1
|
Muino JM, Ruwe H, Qu Y, Maschmann S, Chen W, Zoschke R, Ohler U, Kaufmann K, Schmitz-Linneweber C. MatK impacts differential chloroplast translation by limiting spliced tRNA-K(UUU) abundance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39074058 DOI: 10.1111/tpj.16945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/10/2024] [Accepted: 07/13/2024] [Indexed: 07/31/2024]
Abstract
The protein levels of chloroplast photosynthetic genes and genes related to the chloroplast genetic apparatus vary to adapt to different conditions. However, the underlying mechanisms governing these variations remain unclear. The chloroplast intron Maturase K is encoded within the trnK intron and has been suggested to be required for splicing several group IIA introns, including the trnK intron. In this study, we used RNA immunoprecipitation followed by high-throughput sequencing (RIP-Seq) to identify MatK's preference for binding to group IIA intron domains I and VI within target transcripts. Importantly, these domains are crucial for splice site selection, and we discovered alternative 5'-splice sites in three MatK target introns. The resulting alternative trnK lariat structure showed increased accumulation during heat acclimation. The cognate codon of tRNA-K(UUU) is highly enriched in mRNAs encoding ribosomal proteins and a trnK-matK over-expressor exhibited elevated levels of the spliced tRNA-K(UUU). Ribosome profiling analysis of the overexpressor revealed a significant up-shift in the translation of ribosomal proteins compared to photosynthetic genes. Our findings suggest the existence of a novel regulatory mechanism linked to the abundance of tRNA-K(UUU), enabling the differential expression of functional chloroplast gene groups.
Collapse
Affiliation(s)
- Jose M Muino
- Plant Cell Development, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
- Computational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - Hannes Ruwe
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Yujiao Qu
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Sascha Maschmann
- Molecular Genetics, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Uwe Ohler
- Computational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell Development, Humboldt Universität zu Berlin, Philippstr.13, 10115, Berlin, Germany
| | | |
Collapse
|
2
|
Lihanova Y, Nagel R, Jakob T, Sasso S. Characterization of activating cis-regulatory elements from the histone genes of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:525-539. [PMID: 38693717 DOI: 10.1111/tpj.16781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024]
Abstract
Regulation of gene expression in eukaryotes is controlled by cis-regulatory modules (CRMs). A major class of CRMs are enhancers which are composed of activating cis-regulatory elements (CREs) responsible for upregulating transcription. To date, most enhancers and activating CREs have been studied in angiosperms; in contrast, our knowledge about these key regulators of gene expression in green algae is limited. In this study, we aimed at characterizing putative activating CREs/CRMs from the histone genes of the unicellular model alga Chlamydomonas reinhardtii. To test the activity of four candidates, reporter constructs consisting of a tetramerized CRE, an established promoter, and a gene for the mCerulean3 fluorescent protein were incorporated into the nuclear genome of C. reinhardtii, and their activity was quantified by flow cytometry. Two tested candidates, Eupstr and Ehist cons, significantly upregulated gene expression and were characterized in detail. Eupstr, which originates from highly expressed genes of C. reinhardtii, is an orientation-independent CRE capable of activating both the RBCS2 and β2-tubulin promoters. Ehist cons, which is a CRM from histone genes of angiosperms, upregulates the β2-tubulin promoter in C. reinhardtii over a distance of at least 1.5 kb. The octamer motif present in Ehist cons was identified in C. reinhardtii and the related green algae Chlamydomonas incerta, Chlamydomonas schloesseri, and Edaphochlamys debaryana, demonstrating its high evolutionary conservation. The results of this investigation expand our knowledge about the regulation of gene expression in green algae. Furthermore, the characterized activating CREs/CRMs can be applied as valuable genetic tools.
Collapse
Affiliation(s)
- Yuliia Lihanova
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Raimund Nagel
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Torsten Jakob
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Severin Sasso
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| |
Collapse
|
3
|
Zhang L, Ruan J, Gao F, Xin Q, Che LP, Cai L, Liu Z, Kong M, Rochaix JD, Mi H, Peng L. Thylakoid protein FPB1 synergistically cooperates with PAM68 to promote CP47 biogenesis and Photosystem II assembly. Nat Commun 2024; 15:3122. [PMID: 38600073 PMCID: PMC11006888 DOI: 10.1038/s41467-024-46863-y] [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: 03/08/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
In chloroplasts, insertion of proteins with multiple transmembrane domains (TMDs) into thylakoid membranes usually occurs in a co-translational manner. Here, we have characterized a thylakoid protein designated FPB1 (Facilitator of PsbB biogenesis1) which together with a previously reported factor PAM68 (Photosynthesis Affected Mutant68) is involved in assisting the biogenesis of CP47, a subunit of the Photosystem II (PSII) core. Analysis by ribosome profiling reveals increased ribosome stalling when the last TMD segment of CP47 emerges from the ribosomal tunnel in fpb1 and pam68. FPB1 interacts with PAM68 and both proteins coimmunoprecipitate with SecY/E and Alb3 as well as with some ribosomal components. Thus, our data indicate that, in coordination with the SecY/E translocon and the Alb3 integrase, FPB1 synergistically cooperates with PAM68 to facilitate the co-translational integration of the last two CP47 TMDs and the large loop between them into thylakoids and the PSII core complex.
Collapse
Affiliation(s)
- Lin Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Junxiang Ruan
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Fudan Gao
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qiang Xin
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Li-Ping Che
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lujuan Cai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zekun Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Mengmeng Kong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences / Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, China
| | - Jean-David Rochaix
- Departments of Molecular Biology and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Hualing Mi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences / Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, China
| | - Lianwei Peng
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| |
Collapse
|
4
|
Teyssonniere EM, Shichino Y, Mito M, Friedrich A, Iwasaki S, Schacherer J. Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast. Nucleic Acids Res 2024; 52:2434-2445. [PMID: 38261993 PMCID: PMC10954453 DOI: 10.1093/nar/gkae030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024] Open
Abstract
Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse set of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extent and signature of the post-transcriptional buffering.
