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Guo X, Zhao B, Zhou X, Ni X, Lu D, Chen T, Chen Y, Xiao D. Increased RNA production in Saccharomyces cerevisiae by simultaneously overexpressing FHL1, IFH1, and SSF2 and deleting HRP1. Appl Microbiol Biotechnol 2020; 104:7901-7913. [PMID: 32715361 DOI: 10.1007/s00253-020-10784-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/01/2020] [Accepted: 07/13/2020] [Indexed: 11/25/2022]
Abstract
Ribonucleic acid (RNA) and its degradation products are widely used in the food industry. In this study, we constructed Saccharomyces cerevisiae mutants with FHL1, IFH1, SSF1, and SSF2 overexpression and HRP1 deletion, individually to evaluate the effect on RNA production. The RNA content of recombinant strains W303-1a-FHL1, W303-1a-SSF2, and W303-1a-ΔHRP1 was increased by 14.94%, 24.4%, and 19.36%, respectively, compared with the RNA content of the parent strain. However, W303-1a-IFH1 and W303-1a-SSF1 showed no significant change in RNA production compared with the parent strain. IFH1 and FHL1 encode Ifh1p and Fhl1p, respectively, which combine to form a complex that plays a key role in the transcription of the ribosomal protein (RP) gene. Ssf2p, encoded by SSF2, plays an important role in ribosome biosynthesis and Hrp1p is a negative regulator of cell growth in S. cerevisiae. Subsequently, a high RNA production strain, W112, was constructed by simultaneously overexpressing FHL1, IFH1, and SSF2 and deleting HRP1. The RNA content of W112 was 38.8% higher than the parent strain. The growth performance, RP transcription levels, and rRNA content were also investigated in the recombinant strains. This study provides a new strategy for the construction of S. cerevisiae strains containing large amounts of RNA, and it will make a significant contribution to progress in the nucleic acid industry. KEY POINTS: • Simultaneously overexpressing FHL1, IFH1, and SSF2 and deleting HRP1 can significantly increases RNA production. • The production of RNA increased by 38.8% in Saccharomyces cerevisiae. • The cell size and growth rate of the strains with higher RNA content also increased.
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Affiliation(s)
- Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547, China.
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300457, China.
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, 300457, China.
- Department of Fermentation Engineering, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Bin Zhao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547, China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300457, China
| | - Xinran Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547, China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300457, China
| | - Xiaofeng Ni
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547, China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300457, China
| | - Dongxia Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547, China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300457, China
| | - Tingli Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547, China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547, China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, 300457, China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547, China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, 300457, China
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Abstract
Eukaryotic chromatin is remodelled by the evolutionarily conserved Snf2 family of enzymes in an ATP-dependent manner. Several Snf2 enzymes are part of CRCs (chromatin remodelling complexes). In the present review we focus our attention on the functions of Snf2 enzymes and CRCs in fission yeast. We discuss their molecular mechanisms and roles and in regulating gene expression, DNA recombination, euchromatin and heterochromatin structure.
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Liu H, Luo M, Wen JK. mRNA stability in the nucleus. J Zhejiang Univ Sci B 2014; 15:444-54. [PMID: 24793762 PMCID: PMC4076601 DOI: 10.1631/jzus.b1400088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 04/11/2014] [Indexed: 01/15/2023]
Abstract
Eukaryotic gene expression is controlled by different levels of biological events, such as transcription factors regulating the timing and strength of transcripts production, alteration of transcription rate by RNA processing, and mRNA stability during RNA processing and translation. RNAs, especially mRNAs, are relatively vulnerable molecules in living cells for ribonucleases (RNases). The maintenance of quality and quantity of transcripts is a key issue for many biological processes. Extensive studies draw the conclusion that the stability of RNAs is dedicated-regulated, occurring co- and post-transcriptionally, and translation-coupled as well, either in the nucleus or cytoplasm. Recently, RNA stability in the nucleus has aroused much research interest, especially the stability of newly-made transcripts. In this article, we summarize recent progresses on mRNA stability in the nucleus, especially focusing on quality control of newly-made RNA by RNA polymerase II in eukaryotes.
