and phosphorylate p53 in vitro uniquely in Thr18. Phosphorylation of the p53 protein in response to cellular stresses results in its stabilization by modulating its binding to other proteins. However, p53 phosphorylation also occurs in the absence of stress. Only overexpression of the nuclear VRK2B isoform induces p53 stabilization by post-translational modification, largely due to Thr18 phosphorylation. VRK2B may play a role in controlling the binding specificity of the N-terminal transactivation domain of p53. Indeed, the p53 phosphorylated by VRK2B shows a reduction in ubiquitination by Mdm2 and an increase in acetylation by p300. Endogenous p53 is also phosphorylated in Thr18 by VRK2B, promoting its stabilization and transcriptional activation in A549 cells. The relative phosphorylation of Thr18 by VRK2B is similar in magnitude to that induced by taxol, which might use a different signalling pathway. In this context, VRK2B kinase might functionally replace nuclear VRK1. Therefore, these kinases might be components of a new signalling pathway that is likely to play a role in normal cell proliferation.
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Affiliation(s)
- Sandra Blanco
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, Spain
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47
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Santos CR, Rodríguez-Pinilla M, Vega FM, Rodríguez-Peralto JL, Blanco S, Sevilla A, Valbuena A, Hernández T, van Wijnen AJ, Li F, de Alava E, Sánchez-Céspedes M, Lazo PA. VRK1 signaling pathway in the context of the proliferation phenotype in head and neck squamous cell carcinoma. Mol Cancer Res 2006; 4:177-85. [PMID: 16547155 DOI: 10.1158/1541-7786.mcr-05-0212] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The vaccinia-related kinase (VRK) proteins are a new family with three members in the human kinome. The VRK1 protein phosphorylates several transcription factors and has been postulated to be involved in regulation of cell proliferation. In normal squamous epithelium, VRK1 is expressed in the proliferation area. Because VRK1 can stabilize p53, the expression of the VRK1 protein was analyzed in the context of the p53 pathway and the proliferation phenotype in a series of 73 head and neck squamous cell carcinomas. VRK1 protein level positively correlated with p53 response proteins, particularly hdm2 and p21. The VRK1 protein also correlated positively with several proteins associated with proliferation, such as cyclin-dependent kinase 2 (CDK2), CDK6, cdc2, cyclins B1 and A, topoisomerase II, survivin, and Ki67. The level of VRK1 protein behaves like a proliferation marker in this series of head and neck squamous cell carcinomas. To identify a possible regulatory role for VRK1 and because it regulates gene transcription, the promoters of two genes were studied, CDK2 and SURVIVIN, whose proteins correlated positively with VRK1. VRK1 increases the activity of both the CDK2 and SURVIVIN gene promoters. The expression of VRK1 was analyzed in the context of regulators of the G1-S transition. VRK1 protein levels increase in response to E2F1 and are reduced by retinoblastoma and p16. These data suggest that VRK1 might play a role in cell cycle regulation and is likely to represent the beginning of a new control mechanism of cell cycle, particularly late in the G1-S phase.
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Affiliation(s)
- Claudio R Santos
- Instituto de Biología Molecular y Celular del Cáncer, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Cientificas, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
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48
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Bustos V, Marin O, Meggio F, Cesaro L, Allende C, Allende J, Pinna L. Generation of protein kinase Ck1alpha mutants which discriminate between canonical and non-canonical substrates. Biochem J 2006; 391:417-24. [PMID: 15975091 PMCID: PMC1276941 DOI: 10.1042/bj20050717] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein kinase CK1 denotes a family of pleiotropic serine/threonine protein kinases implicated in a variety of cellular functions. Typically, CK1 acts as a 'phosphate-directed' kinase whose targeting is primed by a single phosphorylated side chain at position n-3 or n-4 relative to serine/threonine, but increasing evidence is accumulating that CK1 can also engage some of its substrates at sites that do not conform to this canonical consensus. In the present paper, we show that CK1a phosphorylates with the same efficiency phosphopeptides primed by a phosphoserine residue at either n-3 [pS(-3)] or n-4 [pS(-4)] positions. The phosphorylation efficiency of the pS(-4) peptide, and to a lesser extent that of the pS(-3) peptide, is impaired by the triple mutation of the lysine residues in the K229KQK232 stretch to alanine residues, promoting 40-fold and 6-fold increases of Km respectively. In both cases, the individual mutation of Lys232 is as detrimental as the triple mutation. A kinetic alanine-scan analysis with a series of substituted peptide substrates in which the priming phosphoserine residue was effectively replaced by a cluster of four aspartate residues was also consistent with a crucial role of Lys232 in the recognition of the acidic determinant at position n-4. In sharp contrast, the phosphorylation of b-catenin and of a peptide including the non-canonical b-catenin site (Ser45) lacking acidic/phosphorylated determinants upstream is not significantly affected by mutations in the KKQK stretch. These data provide a molecular insight into the structural features that underlie the site specificity of CK1a and disclose the possibility of developing strategies for the preferential targeting of subsets of CK1 substrates.
