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Zhang X, Noberini R, Vai A, Bonaldi T, Seidl MF, Collemare J. Detection and quantification of the histone code in the fungal genus Aspergillus. Fungal Genet Biol 2023; 167:103800. [PMID: 37146898 DOI: 10.1016/j.fgb.2023.103800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/30/2023] [Accepted: 04/24/2023] [Indexed: 05/07/2023]
Abstract
In eukaryotes, the combination of different histone post-translational modifications (PTMs) - the histone code - impacts the chromatin organization as compact and transcriptionally silent heterochromatin or accessible and transcriptionally active euchromatin. Although specific histone PTMs have been studied in fungi, an overview of histone PTMs and their relative abundance is still lacking. Here, we used mass spectrometry to detect and quantify histone PTMs in three fungal species belonging to three distinct taxonomic sections of the genus Aspergillus (Aspergillus niger, Aspergillus nidulans (two strains), and Aspergillus fumigatus). We overall detected 23 different histone PTMs, including a majority of lysine methylations and acetylations, and 23 co-occurrence patterns of multiple histone PTMs. Among those, we report for the first time the detection of H3K79me1, H3K79me2, and H4K31ac in Aspergilli. Although all three species harbour the same PTMs, we found significant differences in the relative abundance of H3K9me1/2/3, H3K14ac, H3K36me1 and H3K79me1, as well as the co-occurrence of acetylation on both K18 and K23 of histone H3 in a strain-specific manner. Our results provide novel insights about the underexplored complexity of the histone code in filamentous fungi, and its functional implications on genome architecture and gene regulation.
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Affiliation(s)
- Xin Zhang
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Alessandro Vai
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Haematology-Oncology, University of Milano, Via Santa Sofia 9/1, 20122 Milano, Italy.
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Jérȏme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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2
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In Mitosis You Are Not: The NIMA Family of Kinases in Aspergillus, Yeast, and Mammals. Int J Mol Sci 2022; 23:ijms23074041. [PMID: 35409400 PMCID: PMC8999480 DOI: 10.3390/ijms23074041] [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: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
The Never in mitosis gene A (NIMA) family of serine/threonine kinases is a diverse group of protein kinases implicated in a wide variety of cellular processes, including cilia regulation, microtubule dynamics, mitotic processes, cell growth, and DNA damage response. The founding member of this family was initially identified in Aspergillus and was found to play important roles in mitosis and cell division. The yeast family has one member each, Fin1p in fission yeast and Kin3p in budding yeast, also with functions in mitotic processes, but, overall, these are poorly studied kinases. The mammalian family, the main focus of this review, consists of 11 members named Nek1 to Nek11. With the exception of a few members, the functions of the mammalian Neks are poorly understood but appear to be quite diverse. Like the prototypical NIMA, many members appear to play important roles in mitosis and meiosis, but their functions in the cell go well beyond these well-established activities. In this review, we explore the roles of fungal and mammalian NIMA kinases and highlight the most recent findings in the field.
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Hsu CL, Chong SY, Lin CY, Kao CF. Histone dynamics during DNA replication stress. J Biomed Sci 2021; 28:48. [PMID: 34144707 PMCID: PMC8214274 DOI: 10.1186/s12929-021-00743-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/08/2021] [Indexed: 01/20/2023] Open
Abstract
Accurate and complete replication of the genome is essential not only for genome stability but also for cell viability. However, cells face constant threats to the replication process, such as spontaneous DNA modifications and DNA lesions from endogenous and external sources. Any obstacle that slows down replication forks or perturbs replication dynamics is generally considered to be a form of replication stress, and the past decade has seen numerous advances in our understanding of how cells respond to and resolve such challenges. Furthermore, recent studies have also uncovered links between defects in replication stress responses and genome instability or various diseases, such as cancer. Because replication stress takes place in the context of chromatin, histone dynamics play key roles in modulating fork progression and replication stress responses. Here, we summarize the current understanding of histone dynamics in replication stress, highlighting recent advances in the characterization of fork-protective mechanisms.
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Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Shin Yen Chong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Yeh Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan.
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4
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Peres de Oliveira A, Basei FL, Slepicka PF, de Castro Ferezin C, Melo-Hanchuk TD, de Souza EE, Lima TI, Dos Santos VT, Mendes D, Silveira LR, Menck CFM, Kobarg J. NEK10 interactome and depletion reveal new roles in mitochondria. Proteome Sci 2020; 18:4. [PMID: 32368190 PMCID: PMC7189645 DOI: 10.1186/s12953-020-00160-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/14/2020] [Indexed: 12/29/2022] Open
Abstract
Background Members of the family of NEK protein kinases (NIMA-related kinases) were described to have crucial roles in regulating different aspects of the cell cycle. NEK10 was reported to take part in the maintenance of the G2/M checkpoint after exposure to ultraviolet light. NEK1, NEK5, NEK2 and NEK4 proteins on the other hand have been linked to mitochondrial functions. Methods HEK293T cells were transfected with FLAG empty vector or FLAG-NEK10 and treated or not with Zeocin. For proteomic analysis, proteins co-precipitated with the FLAG constructs were digested by trypsin, and then analyzed via LC-MS/MS. Proteomic data retrieved were next submitted to Integrated Interactome System analysis and differentially expressed proteins were attributed to Gene Ontology biological processes and assembled in protein networks by Cytoscape. For functional, cellular and molecular analyses two stable Nek10 silenced HeLa cell clones were established. Results Here, we discovered the following possible new NEK10 protein interactors, related to mitochondrial functions: SIRT3, ATAD3A, ATAD3B, and OAT. After zeocin treatment, the spectrum of mitochondrial interactors increased by the proteins: FKBP4, TXN, PFDN2, ATAD3B, MRPL12, ATP5J, DUT, YWHAE, CS, SIRT3, HSPA9, PDHB, GLUD1, DDX3X, and APEX1. We confirmed the interaction of NEK10 and GLUD1 by proximity ligation assay and confocal microscopy. Furthermore, we demonstrated that NEK10-depleted cells showed more fragmented mitochondria compared to the control cells. The knock down of NEK10 resulted further in changes in mitochondrial reactive oxygen species (ROS) levels, decreased citrate synthase activity, and culminated in inhibition of mitochondrial respiration, affecting particularly ATP-linked oxygen consumption rate and spare capacity. NEK10 depletion also decreased the ratio of mtDNA amplification, possibly due to DNA damage. However, the total mtDNA content increased, suggesting that NEK10 may be involved in the control of mtDNA content. Conclusions Taken together these data place NEK10 as a novel regulatory player in mitochondrial homeostasis and energy metabolism.
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Affiliation(s)
- Andressa Peres de Oliveira
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,2Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Fernanda Luisa Basei
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,3Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200; Cidade Universitária Zeferino Vaz; Campinas-SP; CEP, São Paulo, 13083-871 Brazil
| | - Priscila Ferreira Slepicka
- 4Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Camila de Castro Ferezin
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,3Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200; Cidade Universitária Zeferino Vaz; Campinas-SP; CEP, São Paulo, 13083-871 Brazil
| | - Talita D Melo-Hanchuk
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Edmarcia Elisa de Souza
- 4Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Tanes I Lima
- 5Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,6Departamento de Bioquímica e Imunologia, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Valquiria Tiago Dos Santos
- 2Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Davi Mendes
- 2Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo Reis Silveira
- 5Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | | | - Jörg Kobarg
- 1Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,3Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200; Cidade Universitária Zeferino Vaz; Campinas-SP; CEP, São Paulo, 13083-871 Brazil
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Karakkat JV, Kaimala S, Sreedharan SP, Jayaprakash P, Adeghate EA, Ansari SA, Guccione E, Mensah-Brown EPK, Starling Emerald B. The metabolic sensor PASK is a histone 3 kinase that also regulates H3K4 methylation by associating with H3K4 MLL2 methyltransferase complex. Nucleic Acids Res 2019; 47:10086-10103. [PMID: 31529049 PMCID: PMC6821284 DOI: 10.1093/nar/gkz786] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/19/2022] Open
Abstract
The metabolic sensor Per-Arnt-Sim (Pas) domain-containing serine/threonine kinase (PASK) is expressed predominantly in the cytoplasm of different cell types, although a small percentage is also expressed in the nucleus. Herein, we show that the nuclear PASK associates with the mammalian H3K4 MLL2 methyltransferase complex and enhances H3K4 di- and tri-methylation. We also show that PASK is a histone kinase that phosphorylates H3 at T3, T6, S10 and T11. Taken together, these results suggest that PASK regulates two different H3 tail modifications involving H3K4 methylation and H3 phosphorylation. Using muscle satellite cell differentiation and functional analysis after loss or gain of Pask expression using the CRISPR/Cas9 system, we provide evidence that some of the regulatory functions of PASK during development and differentiation may occur through the regulation of these histone modifications.
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Affiliation(s)
- Jimsheena V Karakkat
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Suneesh Kaimala
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Sreejisha P Sreedharan
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Princy Jayaprakash
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Ernest A Adeghate
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Suraiya A Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 138673, Singapore
| | - Eric P K Mensah-Brown
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, Abu Dhabi, UAE
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Collemare J, Seidl MF. Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? FEMS Microbiol Rev 2019; 43:591-607. [PMID: 31301226 PMCID: PMC8038932 DOI: 10.1093/femsre/fuz018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/07/2023] Open
Abstract
Fungal secondary metabolites are small molecules that exhibit diverse biological activities exploited in medicine, industry and agriculture. Their biosynthesis is governed by co-expressed genes that often co-localize in gene clusters. Most of these secondary metabolite gene clusters are inactive under laboratory conditions, which is due to a tight transcriptional regulation. Modifications of chromatin, the complex of DNA and histone proteins influencing DNA accessibility, play an important role in this regulation. However, tinkering with well-characterised chemical and genetic modifications that affect chromatin alters the expression of only few biosynthetic gene clusters, and thus the regulation of the vast majority of biosynthetic pathways remains enigmatic. In the past, attempts to activate silent gene clusters in fungi mainly focused on histone acetylation and methylation, while in other eukaryotes many other post-translational modifications are involved in transcription regulation. Thus, how chromatin regulates the expression of gene clusters remains a largely unexplored research field. In this review, we argue that focusing on only few well-characterised chromatin modifications is significantly hampering our understanding of the chromatin-based regulation of biosynthetic gene clusters. Research on underexplored chromatin modifications and on the interplay between different modifications is timely to fully explore the largely untapped reservoir of fungal secondary metabolites.
