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Frangedakis E, Guzman-Chavez F, Rebmann M, Markel K, Yu Y, Perraki A, Tse SW, Liu Y, Rever J, Sauret-Gueto S, Goffinet B, Schneider H, Haseloff J. Construction of DNA Tools for Hyperexpression in Marchantia Chloroplasts. ACS Synth Biol 2021; 10:1651-1666. [PMID: 34097383 PMCID: PMC8296666 DOI: 10.1021/acssynbio.0c00637] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chloroplasts are attractive platforms for synthetic biology applications since they are capable of driving very high levels of transgene expression, if mRNA production and stability are properly regulated. However, plastid transformation is a slow process and currently limited to a few plant species. The liverwort Marchantia polymorpha is a simple model plant that allows rapid transformation studies; however, its potential for protein hyperexpression has not been fully exploited. This is partially due to the fact that chloroplast post-transcriptional regulation is poorly characterized in this plant. We have mapped patterns of transcription in Marchantia chloroplasts. Furthermore, we have obtained and compared sequences from 51 bryophyte species and identified putative sites for pentatricopeptide repeat protein binding that are thought to play important roles in mRNA stabilization. Candidate binding sites were tested for their ability to confer high levels of reporter gene expression in Marchantia chloroplasts, and levels of protein production and effects on growth were measured in homoplastic transformed plants. We have produced novel DNA tools for protein hyperexpression in this facile plant system that is a test-bed for chloroplast engineering.
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Affiliation(s)
- Eftychios Frangedakis
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Fernando Guzman-Chavez
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Marius Rebmann
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Kasey Markel
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Ying Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Artemis Perraki
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Sze Wai Tse
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Yang Liu
- Fairy Lake Botanical Garden & Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Jenna Rever
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Susanna Sauret-Gueto
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269-3043, United States
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
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Castandet B, Germain A, Hotto AM, Stern DB. Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. Nucleic Acids Res 2020; 47:11889-11905. [PMID: 31732725 PMCID: PMC7145512 DOI: 10.1093/nar/gkz1059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/02/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5′ ends corresponding to transcription start sites (TSS), as well as 1628 processed 5′ ends and 1299 3′ ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5′ and 3′ ends, contrasting with the prevailing description of discrete 5′ termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-seq was also implemented for pnp1–1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2000 termini were altered in pnp1–1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.
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Affiliation(s)
- Benoît Castandet
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,Institut des Sciences des Plantes de Paris Saclay (IPS2), UEVE, INRA, CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91192 Gif sur Yvette, France.,Université de Paris, IPS2, F-91192 Gif sur Yvette, France
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Zhang Y, An D, Li C, Zhao Z, Wang W. The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the chloroplast evolution and transcription regulation. BMC Genomics 2020; 21:76. [PMID: 31992185 PMCID: PMC6986005 DOI: 10.1186/s12864-020-6499-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
Background Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. The chloroplast genome sequencing has become routine and less expensive with the delivery of high-throughput sequencing technologies, allowing us to deeply investigate genomics and transcriptomics of duckweed organelles. Results Here, the complete chloroplast genome of Spirodela polyrhiza 7498 (SpV2) is assembled by PacBio sequencing. The length of 168,956 bp circular genome is composed of a pair of inverted repeats of 31,844 bp, a large single copy of 91,210 bp and a small single copy of 14,058 bp. Compared to the previous version (SpV1) assembled from short reads, the integrity and quality of SpV2 are improved, especially with the retrieval of two repeated fragments in ycf2 gene. There are a number of 107 unique genes, including 78 protein-coding genes, 25 tRNA genes and 4 rRNA genes. With the evidence of full-length cDNAs generated from PacBio isoform sequencing, seven genes (ycf3, clpP, atpF, rpoC1, rpl2, rps12 and ndhA) are detected to contain type-II introns. The ndhA intron has 50% more sequence divergence than the species-barcoding marker of atpF-atpH, showing the potential power to discriminate close species. A number of 37 RNA editing sites are recognized to have cytosine (C) to uracil (U) substitutions, eight of which are newly defined including six from the intergenic regions and two from the coding sequences of rpoC2 and ndhA genes. In addition, nine operon classes are identified using transcriptomic data. It is found that the operons contain multiple subunit genes encoding the same functional complexes comprising of ATP synthase, photosynthesis system, ribosomal proteins, et.al., which could be simultaneously transcribed and coordinately translated in response to the cell stimuli. Conclusions The understanding of the chloroplast genomics and the transcriptomics of S.polyrhiza would greatly facilitate the study of phylogenetic evolution and the application of genetically engineering duckweeds.