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Affiliation(s)
- Han Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Min Luo
- Chongqing Institute of Tuberculosis Prevention and Treatment, Chongqing 400050, China
| | - Ji-kai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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Pointner J, Persson J, Prasad P, Norman-Axelsson U, Strålfors A, Khorosjutina O, Krietenstein N, Svensson JP, Ekwall K, Korber P. CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J 2012; 31:4388-403. [PMID: 23103765 DOI: 10.1038/emboj.2012.289] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/28/2012] [Indexed: 11/09/2022] Open
Abstract
Nucleosome positioning governs access to eukaryotic genomes. Many genes show a stereotypic organisation at their 5'end: a nucleosome free region just upstream of the transcription start site (TSS) followed by a regular nucleosomal array over the coding region. The determinants for this pattern are unclear, but nucleosome remodelers are likely critical. Here we study the role of remodelers in global nucleosome positioning in S. pombe and the corresponding changes in expression. We find a striking evolutionary shift in remodeler usage between budding and fission yeast. The S. pombe RSC complex does not seem to be involved in nucleosome positioning, despite its prominent role in S. cerevisiae. While S. pombe lacks ISWI-type remodelers, it has two CHD1-type ATPases, Hrp1 and Hrp3. We demonstrate nucleosome spacing activity for Hrp1 and Hrp3 in vitro, and that together they are essential for linking regular genic arrays to most TSSs in vivo. Impaired arrays in the absence of either or both remodelers may lead to increased cryptic antisense transcription, but overall gene expression levels are only mildly affected.
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Affiliation(s)
- Julia Pointner
- Adolf-Butenandt-Institut, University of Munich, Munich, Germany
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5
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SWI/SNF-like chromatin remodeling factor Fun30 supports point centromere function in S. cerevisiae. PLoS Genet 2012; 8:e1002974. [PMID: 23028372 PMCID: PMC3459985 DOI: 10.1371/journal.pgen.1002974] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 08/08/2012] [Indexed: 12/22/2022] Open
Abstract
Budding yeast centromeres are sequence-defined point centromeres and are, unlike in many other organisms, not embedded in heterochromatin. Here we show that Fun30, a poorly understood SWI/SNF-like chromatin remodeling factor conserved in humans, promotes point centromere function through the formation of correct chromatin architecture at centromeres. Our determination of the genome-wide binding and nucleosome positioning properties of Fun30 shows that this enzyme is consistently enriched over centromeres and that a majority of CENs show Fun30-dependent changes in flanking nucleosome position and/or CEN core micrococcal nuclease accessibility. Fun30 deletion leads to defects in histone variant Htz1 occupancy genome-wide, including at and around most centromeres. FUN30 genetically interacts with CSE4, coding for the centromere-specific variant of histone H3, and counteracts the detrimental effect of transcription through centromeres on chromosome segregation and suppresses transcriptional noise over centromere CEN3. Previous work has shown a requirement for fission yeast and mammalian homologs of Fun30 in heterochromatin assembly. As centromeres in budding yeast are not embedded in heterochromatin, our findings indicate a direct role of Fun30 in centromere chromatin by promoting correct chromatin architecture.
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Shim YS, Choi Y, Kang K, Cho K, Oh S, Lee J, Grewal SIS, Lee D. Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin. EMBO J 2012; 31:4375-87. [PMID: 22990236 DOI: 10.1038/emboj.2012.267] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/03/2012] [Indexed: 11/09/2022] Open
Abstract
The positioning of the nucleosome by ATP-dependent remodellers provides the fundamental chromatin environment for the regulation of diverse cellular processes acting on the underlying DNA. Recently, genome-wide nucleosome mapping has revealed more detailed information on the chromatin-remodelling factors. Here, we report that the Schizosaccharomyces pombe CHD remodeller, Hrp3, is a global regulator that drives proper nucleosome positioning and nucleosome stability. The loss of Hrp3 resulted in nucleosome perturbation across the chromosome, and the production of antisense transcripts in the hrp3Δ cells emphasized the importance of nucleosome architecture for proper transcription. Notably, perturbation of the nucleosome in hrp3 deletion mutant was also associated with destabilization of the DNA-histone interaction and cell cycle-dependent alleviation of heterochromatin silencing. Furthermore, the effect of Hrp3 in the pericentric region was found to be accomplished via a physical interaction with Swi6, and appeared to cooperate with other heterochromatin factors for gene silencing. Taken together, our data indicate that a well-positioned nucleosome by Hrp3 is important for the spatial-temporal control of transcription-associated processes.