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Affiliation(s)
| | - Michael F Seidl
- Corresponding author: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands. E-mail: ; Present address: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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7
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Fry AM, Bayliss R, Roig J. Mitotic Regulation by NEK Kinase Networks. Front Cell Dev Biol 2017; 5:102. [PMID: 29250521 PMCID: PMC5716973 DOI: 10.3389/fcell.2017.00102] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/17/2017] [Indexed: 12/24/2022] Open
Abstract
Genetic studies in yeast and Drosophila led to identification of cyclin-dependent kinases (CDKs), Polo-like kinases (PLKs) and Aurora kinases as essential regulators of mitosis. These enzymes have since been found in the majority of eukaryotes and their cell cycle-related functions characterized in great detail. However, genetic studies in another fungal species, Aspergillus nidulans, identified a distinct family of protein kinases, the NEKs, that are also widely conserved and have key roles in the cell cycle, but which remain less well studied. Nevertheless, it is now clear that multiple NEK family members act in networks to regulate specific events of mitosis, including centrosome separation, spindle assembly and cytokinesis. Here, we describe our current understanding of how the NEK kinases contribute to these processes, particularly through targeted phosphorylation of proteins associated with the microtubule cytoskeleton. We also present the latest findings on molecular events that control the activation state of the NEKs and how these are revealing novel modes of enzymatic regulation relevant not only to other kinases but also to pathological mechanisms of disease.
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Affiliation(s)
- Andrew M. Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Richard Bayliss
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Joan Roig
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
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8
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Abstract
All cells must accurately replicate DNA and partition it to daughter cells. The basic cell cycle machinery is highly conserved among eukaryotes. Most of the mechanisms that control the cell cycle were worked out in fungal cells, taking advantage of their powerful genetics and rapid duplication times. Here we describe the cell cycles of the unicellular budding yeast Saccharomyces cerevisiae and the multicellular filamentous fungus Aspergillus nidulans. We compare and contrast morphological landmarks of G1, S, G2, and M phases, molecular mechanisms that drive cell cycle progression, and checkpoints in these model unicellular and multicellular fungal systems.
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Location and functional analysis of the Aspergillus nidulans Aurora kinase confirm mitotic functions and suggest non-mitotic roles. Fungal Genet Biol 2017; 103:1-15. [DOI: 10.1016/j.fgb.2017.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/12/2017] [Indexed: 11/17/2022]
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10
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Kwon M, Kim JM, Lee K, Park SY, Lim HS, Kim T, Jeong D. Synchronized Cell Cycle Arrest Promotes Osteoclast Differentiation. Int J Mol Sci 2016; 17:ijms17081292. [PMID: 27517906 PMCID: PMC5000689 DOI: 10.3390/ijms17081292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 01/26/2023] Open
Abstract
Osteoclast progenitors undergo cell cycle arrest before differentiation into osteoclasts, induced by exposure to macrophage colony-stimulating factor (M-CSF) and receptor activator of nuclear factor-κB ligand (RANKL). The role of such cell cycle arrest in osteoclast differentiation has remained unclear, however. We here examined the effect of synchronized cell cycle arrest on osteoclast formation. Osteoclast progenitors deprived of M-CSF in culture adopted a uniform morphology and exhibited cell cycle arrest at the G0–G1 phase in association with both down-regulation of cyclins A and D1 as well as up-regulation of the cyclin-dependent kinase inhibitor p27Kip1. Such M-CSF deprivation also promoted the differentiation of osteoclast progenitors into multinucleated osteoclasts expressing high levels of osteoclast marker proteins such as NFATc1, c-Fos, Atp6v0d2, cathepsin K, and integrin β3 on subsequent exposure to M-CSF and RANKL. Our results suggest that synchronized arrest and reprogramming of osteoclast progenitors renders them poised to respond to inducers of osteoclast formation. Further characterization of such effects may facilitate induction of the differentiation of heterogeneous and multipotent cells into desired cell lineages.
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Affiliation(s)
- Minsuk Kwon
- Laboratory of Bone Metabolism and Control, Department of Microbiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
| | - Jin-Man Kim
- Laboratory of Bone Metabolism and Control, Department of Microbiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
| | - Kyunghee Lee
- Laboratory of Bone Metabolism and Control, Department of Microbiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
| | - So-Young Park
- Department of Physiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
| | - Hyun-Sook Lim
- Department of Public Health Administration, Hanyang Women's University, Seoul 04763, Korea.
| | - Taesoo Kim
- Clinical Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Korea.
| | - Daewon Jeong
- Laboratory of Bone Metabolism and Control, Department of Microbiology, Yeungnam University College of Medicine, Daegu 42415, Korea.
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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12
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Zhao Y, Garcia BA. Comprehensive Catalog of Currently Documented Histone Modifications. Cold Spring Harb Perspect Biol 2015; 7:a025064. [PMID: 26330523 DOI: 10.1101/cshperspect.a025064] [Citation(s) in RCA: 257] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Modern techniques in molecular biology, genomics, and mass spectrometry-based proteomics have identified a large number of novel histone posttranslational modifications (PTMs), many of whose functions are still under intense investigation. Here, we catalog histone PTMs under two classes: first, those whose functions have been fairly well studied and, second, those PTMs that have been more recently identified but whose functions remain unclear. We hope that this will be a useful resource for researchers from all biological or technical backgrounds, aiding in their chromatin and epigenetic pursuits.
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Affiliation(s)
- Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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The Set1/COMPASS histone H3 methyltransferase helps regulate mitosis with the CDK1 and NIMA mitotic kinases in Aspergillus nidulans. Genetics 2014; 197:1225-36. [PMID: 24835271 DOI: 10.1534/genetics.114.165647] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Mitosis is promoted and regulated by reversible protein phosphorylation catalyzed by the essential NIMA and CDK1 kinases in the model filamentous fungus Aspergillus nidulans. Protein methylation mediated by the Set1/COMPASS methyltransferase complex has also been shown to regulate mitosis in budding yeast with the Aurora mitotic kinase. We uncover a genetic interaction between An-swd1, which encodes a subunit of the Set1 protein methyltransferase complex, with NIMA as partial inactivation of nimA is poorly tolerated in the absence of swd1. This genetic interaction is additionally seen without the Set1 methyltransferase catalytic subunit. Importantly partial inactivation of NIMT, a mitotic activator of the CDK1 kinase, also causes lethality in the absence of Set1 function, revealing a functional relationship between the Set1 complex and two pivotal mitotic kinases. The main target for Set1-mediated methylation is histone H3K4. Mutational analysis of histone H3 revealed that modifying the H3K4 target residue of Set1 methyltransferase activity phenocopied the lethality seen when either NIMA or CDK1 are partially functional. We probed the mechanistic basis of these genetic interactions and find that the Set1 complex performs functions with CDK1 for initiating mitosis and with NIMA during progression through mitosis. The studies uncover a joint requirement for the Set1 methyltransferase complex with the CDK1 and NIMA kinases for successful mitosis. The findings extend the roles of the Set1 complex to include the initiation of mitosis with CDK1 and mitotic progression with NIMA in addition to its previously identified interactions with Aurora and type 1 phosphatase in budding yeast.
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Govindaraghavan M, McGuire Anglin SL, Shen KF, Shukla N, De Souza CP, Osmani SA. Identification of interphase functions for the NIMA kinase involving microtubules and the ESCRT pathway. PLoS Genet 2014; 10:e1004248. [PMID: 24675878 PMCID: PMC3967960 DOI: 10.1371/journal.pgen.1004248] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 02/03/2014] [Indexed: 12/11/2022] Open
Abstract
The Never in Mitosis A (NIMA) kinase (the founding member of the Nek family of kinases) has been considered a mitotic specific kinase with nuclear restricted roles in the model fungus Aspergillus nidulans. By extending to A. nidulans the results of a synthetic lethal screen performed in Saccharomyces cerevisiae using the NIMA ortholog KIN3, we identified a conserved genetic interaction between nimA and genes encoding proteins of the Endosomal Sorting Complex Required for Transport (ESCRT) pathway. Absence of ESCRT pathway functions in combination with partial NIMA function causes enhanced cell growth defects, including an inability to maintain a single polarized dominant cell tip. These genetic insights suggest NIMA potentially has interphase functions in addition to its established mitotic functions at nuclei. We therefore generated endogenously GFP-tagged NIMA (NIMA-GFP) which was fully functional to follow its interphase locations using live cell spinning disc 4D confocal microscopy. During interphase some NIMA-GFP locates to the tips of rapidly growing cells and, when expressed ectopically, also locates to the tips of cytoplasmic microtubules, suggestive of non-nuclear interphase functions. In support of this, perturbation of NIMA function either by ectopic overexpression or through partial inactivation results in marked cell tip growth defects with excess NIMA-GFP promoting multiple growing cell tips. Ectopic NIMA-GFP was found to locate to the plus ends of microtubules in an EB1 dependent manner, while impairing NIMA function altered the dynamic localization of EB1 and the cytoplasmic microtubule network. Together, our genetic and cell biological analyses reveal novel non-nuclear interphase functions for NIMA involving microtubules and the ESCRT pathway for normal polarized fungal cell tip growth. These insights extend the roles of NIMA both spatially and temporally and indicate that this conserved protein kinase could help integrate cell cycle progression with polarized cell growth.