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Affiliation(s)
- Yating Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong An
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Changsheng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhixuan Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenqin Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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Zhang L, Zhou W, Che L, Rochaix JD, Lu C, Li W, Peng L. PPR Protein BFA2 Is Essential for the Accumulation of the atpH/F Transcript in Chloroplasts. FRONTIERS IN PLANT SCIENCE 2019; 10:446. [PMID: 31031784 PMCID: PMC6474325 DOI: 10.3389/fpls.2019.00446] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 03/25/2019] [Indexed: 05/04/2023]
Abstract
As a fascinating and complicated nanomotor, chloroplast ATP synthase comprises nine subunits encoded by both the nuclear and plastid genomes. Because of its uneven subunit stoichiometry, biogenesis of ATP synthase and expression of plastid-encoded ATP synthase genes requires assistance by nucleus-encoded factors involved in transcriptional, post-transcriptional, and translational steps. In this study, we report a P-class pentatricopeptide repeat (PPR) protein BFA2 (Biogenesis Factor required for ATP synthase 2) that is essential for accumulation of the dicistronic atpH/F transcript in Arabidopsis chloroplasts. A loss-of-function mutation in BFA2 results in a specific reduction of more than 3/4 of chloroplast ATP synthase, which is likely due to the absence of dicistronic atpH/F transcript. BFA2 protein contains 22 putative PPR motifs and exclusively localizes in the chloroplast. Bioinformatics and Electrophoretic Mobility Shift Assays (EMSA) analysis showed that BFA2 binds to the consensus sequence of the atpF-atpA intergenic region in a sequence-specific manner. However, translation initiation of the atpA was not affected in the bfa2 mutant. Thus, we propose that the chloroplast PPR protein BFA2 mainly acts as barrier to prevent the atpH/F transcript degradation by exoribonucleases by binding to the consensus sequence of the atpF-atpA intergenic region.
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Affiliation(s)
- Lin Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wen Zhou
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Liping Che
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Wenjing Li
- College of Life Sciences, Langfang Normal University, Langfang, China
- *Correspondence: Wenjing Li, Lianwei Peng,
| | - Lianwei Peng
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
- *Correspondence: Wenjing Li, Lianwei Peng,
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Zhang L, Pu H, Duan Z, Li Y, Liu B, Zhang Q, Li W, Rochaix JD, Liu L, Peng L. Nucleus-Encoded Protein BFA1 Promotes Efficient Assembly of the Chloroplast ATP Synthase Coupling Factor 1. THE PLANT CELL 2018; 30:1770-1788. [PMID: 30012777 PMCID: PMC6139693 DOI: 10.1105/tpc.18.00075] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/19/2018] [Accepted: 07/16/2018] [Indexed: 05/04/2023]
Abstract
F-type ATP synthases produce nearly all of the ATP found in cells. The catalytic module F1 commonly comprises an α3β3 hexamer surrounding a γ/ε stalk. However, it is unclear how these subunits assemble to form a catalytic motor. In this work, we identified and characterized a chloroplast protein that interacts with the CF1β, γ, and ε subunits of the chloroplast ATP synthase and is required for assembly of its F1 module. We named this protein BIOGENESIS FACTOR REQUIRED FOR ATP SYNTHASE1 (BFA1) and determined its crystal structure at 2.8-Å resolution. BFA1 is comprised primarily of two interacting β-barrels that are oriented nearly perpendicularly to each other. The contact region between BFA1 and the CF1β and γ subunits was further mapped by yeast two-hybrid assays. An in silico molecular docking analysis was performed and revealed close fitting contact sites without steric conflicts between BFA1 and CF1β/γ. We propose that BFA1 acts mainly as a scaffold protein promoting the association of a CF1α/β heterodimer with CF1γ. The subsequent assembly of other CF1α/β heterodimers may shift the position of the CF1γ subunit to complete assembly of the CF1 module. This CF1 assembly process is likely to be valid for other F-type ATP synthases, as their structures are highly conserved.
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Affiliation(s)
- Lin Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Hua Pu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhikun Duan
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yonghong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Bei Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qiqi Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wenjing Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Lin Liu
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Lianwei Peng
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
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Mapping Plastid Transcript Population by Circular Reverse Transcription Polymerase Chain Reaction. Methods Mol Biol 2018. [PMID: 29987728 DOI: 10.1007/978-1-4939-8654-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
During evolution of photosynthetic organisms, the genetic information provided by the internalized cyanobacteria has been transferred to the nucleus. The small genome kept by the chloroplast, the so-called plastome, displays a complex organization, comprising operons under the control of multiples promoters. In addition, polycistronic transcripts undergo multiple processing events, thus generating a complex population of mRNAs from a single gene. This chapter describes a method to investigate the diversity of the mRNA population from a single gene by circular RT-PCR. The protocol provided here allows for the simultaneous mapping of both 5' and 3' ends of the same RNA molecule.
