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van Leeuwe TM, Arentshorst M, Punt PJ, Ram AF. Interrogation of the cell wall integrity pathway in Aspergillus niger identifies a putative negative regulator of transcription involved in chitin deposition. Gene 2021; 763S:100028. [PMID: 32550555 PMCID: PMC7285910 DOI: 10.1016/j.gene.2020.100028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/18/2019] [Accepted: 01/23/2020] [Indexed: 01/26/2023]
Abstract
Post-fermentation fungal biomass waste provides a viable source for chitin. Cell wall chitin of filamentous fungi, and in particular its de-N-acetylated derivative chitosan, has a wide range of commercial applications. Although the cell wall of filamentous fungi comprises 10–30% chitin, these yields are too low for cost-effective production. Therefore, we aimed to identify the genes involved in increased chitin deposition by screening a collection of UV-derived cell wall mutants in Aspergillus niger. This screen revealed a mutant strain (RD15.4#55) that showed a 30–40% increase in cell wall chitin compared to the wild type. In addition to the cell wall chitin phenotype, this strain also exhibited sensitivity to SDS and produces an unknown yellow pigment. Genome sequencing combined with classical genetic linkage analysis identified two mutated genes on chromosome VII that were linked with the mutant phenotype. Single gene knockouts and subsequent complementation analysis revealed that an 8 bp deletion in NRRL3_09595 is solely responsible for the associated phenotypes of RD15.4#55. The mutated gene, which was named cwcA (cell wall chitin A), encodes an orthologue of Saccharomyces cerevisiae Bypass of ESS1 (BYE1), a negative regulator of transcription elongation. We propose that this conserved fungal protein is involved in preventing cell wall integrity signaling under non-inducing conditions, where loss of function results in constitutive activation of the cell wall stress response pathway, and consequently leads to increased chitin content in the mutant cell wall. An Aspergillus niger UV-mutant with increased cell wall chitin was characterized. Causative mutation was identified in a single gene, named cell wall chitin A (cwcA). CwcA is orthologous to yeast Bye1p and exists as a single copy gene. Three relevant domains are found in both CwcA and Bye1p: PHD, TFIIS and SPOC. CwcA acts as negative regulator of CWI signaling.
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Affiliation(s)
- Tim M. van Leeuwe
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Mark Arentshorst
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Peter J. Punt
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Arthur F.J. Ram
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
- Corresponding author at: Leiden University, Institute of Biology, Department Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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2
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Namitz KEW, Zheng T, Canning AJ, Alicea-Velazquez NL, Castañeda CA, Cosgrove MS, Hanes SD. Structure analysis suggests Ess1 isomerizes the carboxy-terminal domain of RNA polymerase II via a bivalent anchoring mechanism. Commun Biol 2021; 4:398. [PMID: 33767358 PMCID: PMC7994582 DOI: 10.1038/s42003-021-01906-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 01/07/2023] Open
Abstract
Accurate gene transcription in eukaryotes depends on isomerization of serine-proline bonds within the carboxy-terminal domain (CTD) of RNA polymerase II. Isomerization is part of the "CTD code" that regulates recruitment of proteins required for transcription and co-transcriptional RNA processing. Saccharomyces cerevisiae Ess1 and its human ortholog, Pin1, are prolyl isomerases that engage the long heptad repeat (YSPTSPS)26 of the CTD by an unknown mechanism. Here, we used an integrative structural approach to decipher Ess1 interactions with the CTD. Ess1 has a rigid linker between its WW and catalytic domains that enforces a distance constraint for bivalent interaction with the ends of long CTD substrates (≥4-5 heptad repeats). Our binding results suggest that the Ess1 WW domain anchors the proximal end of the CTD substrate during isomerization, and that linker divergence may underlie evolution of substrate specificity.