Collapse
Affiliation(s)
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| |
Collapse
|
5
|
Gotsmann VL, Ting MKY, Haase N, Rudorf S, Zoschke R, Willmund F. Utilizing high-resolution ribosome profiling for the global investigation of gene expression in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1614-1634. [PMID: 38047591 DOI: 10.1111/tpj.16577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression. Extraction and sequencing of ribosome-protected fragments (RPFs) and parallel RNA-seq yields genome-wide insight into translational dynamics and post-transcriptional control of gene expression. Here, we provide details on the Ribo-seq method and the subsequent analysis with the unicellular model alga Chlamydomonas reinhardtii (Chlamydomonas) for generating high-resolution data covering more than 10 000 different transcripts. Detailed analysis of the ribosomal offsets on transcripts uncovers presumable transition states during translocation of elongating ribosomes within the 5' and 3' sections of transcripts and characteristics of eukaryotic translation termination, which are fundamentally distinct for chloroplast translation. In chloroplasts, a heterogeneous RPF size distribution along the coding sequence indicates specific regulatory phases during protein synthesis. For example, local accumulation of small RPFs correlates with local slowdown of psbA translation, possibly uncovering an uncharacterized regulatory step during PsbA/D1 synthesis. Further analyses of RPF distribution along specific cytosolic transcripts revealed characteristic patterns of translation elongation exemplified for the major light-harvesting complex proteins, LHCs. By providing high-quality datasets for all subcellular genomes and attaching our data to the Chlamydomonas reference genome, we aim to make ribosome profiles easily accessible for the broad research community. The data can be browsed without advanced bioinformatic background knowledge for translation output levels of specific genes and their splice variants and for monitoring genome annotation.
Collapse
Affiliation(s)
- Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
| | - Michael Kien Yin Ting
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nadin Haase
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Sophia Rudorf
- Institute of Cell Biology and Biophysics, Leibniz University Hanover, Herrenhäuser-Str. 2, 30419, Hanover, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, RPTU Kaiserslautern-Landau, Paul-Ehrlich-Str. 23, 67663, Kaiserslautern, Germany
| |
Collapse
|
6
|
Ries F, Weil HL, Herkt C, Mühlhaus T, Sommer F, Schroda M, Willmund F. Competition co-immunoprecipitation reveals the interactors of the chloroplast CPN60 chaperonin machinery. PLANT, CELL & ENVIRONMENT 2023; 46:3371-3391. [PMID: 37606545 DOI: 10.1111/pce.14697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/28/2023] [Accepted: 08/11/2023] [Indexed: 08/23/2023]
Abstract
The functionality of all metabolic processes in chloroplasts depends on a balanced integration of nuclear- and chloroplast-encoded polypeptides into the plastid's proteome. The chloroplast chaperonin machinery is an essential player in chloroplast protein folding under ambient and stressful conditions, with a more intricate structure and subunit composition compared to the orthologous GroEL/ES chaperonin of Escherichia coli. However, its exact role in chloroplasts remains obscure, mainly because of very limited knowledge about the interactors. We employed the competition immunoprecipitation method for the identification of the chaperonin's interactors in Chlamydomonas reinhardtii. Co-immunoprecipitation of the target complex in the presence of increasing amounts of isotope-labelled competitor epitope and subsequent mass spectrometry analysis specifically allowed to distinguish true interactors from unspecifically co-precipitated proteins. Besides known substrates such as RbcL and the expected complex partners, we revealed numerous new interactors with high confidence. Proteins that qualify as putative substrate proteins differ from bulk chloroplast proteins by a higher content of beta-sheets, lower alpha-helical conformation and increased aggregation propensity. Immunoprecipitations targeted against a subunit of the co-chaperonin lid revealed the ClpP protease as a specific partner complex, pointing to a close collaboration of these machineries to maintain protein homeostasis in the chloroplast.
Collapse
Affiliation(s)
- Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Heinrich Lukas Weil
- Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Plant Physiology/Synmikro, University of Marburg, Marburg, Germany
| |
Collapse
|
7
|
Keller JM, Frieboes MJ, Jödecke L, Kappel S, Wulff N, Rindfleisch T, Sandoval-Ibanez O, Gerlach I, Thiele W, Bock R, Eirich J, Finkemeier I, Schünemann D, Zoschke R, Schöttler MA, Armbruster U. Eukaryote-specific assembly factor DEAP2 mediates an early step of photosystem II assembly in Arabidopsis. PLANT PHYSIOLOGY 2023; 193:1970-1986. [PMID: 37555435 PMCID: PMC10602607 DOI: 10.1093/plphys/kiad446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023]
Abstract
The initial step of oxygenic photosynthesis is the thermodynamically challenging extraction of electrons from water and the release of molecular oxygen. This light-driven process, which is the basis for most life on Earth, is catalyzed by photosystem II (PSII) within the thylakoid membrane of photosynthetic organisms. The biogenesis of PSII requires a controlled step-wise assembly process of which the early steps are considered to be highly conserved between plants and their cyanobacterial progenitors. This assembly process involves auxiliary proteins, which are likewise conserved. In the present work, we used Arabidopsis (Arabidopsis thaliana) as a model to show that in plants, a eukaryote-exclusive assembly factor facilitates the early assembly step, during which the intrinsic antenna protein CP47 becomes associated with the PSII reaction center (RC) to form the RC47 intermediate. This factor, which we named DECREASED ELECTRON TRANSPORT AT PSII (DEAP2), works in concert with the conserved PHOTOSYNTHESIS AFFECTED MUTANT 68 (PAM68) assembly factor. The deap2 and pam68 mutants showed similar defects in PSII accumulation and assembly of the RC47 intermediate. The combined lack of both proteins resulted in a loss of functional PSII and the inability of plants to grow photoautotrophically on the soil. While overexpression of DEAP2 partially rescued the pam68 PSII accumulation phenotype, this effect was not reciprocal. DEAP2 accumulated at 20-fold higher levels than PAM68, together suggesting that both proteins have distinct functions. In summary, our results uncover eukaryotic adjustments to the PSII assembly process, which involve the addition of DEAP2 for the rapid progression from RC to RC47.