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Affiliation(s)
- Young Sam Shim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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7
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Raiola A, Lionetti V, Elmaghraby I, Immerzeel P, Mellerowicz EJ, Salvi G, Cervone F, Bellincampi D. Pectin methylesterase is induced in Arabidopsis upon infection and is necessary for a successful colonization by necrotrophic pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:432-40. [PMID: 21171891 DOI: 10.1094/mpmi-07-10-0157] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The ability of bacterial or fungal necrotrophs to produce enzymes capable of degrading pectin is often related to a successful initiation of the infective process. Pectin is synthesized in a highly methylesterified form and is subsequently de-esterified in muro by pectin methylesterase. De-esterification makes pectin more susceptible to the degradation by pectic enzymes such as endopolygalacturonases (endoPG) and pectate lyases secreted by necrotrophic pathogens during the first stages of infection. We show that, upon infection, Pectobacterium carotovorum and Botrytis cinerea induce in Arabidopsis a rapid expression of AtPME3 that acts as a susceptibility factor and is required for the initial colonization of the host tissue.
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Affiliation(s)
- Alessandro Raiola
- Department of Land, Environment, Agriculture and Forestry, University of Padua, Legnaro (PD) Italy
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8
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Abstract
Chromodomain/helicase/DNA-binding domain (CHD) proteins have been identified in a variety of organisms. Despite common features, such as their chromodomain and helicase domain, they have been described as having multiple roles and interacting partners. However, a common theme for the main role of CHD proteins appears to be linked to their ATP-dependent chromatin-remodeling activity. Their actual activity as either repressor or activator, and their cell or gene specificity, is connected to their interacting partner(s). In this minireview, we attempt to match the members of the CHD family with the presence of structural domains, cofactors, and cellular roles in the regulation of gene expression, recombination, genome organization, and chromatin structure, as well as their potential activity in RNA processing.
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Affiliation(s)
- J Adam Hall
- Department of Biological Sciences, Marshall University, 1 John Marshall Drive, Huntington, WV 25755, USA
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9
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Pal S, Sif S. Interplay between chromatin remodelers and protein arginine methyltransferases. J Cell Physiol 2008; 213:306-15. [PMID: 17708529 DOI: 10.1002/jcp.21180] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chromatin modifying enzymes have emerged as key regulators of all DNA based processes, which control cell growth, development, and differentiation. Recently, it has become clear that different chromatin remodeling and histone-modifying activities are involved in transcriptional activation and repression. Among the enzymes involved in regulating chromatin structure is the family of protein arginine methyltransferases (PRMTs) that specializes in methylating both histones as well as key cellular proteins. There are eleven different PRMT genes (PRMT1-11) whose biological function remains under explored. PRMTs regulate various cellular processes such as DNA repair and transcription, RNA processing, signal transduction, and nucleo-cytoplasmic localization. Like histone lysine methylation, methylation of histone arginine residues can either induce or inhibit transcription depending on the residue being modified and the type of methylation being introduced. In this review, we will focus on the latest findings and biological roles of ATP-dependent chromatin remodeling complexes and PRMT enzymes, and how their aberrant expression is linked to cancer.
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Affiliation(s)
- Sharmistha Pal
- Department of Molecular and Cellular Biochemistry, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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10
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Abstract
Chromodomain/helicase/DNA-binding domain (CHD) proteins have been identified in a variety of organisms. Despite common features, such as their chromodomain and helicase domain, they have been described as having multiple roles and interacting partners. However, a common theme for the main role of CHD proteins appears to be linked to their ATP-dependent chromatin-remodeling activity. Their actual activity as either repressor or activator, and their cell or gene specificity, is connected to their interacting partner(s). In this minireview, we attempt to match the members of the CHD family with the presence of structural domains, cofactors, and cellular roles in the regulation of gene expression, recombination, genome organization, and chromatin structure, as well as their potential activity in RNA processing.
