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Manzoor Y, Aouida M, Ramadoss R, Moovarkumudalvan B, Ahmed N, Sulaiman AA, Mohanty A, Ali R, Mifsud B, Ramotar D. Loss of the yeast transporter Agp2 upregulates the pleiotropic drug-resistant pump Pdr5 and confers resistance to the protein synthesis inhibitor cycloheximide. PLoS One 2024; 19:e0303747. [PMID: 38776347 PMCID: PMC11111045 DOI: 10.1371/journal.pone.0303747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/30/2024] [Indexed: 05/24/2024] Open
Abstract
The transmembrane protein Agp2, initially shown as a transporter of L-carnitine, mediates the high-affinity transport of polyamines and the anticancer drug bleomycin-A5. Cells lacking Agp2 are hyper-resistant to polyamine and bleomycin-A5. In these earlier studies, we showed that the protein synthesis inhibitor cycloheximide blocked the uptake of bleomycin-A5 into the cells suggesting that the drug uptake system may require de novo synthesis. However, our recent findings demonstrated that cycloheximide, instead, induced rapid degradation of Agp2, and in the absence of Agp2 cells are resistant to cycloheximide. These observations raised the possibility that the degradation of Agp2 may allow the cell to alter its drug resistance network to combat the toxic effects of cycloheximide. In this study, we show that membrane extracts from agp2Δ mutants accentuated several proteins that were differentially expressed in comparison to the parent. Mass spectrometry analysis of the membrane extracts uncovered the pleiotropic drug efflux pump, Pdr5, involved in the efflux of cycloheximide, as a key protein upregulated in the agp2Δ mutant. Moreover, a global gene expression analysis revealed that 322 genes were differentially affected in the agp2Δ mutant versus the parent, including the prominent PDR5 gene and genes required for mitochondrial function. We further show that Agp2 is associated with the upstream region of the PDR5 gene, leading to the hypothesis that cycloheximide resistance displayed by the agp2Δ mutant is due to the derepression of the PDR5 gene.
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Affiliation(s)
- Yusra Manzoor
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Ramya Ramadoss
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, India
| | - Balasubramanian Moovarkumudalvan
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, India
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Nisar Ahmed
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Abdallah Alhaj Sulaiman
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Ashima Mohanty
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Reem Ali
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Borbala Mifsud
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Dindial Ramotar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
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2
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Arimbasseri AG, Shukla A, Pradhan AK, Bhargava P. Increased histone acetylation is the signature of repressed state on the genes transcribed by RNA polymerase III. Gene 2024; 893:147958. [PMID: 37923095 DOI: 10.1016/j.gene.2023.147958] [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: 08/10/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Several covalent modifications are found associated with the transcriptionally active chromatin regions constituted by the genes transcribed by RNA polymerase (pol) II. Pol III-transcribed genes code for the small, stable RNA species, which participate in many cellular processes, essential for survival. Pol III transcription is repressed under most of the stress conditions by its negative regulator Maf1. We found that most of the histone acetylations increase with starvation-induced repression on several genes transcribed by the yeast pol III. On one of these genes, SNR6 (coding for the U6snRNA), a strongly positioned nucleosome in the gene upstream region plays regulatory role under repression. On this nucleosome, the changes in H3K9 and H3K14 acetylations show different dynamics. During repression, acetylation levels on H3K9 show steady increase whereas H3K14 acetylation increases with a peak at 40 min after which levels reduce. Both the levels settle by 2 hr to a level higher than the active state, which revert to normal levels with nutrient repletion. The increase in H3 acetylations is seen in the mutants reported to show reduced SNR6 transcription but not in the maf1Δ cells. This increase on a regulatory nucleosome may be part of the signaling mechanisms, which prepare cells for the stress-related quick repression as well as reactivation. The contrasting association of the histone acetylations with pol II and pol III transcription may be an important consideration to make in research studies focused on drug developments targeting histone modifications.
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Affiliation(s)
| | - Ashutosh Shukla
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ashis Kumar Pradhan
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Purnima Bhargava
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India.
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3
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Delorme-Axford E, Wen X, Klionsky DJ. The yeast transcription factor Stb5 acts as a negative regulator of autophagy by modulating cellular metabolism. Autophagy 2023; 19:2719-2732. [PMID: 37345792 PMCID: PMC10472870 DOI: 10.1080/15548627.2023.2228533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 06/02/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
Macroautophagy/autophagy is a highly conserved pathway of cellular degradation and recycling that maintains cell health during homeostatic conditions and facilitates survival during stress. Aberrant cellular autophagy contributes to the pathogenesis of human diseases such as cancer, neurodegeneration, and cardiovascular, metabolic and lysosomal storage disorders. Despite decades of research, there remain unanswered questions as to how autophagy modulates cellular metabolism, and, conversely, how cellular metabolism affects autophagy activity. Here, we have identified the yeast metabolic transcription factor Stb5 as a negative regulator of autophagy. Chromosomal deletion of STB5 in the yeast Saccharomyces cerevisiae enhances autophagy. Loss of Stb5 results in the upregulation of select autophagy-related (ATG) transcripts under nutrient-replete conditions; however, the Stb5-mediated impact on autophagy occurs primarily through its effect on genes involved in NADPH production and the pentose phosphate pathway. This work provides insight into the intersection of Stb5 as a transcription factor that regulates both cellular metabolic responses and autophagy activity.Abbreviations: bp, base pairs; ChIP, chromatin immunoprecipitation; G6PD, glucose-6-phosphate dehydrogenase; GFP, green fluorescent protein; IDR, intrinsically disordered region; NAD, nicotinamide adenine dinucleotide; NADP+, nicotinamide adenine dinucleotide phosphate; NADPH, nicotinamide adenine dinucleotide phosphate (reduced); ORF, open reading frame; PA, protein A; PCR, polymerase chain reaction; PE, phosphatidylethanolamine; PPP, pentose phosphate pathway; prApe1, precursor aminopeptidase I; ROS, reactive oxygen species; RT-qPCR, real-time quantitative PCR; SD, standard deviation; TF, transcription factor; TOR, target of rapamycin; WT, wild-type.
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Affiliation(s)
| | - Xin Wen
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J. Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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4
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Bauer SL, Grochalski TNT, Smialowska A, Åström SU. Sir2 and Reb1 antagonistically regulate nucleosome occupancy in subtelomeric X-elements and repress TERRAs by distinct mechanisms. PLoS Genet 2022; 18:e1010419. [PMID: 36137093 PMCID: PMC9531808 DOI: 10.1371/journal.pgen.1010419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/04/2022] [Accepted: 09/08/2022] [Indexed: 11/19/2022] Open
Abstract
Telomere chromatin structure is pivotal for maintaining genome stability by regulating the binding of telomere-associated proteins and inhibiting the DNA damage response. In Saccharomyces cerevisiae, silent information regulator (Sir) proteins bind to terminal repeats and to subtelomeric X-elements, resulting in transcriptional silencing. Herein, we show that sir2 mutant strains display a specific loss of a nucleosome residing in the X-elements and that this deficiency is remarkably consistent between different telomeres. The X-elements contain several binding sites for the transcription factor Reb1 and we found that Sir2 and Reb1 compete for stabilizing/destabilizing this nucleosome, i.e. inactivation of Reb1 in a sir2 background reinstated the lost nucleosome. The telomeric-repeat-containing RNAs (TERRAs) originate from subtelomeric regions and extend into the terminal repeats. Both Sir2 and Reb1 repress TERRAs and in a sir2 reb1 double mutant, TERRA levels increased synergistically, showing that Sir2 and Reb1 act in different pathways for repressing TERRAs. We present evidence that Reb1 restricts TERRAs by terminating transcription. Mapping the 5′-ends of TERRAs from several telomeres revealed that the Sir2-stabilized nucleosome is the first nucleosome downstream from the transcriptional start site for TERRAs. Finally, moving an X-element to a euchromatic locus changed nucleosome occupancy and positioning, demonstrating that X-element nucleosome structure is dependent on the local telomere environment. Telomeres are specialized structures at the end of linear chromosomes that protect the genetic material from degradation and mistaken recognition as sites of damage. Telomere dysfunction has been linked to several diseases and senescence. The telomeres contain repetitive DNA sequences bound by specialized proteins. Here, we describe two such proteins, Sir2 and Reb1, which regulate the formation of nucleosomes at a repetitive sequence known as the X-element. Sir2 has very important roles in regulating the accessibility of telomeres to the cellular machinery that reads and transcribes the genetic material. Reb1 had not been previously implicated in telomere biology, but is rather known as a general regulator of transcription. We explored the effects of removing either or both of these factors on telomeric features and their relationship in regulating the structure and accessibility of the telomeres in budding yeast. We show that Sir2 and Reb1 have opposing roles in stabilizing and de-stabilizing a nucleosome at the telomeres, but that both inhibit the accumulation of a non-coding RNA molecule transcribed from the telomeres.
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Affiliation(s)
- Stefanie L. Bauer
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Thomas N. T. Grochalski
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Agata Smialowska
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Stefan U. Åström
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- * E-mail:
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Moon IY, Kim JW. Methylation profile of hepatitis B virus is not influenced by interferon α in human liver cancer cells. Mol Med Rep 2021; 24:715. [PMID: 34396432 PMCID: PMC8383030 DOI: 10.3892/mmr.2021.12354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 07/12/2021] [Indexed: 12/17/2022] Open
Abstract
Interferon (IFN) α is used for the treatment of chronic hepatitis B virus (HBV) infection, but the molecular mechanisms underlying its antiviral effect have not been fully elucidated. Epigenetic modifications regulate the transcriptional activity of covalently closed circular DNA (cccDNA) in cells with chronic HBV infection. IFN‑α has been shown to modify cccDNA‑bound histones, but it is not known whether the anti‑HBV effect of IFN‑α involves methylation of cccDNA. The present study aimed to determine whether IFN‑α induced methylation of HBV cccDNA in a cell‑based model in which HepG2 cells were directly infected with wild‑type HBV virions. Methylation status of HBV cccDNA was assessed using global DNA methylation ELISA assay, methylation‑specific PCR and bisulfite sequencing. IFN‑α suppressed HBV DNA and RNA transcripts, but methylation profiles were similar between the control and IFN‑α treated groups. Chromatin immunoprecipitation results revealed binding of DNA methyltransferases (DNMT) 3A and DNMT3B to HBV cccDNA and treatment with IFN‑α suppressed the recruitment of DNMT3B to cccDNA. Taken together, these results suggest that IFN‑α does not induce methylation of HBV cccDNA. Therefore, it was concluded that methylation is unlikely to contribute to the anti‑HBV effect of IFN‑α in HepG2 cells, and that alternative mechanisms need to be sought to enhance cccDNA methylation as a novel therapy against HBV.
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Affiliation(s)
- In Young Moon
- Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620, Republic of Korea
| | - Jin-Wook Kim
- Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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6
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FBXO32 links ubiquitination to epigenetic reprograming of melanoma cells. Cell Death Differ 2021; 28:1837-1848. [PMID: 33462405 PMCID: PMC8184796 DOI: 10.1038/s41418-020-00710-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022] Open
Abstract
Ubiquitination by serving as a major degradation signal of proteins, but also by controlling protein functioning and localization, plays critical roles in most key cellular processes. Here, we show that MITF, the master transcription factor in melanocytes, controls ubiquitination in melanoma cells. We identified FBXO32, a component of the SCF E3 ligase complex as a new MITF target gene. FBXO32 favors melanoma cell migration, proliferation, and tumor development in vivo. Transcriptomic analysis shows that FBXO32 knockdown induces a global change in melanoma gene expression profile. These include the inhibition of CDK6 in agreement with an inhibition of cell proliferation and invasion upon FBXO32 silencing. Furthermore, proteomic analysis identifies SMARC4, a component of the chromatin remodeling complexes BAF/PBAF, as a FBXO32 partner. FBXO32 and SMARCA4 co-localize at loci regulated by FBXO32, such as CDK6 suggesting that FBXO32 controls transcription through the regulation of chromatin remodeling complex activity. FBXO32 and SMARCA4 are the components of a molecular cascade, linking MITF to epigenetics, in melanoma cells.