Collapse
Affiliation(s)
- Jakob-Maximilian Keller
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Maureen Julia Frieboes
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Ludwig Jödecke
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Sandrine Kappel
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Natalia Wulff
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Tobias Rindfleisch
- Computational Biology Unit, Department of Chemistry, University of Bergen, 5008 Bergen, Norway
| | - Omar Sandoval-Ibanez
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Ines Gerlach
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Jürgen Eirich
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr University Bochum, 44780 Bochum, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Mark Aurel Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Ute Armbruster
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
- Institute of Molecular Photosynthesis, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|
8
|
Zhang Y, Tian L, Lu C. Chloroplast gene expression: Recent advances and perspectives. PLANT COMMUNICATIONS 2023; 4:100611. [PMID: 37147800 PMCID: PMC10504595 DOI: 10.1016/j.xplc.2023.100611] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 05/07/2023]
Abstract
Chloroplasts evolved from an ancient cyanobacterial endosymbiont more than 1.5 billion years ago. During subsequent coevolution with the nuclear genome, the chloroplast genome has remained independent, albeit strongly reduced, with its own transcriptional machinery and distinct features, such as chloroplast-specific innovations in gene expression and complicated post-transcriptional processing. Light activates the expression of chloroplast genes via mechanisms that optimize photosynthesis, minimize photodamage, and prioritize energy investments. Over the past few years, studies have moved from describing phases of chloroplast gene expression to exploring the underlying mechanisms. In this review, we focus on recent advances and emerging principles that govern chloroplast gene expression in land plants. We discuss engineering of pentatricopeptide repeat proteins and its biotechnological effects on chloroplast RNA research; new techniques for characterizing the molecular mechanisms of chloroplast gene expression; and important aspects of chloroplast gene expression for improving crop yield and stress tolerance. We also discuss biological and mechanistic questions that remain to be answered in the future.
Collapse
Affiliation(s)
- Yi Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lin Tian
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Congming Lu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
| |
Collapse
|
9
|
Zoclanclounon YAB, Thamilarasan SK, Mo Y, Ahn BO, Kim JG, Lee K. Insights into chloroplast genome structure and phylogenetic relationships within the Sesamum species complex (Pedaliaceae). Front Genet 2023; 14:1207306. [PMID: 37323670 PMCID: PMC10267711 DOI: 10.3389/fgene.2023.1207306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Background: In the Sesamum species complex, the lack of wild species genomic resources hinders the evolutionary comprehension of phylogenetic relationships. Results: In the present study, we generated complete chloroplast genomes of six wild relatives (Sesamum alatum, Sesamum angolense, Sesamum pedaloides, Ceratotheca sesamoides (syn. Sesamum sesamoides), Ceratotheca triloba (syn. Sesamum trilobum), and Sesamum radiatum) and a Korean cultivar, Sesamum indicum cv. Goenbaek. A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed. A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted. The chloroplast genomes (152, 863-153, 338 bp) exhibited the IR contraction/expansion phenomenon and were quite conserved in both coding and non-coding regions. However, high values of the nucleotide diversity index were found in several genes, including ndhA, ndhE, ndhF, ycf1, and psaC-ndhD. Concordant tree topologies suggest ndhF as a useful marker for taxon discrimination. The phylogenetic inference and time divergence dating indicate that S. radiatum (2n = 64) occurred concomitantly with the sister species C. sesamoides (2n = 32) approximately 0.05 million years ago (Mya). In addition, S. alatum was clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others. Conclusion: Altogether, we propose to rename C. sesamoides and C. triloba as S. sesamoides and S. trilobum, respectively, as suggested previously based on the morphological description. This study provides the first insight into the phylogenetic relationships among the cultivated and wild African native relatives. The chloroplast genome data lay a foundation for speciation genomics in the Sesamum species complex.
Collapse
Affiliation(s)
- Yedomon Ange Bovys Zoclanclounon
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Senthil Kumar Thamilarasan
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Youngjun Mo
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Byoung-Ohg Ahn
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Jeong-Gu Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Keunpyo Lee
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| |
Collapse
|
10
|
Ghandour R, Gao Y, Laskowski J, Barahimipour R, Ruf S, Bock R, Zoschke R. Transgene insertion into the plastid genome alters expression of adjacent native chloroplast genes at the transcriptional and translational levels. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:711-725. [PMID: 36529916 PMCID: PMC10037153 DOI: 10.1111/pbi.13985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 11/14/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
In plant biotechnology and basic research, chloroplasts have been used as chassis for the expression of various transgenes. However, potential unintended side effects of transgene insertion and high-level transgene expression on the expression of native chloroplast genes are often ignored and have not been studied comprehensively. Here, we examined expression of the chloroplast genome at both the transcriptional and translational levels in five transplastomic tobacco (Nicotiana tabacum) lines carrying the identical aadA resistance marker cassette in diverse genomic positions. Although none of the lines exhibits a pronounced visible phenotype, the analysis of three lines that contain the aadA insertion in different locations within the petL-petG-psaJ-rpl33-rps18 transcription unit demonstrates that transcriptional read-through from the aadA resistance marker is unavoidable, and regularly causes overexpression of downstream sense-oriented chloroplast genes at the transcriptional and translational levels. Investigation of additional lines that harbour the aadA intergenically and outside of chloroplast transcription units revealed that expression of the resistance marker can also cause antisense effects by interference with transcription/transcript accumulation and/or translation of downstream antisense-oriented genes. In addition, we provide evidence for a previously suggested role of genomically encoded tRNAs in chloroplast transcription termination and/or transcript processing. Together, our data uncover principles of neighbouring effects of chloroplast transgenes and suggest general strategies for the choice of transgene insertion sites and expression elements to minimize unintended consequences of transgene expression on the transcription and translation of native chloroplast genes.
Collapse
Affiliation(s)
- Rabea Ghandour
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Yang Gao
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | | | | | - Stephanie Ruf
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| |
Collapse
|
11
|
Wang F, Dischinger K, Westrich LD, Meindl I, Egidi F, Trösch R, Sommer F, Johnson X, Schroda M, Nickelsen J, Willmund F, Vallon O, Bohne AV. One-helix protein 2 is not required for the synthesis of photosystem II subunit D1 in Chlamydomonas. PLANT PHYSIOLOGY 2023; 191:1612-1633. [PMID: 36649171 PMCID: PMC10022639 DOI: 10.1093/plphys/kiad015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
In land plants and cyanobacteria, co-translational association of chlorophyll (Chl) to the nascent D1 polypeptide, a reaction center protein of photosystem II (PSII), requires a Chl binding complex consisting of a short-chain dehydrogenase (high chlorophyll fluorescence 244 [HCF244]/uncharacterized protein 39 [Ycf39]) and one-helix proteins (OHP1 and OHP2 in chloroplasts) of the light-harvesting antenna complex superfamily. Here, we show that an ohp2 mutant of the green alga Chlamydomonas (Chlamydomonas reinhardtii) fails to accumulate core PSII subunits, in particular D1 (encoded by the psbA mRNA). Extragenic suppressors arose at high frequency, suggesting the existence of another route for Chl association to PSII. The ohp2 mutant was complemented by the Arabidopsis (Arabidopsis thaliana) ortholog. In contrast to land plants, where psbA translation is prevented in the absence of OHP2, ribosome profiling experiments showed that the Chlamydomonas mutant translates the psbA transcript over its full length. Pulse labeling suggested that D1 is degraded during or immediately after translation. The translation of other PSII subunits was affected by assembly-controlled translational regulation. Proteomics showed that HCF244, a translation factor which associates with and is stabilized by OHP2 in land plants, still partly accumulates in the Chlamydomonas ohp2 mutant, explaining the persistence of psbA translation. Several Chl biosynthesis enzymes overaccumulate in the mutant membranes. Partial inactivation of a D1-degrading protease restored a low level of PSII activity in an ohp2 background, but not photoautotrophy. Taken together, our data suggest that OHP2 is not required for psbA translation in Chlamydomonas, but is necessary for D1 stabilization.