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11
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Hirota K, Mizuno KI, Shibata T, Ohta K. Distinct chromatin modulators regulate the formation of accessible and repressive chromatin at the fission yeast recombination hotspot ade6-M26. Mol Biol Cell 2008; 19:1162-73. [PMID: 18199689 DOI: 10.1091/mbc.e07-04-0377] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Histone acetyltransferases (HATs) and ATP-dependent chromatin remodeling factors (ADCRs) regulate transcription and recombination via alteration of local chromatin configuration. The ade6-M26 allele of Schizosaccharomyces pombe creates a meiotic recombination hotspot that requires a cAMP-responsive element (CRE)-like sequence M26, the Atf1/Pcr1 heterodimeric ATF/CREB transcription factor, the Gcn5 HAT, and the Snf22 SWI2/SNF2 family ADCR. Chromatin alteration occurs meiotically around M26, leading to the activation of meiotic recombination. We newly report the roles of other chromatin remodeling factors that function positively and negatively in chromatin alteration at M26: two CHD-1 family ADCRs (Hrp1 and Hrp3), a Spt-Ada-Gcn5 acetyltransferase component (Ada2), and a member of Moz-Ybf2/Sas3-Sas2-Tip60 family (Mst2). Ada2, Mst2, and Hrp3 are required for the full activation of chromatin changes around M26 and meiotic recombination. Acetylation of histone H3 around M26 is remarkably reduced in gcn5Delta, ada2Delta and snf22Delta, suggesting cooperative functions of these HAT complexes and Snf22. Conversely, Hrp1, another CHD-1 family ADCR, maintains repressive chromatin configuration at ade6-M26. Interestingly, transcriptional initiation site is shifted to a site around M26 from the original initiation sites, in couple with the histone acetylation and meiotic chromatin alteration induced around 3' region of M26, suggesting a collaboration between these chromatin modulators and the transcriptional machinery to form accessible chromatin. These HATs and ADCRs are also required for the regulation of transcription and chromatin structure around M26 in response to osmotic stress. Thus, we propose that multiple chromatin modulators regulate chromatin structure reversibly and participate in the regulation of both meiotic recombination and stress-induced transcription around CRE-like sequences.
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Affiliation(s)
- Kouji Hirota
- Shibata Distinguished Senior Scientist Laboratory, RIKEN Discovery Research Institute, Wako-shi, Saitama 351-0198, Japan.
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12
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Sillibourne JE, Delaval B, Redick S, Sinha M, Doxsey SJ. Chromatin remodeling proteins interact with pericentrin to regulate centrosome integrity. Mol Biol Cell 2007; 18:3667-80. [PMID: 17626165 PMCID: PMC1951766 DOI: 10.1091/mbc.e06-07-0604] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Pericentrin is an integral centrosomal component that anchors regulatory and structural molecules to centrosomes. In a yeast two-hybrid screen with pericentrin we identified chromodomain helicase DNA-binding protein 4 (CHD4/Mi2beta). CHD4 is part of the multiprotein nucleosome remodeling deacetylase (NuRD) complex. We show that many NuRD components interacted with pericentrin by coimmunoprecipitation and that they localized to centrosomes and midbodies. Overexpression of the pericentrin-binding domain of CHD4 or another family member (CHD3) dissociated pericentrin from centrosomes. Depletion of CHD3, but not CHD4, by RNA interference dissociated pericentrin and gamma-tubulin from centrosomes. Microtubule nucleation/organization, cell morphology, and nuclear centration were disrupted in CHD3-depleted cells. Spindles were disorganized, the majority showing a prometaphase-like configuration. Time-lapse imaging revealed mitotic failure before chromosome segregation and cytokinesis failure. We conclude that pericentrin forms complexes with CHD3 and CHD4, but a distinct CHD3-pericentrin complex is required for centrosomal anchoring of pericentrin/gamma-tubulin and for centrosome integrity.