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Affiliation(s)
- Meera Govindaraghavan
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | | | - Kuo-Fang Shen
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Nandini Shukla
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, United States of America
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, United States of America
| | - Colin P. De Souza
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Stephen A. Osmani
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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15
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Shen KF, Osmani AH, Govindaraghavan M, Osmani SA. Mitotic regulation of fungal cell-to-cell connectivity through septal pores involves the NIMA kinase. Mol Biol Cell 2014; 25:763-75. [PMID: 24451264 PMCID: PMC3952847 DOI: 10.1091/mbc.e13-12-0718] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Septal pores—the intercellular bridges of fungi—are open during interphase but closed at mitosis. The NIMA kinase mitotically regulates septal pore closing and opening potentially via mechanisms analogous to how it regulates mitotic nuclear pores. The findings explain how and why physically connected Aspergillus cells can maintain mitotic autonomy. Intercellular bridges are a conserved feature of multicellular organisms. In multicellular fungi, cells are connected directly via intercellular bridges called septal pores. Using Aspergillus nidulans, we demonstrate for the first time that septal pores are regulated to be opened during interphase but closed during mitosis. Septal pore–associated proteins display dynamic cell cycle–regulated locations at mature septa. Of importance, the mitotic NIMA kinase locates to forming septa and surprisingly then remains at septa throughout interphase. However, during mitosis, when NIMA transiently locates to nuclei to promote mitosis, its levels at septa drop. A model is proposed in which NIMA helps keep septal pores open during interphase and then closed when it is removed from them during mitosis. In support of this hypothesis, NIMA inactivation is shown to promote interphase septal pore closing. Because NIMA triggers nuclear pore complex opening during mitosis, our findings suggest that common cell cycle regulatory mechanisms might control septal pores and nuclear pores such that they are opened and closed out of phase to each other during cell cycle progression. The study provides insights into how and why cytoplasmically connected Aspergillus cells maintain mitotic autonomy.
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Affiliation(s)
- Kuo-Fang Shen
- Department of Molecular Genetics and Molecular, Cellular and Developmental Biology Program, Ohio State University, Columbus, OH 43210
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16
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Insights into dynamic mitotic chromatin organization through the NIMA kinase suppressor SonC, a chromatin-associated protein involved in the DNA damage response. Genetics 2013; 196:177-95. [PMID: 24214344 DOI: 10.1534/genetics.113.156745] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nuclear pore complex proteins SonA and SonB, the orthologs of mammalian RAE1 and NUP98, respectively, were identified in Aspergillus nidulans as cold-sensitive suppressors of a temperature-sensitive allele of the essential mitotic NIMA kinase (nimA1). Subsequent analyses found that sonB1 mutants exhibit temperature-dependent DNA damage sensitivity. To understand this pathway further, we performed a genetic screen to isolate additional conditional DNA damage-sensitive suppressors of nimA1. We identified two new alleles of SonA and four intragenic nimA mutations that suppress the temperature sensitivity of the nimA1 mutant. In addition, we identified SonC, a previously unstudied binuclear zinc cluster protein involved with NIMA and the DNA damage response. Like sonA and sonB, sonC is an essential gene. SonC localizes to nuclei and partially disperses during mitosis. When the nucleolar organizer region (NOR) undergoes mitotic condensation and removal from the nucleolus, nuclear SonC and histone H1 localize in a mutually exclusive manner with H1 being removed from the NOR region and SonC being absent from the end of the chromosome beyond the NOR. This region of chromatin is adjacent to a cluster of nuclear pore complexes to which NIMA localizes last during its progression around the nuclear envelope during initiation of mitosis. The results genetically extend the NIMA regulatory system to include a protein with selective large-scale chromatin location observed during mitosis. The data suggest a model in which NIMA and SonC, its new chromatin-associated suppressor, might help to orchestrate global chromatin states during mitosis and the DNA damage response.
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17
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Mahmoud SA, Poizat C. Epigenetics and chromatin remodeling in adult cardiomyopathy. J Pathol 2013; 231:147-57. [PMID: 23813473 PMCID: PMC4285861 DOI: 10.1002/path.4234] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 06/22/2013] [Accepted: 06/24/2013] [Indexed: 12/19/2022]
Abstract
The manipulation of chromatin structure regulates gene expression and the flow of genetic information. Histone modifications and ATP-dependent chromatin remodeling together with DNA methylation are dynamic processes that modify chromatin architecture and profoundly modulate gene expression. Their coordinated control is key to ensuring proper cell commitment and organ development, as well as adaption to environmental cues. Recent studies indicate that abnormal epigenetic status of the genome, in concert with alteration of transcriptional networks, contribute to the development of adult cardiomyopathy such as pathological cardiac hypertrophy. Here we consider the emerging role of different classes of chromatin regulators and how their dysregulation in the adult heart alters specific gene programs with subsequent development of major cardiomyopathies. Understanding the functional significance of the different epigenetic marks as points of genetic control may represent a promising future therapeutic tool.
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Affiliation(s)
- Salma Awad Mahmoud
- Cardiovascular Research Program, King Faisal Specialist Hospital & Research Centre, PO Box 3354, Riyadh, 11211, Kingdom of Saudi Arabia
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18
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The NIMA kinase is required to execute stage-specific mitotic functions after initiation of mitosis. EUKARYOTIC CELL 2013; 13:99-109. [PMID: 24186954 DOI: 10.1128/ec.00231-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The G2-M transition in Aspergillus nidulans requires the NIMA kinase, the founding member of the Nek kinase family. Inactivation of NIMA results in a late G2 arrest, while overexpression of NIMA is sufficient to promote mitotic events independently of cell cycle phase. Endogenously tagged NIMA-GFP has dynamic mitotic localizations appearing first at the spindle pole body and then at nuclear pore complexes before transitioning to within nuclei and the mitotic spindle and back at the spindle pole bodies at mitotic exit, suggesting that it functions sequentially at these locations. Since NIMA is indispensable for mitotic entry, it has been difficult to determine the requirement of NIMA for subaspects of mitosis. We show here that when NIMA is partially inactivated, although mitosis can be initiated, a proportion of cells fail to successfully generate two daughter nuclei. We further define the mitotic defects to show that normal NIMA function is required for the formation of a bipolar spindle, nuclear pore complex disassembly, completion of chromatin segregation, and the normal structural rearrangements of the nuclear envelope required to generate two nuclei from one. In the remaining population of cells that enter mitosis with inadequate NIMA, two daughter nuclei are generated in a manner dependent on the spindle assembly checkpoint, indicating highly penetrant defects in mitotic progression without sufficient NIMA activity. This study shows that NIMA is required not only for mitotic entry but also sequentially for successful completion of stage-specific mitotic events.
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Shen KF, Osmani SA. Regulation of mitosis by the NIMA kinase involves TINA and its newly discovered partner, An-WDR8, at spindle pole bodies. Mol Biol Cell 2013; 24:3842-56. [PMID: 24152731 PMCID: PMC3861081 DOI: 10.1091/mbc.e13-07-0422] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The NIMA kinase is required for mitotic nuclear pore complex disassembly and potentially controls other mitotic-specific events. To investigate this possibility, we imaged NIMA-green fluorescent protein (GFP) using four-dimensional spinning disk confocal microscopy. At mitosis NIMA-GFP locates to spindle pole bodies (SPBs), which contain Cdk1/cyclin B, followed by Aurora, TINA, and the BimC kinesin. NIMA promotes NPC disassembly in a spatially regulated manner starting near SPBs. NIMA is also required for TINA, a NIMA-interacting protein, to locate to SPBs during initiation of mitosis, and TINA is then necessary for locating NIMA back to SPBs during mitotic progression. To help expand the NIMA-TINA pathway, we affinity purified TINA and found it to uniquely copurify with An-WDR8, a WD40-domain protein conserved from humans to plants. Like TINA, An-WDR8 accumulates within nuclei during G2 but disperses from nuclei before locating to mitotic SPBs. Without An-WDR8, TINA levels are greatly reduced, whereas TINA is necessary for mitotic targeting of An-WDR8. Finally, we show that TINA is required to anchor mitotic microtubules to SPBs and, in combination with An-WDR8, for successful mitosis. The findings provide new insights into SPB targeting and indicate that the mitotic microtubule-anchoring system at SPBs involves WDR8 in complex with TINA.
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Affiliation(s)
- Kuo-Fang Shen
- Department of Molecular Genetics and Molecular, Cellular and Developmental Biology Program, Ohio State University, Columbus, OH 43210
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20
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Awad S, Kunhi M, Little GH, Bai Y, An W, Bers D, Kedes L, Poizat C. Nuclear CaMKII enhances histone H3 phosphorylation and remodels chromatin during cardiac hypertrophy. Nucleic Acids Res 2013; 41:7656-72. [PMID: 23804765 PMCID: PMC3763528 DOI: 10.1093/nar/gkt500] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) plays a central role in pathological cardiac hypertrophy, but the mechanisms by which it modulates gene activity in the nucleus to mediate hypertrophic signaling remain unclear. Here, we report that nuclear CaMKII activates cardiac transcription by directly binding to chromatin and regulating the phosphorylation of histone H3 at serine-10. These specific activities are demonstrated both in vitro and in primary neonatal rat cardiomyocytes. Activation of CaMKII signaling by hypertrophic agonists increases H3 phosphorylation in primary cardiac cells and is accompanied by concomitant cellular hypertrophy. Conversely, specific silencing of nuclear CaMKII using RNA interference reduces both H3 phosphorylation and cellular hypertrophy. The hyper-phosphorylation of H3 associated with increased chromatin binding of CaMKII occurs at specific gene loci reactivated during cardiac hypertrophy. Importantly, H3 Ser-10 phosphorylation and CaMKII recruitment are associated with increased chromatin accessibility and are required for chromatin-mediated transcription of the Mef2 transcription factor. Unlike phosphorylation of H3 by other kinases, which regulates cellular proliferation and immediate early gene activation, CaMKII-mediated signaling to H3 is associated with hypertrophic growth. These observations reveal a previously unrecognized function of CaMKII as a kinase signaling to histone H3 and remodeling chromatin. They suggest a new epigenetic mechanism controlling cardiac hypertrophy.