Collapse
Affiliation(s)
- Fei Wang
- Molecular Plant Sciences, LMU Munich, Planegg-Martinsried 82152, Germany
- UMR 7141, Centre National de la Recherche Scientifique/Sorbonne Université, Institut de Biologie Physico-Chimique, Paris 75005, France
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | | | - Lisa Désirée Westrich
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Irene Meindl
- Molecular Plant Sciences, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Felix Egidi
- Molecular Plant Sciences, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Xenie Johnson
- UMR 7141, Centre National de la Recherche Scientifique/Sorbonne Université, Institut de Biologie Physico-Chimique, Paris 75005, France
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Joerg Nickelsen
- Molecular Plant Sciences, LMU Munich, Planegg-Martinsried 82152, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Olivier Vallon
- UMR 7141, Centre National de la Recherche Scientifique/Sorbonne Université, Institut de Biologie Physico-Chimique, Paris 75005, France
| | | |
Collapse
|
12
|
Liu P, Ye DM, Chen M, Zhang J, Huang XH, Shen LL, Xia KK, Xu XJ, Xu YC, Guo YL, Wang YC, Huang F. Scaling-up and proteomic analysis reveals photosynthetic and metabolic insights toward prolonged H 2 photoproduction in Chlamydomonas hpm91 mutant lacking proton gradient regulation 5 (PGR5). PHOTOSYNTHESIS RESEARCH 2022; 154:397-411. [PMID: 35974136 PMCID: PMC9722884 DOI: 10.1007/s11120-022-00945-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Clean and sustainable H2 production is crucial to a carbon-neutral world. H2 generation by Chlamydomonas reinhardtii is an attractive approach for solar-H2 from H2O. However, it is currently not large-scalable because of lacking desirable strains with both optimal H2 productivity and sufficient knowledge of underlying molecular mechanism. We hereby carried out extensive and in-depth investigations of H2 photoproduction of hpm91 mutant lacking PGR5 (Proton Gradient Regulation 5) toward its up-scaling and fundamental mechanism issues. We show that hpm91 is at least 100-fold scalable (up to 10 L) with continuous H2 collection of 7287 ml H2/10L-HPBR in averagely 26 days under sulfur deprivation. Also, we show that hpm91 is robust and active during sustained H2 photoproduction, most likely due to decreased intracellular ROS relative to wild type. Moreover, we obtained quantitative proteomic profiles of wild type and hpm91 at four representing time points of H2 evolution, leading to 2229 and 1350 differentially expressed proteins, respectively. Compared to wild type, major proteome alterations of hpm91 include not only core subunits of photosystems and those related to anti-oxidative responses but also essential proteins in photosynthetic antenna, C/N metabolic balance, and sulfur assimilation toward both cysteine biosynthesis and sulfation of metabolites during sulfur-deprived H2 production. These results reveal not only new insights of cellular and molecular basis of enhanced H2 production in hpm91 but also provide additional candidate gene targets and modules for further genetic modifications and/or in artificial photosynthesis mimics toward basic and applied research aiming at advancing solar-H2 technology.
Collapse
Affiliation(s)
- Peng Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Min Ye
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mei Chen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia-He Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li-Li Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke-Ke Xia
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiao-Jing Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ying-Chun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Fang Huang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| |
Collapse
|
13
|
Loiacono FV, Walther D, Seeger S, Thiele W, Gerlach I, Karcher D, Schöttler MA, Zoschke R, Bock R. Emergence of Novel RNA-Editing Sites by Changes in the Binding Affinity of a Conserved PPR Protein. Mol Biol Evol 2022; 39:6760358. [PMID: 36227729 PMCID: PMC9750133 DOI: 10.1093/molbev/msac222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/07/2023] Open
Abstract
RNA editing converts cytidines to uridines in plant organellar transcripts. Editing typically restores codons for conserved amino acids. During evolution, specific C-to-U editing sites can be lost from some plant lineages by genomic C-to-T mutations. By contrast, the emergence of novel editing sites is less well documented. Editing sites are recognized by pentatricopeptide repeat (PPR) proteins with high specificity. RNA recognition by PPR proteins is partially predictable, but prediction is often inadequate for PPRs involved in RNA editing. Here we have characterized evolution and recognition of a recently gained editing site. We demonstrate that changes in the RNA recognition motifs that are not explainable with the current PPR code allow an ancient PPR protein, QED1, to uniquely target the ndhB-291 site in Brassicaceae. When expressed in tobacco, the Arabidopsis QED1 edits 33 high-confident off-target sites in chloroplasts and mitochondria causing a spectrum of mutant phenotypes. By manipulating the relative expression levels of QED1 and ndhB-291, we show that the target specificity of the PPR protein depends on the RNA:protein ratio. Finally, our data suggest that the low expression levels of PPR proteins are necessary to ensure the specificity of editing site selection and prevent deleterious off-target editing.
Collapse
Affiliation(s)
- F Vanessa Loiacono
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Dirk Walther
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stefanie Seeger
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Wolfram Thiele
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ines Gerlach
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Reimo Zoschke
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | | |
Collapse
|
14
|
Abstract
Cilium formation and regeneration requires new protein synthesis, but the underlying cytosolic translational reprogramming remains largely unknown. Using ribosome footprinting, we performed global translatome profiling during cilia regeneration in Chlamydomonas and uncovered that flagellar genes undergo an early transcriptional activation but late translational repression. This pattern guided our identification of sphingolipid metabolism enzymes, including serine palmitoyltransferase (SPT), as essential regulators for ciliogenesis. Cryo-electron tomography showed that ceramide loss abnormally increased the membrane-axoneme distance and generated bulged cilia. We found that ceramides interact with intraflagellar transport (IFT) particle proteins that IFT motors transport along axoneme microtubules (MTs), suggesting that ceramide-IFT particle-IFT motor-MT interactions connect the ciliary membrane with the axoneme to form rod-shaped cilia. SPT-deficient vertebrate cells were defective in ciliogenesis, and SPT mutations from patients with hereditary sensory neuropathy disrupted cilia, which could be restored by sphingolipid supplementation. These results reveal a conserved role of sphingolipid in cilium formation and link compromised sphingolipid production with ciliopathies.
