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Shen X, Peng X, Guo Y, Dai Z, Cui L, Yu W, Liu Y, Liu CY. YAP/TAZ enhances P-body formation to promote tumorigenesis. eLife 2024; 12:RP88573. [PMID: 39046443 PMCID: PMC11268890 DOI: 10.7554/elife.88573] [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] [Indexed: 07/25/2024] Open
Abstract
The role of processing bodies (P-bodies) in tumorigenesis and tumor progression is not well understood. Here, we showed that the oncogenes YAP/TAZ promote P-body formation in a series of cancer cell lines. Mechanistically, both transcriptional activation of the P-body-related genes SAMD4A, AJUBA, and WTIP and transcriptional suppression of the tumor suppressor gene PNRC1 are involved in enhancing the effects of YAP/TAZ on P-body formation in colorectal cancer (CRC) cells. By reexpression of PNRC1 or knockdown of P-body core genes (DDX6, DCP1A, and LSM14A), we determined that disruption of P-bodies attenuates cell proliferation, cell migration, and tumor growth induced by overexpression of YAP5SA in CRC. Analysis of a pancancer CRISPR screen database (DepMap) revealed co-dependencies between YAP/TEAD and the P-body core genes and correlations between the mRNA levels of SAMD4A, AJUBA, WTIP, PNRC1, and YAP target genes. Our study suggests that the P-body is a new downstream effector of YAP/TAZ, which implies that reexpression of PNRC1 or disruption of P-bodies is a potential therapeutic strategy for tumors with active YAP.
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Affiliation(s)
- Xia Shen
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Xiang Peng
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - YueGui Guo
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Zhujiang Dai
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Long Cui
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Wei Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan UniversityShanghaiChina
| | - Yun Liu
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
| | - Chen-Ying Liu
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Colorectal Cancer Research CenterShanghaiChina
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Kim MH, Jeon J, Lee S, Lee JH, Gao L, Lee BH, Park JM, Kim YJ, Kwak JM. Proteasome subunit RPT2a promotes PTGS through repressing RNA quality control in Arabidopsis. NATURE PLANTS 2019; 5:1273-1282. [PMID: 31740770 DOI: 10.1038/s41477-019-0546-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/09/2019] [Indexed: 05/12/2023]
Abstract
RNA quality control (RQC) and post-transcriptional gene silencing (PTGS) target and degrade aberrant endogenous RNAs and foreign RNAs, contributing to homeostasis of cellular RNAs. In plants, RQC and PTGS compete for foreign and selected endogenous RNAs; however, little is known about the mechanism interconnecting the two pathways. Using a reporter system designed for monitoring PTGS, we revealed that the 26S proteasome subunit RPT2a enhances transgene PTGS by promoting the accumulation of transgene-derived short interfering RNAs without affecting their biogenesis. RPT2a physically associated with a subset of RQC components and downregulated the protein level. Overexpression of the RQC components interfered with transgene silencing, and impairment of the RQC machinery reinforced transgene PTGS attenuated by rpt2a. Overall, we demonstrate that the 26S proteasome subunit RPT2a promotes PTGS by repressing the RQC machinery to control foreign RNAs.
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Affiliation(s)
- Myung-Hee Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Jieun Jeon
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Seulbee Lee
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Jae Ho Lee
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Byung-Hoon Lee
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Jeong Mee Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yun Ju Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea.
| | - June M Kwak
- Department of New Biology, DGIST, Daegu, Republic of Korea.