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7
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Grünberger F, Reichelt R, Waege I, Ned V, Bronner K, Kaljanac M, Weber N, El Ahmad Z, Knauss L, Madej MG, Ziegler C, Grohmann D, Hausner W. CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis in Pyrococcus furiosus. Front Microbiol 2021; 11:613532. [PMID: 33505379 PMCID: PMC7830388 DOI: 10.3389/fmicb.2020.613532] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/09/2020] [Indexed: 11/24/2022] Open
Abstract
Although copper is in many cases an essential micronutrient for cellular life, higher concentrations are toxic. Therefore, all living cells have developed strategies to maintain copper homeostasis. In this manuscript, we have analyzed the transcriptome-wide response of Pyrococcus furiosus to increased copper concentrations and described the essential role of the putative copper-sensing metalloregulator CopR in the detoxification process. To this end, we employed biochemical and biophysical methods to characterize the role of CopR. Additionally, a copR knockout strain revealed an amplified sensitivity in comparison to the parental strain towards increased copper levels, which designates an essential role of CopR for copper homeostasis. To learn more about the CopR-regulated gene network, we performed differential gene expression and ChIP-seq analysis under normal and 20 μM copper-shock conditions. By integrating the transcriptome and genome-wide binding data, we found that CopR binds to the upstream regions of many copper-induced genes. Negative-stain transmission electron microscopy and 2D class averaging revealed an octameric assembly formed from a tetramer of dimers for CopR, similar to published crystal structures from the Lrp family. In conclusion, we propose a model for CopR-regulated transcription and highlight the regulatory network that enables Pyrococcus to respond to increased copper concentrations.
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Affiliation(s)
- Felix Grünberger
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Ingrid Waege
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Verena Ned
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Korbinian Bronner
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Marcell Kaljanac
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Nina Weber
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Zubeir El Ahmad
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Lena Knauss
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - M. Gregor Madej
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Christine Ziegler
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Winfried Hausner
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
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8
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Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [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: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
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9
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Yang X, Zhang W, Wen X, Bulinski PJ, Chomchai DA, Arines FM, Liu YY, Sprenger S, Teis D, Klionsky DJ, Li M. TORC1 regulates vacuole membrane composition through ubiquitin- and ESCRT-dependent microautophagy. J Cell Biol 2020; 219:133713. [PMID: 32045480 PMCID: PMC7055007 DOI: 10.1083/jcb.201902127] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 11/22/2019] [Accepted: 01/07/2020] [Indexed: 01/12/2023] Open
Abstract
Cellular adaptation in response to nutrient limitation requires the induction of autophagy and lysosome biogenesis for the efficient recycling of macromolecules. Here, we discovered that starvation and TORC1 inactivation not only lead to the up-regulation of autophagy and vacuole proteins involved in recycling but also result in the down-regulation of many vacuole membrane proteins to supply amino acids as part of a vacuole remodeling process. Down-regulation of vacuole membrane proteins is initiated by ubiquitination, which is accomplished by the coordination of multiple E3 ubiquitin ligases, including Rsp5, the Dsc complex, and a newly characterized E3 ligase, Pib1. The Dsc complex is negatively regulated by TORC1 through the Rim15-Ume6 signaling cascade. After ubiquitination, vacuole membrane proteins are sorted into the lumen for degradation by ESCRT-dependent microautophagy. Thus, our study uncovered a complex relationship between TORC1 inactivation and vacuole biogenesis.
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Affiliation(s)
- Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Weichao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Xin Wen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI.,Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Patrick J Bulinski
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Dominic A Chomchai
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Yun-Yu Liu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Simon Sprenger
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - David Teis
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniel J Klionsky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI.,Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
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Puts G, Jarrett S, Leonard M, Matsangos N, Snyder D, Wang Y, Vincent R, Portney B, Abbotts R, McLaughlin L, Zalzman M, Rassool F, Kaetzel D. Metastasis Suppressor NME1 Modulates Choice of Double-Strand Break Repair Pathways in Melanoma Cells by Enhancing Alternative NHEJ while Inhibiting NHEJ and HR. Int J Mol Sci 2020; 21:ijms21165896. [PMID: 32824412 PMCID: PMC7460576 DOI: 10.3390/ijms21165896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 01/15/2023] Open
Abstract
Reduced NME1 expression in melanoma cell lines, mouse models of melanoma, and melanoma specimens in human patients is associated with increased metastatic activity. Herein, we investigate the role of NME1 in repair of double-stranded breaks (DSBs) and choice of double-strand break repair (DSBR) pathways in melanoma cells. Using chromatin immunoprecipitation, NME1 was shown to be recruited rapidly and directly to DSBs generated by the homing endonuclease I-PpoI. NME1 was recruited to DSBs within 30 min, in concert with recruitment of ataxia-telangiectasia mutated (ATM) protein, an early step in DSBR complex formation, as well as loss of histone 2B. NME1 was detected up to 5 kb from the break site after DSB induction, suggesting a role in extending chromatin reorganization away from the repair site. shRNA-mediated silencing of NME1 expression led to increases in the homologous recombination (HR) and non-homologous end-joining (NHEJ) pathways of double-strand break repair (DSBR), and reduction in the low fidelity, alternative-NHEJ (A-NHEJ) pathway. These findings suggest low expression of NME1 drives DSBR towards higher fidelity pathways, conferring enhanced genomic stability necessary for rapid and error-free proliferation in invasive and metastatic cells. The novel mechanism highlighted in the current study appears likely to impact metastatic potential and therapy-resistance in advanced melanoma and other cancers.
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Affiliation(s)
- Gemma Puts
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Stuart Jarrett
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA;
| | - Mary Leonard
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Nicolette Matsangos
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Devin Snyder
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Ying Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Richard Vincent
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Benjamin Portney
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Rachel Abbotts
- Department of Radiation Oncology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (R.A.); (L.M.); (F.R.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
| | - Lena McLaughlin
- Department of Radiation Oncology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (R.A.); (L.M.); (F.R.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
| | - Michal Zalzman
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
- Department of Otorhinolaryngology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Feyruz Rassool
- Department of Radiation Oncology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (R.A.); (L.M.); (F.R.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
| | - David Kaetzel
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
- Correspondence: ; Tel.: +1-410-706-5080; Fax: +1-410-706-8297
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11
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Muhammad II, Kong SL, Akmar Abdullah SN, Munusamy U. RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism. Int J Mol Sci 2019; 21:E167. [PMID: 31881735 PMCID: PMC6981605 DOI: 10.3390/ijms21010167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.
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Affiliation(s)
- Isiaka Ibrahim Muhammad
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Sze Ling Kong
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Siti Nor Akmar Abdullah
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Selangor 43400, Malaysia
| | - Umaiyal Munusamy
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
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12
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House NC, Polleys EJ, Quasem I, De la Rosa Mejia M, Joyce CE, Takacsi-Nagy O, Krebs JE, Fuchs SM, Freudenreich CH. Distinct roles for S. cerevisiae H2A copies in recombination and repeat stability, with a role for H2A.1 threonine 126. eLife 2019; 8:53362. [PMID: 31804179 PMCID: PMC6927750 DOI: 10.7554/elife.53362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/26/2019] [Indexed: 01/14/2023] Open
Abstract
CAG/CTG trinuncleotide repeats are fragile sequences that when expanded form DNA secondary structures and cause human disease. We evaluated CAG/CTG repeat stability and repair outcomes in histone H2 mutants in S. cerevisiae. Although the two copies of H2A are nearly identical in amino acid sequence, CAG repeat stability depends on H2A copy 1 (H2A.1) but not copy 2 (H2A.2). H2A.1 promotes high-fidelity homologous recombination, sister chromatid recombination (SCR), and break-induced replication whereas H2A.2 does not share these functions. Both decreased SCR and the increase in CAG expansions were due to the unique Thr126 residue in H2A.1 and hta1Δ or hta1-T126A mutants were epistatic to deletion of the Polδ subunit Pol32, suggesting a role for H2A.1 in D-loop extension. We conclude that H2A.1 plays a greater repair-specific role compared to H2A.2 and may be a first step towards evolution of a repair-specific function for H2AX compared to H2A in mammalian cells.
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Affiliation(s)
- Nealia Cm House
- Department of Biology, Tufts University, Medford, United States
| | - Erica J Polleys
- Department of Biology, Tufts University, Medford, United States
| | | | | | - Cailin E Joyce
- Department of Biology, Tufts University, Medford, United States
| | | | - Jocelyn E Krebs
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, United States
| | - Stephen M Fuchs
- Department of Biology, Tufts University, Medford, United States
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, United States.,Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, United States
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13
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Trinh DA, Shirakawa R, Kimura T, Sakata N, Goto K, Horiuchi H. Inhibitor of Growth 4 (ING4) is a positive regulator of rRNA synthesis. Sci Rep 2019; 9:17235. [PMID: 31754246 PMCID: PMC6872537 DOI: 10.1038/s41598-019-53767-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 08/30/2019] [Indexed: 01/29/2023] Open
Abstract
Ribosome biogenesis is essential for maintaining basic cellular activities although its mechanism is not fully understood. Inhibitor of growth 4 (ING4) is a member of ING family while its cellular functions remain controversial. Here, we identified several nucleolar proteins as novel ING4 interacting proteins. ING4 localized in the nucleus with strong accumulation in the nucleolus through its plant homeodomain, which is known to interact with histone trimethylated H3K4, commonly present in the promoter of active genes. ING4 deficient cells exhibited slower proliferation and the alteration in nucleolar structure with reduced rRNA transcription, which was rescued by exogenous expression of GFP-ING4 to the similar levels of wild type cells. In the ING4 deficient cells, histone H3K9 acetylation and the key rRNA transcription factor UBF at the promoter of rDNA were reduced, both of which were also recovered by exogenous GFP-ING4 expression. Thus, ING4 could positively regulate rRNA transcription through modulation of histone modifications at the rDNA promoter.
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Affiliation(s)
- Duc-Anh Trinh
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan.,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Tomohiro Kimura
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Research Center for Molecular Genetics, Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, Yamagata, Yamagata, Japan
| | - Natsumi Sakata
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kota Goto
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hisanori Horiuchi
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan. .,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
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14
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Wen X, Gatica D, Yin Z, Hu Z, Dengjel J, Klionsky DJ. The transcription factor Spt4-Spt5 complex regulates the expression of ATG8 and ATG41. Autophagy 2019; 16:1172-1185. [PMID: 31462158 DOI: 10.1080/15548627.2019.1659573] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroautophagy/autophagy, a highly conserved dynamic process, is one of the major degradative pathways in cells. So far, over 40 autophagy-related (ATG) genes have been identified in Saccharomyces cerevisiae, most of which have homologs in more complex eukaryotes. Autophagy plays a crucial role in cell survival and maintenance, and its dysfunction is related to various diseases, indicating that the proper regulation of autophagy is important. Although the overall process of autophagy has been extensively studied, in particular with regard to the function of the Atg proteins, relatively little is known about the regulatory mechanisms that control autophagy activity. Spt5 is one of the transcriptional factors that is universally conserved across all domains. This protein can form a complex with Spt4, together playing a central role in transcription. In complex eukaryotic cells, the Spt4-Spt5 complex plays a dual role in gene regulation, acting both to delay transcription through promoter-proximal pausing, and to facilitate transcriptional elongation. In contrast, in S. cerevisiae, only the positive function of the Spt4-Spt5 complex has been identified. Here, we show for the first time that the Spt4-Spt5 transcription factor complex negatively regulates ATG genes in S. cerevisiae, inhibiting autophagy activity during active growth. Under autophagy-inducing conditions, the repression is released by Spt5 phosphorylation, allowing an upregulation of autophagy activity. ABBREVIATIONS AID: auxin-inducible degron; ATG: autophagy-related; ChIP: chromatin immunoprecipitation;Cvt: cytoplasm-to-vacuole targeting; DSIF: DRB sensitivity-inducible factor; NELF: negativeelongation factor; ORF: open reading frame; PA: protein A; PE: phosphatidylethanolamine;prApe1: precursor aminopeptidase I; RT-qPCR: real-time quantitative PCR; RNAP II: RNApolymerase II; TSS: transcription start site; WT: wild-type.