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Karahan G, Sayar N, Gozum G, Bozkurt B, Konu O, Yulug IG. Relative expression of rRNA transcripts and 45S rDNA promoter methylation status are dysregulated in tumors in comparison with matched-normal tissues in breast cancer. Oncol Rep 2015; 33:3131-45. [PMID: 25962577 DOI: 10.3892/or.2015.3940] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/14/2015] [Indexed: 11/06/2022] Open
Abstract
Ribosomal RNA (rRNA) expression, one of the most important factors regulating ribosome production, is primarily controlled by a CG-rich 45 S rDNA promoter. However, the DNA methylation state of the 45 S rDNA promoter, as well as its effect on rRNA gene expression in types of human cancers is controversial. In the present study we analyzed the methylation status of the rDNA promoter (-380 to +53 bp) as well as associated rRNA expression levels in breast cancer cell lines and breast tumor-normal tissue pairs. We found that the aforementioned regulatory region was extensively methylated (74-96%) in all cell lines and in 68% (13/19 tumor-normal pairs) of the tumors. Expression levels of rRNA transcripts 18 S, 28 S, 5.8 S and 45 S external transcribed spacer (45 S ETS) greatly varied in the breast cancer cell lines regardless of their methylation status. Analyses of rRNA transcript expression levels in the breast tumor and normal matched tissues showed no significant difference when normalized with TBP. On the other hand, using the geometric mean of the rRNA expression values (GM-rRNA) as reference enabled us to identify significant changes in the relative expression of rRNAs in the tissue samples. We propose GM-rRNA normalization as a novel strategy to analyze expression differences between rRNA transcripts. Accordingly, the 18S rRNA/GM-rRNA ratio was significantly higher whereas the 5.8S rRNA/GM-rRNA ratio was significantly lower in breast tumor samples than this ratio in the matched normal samples. Moreover, the 18S rRNA/GM-rRNA ratio was negatively correlated with the 45 S rDNA promoter methylation level in the normal breast tissue samples, yet not in the breast tumors. Significant correlations observed between the expression levels of rRNA transcripts in the normal samples were lost in the tumor samples. We showed that the expression of rRNA transcripts may not be based solely on promoter methylation. Carcinogenesis may cause dysregulation of the correlation between spliced rRNA expression levels, possibly due to changes in rRNA processing, which requires further investigation.
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Affiliation(s)
- Gurbet Karahan
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Nilufer Sayar
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Gokcen Gozum
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Betul Bozkurt
- Department of General Surgery, Ankara Numune Research and Teaching Hospital, TR-06100 Ankara, Turkey
| | - Ozlen Konu
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Isik G Yulug
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
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Emerging functions of mammalian and plant mTERFs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:786-97. [PMID: 25582570 DOI: 10.1016/j.bbabio.2014.12.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/21/2014] [Indexed: 11/24/2022]
Abstract
Organellar gene expression (OGE) is crucial for plant development, respiration and photosynthesis, but the mechanisms that control it are still largely unclear. Thus, OGE requires various nucleus-encoded proteins that promote transcription, splicing, trimming and editing of organellar RNAs, and regulate their translation. In mammals, members of the mitochondrial transcription termination factor (mTERF) family play important roles in OGE. Intriguingly, three of the four mammalian mTERFs do not actually terminate transcription, as their designation suggests, but appear to function in antisense transcription termination and ribosome biogenesis. During the evolution of land plants, the mTERF family has expanded to approximately 30 members, but knowledge of their function in photosynthetic organisms remains sparse. Here, we review recent advances in the characterization of mterf mutants in mammals and photosynthetic organisms, focusing particularly on the progress made in elucidating their molecular functions in the last two years. This article is part of a Special Issue entitled: Chloroplast biogenesis.
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Lefebvre-Legendre L, Merendino L, Rivier C, Goldschmidt-Clermont M. On the Complexity of Chloroplast RNA Metabolism: psaA Trans-splicing Can be Bypassed in Chlamydomonas. Mol Biol Evol 2014; 31:2697-707. [DOI: 10.1093/molbev/msu215] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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