151
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Martin LBB, Fei Z, Giovannoni JJ, Rose JKC. Catalyzing plant science research with RNA-seq. FRONTIERS IN PLANT SCIENCE 2013; 4:66. [PMID: 23554602 PMCID: PMC3612697 DOI: 10.3389/fpls.2013.00066] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 03/10/2013] [Indexed: 05/18/2023]
Abstract
Next generation DNA sequencing technologies are driving increasingly rapid, affordable and high resolution analyses of plant transcriptomes through sequencing of their associated cDNA (complementary DNA) populations; an analytical platform commonly referred to as RNA-sequencing (RNA-seq). Since entering the arena of whole genome profiling technologies only a few years ago, RNA-seq has proven itself to be a powerful tool with a remarkably diverse range of applications, from detailed studies of biological processes at the cell type-specific level, to providing insights into fundamental questions in plant biology on an evolutionary time scale. Applications include generating genomic data for heretofore unsequenced species, thus expanding the boundaries of what had been considered "model organisms," elucidating structural and regulatory gene networks, revealing how plants respond to developmental cues and their environment, allowing a better understanding of the relationships between genes and their products, and uniting the "omics" fields of transcriptomics, proteomics, and metabolomics into a now common systems biology paradigm. We provide an overview of the breadth of such studies and summarize the range of RNA-seq protocols that have been developed to address questions spanning cell type-specific-based transcriptomics, transcript secondary structure and gene mapping.
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Affiliation(s)
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant ResearchIthaca, NY, USA
- Robert W. Holly Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research ServiceIthaca, NY, USA
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant ResearchIthaca, NY, USA
- Robert W. Holly Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research ServiceIthaca, NY, USA
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152
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Germain A, Hotto AM, Barkan A, Stern DB. RNA processing and decay in plastids. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:295-316. [PMID: 23536311 DOI: 10.1002/wrna.1161] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Plastids were derived through endosymbiosis from a cyanobacterial ancestor, whose uptake was followed by massive gene transfer to the nucleus, resulting in the compact size and modest coding capacity of the extant plastid genome. Plastid gene expression is essential for plant development, but depends on nucleus-encoded proteins recruited from cyanobacterial or host-cell origins. The plastid genome is heavily transcribed from numerous promoters, giving posttranscriptional events a critical role in determining the quantity and sizes of accumulating RNA species. The major events reviewed here are RNA editing, which restores protein conservation or creates correct open reading frames by converting C residues to U, RNA splicing, which occurs both in cis and trans, and RNA cleavage, which relies on a variety of exoribonucleases and endoribonucleases. Because the RNases have little sequence specificity, they are collectively able to remove extraneous RNAs whose ends are not protected by RNA secondary structures or sequence-specific RNA-binding proteins (RBPs). Other plastid RBPs, largely members of the helical-repeat superfamily, confer specificity to editing and splicing reactions. The enzymes that catalyze RNA processing are also the main actors in RNA decay, implying that these antagonistic roles are optimally balanced. We place the actions of RBPs and RNases in the context of a recent proteomic analysis that identifies components of the plastid nucleoid, a protein-DNA complex with multiple roles in gene expression. These results suggest that sublocalization and/or concentration gradients of plastid proteins could underpin the regulation of RNA maturation and degradation.
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153
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Shi C, Liu Y, Huang H, Xia EH, Zhang HB, Gao LZ. Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms. PLoS One 2013; 8:e59620. [PMID: 23527231 PMCID: PMC3601113 DOI: 10.1371/journal.pone.0059620] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/15/2013] [Indexed: 11/19/2022] Open
Abstract
Plant chloroplast genes are usually co-transcribed while its posttranscriptional splicing is fairly complex and remains largely unsolved. On basis of sequencing the three complete Camellia (Theaceae) chloroplast genomes for the first time, we comprehensively analyzed the evolutionary patterns of ycf15, a plastid gene quite paradoxical in terms of its function and evolution, along the inferred angiosperm phylogeny. Although many species in separate lineages including the three species reported here contained an intact ycf15 gene in their chloroplast genomes, the phylogenetic mixture of both intact and obviously disabled ycf15 genes imply that they are all non-functional. Both intracellular gene transfer (IGT) and horizontal gene transfer (HGT) failed to explain such distributional anomalies. While, transcriptome analyses revealed that ycf15 was transcribed as precursor polycistronic transcript which contained ycf2, ycf15 and antisense trnL-CAA. The transcriptome assembly was surprisingly found to cover near the complete Camellia chloroplast genome. Many non-coding regions including pseudogenes were mapped by multiple transcripts, indicating the generality of pseudogene transcriptions. Our results suggest that plastid DNA posttranscriptional splicing may involve complex cleavage of non-functional genes.