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Affiliation(s)
- Xin Wen
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Damián Gatica
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Zhangyuan Yin
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Zehan Hu
- Department of Biology, University of Fribourg , Fribourg, Switzerland
| | - Jörn Dengjel
- Department of Biology, University of Fribourg , Fribourg, Switzerland
| | - Daniel J Klionsky
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
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15
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Geisberg JV, Moqtaderi Z. Protein Binding to mRNA 3' Isoforms. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2019; 128:e101. [PMID: 31503412 PMCID: PMC6741434 DOI: 10.1002/cpmb.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Here we describe CLIP-READS, a technique that combines elements of crosslinking and immunoprecipitation (CLIP) and 3' region extraction and deep sequencing (READS), to provide a genome-wide map of mRNA 3' isoform binding by a given messenger ribonucleoprotein (mRNP). In CLIP-READS, cells are grown to logarithmic phase and are irradiated with UV light (254 nm) to form RNA-protein adducts. The protein-mRNA complexes are immunoprecipitated from cell extracts with an antibody specific to the protein of interest, after which the protein component is digested away with Pronase. Messenger RNAs are then subjected to 3' READS. An input sample processed by 3' READS in parallel allows for the relative quantification of isoform-specific binding by the mRNP of interest. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Joseph V Geisberg
- Harvard Medical School, Department of BCMP, 240 Longwood Avenue, Boston, MA 02115
| | - Zarmik Moqtaderi
- Harvard Medical School, Department of BCMP, 240 Longwood Avenue, Boston, MA 02115
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16
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Will WR, Whitham PJ, Reid PJ, Fang FC. Modulation of H-NS transcriptional silencing by magnesium. Nucleic Acids Res 2019; 46:5717-5725. [PMID: 29757411 PMCID: PMC6009595 DOI: 10.1093/nar/gky387] [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: 08/14/2017] [Accepted: 04/30/2018] [Indexed: 11/15/2022] Open
Abstract
The bacterial histone-like protein H-NS silences AT-rich DNA, binding DNA as 'stiffened' filaments or 'bridged' intrastrand loops. The switch between these modes has been suggested to depend on the concentration of divalent cations, in particular Mg2+, with elevated Mg2+ concentrations associated with a transition to bridging. Here we demonstrate that the observed binding mode is a function of the local concentration of H-NS and its cognate binding sites, as well as the affinity of the interactions between them. Mg2+ does not control a binary switch between these two modes but rather modulates the affinity of this interaction, inhibiting the DNA-binding and silencing activity of H-NS in a continuous linear fashion. The direct relationship between conditions that favor stiffening and transcriptional silencing activity suggests that although both modes can occur in the cell, stiffening is the predominant mode of binding at silenced genes.
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Affiliation(s)
- W Ryan Will
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Patrick J Whitham
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Philip J Reid
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ferric C Fang
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.,Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
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17
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Abstract
The programmed release of apoptogenic proteins from mitochondria is a core event of apoptosis, although ancestral roles of this phenomenon are not known. In mammals, one such apoptogenic protein is Endonuclease G (EndoG), a conserved mitochondrial nuclease that fragments the DNA of dying cells. In this work, we show that budding yeast executes meiotically programmed mitochondrial release of an EndoG homolog, Nuc1, during sporulation. In contrast to EndoG's ostensible pro-death function during apoptosis, Nuc1 mitochondrial release is pro-survival, attenuating the cytosolic L-A and Killer double-stranded RNA mycoviruses and protecting meiotic progeny from the catastrophic consequences of their derepression. The protective viral attenuation role of this pathway illuminates a primordial role for mitochondrial release of EndoG, and perhaps of apoptosis itself.
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18
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Moon IY, Choi JH, Chung JW, Jang ES, Jeong SH, Kim JW. MicroRNA‑20 induces methylation of hepatitis B virus covalently closed circular DNA in human hepatoma cells. Mol Med Rep 2019; 20:2285-2293. [PMID: 31257511 PMCID: PMC6691198 DOI: 10.3892/mmr.2019.10435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023] Open
Abstract
Methylation was suggested to suppress the transcriptional activity of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) in hepatocytes. This may be associated with its low replicative activity during the inactive stage of chronic HBV infection; however, the exact mechanisms of methylation in HBV infection remain unknown. We have previously shown that short hairpin RNAs induced the methylation of the HBV genome in hepatoma cell lines. We also reported that the microRNA (miR) 17–92 cluster negatively regulates HBV replication in human hepatoma cells. In addition, miR-20a, a member of the miR 17–92 cluster, has sequence homology with the short hairpin RNA that induces HBV methylation. In the present study, we investigated whether miR-20a can function as an endogenous effector of HBV DNA methylation. The results indicated that overexpression of miR-20a could suppress the replicative activity of HBV and increased the degree of methylation of HBV cccDNA in the HepAD38 hepatoma cell line. Argonaute (AGO)1 and AGO2, effectors of the RNA-induced silencing complex, were detected in the nucleus of HepAD38 cells; however, only AGO2 was bound to HBV cccDNA. In addition, intranuclear AGO2 was determined to be bound with miR-20a. In conclusion, miR-20a may be loaded onto AGO2, prior to its translocation into the nucleus, inducing the methylation of HBV DNA in human hepatoma cells, leading to the suppression of HBV replication.
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Affiliation(s)
- In Young Moon
- Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620, Republic of Korea
| | - Jae Hee Choi
- Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620, Republic of Korea
| | - Jung Wha Chung
- Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620, Republic of Korea
| | - Eun Sun Jang
- Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620, Republic of Korea
| | - Sook-Hyang Jeong
- Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620, Republic of Korea
| | - Jin-Wook Kim
- Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620, Republic of Korea
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19
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Höpfler M, Kern MJ, Straub T, Prytuliak R, Habermann BH, Pfander B, Jentsch S. Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance. EMBO J 2019; 38:embj.2018100368. [PMID: 31015336 PMCID: PMC6545562 DOI: 10.15252/embj.2018100368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 12/27/2022] Open
Abstract
Chromatin is a highly regulated environment, and protein association with chromatin is often controlled by post‐translational modifications and the corresponding enzymatic machinery. Specifically, SUMO‐targeted ubiquitin ligases (STUbLs) have emerged as key players in nuclear quality control, genome maintenance, and transcription. However, how STUbLs select specific substrates among myriads of SUMOylated proteins on chromatin remains unclear. Here, we reveal a remarkable co‐localization of the budding yeast STUbL Slx5/Slx8 and ubiquitin at seven genomic loci that we term “ubiquitin hotspots”. Ubiquitylation at these sites depends on Slx5/Slx8 and protein turnover on the Cdc48 segregase. We identify the transcription factor‐like Ymr111c/Euc1 to associate with these sites and to be a critical determinant of ubiquitylation. Euc1 specifically targets Slx5/Slx8 to ubiquitin hotspots via bipartite binding of Slx5 that involves the Slx5 SUMO‐interacting motifs and an additional, novel substrate recognition domain. Interestingly, the Euc1‐ubiquitin hotspot pathway acts redundantly with chromatin modifiers of the H2A.Z and Rpd3L pathways in specific stress responses. Thus, our data suggest that STUbL‐dependent ubiquitin hotspots shape chromatin during stress adaptation.
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Affiliation(s)
- Markus Höpfler
- Max Planck Institute of Biochemistry, Molecular Cell Biology, Martinsried, Germany
| | - Maximilian J Kern
- Max Planck Institute of Biochemistry, Molecular Cell Biology, Martinsried, Germany
| | - Tobias Straub
- Biomedizinisches Centrum, Core Facility Bioinformatics, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Roman Prytuliak
- Max Planck Institute of Biochemistry, Computational Biology Group, Martinsried, Germany
| | - Bianca H Habermann
- Max Planck Institute of Biochemistry, Computational Biology Group, Martinsried, Germany.,Aix-Marseille Univ, CNRS, IBDM UMR 7288, Marseille Cedex 9, France
| | - Boris Pfander
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
| | - Stefan Jentsch
- Max Planck Institute of Biochemistry, Molecular Cell Biology, Martinsried, Germany
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20
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Will WR, Brzovic P, Le Trong I, Stenkamp RE, Lawrenz MB, Karlinsey JE, Navarre WW, Main-Hester K, Miller VL, Libby SJ, Fang FC. The Evolution of SlyA/RovA Transcription Factors from Repressors to Countersilencers in Enterobacteriaceae. mBio 2019; 10:e00009-19. [PMID: 30837332 PMCID: PMC6401476 DOI: 10.1128/mbio.00009-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/29/2019] [Indexed: 02/02/2023] Open
Abstract
Gene duplication and subsequent evolutionary divergence have allowed conserved proteins to develop unique roles. The MarR family of transcription factors (TFs) has undergone extensive duplication and diversification in bacteria, where they act as environmentally responsive repressors of genes encoding efflux pumps that confer resistance to xenobiotics, including many antimicrobial agents. We have performed structural, functional, and genetic analyses of representative members of the SlyA/RovA lineage of MarR TFs, which retain some ancestral functions, including repression of their own expression and that of divergently transcribed multidrug efflux pumps, as well as allosteric inhibition by aromatic carboxylate compounds. However, SlyA and RovA have acquired the ability to countersilence horizontally acquired genes, which has greatly facilitated the evolution of Enterobacteriaceae by horizontal gene transfer. SlyA/RovA TFs in different species have independently evolved novel regulatory circuits to provide the enhanced levels of expression required for their new role. Moreover, in contrast to MarR, SlyA is not responsive to copper. These observations demonstrate the ability of TFs to acquire new functions as a result of evolutionary divergence of both cis-regulatory sequences and in trans interactions with modulatory ligands.IMPORTANCE Bacteria primarily evolve via horizontal gene transfer, acquiring new traits such as virulence and antibiotic resistance in single transfer events. However, newly acquired genes must be integrated into existing regulatory networks to allow appropriate expression in new hosts. This is accommodated in part by the opposing mechanisms of xenogeneic silencing and countersilencing. An understanding of these mechanisms is necessary to understand the relationship between gene regulation and bacterial evolution. Here we examine the functional evolution of an important lineage of countersilencers belonging to the ancient MarR family of classical transcriptional repressors. We show that although members of the SlyA lineage retain some ancestral features associated with the MarR family, their cis-regulatory sequences have evolved significantly to support their new function. Understanding the mechanistic requirements for countersilencing is critical to understanding the pathoadaptation of emerging pathogens and also has practical applications in synthetic biology.