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Affiliation(s)
- Kevin E. W. Namitz
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.29857.310000 0001 2097 4281Present Address: Department of Chemistry, Pennsylvania State University, University Park, PA USA
| | - Tongyin Zheng
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Ashley J. Canning
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Nilda L. Alicea-Velazquez
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.247980.00000 0001 2184 3689Present Address: Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT USA
| | - Carlos A. Castañeda
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Michael S. Cosgrove
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Steven D. Hanes
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
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3
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H3K4 Methylation Dependent and Independent Chromatin Regulation by JHD2 and SET1 in Budding Yeast. G3-GENES GENOMES GENETICS 2018; 8:1829-1839. [PMID: 29599176 PMCID: PMC5940172 DOI: 10.1534/g3.118.200151] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Set1 and Jhd2 regulate the methylation state of histone H3 lysine-4 (H3K4me) through their opposing methyltransferase and demethylase activities in the budding yeast Saccharomyces cerevisiae. H3K4me associates with actively transcribed genes and, like both SET1 and JHD2 themselves, is known to regulate gene expression diversely. It remains unclear, however, if Set1 and Jhd2 act solely through H3K4me. Relevantly, Set1 methylates lysine residues in the kinetochore protein Dam1 while genetic studies of the S. pombe SET1 ortholog suggest the existence of non-H3K4 Set1 targets relevant to gene regulation. We interrogated genetic interactions of JHD2 and SET1 with essential genes involved in varied aspects of the transcription cycle. Our findings implicate JHD2 in genetic inhibition of the histone chaperone complexes Spt16-Pob3 (FACT) and Spt6-Spn1. This targeted screen also revealed that JHD2 inhibits the Nrd1-Nab3-Sen1 (NNS) transcription termination complex. We find that while Jhd2’s impact on these transcription regulatory complexes likely acts via H3K4me, Set1 governs the roles of FACT and NNS through opposing H3K4-dependent and -independent functions. We also identify diametrically opposing consequences for mutation of H3K4 to alanine or arginine, illuminating that caution must be taken in interpreting histone mutation studies. Unlike FACT and NNS, detailed genetic studies suggest an H3K4me-centric mode of Spt6-Spn1 regulation by JHD2 and SET1. Chromatin immunoprecipitation and transcript quantification experiments show that Jhd2 opposes the positioning of a Spt6-deposited nucleosome near the transcription start site of SER3, a Spt6-Spn1 regulated gene, leading to hyper-induction of SER3. In addition to confirming and extending an emerging role for Jhd2 in the control of nucleosome occupancy near transcription start sites, our findings suggest some of the chromatin regulatory functions of Set1 are independent of H3K4 methylation.
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4
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Harlen KM, Churchman LS. Subgenic Pol II interactomes identify region-specific transcription elongation regulators. Mol Syst Biol 2017; 13:900. [PMID: 28043953 PMCID: PMC5293154 DOI: 10.15252/msb.20167279] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Transcription, RNA processing, and chromatin‐related factors all interact with RNA polymerase II (Pol II) to ensure proper timing and coordination of transcription and co‐transcriptional processes. Many transcription elongation regulators must function simultaneously to coordinate these processes, yet few strategies exist to explore the complement of factors regulating specific stages of transcription. To this end, we developed a strategy to purify Pol II elongation complexes from subgenic regions of a single gene, namely the 5′ and 3′ regions, using sequences in the nascent RNA. Applying this strategy to Saccharomyces cerevisiae, we determined the specific set of factors that interact with Pol II at precise stages during transcription. We identify many known region‐specific factors as well as determine unappreciated associations of regulatory factors during early and late stages of transcription. These data reveal a role for the transcription termination factor, Rai1, in regulating the early stages of transcription genome‐wide and support the role of Bye1 as a negative regulator of early elongation. We also demonstrate a role for the ubiquitin ligase, Bre1, in regulating Pol II dynamics during the latter stages of transcription. These data and our approach to analyze subgenic transcription elongation complexes will shed new light on the myriad factors that regulate the different stages of transcription and coordinate co‐transcriptional processes.
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Affiliation(s)
- Kevin M Harlen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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5
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Functional characterisation of parvulin-type peptidyl prolyl cis-trans isomerase, PinA in Dictyostelium discoideum. Biochem Biophys Res Commun 2017; 482:208-214. [DOI: 10.1016/j.bbrc.2016.11.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 11/08/2016] [Indexed: 11/22/2022]
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6
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Ahn JH, Rechsteiner A, Strome S, Kelly WG. A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans. PLoS Genet 2016; 12:e1006227. [PMID: 27541139 PMCID: PMC4991786 DOI: 10.1371/journal.pgen.1006227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/08/2016] [Indexed: 01/22/2023] Open
Abstract
The elongation phase of transcription by RNA Polymerase II (Pol II) involves numerous events that are tightly coordinated, including RNA processing, histone modification, and chromatin remodeling. RNA splicing factors are associated with elongating Pol II, and the interdependent coupling of splicing and elongation has been documented in several systems. Here we identify a conserved, multi-domain cyclophilin family member, SIG-7, as an essential factor for both normal transcription elongation and co-transcriptional splicing. In embryos depleted for SIG-7, RNA levels for over a thousand zygotically expressed genes are substantially reduced, Pol II becomes significantly reduced at the 3' end of genes, marks of transcription elongation are reduced, and unspliced mRNAs accumulate. Our findings suggest that SIG-7 plays a central role in both Pol II elongation and co-transcriptional splicing and may provide an important link for their coordination and regulation.