Collapse
|
15
|
Sandoval-Ibáñez O, Rolo D, Ghandour R, Hertle AP, Armarego-Marriott T, Sampathkumar A, Zoschke R, Bock R. De-etiolation-induced protein 1 (DEIP1) mediates assembly of the cytochrome b 6f complex in Arabidopsis. Nat Commun 2022; 13:4045. [PMID: 35831297 PMCID: PMC9279372 DOI: 10.1038/s41467-022-31758-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/01/2022] [Indexed: 11/26/2022] Open
Abstract
The conversion of light energy to chemical energy by photosynthesis requires the concerted action of large protein complexes in the thylakoid membrane. Recent work has provided fundamental insights into the three-dimensional structure of these complexes, but how they are assembled from hundreds of parts remains poorly understood. Particularly little is known about the biogenesis of the cytochrome b6f complex (Cytb6f), the redox-coupling complex that interconnects the two photosystems. Here we report the identification of a factor that guides the assembly of Cytb6f in thylakoids of chloroplasts. The protein, DE-ETIOLATION-INDUCED PROTEIN 1 (DEIP1), resides in the thylakoid membrane and is essential for photoautotrophic growth. Knock-out mutants show a specific loss of Cytb6f, and are defective in complex assembly. We demonstrate that DEIP1 interacts with the two cytochrome subunits of the complex, PetA and PetB, and mediates the assembly of intermediates in Cytb6f biogenesis. The identification of DEIP1 provides an entry point into the study of the assembly pathway of a crucial complex in photosynthetic electron transfer. The Cytb6f complex is a multi-subunit enzyme that couples the two photosystems during the light reactions of photosynthesis. Here the authors show that the thylakoid-localized DEIP1 protein interacts with the PetA and PetB subunits, and is essential for Cytb6f complex assembly in Arabidopsis.
Collapse
Affiliation(s)
- Omar Sandoval-Ibáñez
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - David Rolo
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rabea Ghandour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alexander P Hertle
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Tegan Armarego-Marriott
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| |
Collapse
|
16
|
Trösch R, Ries F, Westrich LD, Gao Y, Herkt C, Hoppstädter J, Heck-Roth J, Mustas M, Scheuring D, Choquet Y, Räschle M, Zoschke R, Willmund F. Fast and global reorganization of the chloroplast protein biogenesis network during heat acclimation. THE PLANT CELL 2022; 34:1075-1099. [PMID: 34958373 PMCID: PMC8894945 DOI: 10.1093/plcell/koab317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/20/2021] [Indexed: 06/02/2023]
Abstract
Photosynthesis is a central determinant of plant biomass production, but its homeostasis is increasingly challenged by heat. Little is known about the sensitive regulatory principles involved in heat acclimation that underly the biogenesis and repair of chloroplast-encoded core subunits of photosynthetic complexes. Employing time-resolved ribosome and transcript profiling together with selective ribosome proteomics, we systematically deciphered these processes in chloroplasts of Chlamydomonas reinhardtii. We revealed protein biosynthesis and altered translation elongation as central processes for heat acclimation and showed that these principles are conserved between the alga and the flowering plant Nicotiana tabacum. Short-term heat exposure resulted in specific translational repression of chlorophyll a-containing core antenna proteins of photosystems I and II. Furthermore, translocation of ribosome nascent chain complexes to thylakoid membranes was affected, as reflected by the increased accumulation of stromal cpSRP54-bound ribosomes. The successful recovery of synthesizing these proteins under prolonged acclimation of nonlethal heat conditions was associated with specific changes of the co-translational protein interaction network, including increased ribosome association of chlorophyll biogenesis enzymes and acclimation factors responsible for complex assembly. We hypothesize that co-translational cofactor binding and targeting might be bottlenecks under heat but become optimized upon heat acclimation to sustain correct co-translational protein complex assembly.
Collapse
Affiliation(s)
- Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Lisa Désirée Westrich
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Julia Hoppstädter
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Johannes Heck-Roth
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Matthieu Mustas
- Biologie du Chloroplaste et Perception de la Lumieère Chez les Microalgues, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC, Paris 7141, France
| | - David Scheuring
- Plant Pathology, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Yves Choquet
- Biologie du Chloroplaste et Perception de la Lumieère Chez les Microalgues, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC, Paris 7141, France
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern 67663, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Kaiserslautern 67663, Germany
| |
Collapse
|
17
|
HERNÁNDEZ-CRUZ K, JIMÉNEZ-MARTÍNEZ C, PERUCINI-AVENDAÑO M, MATEO CID LE, PEREA-FLORES MDJ, GUTIÉRREZ-LÓPEZ GF, DÁVILA-ORTIZ G. Chemical and microstructural characterization of three seaweed species from two locations of Veracruz, Mexico. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.41421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
18
|
DeTar RA, Barahimipour R, Manavski N, Schwenkert S, Höhner R, Bölter B, Inaba T, Meurer J, Zoschke R, Kunz HH. Loss of inner-envelope K+/H+ exchangers impairs plastid rRNA maturation and gene expression. THE PLANT CELL 2021; 33:2479-2505. [PMID: 34235544 PMCID: PMC8364240 DOI: 10.1093/plcell/koab123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/30/2021] [Indexed: 05/08/2023]
Abstract
The inner-envelope K+ EFFLUX ANTIPORTERS (KEA) 1 and 2 are critical for chloroplast development, ion homeostasis, and photosynthesis. However, the mechanisms by which changes in ion flux across the envelope affect organelle biogenesis remained elusive. Chloroplast development requires intricate coordination between the nuclear genome and the plastome. Many mutants compromised in plastid gene expression (PGE) display a virescent phenotype, that is delayed greening. The phenotypic appearance of Arabidopsis thaliana kea1 kea2 double mutants fulfills this criterion, yet a link to PGE has not been explored. Here, we show that a simultaneous loss of KEA1 and KEA2 results in maturation defects of the plastid ribosomal RNAs. This may be caused by secondary structure changes of rRNA transcripts and concomitant reduced binding of RNA-processing proteins, which we documented in the presence of skewed ion homeostasis in kea1 kea2. Consequently, protein synthesis and steady-state levels of plastome-encoded proteins remain low in mutants. Disturbance in PGE and other signs of plastid malfunction activate GENOMES UNCOUPLED 1-dependent retrograde signaling in kea1 kea2, resulting in a dramatic downregulation of GOLDEN2-LIKE transcription factors to halt expression of photosynthesis-associated nuclear-encoded genes (PhANGs). PhANG suppression delays the development of fully photosynthesizing kea1 kea2 chloroplasts, probably to avoid progressing photo-oxidative damage. Overall, our results reveal that KEA1/KEA2 function impacts plastid development via effects on RNA-metabolism and PGE.
