1
|
Sun T, Tang Y, Zhou L, Qiao X, Ma X, Qin H, Han Y, Sui C. Characterization of the complete chloroplast genome of Rhodiola sachalinensis and comparative analysis with its congeneric plants. FEBS Open Bio 2024. [PMID: 38965647 DOI: 10.1002/2211-5463.13854] [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: 03/16/2024] [Revised: 05/29/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024] Open
Abstract
Rhodiola, belonging to the Crassulaceae family, is a perennial herbaceous plant genus. There are about 90 Rhodiola species worldwide, some of which have been reported to have medicinal properties. Rhodiola sachalinensis is a perennial medicinal herb within this genus and, in the present study, its chloroplast genome was sequenced, assembled, annotated and compared with 24 other Rhodiola species. The results obtained show that the chloroplast genome of R. sachalinensis is 151 595 bp long and has a CG content of 37.7%. The inverted repeats (IR) region of the Rhodiola chloroplast genome is the most conserved region, with the main differences being observed in the ycf1 and ndhF genes at the IRb-small single copy boundary, and rps19 and trnH genes at the IRa-large single copy boundary. Phylogenetic analysis showed that Rhodiola species form two major clades, and species with recorded medicinal properties, clustered together in one branch except for R. dumulosa. Within the genus, R. sachalinensis is most closely related to Rhodiola rosea, although comparative analyses showed that only R. sachalinensis and Rhodiola subopposita contained the psbZ gene, which encodes a highly conserved protein subunit of the Photosystem II core complex. Overall, the present study contributes to the understanding of the chloroplast genome of Rhodiola species, and provides a theoretical basis for the study of their genetic diversity and possible use as medicinal plants.
Collapse
Affiliation(s)
- Tianqi Sun
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College (Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials), Beijing, China
| | - Yuman Tang
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College (Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials), Beijing, China
| | - Lei Zhou
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College (Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials), Beijing, China
| | - Xu Qiao
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College (Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials), Beijing, China
| | - Xuan Ma
- New Cicon Pharmaceutical Co., Ltd, Urumqi, China
| | - Huaxia Qin
- New Cicon Pharmaceutical Co., Ltd, Urumqi, China
| | - Yu Han
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College (Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials), Beijing, China
| | - Chun Sui
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College (Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials), Beijing, China
| |
Collapse
|
2
|
He L, Xu S, Cheng X, Huang H, Dai H, Wang X, Ding Z, Xu M, Gu H, Yan N, Wang C. Chloroplast genomes in seven Lagerstroemia species provide new insights into molecular evolution of photosynthesis genes. Front Genet 2024; 15:1378403. [PMID: 38628576 PMCID: PMC11019025 DOI: 10.3389/fgene.2024.1378403] [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: 01/29/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Lagerstroemia indica is an important commercial tree known for the ornamental value. In this study, the complete chloroplast genome sequence of Lagerstroemia indica "Pink Velour" (Lagerstroemia "Pink Velour") was 152,174 bp in length with a GC content of 39.50%. It contained 85 protein coding genes (PCGs), 37 tRNAs, and 8 rRNA genes. 207 simple sequence repeats (SSRs) and 31 codons with relative synonymous codon (RSCU)value > 1 were detected. Phylogenetic analysis divided 10 Lagerstroemia species into evolutionary branches of clade A and clade B. We conducted a comparative analysis of Lagerstroemia "Pink Velours" complete chloroplast genome with the genomes of six closely related Lagerstroemia species from different origins. The structural features of all seven species were similar, except for the deletion of ycf1 nucleobases at the JSA boundary. The large single-copy (LSC) and the small single-copy (SSC) had a higher sequence divergence than the IR region, and 8 genes that were highly divergent (trnK-UUU, petN, psbF, psbJ, ndhE, ndhD, ndhI, ycf1) had been identified and could be used as molecular markers in future studies. High nucleotide diversity was present in genes belonging to the photosynthesis category. Mutation of single nucleic acid was mainly influenced by codon usage. The value percentage of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) in 6 Lagerstroemia species revealed that more photosynthesis genes have Ka or Ks only in Lagerstroemia fauriei, Lagerstroemia limii, and Lagerstroemia subcostata. These advances will facilitate the breeding of closely related Lagerstroemia species and deepen understanding on climatic adaptation of Lagerstroemia plants.