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Affiliation(s)
- Chao Shi
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yuan Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Hai-Bin Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, China
- * E-mail:
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154
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Xie Z. PROG BIOCHEM BIOPHYS 2013; 39:1174-1177. [DOI: 10.3724/sp.j.1206.2012.00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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155
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Hotto AM, Germain A, Stern DB. Plastid non-coding RNAs: emerging candidates for gene regulation. TRENDS IN PLANT SCIENCE 2012; 17:737-44. [PMID: 22981395 DOI: 10.1016/j.tplants.2012.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/27/2012] [Accepted: 08/05/2012] [Indexed: 05/08/2023]
Abstract
Recent advances in transcriptomics and bioinformatics, specifically strand-specific RNA sequencing, have allowed high-throughput, comprehensive detection of low-abundance transcripts typical of the non-coding RNAs studied in bacteria and eukaryotes. Before this, few plastid non-coding RNAs (pncRNAs) had been identified, and even fewer had been investigated for any functional role in gene regulation. Relaxed plastid transcription initiation and termination result in full transcription of both chloroplast DNA strands. Following this, post-transcriptional processing produces a pool of metastable RNA species, including distinct pncRNAs. Here we review pncRNA biogenesis and possible functionality, and speculate that this RNA class may have an underappreciated role in plastid gene regulation.
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Affiliation(s)
- Amber M Hotto
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
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156
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Udy DB, Belcher S, Williams-Carrier R, Gualberto JM, Barkan A. Effects of reduced chloroplast gene copy number on chloroplast gene expression in maize. PLANT PHYSIOLOGY 2012; 160:1420-31. [PMID: 22977281 PMCID: PMC3490597 DOI: 10.1104/pp.112.204198] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/12/2012] [Indexed: 05/18/2023]
Abstract
Chloroplasts and other members of the plastid organelle family contain a small genome of bacterial ancestry. Young chloroplasts contain hundreds of genome copies, but the functional significance of this high genome copy number has been unclear. We describe molecular phenotypes associated with mutations in a nuclear gene in maize (Zea mays), white2 (w2), encoding a predicted organellar DNA polymerase. Weak and strong mutant alleles cause a moderate (approximately 5-fold) and severe (approximately 100-fold) decrease in plastid DNA copy number, respectively, as assayed by quantitative PCR and Southern-blot hybridization of leaf DNA. Both alleles condition a decrease in most chloroplast RNAs, with the magnitude of the RNA deficiencies roughly paralleling that of the DNA deficiency. However, some RNAs are more sensitive to a decrease in genome copy number than others. The rpoB messenger RNA (mRNA) exhibited a unique response, accumulating to dramatically elevated levels in response to a moderate reduction in plastid DNA. Subunits of photosynthetic enzyme complexes were reduced more severely than were plastid mRNAs, possibly because of impaired translation resulting from limiting ribosomal RNA, transfer RNA, and ribosomal protein mRNA. These results indicate that chloroplast genome copy number is a limiting factor for the expression of a subset of chloroplast genes in maize. Whereas in Arabidopsis (Arabidopsis thaliana) a pair of orthologous genes function redundantly to catalyze DNA replication in both mitochondria and chloroplasts, the w2 gene is responsible for virtually all chloroplast DNA replication in maize. Mitochondrial DNA copy number was reduced approximately 2-fold in mutants harboring strong w2 alleles, suggesting that w2 also contributes to mitochondrial DNA replication.