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Affiliation(s)
- Salma Awad
- Cardiovascular Research Program, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Kingdom of Saudi Arabia, Institute for Genetic Medicine, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90033, USA, Department of Biochemistry and Molecular Biology, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90089, USA, Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA and Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Muhammad Kunhi
- Cardiovascular Research Program, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Kingdom of Saudi Arabia, Institute for Genetic Medicine, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90033, USA, Department of Biochemistry and Molecular Biology, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90089, USA, Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA and Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Gillian H. Little
- Cardiovascular Research Program, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Kingdom of Saudi Arabia, Institute for Genetic Medicine, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90033, USA, Department of Biochemistry and Molecular Biology, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90089, USA, Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA and Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Yan Bai
- Cardiovascular Research Program, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Kingdom of Saudi Arabia, Institute for Genetic Medicine, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90033, USA, Department of Biochemistry and Molecular Biology, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90089, USA, Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA and Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Woojin An
- Cardiovascular Research Program, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Kingdom of Saudi Arabia, Institute for Genetic Medicine, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90033, USA, Department of Biochemistry and Molecular Biology, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90089, USA, Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA and Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Donald Bers
- Cardiovascular Research Program, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Kingdom of Saudi Arabia, Institute for Genetic Medicine, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90033, USA, Department of Biochemistry and Molecular Biology, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90089, USA, Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA and Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Larry Kedes
- Cardiovascular Research Program, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Kingdom of Saudi Arabia, Institute for Genetic Medicine, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90033, USA, Department of Biochemistry and Molecular Biology, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90089, USA, Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA and Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Coralie Poizat
- Cardiovascular Research Program, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211, Kingdom of Saudi Arabia, Institute for Genetic Medicine, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90033, USA, Department of Biochemistry and Molecular Biology, University of Southern California 2250 Alcazar Street, Los Angeles, CA 90089, USA, Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA and Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA,*To whom correspondence should be addressed. Tel: +966 1 464 7272 (ext. 32984); Fax: +966 1 464 7858; or
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21
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Kumar A, Rajendran V, sethumadhavan R, Purohit R. Insight into Nek2A activity regulation and its pharmacological prospects. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2013. [DOI: 10.1016/j.ejmhg.2012.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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22
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Cappello P, Blaser H, Gorrini C, Lin DCC, Elia AJ, Wakeham A, Haider S, Boutros PC, Mason JM, Miller NA, Youngson B, Done SJ, Mak TW. Role of Nek2 on centrosome duplication and aneuploidy in breast cancer cells. Oncogene 2013; 33:2375-84. [PMID: 23708664 DOI: 10.1038/onc.2013.183] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 04/04/2013] [Accepted: 04/04/2013] [Indexed: 11/09/2022]
Abstract
Breast cancer is the most common solid tumor and the second most common cause of death in women. Despite a large body of literature and progress in breast cancer research, many molecular aspects of this complex disease are still poorly understood, hindering the design of specific and effective therapeutic strategies. To identify the molecules important in breast cancer progression and metastasis, we tested the in vivo effects of inhibiting the functions of various kinases and genes involved in the regulation/modulation of the cytoskeleton by downregulating them in mouse PyMT mammary tumor cells and human breast cancer cell lines. These kinases and cytoskeletal regulators were selected based on their prognostic values for breast cancer patient survival. PyMT tumor cells, in which a selected gene was stably knocked down were injected into the tail veins of mice, and the formation of tumors in the lungs was monitored. One of the several genes found to be important for tumor growth in the lungs was NIMA-related kinases 2 (Nek2), a cell cycle-related protein kinase. Furthermore, Nek2 was also important for tumor growth in the mammary fat pad. In various human breast cancer cell lines, Nek2 knockdown induced aneuploidy and cell cycle arrest that led to cell death. Significantly, the breast cancer cell line most sensitive to Nek2 depletion was of the triple negative breast cancer subtype. Our data indicate that Nek2 has a pivotal role in breast cancer growth at primary and secondary sites, and thus may be an attractive and novel therapeutic target for this disease.
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Affiliation(s)
- P Cappello
- 1] The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada [2] Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - H Blaser
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada
| | - C Gorrini
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada
| | - D C C Lin
- The Campbell Family Institute for Breast Cancer Research, University Health Network, TMDT East Tower, MaRS Centre, Toronto, Ontario, Canada
| | - A J Elia
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada
| | - A Wakeham
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada
| | - S Haider
- Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - P C Boutros
- Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - J M Mason
- The Campbell Family Institute for Breast Cancer Research, University Health Network, TMDT East Tower, MaRS Centre, Toronto, Ontario, Canada
| | - N A Miller
- 1] Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada [2] Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - B Youngson
- 1] Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada [2] Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - S J Done
- 1] The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada [2] Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada [3] Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - T W Mak
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada
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23
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Matsunaga S, Katagiri Y, Nagashima Y, Sugiyama T, Hasegawa J, Hayashi K, Sakamoto T. New insights into the dynamics of plant cell nuclei and chromosomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 305:253-301. [PMID: 23890384 DOI: 10.1016/b978-0-12-407695-2.00006-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The plant lamin-like protein NMCP/AtLINC and orthologues of the SUN-KASH complex across the nuclear envelope (NE) show the universality of nuclear structure in eukaryotes. However, depletion of components in the connection complex of the NE in plants does not induce severe defects, unlike in animals. Appearance of the Rabl configuration is not dependent on genome size in plant species. Topoisomerase II and condensin II are not essential for plant chromosome condensation. Plant endoreduplication shares several common characteristics with animals, including involvement of cyclin-dependent kinases and E2F transcription factors. Recent finding regarding endomitosis regulator GIG1 shed light on the suppression mechanism of endomitosis in plants. The robustness of plants, compared with animals, is reflected in their genome redundancy. Spatiotemporal functional analyses using chromophore-assisted light inactivation, super-resolution microscopy, and 4D (3D plus time) imaging will reveal new insights into plant nuclear and chromosomal dynamics.
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Affiliation(s)
- Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
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24
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Fry AM, O'Regan L, Sabir SR, Bayliss R. Cell cycle regulation by the NEK family of protein kinases. J Cell Sci 2012; 125:4423-33. [PMID: 23132929 DOI: 10.1242/jcs.111195] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Genetic screens for cell division cycle mutants in the filamentous fungus Aspergillus nidulans led to the discovery of never-in-mitosis A (NIMA), a serine/threonine kinase that is required for mitotic entry. Since that discovery, NIMA-related kinases, or NEKs, have been identified in most eukaryotes, including humans where eleven genetically distinct proteins named NEK1 to NEK11 are expressed. Although there is no evidence that human NEKs are essential for mitotic entry, it is clear that several NEK family members have important roles in cell cycle control. In particular, NEK2, NEK6, NEK7 and NEK9 contribute to the establishment of the microtubule-based mitotic spindle, whereas NEK1, NEK10 and NEK11 have been implicated in the DNA damage response. Roles for NEKs in other aspects of mitotic progression, such as chromatin condensation, nuclear envelope breakdown, spindle assembly checkpoint signalling and cytokinesis have also been proposed. Interestingly, NEK1 and NEK8 also function within cilia, the microtubule-based structures that are nucleated from basal bodies. This has led to the current hypothesis that NEKs have evolved to coordinate microtubule-dependent processes in both dividing and non-dividing cells. Here, we review the functions of the human NEKs, with particular emphasis on those family members that are involved in cell cycle control, and consider their potential as therapeutic targets in cancer.
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Affiliation(s)
- Andrew M Fry
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK.
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25
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De Benedetti A. The Tousled-Like Kinases as Guardians of Genome Integrity. ISRN MOLECULAR BIOLOGY 2012; 2012:627596. [PMID: 23869254 PMCID: PMC3712517 DOI: 10.5402/2012/627596] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Tousled-like kinases (TLKs) function in processes of chromatin assembly, including replication, transcription, repair, and chromosome segregation. TLKs interact specifically (and phosphorylate) with the chromatin assembly factor Asf1, a histone H3-H4 chaperone, histone H3 itself at Ser10, and also Rad9, a key protein involved in DNA repair and cell cycle signaling following DNA damage. These interactions are believed to be responsible for the action of TLKs in double-stranded break repair and radioprotection and also in the propagation of the DNA damage response. Hence, I propose that TLKs play key roles in maintenance of genome integrity in many organisms of both kingdoms. In this paper, I highlight key issues of the known roles of these proteins, particularly in the context of DNA repair (IR and UV), their possible relevance to genome integrity and cancer development, and as possible targets for intervention in cancer management.
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Affiliation(s)
- Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA 71130, USA
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26
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Moniz L, Dutt P, Haider N, Stambolic V. Nek family of kinases in cell cycle, checkpoint control and cancer. Cell Div 2011; 6:18. [PMID: 22040655 PMCID: PMC3222597 DOI: 10.1186/1747-1028-6-18] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 10/31/2011] [Indexed: 12/02/2022] Open
Abstract
Early studies in lower Eukaryotes have defined a role for the members of the NimA related kinase (Nek) family of protein kinases in cell cycle control. Expansion of the Nek family throughout evolution has been accompanied by their broader involvement in checkpoint regulation and cilia biology. Moreover, mutations of Nek family members have been identified as drivers behind the development of ciliopathies and cancer. Recent advances in studying the physiological roles of Nek family members utilizing mouse genetics and RNAi-mediated knockdown are revealing intricate associations of Nek family members with fundamental biological processes. Here, we aim to provide a comprehensive account of our understanding of Nek kinase biology and their involvement in cell cycle, checkpoint control and cancer.
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Affiliation(s)
- Larissa Moniz
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 2M9, Canada.