Collapse
Affiliation(s)
- Ling He
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Sujuan Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinnian Cheng
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Hanlin Huang
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Hongyu Dai
- College of Medicine, Southeast University, Nanjing, China
| | - Xin Wang
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Zhiyang Ding
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Ming Xu
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Haoran Gu
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Na Yan
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| | - Chunyan Wang
- College of Horticulture and Landscape Architecture, Jinling Institute of Technology, Nanjing, China
| |
Collapse
|
3
|
Köhler M, Reginato M, Jin JJ, Majure LC. More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae). ANNALS OF BOTANY 2023; 132:771-786. [PMID: 37467174 PMCID: PMC10799996 DOI: 10.1093/aob/mcad098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far. METHODS Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes. KEY RESULTS Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny. CONCLUSIONS Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.
Collapse
Affiliation(s)
- Matias Köhler
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jian-Jun Jin
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Lucas C Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
| |
Collapse
|
4
|
Rochaix J. Chloroplast protein import machinery and quality control. FEBS J 2022; 289:6908-6918. [PMID: 35472255 PMCID: PMC9790281 DOI: 10.1111/febs.16464] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/20/2022] [Accepted: 04/25/2022] [Indexed: 01/13/2023]
Abstract
Most chloroplast proteins are nucleus-encoded, translated on cytoplasmic ribosomes as precursor proteins, and imported into chloroplasts through TOC and TIC, the translocons of the outer and inner chloroplast envelope membranes. While the composition of the TOC complex is well established, there is still some controversy about the importance of a recently identified TIC complex consisting of Tic20, Tic214, Tic100, and Tic56. TOC and TIC form a supercomplex with a protein channel at the junction of the outer and inner envelope membranes through which preproteins are pulled into the stroma by the ATP-powered Ycf2 complex consisting of several FtsH-like ATPases and/or by chloroplast Hsp proteins. Several components of the TOC/TIC system are moonlighting proteins with additional roles in chloroplast gene expression and metabolism. Chaperones and co-chaperones, associated with TOC and TIC on the cytoplasmic and stromal side of the chloroplast envelope, participate in the unfolding and folding of the precursor proteins and act together with the ubiquitin-proteasome system in protein quality control. Chloroplast protein import is also intimately linked with retrograde signaling, revealing altogether an unsuspected complexity in the regulation of this process.
Collapse
Affiliation(s)
- Jean‐David Rochaix
- Departments of Molecular Biology and Plant BiologyUniversity of GenevaSwitzerland
| |
Collapse
|
5
|
Smith LT, Magdalena C, Przelomska NAS, Pérez-Escobar OA, Melgar-Gómez DG, Beck S, Negrão R, Mian S, Leitch IJ, Dodsworth S, Maurin O, Ribero-Guardia G, Salazar CD, Gutierrez-Sibauty G, Antonelli A, Monro AK. Revised Species Delimitation in the Giant Water Lily Genus Victoria (Nymphaeaceae) Confirms a New Species and Has Implications for Its Conservation. FRONTIERS IN PLANT SCIENCE 2022; 13:883151. [PMID: 35860537 PMCID: PMC9289450 DOI: 10.3389/fpls.2022.883151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Reliably documenting plant diversity is necessary to protect and sustainably benefit from it. At the heart of this documentation lie species concepts and the practical methods used to delimit taxa. Here, we apply a total-evidence, iterative methodology to delimit and document species in the South American genus Victoria (Nymphaeaceae). The systematics of Victoria has thus far been poorly characterized due to difficulty in attributing species identities to biological collections. This research gap stems from an absence of type material and biological collections, also the confused diagnosis of V. cruziana. With the goal of improving systematic knowledge of the genus, we compiled information from historical records, horticulture and geography and assembled a morphological dataset using citizen science and specimens from herbaria and living collections. Finally, we generated genomic data from a subset of these specimens. Morphological and geographical observations suggest four putative species, three of which are supported by nuclear population genomic and plastid phylogenomic inferences. We propose these three confirmed entities as robust species, where two correspond to the currently recognized V. amazonica and V. cruziana, the third being new to science, which we describe, diagnose and name here as V. boliviana Magdalena and L. T. Sm. Importantly, we identify new morphological and molecular characters which serve to distinguish the species and underpin their delimitations. Our study demonstrates how combining different types of character data into a heuristic, total-evidence approach can enhance the reliability with which biological diversity of morphologically challenging groups can be identified, documented and further studied.