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157
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Sosso D, Canut M, Gendrot G, Dedieu A, Chambrier P, Barkan A, Consonni G, M. Rogowsky P. PPR8522 encodes a chloroplast-targeted pentatricopeptide repeat protein necessary for maize embryogenesis and vegetative development. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5843-57. [PMID: 22945943 PMCID: PMC3467297 DOI: 10.1093/jxb/ers232] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The pentatricopeptide repeat (PPR) domain is an RNA binding domain allowing members of the PPR superfamily to participate in post-transcriptional processing of organellar RNA. Loss of PPR8522 from maize (Zea mays) confers an embryo-specific (emb) phenotype. The emb8522 mutation was isolated in an active Mutator (Mu) population and co-segregation analysis revealed that it was tightly linked to a MuDR insertion in the first exon of PPR8522. Independent evidence that disruption of PPR8522 caused the emb phenotype was provided by fine mapping to a region of 116kb containing no other gene than PPR8522 and complementation of the emb8522 mutant by a PPR8522 cDNA. The deduced PPR8522 amino acid sequence of 832 amino acids contains 10 PPR repeats and a chloroplast target peptide, the function of which was experimentally demonstrated by transient expression in Nicotiana benthamiana. Whereas mutant endosperm is apparently normal, mutant embryos deviate from normal development as early as 3 days after pollination, are reduced in size, exhibit more or less severe morphological aberrations depending on the genetic background, and generally do not germinate. The emb8522 mutation is the first to associate the loss of a PPR gene with an embryo-lethal phenotype in maize. Analyses of mutant plantlets generated by embryo-rescue experiments indicate that emb8522 also affects vegetative plant growth and chloroplast development. The loss of chloroplast transcription dependent on plastid-encoded RNA polymerase is the likely cause for the lack of an organized thylakoid network and an albino, seedling-lethal phenotype.
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Affiliation(s)
- Davide Sosso
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
- Dipartimento di Produzione Vegetale, Università degli Studi di
Milano,20133 Milan,Italy
| | - Matthieu Canut
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
| | - Ghislaine Gendrot
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
| | - Annick Dedieu
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
| | - Pierre Chambrier
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, EugeneOR 97403,USA
| | - Gabriella Consonni
- Dipartimento di Produzione Vegetale, Università degli Studi di
Milano,20133 Milan,Italy
| | - Peter M. Rogowsky
- Université de Lyon, Ecole Normale Supérieure de Lyon,
Université Lyon 1, Unité Reproduction et Développement des
Plantes,F-69364 Lyon,France
- INRA, UMR879 Reproduction et Développement des Plantes,F-69364 Lyon,France
- CNRS, UMR5667 Reproduction et Développement des Plantes,F-69364 Lyon,France
- To whom correspondence should be addressed: E-mail:
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158
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Sakurai I, Stazic D, Eisenhut M, Vuorio E, Steglich C, Hess WR, Aro EM. Positive regulation of psbA gene expression by cis-encoded antisense RNAs in Synechocystis sp. PCC 6803. PLANT PHYSIOLOGY 2012; 160:1000-10. [PMID: 22858634 PMCID: PMC3461525 DOI: 10.1104/pp.112.202127] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The D1 protein of photosystem II in the thylakoid membrane of photosynthetic organisms is encoded by psbA genes, which in cyanobacteria occur in the form of a small gene family. Light-dependent up-regulation of psbA gene expression is crucial to ensure the proper replacement of the D1 protein. To gain a high level of gene expression, psbA transcription can be enhanced by several orders of magnitude. Recent transcriptome analyses demonstrated a high number of cis-encoded antisense RNAs (asRNAs) in bacteria, but very little is known about their possible functions. Here, we show the presence of two cis-encoded asRNAs (PsbA2R and PsbA3R) of psbA2 and psbA3 from Synechocystis sp. PCC 6803. These asRNAs are located in the 5' untranslated region of psbA2 and psbA3 genes. Their expression becomes up-regulated by light and down-regulated by darkness, similar to their target mRNAs. In the PsbA2R-suppressing strain [PsbA2R(-)], the amount of psbA2 mRNA was only about 50% compared with the control strain. Likewise, we identified a 15% lowered activity of photosystem II and a reduced amount of the D1 protein in PsbA2R(-) compared with the control strain. The function of PsbA2R in the stabilization of psbA2 mRNA was shown from in vitro RNase E assay when the AU box and the ribosome-binding site in the 5' untranslated region of psbA2 mRNA were both covered by PsbA2R. These results add another layer of complexity to the mechanisms that contribute to psbA gene expression and show PsbA2R as a positively acting factor to achieve a maximum level of D1 synthesis.