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Affiliation(s)
- Jeong H. Ahn
- Biology Department, Emory University, Atlanta, Georgia, United States of America
- Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, United States of America
| | - Andreas Rechsteiner
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - William G. Kelly
- Biology Department, Emory University, Atlanta, Georgia, United States of America
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7
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Allepuz-Fuster P, Martínez-Fernández V, Garrido-Godino AI, Alonso-Aguado S, Hanes SD, Navarro F, Calvo O. Rpb4/7 facilitates RNA polymerase II CTD dephosphorylation. Nucleic Acids Res 2014; 42:13674-88. [PMID: 25416796 PMCID: PMC4267648 DOI: 10.1093/nar/gku1227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/04/2014] [Accepted: 11/10/2014] [Indexed: 12/11/2022] Open
Abstract
The Rpb4 and Rpb7 subunits of eukaryotic RNA polymerase II (RNAPII) participate in a variety of processes from transcription, DNA repair, mRNA export and decay, to translation regulation and stress response. However, their mechanism(s) of action remains unclear. Here, we show that the Rpb4/7 heterodimer in Saccharomyces cerevisiae plays a key role in controlling phosphorylation of the carboxy terminal domain (CTD) of the Rpb1 subunit of RNAPII. Proper phosphorylation of the CTD is critical for the synthesis and processing of RNAPII transcripts. Deletion of RPB4, and mutations that disrupt the integrity of Rpb4/7 or its recruitment to the RNAPII complex, increased phosphorylation of Ser2, Ser5, Ser7 and Thr4 within the CTD. RPB4 interacted genetically with genes encoding CTD phosphatases (SSU72, FCP1), CTD kinases (KIN28, CTK1, SRB10) and a prolyl isomerase that targets the CTD (ESS1). We show that Rpb4 is important for Ssu72 and Fcp1 phosphatases association, recruitment and/or accessibility to the CTD, and that this correlates strongly with Ser5P and Ser2P levels, respectively. Our data also suggest that Fcp1 is the Thr4P phosphatase in yeast. Based on these and other results, we suggest a model in which Rpb4/7 helps recruit and potentially stimulate the activity of CTD-modifying enzymes, a role that is central to RNAPII function.
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Affiliation(s)
- Paula Allepuz-Fuster
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Verónica Martínez-Fernández
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Ana I. Garrido-Godino
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Sergio Alonso-Aguado
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Steven D. Hanes
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY 13210, USA
| | - Francisco Navarro
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
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8
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Hanes SD. Prolyl isomerases in gene transcription. Biochim Biophys Acta Gen Subj 2014; 1850:2017-34. [PMID: 25450176 DOI: 10.1016/j.bbagen.2014.10.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/20/2014] [Accepted: 10/23/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Peptidyl-prolyl isomerases (PPIases) are enzymes that assist in the folding of newly-synthesized proteins and regulate the stability, localization, and activity of mature proteins. They do so by catalyzing reversible (cis-trans) rotation about the peptide bond that precedes proline, inducing conformational changes in target proteins. SCOPE OF REVIEW This review will discuss how PPIases regulate gene transcription by controlling the activity of (1) DNA-binding transcription regulatory proteins, (2) RNA polymerase II, and (3) chromatin and histone modifying enzymes. MAJOR CONCLUSIONS Members of each family of PPIase (cyclophilins, FKBPs, and parvulins) regulate gene transcription at multiple levels. In all but a few cases, the exact mechanisms remain elusive. Structure studies, development of specific inhibitors, and new methodologies for studying cis/trans isomerization in vivo represent some of the challenges in this new frontier that merges two important fields. GENERAL SIGNIFICANCE Prolyl isomerases have been found to play key regulatory roles in all phases of the transcription process. Moreover, PPIases control upstream signaling pathways that regulate gene-specific transcription during development, hormone response and environmental stress. Although transcription is often rate-limiting in the production of enzymes and structural proteins, post-transcriptional modifications are also critical, and PPIases play key roles here as well (see other reviews in this issue). This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Steven D Hanes
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E Adams St., Syracuse, NY 13210 USA.