Collapse
Affiliation(s)
- Lucy T. Smith
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Natalia A. S. Przelomska
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | | | - Darío G. Melgar-Gómez
- Herbario German Coimbra Sanz, Jardín Botánico Municipal de Santa Cruz de la Sierra, Santa Cruz de la Sierra, Bolivia
| | - Stephan Beck
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Raquel Negrão
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Sahr Mian
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | | | | | | | - Gloria Gutierrez-Sibauty
- Herbario German Coimbra Sanz, Jardín Botánico Municipal de Santa Cruz de la Sierra, Santa Cruz de la Sierra, Bolivia
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
6
|
Peng J, Zhao Y, Dong M, Liu S, Hu Z, Zhong X, Xu Z. Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes. BMC Ecol Evol 2021; 21:71. [PMID: 33931026 PMCID: PMC8086295 DOI: 10.1186/s12862-021-01800-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/22/2021] [Indexed: 01/18/2023] Open
Abstract
Background Cultivated tea is one of the most important economic and ecological trees distributed worldwide. Cultivated tea suffer from long-term targeted selection of traits and overexploitation of habitats by human beings, which may have changed its genetic structure. The chloroplast is an organelle with a conserved cyclic genomic structure, and it can help us better understand the evolutionary relationship of Camellia plants. Results We conducted comparative and evolutionary analyses on cultivated tea and wild tea, and we detected the evolutionary characteristics of cultivated tea. The chloroplast genome sizes of cultivated tea were slightly different, ranging from 157,025 to 157,100 bp. In addition, the cultivated species were more conserved than the wild species, in terms of the genome length, gene number, gene arrangement and GC content. However, comparing Camellia sinensis var. sinensis and Camellia sinensis var. assamica with their cultivars, the IR length variation was approximately 20 bp and 30 bp, respectively. The nucleotide diversity of 14 sequences in cultivated tea was higher than that in wild tea. Detailed analysis on the genomic variation and evolution of Camellia sinensis var. sinensis cultivars revealed 67 single nucleotide polymorphisms (SNPs), 46 insertions/deletions (indels), and 16 protein coding genes with nucleotide substitutions, while Camellia sinensis var. assamica cultivars revealed 4 indels. In cultivated tea, the most variable gene was ycf1. The largest number of nucleotide substitutions, five amino acids exhibited site-specific selection, and a 9 bp sequence insertion were found in the Camellia sinensis var. sinensis cultivars. In addition, phylogenetic relationship in the ycf1 tree suggested that the ycf1 gene has diverged in cultivated tea. Because C. sinensis var. sinensis and its cultivated species were not tightly clustered. Conclusions The cultivated species were more conserved than the wild species in terms of architecture and linear sequence order. The variation of the chloroplast genome in cultivated tea was mainly manifested in the nucleotide polymorphisms and sequence insertions. These results provided evidence regarding the influence of human activities on tea. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01800-1.