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159
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Wang Y, Ding J, Daniell H, Hu H, Li X. Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins. PLANT MOLECULAR BIOLOGY 2012; 80:177-87. [PMID: 22733202 DOI: 10.1007/s11103-012-9938-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/15/2012] [Indexed: 06/01/2023]
Abstract
Chloroplasts play critical roles in land plant cells. Despite their importance and the availability of at least 200 sequenced chloroplast genomes, the number of known DNA regulatory sequences in chloroplast genomes are limited. In this paper, we designed computational methods to systematically study putative DNA regulatory sequences in intergenic regions near chloroplast genes in seven plant species and in promoter sequences of nuclear genes in Arabidopsis and rice. We found that -35/-10 elements alone cannot explain the transcriptional regulation of chloroplast genes. We also concluded that there are unlikely motifs shared by intergenic sequences of most of chloroplast genes, indicating that these genes are regulated differently. Finally and surprisingly, we found five conserved motifs, each of which occurs in no more than six chloroplast intergenic sequences, are significantly shared by promoters of nuclear-genes encoding chloroplast proteins. By integrating information from gene function annotation, protein subcellular localization analyses, protein-protein interaction data, and gene expression data, we further showed support of the functionality of these conserved motifs. Our study implies the existence of unknown nuclear-encoded transcription factors that regulate both chloroplast genes and nuclear genes encoding chloroplast protein, which sheds light on the understanding of the transcriptional regulation of chloroplast genes.
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Affiliation(s)
- Ying Wang
- Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA
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160
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Eisenhut M, Georg J, Klähn S, Sakurai I, Mustila H, Zhang P, Hess WR, Aro EM. The antisense RNA As1_flv4 in the Cyanobacterium Synechocystis sp. PCC 6803 prevents premature expression of the flv4-2 operon upon shift in inorganic carbon supply. J Biol Chem 2012; 287:33153-62. [PMID: 22854963 PMCID: PMC3460422 DOI: 10.1074/jbc.m112.391755] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The functional relevance of natural cis-antisense transcripts is mostly unknown. Here we have characterized the association of three antisense RNAs and one intergenically encoded noncoding RNA with an operon that plays a crucial role in photoprotection of photosystem II under low carbon conditions in the cyanobacterium Synechocystis sp. PCC 6803. Cyanobacteria show strong gene expression dynamics in response to a shift of cells from high carbon to low levels of inorganic carbon (Ci), but the regulatory mechanisms are poorly understood. Among the most up-regulated genes in Synechocystis are flv4, sll0218, and flv2, which are organized in the flv4-2 operon. The flavodiiron proteins encoded by this operon open up an alternative electron transfer route, likely starting from the QB site in photosystem II, under photooxidative stress conditions. Our expression analysis of cells shifted from high carbon to low carbon demonstrated an inversely correlated transcript accumulation of the flv4-2 operon mRNA and one antisense RNA to flv4, designated as As1_flv4. Overexpression of As1_flv4 led to a decrease in flv4-2 mRNA. The promoter activity of as1_flv4 was transiently stimulated by Ci limitation and negatively regulated by the AbrB-like transcription regulator Sll0822, whereas the flv4-2 operon was positively regulated by the transcription factor NdhR. The results indicate that the tightly regulated antisense RNA As1_flv4 establishes a transient threshold for flv4-2 expression in the early phase after a change in Ci conditions. Thus, it prevents unfavorable synthesis of the proteins from the flv4-2 operon.
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Affiliation(s)
- Marion Eisenhut
- Department of Biochemistry and Food Science, Plant Physiology and Molecular Biology, University of Turku, Turku FI-20014, Finland
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161
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Malik Ghulam M, Zghidi-Abouzid O, Lambert E, Lerbs-Mache S, Merendino L. Transcriptional organization of the large and the small ATP synthase operons, atpI/H/F/A and atpB/E, in Arabidopsis thaliana chloroplasts. PLANT MOLECULAR BIOLOGY 2012; 79:259-72. [PMID: 22527751 DOI: 10.1007/s11103-012-9910-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 03/30/2012] [Indexed: 05/04/2023]
Abstract
The ATP synthase is a ubiquitous enzyme which is found in bacteria and eukaryotic organelles. It is essential in the photosynthetic and respiratory processes, by transforming the electrochemical proton gradient into ATP energy via proton transport across the membranes. In Escherichia coli, the atp genes coding for the subunits of the ATP synthase enzyme are grouped in the same transcriptional unit, while in higher plants the plastid atp genes are organized into a large (atpI/H/F/A) and a small (atpB/E) atp operon. By using the model plant Arabidopsis thaliana, we have investigated the strategy evolved in chloroplasts to overcome the physical separation of the atp gene clusters and to coordinate their transcription. We show that all the identified promoters in the two atp operons are PEP dependent and require sigma factors for specific recognition. Our results indicate that transcription of the two atp operons is initiated by at least one common factor, the essential SIG2 factor. Our data show that SIG3 and SIG6 also participate in transcription initiation of the large and the small atp operon, respectively. We propose that SIG2 might be the factor responsible for coordinating the basal transcription of the plastid atp genes and that SIG3 and SIG6 might serve to modulate plastid atp expression with respect to physiological and environmental conditions. However, we observe that in the sigma mutants (sig2, sig3 and sig6) the deficiency in the recognition of specific atp promoters is largely balanced by mRNA stabilization and/or by activation of otherwise silent promoters, indicating that the rate-limiting step for expression of the atp operons is mostly post-transcriptional.