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3
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Guedes-Monteiro RF, Franco LV, Moda BS, Tzagoloff A, Barros MH. 5′ processing of Saccharomyces cerevisiae mitochondrial tRNAs requires expression of multiple genes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:806-818. [DOI: 10.1016/j.bbamcr.2019.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/31/2019] [Accepted: 02/03/2019] [Indexed: 01/02/2023]
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Cary GA, Vinh DBN, May P, Kuestner R, Dudley AM. Proteomic Analysis of Dhh1 Complexes Reveals a Role for Hsp40 Chaperone Ydj1 in Yeast P-Body Assembly. G3 (BETHESDA, MD.) 2015; 5:2497-511. [PMID: 26392412 PMCID: PMC4632068 DOI: 10.1534/g3.115.021444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/16/2015] [Indexed: 12/18/2022]
Abstract
P-bodies (PB) are ribonucleoprotein (RNP) complexes that aggregate into cytoplasmic foci when cells are exposed to stress. Although the conserved mRNA decay and translational repression machineries are known components of PB, how and why cells assemble RNP complexes into large foci remain unclear. Using mass spectrometry to analyze proteins immunoisolated with the core PB protein Dhh1, we show that a considerable number of proteins contain low-complexity sequences, similar to proteins highly represented in mammalian RNP granules. We also show that the Hsp40 chaperone Ydj1, which contains an low-complexity domain and controls prion protein aggregation, is required for the formation of Dhh1-GFP foci on glucose depletion. New classes of proteins that reproducibly coenrich with Dhh1-GFP during PB induction include proteins involved in nucleotide or amino acid metabolism, glycolysis, transfer RNA aminoacylation, and protein folding. Many of these proteins have been shown to form foci in response to other stresses. Finally, analysis of RNA associated with Dhh1-GFP shows enrichment of mRNA encoding the PB protein Pat1 and catalytic RNAs along with their associated mitochondrial RNA-binding proteins. Thus, global characterization of PB composition has uncovered proteins important for PB assembly and evidence suggesting an active role for RNA in PB function.
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Affiliation(s)
- Gregory A Cary
- Institute for Systems Biology, Seattle, Washington 98109 Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Dani B N Vinh
- Institute for Systems Biology, Seattle, Washington 98109
| | - Patrick May
- Institute for Systems Biology, Seattle, Washington 98109 Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Esch-sur-Alzette, Luxembourg L-4362
| | - Rolf Kuestner
- Institute for Systems Biology, Seattle, Washington 98109
| | - Aimée M Dudley
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195 Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
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5
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Mota S, Vieira N, Barbosa S, Delaveau T, Torchet C, Le Saux A, Garcia M, Pereira A, Lemoine S, Coulpier F, Darzacq X, Benard L, Casal M, Devaux F, Paiva S. Role of the DHH1 gene in the regulation of monocarboxylic acids transporters expression in Saccharomyces cerevisiae. PLoS One 2014; 9:e111589. [PMID: 25365506 PMCID: PMC4218774 DOI: 10.1371/journal.pone.0111589] [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: 07/21/2014] [Accepted: 09/26/2014] [Indexed: 01/05/2023] Open
Abstract
Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2 (Paiva S, Althoff S, Casal M, Leao C. FEMS Microbiol Lett, 1999, 170:301-306). In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. In these conditions, the stabilized JEN1 mRNA was associated to polysomes but no Jen1 protein could be detected, either by measurable lactate carrier activity, Jen1-GFP fluorescence detection or western blots. These results revealed the complexity of the expression regulation of JEN1 in S. cerevisiae and evidenced the importance of DHH1 in this process. Additionally, microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects.
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Affiliation(s)
- Sandra Mota
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Centre of Health and Environmental Research (CISA), School of Allied Health Sciences, Polytechnic Institute of Porto, Vila Nova de Gaia, Portugal
| | - Neide Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Sónia Barbosa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Thierry Delaveau
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
- CNRS, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
| | - Claire Torchet
- CNRS, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie UPMC, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Paris, France
| | - Agnès Le Saux
- CNRS, FRE3630, Laboratoire de l’Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris, France
| | - Mathilde Garcia
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
- CNRS, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
| | - Ana Pereira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Sophie Lemoine
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
- Inserm, U1024, Paris, France
- CNRS, UMR 8197, Paris, France
| | - Fanny Coulpier
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
- Inserm, U1024, Paris, France
- CNRS, UMR 8197, Paris, France
| | - Xavier Darzacq
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, Paris, France
- Inserm, U1024, Paris, France
- CNRS, UMR 8197, Paris, France
| | - Lionel Benard
- CNRS, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie UPMC, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Paris, France
| | - Margarida Casal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Frédéric Devaux
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
- CNRS, UMR7238, Laboratoire de Biologie computationnelle et quantitative, Paris, France
| | - Sandra Paiva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
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Herbert CJ, Golik P, Bonnefoy N. Yeast PPR proteins, watchdogs of mitochondrial gene expression. RNA Biol 2013; 10:1477-94. [PMID: 24184848 DOI: 10.4161/rna.25392] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
PPR proteins are a family of ubiquitous RNA-binding factors, found in all the Eukaryotic lineages, and are particularly numerous in higher plants. According to recent bioinformatic analyses, yeast genomes encode from 10 (in S. pombe) to 15 (in S. cerevisiae) PPR proteins. All of these proteins are mitochondrial and very often interact with the mitochondrial membrane. Apart from the general factors, RNA polymerase and RNase P, most yeast PPR proteins are involved in the stability and/or translation of mitochondrially encoded RNAs. At present, some information concerning the target RNA(s) of most of these proteins is available, the next challenge will be to refine our understanding of the function of the proteins and to resolve the yeast PPR-RNA-binding code, which might differ significantly from the plant PPR code.