Collapse
Affiliation(s)
- Jiao Peng
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, 410004, Hunan, People's Republic of China.,Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, 410004, Hunan, People's Republic of China.,Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Meng Dong
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Shiquan Liu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Zhiyuan Hu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Xiaofen Zhong
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, 410004, Hunan, People's Republic of China. .,Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China. .,Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China.
| |
Collapse
|
7
|
Protein import into chloroplasts and its regulation by the ubiquitin-proteasome system. Biochem Soc Trans 2020; 48:71-82. [PMID: 31922184 PMCID: PMC7054747 DOI: 10.1042/bst20190274] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 02/08/2023]
Abstract
Chloroplasts are photosynthetic plant organelles descended from a bacterial ancestor. The vast majority of chloroplast proteins are synthesized in the cytosol and then imported into the chloroplast post-translationally. Translocation complexes exist in the organelle's outer and inner envelope membranes (termed TOC and TIC, respectively) to facilitate protein import. These systems recognize chloroplast precursor proteins and mediate their import in an energy-dependent manner. However, many unanswered questions remain regarding mechanistic details of the import process and the participation and functions of individual components; for example, the cytosolic events that mediate protein delivery to chloroplasts, the composition of the TIC apparatus, and the nature of the protein import motor all require resolution. The flux of proteins through TOC and TIC varies greatly throughout development and in response to specific environmental cues. The import process is, therefore, tightly regulated, and it has emerged that the ubiquitin-proteasome system (UPS) plays a key role in this regard, acting at several different steps in the process. The UPS is involved in: the selective degradation of transcription factors that co-ordinate the expression of chloroplast precursor proteins; the removal of unimported chloroplast precursor proteins in the cytosol; the inhibition of chloroplast biogenesis pre-germination; and the reconfiguration of the TOC apparatus in response to developmental and environmental signals in a process termed chloroplast-associated protein degradation. In this review, we highlight recent advances in our understanding of protein import into chloroplasts and how this process is regulated by the UPS.
Collapse
|
8
|
Jiang J, Chai X, Manavski N, Williams-Carrier R, He B, Brachmann A, Ji D, Ouyang M, Liu Y, Barkan A, Meurer J, Zhang L, Chi W. An RNA Chaperone-Like Protein Plays Critical Roles in Chloroplast mRNA Stability and Translation in Arabidopsis and Maize. THE PLANT CELL 2019; 31:1308-1327. [PMID: 30962391 PMCID: PMC6588297 DOI: 10.1105/tpc.18.00946] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/19/2019] [Accepted: 04/07/2019] [Indexed: 05/18/2023]
Abstract
A key characteristic of chloroplast gene expression is the predominance of posttranscriptional control via numerous nucleus-encoded RNA binding factors. Here, we explored the essential roles of the S1-domain-containing protein photosynthetic electron transfer B (petB)/ petD Stabilizing Factor (BSF) in the stabilization and translation of chloroplast mRNAs. BSF binds to the intergenic region of petB-petD, thereby stabilizing 3' processed petB transcripts and stimulating petD translation. BSF also binds to the 5' untranslated region of petA and activates its translation. BSF displayed nucleic-acid-melting activity in vitro, and its absence induces structural changes to target RNAs in vivo, suggesting that BSF functions as an RNA chaperone to remodel RNA structure. BSF physically interacts with the pentatricopeptide repeat protein Chloroplast RNA Processing 1 (AtCRP1) and the ribosomal release factor-like protein Peptide chain Release Factor 3 (PrfB3), whose established RNA ligands overlap with those of BSF. In addition, PrfB3 stimulated the RNA binding ability of BSF in vitro. We propose that BSF and PrfB3 cooperatively reduce the formation of secondary RNA structures within target mRNAs and facilitate AtCRP1 binding. The translation activation function of BSF for petD is conserved in Arabidopsis (Arabidopsis thaliana) and maize (Zea mays), but that for petA operates specifically in Arabidopsis. Our study sheds light on the mechanisms by which RNA binding proteins cooperatively regulate mRNA stability and translation in chloroplasts.