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Regulated inactivation of the spindle assembly checkpoint without functional mitotic spindles. EMBO J 2011; 30:2648-61. [PMID: 21642954 DOI: 10.1038/emboj.2011.176] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 05/09/2011] [Indexed: 12/13/2022] Open
Abstract
The spindle assembly checkpoint (SAC) arrests mitosis until bipolar attachment of spindle microtubules to all chromosomes is accomplished. However, when spindle formation is prevented and the SAC cannot be satisfied, mammalian cells can eventually overcome the mitotic arrest while the checkpoint is still activated. We find that Aspergillus nidulans cells, which are unable to satisfy the SAC, inactivate the checkpoint after a defined period of mitotic arrest. Such SAC inactivation allows normal nuclear reassembly and mitotic exit without DNA segregation. We demonstrate that the mechanisms, which govern such SAC inactivation, require protein synthesis and can occur independently of inactivation of the major mitotic regulator Cdk1/Cyclin B or mitotic exit. Moreover, in the continued absence of spindle function cells transit multiple cell cycles in which the SAC is reactivated each mitosis before again being inactivated. Such cyclic activation and inactivation of the SAC suggests that it is subject to cell-cycle regulation that is independent of bipolar spindle function.
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Strauss J, Reyes-Dominguez Y. Regulation of secondary metabolism by chromatin structure and epigenetic codes. Fungal Genet Biol 2011; 48:62-9. [PMID: 20659575 PMCID: PMC3935439 DOI: 10.1016/j.fgb.2010.07.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 07/02/2010] [Accepted: 07/19/2010] [Indexed: 01/07/2023]
Abstract
Chromatin, composed of DNA wrapped around an octamer of histones, is the relevant substrate for all genetic processes in eukaryotic nuclei. Changes in chromatin structure are associated with the activation and silencing of gene transcription and reversible post-translational modifications of histones are now known to direct chromatin structure transitions. Recent studies in several fungal species have identified a chromatin-based regulation of secondary metabolism (SM) gene clusters representing an upper-hierarchical level for the coordinated control of large chromosomal elements. Regulation by chromatin transition processes provides a mechanistic model to explain how different SM clusters located at dispersed genomic regions can be simultaneously silenced during primary metabolism. Activation of SM clusters has been shown to be associated with increased acetylation of histones H3 and H4 and, consequently, inhibition of histone de-acetylase activities also leads to increased production of secondary metabolites. New findings suggest that SM clusters are silenced by heterochromatic histone marks and that the "closed" heterochromatic structures are reversed during SM activation. This process is mediated by the conserved activator of SM, LaeA. Despite the increase in knowledge about these processes, much remains to be learned from chromatin-level regulation of SM. For example, which proteins "position" the chromatin restructuring signal onto SM clusters or how exactly LaeA works to mediate the low level of heterochromatic marks inside different clusters remain open questions. Answers to these and other chromatin-related questions would certainly complete our understanding of SM gene regulation and signaling and, because for many predicted SM clusters corresponding products have not been identified so far, anti-silencing strategies would open new ways for the identification of novel bioactive substances.
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Affiliation(s)
- Joseph Strauss
- Corresponding author. Fax: +43 1 36006 6392. (J. Strauss)
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Nassirpour R, Shao L, Flanagan P, Abrams T, Jallal B, Smeal T, Yin MJ. Nek6 mediates human cancer cell transformation and is a potential cancer therapeutic target. Mol Cancer Res 2010; 8:717-28. [PMID: 20407017 DOI: 10.1158/1541-7786.mcr-09-0291] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We investigated the role of Nek6, a member of the NIMA-related serine/threonine kinase family, in tumorigenesis. Transcript, protein, and kinase activity levels of Nek6 were highly elevated in the malignant tumors and human cancer cell lines compared with normal tissue and fibroblast cells. Expression of exogenous wild-type Nek6 increased anchorage-independent growth of a variety of human cancer cell lines, whereas overexpression of the kinase-dead Nek6 and RNAi knockdown of endogenous Nek6 suppressed cancer cell transformation and induced apoptosis. Additionally, in in vivo xenograft nude mouse model, knockdown of Nek6 in HeLa cells resulted in reduction of tumor size relative to control siRNA tumors. Most importantly, knocking down endogenous Nek6 levels or exogenous expression of the kinase-dead form did not inhibit cell proliferation, nor did it induce apoptosis in normal fibroblast cells. Taken together, our data indicate a pivotal role for Nek6 in tumorigenesis and establish Nek6 as a potential target for treatment of a variety of human cancers.
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Affiliation(s)
- Rounak Nassirpour
- Pfizer Global Research and Development, La Jolla Laboratories, 10724 Science Center Drive, San Diego, CA 92121, USA
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Pérez-Cadahía B, Drobic B, Davie JR. H3 phosphorylation: dual role in mitosis and interphase. Biochem Cell Biol 2010; 87:695-709. [PMID: 19898522 DOI: 10.1139/o09-053] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromatin condensation and subsequent decondensation are processes required for proper execution of various cellular events. During mitosis, chromatin compaction is at its highest, whereas relaxation of chromatin is necessary for DNA replication, repair, recombination, and gene transcription. Since histone proteins are directly complexed with DNA in the form of a nucleosome, great emphasis is put on deciphering histone post-translational modifications that control the chromatin condensation state. Histone H3 phosphorylation is a mark present in mitosis, where chromatin condensation is necessary, and in transcriptional activation of genes, when chromatin needs to be decondensed. There are four characterized phospho residues within the H3 N-terminal tail during mitosis: Thr3, Ser10, Thr11, and Ser28. Interestingly, H3 phosphorylated at Ser10, Thr11, and Ser28 has been observed on genomic regions of transcriptionally active genes. Therefore, H3 phosphorylation is involved in processes requiring opposing chromatin states. The level of H3 phosphorylation is mediated by opposing actions of specific kinases and phosphatases during mitosis and gene transcription. The cellular contexts under which specific residues on H3 are phosphorylated in mitosis and interphase are known to some extent. However, the functional consequences of H3 phosphorylation are still unclear.
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Affiliation(s)
- Beatriz Pérez-Cadahía
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E0V9, Canada
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Markaki Y, Christogianni A, Politou AS, Georgatos SD. Phosphorylation of histone H3 at Thr3 is part of a combinatorial pattern that marks and configures mitotic chromatin. J Cell Sci 2009; 122:2809-19. [DOI: 10.1242/jcs.043810] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We have previously shown that histone H3 is transiently phosphorylated at Thr3 during mitosis. Extending these studies, we now report that phosphorylated Thr3 is always in cis to trimethylated Lys4 and dimethylated Arg8, forming a new type of combinatorial modification, which we have termed PMM. PMM-marked chromatin emerges at multiple, peripheral sites of the prophase nucleus, then forms distinct clusters at the centric regions of metaphase chromosomes, and finally spreads (as it wanes) to the distal areas of segregating chromatids. The characteristic prophase pattern can be reproduced by expressing ectopically the kinase haspin at interphase, suggesting that the formation of the PMM signature does not require a pre-existing mitotic environment. On the other hand, the `dissolution' and displacement of PMM clusters from a centric to distal position can be induced by partial dephosphorylation or chromosome unravelling, indicating that these changes reflect the regulated grouping and scrambling of PMM subdomains during cell division. Formation of PMM is prevented by haspin knockdown and leads to delayed exit from mitosis. However, PMM-negative cells do not exhibit major chromosomal defects, suggesting that the local structures formed by PMM chromatin may serve as a `licensing system' that allows quick clearance through the metaphase-anaphase checkpoint.
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Affiliation(s)
- Yolanda Markaki
- Laboratory of Biology, Stem Cell and Chromatin Group, The University of Ioannina School of Medicine and The Biomedical Institute of Ioannina (BRI/FORTH), Dourouti, 45 110 Ioannina, Greece
| | - Anastasia Christogianni
- Laboratory of Biology, Stem Cell and Chromatin Group, The University of Ioannina School of Medicine and The Biomedical Institute of Ioannina (BRI/FORTH), Dourouti, 45 110 Ioannina, Greece
| | - Anastasia S. Politou
- Laboratory of Biological Chemistry, Stem Cell and Chromatin Group, The University of Ioannina School of Medicine and The Biomedical Institute of Ioannina (BRI/FORTH), Dourouti, 45 110 Ioannina, Greece
| | - Spyros D. Georgatos
- Laboratory of Biology, Stem Cell and Chromatin Group, The University of Ioannina School of Medicine and The Biomedical Institute of Ioannina (BRI/FORTH), Dourouti, 45 110 Ioannina, Greece
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Demidov D, Hesse S, Tewes A, Rutten T, Fuchs J, Ashtiyani RK, Lein S, Fischer A, Reuter G, Houben A. Aurora1 phosphorylation activity on histone H3 and its cross-talk with other post-translational histone modifications in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:221-30. [PMID: 19582900 DOI: 10.1111/j.1365-313x.2009.03861.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The enzymological properties of AtAurora1, a kinase responsible for the cell cycle-dependent phosphorylation of histone H3 at S10, and its cross-talk with other post-translational histone modifications, were determined. In vitro phosphorylation of H3S10 by AtAurora1 is strongly increased by K9 acetylation, and decreased by K14 acetylation and T11 phosphorylation. However, S10 phosphorylation activity is unaltered by mono-, di- or trimethylation of K9. An interference of H3K9 dimethylation by SUVR4 occurs by a pre-existing phosphorylation at S10. Hence, cross-talk in plants exists between phosphorylation of H3S10 and methylation, acetylation or phosphorylation of neighbouring amino acid residues. AtAurora1 undergoes autophosphorylation in vivo regardless of the presence of substrate, and forms dimers in planta. Of the three ATP-competitive Aurora inhibitors tested, Hesperadin was most effective in reducing the in vivo kinase activity of AtAurora1. Hesperadin consistently inhibited histone H3S10 phosphorylation during mitosis in Arabidopsis cells, but did not affect other H3 post-translational modifications, suggesting a specific inhibition of AtAurora in vivo. Inactivation of AtAurora also caused lagging chromosomes in a number of anaphase cells, but, unlike the situation in mammalian cells, Hesperadin did not influence the microtubule dynamics in dividing cells.