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Affiliation(s)
- W Ryan Will
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Peter Brzovic
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Isolde Le Trong
- Department of Biological Structure, University of Washington, Seattle, Washington, USA
| | - Ronald E Stenkamp
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Department of Biological Structure, University of Washington, Seattle, Washington, USA
| | - Matthew B Lawrenz
- Department of Microbiology and Immunology and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Joyce E Karlinsey
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - William W Navarre
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Kara Main-Hester
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Virginia L Miller
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Stephen J Libby
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Ferric C Fang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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21
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Chiarella AM, Quimby AL, Mehrab-Mohseni M, Velasco B, Kasoji SK, Davis IJ, Dayton PA, Hathaway NA, Pattenden SG. Cavitation Enhancement Increases the Efficiency and Consistency of Chromatin Fragmentation from Fixed Cells for Downstream Quantitative Applications. Biochemistry 2018; 57:2756-2761. [PMID: 29658277 DOI: 10.1021/acs.biochem.8b00075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the most sensitive, time-consuming, and variable steps of chromatin immunoprecipitation (ChIP) is chromatin sonication. Traditionally, this process can take hours to properly sonicate enough chromatin for multiple ChIP assays. Further, the length of sheared DNA is often inconsistent. In order to faithfully measure chemical and structural changes at the chromatin level, sonication needs to be reliable. Thus, chromatin fragmentation by sonication represents a significant bottleneck to downstream quantitative analysis. To improve the consistency and efficiency of chromatin sonication, we developed and tested a cavitation enhancing reagent based on sonically active nanodroplets. Here, we show that nanodroplets increase sonication efficiency by 16-fold and provide more consistent levels of chromatin fragmentation. Using the previously characterized chromatin in vivo assay (CiA) platform, we generated two distinct chromatin states in order to test nanodroplet-assisted sonication sensitivity in measuring post-translational chromatin marks. By comparing euchromatin to chemically induced heterochromatin at the same CiA:Oct4 locus, we quantitatively measure the capability of our new sonication technique to resolve differences in chromatin structure. We confirm that nanodroplet-assisted sonication results are indistinguishable from those of samples processed with traditional sonication in downstream applications. While the processing time for each sample was reduced from 38.4 to 2.3 min, DNA fragment distribution sizes were significantly more consistent with a coefficient of variation 2.7 times lower for samples sonicated in the presence of nanodroplets. In conclusion, sonication utilizing the nanodroplet cavitation enhancement reagent drastically reduces the amount of processing time and provides consistently fragmented chromatin of high quality for downstream applications.
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Affiliation(s)
- Anna M Chiarella
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Curriculum in Genetics and Molecular Biology , The University of North Carolina , Chapel Hill , North Carolina 27514 , United States
| | - Austin L Quimby
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Marjan Mehrab-Mohseni
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Joint Department of Biomedical Engineering , The University of North Carolina and North Carolina State University , Chapel Hill , North Carolina 27599 , United States
| | - Brian Velasco
- Joint Department of Biomedical Engineering , The University of North Carolina and North Carolina State University , Chapel Hill , North Carolina 27599 , United States
| | - Sandeep K Kasoji
- Joint Department of Biomedical Engineering , The University of North Carolina and North Carolina State University , Chapel Hill , North Carolina 27599 , United States
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Departments of Genetics and Pediatrics , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Paul A Dayton
- Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Joint Department of Biomedical Engineering , The University of North Carolina and North Carolina State University , Chapel Hill , North Carolina 27599 , United States
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Curriculum in Genetics and Molecular Biology , The University of North Carolina , Chapel Hill , North Carolina 27514 , United States.,Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Samantha G Pattenden
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States
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22
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Newman SL, Will WR, Libby SJ, Fang FC. The curli regulator CsgD mediates stationary phase counter-silencing of csgBA in Salmonella Typhimurium. Mol Microbiol 2018; 108:101-114. [PMID: 29388265 DOI: 10.1111/mmi.13919] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 12/23/2022]
Abstract
Integration of horizontally acquired genes into transcriptional networks is essential for the regulated expression of virulence in bacterial pathogens. In Salmonella enterica, expression of such genes is repressed by the nucleoid-associated protein H-NS, which recognizes and binds to AT-rich DNA. H-NS-mediated silencing must be countered by other DNA-binding proteins to allow expression under appropriate conditions. Some genes that can be transcribed by RNA polymerase (RNAP) associated with the alternative sigma factor σS or the housekeeping sigma factor σ70 in vitro appear to be preferentially transcribed by σS in the presence of H-NS, suggesting that σS may act as a counter-silencer. To determine whether σS directly counters H-NS-mediated silencing and whether co-regulation by H-NS accounts for the σS selectivity of certain promoters, we examined the csgBA operon, which is required for curli fimbriae expression and is known to be regulated by both H-NS and σS . Using genetics and in vitro biochemical analyses, we found that σS is not directly required for csgBA transcription, but rather up-regulates csgBA via an indirect upstream mechanism. Instead, the biofilm master regulator CsgD directly counter-silences the csgBA promoter by altering the DNA-protein complex structure to disrupt H-NS-mediated silencing in addition to directing the binding of RNAP.
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Affiliation(s)
- S L Newman
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - W R Will
- Department of Microbiology, University of Washington, Seattle WA, USA
| | - S J Libby
- Department of Microbiology, University of Washington, Seattle WA, USA
| | - F C Fang
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.,Department of Microbiology, University of Washington, Seattle WA, USA
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23
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Abstract
Chromatin immunoprecipitation (ChIP) is a sensitive, accurate, and reliable technique widely used to analyze protein-DNA interactions at specific binding sites in vivo. It has been a particularly powerful technique for mapping of histone modification patterns both at individual loci and genome-wide. Here we provide a detailed protocol for ChIP of histone modifications associated with active transcription in fission yeast (Schizosaccharomyces pombe).
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Affiliation(s)
- Jean Mbogning
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
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24
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Zaidi H, Hoffman EA, Shetty SJ, Bekiranov S, Auble DT. Second-generation method for analysis of chromatin binding with formaldehyde-cross-linking kinetics. J Biol Chem 2017; 292:19338-19355. [PMID: 28972159 DOI: 10.1074/jbc.m117.796441] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/21/2017] [Indexed: 11/06/2022] Open
Abstract
Formaldehyde-cross-linking underpins many of the most commonly used experimental approaches in the chromatin field, especially in capturing site-specific protein-DNA interactions. Extending such assays to assess the stability and binding kinetics of protein-DNA interactions is more challenging, requiring absolute measurements with a relatively high degree of physical precision. We previously described an experimental framework called the cross-linking kinetics (CLK) assay, which uses time-dependent formaldehyde-cross-linking data to extract kinetic parameters of chromatin binding. Many aspects of formaldehyde behavior in cells are unknown or undocumented, however, and could potentially affect CLK data analyses. Here, we report biochemical results that better define the properties of formaldehyde-cross-linking in budding yeast cells. These results have the potential to inform interpretations of "standard" chromatin assays, including chromatin immunoprecipitation. Moreover, the chemical complexity we uncovered resulted in the development of an improved method for measuring binding kinetics with the CLK approach. Optimum conditions included an increased formaldehyde concentration and more robust glycine-quench conditions. Notably, we observed that formaldehyde-cross-linking rates can vary dramatically for different protein-DNA interactions in vivo Some interactions were cross-linked much faster than the in vivo macromolecular interactions, making them suitable for kinetic analysis. For other interactions, we found the cross-linking reaction occurred on the same time scale or slower than binding dynamics; for these interactions, it was sometimes possible to compute the in vivo equilibrium-binding constant but not binding on- and off-rates. This improved method yields more accurate in vivo binding kinetics estimates on the minute time scale.
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Affiliation(s)
- Hussain Zaidi
- From the School of Medicine Research Computing, University of Virginia and
| | - Elizabeth A Hoffman
- the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Savera J Shetty
- the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Stefan Bekiranov
- the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - David T Auble
- the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
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25
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Mulla WA, Seidel CW, Zhu J, Tsai HJ, Smith SE, Singh P, Bradford WD, McCroskey S, Nelliat AR, Conkright J, Peak A, Malanowski KE, Perera AG, Li R. Aneuploidy as a cause of impaired chromatin silencing and mating-type specification in budding yeast. eLife 2017; 6:27991. [PMID: 28841138 PMCID: PMC5779231 DOI: 10.7554/elife.27991] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/24/2017] [Indexed: 01/12/2023] Open
Abstract
Aneuploidy and epigenetic alterations have long been associated with carcinogenesis, but it was unknown whether aneuploidy could disrupt the epigenetic states required for cellular differentiation. In this study, we found that ~3% of random aneuploid karyotypes in yeast disrupt the stable inheritance of silenced chromatin during cell proliferation. Karyotype analysis revealed that this phenotype was significantly correlated with gains of chromosomes III and X. Chromosome X disomy alone was sufficient to disrupt chromatin silencing and yeast mating-type identity as indicated by a lack of growth response to pheromone. The silencing defect was not limited to cryptic mating type loci and was associated with broad changes in histone modifications and chromatin localization of Sir2 histone deacetylase. The chromatin-silencing defect of disome X can be partially recapitulated by an extra copy of several genes on chromosome X. These results suggest that aneuploidy can directly cause epigenetic instability and disrupt cellular differentiation.
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Affiliation(s)
- Wahid A Mulla
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Chris W Seidel
- Stowers Institute for Medical Research, Missouri, United States
| | - Jin Zhu
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Hung-Ji Tsai
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sarah E Smith
- Stowers Institute for Medical Research, Missouri, United States
| | - Pushpendra Singh
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States
| | | | - Scott McCroskey
- Stowers Institute for Medical Research, Missouri, United States
| | - Anjali R Nelliat
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
| | | | - Allison Peak
- Stowers Institute for Medical Research, Missouri, United States
| | | | - Anoja G Perera
- Stowers Institute for Medical Research, Missouri, United States
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, United States
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26
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Keck KM, Moquin SA, He A, Fernandez SG, Somberg JJ, Liu SM, Martinez DM, Miranda JL. Bromodomain and extraterminal inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps. J Biol Chem 2017; 292:13284-13295. [PMID: 28588024 PMCID: PMC5555189 DOI: 10.1074/jbc.m116.751644] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 05/15/2017] [Indexed: 12/17/2022] Open
Abstract
Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. Proteins in the bromodomain and extraterminal (BET) family regulate multiple stages of viral life cycles and provide promising intervention targets. Synthetic small molecules can bind to the bromodomains and disrupt function by preventing recognition of acetylated lysine substrates. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV lytic cycle. BET inhibitors prevent expression of the viral immediate-early protein BZLF1. JQ1 alters transcription of genes controlled by the host protein BACH1, and BACH1 knockdown reduces BZLF1 expression. BET proteins also localize to the lytic origin of replication (OriLyt) genetic elements, and BET inhibitors prevent viral late gene expression. There JQ1 reduces BRD4 recruitment during reactivation to preclude replication initiation. This represents a rarely observed dual mode of action for drugs.
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Affiliation(s)
- Kristin M Keck
- the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Stephanie A Moquin
- the Gladstone Institute of Virology and Immunology, San Francisco, California 94158.,From the Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF), California 94158 and
| | - Amanda He
- the Gladstone Institute of Virology and Immunology, San Francisco, California 94158.,From the Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF), California 94158 and
| | - Samantha G Fernandez
- the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Jessica J Somberg
- the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Stephanie M Liu
- the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Delsy M Martinez
- the Gladstone Institute of Virology and Immunology, San Francisco, California 94158.,From the Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF), California 94158 and
| | - Jj L Miranda
- the Gladstone Institute of Virology and Immunology, San Francisco, California 94158 .,From the Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF), California 94158 and
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27
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Sankella S, Garg A, Agarwal AK. Characterization of the Mouse and Human Monoacylglycerol O-Acyltransferase 1 (Mogat1) Promoter in Human Kidney Proximal Tubule and Rat Liver Cells. PLoS One 2016; 11:e0162504. [PMID: 27611931 PMCID: PMC5017789 DOI: 10.1371/journal.pone.0162504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/23/2016] [Indexed: 12/22/2022] Open
Abstract
Monoacylglycerol acyltransferase 1 (Mogat1) catalyzes the conversion of monoacylglycerols (MAG) to diacylglycerols (DAG), the precursor of several physiologically important lipids such as phosphatidylcholine, phosphatidylethanolamine and triacylglycerol (TAG). Expression of Mogat1 is tissue restricted and it is highly expressed in the kidney, stomach and adipose tissue but minimally in the normal adult liver. To understand the transcriptional regulation of Mogat1, we characterized the mouse and human Mogat1 promoters in human kidney proximal tubule-2 (HK-2) cells. In-silico analysis revealed several peroxisome proliferator response element (PPRE) binding sites in the promoters of both human and mouse Mogat1. These sites responded to all three peroxisome proliferator activated receptor (PPAR) isoforms such that their respective agonist or antagonist activated or inhibited the expression of Mogat1. PPRE site mutagenesis revealed that sites located at -592 and -2518 are very effective in decreasing luciferase reporter gene activity. Chromatin immunoprecipitation (ChIP) assay using PPARα antibody further confirmed the occupancy of these sites by PPARα. While these assays revealed the core promoter elements necessary for Mogat1 expression, there are additional elements required to regulate its tissue specific expression. Chromosome conformation capture (3C) assay revealed additional cis-elements located ~10–15 kb upstream which interact with the core promoter. These chromosomal regions are responsive to both PPARα agonist and antagonist.