Collapse
Affiliation(s)
- Jingjing Jiang
- 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
| | - Xin Chai
- 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
| | - Nikolay Manavski
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology, 82152 Planegg-Martinsried, Germany
| | | | - Baoye He
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Andreas Brachmann
- Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Daili Ji
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yini Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Jörg Meurer
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology, 82152 Planegg-Martinsried, Germany
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wei Chi
- 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
| |
Collapse
|
9
|
Schäfer P, Helm S, Köhler D, Agne B, Baginsky S. Consequences of impaired 1-MDa TIC complex assembly for the abundance and composition of chloroplast high-molecular mass protein complexes. PLoS One 2019; 14:e0213364. [PMID: 30865669 PMCID: PMC6415892 DOI: 10.1371/journal.pone.0213364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/20/2019] [Indexed: 12/28/2022] Open
Abstract
We report a systematic analysis of chloroplast high-molecular mass protein complexes using a combination of native gel electrophoresis and absolute protein quantification by MSE. With this experimental setup, we characterized the effect of the tic56-3 mutation in the 1-MDa inner envelope translocase (TIC) on the assembly of the chloroplast proteome. We show that the tic56-3 mutation results in a reduction of the 1-MDa TIC complex to approximately 10% of wildtype levels. Hierarchical clustering confirmed the association of malate dehydrogenase (MDH) with an envelope-associated FtsH/FtsHi complex and suggested the association of a glycine-rich protein with the 1-MDa TIC complex. Depletion of this complex leads to a reduction of chloroplast ATPase to approx. 75% of wildtype levels, while the abundance of the FtsH/FtsHi complex is increased to approx. 140% of wildtype. The accumulation of the major photosynthetic complexes is not affected by the mutation, suggesting that tic56-3 plants can sustain a functional photosynthetic machinery despite a significant reduction of the 1-MDa TIC complex. Together our analysis expands recent efforts to catalogue the native molecular masses of chloroplast proteins and provides information on the consequences of impaired accumulation of the 1-MDa TIC translocase for chloroplast proteome assembly.
Collapse
Affiliation(s)
- Peter Schäfer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
- * E-mail:
| |
Collapse
|
10
|
Simkin AJ, López-Calcagno PE, Raines CA. Feeding the world: improving photosynthetic efficiency for sustainable crop production. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1119-1140. [PMID: 30772919 PMCID: PMC6395887 DOI: 10.1093/jxb/ery445] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/27/2018] [Indexed: 05/18/2023]
Abstract
A number of recent studies have provided strong support demonstrating that improving the photosynthetic processes through genetic engineering can provide an avenue to improve yield potential. The major focus of this review is on improvement of the Calvin-Benson cycle and electron transport. Consideration is also given to how altering regulatory process may provide an additional route to increase photosynthetic efficiency. Here we summarize some of the recent successes that have been observed through genetic manipulation of photosynthesis, showing that, in both the glasshouse and the field, yield can be increased by >40%. These results provide a clear demonstration of the potential for increasing yield through improvements in photosynthesis. In the final section, we consider the need to stack improvement in photosynthetic traits with traits that target the yield gap in order to provide robust germplasm for different crops across the globe.
Collapse
Affiliation(s)
- Andrew J Simkin
- NIAB EMR, New Road, East Malling, Kent, UK
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
| | | | - Christine A Raines
- School of Biological Sciences, Wivenhoe Park, University of Essex, Colchester, UK
| |
Collapse
|
11
|
Nowack ECM, Weber APM. Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:51-84. [PMID: 29489396 DOI: 10.1146/annurev-arplant-042817-040209] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles. Furthermore, we discuss the preconditions for the evolution of nitrogen-fixing organelles. Recent genomic data on previously undersampled cyanobacterial and protist taxa provide new clues to the origins of the host cell and endosymbiont, and proteomic approaches allow insights into the rearrangement of the endosymbiont proteome during organellogenesis. We conclude that in addition to endosymbiotic gene transfers, horizontal gene acquisitions from a broad variety of prokaryotic taxa were crucial to organelle evolution.