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9
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Abstract
The Ess1 prolyl isomerase from Saccharomyces cerevisiae and its human ortholog, Pin1, play critical roles in transcription by regulating RNA polymerase II. In human cells, Pin1 also regulates a variety of signaling proteins, and Pin1 misexpression is linked to several human diseases. To gain insight into Ess1/Pin1 function, we carried out a synthetic genetic array screen to identify novel targets of Ess1 in yeast. We identified potential targets of Ess1 in transcription, stress, and cell-cycle pathways. We focused on the cell-cycle regulators Swi6 and Whi5, both of which show highly regulated nucleocytoplasmic shuttling during the cell cycle. Surprisingly, Ess1 did not control their transcription but instead was necessary for their nuclear localization. Ess1 associated with Swi6 and Whi5 in vivo and bound directly to peptides corresponding to their nuclear localization sequences in vitro. Binding by Ess1 was significant only if the Swi6 and Whi5 peptides were phosphorylated at Ser-Pro motifs, the target sites of cyclin-dependent kinases. On the basis of these results, we propose a model in which Ess1 induces a conformational switch (cis-trans isomerization) at phospho-Ser-Pro sites within the nuclear targeting sequences of Swi6 and Whi5. This switch would promote nuclear entry and/or retention during late M and G1 phases and might work by stimulating dephosphorylation at these sites by the Cdc14 phosphatase. This is the first study to identify targets of Ess1 in yeast other than RNA polymerase II.
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10
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The Ess1 prolyl isomerase: traffic cop of the RNA polymerase II transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:316-33. [PMID: 24530645 DOI: 10.1016/j.bbagrm.2014.02.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 02/01/2014] [Accepted: 02/03/2014] [Indexed: 11/23/2022]
Abstract
Ess1 is a prolyl isomerase that regulates the structure and function of eukaryotic RNA polymerase II. Ess1 works by catalyzing the cis/trans conversion of pSer5-Pro6 bonds, and to a lesser extent pSer2-Pro3 bonds, within the carboxy-terminal domain (CTD) of Rpb1, the largest subunit of RNA pol II. Ess1 is conserved in organisms ranging from yeast to humans. In budding yeast, Ess1 is essential for growth and is required for efficient transcription initiation and termination, RNA processing, and suppression of cryptic transcription. In mammals, Ess1 (called Pin1) functions in a variety of pathways, including transcription, but it is not essential. Recent work has shown that Ess1 coordinates the binding and release of CTD-binding proteins that function as co-factors in the RNA pol II complex. In this way, Ess1 plays an integral role in writing (and reading) the so-called CTD code to promote production of mature RNA pol II transcripts including non-coding RNAs and mRNAs.
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11
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Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55. [PMID: 24040939 PMCID: PMC3988834 DOI: 10.1021/cr400158h] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore Maryland 21205, United States
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12
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Jeronimo C, Bataille AR, Robert F. The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code. Chem Rev 2013; 113:8491-522. [DOI: 10.1021/cr4001397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - Alain R. Bataille
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
- Département
de Médecine,
Faculté de Médecine, Université de Montréal, Montréal, Québec,
Canada H3T 1J4
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13
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Campos BM, Sforça ML, Ambrosio ALB, Domingues MN, Brasil de Souza TDAC, Barbosa JARG, Leme AFP, Perez CA, Whittaker SBM, Murakami MT, Zeri ACDM, Benedetti CE. A redox 2-Cys mechanism regulates the catalytic activity of divergent cyclophilins. PLANT PHYSIOLOGY 2013; 162:1311-23. [PMID: 23709667 PMCID: PMC3707534 DOI: 10.1104/pp.113.218339] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 05/23/2013] [Indexed: 05/20/2023]
Abstract
The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism.