Collapse
Affiliation(s)
- Rachael Ann DeTar
- Plant Physiology, School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
| | - Rouhollah Barahimipour
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Nikolay Manavski
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Serena Schwenkert
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Ricarda Höhner
- Plant Physiology, School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
| | - Bettina Bölter
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Takehito Inaba
- Department of Agricultural and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Jörg Meurer
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Hans-Henning Kunz
- Plant Physiology, School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
- Plant Sciences, Department I, LMU Munich, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
- Author for correspondence:
| |
Collapse
|
19
|
Fu HY, Ghandour R, Ruf S, Zoschke R, Bock R, Schöttler MA. The availability of neither D2 nor CP43 limits the biogenesis of photosystem II in tobacco. PLANT PHYSIOLOGY 2021; 185:1111-1130. [PMID: 33793892 PMCID: PMC8133689 DOI: 10.1093/plphys/kiaa052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
The pathway of photosystem II (PSII) assembly is well understood, and multiple auxiliary proteins supporting it have been identified, but little is known about rate-limiting steps controlling PSII biogenesis. In the cyanobacterium Synechocystis PCC6803 and the green alga Chlamydomonas reinhardtii, indications exist that the biosynthesis of the chloroplast-encoded D2 reaction center subunit (PsbD) limits PSII accumulation. To determine the importance of D2 synthesis for PSII accumulation in vascular plants and elucidate the contributions of transcriptional and translational regulation, we modified the 5'-untranslated region of psbD via chloroplast transformation in tobacco (Nicotiana tabacum). A drastic reduction in psbD mRNA abundance resulted in a strong decrease in PSII content, impaired photosynthetic electron transport, and retarded growth under autotrophic conditions. Overexpression of the psbD mRNA also increased transcript abundance of psbC (the CP43 inner antenna protein), which is co-transcribed with psbD. Because translation efficiency remained unaltered, translation output of pbsD and psbC increased with mRNA abundance. However, this did not result in increased PSII accumulation. The introduction of point mutations into the Shine-Dalgarno-like sequence or start codon of psbD decreased translation efficiency without causing pronounced effects on PSII accumulation and function. These data show that neither transcription nor translation of psbD and psbC are rate-limiting for PSII biogenesis in vascular plants and that PSII assembly and accumulation in tobacco are controlled by different mechanisms than in cyanobacteria or in C. reinhardtii.
Collapse
Affiliation(s)
- Han-Yi Fu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Rabea Ghandour
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Reimo Zoschke
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Mark Aurel Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
| |
Collapse
|
20
|
Kleine T, Nägele T, Neuhaus HE, Schmitz-Linneweber C, Fernie AR, Geigenberger P, Grimm B, Kaufmann K, Klipp E, Meurer J, Möhlmann T, Mühlhaus T, Naranjo B, Nickelsen J, Richter A, Ruwe H, Schroda M, Schwenkert S, Trentmann O, Willmund F, Zoschke R, Leister D. Acclimation in plants - the Green Hub consortium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:23-40. [PMID: 33368770 DOI: 10.1111/tpj.15144] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 05/04/2023]
Abstract
Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to 'smart breeding' methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast-related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted.
Collapse
Affiliation(s)
- Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - H Ekkehard Neuhaus
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | | | - Alisdair R Fernie
- Central Metabolism, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Peter Geigenberger
- Plant Metabolism, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Bernhard Grimm
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Edda Klipp
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Torsten Möhlmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Belen Naranjo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Jörg Nickelsen
- Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Andreas Richter
- Physiology of Plant Organelles, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Michael Schroda
- Molecular Biotechnology & Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Serena Schwenkert
- Plant Biochemistry and Physiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Oliver Trentmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Reimo Zoschke
- Translational Regulation in Plants, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| |
Collapse
|
21
|
Méteignier LV, Ghandour R, Zimmerman A, Kuhn L, Meurer J, Zoschke R, Hammani K. Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo. Nucleic Acids Res 2021; 49:1114-1132. [PMID: 33398331 PMCID: PMC7826268 DOI: 10.1093/nar/gkaa1244] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/07/2020] [Accepted: 12/13/2020] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.
Collapse
Affiliation(s)
- Louis-Valentin Méteignier
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Rabea Ghandour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Aude Zimmerman
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Jörg Meurer
- Plant Sciences, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Kamel Hammani
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| |
Collapse
|
22
|
Nehal N, Choudhary B, Nagpure A, Gupta RK. DNA barcoding: a modern age tool for detection of adulteration in food. Crit Rev Biotechnol 2021; 41:767-791. [PMID: 33530758 DOI: 10.1080/07388551.2021.1874279] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Globalization of the food trade requires precise and exact information about the origin, methods of production, transformation technologies, authentication, and the traceability of foodstuffs. New challenges in food supply chains such as deliberate fraudulent substitution, tampering or mislabeling of food and its ingredients or food packaging incapacitates the market and eventually the national economy. Currently, no proper standards have been established for the authentication of most of the food materials. However, in order to control food fraud, various robust and cost-effective technologies have been employed, like a spectrophotometer, GC-MS, HPLC, and DNA barcoding. Among these techniques, DNA barcoding is a biotechnology advantage with the principle of using 400-800 bp long standardized unique DNA sequences of mitochondrial (e.g. COI) or plastidial (e.g. rbcL) of nuclear origin (e.g. ITS) to analyze and classify the food commodities. This review covers several traded food commodities like legumes, seafood, oils, herbal products, spices, fruits, cereals, meat, and their unique barcodes which are critically analyzed to detect adulteration or fraud. DNA barcoding is a global initiative and it is being accepted as a global standard/marker for species identification or authentication. The research laboratories and industries should collaborate to realize its potential in setting standards for quality assurance, quality control, and food safety for different food products.