Collapse
Affiliation(s)
- Eva C M Nowack
- Microbial Symbiosis and Organelle Evolution Group, Biology Department, Heinrich Heine University, 40225 Düsseldorf, Germany;
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany;
| |
Collapse
|
12
|
Simkin AJ, McAusland L, Lawson T, Raines CA. Overexpression of the RieskeFeS Protein Increases Electron Transport Rates and Biomass Yield. PLANT PHYSIOLOGY 2017; 175:134-145. [PMID: 28754840 DOI: 10.1101/133702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/27/2017] [Indexed: 05/22/2023]
Abstract
In this study, we generated transgenic Arabidopsis (Arabidopsis thaliana) plants overexpressing the Rieske FeS protein (PetC), a component of the cytochrome b6f (cyt b6f) complex. Increasing the levels of this protein resulted in concomitant increases in the levels of cyt f (PetA) and cyt b6 (PetB), core proteins of the cyt b6f complex. Interestingly, an increase in the levels of proteins in both the photosystem I (PSI) and PSII complexes also was seen in the Rieske FeS overexpression plants. Although the mechanisms leading to these changes remain to be identified, the transgenic plants presented here provide novel tools to explore this. Importantly, overexpression of the Rieske FeS protein resulted in substantial and significant impacts on the quantum efficiency of PSI and PSII, electron transport, biomass, and seed yield in Arabidopsis plants. These results demonstrate the potential for manipulating electron transport processes to increase crop productivity.
Collapse
Affiliation(s)
- Andrew J Simkin
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Lorna McAusland
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Tracy Lawson
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Christine A Raines
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| |
Collapse
|
13
|
Simkin AJ, McAusland L, Lawson T, Raines CA. Overexpression of the RieskeFeS Protein Increases Electron Transport Rates and Biomass Yield. PLANT PHYSIOLOGY 2017; 175:134-145. [PMID: 28754840 PMCID: PMC5580758 DOI: 10.1104/pp.17.00622] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/27/2017] [Indexed: 05/18/2023]
Abstract
In this study, we generated transgenic Arabidopsis (Arabidopsis thaliana) plants overexpressing the Rieske FeS protein (PetC), a component of the cytochrome b6f (cyt b6f) complex. Increasing the levels of this protein resulted in concomitant increases in the levels of cyt f (PetA) and cyt b6 (PetB), core proteins of the cyt b6f complex. Interestingly, an increase in the levels of proteins in both the photosystem I (PSI) and PSII complexes also was seen in the Rieske FeS overexpression plants. Although the mechanisms leading to these changes remain to be identified, the transgenic plants presented here provide novel tools to explore this. Importantly, overexpression of the Rieske FeS protein resulted in substantial and significant impacts on the quantum efficiency of PSI and PSII, electron transport, biomass, and seed yield in Arabidopsis plants. These results demonstrate the potential for manipulating electron transport processes to increase crop productivity.