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Affiliation(s)
- Dmitri Demidov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
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The Nek6 and Nek7 protein kinases are required for robust mitotic spindle formation and cytokinesis. Mol Cell Biol 2009; 29:3975-90. [PMID: 19414596 PMCID: PMC2704745 DOI: 10.1128/mcb.01867-08] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nek6 and Nek7 are members of the NIMA-related serine/threonine kinase family. Previous work showed that they contribute to mitotic progression downstream of another NIMA-related kinase, Nek9, although the roles of these different kinases remain to be defined. Here, we carried out a comprehensive analysis of the regulation and function of Nek6 and Nek7 in human cells. By generating specific antibodies, we show that both Nek6 and Nek7 are activated in mitosis and that interfering with their activity by either depletion or expression of reduced-activity mutants leads to mitotic arrest and apoptosis. Interestingly, while completely inactive mutants and small interfering RNA-mediated depletion delay cells at metaphase with fragile mitotic spindles, hypomorphic mutants or RNA interference treatment combined with a spindle assembly checkpoint inhibitor delays cells at cytokinesis. Importantly, depletion of either Nek6 or Nek7 leads to defective mitotic progression, indicating that although highly similar, they are not redundant. Indeed, while both kinases localize to spindle poles, only Nek6 obviously localizes to spindle microtubules in metaphase and anaphase and to the midbody during cytokinesis. Together, these data lead us to propose that Nek6 and Nek7 play independent roles not only in robust mitotic spindle formation but also potentially in cytokinesis.
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Pagès G. MAP kinase phosphatase-1: a link between cell signaling and histone phosphorylation. Focus on “Histone H3 as a novel substrate for MAP kinase phosphatase-1”. Am J Physiol Cell Physiol 2009; 296:C233-4. [DOI: 10.1152/ajpcell.00637.2008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Copy number suppressors of the Aspergillus nidulans nimA1 mitotic kinase display distinctive and highly dynamic cell cycle-regulated locations. EUKARYOTIC CELL 2008; 7:2087-99. [PMID: 18931041 DOI: 10.1128/ec.00278-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Aspergillus nidulans NIMA kinase is essential for mitosis and is the founding member of the conserved NIMA-related kinase (Nek) family of protein kinases. To gain insight into NIMA function, a copy number suppression screen has been completed that defines three proteins termed MCNA, MCNB, and MCNC (multi-copy-number suppressor of nimA1 A, B, and C). All display a distinctive and dynamic cell cycle-specific distribution. MCNC has weak similarity to Saccharomyces cerevisiae Def1 within a shared CUE-like domain. MCNC, like Def1, is a cytoplasmic protein with slow mobility during sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and its deletion causes polarization defects and a small colony phenotype. MCNC enters nuclei during mitosis. In contrast, MCNB is a nuclear protein displaying increased nuclear levels as cells progress through interphase but is lost from nuclei at mitosis. MCNB is highly related to the Schizosaccharomyces pombe forkhead transcription factor Sep1 and is likely a transcriptional activator of nimA. Most surprisingly, MCNA, a protein restricted to the aspergilli and pathogenic systemic dimorphic fungi (the Eurotiomycetes), defines a nuclear body located near nucleoli at the nuclear periphery of G(2) nuclei. During progression through mitosis, the MCNA body is excluded from nuclei. Cytoplasmic MCNA bodies then diminish during early stages of interphase, and single MCNA bodies are formed within nuclei as interphase progresses. Three sites of MCNA phosphorylation were mapped and mutated to implicate proline-directed phosphorylation in the equal segregation of MCNA during the cell cycle. The data indicate all three MCN proteins likely have cell cycle functions.
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Sanchez MDLP, Caro E, Desvoyes B, Ramirez-Parra E, Gutierrez C. Chromatin dynamics during the plant cell cycle. Semin Cell Dev Biol 2008; 19:537-46. [PMID: 18707013 DOI: 10.1016/j.semcdb.2008.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 07/23/2008] [Accepted: 07/24/2008] [Indexed: 11/30/2022]
Abstract
Cell cycle progression depends on a highly regulated series of events of which transcriptional control plays a major role. In addition, during the S-phase not only DNA but chromatin as a whole needs to be faithfully duplicated. Therefore, both nucleosome dynamics as well as local changes in chromatin organization, including introduction and/or removal of covalent DNA and histone modifications, at genes with a key role in cell proliferation, are of primary relevance. Chromatin duplication during the S-phase and the chromosome segregation during mitosis are cell cycle stages critical for maintenance of epigenetic marks or for allowing the daughter products to acquire a distinct epigenetic landscape and, consequently, a unique cell fate decision. These aspects of chromatin dynamics together with the strict coupling of cell proliferation, cell differentiation and post-embryonic organogenesis have a profound impact on plant growth, development and response to external signals.
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Affiliation(s)
- María de la Paz Sanchez
- Centro de Biologia Molecular "Severo Ochoa", Consejo Superior de Investigaciones Cientificas, Universidad Autonoma de Madrid, Nicolas Cabrera 1, Cantoblanco, Madrid, Spain
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Helmstaedt K, Laubinger K, Vosskuhl K, Bayram O, Busch S, Hoppert M, Valerius O, Seiler S, Braus GH. The nuclear migration protein NUDF/LIS1 forms a complex with NUDC and BNFA at spindle pole bodies. EUKARYOTIC CELL 2008; 7:1041-52. [PMID: 18390647 PMCID: PMC2446659 DOI: 10.1128/ec.00071-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Accepted: 03/25/2008] [Indexed: 11/20/2022]
Abstract
Nuclear migration depends on microtubules, the dynein motor complex, and regulatory components like LIS1 and NUDC. We sought to identify new binding partners of the fungal LIS1 homolog NUDF to clarify its function in dynein regulation. We therefore analyzed the association between NUDF and NUDC in Aspergillus nidulans. NUDF and NUDC directly interacted in yeast two-hybrid experiments via NUDF's WD40 domain. NUDC-green fluorescent protein (NUDC-GFP) was localized to immobile dots in the cytoplasm and at the hyphal cortex, some of which were spindle pole bodies (SPBs). We showed by bimolecular fluorescence complementation microscopy that NUDC directly interacted with NUDF at SPBs at different stages of the cell cycle. Applying tandem affinity purification, we isolated the NUDF-associated protein BNFA (for binding to NUDF). BNFA was dispensable for growth and for nuclear migration. GFP-BNFA fusions localized to SPBs at different stages of the cell cycle. This localization depended on NUDF, since the loss of NUDF resulted in the cytoplasmic accumulation of BNFA. BNFA did not bind to NUDC in a yeast two-hybrid assay. These results show that the conserved NUDF and NUDC proteins play a concerted role at SPBs at different stages of the cell cycle and that NUDF recruits additional proteins specifically to the dynein complex at SPBs.
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Affiliation(s)
- Kerstin Helmstaedt
- Molekulare Mikrobiologie und Genetik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
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38
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Bui HT, Van Thuan N, Kishigami S, Wakayama S, Hikichi T, Ohta H, Mizutani E, Yamaoka E, Wakayama T, Miyano T. Regulation of chromatin and chromosome morphology by histone H3 modifications in pig oocytes. Reproduction 2007; 133:371-82. [PMID: 17307905 DOI: 10.1530/rep-06-0099] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Oocyte growth, maturation, and activation are complex processes that include transcription, heterochromatin formation, chromosome condensation and decondensation, two consecutive chromosome separations, and genomic imprinting. The objective of this study was to investigate changes in histone H3 modifications in relation to chromatin/chromosome morphology in pig oocytes during their growth, maturation, and activation. During the growth phase, histone H3 was acetylated at lysines 9, 14, and 18 (K9, K14, and K18), and became methylated at K9 when the follicles developed to the antral stage (oocyte diameter, 90 mum). When the fully grown oocytes (diameter, 120 mum) started their maturation, histone H3 became phosphorylated at serine 28 (S28) and then at S10, and deacetylated at K9, K14, and K18 as the chromosomes condensed. After the electroactivation of mature oocytes, histone H3 was reacetylated and dephosphorylated concomitant with the decondensation of the chromosomes. Histone H3 kinase activity increased over a similar time course to that of the phosphorylation of histone H3-S28 during oocyte maturation, and this activity decreased as histone H3-S10 and H3-S28 began to be dephosphorylated after the activation of the mature oocytes. These results suggest that the chromatin morphology of pig oocytes is regulated by the acetylation/deacetylation and the phosphorylation/dephosphorylation of histone H3, and the phosphorylation of histone H3 is the key event in meiotic chromosome condensation in oocytes. The inhibition of histone deacetylase with trichostatin A (TSA) inhibited the deacetylation and phosphorylation of histone H3, and chromosome condensation. Therefore, the deacetylation of histone H3 is thought to be required for its phosphorylation in meiosis. Although histone H3 acetylation and phosphorylation were reversible, the histone methylation that was established during the oocyte growth phase was stable throughout the course of oocyte maturation and activation.
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Affiliation(s)
- Hong-Thuy Bui
- RIKEN-Kobe, Center for Developmental Biology, 2-2-3 Minamimachi Chuo-ku, Kobe 650-0047, Japan.