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Affiliation(s)
- Christopher J Herbert
- Centre de Génétique Moléculaire du CNRS; UPR3404; FRC3115; Gif-sur-Yvette; Paris, France
| | - Pawel Golik
- Department of Genetics and Biotechnology; Faculty of Biology; University of Warsaw; Pawinskiego 5A; Warsaw, Poland
| | - Nathalie Bonnefoy
- Centre de Génétique Moléculaire du CNRS; UPR3404; FRC3115; Gif-sur-Yvette; Paris, France
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7
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Weil D, Hollien J. Cytoplasmic organelles on the road to mRNA decay. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:725-31. [PMID: 23337852 DOI: 10.1016/j.bbagrm.2013.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 01/02/2013] [Accepted: 01/03/2013] [Indexed: 11/27/2022]
Abstract
Localization of both mRNAs and mRNA decay factors to internal membranes of eukaryotic cells provides a means of coordinately regulating mRNAs with common functions as well as coupling organelle function to mRNA turnover. The classic mechanism of mRNA localization to membranes is the signal sequence-dependent targeting of mRNAs encoding membrane and secreted proteins to the cytoplasmic surface of the endoplasmic reticulum. More recently, however, mRNAs encoding proteins with cytosolic or nuclear functions have been found associated with various organelles, in many cases through unknown mechanisms. Furthermore, there are several types of RNA granules, many of which are sites of mRNA degradation; these are frequently found associated with membrane-bound organelles such as endosomes and mitochondria. In this review we summarize recent findings that link organelle function and mRNA localization to mRNA decay. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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8
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The discovery and analysis of P Bodies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:23-43. [PMID: 23224963 DOI: 10.1007/978-1-4614-5107-5_3] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Ernoult-Lange M, Bénard M, Kress M, Weil D. P-bodies and mitochondria: which place in RNA interference? Biochimie 2012; 94:1572-7. [PMID: 22445682 DOI: 10.1016/j.biochi.2012.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 03/07/2012] [Indexed: 11/25/2022]
Abstract
Micro-RNAs (miRNAs) are major actors of RNA interference (RNAi), a regulation pathway which leads to translational repression and/or degradation of specific mRNAs. They provide target specificity by incorporating into the RISC complex and guiding its binding to mRNA. Since the discovery of RNAi, many progresses have been made on the mechanism of action of the RISC complex and on the identification of target mRNAs. However, the regulation of RNAi has been poorly investigated so far. Recently, various studies have revealed physical and functional relationships between RNAi, P-bodies and mitochondria. This review intends to recapitulate these data and discuss their potential importance in cell metabolism.
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10
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Huang X, Liu J, Dickson RC. Down-regulating sphingolipid synthesis increases yeast lifespan. PLoS Genet 2012; 8:e1002493. [PMID: 22319457 PMCID: PMC3271065 DOI: 10.1371/journal.pgen.1002493] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/07/2011] [Indexed: 12/14/2022] Open
Abstract
Knowledge of the mechanisms for regulating lifespan is advancing rapidly, but lifespan is a complex phenotype and new features are likely to be identified. Here we reveal a novel approach for regulating lifespan. Using a genetic or a pharmacological strategy to lower the rate of sphingolipid synthesis, we show that Saccharomyces cerevisiae cells live longer. The longer lifespan is due in part to a reduction in Sch9 protein kinase activity and a consequent reduction in chromosomal mutations and rearrangements and increased stress resistance. Longer lifespan also arises in ways that are independent of Sch9 or caloric restriction, and we speculate on ways that sphingolipids might mediate these aspects of increased lifespan. Sch9 and its mammalian homolog S6 kinase work downstream of the target of rapamycin, TOR1, protein kinase, and play evolutionarily conserved roles in regulating lifespan. Our data establish Sch9 as a focal point for regulating lifespan by integrating nutrient signals from TOR1 with growth and stress signals from sphingolipids. Sphingolipids are found in all eukaryotes and our results suggest that pharmacological down-regulation of one or more sphingolipids may provide a means to reduce age-related diseases and increase lifespan in other eukaryotes.