Collapse
Affiliation(s)
- Andrew J Simkin
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Lorna McAusland
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Tracy Lawson
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Christine A Raines
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| |
Collapse
|
14
|
Yerramsetty P, Agar EM, Yim WC, Cushman JC, Berry JO. An rbcL mRNA-binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4635-4649. [PMID: 28981775 PMCID: PMC5853808 DOI: 10.1093/jxb/erx264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Nuclear-encoded RLSB protein binds chloroplastic rbcL mRNA encoding the Rubisco large subunit. RLSB is highly conserved across all groups of land plants and is associated with positive post-transcriptional regulation of rbcL expression. In C3 leaves, RLSB and Rubisco occur in all chlorenchyma cell chloroplasts, while in C4 leaves these accumulate only within bundle sheath (BS) chloroplasts. RLSB's role in rbcL expression makes modification of its localization a likely prerequisite for the evolutionary restriction of Rubisco to BS cells. Taking advantage of evolutionarily conserved RLSB orthologs in several C3, C3-C4, C4-like, and C4 photosynthetic types within the genus Flaveria, we show that low level RLSB sequence divergence and modification to BS specificity coincided with ontogeny of Rubisco specificity and Kranz anatomy during C3 to C4 evolution. In both C3 and C4 species, Rubisco production reflected RLSB production in all cell types, tissues, and conditions examined. Co-localization occurred only in photosynthetic tissues, and both proteins were co-ordinately induced by light at post-transcriptional levels. RLSB is currently the only mRNA-binding protein to be associated with rbcL gene regulation in any plant, with variations in sequence and acquisition of cell type specificity reflecting the progression of C4 evolution within the genus Flaveria.
Collapse
Affiliation(s)
- Pradeep Yerramsetty
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Erin M Agar
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
| | - Won C Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - James O Berry
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
| |
Collapse
|
15
|
Graham SW, Lam VKY, Merckx VSFT. Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes. THE NEW PHYTOLOGIST 2017; 214:48-55. [PMID: 28067952 DOI: 10.1111/nph.14398] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/14/2016] [Indexed: 05/23/2023]
Abstract
Contents 48 I. 48 II. 50 III. 53 54 References 54 SUMMARY: We examine recent evidence for ratchet-like genome degradation in mycoheterotrophs, plants that obtain nutrition from fungi. Initial loss of the NADH dehydrogenase-like (NDH) complex may often set off an irreversible evolutionary cascade of photosynthetic gene losses. Genes for plastid-encoded subunits of RNA polymerase and photosynthetic enzymes with secondary functions (Rubisco and ATP synthase) can persist initially, with nonsynchronous and quite broad windows in the relative timing of their loss. Delayed losses of five core nonbioenergetic genes (especially trnE and accD, which respectively code for glutamyl tRNA and a subunit of acetyl-CoA carboxylase) probably explain long-term persistence of heterotrophic plastomes. The observed range of changes of mycoheterotroph plastomes is similar to that of holoparasites, although greater diversity of both probably remains to be discovered. These patterns of gene loss/retention can inform research programs on plastome function.
Collapse
Affiliation(s)
- Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Vincent S F T Merckx
- Understanding Evolution Group, Naturalis Biodiversity Center, Vondellaan 55, 2332 AA, Leiden, the Netherlands
| |
Collapse
|
16
|
Agne B, Köhler D, Baginsky S. Protein import-independent functions of Tic56, a component of the 1-MDa translocase at the inner chloroplast envelope membrane. PLANT SIGNALING & BEHAVIOR 2017; 12:e1284726. [PMID: 28125316 PMCID: PMC5399903 DOI: 10.1080/15592324.2017.1284726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Tic56 is an essential subunit of a 1-MDa protein complex at the inner chloroplast envelope membrane that comprises Tic100, Tic214 and the protein conducting channel protein Tic20-I. The complex was characterized as the "general protein import translocase" because mutants in either of its subunits have a severe growth phenotype and fail to assemble a photosynthetic machinery. In a recent publication we show that the albino phenotype of tic56-1 mutants results at least in part from a defect in ribosome assembly and a deficiency in plastid translation. We furthermore could not detect any impairment of protein import activity with plastids from tic56-3 mutants, despite a lack of full-length Tic56 and a decreased abundance of other 1-MDa complex subunits. These findings suggest that the 1-MDa complex consists of subunits that have functions other than protein import.