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Affiliation(s)
- Victor H. Bustos
- *Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Casilla 70086, Santiago 7, Chile
| | - Oriano Marin
- †Dipartimento di Chimica Biologica, Università di Padova, viale G. Colombo 3, 35121 Padova, Italy
- ‡Istituto Veneto di Medicina Molecolare, via Orus 2, 35129 Padova, Italy
| | - Flavio Meggio
- †Dipartimento di Chimica Biologica, Università di Padova, viale G. Colombo 3, 35121 Padova, Italy
- ‡Istituto Veneto di Medicina Molecolare, via Orus 2, 35129 Padova, Italy
| | - Luca Cesaro
- †Dipartimento di Chimica Biologica, Università di Padova, viale G. Colombo 3, 35121 Padova, Italy
- ‡Istituto Veneto di Medicina Molecolare, via Orus 2, 35129 Padova, Italy
| | - Catherine C. Allende
- *Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Casilla 70086, Santiago 7, Chile
| | - Jorge E. Allende
- *Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Casilla 70086, Santiago 7, Chile
| | - Lorenzo A. Pinna
- †Dipartimento di Chimica Biologica, Università di Padova, viale G. Colombo 3, 35121 Padova, Italy
- ‡Istituto Veneto di Medicina Molecolare, via Orus 2, 35129 Padova, Italy
- To whom correspondence should be addressed (email )
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Okamura A, Iwata N, Tamekane A, Yakushijin K, Nishikawa S, Hamaguchi M, Fukui C, Yamamoto K, Matsui T. Casein kinase Iepsilon down-regulates phospho-Akt via PTEN, following genotoxic stress-induced apoptosis in hematopoietic cells. Life Sci 2005; 78:1624-9. [PMID: 16274701 DOI: 10.1016/j.lfs.2005.07.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2005] [Accepted: 07/26/2005] [Indexed: 11/30/2022]
Abstract
Here, we show a functional role of casein kinase I (CKI) epsilon in hematopoietic cell survival through the modification of phosphatidylinositol 3-kinase (PI3K)/Akt signaling. Introduction of wild-type (WT)-CKIepsilon into interleukin-3 (IL-3)-dependent 32D cells increased the sensitivity to genotoxic stresses, such as gamma-irradiation, etoposide, and IL-3 deprivation, whereas kinase-negative (KN)-CKIepsilon suppressed it. Contrary to KN-CKIepsilon, WT-CKIepsilon attenuated the IL-3-induced activation of Akt with the increase of PTEN activity. Similarly, the increase of Akt activation, as well as PTEN inactivation, was accompanied both by a decrease of CKIepsilon expression induced by all-trans retinoic acid and by the addition of a specific inhibitor for CKIepsilon in HL-60 cells. CKIepsilon seems to activate PTEN by physical interaction. These results suggest that the CKIepsilon-induced down-regulation of PI3K/Akt signaling through PTEN lead to amplified sensitivity to apoptosis. Thus, the suppression of CKIepsilon in many human leukemia cell lines may play a role in the cell immortalization.
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Affiliation(s)
- Atsuo Okamura
- Hematology/Oncology, Department of Medicine, Kobe University Graduate School of Medicine 7-5-2, Chuo-ku, Kobe 650-0017, Japan
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van de Sande WWJ, Gorkink R, Simons G, Ott A, Ahmed AOA, Verbrugh H, van Belkum A. Genotyping of Madurella mycetomatis by selective amplification of restriction fragments (amplified fragment length polymorphism) and subtype correlation with geographical origin and lesion size. J Clin Microbiol 2005; 43:4349-56. [PMID: 16145076 PMCID: PMC1234066 DOI: 10.1128/jcm.43.9.4349-4356.2005] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the causative organisms of mycetoma is the fungus Madurella mycetomatis. Previously, extensive molecular typing studies identified Sudanese isolates of this fungus as clonal, but polymorphic genetic markers have not yet been identified. Here, we report on the selective amplification of restriction fragment (AFLP) analysis of 37 Sudanese clinical isolates of M. mycetomatis. Of 93 AFLP fragments generated, 25 were polymorphic, and 12 of these 25 polymorphic fragments were found in a large fraction of the strains. Comparative analysis resulted into a tree, composed of two main (clusters I and II) and one minor cluster (cluster III). Seventy-five percent of the strains found in cluster I originated from central Sudan, while the origin of the strains in cluster II was more heterogeneous. Furthermore, the strains found in cluster I were generally obtained from lesions larger than those from which the strains found in cluster II were obtained (chi-square test for trend, P = 0.03). Among the 12 more commonly found polymorphisms, 4 showed sequence homology with known genes. Marker A7 was homologous to an endo-1,4-beta-glucanase from Aspergillus oryzae, 97% identical markers A12 and B3 matched a hypothetical protein from Gibberella zeae, and marker B4 was homologous to casein kinase I from Danio rerio. The last marker seemed to be associated with strains originating from central Sudan (P = 0.001). This is the first report on a genotypic study where genetic markers which may be used to study pathogenicity in M. mycetomatis were obtained.
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Affiliation(s)
- Wendy W J van de Sande
- Erasmus MC University Medical Center Rotterdam, Department of Medical Microbiology & Infectious Diseases, The Netherlands.
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