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Affiliation(s)
- Bruna Medéia Campos
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Mauricio Luis Sforça
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Andre Luis Berteli Ambrosio
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Mariane Noronha Domingues
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | | | | | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Carlos Alberto Perez
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Sara Britt-Marie Whittaker
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Mario Tyago Murakami
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
| | - Ana Carolina de Matos Zeri
- Laboratório Nacional de Biociências (B.M.C., M.L.S., A.L.B.A., M.N.D., T.d.A.C.B.d.S., J.A.R.G.B., A.F.P.L., M.T.M., A.C.d.M.Z., C.E.B.) and Laboratório Nacional de Luz Síncrotron (C.A.P.), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP CP6192, Brazil; and
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom (S.B.-M.W.)
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14
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Samaranayake D, Atencio D, Morse R, Wade JT, Chaturvedi V, Hanes SD. Role of Ess1 in growth, morphogenetic switching, and RNA polymerase II transcription in Candida albicans. PLoS One 2013; 8:e59094. [PMID: 23516603 PMCID: PMC3597612 DOI: 10.1371/journal.pone.0059094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 02/12/2013] [Indexed: 11/18/2022] Open
Abstract
Candida albicans is a fungal pathogen that causes potentially fatal infections among immune-compromised individuals. The emergence of drug resistant C. albicans strains makes it important to identify new antifungal drug targets. Among potential targets are enzymes known as peptidyl-prolyl cis/trans isomerases (PPIases) that catalyze isomerization of peptide bonds preceding proline. We are investigating a PPIase called Ess1, which is conserved in all major human pathogenic fungi. Previously, we reported that C. albicans Ess1 is essential for growth and morphogenetic switching. In the present study, we re-evaluated these findings using more rigorous genetic analyses, including the use of additional CaESS1 mutant alleles, distinct marker genes, and the engineering of suitably-matched isogenic control strains. The results confirm that CaEss1 is essential for growth in C. albicans, but show that reduction of CaESS1 gene dosage by half (δ/+) does not interfere with morphogenetic switching. However, further reduction of CaEss1 levels using a conditional allele does reduce morphogenetic switching. We also examine the role of the linker α-helix that distinguishes C. albicans Ess1 from the human Pin1 enzyme, and present results of a genome-wide transcriptome analysis. The latter analysis indicates that CaEss1 has a conserved role in regulation of RNA polymerase II function, and is required for efficient termination of small nucleolar RNAs and repression of cryptic transcription in C. albicans.
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Affiliation(s)
- Dhanushki Samaranayake
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
| | - David Atencio
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York, United States of America
| | - Randall Morse
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
| | - Joseph T. Wade
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Division of Genetics, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
| | - Vishnu Chaturvedi
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Mycology Laboratory, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
| | - Steven D. Hanes
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York, United States of America
- Division of Infectious Disease, Wadsworth Center, NY State Department of Health, Albany, New York, United States of America
- Department of Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, Syracuse, New York, United States of America
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15
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Bannikova O, Zywicki M, Marquez Y, Skrahina T, Kalyna M, Barta A. Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity. Nucleic Acids Res 2012; 41:1783-96. [PMID: 23248006 PMCID: PMC3561992 DOI: 10.1093/nar/gks1252] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AtCyp59 is a multidomain cyclophilin containing a peptidyl-prolyl cis/trans isomerase (PPIase) domain and an evolutionarily highly conserved RRM domain. Deregulation of this class of cyclophilins has been shown to affect transcription and to influence phosphorylation of the C-terminal repeat domain of the largest subunit of the RNA polymerase II. We used a genomic SELEX method for identifying RNA targets of AtCyp59. Analysis of the selected RNAs revealed an RNA-binding motif (G[U/C]N[G/A]CC[A/G]) and we show that it is evolutionarily conserved. Binding to this motif was verified by gel shift assays in vitro and by RNA immunopreciptation assays of AtCyp59 in vivo. Most importantly, we show that binding also occurs on unprocessed transcripts in vivo and that binding of specific RNAs inhibits the PPIase activity of AtCyp59 in vitro. Surprisingly, genome-wide analysis showed that the RNA motif is present in about 70% of the annotated transcripts preferentially in exons. Taken together, the available data suggest that these cyclophilins might have an important function in transcription regulation.
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Affiliation(s)
- Olga Bannikova
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria
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