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Affiliation(s)
- Mustafa Malik Ghulam
- CEA, IRTSV, Laboratoire Physiologie Cellulaire et Végétale, 38054 Grenoble, France
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162
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RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proc Natl Acad Sci U S A 2012; 109:E1453-61. [PMID: 22566615 DOI: 10.1073/pnas.1121465109] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Transcripts of plant organelle genes are modified by cytidine-to-uridine (C-to-U) RNA editing, often changing the encoded amino acid predicted from the DNA sequence. Members of the PLS subclass of the pentatricopeptide repeat (PPR) motif-containing family are site-specific recognition factors for either chloroplast or mitochondrial C targets of editing. However, other than PPR proteins and the cis-elements on the organelle transcripts, no other components of the editing machinery in either organelle have previously been identified. The Arabidopsis chloroplast PPR protein Required for AccD RNA Editing 1 (RARE1) specifies editing of a C in the accD transcript. RARE1 was detected in a complex of >200 kDa. We immunoprecipitated epitope-tagged RARE1, and tandem MS/MS analysis identified a protein of unknown function lacking PPR motifs; we named it RNA-editing factor interacting protein 1 (RIP1). Yeast two-hybrid analysis confirmed RIP1 interaction with RARE1, and RIP1-GFP fusions were found in both chloroplasts and mitochondria. Editing assays for all 34 known Arabidopsis chloroplast targets in a rip1 mutant revealed altered efficiency of 14 editing events. In mitochondria, 266 editing events were found to have reduced efficiency, with major loss of editing at 108 C targets. Virus-induced gene silencing of RIP1 confirmed the altered editing efficiency. Transient introduction of a WT RIP1 allele into rip1 improved the defective RNA editing. The presence of RIP1 in a protein complex along with chloroplast editing factor RARE1 indicates that RIP1 is an important component of the RNA editing apparatus that acts on many chloroplast and mitochondrial C targets.
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163
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Eckardt NA. Mapping the barley chloroplast transcriptome. THE PLANT CELL 2012; 24:3. [PMID: 22286135 PMCID: PMC3289563 DOI: 10.1105/tpc.112.240112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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164
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Zubo YO, Kusnetsov VV, Börner T, Liere K. Reverse protection assay: a tool to analyze transcriptional rates from individual promoters. PLANT METHODS 2011; 7:47. [PMID: 22185205 PMCID: PMC3259058 DOI: 10.1186/1746-4811-7-47] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 12/20/2011] [Indexed: 05/08/2023]
Abstract
Transcriptional activity of entire genes in chloroplasts is usually assayed by run-on analyses. To determine not only the overall intensity of transcription of a gene, but also the rate of transcription from a particular promoter, we created the Reverse RNase Protection Assay (RePro): in-organello run-on transcription coupled to RNase protection to define distinct transcript ends during transcription. We demonstrate successful application of RePro in plastid promoter analysis and transcript 3' end processing.
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Affiliation(s)
- Yan O Zubo
- Institut für Biologie (Genetik), Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
- Timiriazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, Moscow, 127276 Russia
- Department of Biological Sciences, Dartmouth College, Hanover NH 03755, USA
| | - Victor V Kusnetsov
- Timiriazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, Moscow, 127276 Russia
| | - Thomas Börner
- Institut für Biologie (Genetik), Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
| | - Karsten Liere
- Institut für Biologie (Genetik), Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
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