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Affiliation(s)
- Shireesha Sankella
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine and Center for Human Nutrition, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390, United States of America
| | - Abhimanyu Garg
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine and Center for Human Nutrition, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390, United States of America
| | - Anil K. Agarwal
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine and Center for Human Nutrition, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390, United States of America
- * E-mail:
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28
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Kakiuchi T, Takahara T, Kasugai Y, Arita K, Yoshida N, Karube K, Suguro M, Matsuo K, Nakanishi H, Kiyono T, Nakamura S, Osada H, Sekido Y, Seto M, Tsuzuki S. Modeling mesothelioma utilizing human mesothelial cells reveals involvement of phospholipase-C beta 4 in YAP-active mesothelioma cell proliferation. Carcinogenesis 2016; 37:1098-1109. [PMID: 27559111 DOI: 10.1093/carcin/bgw084] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/13/2016] [Accepted: 08/06/2016] [Indexed: 12/17/2022] Open
Abstract
Mesotheliomas are frequently characterized by disruption of Hippo pathway due to deletion and/or mutation in genes, such as neurofibromin 2 ( NF2 ). Hippo disruption attenuates yes-associated protein (YAP) phosphorylation allowing YAP to translocate to the nucleus and regulate gene expression. The role of disrupted Hippo pathway in maintenance of established mesotheliomas has been extensively investigated using cell lines; however, its involvement in development of human mesothelioma has not been explored much. Here, we employed immortalized human mesothelial cells to disrupt Hippo pathway. YAP phosphorylation was reduced on NF2 knockdown and the cells exhibited altered growth in vitro , developing tumors when transplanted into nude mice. Similar results were obtained from enforced expression of wild-type or constitutively active (S127A) YAP, indicating the crucial role of activated YAP in the transformation of mesothelial cells. Gene expression analysis comparing control- and YAP-transduced immortalized human mesothelial cells revealed phospholipase-C beta 4 ( PLCB4 ) to be among the genes highly upregulated by YAP. PLCB4 was upregulated by YAP in immortalized human mesothelial cells and downregulated on YAP knockdown in Hippo-disrupted mesothelioma cell lines. PLCB4 knockdown attenuated the growth of YAP-transduced immortalized mesothelial cells and YAP-active, but not YAP-nonactive, mesothelioma cell lines. Our model system thus provides a versatile tool to investigate the mechanisms underlying mesothelioma development. We suggest that PLCB4 may be an attractive drug target for the treatment of mesothelioma.
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Affiliation(s)
- Tatsuo Kakiuchi
- Division of Molecular Medicine, Aichi Cancer Center Research Institute , Nagoya 464-8681 , Japan.,Department of Pathology and Clinical Laboratories, Nagoya University Hospital , Nagoya 466-0065 , Japan
| | - Taishi Takahara
- Division of Molecular Medicine, Aichi Cancer Center Research Institute , Nagoya 464-8681 , Japan.,Department of Pathology and Clinical Laboratories, Nagoya University Hospital , Nagoya 466-0065 , Japan
| | - Yumiko Kasugai
- Division of Molecular Medicine, Aichi Cancer Center Research Institute , Nagoya 464-8681 , Japan
| | - Kotaro Arita
- Third Department of Internal Medicine, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama , Toyama 930-0194 , Japan
| | - Noriaki Yoshida
- Department of Pathology, Kurume University School of Medicine , Kurume 830-0011 , Japan.,Present address: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kennosuke Karube
- Laboratory of Cytopathology, Faculty of Medicine, University of the Ryukyus , Okinawa 903-0215 , Japan
| | - Miyuki Suguro
- Division of Molecular Medicine, Aichi Cancer Center Research Institute , Nagoya 464-8681 , Japan
| | - Keitaro Matsuo
- Division of Molecular Medicine, Aichi Cancer Center Research Institute , Nagoya 464-8681 , Japan
| | - Hayao Nakanishi
- Laboratory of Pathology and Clinical Research, Aichi Cancer Center , Aichi Hospital, Okazaki 444-0011 , Japan
| | - Tohru Kiyono
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute , Tokyo 104-0045 , Japan
| | - Shigeo Nakamura
- Department of Pathology and Clinical Laboratories, Nagoya University Hospital , Nagoya 466-0065 , Japan
| | - Hirotaka Osada
- Division of Molecular Oncology, Aichi Cancer Center Research Institute , Nagoya 464-8681 , Japan.,Department of Cancer Genetics, Program in Function Construction Medicine, Nagoya University Graduate School of Medicine , Nagoya 466-8550 , Japan and
| | - Yoshitaka Sekido
- Division of Molecular Oncology, Aichi Cancer Center Research Institute , Nagoya 464-8681 , Japan.,Department of Cancer Genetics, Program in Function Construction Medicine, Nagoya University Graduate School of Medicine , Nagoya 466-8550 , Japan and
| | - Masao Seto
- Department of Pathology, Kurume University School of Medicine , Kurume 830-0011 , Japan
| | - Shinobu Tsuzuki
- Division of Molecular Medicine, Aichi Cancer Center Research Institute , Nagoya 464-8681 , Japan.,Department of Biochemistry, Aichi Medical University School of Medicine , Nagakute, Aichi 480-1195 , Japan
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29
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Histone Deacetylases with Antagonistic Roles in Saccharomyces cerevisiae Heterochromatin Formation. Genetics 2016; 204:177-90. [PMID: 27489001 DOI: 10.1534/genetics.116.190835] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/14/2016] [Indexed: 12/18/2022] Open
Abstract
As the only catalytic member of the Sir-protein gene-silencing complex, Sir2's catalytic activity is necessary for silencing. The only known role for Sir2's catalytic activity in Saccharomyces cerevisiae silencing is to deacetylate N-terminal tails of histones H3 and H4, creating high-affinity binding sites for the Sir-protein complex, resulting in association of Sir proteins across the silenced domain. This histone deacetylation model makes the simple prediction that preemptively removing Sir2's H3 and H4 acetyl substrates, by mutating these lysines to unacetylatable arginines, or removing the acetyl transferase responsible for their acetylation, should restore silencing in the Sir2 catalytic mutant. However, this was not the case. We conducted a genetic screen to explore what aspect of Sir2's catalytic activity has not been accounted for in silencing. Mutation of a nonsirtuin histone deacetylase, Rpd3, restored Sir-protein-based silencing in the absence of Sir2's catalytic activity. Moreover, this antagonism could be mediated by either the large or the small Rpd3-containing complex. Interestingly, this restoration of silencing appeared independent of any known histone H3 or H4 substrates of Rpd3 Investigation of Sir-protein association in the Rpd3 mutant revealed that the restoration of silencing was correlated with an increased association of Sir proteins at the silencers, suggesting that Rpd3 was an antagonist of Sir2's function in nucleation of Sir proteins to the silencer. Additionally, restoration of silencing by Rpd3 was dependent on another sirtuin family member, Hst3, indicating multiple antagonistic roles for deacetylases in S. cerevisiae silencing.
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30
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Tramantano M, Sun L, Au C, Labuz D, Liu Z, Chou M, Shen C, Luk E. Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex. eLife 2016; 5. [PMID: 27438412 PMCID: PMC4995100 DOI: 10.7554/elife.14243] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 07/12/2016] [Indexed: 12/17/2022] Open
Abstract
The assembly of the preinitiation complex (PIC) occurs upstream of the +1 nucleosome which, in yeast, obstructs the transcription start site and is frequently assembled with the histone variant H2A.Z. To understand the contribution of the transcription machinery in the disassembly of the +1 H2A.Z nucleosome, conditional mutants were used to block PIC assembly. A quantitative ChIP-seq approach, which allows detection of global occupancy change, was employed to measure H2A.Z occupancy. Blocking PIC assembly resulted in promoter-specific H2A.Z accumulation, indicating that the PIC is required to evict H2A.Z. By contrast, H2A.Z eviction was unaffected upon depletion of INO80, a remodeler previously reported to displace nucleosomal H2A.Z. Robust PIC-dependent H2A.Z eviction was observed at active and infrequently transcribed genes, indicating that constitutive H2A.Z turnover is a general phenomenon. Finally, sites with strong H2A.Z turnover precisely mark transcript starts, providing a new metric for identifying cryptic and alternative sites of initiation. DOI:http://dx.doi.org/10.7554/eLife.14243.001 To fit the genetic information of an animal, yeast or other eukaryote into cells, DNA is tightly wound around proteins called histones to form repeating units known as nucleosomes. However, this tight winding prevents proteins from accessing the DNA, and so prevents gene transcription – the first stage of producing the molecules encoded by a gene. For transcription to take place, nucleosomes at DNA sequences called promoters must be reorganized and disassembled, thereby allowing proteins to bind to and engage these sequences and to turn nearby genes on. H2A is a histone protein that is found in the majority of nucleosomes in yeast cells. A different form of this histone – called H2A.Z – is found in nucleosomes near the promoter of almost every gene. It is thought that nucleosomes that contain H2A.Z are recognized and disassembled as the gene turns on, but it is unclear how this happens. To investigate how H2A.Z nucleosomes are disassembled, Tramantano et al. depleted yeast cells of various proteins thought to play a role in the disassembly process. This indicated that the proteins that transcribe genes play crucial roles in the process of disassembling the H2A.Z nucleosomes, because H2A.Z accumulated at promoters in cells that are depleted of these proteins. Further investigation revealed that disassembled H2A.Z nucleosomes are reassembled with H2A histones, before being converted back to the H2A.Z form by an enzyme called SWR1. This turnover of H2A.Z was seen at active genes and those that are infrequently transcribed, suggesting that it is a general phenomenon. Tramantano et al. also found that the turnover rate of H2A.Z can be used to accurately predict the sites in the DNA where transcription starts. This observation could therefore help to identify previously unknown transcription start sites. Future work could address further questions about how H2A.Z nucleosomes are disassembled. For example, what is the mechanical force that drives this process? And at what step of the transcription process does it occur? DOI:http://dx.doi.org/10.7554/eLife.14243.002
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Affiliation(s)
- Michael Tramantano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Lu Sun
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Christy Au
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Daniel Labuz
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Zhimin Liu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Mindy Chou
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Chen Shen
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Ed Luk
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
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31
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Singh D, Chetia H, Kabiraj D, Sharma S, Kumar A, Sharma P, Deka M, Bora U. A comprehensive view of the web-resources related to sericulture. Database (Oxford) 2016; 2016:baw086. [PMID: 27307138 PMCID: PMC4909305 DOI: 10.1093/database/baw086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/25/2016] [Accepted: 05/02/2016] [Indexed: 12/03/2022]
Abstract
Recent progress in the field of sequencing and analysis has led to a tremendous spike in data and the development of data science tools. One of the outcomes of this scientific progress is development of numerous databases which are gaining popularity in all disciplines of biology including sericulture. As economically important organism, silkworms are studied extensively for their numerous applications in the field of textiles, biomaterials, biomimetics, etc. Similarly, host plants, pests, pathogens, etc. are also being probed to understand the seri-resources more efficiently. These studies have led to the generation of numerous seri-related databases which are extremely helpful for the scientific community. In this article, we have reviewed all the available online resources on silkworm and its related organisms, including databases as well as informative websites. We have studied their basic features and impact on research through citation count analysis, finally discussing the role of emerging sequencing and analysis technologies in the field of seri-data science. As an outcome of this review, a web portal named SeriPort, has been created which will act as an index for the various sericulture-related databases and web resources available in cyberspace.Database URL: http://www.seriport.in/.