Collapse
Affiliation(s)
- Nazish Nehal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, India
| | - Bharti Choudhary
- School of Studies in Biotechnology, Pt. Ravi Shankar Shukla University, Raipur, India
| | - Anand Nagpure
- Biology Division, State Forensic Science Laboratory, Bhopal, India
| | - Rajinder K Gupta
- Department of Applied Chemistry, Delhi Technological University, Delhi, India
| |
Collapse
|
23
|
Westrich LD, Gotsmann VL, Herkt C, Ries F, Kazek T, Trösch R, Armbruster L, Mühlenbeck JS, Ramundo S, Nickelsen J, Finkemeier I, Wirtz M, Storchová Z, Räschle M, Willmund F. The versatile interactome of chloroplast ribosomes revealed by affinity purification mass spectrometry. Nucleic Acids Res 2021; 49:400-415. [PMID: 33330923 PMCID: PMC7797057 DOI: 10.1093/nar/gkaa1192] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
In plant cells, chloroplast gene expression is predominantly controlled through post-transcriptional regulation. Such fine-tuning is vital for precisely orchestrating protein complex assembly as for the photosynthesis machinery and for quickly responding to environmental changes. While regulation of chloroplast protein synthesis is of central importance, little is known about the degree and nature of the regulatory network, mainly due to challenges associated with the specific isolation of transient ribosome interactors. Here, we established a ribosome affinity purification method, which enabled us to broadly uncover putative ribosome-associated proteins in chloroplasts. Endogenously tagging of a protein of the large or small subunit revealed not only interactors of the holo complex, but also preferential interactors of the two subunits. This includes known canonical regulatory proteins as well as several new proteins belonging to the categories of protein and RNA regulation, photosystem biogenesis, redox control and metabolism. The sensitivity of the here applied screen was validated for various transiently interacting proteins. We further provided evidence for the existence of a ribosome-associated Nα-acetyltransferase in chloroplasts and its ability to acetylate substrate proteins at their N-terminus. The broad set of ribosome interactors underscores the potential to regulate chloroplast gene expression on the level of protein synthesis.
Collapse
Affiliation(s)
- Lisa Désirée Westrich
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Tanja Kazek
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Jens Stephan Mühlenbeck
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, 48149 Münster, Germany
| | - Silvia Ramundo
- Department of Biochemistry and Biophysics, University of California, 600 16th St, N316, San Francisco, CA 94143, USA
| | - Jörg Nickelsen
- Department of Molecular Plant Science, University of Munich, Grosshaderner-Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, 48149 Münster, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Zuzana Storchová
- Molecular Genetics, University of Kaiserslautern, Paul-Ehrlich-Str. 24, 67663 Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Paul-Ehrlich-Str. 24, 67663 Kaiserslautern, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| |
Collapse
|
24
|
Kage U, Powell JJ, Gardiner DM, Kazan K. Ribosome profiling in plants: what is not lost in translation? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5323-5332. [PMID: 32459844 DOI: 10.1093/jxb/eraa227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/05/2020] [Indexed: 05/03/2023]
Abstract
Translation is a highly dynamic cellular process whereby genetic information residing in an mRNA molecule is converted into a protein that in turn executes specific functions. However, pre-synthesized mRNA levels do not always correlate with corresponding protein levels, suggesting that translational control plays an essential role in gene regulation. A better understanding of how gene expression is regulated during translation will enable the discovery of new genes and mechanisms that control important traits in plants. Therefore, in recent years, several methods have been developed to analyse the translatome; that is, all mRNAs being actively translated at a given time, tissue, and/or developmental stage. Ribosome profiling or ribo-seq is one such technology revolutionizing our ability to analyse the translatome and in turn understand translational control of gene expression. Ribo-seq involves isolating mRNA-ribosome complexes, treating them with a RNase, and then identifying ribosome-protected mRNA regions by deep sequencing. Here, we briefly review recent ribosome profiling studies that revealed new insights into plant biology. Manipulation of novel genes identified using ribosome profiling could prove useful for increasing yield through improved biotic and abiotic stress tolerance.
Collapse
Affiliation(s)
- Udaykumar Kage
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| | - Jonathan J Powell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| | - Donald M Gardiner
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, St Lucia, QLD, Australia
| |
Collapse
|
25
|
Weiner I, Feldman Y, Shahar N, Yacoby I, Tuller T. CSO – A sequence optimization software for engineering chloroplast expression in Chlamydomonas reinhardtii. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
26
|
Trösch R, Willmund F. The conserved theme of ribosome hibernation: from bacteria to chloroplasts of plants. Biol Chem 2020; 400:879-893. [PMID: 30653464 DOI: 10.1515/hsz-2018-0436] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 12/21/2022]
Abstract
Cells are highly adaptive systems that respond and adapt to changing environmental conditions such as temperature fluctuations or altered nutrient availability. Such acclimation processes involve reprogramming of the cellular gene expression profile, tuning of protein synthesis, remodeling of metabolic pathways and morphological changes of the cell shape. Nutrient starvation can lead to limited energy supply and consequently, remodeling of protein synthesis is one of the key steps of regulation since the translation of the genetic code into functional polypeptides may consume up to 40% of a cell's energy during proliferation. In eukaryotic cells, downregulation of protein synthesis during stress is mainly mediated by modification of the translation initiation factors. Prokaryotic cells suppress protein synthesis by the active formation of dimeric so-called 'hibernating' 100S ribosome complexes. Such a transition involves a number of proteins which are found in various forms in prokaryotes but also in chloroplasts of plants. Here, we review the current understanding of these hibernation factors and elaborate conserved principles which are shared between species.