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Bakshi R, Mehta AK, Sharma R, Maiti S, Pasha S, Brahmachari V. Characterization of a human SWI2/SNF2 like protein hINO80: demonstration of catalytic and DNA binding activity. Biochem Biophys Res Commun 2005; 339:313-20. [PMID: 16298340 DOI: 10.1016/j.bbrc.2005.10.206] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2005] [Accepted: 10/27/2005] [Indexed: 11/29/2022]
Abstract
The proteins belonging to SWI2/SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. We have identified a human gene with a putative DNA binding domain, which belongs to the INO80 subfamily of SWI2/SNF2 proteins. Here we report the cloning, expression, and functional activity of the domains from hINO80 gene both in terms of the DNA dependent ATPase as well as DNA binding activity. A differential expression of the various domains within this gene is detected in human tissues while a ubiquitous expression is detected in mice. The intranuclear localization is demonstrated using antibodies directed against the DBINO domain of hINO80.
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Affiliation(s)
- Rachit Bakshi
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India
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14
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Bouazoune K, Brehm A. dMi-2 chromatin binding and remodeling activities are regulated by dCK2 phosphorylation. J Biol Chem 2005; 280:41912-20. [PMID: 16223721 DOI: 10.1074/jbc.m507084200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A plethora of ATP-dependent chromatin-remodeling enzymes have been identified during the last decade. Many have been shown to play pivotal roles in the organization and expression of eukaryotic genomes. It is clear that their activities need to be tightly regulated to ensure their coordinated action. However, little is known about how ATP-dependent remodelers are regulated at the molecular level. Here, we have investigated the ATP-dependent chromatin remodeling enzyme Mi-2 of Drosophila melanogaster. Radioactive labeling of S2 cells reveals that dMi-2 is a phosphoprotein in vivo. dMi-2 phosphorylation is constitutive, and we identify dCK2 as a major dMi-2 kinase in cell extracts. dCK2 binds to and phosphorylates a dMi-2 N-terminal region. Dephosphorylation of recombinant dMi-2 increases its affinity for the nucleosome substrate, nucleosome-stimulated ATPase, and ATP-dependent nucleosome mobilization activities. Our results reveal a potential mechanism for regulation of the dMi-2 enzyme and point toward CK2 phosphorylation as a common feature of CHD family ATPases.
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Affiliation(s)
- Karim Bouazoune
- Adolf-Butenandt-Institut, Lehrstuhl für Molekularbiologie, Ludwig-Maximilians-Universität, Schillerstrasse 44, 80336 München, Germany
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15
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Vázquez-Novelle MD, Esteban V, Bueno A, Sacristán MP. Functional Homology among Human and Fission Yeast Cdc14 Phosphatases. J Biol Chem 2005; 280:29144-50. [PMID: 15911625 DOI: 10.1074/jbc.m413328200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Budding and fission yeast Cdc14 homologues, a conserved family of serine-threonine phosphatases, play a role in the inactivation of mitotic cyclin-dependent kinases (CDKs) by molecularly distinct mechanisms. Saccharomyces cerevisiae Cdc14 protein phosphatase inactivates CDKs by promoting mitotic cyclin degradation and the accumulation of a CDK inhibitor to allow budding yeast cells to exit from mitosis. Schizosaccharomyces pombe Flp1 phosphatase down-regulates CDK/cyclin activity, controlling the degradation of the Cdc25 tyrosine phosphatase for fission yeast cells to undergo cytokinesis. In the present work, we show that human Cdc14 homologues (hCdc14A and hCdc14B) rescued flp1-deficient fission yeast strains, indicating functional homology. We also show that hCdc14A and B interacted in vivo with S. pombe Cdc25 and that hCdc14A dephosphorylated this mitotic inducer both in vitro and in vivo. Our results support a Cdc14 conserved inhibitory mechanism acting on S. pombe Cdc25 protein and suggest that human cells may regulate Cdc25 in a similar manner to inactivate Cdk1-mitotic cyclin complexes.