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Affiliation(s)
- Deepika Singh
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Hasnahana Chetia
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Debajyoti Kabiraj
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Swagata Sharma
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Anil Kumar
- Centre for Biological Sciences (Bioinformatics), Central University of South Bihar (CUSB), Patna 800014, India
| | - Pragya Sharma
- Department of Bioengineering & Technology, Gauhati University Institute of Science & Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Manab Deka
- Department of Bioengineering & Technology, Gauhati University Institute of Science & Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Utpal Bora
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India Mugagen Laboratories Pvt. Ltd, Technology Incubation Centre, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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32
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Lai K, Luo C, Zhang X, Ye P, Zhang Y, He J, Yao K. Regulation of angiogenin expression and epithelial-mesenchymal transition by HIF-1α signaling in hypoxic retinal pigment epithelial cells. Biochim Biophys Acta Mol Basis Dis 2016; 1862:1594-607. [PMID: 27259982 DOI: 10.1016/j.bbadis.2016.05.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/05/2016] [Accepted: 05/27/2016] [Indexed: 01/13/2023]
Abstract
Choroidal neovascularization (CNV) is a major cause of vision loss in many retinal diseases. Hypoxia is determined to be a key inducer of CNV and hypoxia-inducible factor-1 (HIF-1) is an important transcription factor. Epithelial-mesenchymal transition (EMT) and the synthesis of proangiogenic cytokines make great contributions to the development of CNV. In the present study, the role of HIF-1α signaling in the regulation of angiogenin (ANG) expression and EMT in hypoxic retinal pigment epithelial cells was investigated. A significant elevation expression of ANG expression level in a mouse model of laser-induced CNV was demonstrated. In a hypoxic model of ARPE-19, an increased expression level of ANG and induction of EMT accompanied with stabilization and nucleus translocation of HIF-1α. Blockage of HIF-1α signaling resulted in inhibition of high expression of ANG and EMT features. The direct interaction between HIF-1α and ANG promoter region was identified by ChIP-qPCR. The association of RNase 4 mRNA level with HIF-1α signaling was also clarified in APRE-19. Moreover, the exogenous ANG translocated into the nucleus, enhanced 45S rRNA transcription, promoted cell proliferation and tube formation in human retinal microvascular endothelial cells. In conclusion, the hypoxic conditions regulate the expression of ANG and EMT via an activation of HIF-1α signaling. It provides molecular evidence for potential therapy strategies of treating CNV.
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Affiliation(s)
- Kairan Lai
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory of Ophthalmology, Hangzhou, China
| | - Chenqi Luo
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory of Ophthalmology, Hangzhou, China
| | - Xiaobo Zhang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Panpan Ye
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yidong Zhang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiliang He
- Institutes of Environmental Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ke Yao
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory of Ophthalmology, Hangzhou, China.
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33
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Ellahi A, Rine J. Evolution and Functional Trajectory of Sir1 in Gene Silencing. Mol Cell Biol 2016; 36:1164-79. [PMID: 26811328 PMCID: PMC4800792 DOI: 10.1128/mcb.01013-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/08/2015] [Accepted: 01/21/2016] [Indexed: 01/28/2023] Open
Abstract
We used the budding yeasts Saccharomyces cerevisiae and Torulaspora delbrueckii to examine the evolution of Sir-based silencing, focusing on Sir1, silencers, the molecular topography of silenced chromatin, and the roles of SIR and RNA interference (RNAi) genes in T. delbrueckii. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) analysis of Sir proteins in T. delbrueckii revealed a different topography of chromatin at the HML and HMR loci than was observed in S. cerevisiae. S. cerevisiae Sir1, enriched at the silencers of HMLα and HMR A: , was absent from telomeres and did not repress subtelomeric genes. In contrast to S. cerevisiae SIR1's partially dispensable role in silencing, the T. delbrueckii SIR1 paralog KOS3 was essential for silencing. KOS3 was also found at telomeres with T. delbrueckii Sir2 (Td-Sir2) and Td-Sir4 and repressed subtelomeric genes. Silencer mapping in T. delbrueckii revealed single silencers at HML and HMR, bound by Td-Kos3, Td-Sir2, and Td-Sir4. The KOS3 gene mapped near HMR, and its expression was regulated by Sir-based silencing, providing feedback regulation of a silencing protein by silencing. In contrast to the prominent role of Sir proteins in silencing, T. delbrueckii RNAi genes AGO1 and DCR1 did not function in heterochromatin formation. These results highlighted the shifting role of silencing genes and the diverse chromatin architectures underlying heterochromatin.
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Affiliation(s)
- Aisha Ellahi
- Department of Molecular and Cell Biology and California Institute of Quantitative Biology, University of California Berkeley, Berkeley, California, USA
| | - Jasper Rine
- Department of Molecular and Cell Biology and California Institute of Quantitative Biology, University of California Berkeley, Berkeley, California, USA
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34
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Richardson CD, Ray GJ, DeWitt MA, Curie GL, Corn JE. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol 2016; 34:339-44. [PMID: 26789497 DOI: 10.1038/nbt.3481] [Citation(s) in RCA: 732] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/13/2016] [Indexed: 12/31/2022]
Abstract
Targeted genomic manipulation by Cas9 can efficiently generate knockout cells and organisms via error-prone nonhomologous end joining (NHEJ), but the efficiency of precise sequence replacement by homology-directed repair (HDR) is substantially lower. Here we investigate the interaction of Cas9 with target DNA and use our findings to improve HDR efficiency. We show that dissociation of Cas9 from double-stranded DNA (dsDNA) substrates is slow (lifetime ∼6 h) but that, before complete dissociation, Cas9 asymmetrically releases the 3' end of the cleaved DNA strand that is not complementary to the sgRNA (nontarget strand). By rationally designing single-stranded DNA (ssDNA) donors of the optimal length complementary to the strand that is released first, we increase the rate of HDR in human cells when using Cas9 or nickase variants to up to 60%. We also demonstrate HDR rates of up to 0.7% using a catalytically inactive Cas9 mutant (dCas9), which binds DNA without cleaving it.
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Affiliation(s)
- Christopher D Richardson
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Graham J Ray
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Mark A DeWitt
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Gemma L Curie
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jacob E Corn
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
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35
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Boucherat O, Landry-Truchon K, Bérubé-Simard FA, Houde N, Beuret L, Lezmi G, Foulkes WD, Delacourt C, Charron J, Jeannotte L. Epithelial inactivation of Yy1 abrogates lung branching morphogenesis. Development 2015; 142:2981-95. [PMID: 26329601 DOI: 10.1242/dev.120469] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Yin Yang 1 (YY1) is a multifunctional zinc-finger-containing transcription factor that plays crucial roles in numerous biological processes by selectively activating or repressing transcription, depending upon promoter contextual differences and specific protein interactions. In mice, Yy1 null mutants die early in gestation whereas Yy1 hypomorphs die at birth from lung defects. We studied how the epithelial-specific inactivation of Yy1 impacts on lung development. The Yy1 mutation in lung epithelium resulted in neonatal death due to respiratory failure. It impaired tracheal cartilage formation, altered cell differentiation, abrogated lung branching and caused airway dilation similar to that seen in human congenital cystic lung diseases. The cystic lung phenotype in Yy1 mutants can be partly explained by the reduced expression of Shh, a transcriptional target of YY1, in lung endoderm, and the subsequent derepression of mesenchymal Fgf10 expression. Accordingly, SHH supplementation partially rescued the lung phenotype in vitro. Analysis of human lung tissues revealed decreased YY1 expression in children with pleuropulmonary blastoma (PPB), a rare pediatric lung tumor arising during fetal development and associated with DICER1 mutations. No evidence for a potential genetic interplay between murine Dicer and Yy1 genes during lung morphogenesis was observed. However, the cystic lung phenotype resulting from the epithelial inactivation of Dicer function mimics the Yy1 lung malformations with similar changes in Shh and Fgf10 expression. Together, our data demonstrate the crucial requirement for YY1 in lung morphogenesis and identify Yy1 mutant mice as a potential model for studying the genetic basis of PPB.
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Affiliation(s)
- Olivier Boucherat
- Centre de Recherche sur le Cancer de l'Université Laval; CRCHUQ, L'Hôtel-Dieu de Québec, Québec, G1R 3S3, Canada
| | - Kim Landry-Truchon
- Centre de Recherche sur le Cancer de l'Université Laval; CRCHUQ, L'Hôtel-Dieu de Québec, Québec, G1R 3S3, Canada
| | - Félix-Antoine Bérubé-Simard
- Centre de Recherche sur le Cancer de l'Université Laval; CRCHUQ, L'Hôtel-Dieu de Québec, Québec, G1R 3S3, Canada
| | - Nicolas Houde
- Centre de Recherche sur le Cancer de l'Université Laval; CRCHUQ, L'Hôtel-Dieu de Québec, Québec, G1R 3S3, Canada
| | - Laurent Beuret
- Centre de Recherche sur le Cancer de l'Université Laval; CRCHUQ, L'Hôtel-Dieu de Québec, Québec, G1R 3S3, Canada
| | - Guillaume Lezmi
- AP-HP, Hôpital Necker-Enfants Malades, Service de Pneumologie Pédiatrique, Université Paris-Descartes, Paris, 75015, France Inserm U955, IMRB, Equipe 04, Créteil, 94011, France
| | - William D Foulkes
- Department of Medical Genetics, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montréal, H3G 1A4, Canada
| | - Christophe Delacourt
- AP-HP, Hôpital Necker-Enfants Malades, Service de Pneumologie Pédiatrique, Université Paris-Descartes, Paris, 75015, France Inserm U955, IMRB, Equipe 04, Créteil, 94011, France
| | - Jean Charron
- Centre de Recherche sur le Cancer de l'Université Laval; CRCHUQ, L'Hôtel-Dieu de Québec, Québec, G1R 3S3, Canada
| | - Lucie Jeannotte
- Centre de Recherche sur le Cancer de l'Université Laval; CRCHUQ, L'Hôtel-Dieu de Québec, Québec, G1R 3S3, Canada
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36
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Hoffman EA, Frey BL, Smith LM, Auble DT. Formaldehyde crosslinking: a tool for the study of chromatin complexes. J Biol Chem 2015; 290:26404-11. [PMID: 26354429 DOI: 10.1074/jbc.r115.651679] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formaldehyde has been used for decades to probe macromolecular structure and function and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is routinely employed for detection and quantification of protein-DNA interactions, interactions between chromatin proteins, and interactions between distal segments of the chromatin fiber. Despite widespread use and a rich biochemical literature, important aspects of formaldehyde behavior in cells have not been well described. Here, we highlight features of formaldehyde chemistry relevant to its use in analyses of chromatin complexes, focusing on how its properties may influence studies of chromatin structure and function.
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Affiliation(s)
- Elizabeth A Hoffman
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and
| | - Brian L Frey
- the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - Lloyd M Smith
- the Department of Chemistry and Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706
| | - David T Auble
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908 and
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37
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Steakley DL, Rine J. On the Mechanism of Gene Silencing in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2015; 5:1751-63. [PMID: 26082137 PMCID: PMC4528331 DOI: 10.1534/g3.115.018515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/15/2015] [Indexed: 11/18/2022]
Abstract
Multiple mechanisms have been proposed for gene silencing in Saccharomyces cerevisiae, ranging from steric occlusion of DNA binding proteins from their recognition sequences in silenced chromatin to a specific block in the formation of the preinitiation complex to a block in transcriptional elongation. This study provided strong support for the steric occlusion mechanism by the discovery that RNA polymerase of bacteriophage T7 could be substantially blocked from transcribing from its cognate promoter when embedded in silenced chromatin. Moreover, unlike previous suggestions, we found no evidence for stalled RNA polymerase II within silenced chromatin. The effectiveness of the Sir protein-based silencing mechanism to block transcription activated by Gal4 at promoters in the domain of silenced chromatin was marginal, yet it improved when tested against mutant forms of the Gal4 protein, highlighting a role for specific activators in their sensitivity to gene silencing.