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Mitotic histone H3 phosphorylation by vaccinia-related kinase 1 in mammalian cells. Mol Cell Biol 2007; 27:8533-46. [PMID: 17938195 DOI: 10.1128/mcb.00018-07] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitotic chromatin condensation is essential for cell division in eukaryotes. Posttranslational modification of the N-terminal tail of histone proteins, particularly by phosphorylation by mitotic histone kinases, may facilitate this process. In mammals, aurora B is believed to be the mitotic histone H3 Ser10 kinase; however, it is not sufficient to phosphorylate H3 Ser10 with aurora B alone. We show that histone H3 is phosphorylated by vaccinia-related kinase 1 (VRK1). Direct phosphorylation of Thr3 and Ser10 in H3 by VRK1 both in vitro and in vivo was observed. Loss of VRK1 activity was associated with a marked decrease in H3 phosphorylation during mitosis. Phosphorylation of Ser10 by VRK1 is similar to that by aurora B. Moreover, expression and chromatin localization of VRK1 depended on the cell cycle phase. Overexpression of VRK1 resulted in a dramatic condensation of nuclei. Our findings collectively support a role of VRK1 as a novel mitotic histone H3 kinase in mammals.
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O'Regan L, Blot J, Fry AM. Mitotic regulation by NIMA-related kinases. Cell Div 2007; 2:25. [PMID: 17727698 PMCID: PMC2018689 DOI: 10.1186/1747-1028-2-25] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Accepted: 08/29/2007] [Indexed: 11/22/2022] Open
Abstract
The NIMA-related kinases represent a family of serine/threonine kinases implicated in cell cycle control. The founding member of this family, the NIMA kinase of Aspergillus nidulans, as well as the fission yeast homologue Fin1, contribute to multiple aspects of mitotic progression including the timing of mitotic entry, chromatin condensation, spindle organization and cytokinesis. Mammals contain a large family of eleven NIMA-related kinases, named Nek1 to Nek11. Of these, there is now substantial evidence that Nek2, Nek6, Nek7 and Nek9 also regulate mitotic events. At least three of these kinases, as well as NIMA and Fin1, have been localized to the microtubule organizing centre of their respective species, namely the centrosome or spindle pole body. Here, they have important functions in microtubule organization and mitotic spindle assembly. Other Nek kinases have been proposed to play microtubule-dependent roles in non-dividing cells, most notably in regulating the axonemal microtubules of cilia and flagella. In this review, we discuss the evidence that NIMA-related kinases make a significant contribution to the orchestration of mitotic progression and thereby protect cells from chromosome instability. Furthermore, we highlight their potential as novel chemotherapeutic targets.
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Affiliation(s)
- Laura O'Regan
- Department of Biochemistry, University of Leicester, Leicester, UK
| | - Joelle Blot
- Department of Biochemistry, University of Leicester, Leicester, UK
| | - Andrew M Fry
- Department of Biochemistry, University of Leicester, Leicester, UK
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Wu W, Baxter JE, Wattam SL, Hayward DG, Fardilha M, Knebel A, Ford EM, da Cruz e Silva EF, Fry AM. Alternative splicing controls nuclear translocation of the cell cycle-regulated Nek2 kinase. J Biol Chem 2007; 282:26431-40. [PMID: 17626005 DOI: 10.1074/jbc.m704969200] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nek2 is a cell cycle-regulated serine/threonine protein kinase that is up-regulated in human cancers. Functionally, it is implicated in control of centrosome separation and bipolar spindle formation in mitotic cells and chromatin condensation in meiotic cells. Two major splice variants have been described in vertebrates, Nek2A and Nek2B, that differ in their non-catalytic C termini. Recently, a third splice variant, Nek2C, was identified that lacks an eight-amino acid internal sequence within the C-terminal domain of Nek2A. This excision occurs at the same position as the Nek2A/Nek2B splice point. As predicted from their high degree of similarity, we show here that Nek2C shares many properties with Nek2A including kinase activity, dimerization, protein phosphatase 1 interaction, mitotic degradation, microtubule binding, and centrosome localization. Unexpectedly, though, the non-centrosomal pool of protein exhibits a marked difference in distribution for the three splice variants. Nek2C is mainly nuclear, Nek2B is mainly cytoplasmic, and Nek2A is evenly distributed within nuclei and cytoplasm. Mutagenesis experiments revealed a functional bipartite nuclear localization sequence (NLS) that spans the splice site leading to Nek2C having a strong NLS, Nek2A having a weak NLS, and Nek2B having no NLS. Finally, we identified a 28-kDa protein in nuclear extracts as a potential novel substrate of Nek2. Thus, alternative splicing provides an unusual mechanism for modulating Nek2 localization, enabling it to have both nuclear and cytoplasmic functions.
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Affiliation(s)
- Wenjuan Wu
- Laboratório de Transdução de Sinais, Centro de Biologia Celular, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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Kim S, Lee K, Rhee K. NEK7 is a centrosomal kinase critical for microtubule nucleation. Biochem Biophys Res Commun 2007; 360:56-62. [PMID: 17586473 DOI: 10.1016/j.bbrc.2007.05.206] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Accepted: 05/31/2007] [Indexed: 01/19/2023]
Abstract
NIMA in Aspergillus nidulans is a mitotic kinase for chromosome condensation and segregation. We characterized NEK7, a human homologue of Aspergillus NIMA. NEK7 was located at the centrosome throughout the cell cycle. Temporal localization of NEK7 at midbody of the cytokinetic cell was also observed. NEK7 knockdown by RNAi caused a prometaphase arrest of the cell cycle with monopolar or disorganized spindle. We propose that such defects in spindle assembly are resulted from reduction in microtubule nucleation activity at the centrosome. In consistent to the proposal, we observed a decrease in the centrosomal gamma-tubulin levels and reduction of the microtubule re-growth activity in the NEK7-suppressed cells. In addition, it was evident that NEK7 was directly involved in cytokinesis.
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Affiliation(s)
- Sunghwan Kim
- Department of Biological Sciences and Research Center for Functional Cellulomics, Seoul National University, Seoul 151-742, Republic of Korea
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Houben A, Demidov D, Caperta AD, Karimi R, Agueci F, Vlasenko L. Phosphorylation of histone H3 in plants--a dynamic affair. ACTA ACUST UNITED AC 2007; 1769:308-15. [PMID: 17320987 DOI: 10.1016/j.bbaexp.2007.01.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Revised: 01/08/2007] [Accepted: 01/11/2007] [Indexed: 01/15/2023]
Abstract
Histones are the main protein components of chromatin: they undergo extensive post-translational modifications, particularly acetylation, methylation, phosphorylation, ubiquitination and ADP-ribosylation which modify the structural/functional properties of chromatin. Post-translational modifications of the N-terminal tails of the core histones within the nucleosome particle are thought to act as signals from the chromatin to the cell, for various processes. Thus, in many ways histone tails can be viewed as complex protein-protein interaction surfaces that are regulated by numerous post-translational modifications. Histone phosphorylation has been linked to chromosome condensation/segregation, activation of transcription, apoptosis and DNA damage repair. In plants, the cell cycle dependent phosphorylation of histone H3 has been described; it is hyperphosphorylated at serines 10/28 and at threonines 3/11 during both mitosis and meiosis in patterns that are specifically coordinated in both space and time. Although this post-translational modification is highly conserved, data show that the chromosomal distribution of individual modifications can differ between groups of eukaryotes. Initial results indicate that members of the plant Aurora kinase family have the capacity to control cell cycle regulated histone H3 phosphorylation, and in addition we describe other potential H3 kinases and discuss their functions.
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Affiliation(s)
- Andreas Houben
- Leibniz-Institute of Plant Genetics and Crop Plant Research, Chromosome Structure and Function Group, Corrensstrasse 3, D-06466 Gatersleben, Germany.
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Yissachar N, Salem H, Tennenbaum T, Motro B. Nek7 kinase is enriched at the centrosome, and is required for proper spindle assembly and mitotic progression. FEBS Lett 2006; 580:6489-95. [PMID: 17101132 DOI: 10.1016/j.febslet.2006.10.069] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 10/27/2006] [Accepted: 10/30/2006] [Indexed: 11/23/2022]
Abstract
Members of the NIMA-related kinases (NRK) family are recently emerging as central regulators of various aspects of the cell cycle. However, the cellular roles of the mammalian NRK, Nek7, remain obscure. We show here that the endogenous Nek7 protein is enriched at the centrosome in a microtubule-independent manner. Overexpression of wt or kinase-defective Nek7 resulted in cells of rounder appearance, and higher proportions of multinuclear and apoptotic cells. Down-regulation of Nek7 using a small interfering RNA approach resulted in a significant increase in mitotic cells presenting multipolar spindle phenotype. These results suggest a role for Nek7 in regulating proper spindle assembly and mitotic progression.
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Affiliation(s)
- Nissan Yissachar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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De Souza CPC, Hashmi SB, Horn KP, Osmani SA. A point mutation in the Aspergillus nidulans sonBNup98 nuclear pore complex gene causes conditional DNA damage sensitivity. Genetics 2006; 174:1881-93. [PMID: 17028324 PMCID: PMC1698649 DOI: 10.1534/genetics.106.063438] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nuclear pore complex (NPC) is embedded in the nuclear envelope where it mediates transport between the cytoplasm and nucleus and helps to organize nuclear architecture. We previously isolated sonB1, a mutation encoding a single amino acid substitution within the Aspergillus nidulans SONBnNup98 NPC protein (nucleoporin). Here we demonstrate that this mutation causes marked DNA damage sensitivity at 42 degrees . Although SONBnNup98 has roles in the G2 transition, we demonstrate that the G2 DNA damage checkpoint is functional in the sonB1 mutant at 42 degrees . The MRN complex is composed of MRE11, RAD50, and NBS1 and functions in checkpoint signaling, DNA repair, and telomere maintenance. At 42 degrees we find that the DNA damage response defect of sonB1 mutants causes synthetic lethality when combined with mutations in scaANBS1, the A. nidulans homolog of NBS1. We provide evidence that this synthetic lethality is independent of MRN cell cycle checkpoint functions or MREAMRE11-mediated DNA repair functions. We also demonstrate that the single A. nidulans histone H2A gene contains the C-terminal SQE motif of histone H2AX isoforms and that this motif is required for the DNA damage response. We propose that the sonB1 nucleoporin mutation causes a defect in a novel part of the DNA damage response.