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Affiliation(s)
- M Dolores Vázquez-Novelle
- Centro de Investigación del Cáncer and Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca/Consejo Superior de Investigaciones Científicas, 37007 Salamanca, Spain
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16
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Martienssen RA, Zaratiegui M, Goto DB. RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe. Trends Genet 2005; 21:450-6. [PMID: 15979194 DOI: 10.1016/j.tig.2005.06.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Revised: 05/17/2005] [Accepted: 06/08/2005] [Indexed: 10/25/2022]
Abstract
Fission yeast is a useful model for RNA interference because it has single-copy genes for components of the RNAi pathway such as argonaute, dicer and RNA-dependent RNA polymerase (RdRP). Functions for RNAi revealed in S. pombe, such as heterochromatic silencing and chromosome segregation, are likely to be ancient because they are shared with some other eukaryotes. The underlying mechanisms are being rapidly unraveled.
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17
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Walfridsson J, Bjerling P, Thalen M, Yoo EJ, Park SD, Ekwall K. The CHD remodeling factor Hrp1 stimulates CENP-A loading to centromeres. Nucleic Acids Res 2005; 33:2868-79. [PMID: 15908586 PMCID: PMC1133792 DOI: 10.1093/nar/gki579] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Centromeres of fission yeast are arranged with a central core DNA sequence flanked by repeated sequences. The centromere-associated histone H3 variant Cnp1 (SpCENP-A) binds exclusively to central core DNA, while the heterochromatin proteins and cohesins bind the surrounding outer repeats. CHD (chromo-helicase/ATPase DNA binding) chromatin remodeling factors were recently shown to affect chromatin assembly in vitro. Here, we report that the CHD protein Hrp1 plays a key role at fission yeast centromeres. The hrp1Δ mutant disrupts silencing of the outer repeats and central core regions of the centromere and displays chromosome segregation defects characteristic for dysfunction of both regions. Importantly, Hrp1 is required to maintain high levels of Cnp1 and low levels of histone H3 and H4 acetylation at the central core region. Hrp1 interacts directly with the centromere in early S-phase when centromeres are replicated, suggesting that Hrp1 plays a direct role in chromatin assembly during DNA replication.
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Affiliation(s)
| | | | | | - Eung-Jae Yoo
- School of Biological Sciences, Seoul National UniversitySeoul 151-742, Korea
| | - Sang Dai Park
- School of Biological Sciences, Seoul National UniversitySeoul 151-742, Korea
| | - Karl Ekwall
- To whom correspondence should be addressed. Tel: +46 8 6084713; Fax: +46 8 6084510;
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18
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DiPaolo C, Kieft R, Cross M, Sabatini R. Regulation of trypanosome DNA glycosylation by a SWI2/SNF2-like protein. Mol Cell 2005; 17:441-51. [PMID: 15694344 DOI: 10.1016/j.molcel.2004.12.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2004] [Revised: 11/16/2004] [Accepted: 12/10/2004] [Indexed: 11/16/2022]
Abstract
Synthesis of the modified thymine base beta-D-glucosyl-hydroxymethyluracil, or J, within telomeric DNA of Trypanosoma brucei correlates with the bloodstream-form-specific epigenetic silencing of telomeric variant surface glycoprotein genes involved in antigenic variation. The mechanism of developmental and telomeric-specific regulation of J synthesis is unknown. We have previously identified a J binding protein (JBP1) involved in propagating J synthesis. We have now identified a homolog of JBP1, JBP2, containing a domain related to the SWI2/SNF2 family of chromatin remodeling proteins that is upregulated in bloodstream form cells and interacts with nuclear chromatin. We show that expression of JBP2 in procyclic form cells leads to de novo J synthesis within telomeric regions of the chromosome and that this activity is inhibited after mutagenesis of conserved residues critical for SWI2/SNF2 function. We propose a model in which chromatin remodeling by JBP2 regulates the initial sites of J synthesis within bloodstream form trypanosome DNA, with further propagation and maintenance of J by JBP1.
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Affiliation(s)
- Courtney DiPaolo
- Global Infectious Diseases Program, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 2004; 68:1-108. [PMID: 15007097 PMCID: PMC362109 DOI: 10.1128/mmbr.68.1.1-108.2004] [Citation(s) in RCA: 434] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.