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Affiliation(s)
- David Lee Steakley
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, Stanley Hall, University of California Berkeley, Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, Stanley Hall, University of California Berkeley, Berkeley, California 94720
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38
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Monaghan RM, Barnes RG, Fisher K, Andreou T, Rooney N, Poulin GB, Whitmarsh AJ. A nuclear role for the respiratory enzyme CLK-1 in regulating mitochondrial stress responses and longevity. Nat Cell Biol 2015; 17:782-92. [PMID: 25961505 PMCID: PMC4539581 DOI: 10.1038/ncb3170] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/27/2015] [Indexed: 12/12/2022]
Abstract
The coordinated regulation of mitochondrial and nuclear activities is essential for cellular respiration and its disruption leads to mitochondrial dysfunction, a hallmark of ageing. Mitochondria communicate with nuclei through retrograde signalling pathways that modulate nuclear gene expression to maintain mitochondrial homeostasis. The monooxygenase CLK-1 (human homologue COQ7) was previously reported to be mitochondrial, with a role in respiration and longevity. We have uncovered a distinct nuclear form of CLK-1 that independently regulates lifespan. Nuclear CLK-1 mediates a retrograde signalling pathway that is conserved from Caenorhabditis elegans to humans and is responsive to mitochondrial reactive oxygen species, thus acting as a barometer of oxidative metabolism. We show that, through modulation of gene expression, the pathway regulates both mitochondrial reactive oxygen species metabolism and the mitochondrial unfolded protein response. Our results demonstrate that a respiratory enzyme acts in the nucleus to control mitochondrial stress responses and longevity.
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Affiliation(s)
- Richard M. Monaghan
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Robert G. Barnes
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Kate Fisher
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Tereza Andreou
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Nicholas Rooney
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Gino B. Poulin
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Alan J. Whitmarsh
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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39
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Shao M, Sun Y, Zhou S. Identifying TF-MiRNA Regulatory Relationships Using Multiple Features. PLoS One 2015; 10:e0125156. [PMID: 25922940 PMCID: PMC4414601 DOI: 10.1371/journal.pone.0125156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 03/20/2015] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs are known to play important roles in the transcriptional and post-transcriptional regulation of gene expression. While intensive research has been conducted to identify miRNAs and their target genes in various genomes, there is only limited knowledge about how microRNAs are regulated. In this study, we construct a pipeline that can infer the regulatory relationships between transcription factors and microRNAs from ChIP-Seq data with high confidence. In particular, after identifying candidate peaks from ChIP-Seq data, we formulate the inference as a PU learning (learning from only positive and unlabeled examples) problem. Multiple features including the statistical significance of the peaks, the location of the peaks, the transcription factor binding site motifs, and the evolutionary conservation are derived from peaks for training and prediction. To further improve the accuracy of our inference, we also apply a mean reciprocal rank (MRR)-based method to the candidate peaks. We apply our pipeline to infer TF-miRNA regulatory relationships in mouse embryonic stem cells. The experimental results show that our approach provides very specific findings of TF-miRNA regulatory relationships.
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Affiliation(s)
- Mingyu Shao
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai 200433, China
- Department of Computer Science and Engineering, Michigan State University, 428 S. Shaw Lane, East Lansing, 48824, USA
| | - Yanni Sun
- Department of Computer Science and Engineering, Michigan State University, 428 S. Shaw Lane, East Lansing, 48824, USA
- * E-mail: (YS); (SZ)
| | - Shuigeng Zhou
- School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, 220 Handan Road, Shanghai 200433, China
- * E-mail: (YS); (SZ)
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40
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Vanacloig-Pedros E, Bets-Plasencia C, Pascual-Ahuir A, Proft M. Coordinated gene regulation in the initial phase of salt stress adaptation. J Biol Chem 2015; 290:10163-75. [PMID: 25745106 DOI: 10.1074/jbc.m115.637264] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 01/24/2023] Open
Abstract
Stress triggers complex transcriptional responses, which include both gene activation and repression. We used time-resolved reporter assays in living yeast cells to gain insights into the coordination of positive and negative control of gene expression upon salt stress. We found that the repression of "housekeeping" genes coincides with the transient activation of defense genes and that the timing of this expression pattern depends on the severity of the stress. Moreover, we identified mutants that caused an alteration in the kinetics of this transcriptional control. Loss of function of the vacuolar H(+)-ATPase (vma1) or a defect in the biosynthesis of the osmolyte glycerol (gpd1) caused a prolonged repression of housekeeping genes and a delay in gene activation at inducible loci. Both mutants have a defect in the relocation of RNA polymerase II complexes at stress defense genes. Accordingly salt-activated transcription is delayed and less efficient upon partially respiratory growth conditions in which glycerol production is significantly reduced. Furthermore, the loss of Hog1 MAP kinase function aggravates the loss of RNA polymerase II from housekeeping loci, which apparently do not accumulate at inducible genes. Additionally the Def1 RNA polymerase II degradation factor, but not a high pool of nuclear polymerase II complexes, is needed for efficient stress-induced gene activation. The data presented here indicate that the finely tuned transcriptional control upon salt stress is dependent on physiological functions of the cell, such as the intracellular ion balance, the protective accumulation of osmolyte molecules, and the RNA polymerase II turnover.
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Affiliation(s)
- Elena Vanacloig-Pedros
- the Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Carolina Bets-Plasencia
- the Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Amparo Pascual-Ahuir
- the Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Markus Proft
- From the Department of Mechanisms of Plant Stress Responses, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, and
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41
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Sanchez-Casalongue ME, Lee J, Diamond A, Shuldiner S, Moir RD, Willis IM. Differential phosphorylation of a regulatory subunit of protein kinase CK2 by target of rapamycin complex 1 signaling and the Cdc-like kinase Kns1. J Biol Chem 2015; 290:7221-33. [PMID: 25631054 DOI: 10.1074/jbc.m114.626523] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transcriptional regulation of ribosome and tRNA synthesis plays a central role in determining protein synthetic capacity and is tightly controlled in response to nutrient availability and cellular stress. In Saccharomyces cerevisiae, the regulation of ribosome and tRNA synthesis was recently shown to involve the Cdc-like kinase Kns1 and the GSK-3 kinase Mck1. In this study, we explored additional roles for these conserved kinases in processes connected to the target of rapamycin complex 1 (TORC1). We conducted a synthetic chemical-genetic screen in a kns1Δ mck1Δ strain and identified many novel rapamycin-hypersensitive genes. Gene ontology analysis showed enrichment for TORC1-regulated processes (vesicle-mediated transport, autophagy, and regulation of cell size) and identified new connections to protein complexes including the protein kinase CK2. CK2 is considered to be a constitutively active kinase and in budding yeast, the holoenzyme comprises two regulatory subunits, Ckb1 and Ckb2, and two catalytic subunits, Cka1 and Cka2. We show that Ckb1 is differentially phosphorylated in vivo and that Kns1 mediates this phosphorylation when nutrients are limiting and under all tested stress conditions. We determined that the phosphorylation of Ckb1 does not detectably affect the stability of the CK2 holoenzyme but correlates with the reduced occupancy of Ckb1 on tRNA genes after rapamycin treatment. Thus, the differential occupancy of tRNA genes by CK2 is likely to modulate its activation of RNA polymerase III transcription. Our data suggest that TORC1, via its effector kinase Kns1, may regulate the association of CK2 with some of its substrates by phosphorylating Ckb1.
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Affiliation(s)
| | | | | | | | | | - Ian M Willis
- From the Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461
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42
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Aldawsari FS, Elshenawy OH, El Gendy MAM, Aguayo-Ortiz R, Baksh S, El-Kadi AOS, Velázquez-Martínez CA. Design and synthesis of resveratrol–salicylate hybrid derivatives as CYP1A1 inhibitors. J Enzyme Inhib Med Chem 2014; 30:884-95. [DOI: 10.3109/14756366.2014.979347] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fahad S. Aldawsari
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada,
| | - Osama H. Elshenawy
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada,
| | - Mohamed A. M. El Gendy
- Experimental Oncology Unit, Department of Oncology, University of Alberta, Edmonton, Alberta, Canada,
- Department of Pharmacognosy, Pharmaceutical Sciences Division, Natural Research Centre, Dokki, Giza, Egypt,
| | - Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, México,
| | - Shairaz Baksh
- Department of Pediatrics, Oncology and Biochemistry, University of Alberta, Edmonton, Alberta, Canada, and
- Alberta Inflammatory Bowel Disease Consortium, Alberta, Canada
| | - Ayman O. S. El-Kadi
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada,
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43
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Abstract
The extent of chromatin compaction is a fundamental driver of nuclear metabolism . Yta7 is a chromatin-associated AAA-ATPase, the human ortholog of which, ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. Yta7 directly binds histone H3, and bulk chromatin exhibits increased nucleosomal density in yta7Δ mutants. The suppression of yta7Δ mutant growth and transcriptional phenotypes in budding yeast by decreased dosage of histones H3 and H4 indicates the acute sensitivity of cells to deviations in nucleosome spacing. This study investigated the global changes in chromatin structure upon Yta7 loss or overexpression and determined which of these effects reflected direct Yta7 activity. Metagene analysis of Yta7's genome-wide localization indicated peak binding of Yta7 just downstream of the transcription start site. Cells lacking Yta7 exhibited increased nucleosome density within genes downstream of the +1 nucleosome, as defined by decreased internucleosomal distance, resulting in progressively 5'-shifted nucleosomes within the gene. In contrast, cells overexpressing Yta7 displayed profound 3'-shifts in nucleosome position and reduced nucleosome density within genes. Importantly, Yta7-bound regions were enriched for nucleosomal shifts, indicating that Yta7 acted locally to modulate nucleosome spacing. The phenotype of cells lacking both Yta7 and Rtt106, the histone H3/H4 chaperone, indicated that Yta7 functions in both Rtt106-dependent and Rtt106-independent ways to modulate nucleosome spacing within genes. This study suggested that Yta7 affected nucleosome density throughout the gene by both blocking Rtt106 from entering the gene, as shown previously at HTA1, and facilitating the loss of nucleosomes from the 5'-end.
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44
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Evolutionary expansion of a regulatory network by counter-silencing. Nat Commun 2014; 5:5270. [PMID: 25348042 PMCID: PMC4215172 DOI: 10.1038/ncomms6270] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 09/15/2014] [Indexed: 11/09/2022] Open
Abstract
Horizontal gene transfer plays a major role in bacterial evolution. Successful acquisition of new genes requires their incorporation into existing regulatory networks. This study compares the regulation of conserved genes in the PhoPQ regulon of Salmonella enterica serovar Typhimurium with that of PhoPQ-regulated horizontally-acquired genes, which are silenced by the histone-like protein H-NS. We demonstrate that PhoP up-regulates conserved and horizontally-acquired genes by distinct mechanisms. Conserved genes are regulated by classical PhoP-mediated activation and are invariant in promoter architecture, whereas horizontally-acquired genes exhibit variable promoter architecture and are regulated by PhoP-mediated counter-silencing. Biochemical analyses show that a horizontally-acquired promoter adopts different structures in the silenced and counter-silenced states, implicating the remodeling of the H-NS nucleoprotein filament and the subsequent restoration of open complex formation as the central mechanism of counter-silencing. Our results indicate that counter-silencing is favored in the regulatory integration of newly-acquired genes because it is able to accommodate multiple promoter architectures.