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Affiliation(s)
- Xinhe Huang
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky, United States of America
| | - Jun Liu
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky, United States of America
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Robert C. Dickson
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky, United States of America
- * E-mail:
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11
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Rossmanith W. Of P and Z: mitochondrial tRNA processing enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:1017-26. [PMID: 22137969 PMCID: PMC3790967 DOI: 10.1016/j.bbagrm.2011.11.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/11/2011] [Accepted: 11/15/2011] [Indexed: 12/18/2022]
Abstract
Mitochondrial tRNAs are generally synthesized as part of polycistronic transcripts. Release of tRNAs from these precursors is thus not only required to produce functional adaptors for translation, but also responsible for the maturation of other mitochondrial RNA species. Cleavage of mitochondrial tRNAs appears to be exclusively accomplished by endonucleases. 5'-end maturation in the mitochondria of different Eukarya is achieved by various kinds of RNase P, representing the full range of diversity found in this enzyme family. While ribonucleoprotein enzymes with RNA components of bacterial-like appearance are found in a few unrelated protists, algae, and fungi, highly degenerate RNAs of dramatic size variability are found in the mitochondria of many fungi. The majority of mitochondrial RNase P enzymes, however, appear to be pure protein enzymes. Human mitochondrial RNase P, the first to be identified and possibly the prototype of all animal mitochondrial RNases P, is composed of three proteins. Homologs of its nuclease subunit MRPP3/PRORP, are also found in plants, algae and several protists, where they are apparently responsible for RNase P activity in mitochondria (and beyond) without the help of extra subunits. The diversity of RNase P enzymes is contrasted by the uniformity of mitochondrial RNases Z, which are responsible for 3'-end processing. Only the long form of RNase Z, which is restricted to eukarya, is found in mitochondria, even when an additional short form is present in the same organism. Mitochondrial tRNA processing thus appears dominated by new, eukaryal inventions rather than bacterial heritage. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Austria.
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12
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Lipinski KA, Puchta O, Surendranath V, Kudla M, Golik P. Revisiting the yeast PPR proteins--application of an Iterative Hidden Markov Model algorithm reveals new members of the rapidly evolving family. Mol Biol Evol 2011; 28:2935-48. [PMID: 21546354 DOI: 10.1093/molbev/msr120] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are the largest known RNA-binding protein family, and are found in all eukaryotes, being particularly abundant in higher plants. PPR proteins localize mostly to mitochondria and chloroplasts, and many were shown to modulate organellar genome expression on the posttranscriptional level. Although the genomes of land plants encode hundreds of PPR proteins, only a few have been identified in Fungi and Metazoa. As the current PPR motif profiles are built mainly on the basis of the predominant plant sequences, they are unlikely to be optimal for detecting fungal and animal members of the family, and many putative PPR proteins in these genomes may remain undetected. In order to verify this hypothesis, we designed a hidden Markov model-based bioinformatic tool called Supervised Clustering-based Iterative Phylogenetic Hidden Markov Model algorithm for the Evaluation of tandem Repeat motif families (SCIPHER) using sequence data from orthologous clusters from available yeast genomes. This approach allowed us to assign 12 new proteins in Saccharomyces cerevisiae to the PPR family. Similarly, in other yeast species, we obtained a 5-fold increase in the detection of PPR motifs, compared with the previous tools. All the newly identified S. cerevisiae PPR proteins localize in the mitochondrion and are a part of the RNA processing interaction network. Furthermore, the yeast PPR proteins seem to undergo an accelerated divergent evolution. Analysis of single and double amino acid substitutions in the Dmr1 protein of S. cerevisiae suggests that cooperative interactions between motifs and pseudoreversion could be the force driving this rapid evolution.