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Affiliation(s)
- Katherine A Borkovich
- Department of Plant Pathology, University of California, Riverside, California 92521, USA. Katherine/
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Tajul-Arifin K, Teasdale R, Ravasi T, Hume DA, Mattick JS. Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome. Genome Res 2003; 13:1416-29. [PMID: 12819141 PMCID: PMC403676 DOI: 10.1101/gr.1015703] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The chromodomain is 40-50 amino acids in length and is conserved in a wide range of chromatic and regulatory proteins involved in chromatin remodeling. Chromodomain-containing proteins can be classified into families based on their broader characteristics, in particular the presence of other types of domains, and which correlate with different subclasses of the chromodomains themselves. Hidden Markov model (HMM)-generated profiles of different subclasses of chromodomains were used here to identify sequences encoding chromodomain-containing proteins in the mouse transcriptome and genome. A total of 36 different loci encoding proteins containing chromodomains, including 17 novel loci, were identified. Six of these loci (including three apparent pseudogenes, a novel HP1 ortholog, and two novel Msl-3 transcription factor-like proteins) are not present in the human genome, whereas the human genome contains four loci (two CDY orthologs and two apparent CDY pseudogenes) that are not present in mouse. A number of these loci exhibit alternative splicing to produce different isoforms, including 43 novel variants, some of which lack the chromodomain. The likely functions of these proteins are discussed in relation to the known functions of other chromodomain-containing proteins within the same family.
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Affiliation(s)
- Khairina Tajul-Arifin
- ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St.Lucia, Queensland 4072, Australia
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21
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Manzanero S, Puertas MJ. Rye terminal neocentromeres: characterisation of the underlying DNA and chromatin structure. Chromosoma 2003; 111:408-15. [PMID: 12644955 DOI: 10.1007/s00412-002-0224-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2002] [Revised: 11/04/2002] [Accepted: 11/15/2002] [Indexed: 10/22/2022]
Abstract
We have studied rye plants with neocentromeres on the terminal regions of the chromosomes. These neocentromeres only appear in meiosis, they are active together with the normal centromere and move the chromosomal arms polewards from prometaphase to anaphase at both the first and second meiotic divisions. All chromosomes of the normal set may show neocentric activity, but chromosomal arms with terminal heterochromatic blocks, as assessed by C-banding, are significantly more susceptible than those that do not have them. At least three repetitive sequences underlie the neocentromeres: pSc34, pSc74 and pSc200. These sequences are not detectable in B chromosomes, which never showed neocentric activity. Fluorescence in situ hybridisation with these sequences used as probes revealed elongated chromatin extensions on the neocentromeres that have not been observed using other staining techniques. These extensions were never observed in control plants. They suggest a modified chromatin structure, which might be responsible for the interaction with proteins involved in chromosomal movement on the spindle.
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Affiliation(s)
- Silvia Manzanero
- Departamento de Genética, Facultad de Biología, Universidad Complutense, 28040 Madrid, Spain
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Brzeski J, Jerzmanowski A. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J Biol Chem 2003; 278:823-8. [PMID: 12403775 DOI: 10.1074/jbc.m209260200] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deficient in DNA Methylation 1 (DDM1) protein is required to maintain the DNA methylation status of Arabidopsis thaliana. DDM1 is a member of the broad SWI2/SNF2 protein family. Because of its phylogenetic position, DDM1 has been speculated to act as a chromatin-remodeling factor. Here we used a purified recombinant DDM1 protein to investigate whether it can remodel chromatin in vitro. We show that DDM1 is an ATPase stimulated by both naked and nucleosomal DNA. DDM1 binds to the nucleosome and promotes chromatin remodeling in an ATP-dependent manner. Specifically, it induces nucleosome repositioning on a short DNA fragment. The enzymatic activity of DDM1 is not affected by DNA methylation. The relevance of these findings to the in vivo role of DDM1 is discussed.