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45
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House NCM, Yang JH, Walsh SC, Moy JM, Freudenreich CH. NuA4 initiates dynamic histone H4 acetylation to promote high-fidelity sister chromatid recombination at postreplication gaps. Mol Cell 2014; 55:818-828. [PMID: 25132173 PMCID: PMC4169719 DOI: 10.1016/j.molcel.2014.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 04/16/2014] [Accepted: 07/10/2014] [Indexed: 11/24/2022]
Abstract
CAG/CTG trinucleotide repeats are unstable, fragile sequences that strongly position nucleosomes, but little is known about chromatin modifications required to prevent genomic instability at these or other structure-forming sequences. We discovered that regulated histone H4 acetylation is required to maintain CAG repeat stability and promote gap-induced sister chromatid recombination. CAG expansions in the absence of H4 HATs NuA4 and Hat1 and HDACs Sir2, Hos2, and Hst1 depended on Rad52, Rad57, and Rad5 and were therefore arising through homology-mediated postreplication repair (PRR) events. H4K12 and H4K16 acetylation were required to prevent Rad5-dependent CAG repeat expansions, and H4K16 acetylation was enriched at CAG repeats during S phase. Genetic experiments placed the RSC chromatin remodeler in the same PRR pathway, and Rsc2 recruitment was coincident with H4K16 acetylation. Here we have utilized a repetitive DNA sequence that induces endogenous DNA damage to identify histone modifications that regulate recombination efficiency and fidelity during postreplication gap repair.
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Affiliation(s)
| | - Jiahui H Yang
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Stephen C Walsh
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jonathan M Moy
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA 02155, USA; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA.
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46
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Richardson CD, Li JJ. Regulatory mechanisms that prevent re-initiation of DNA replication can be locally modulated at origins by nearby sequence elements. PLoS Genet 2014; 10:e1004358. [PMID: 24945837 PMCID: PMC4063666 DOI: 10.1371/journal.pgen.1004358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/24/2014] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic cells must inhibit re-initiation of DNA replication at each of the thousands of origins in their genome because re-initiation can generate genomic alterations with extraordinary frequency. To minimize the probability of re-initiation from so many origins, cells use a battery of regulatory mechanisms that reduce the activity of replication initiation proteins. Given the global nature of these mechanisms, it has been presumed that all origins are inhibited identically. However, origins re-initiate with diverse efficiencies when these mechanisms are disabled, and this diversity cannot be explained by differences in the efficiency or timing of origin initiation during normal S phase replication. This observation raises the possibility of an additional layer of replication control that can differentially regulate re-initiation at distinct origins. We have identified novel genetic elements that are necessary for preferential re-initiation of two origins and sufficient to confer preferential re-initiation on heterologous origins when the control of re-initiation is partially deregulated. The elements do not enhance the S phase timing or efficiency of adjacent origins and thus are specifically acting as re-initiation promoters (RIPs). We have mapped the two RIPs to ∼60 bp AT rich sequences that act in a distance- and sequence-dependent manner. During the induction of re-replication, Mcm2-7 reassociates both with origins that preferentially re-initiate and origins that do not, suggesting that the RIP elements can overcome a block to re-initiation imposed after Mcm2-7 associates with origins. Our findings identify a local level of control in the block to re-initiation. This local control creates a complex genomic landscape of re-replication potential that is revealed when global mechanisms preventing re-replication are compromised. Hence, if re-replication does contribute to genomic alterations, as has been speculated for cancer cells, some regions of the genome may be more susceptible to these alterations than others. Eukaryotic organisms have hundreds to thousands of DNA replication origins distributed throughout their genomes. Faithful duplication of these genomes requires a multitude of global controls that ensure that every replication origin initiates at most once per cell cycle. Disruptions in these controls can result in re-initiation of origins and localized re-replication of the surrounding genome. Such re-replicated genomic segments are converted to stable chromosomal alterations with extraordinarily efficiency and could provide a potential source of genomic alterations associated with cancer cells. This publication establishes the existence of a local layer of replication control by identifying new genetic elements, termed re-initiation promoters (RIPs) that can locally override some of the global mechanisms preventing re-initiation. Origins adjacent to RIP elements are not as tightly controlled and thus more susceptible to re-initiation, especially when these global controls are compromised. We speculate that RIP elements contribute to genomic variability in origin control and make some regions of the genome more susceptible to re-replication induced genomic instability.
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Affiliation(s)
- Christopher D. Richardson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Joachim J. Li
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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The transcription factors Tec1 and Ste12 interact with coregulators Msa1 and Msa2 to activate adhesion and multicellular development. Mol Cell Biol 2014; 34:2283-93. [PMID: 24732795 DOI: 10.1128/mcb.01599-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In Saccharomyces cerevisiae and related yeast species, the TEA transcription factor Tec1, together with a second transcription factor, Ste12, controls development, including cell adhesion and filament formation. Tec1-Ste12 complexes control target genes through Tec1 binding sites (TEA consensus sequences [TCSs]) that can be further combined with Ste12 binding sites (pheromone response elements [PREs]) for cooperative DNA binding. The activity of Tec1-Ste12 complexes is known to be under negative control of the Dig1 and Dig2 (Dig1/2) transcriptional corepressors that confer regulation by upstream signaling pathways. Here, we found that Tec1 and Ste12 can associate with the transcriptional coregulators Msa1 and Msa2 (Msa1/2), which were previously found to associate with the cell cycle transcription factor complexes SBF (Swi4/Swi6 cell cycle box binding factor) and MBF (Mbp1/Swi6 cell cycle box binding factor) to control G1-specific transcription. We further show that Tec1-Ste12-Msa1/2 complexes (i) do not contain Swi4 or Mbp1, (ii) assemble at single TCSs or combined TCS-PREs in vitro, and (iii) coregulate genes involved in adhesive and filamentous growth by direct promoter binding in vivo. Finally, we found that, in contrast to Dig proteins, Msa1/2 seem to act as coactivators that enhance the transcriptional activity of Tec1-Ste12. Taken together, our findings add an additional layer of complexity to our understanding of the control mechanisms exerted by the evolutionarily conserved TEA domain and Ste12-like transcription factors.
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Abstract
Heterochromatin imparts regional, promoter-independent repression of genes and is epigenetically heritable. Understanding how silencing achieves this regional repression is a fundamental problem in genetics and development. Current models of yeast silencing posit that Sir proteins, recruited by transcription factors bound to the silencers, spread throughout the silenced region. To test this model directly at high resolution, we probed the silenced chromatin architecture by chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-seq) of Sir proteins, histones, and a key histone modification, H4K16-acetyl. These analyses revealed that Sir proteins are strikingly concentrated at and immediately adjacent to the silencers, with lower levels of enrichment over the promoters at HML and HMR, the critical targets for transcriptional repression. The telomeres also showed discrete peaks of Sir enrichment yet a continuous domain of hypoacetylated histone H4K16. Surprisingly, ChIP-seq of cross-linked chromatin revealed a distribution of nucleosomes at silenced loci that was similar to Sir proteins, whereas native nucleosome maps showed a regular distribution throughout silenced loci, indicating that cross-linking captured a specialized chromatin organization imposed by Sir proteins. This specialized chromatin architecture observed in yeast informs the importance of a steric contribution to regional repression in other organisms.
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Affiliation(s)
- Deborah M Thurtle
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
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Anwar-Mohamed A, Elshenawy OH, Soshilov AA, Denison MS, Chris Le X, Klotz LO, El-Kadi AOS. Methylated pentavalent arsenic metabolites are bifunctional inducers, as they induce cytochrome P450 1A1 and NAD(P)H:quinone oxidoreductase through AhR- and Nrf2-dependent mechanisms. Free Radic Biol Med 2014; 67:171-87. [PMID: 24161444 DOI: 10.1016/j.freeradbiomed.2013.10.810] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 09/29/2013] [Accepted: 10/16/2013] [Indexed: 02/06/2023]
Abstract
Activation of the aryl hydrocarbon receptor (AhR) ultimately leads to the induction of the carcinogen-activating enzyme cytochrome P450 1A1 (CYP1A1), and activation of the nuclear factor-erythroid 2 p45-related factor 2 (Nrf2) in addition to the AhR pathway induces the expression of the NADP(H):quinone oxidoreductase (NQO1). Therefore, the aim of this study was to examine the effect of As(III) pentavalent metabolites, MMA(V), DMA(V), and TMA(V), on AhR and Nrf2 activation and on the expression of their prototypical downstream targets CYP1A1 and NQO1, respectively. Our results showed that treatment of HepG2 cells with MMA(V), DMA(V), or TMA(V) in the absence and presence of 2,3,7,8-tetrachlorodibenzo-p-dioxin or sulforaphane significantly induced both CYP1A1 and NQO1 at the mRNA, protein, and catalytic activity levels. Furthermore, these metabolites increased the AhR-dependent XRE-driven and the Nrf2-dependent ARE-driven luciferase reporter activities, which coincided with increased nuclear accumulation of both transcription factors. However, none of these metabolites were shown to be AhR ligands. The induction of CYP1A1 by these metabolites seems to be ligand-independent, possibly through a decrease in HSP90 protein expression levels. The metabolites also increased ROS production, which was significantly higher than that produced by As(III). Upon knockdown of AhR and Nrf2 the MMA(V)-, DMA(V)-, and TMA(V)-mediated induction of both CYP1A1 and NQO1 proteins was significantly decreased. In conclusion, this study demonstrates for the first time that methylated pentavalent arsenic metabolites are bifunctional inducers, as they increase CYP1A1 by activating the AhR/XRE signaling pathway and they increase NQO1 by activating the Nrf2/ARE signaling pathway in addition to the AhR/XRE pathway.
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Affiliation(s)
- Anwar Anwar-Mohamed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E1
| | - Osama H Elshenawy
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E1
| | - Anatoly A Soshilov
- Department of Environmental Toxicology, University of California at Davis, Davis, CA 95616, USA
| | - Michael S Denison
- Department of Environmental Toxicology, University of California at Davis, Davis, CA 95616, USA
| | - X Chris Le
- Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada T6G 2G3
| | - Lars-Oliver Klotz
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E1
| | - Ayman O S El-Kadi
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E1; College of Pharmacy, Qatar University, Doha 02713, Qatar.
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Distinct roles of the Salmonella enterica serovar Typhimurium CyaY and YggX proteins in the biosynthesis and repair of iron-sulfur clusters. Infect Immun 2014; 82:1390-401. [PMID: 24421039 DOI: 10.1128/iai.01022-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Labile [4Fe-4S](2+) clusters found at the active sites of many dehydratases are susceptible to damage by univalent oxidants that convert the clusters to an inactive [3Fe-4S](1+) form. Bacteria repair damaged clusters in a process that does not require de novo protein synthesis or the Isc and Suf cluster assembly pathways. The current study investigates the participation of the bacterial frataxin ortholog CyaY and the YggX protein, which are proposed to play roles in iron trafficking and iron-sulfur cluster repair. Previous reports found that individual mutations in cyaY or yggX were not associated with phenotypic changes in Escherichia coli and Salmonella enterica serovar Typhimurium, suggesting that CyaY and YggX might have functionally redundant roles. However, we have found that individual mutations in cyaY or yggX confer enhanced susceptibility to hydrogen peroxide in Salmonella enterica serovar Typhimurium. In addition, inactivation of the stm3944 open reading frame, which is located immediately upstream of cyaY and which encodes a putative inner membrane protein, dramatically enhances the hydrogen peroxide sensitivity of a cyaY mutant. Overexpression of STM3944 reduces the elevated intracellular free iron levels observed in an S. Typhimurium fur mutant and also reduces the total cellular iron content under conditions of iron overload, suggesting that the stm3944-encoded protein may mediate iron efflux. Mutations in cyaY and yggX have different effects on the activities of the iron-sulfur cluster-containing aconitase, serine deaminase, and NADH dehydrogenase I enzymes of S. Typhimurium under basal conditions or following recovery from oxidative stress. In addition, cyaY and yggX mutations have additive effects on 6-phosphogluconate dehydratase-dependent growth during nitrosative stress, and a cyaY mutation reduces Salmonella virulence in mice. Collectively, these results indicate that CyaY and YggX play distinct supporting roles in iron-sulfur cluster biosynthesis and the repair of labile clusters damaged by univalent oxidants. Salmonella experiences oxidative and nitrosative stress within host phagocytes, and CyaY-dependent maintenance of labile iron-sulfur clusters appears to be important for Salmonella virulence.
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