Collapse
Affiliation(s)
- Raphael Trösch
- Department of Biology, Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Straße 23, D-67663 Kaiserslautern, Germany
| | - Felix Willmund
- Department of Biology, Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Straße 23, D-67663 Kaiserslautern, Germany
| |
Collapse
|
27
|
Exploring the Link between Photosystem II Assembly and Translation of the Chloroplast psbA mRNA. PLANTS 2020; 9:plants9020152. [PMID: 31991763 PMCID: PMC7076361 DOI: 10.3390/plants9020152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/16/2020] [Accepted: 01/21/2020] [Indexed: 12/12/2022]
Abstract
Photosystem II (PSII) in chloroplasts and cyanobacteria contains approximately fifteen core proteins, which organize numerous pigments and prosthetic groups that mediate the light-driven water-splitting activity that drives oxygenic photosynthesis. The PSII reaction center protein D1 is subject to photodamage, whose repair requires degradation of damaged D1 and its replacement with nascent D1. Mechanisms that couple D1 synthesis with PSII assembly and repair are poorly understood. We address this question by using ribosome profiling to analyze the translation of chloroplast mRNAs in maize and Arabidopsis mutants with defects in PSII assembly. We found that OHP1, OHP2, and HCF244, which comprise a recently elucidated complex involved in PSII assembly and repair, are each required for the recruitment of ribosomes to psbA mRNA, which encodes D1. By contrast, HCF136, which acts upstream of the OHP1/OHP2/HCF244 complex during PSII assembly, does not have this effect. The fact that the OHP1/OHP2/HCF244 complex brings D1 into proximity with three proteins with dual roles in PSII assembly and psbA ribosome recruitment suggests that this complex is the hub of a translational autoregulatory mechanism that coordinates D1 synthesis with need for nascent D1 during PSII biogenesis and repair.
Collapse
|
28
|
Fujita T, Kurihara Y, Iwasaki S. The Plant Translatome Surveyed by Ribosome Profiling. PLANT & CELL PHYSIOLOGY 2019; 60:1917-1926. [PMID: 31004488 DOI: 10.1093/pcp/pcz059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/31/2019] [Indexed: 06/09/2023]
Abstract
Although transcriptome changes have long been recognized as a mechanism to induce tentative substitution of expressed genes in diverse biological processes in plants, the regulation of translation-the final step of the central dogma of molecular biology-emerged as an alternative and prominent layer in defining the output of genes. Despite these demands, the genome-wide analysis of protein synthesis has posed technical challenges, resulting in the plant translatome being poorly understood. The development of ribosome profiling promises to address the hidden aspects of translation, and its application to plants is revolutionizing our knowledge of the translatome. This review outlines the array of recent findings provided by ribosome profiling and illustrates the power of the versatile technique in green organisms.
Collapse
Affiliation(s)
- Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| |
Collapse
|
29
|
Comprehensive Analysis of Rhodomyrtus tomentosa Chloroplast Genome. PLANTS 2019; 8:plants8040089. [PMID: 30987338 PMCID: PMC6524380 DOI: 10.3390/plants8040089] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 11/16/2022]
Abstract
In the last decade, several studies have relied on a small number of plastid genomes to deduce deep phylogenetic relationships in the species-rich Myrtaceae. Nevertheless, the plastome of Rhodomyrtus tomentosa, an important representative plant of the Rhodomyrtus (DC.) genera, has not yet been reported yet. Here, we sequenced and analyzed the complete chloroplast (CP) genome of R. tomentosa, which is a 156,129-bp-long circular molecule with 37.1% GC content. This CP genome displays a typical quadripartite structure with two inverted repeats (IRa and IRb), of 25,824 bp each, that are separated by a small single copy region (SSC, 18,183 bp) and one large single copy region (LSC, 86,298 bp). The CP genome encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes and three pseudogenes (ycf1, rps19, ndhF). A considerable number of protein-coding genes have a universal ATG start codon, except for psbL and ndhD. Premature termination codons (PTCs) were found in one protein-coding gene, namely atpE, which is rarely reported in the CP genome of plants. Phylogenetic analysis revealed that R. tomentosa has a sister relationship with Eugenia uniflora and Psidium guajava. In conclusion, this study identified unique characteristics of the R. tomentosa CP genome providing valuable information for further investigations on species identification and the phylogenetic evolution between R. tomentosa and related species.
Collapse
|
30
|
Macedo-Osorio KS, Pérez-España VH, Garibay-Orijel C, Guzmán-Zapata D, Durán-Figueroa NV, Badillo-Corona JA. Intercistronic expression elements (IEE) from the chloroplast of Chlamydomonas reinhardtii can be used for the expression of foreign genes in synthetic operons. PLANT MOLECULAR BIOLOGY 2018; 98:303-317. [PMID: 30225747 DOI: 10.1007/s11103-018-0776-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/31/2018] [Indexed: 05/21/2023]
Abstract
Two intercistronic regions were identified as functional intercistronic expression elements (IEE) for the simultaneous expression of aphA-6 and gfp in a synthetic operon in the chloroplast of C. reinhardtii. Chlamydomonas reinhardtii, a biflagellate photosynthetic microalga, has been widely used in basic and applied science. Already three decades ago, Chlamydomonas had its chloroplast genome transformed and to this day constitutes the only alga routinely used in transplastomic technology. Despite the fact that over a 100 foreign genes have been expressed from the chloroplast genome, little has been done to address the challenge of expressing multiple genes in the form of operons, a development that is needed and crucial to push forward metabolic engineering and synthetic biology in this organism. Here, we studied five intercistronic regions and investigated if they can be used as intercistronic expression elements (IEE) in synthetic operons to drive the expression of foreign genes in the chloroplast of C. reinhardtii. The intercistronic regions were those from the psbB-psbT, psbN-psbH, psaC-petL, petL-trnN and tscA-chlN chloroplast operons, and the foreign genes were the aminoglycoside 3'-phosphotransferase (aphA-6), which confers resistance to kanamycin, and the green fluorescent protein gene (gfp). While all the intercistronic regions yielded lines that were resistant to kanamycin, only two (obtained with intercistronic regions from psbN-psbH and tscA-chlN) were identified as functional IEEs, yielding lines in which the second cistron (gfp) was translated and generated GFP. The IEEs we have identified could be useful for the stacking of genes for metabolic engineering or synthetic biology circuits in the chloroplast of C. reinhardtii.
Collapse
Affiliation(s)
- Karla S Macedo-Osorio
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticoman, Mexico City, Mexico
| | - Víctor H Pérez-España
- Universidad Autónoma del Estado de Hidalgo, Escuela Superior de Apan, Carretera Apan Calpulalpan km 8, Col. Chimalpa-Tlalayote, Apan, Hidalgo, Mexico
| | - Claudio Garibay-Orijel
- Labcitec, Camino a Atzacoalco 99, Col. Constitución de la República, Mexico City, Mexico
| | - Daniel Guzmán-Zapata
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticoman, Mexico City, Mexico
| | - Noé V Durán-Figueroa
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticoman, Mexico City, Mexico
| | - Jesús A Badillo-Corona
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto SN, Col. Barrio la Laguna Ticoman, Mexico City, Mexico.
| |
Collapse
|