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Affiliation(s)
- Jan Brzeski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
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Abstract
It has been a long-standing challenge to decipher the principles that enable cells to both organize their genomes into compact chromatin and ensure that the genetic information remains accessible to regulatory factors and enzymes within the confines of the nucleus. The discovery of nucleosome remodeling activities that utilize the energy of ATP to render nucleosomal DNA accessible has been a great leap forward. In vitro, these enzymes weaken the tight wrapping of DNA around the histone octamers, thereby facilitating the sliding of histone octamers to neighboring DNA segments, their displacement to unlinked DNA, and the accumulation of patches of accessible DNA on the surface of nucleosomes. It is presumed that the collective action of these enzymes endows chromatin with dynamic properties that govern all nuclear functions dealing with chromatin as a substrate. The diverse set of ATPases that qualify as the molecular motors of the nucleosome remodeling process have a common history and are part of a superfamily. The physiological context of their remodeling action builds on the association with a wide range of other proteins to form distinct complexes for nucleosome remodeling. This review summarizes the recent progress in our understanding of the mechanisms underlying the nucleosome remodeling reaction, the targeting of remodeling machines to selected sites in chromatin, and their integration into complex regulatory schemes.
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Affiliation(s)
- Peter B Becker
- Adolf-Butenandt-Institut, Molekularbiologie, 80336 Munich, Germany.
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Jae Yoo E, Kyu Jang Y, Ae Lee M, Bjerling P, Bum Kim J, Ekwall K, Hyun Seong R, Dai Park S. Hrp3, a chromodomain helicase/ATPase DNA binding protein, is required for heterochromatin silencing in fission yeast. Biochem Biophys Res Commun 2002; 295:970-4. [PMID: 12127990 DOI: 10.1016/s0006-291x(02)00797-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Hrp3, a paralog of Hrp1, is a novel member of the CHD1 (chromo-helicase/ATPase-DNA binding 1) protein family of Schizosaccharomyces pombe. Although it has been considered that CHD1 proteins are required for chromatin modifications in transcriptional regulations, little is known about their roles in vivo. In this study, we examined the effects of Hrp3 on heterochromatin silencing using several S. pombe reporter strains. The phenotypic analysis revealed that hrp3(+) is not an essential gene for cell viability. However, Hrp3 is required for transcriptional repression at silence loci of mat3. A chromatin immunoprecipitation assay showed that Hrp3 directly associates with mat3 chromatin. Thus, our results strongly suggest that Hrp3 is involved in heterochromatin silencing and plays a direct role as a chromatin remodeling factor at mat3 in vivo.
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Affiliation(s)
- Eung Jae Yoo
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
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Kim WJ, Lee H, Park EJ, Park JK, Park SD. Gain- and loss-of-function of Rhp51, a Rad51 homolog in fission yeast, reveals dissimilarities in chromosome integrity. Nucleic Acids Res 2001; 29:1724-32. [PMID: 11292845 PMCID: PMC31306 DOI: 10.1093/nar/29.8.1724] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2000] [Revised: 02/20/2001] [Accepted: 02/20/2001] [Indexed: 02/02/2023] Open
Abstract
Rad51 is crucial not only in homologous recombination and recombinational repair but also in normal cellular growth. To address the role of Rad51 in normal cell growth we investigated morphological changes of cells after overexpression of wild-type and a dominant negative form of Rad51 in fission yeast. Rhp51, a Rad51 homolog in Schizosaccharomyces pombe, has a highly conserved ATP-binding motif. Rhp51 K155A, which has a single substitution in this motif, failed to rescue hypersensitivity of a rhp51 mutant to methyl methanesulfonate (MMS) and UV, whereas it binds normally to Rhp51 and Rad22, a Rad52 homolog. Two distinct cellular phenotypes were observed when Rhp51 or Rhp51 K155A was overexpressed in normal cells. Overexpression of Rhp51 caused lethality in the absence of DNA-damaging agents, with acquisition of a cell cycle mutant phenotype and accumulation of a 1C DNA population. On the other hand, overexpression of Rhp51 K155A led to a delay in G(2) with decondensed nuclei, which resembled the phenotype of rhp51. The latter also exhibited MMS and UV sensitivity, indicating that Rhp51 K155A has a dominant negative effect. These results suggest an association between DNA replication and Rad51 function.
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Affiliation(s)
- W J Kim
- School of Biological Sciences, Seoul National University, Kwanak-Ku, Shilim-dong, Seoul 151-742, Republic of Korea
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