Collapse
Affiliation(s)
- Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg, Halle (Saale), Germany
| | - Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg, Halle (Saale), Germany
- CONTACT Sacha Baginsky Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| |
Collapse
|
17
|
Sjuts I, Soll J, Bölter B. Import of Soluble Proteins into Chloroplasts and Potential Regulatory Mechanisms. FRONTIERS IN PLANT SCIENCE 2017; 8:168. [PMID: 28228773 PMCID: PMC5296341 DOI: 10.3389/fpls.2017.00168] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/26/2017] [Indexed: 05/20/2023]
Abstract
Chloroplasts originated from an endosymbiotic event in which a free-living cyanobacterium was engulfed by an ancestral eukaryotic host. During evolution the majority of the chloroplast genetic information was transferred to the host cell nucleus. As a consequence, proteins formerly encoded by the chloroplast genome are now translated in the cytosol and must be subsequently imported into the chloroplast. This process involves three steps: (i) cytosolic sorting procedures, (ii) binding to the designated receptor-equipped target organelle and (iii) the consecutive translocation process. During import, proteins have to overcome the two barriers of the chloroplast envelope, namely the outer envelope membrane (OEM) and the inner envelope membrane (IEM). In the majority of cases, this is facilitated by two distinct multiprotein complexes, located in the OEM and IEM, respectively, designated TOC and TIC. Plants are constantly exposed to fluctuating environmental conditions such as temperature and light and must therefore regulate protein composition within the chloroplast to ensure optimal functioning of elementary processes such as photosynthesis. In this review we will discuss the recent models of each individual import stage with regard to short-term strategies that plants might use to potentially acclimate to changes in their environmental conditions and preserve the chloroplast protein homeostasis.
Collapse
Affiliation(s)
- Inga Sjuts
- Department Biologie I-Botanik, Ludwig-Maximilians-UniversitätPlanegg-Martinsried, Germany
| | - Jürgen Soll
- Department Biologie I-Botanik, Ludwig-Maximilians-UniversitätPlanegg-Martinsried, Germany
- Munich Center for Integrated Protein Science CiPSM, Ludwig-Maximilians-UniversitätMunich, Germany
| | - Bettina Bölter
- Department Biologie I-Botanik, Ludwig-Maximilians-UniversitätPlanegg-Martinsried, Germany
- Munich Center for Integrated Protein Science CiPSM, Ludwig-Maximilians-UniversitätMunich, Germany
- *Correspondence: Bettina Bölter,
| |
Collapse
|
18
|
Bölter B, Soll J. Once upon a Time - Chloroplast Protein Import Research from Infancy to Future Challenges. MOLECULAR PLANT 2016; 9:798-812. [PMID: 27142186 DOI: 10.1016/j.molp.2016.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/25/2016] [Accepted: 04/27/2016] [Indexed: 05/08/2023]
Abstract
Protein import into chloroplasts has been a focus of research for several decades. The first publications dealing with this fascinating topic appeared in the 1970s. From the initial realization that many plastid proteins are being encoded for in the nucleus and require transport into their target organelle to the identification of import components in the cytosol, chloroplast envelopes, and stroma, as well as elucidation of some mechanistic details, more fascinating aspects are still being unraveled. With this overview, we present a survey of the beginnings of chloroplast protein import research, the first steps on this winding road, and end with a glimpse into the future.
Collapse
Affiliation(s)
- Bettina Bölter
- Department Biologie I-Botanik, Ludwig-Maximilians-Universität, Großhaderner Straße 2-4, 82152 Planegg-Martinsried, Germany; Munich Center for Integrated Protein Science CiPSM, Ludwig-Maximilians-Universität, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
| | - Jürgen Soll
- Department Biologie I-Botanik, Ludwig-Maximilians-Universität, Großhaderner Straße 2-4, 82152 Planegg-Martinsried, Germany; Munich Center for Integrated Protein Science CiPSM, Ludwig-Maximilians-Universität, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| |
Collapse
|