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Affiliation(s)
- Colin P C De Souza
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA
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Takahashi H, Murai Y, Tsuneyama K, Nomoto K, Okada E, Fujita H, Takano Y. Overexpression of Phosphorylated Histone H3 is an Indicator of Poor Prognosis in Gastric Adenocarcinoma Patients. Appl Immunohistochem Mol Morphol 2006; 14:296-302. [PMID: 16932020 DOI: 10.1097/00129039-200609000-00007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ki-67 immunostaining is commonly used for assessing cell proliferation, but studies of its use as a prognostic indicator have revealed discordant results in gastric cancer patients. Recently, antibodies for phosphorylated histone H3 have been used to identify dividing cells because of its precise overexpression in mitosis. The authors tested the hypothesis that phosphorylated histone H3 overexpression might be a good prognostic indicator for gastric cancer patients by conducting an immunohistochemical comparison with Ki-67 in gastric cancer samples. One hundred twenty-two surgically resected primary cases were selected and histologically categorized in accordance with Lauren's classification. No correlation was found between phosphorylated histone H3 and Ki-67 regarding overexpression. However, correlations between phosphorylated histone H3 overexpression and clinicopathologic variables were noted for histologic type (intestinal type predominant in high labeling indices [LIs], defined as over the value of the 75th percentile; P<0.01), vessel invasion (positive in high LIs; P=0.05), and lymph node metastasis (positive in high LIs; P=0.04). With regard to Ki-67 overexpression, no correlation was evident with the clinicopathologic variables except histologic type (intestinal type predominant; P=0.05). By the Kaplan-Meier method with the log-rank test, cases overexpressing phosphorylated histone H3 showed a poorer prognosis than cases with low expression (P<0.01). In contrast, Ki-67 expression did not influence prognosis. Multivariate analyses indicated phosphorylated histone H3 overexpression to be an independent prognostic factor, together with lymphatic invasion and venous invasion (P<0.01). In conclusion, it seems likely that phosphorylated histone H3 plays an important role in the prognosis of gastric cancer, and its immunohistochemical investigation is useful for the prediction of prognosis in gastric cancer.
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Affiliation(s)
- Hiroyuki Takahashi
- First Department of Pathology, Toyama Medical and Pharmaceutical University School of Medicine, Toyama, Japan
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Feige E, Shalom O, Tsuriel S, Yissachar N, Motro B. Nek1 shares structural and functional similarities with NIMA kinase. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:272-81. [PMID: 16603261 DOI: 10.1016/j.bbamcr.2006.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2005] [Revised: 01/12/2006] [Accepted: 01/17/2006] [Indexed: 11/28/2022]
Abstract
The Aspergillus NIMA serine/threonine kinase plays a pivotal role in controlling entrance into mitosis. A major function attributed to NIMA is the induction of chromatin condensation. We show here that the founder murine NIMA-related kinase, Nek1, is larger than previously reported, and that the full-length protein conserves the structural hallmarks of NIMA. Even though Nek1 bears two classical nuclear localization signals (NLS), the endogenous protein localizes to the cytoplasm. Ectopic overexpression of various Nek1 constructs suggests that the C-terminus of Nek1 bears cytoplasmic localization signal(s). Overexpression of nuclear constructs of Nek1 resulted in abnormal chromatin condensation, with the DNA mainly confined to the periphery of the nucleus. Advanced condensation phenotype was associated with nuclear pore complex dispersal. The condensation was not accompanied by up-regulation of mitotic or apoptotic markers. A similar phenotype has been described following NIMA overexpression, strengthening the notion that the mammalian Nek1 kinase has functional similarity to NIMA.
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Affiliation(s)
- Erez Feige
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Cha H, Dangi S, Machamer CE, Shapiro P. Inhibition of mixed-lineage kinase (MLK) activity during G2-phase disrupts microtubule formation and mitotic progression in HeLa cells. Cell Signal 2006; 18:93-104. [PMID: 15923109 PMCID: PMC2835151 DOI: 10.1016/j.cellsig.2005.03.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Revised: 03/18/2005] [Accepted: 03/18/2005] [Indexed: 10/25/2022]
Abstract
The mixed-lineage kinases (MLK) are serine/threonine protein kinases that regulate mitogen-activated protein (MAP) kinase signaling pathways in response to extracellular signals. Recent studies indicate that MLK activity may promote neuronal cell death through activation of the c-Jun NH2-terminal kinase (JNK) family of MAP kinases. Thus, inhibitors of MLK activity may be clinically useful for delaying the progression of neurodegenerative diseases, such as Parkinson's. In proliferating non-neuronal cells, MLK may have the opposite effect of promoting cell proliferation. In the current studies we examined the requirement for MLK proteins in regulating cell proliferation by examining MLK function during G2 and M-phase of the cell cycle. The MLK inhibitor CEP-11004 prevented HeLa cell proliferation by delaying mitotic progression. Closer examination revealed that HeLa cells treated with CEP-11004 during G2-phase entered mitosis similar to untreated G2-phase cells. However, CEP-11004 treated cells failed to properly exit mitosis and arrested in a pro-metaphase state. Partial reversal of the CEP-11004 induced mitotic arrest could be achieved by overexpression of exogenous MLK3. The effects of CEP-11004 treatment on mitotic events included the inhibition of histone H3 phosphorylation during prophase and prior to nuclear envelope breakdown and the formation of aberrant mitotic spindles. These data indicate that MLK3 might be a unique target to selectively inhibit transformed cell proliferation by disrupting mitotic spindle formation resulting in mitotic arrest.
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Affiliation(s)
- Hyukjin Cha
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy Baltimore, Maryland, USA
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Cloutier M, Vigneault F, Lachance D, Séguin A. Characterization of a poplar NIMA-related kinase PNek1 and its potential role in meristematic activity. FEBS Lett 2005; 579:4659-65. [PMID: 16098516 DOI: 10.1016/j.febslet.2005.07.036] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Revised: 07/11/2005] [Accepted: 07/12/2005] [Indexed: 12/14/2022]
Abstract
Meristems are sites of undifferentiated cell division, which carry on developing into functional organs. Using the two-hybrid system with a poplar 14-3-3, we uncovered poplar NIMA-related kinase 1 (PNek1) as an interacting protein. PNek1 shows high homology to the mammalian NIMA-related kinases, which are thought to be involved in cell cycle progression. Using a synchronized poplar cell suspension, we observed an accumulation of PNek1 mRNA at the G1/S transition and throughout the G2-to-M progression. Moreover, PNek1-GFP fusion protein localized in the cytoplasm and in both the nuclear and nucleolar regions. Overexpression of PNek1-GFP in Arabidopsis caused morphological abnormalities in flower and siliques. Overall, these results suggest that PNek1 is involved in plant development.
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Affiliation(s)
- Monikca Cloutier
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 3800, Sainte-Foy, Que., Canada
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Sunavala-Dossabhoy G, Balakrishnan SK, Sen S, Nuthalapaty S, De Benedetti A. The radioresistance kinase TLK1B protects the cells by promoting repair of double strand breaks. BMC Mol Biol 2005; 6:19. [PMID: 16156902 PMCID: PMC1242231 DOI: 10.1186/1471-2199-6-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Accepted: 09/12/2005] [Indexed: 11/10/2022] Open
Abstract
Background The mammalian protein kinase TLK1 is a homologue of Tousled, a gene involved in flower development in Arabidopsis thaliana. The function of TLK1 is not well known, although knockout of the gene in Drosophila or expression of a dominant negative mutant in mouse cells causes loss of nuclear divisions and missegregation of chromosomes probably, due to alterations in chromatin remodeling capacity. Overexpression of TLK1B, a spliced variant of the TLK1 mRNA, in a model mouse cell line increases it's resistance to ionizing radiation (IR) or the radiomimetic drug doxorubicin, also likely due to changes in chromatin remodeling. TLK1B is translationally regulated by the availability of the translation factor eIF4E, and its synthesis is activated by IR. The reason for this mechanism of regulation is likely to provide a rapid means of promoting repair of DSBs. TLK1B specifically phosphorylates histone H3 and Asf1, likely resulting in changes in chromatin structure, particularly at double strand breaks (DSB) sites. Results In this work, we provide several lines of evidence that TLK1B protects the cells from IR by facilitating the repair of DSBs. First, the pattern of phosphorylation and dephosphorylation of H2AX and H3 indicated that cells overexpressing TLK1B return to pre-IR steady state much more rapidly than controls. Second, the repair of episomes damaged with DSBs was much more rapid in cells overexpressing TLK1B. This was also true for repair of genomic damage. Lastly, we demonstrate with an in vitro repair system that the addition of recombinant TLK1B promotes repair of a linearized plasmid incubated with nuclear extract. In addition, TLK1B in this in vitro system promotes the assembly of chromatin as shown by the formation of more highly supercoiled topomers of the plasmid. Conclusion In this work, we provide evidence that TLK1B promotes the repair of DSBs, likely as a consequence of a change in chromatin remodeling capacity that must precede the assembly of repair complexes at the sites of damage.
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Affiliation(s)
- Gulshan Sunavala-Dossabhoy
- Department of Biochemistry and Molecular Biology and the Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center. 1501 Kings Highway, Shreveport, LA 71130-3932, USA
| | - Sri Kripa Balakrishnan
- Department of Biochemistry and Molecular Biology and the Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center. 1501 Kings Highway, Shreveport, LA 71130-3932, USA
| | - Siddhartha Sen
- Department of Biochemistry and Molecular Biology and the Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center. 1501 Kings Highway, Shreveport, LA 71130-3932, USA
| | - Sam Nuthalapaty
- Department of Biochemistry and Molecular Biology and the Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center. 1501 Kings Highway, Shreveport, LA 71130-3932, USA
| | - Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology and the Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center. 1501 Kings Highway, Shreveport, LA 71130-3932, USA
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