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Affiliation(s)
- Kamil A Lipinski
- Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
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13
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Abstract
P-bodies (processing bodies) are cytoplasmic foci visible by light microscopy in somatic cells of vertebrate and invertebrate origin as well as in yeast, plants and trypanosomes. At the molecular level, P-bodies are dynamic aggregates of specific mRNAs and proteins that serve a dual function: first, they harbour mRNAs that are translationally silenced, and such mRNA can exit again from P-bodies to re-engage in translation. Secondly, P-bodies recruit mRNAs that are targeted for deadenylation and degradation by the decapping/Xrn1 pathway. Whereas certain proteins are core constituents of P-bodies, others involved in recognizing short-lived mRNAs can only be trapped in P-bodies when mRNA decay is attenuated. This reflects the very transient interactions by which many proteins associate with P-bodies. In the present review, we summarize recent findings on the function, assembly and motility of P-bodies. An updated list of proteins and RNAs that localize to P-bodies will help in keeping track of this fast-growing field.
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Abstract
Eukaryotic cells contain at least two types of cytoplasmic RNA-protein (RNP) granules that contain nontranslating mRNAs. One such RNP granule is a P-body, which contains translationally inactive mRNAs and proteins involved in mRNA degradation and translation repression. A second such RNP granule is a stress granule which also contains mRNAs, some RNA binding proteins and several translation initiation factors, suggesting these granules contain mRNAs stalled in translation initiation. In this chapter, we describe methods to analyze P-bodies and stress granules in Saccharomyces cerevisiae, including procedures to determine if a protein or mRNA can accumulate in either granule, if an environmental perturbation or mutation affects granule size and number, and granule quantification methods.
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15
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Lipinski KA, Kaniak-Golik A, Golik P. Maintenance and expression of the S. cerevisiae mitochondrial genome--from genetics to evolution and systems biology. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1086-98. [PMID: 20056105 DOI: 10.1016/j.bbabio.2009.12.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 12/18/2009] [Accepted: 12/24/2009] [Indexed: 10/20/2022]
Abstract
As a legacy of their endosymbiotic eubacterial origin, mitochondria possess a residual genome, encoding only a few proteins and dependent on a variety of factors encoded by the nuclear genome for its maintenance and expression. As a facultative anaerobe with well understood genetics and molecular biology, Saccharomyces cerevisiae is the model system of choice for studying nucleo-mitochondrial genetic interactions. Maintenance of the mitochondrial genome is controlled by a set of nuclear-coded factors forming intricately interconnected circuits responsible for replication, recombination, repair and transmission to buds. Expression of the yeast mitochondrial genome is regulated mostly at the post-transcriptional level, and involves many general and gene-specific factors regulating splicing, RNA processing and stability and translation. A very interesting aspect of the yeast mitochondrial system is the relationship between genome maintenance and gene expression. Deletions of genes involved in many different aspects of mitochondrial gene expression, notably translation, result in an irreversible loss of functional mtDNA. The mitochondrial genetic system viewed from the systems biology perspective is therefore very fragile and lacks robustness compared to the remaining systems of the cell. This lack of robustness could be a legacy of the reductive evolution of the mitochondrial genome, but explanations involving selective advantages of increased evolvability have also been postulated.
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Affiliation(s)
- Kamil A Lipinski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
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16
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Abstract
The "RNA World" hypothesis suggests that life developed from RNA enzymes termed ribozymes, which carry out reactions without assistance from proteins. Ribonuclease (RNase) P is one ribozyme that appears to have adapted these origins to modern cellular life by adding protein to the RNA core in order to broaden the potential functions. This RNA-protein complex plays diverse roles in processing RNA, but its best-understood reaction is pre-tRNA maturation, resulting in mature 5' ends of tRNAs. The core catalytic activity resides in the RNA subunit of almost all RNase P enzymes but broader substrate tolerance is required for recognizing not only the diverse sequences of tRNAs, but also additional cellular RNA substrates. This broader substrate tolerance is provided by the addition of protein to the RNA core and allows RNase P to selectively recognize different RNAs, and possibly ribonucleoprotein (RNP) substrates. Thus, increased protein content correlated with evolution from bacteria to eukaryotes has further enhanced substrate potential enabling the enzyme to function in a complex cellular environment.
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Affiliation(s)
- Michael C. Marvin
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, Michigan 48109-0606
| | - David R. Engelke
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, Michigan 48109-0606
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