1
|
He X, Yang Y, Zhang X, Zhao W, Zhang Q, Luo C, Xie Y, Li Z, Wang X. Comparative Chloroplast Genomics of Actinidia deliciosa Cultivars: Insights into Positive Selection and Population Evolution. Int J Mol Sci 2025; 26:4387. [PMID: 40362623 PMCID: PMC12072308 DOI: 10.3390/ijms26094387] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 05/03/2025] [Accepted: 05/04/2025] [Indexed: 05/15/2025] Open
Abstract
The chloroplast genome, as an important evolutionary marker, can provide a new breakthrough direction for the population evolution of plant species. Actinidia deliciosa represents one of the most economically significant and widely cultivated fruit species in the genus Actinidia. In this study, we sequenced and analyzed the complete chloroplast genomes of seven cultivars of Actinidia. deliciosa to detect the structural variation and population evolutionary characteristics. The total genome size ranged from 156,404 bp (A. deliciosa cv. Hayward) to 156,495 bp (A. deliciosa cv. Yate). A total of 321 simple sequence repeats (SSRs) and 1335 repetitive sequences were identified. Large-scale repeat sequences may facilitate indels and substitutions, molecular variations in A. deliciosa varieties' chloroplast genomes. Additionally, four polymorphic chloroplast DNA loci (atpF-atpH, atpH-atpI, atpB, and accD) were detected, which could potentially provide useful molecular genetic markers for further population genetics studies within A. deliciosa varieties. Site-specific selection analysis revealed that six genes (atpA, rps3, rps7, rpl22, rbcL, and ycf2) underwent protein sequence evolution. These genes may have played key roles in the adaptation of A. deliciosa to various environments. The population evolutionary analysis suggested that A. deliciosa cultivars were clustered into an individual evolutionary branch with moderate-to-high support values. These results provided a foundational genomic resource that will be a major contribution to future studies of population genetics, adaptive evolution, and genetic improvement in Actinidia.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Zhonghu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (X.H.); (Y.Y.); (X.Z.); (W.Z.); (Q.Z.); (C.L.); (Y.X.)
| | - Xiaojuan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (X.H.); (Y.Y.); (X.Z.); (W.Z.); (Q.Z.); (C.L.); (Y.X.)
| |
Collapse
|
2
|
Lenzen B, Rösch F, Legen J, Ruwe H, Kachariya N, Sattler M, Small I, Schmitz-Linneweber C. The chloroplast RNA-binding protein CP29A supports rbcL expression during cold acclimation. Proc Natl Acad Sci U S A 2025; 122:e2403969122. [PMID: 39879235 PMCID: PMC11804644 DOI: 10.1073/pnas.2403969122] [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: 02/26/2024] [Accepted: 12/17/2024] [Indexed: 01/31/2025] Open
Abstract
The chloroplast genome encodes key components of the photosynthetic light reaction machinery as well as the large subunit of the enzyme central for carbon fixation, Ribulose-1,5-bisphosphat-carboxylase/-oxygenase (RuBisCo). Its expression is predominantly regulated posttranscriptionally, with nuclear-encoded RNA-binding proteins (RBPs) playing a key role. Mutants of chloroplast gene expression factors often exhibit impaired chloroplast biogenesis, especially in cold conditions. Low temperatures pose a challenge for plants as this leads to electron imbalances and oxidative damage. A well-known response of plants to this problem is to increase the production of RuBisCo and other Calvin Cycle enzymes in the cold, but how this is achieved is unclear. The chloroplast RBP CP29A has been shown to be essential for cold resistance in growing leaf tissue of Arabidopsis thaliana. Here, we examined CP29A-RNA interaction sites at nucleotide resolution. We found that CP29A preferentially binds to the 5'-untranslated region of rbcL, downstream of the binding site of the pentatricopeptide repeat protein MATURATION OF RBCL 1 (MRL1). MRL1 is an RBP known to be necessary for the accumulation of rbcL. In Arabidopsis mutants lacking CP29A, we were unable to observe significant effects on rbcL, possibly due to CP29A's restricted role in a limited number of cells at the base of leaves. In contrast, CRISPR/Cas9-induced mutants of tobacco NtCP29A exhibit cold-dependent photosynthetic deficiencies throughout the entire leaf blade. This is associated with a parallel reduction in rbcL mRNA and RbcL protein accumulation. Our work indicates that a chloroplast RNA-binding protein contributes to cold acclimation of RbcL production.
Collapse
Affiliation(s)
- Benjamin Lenzen
- Molecular Genetics, Institute of Biology, Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin10115, Germany
| | - Florian Rösch
- Molecular Genetics, Institute of Biology, Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin10115, Germany
| | - Julia Legen
- Molecular Genetics, Institute of Biology, Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin10115, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin10115, Germany
| | - Nitin Kachariya
- Molecular Targets and Therapeutics Center, Helmholtz Munich, Institute of Structural Biology, Neuherberg85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University Munich School of Natural Sciences, Technical University of Munich, Garching85747, Germany
| | - Michael Sattler
- Molecular Targets and Therapeutics Center, Helmholtz Munich, Institute of Structural Biology, Neuherberg85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University Munich School of Natural Sciences, Technical University of Munich, Garching85747, Germany
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA6009, Australia
| | - Christian Schmitz-Linneweber
- Molecular Genetics, Institute of Biology, Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin10115, Germany
| |
Collapse
|
3
|
Wu H, Li DZ, Ma PF. Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 2024; 22:97. [PMID: 38679718 PMCID: PMC11057118 DOI: 10.1186/s12915-024-01890-5] [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: 07/27/2023] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a "small-large-moderate" trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. CONCLUSIONS The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.
Collapse
Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
4
|
Tian Y, Liu X, Xu Y, Yu B, Wang L, Qu X. Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et S. C. Chen plastomes and utility of plastomes mutational hotspots. Sci Rep 2023; 13:15622. [PMID: 37730791 PMCID: PMC10511529 DOI: 10.1038/s41598-023-42945-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023] Open
Abstract
Tiandong is a vital traditional Chinese herbal medicine. It is derived from the tuber root of the Asparagus cochinchinensis according to the Pharmacopoeia of the people's republic of China (2020 Edition). On account of the similar morphology, Asparagus meioclados and Asparagus munitus were used as Tian-Dong in southwest China. Chloroplast (cp) genomes are highly active genetic components of plants and play an extremely important role in improving the efficiency of the identification of plant species. To differentiate the medicinal plants belonging to the genus Asparagus, we sequenced and analyzed the complete plastomes (plastid genomes) of A. meioclados and A. munitus and obtained two plastomes whose length changed to 156,515 bp and 156,381 bp, respectively. A total of 111 unique genes have been detected in plastome, which included 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In plastomes of A. meioclados and A. munitus, 14,685 and 14,987 codons were detected, among which 9942 and 10,207 had the relative synonymous codon usage (RSCU) values higher than 1, respectively. A. meioclados and A. munitus have 26 SSRs patterns, among which A. meioclados was 25 and A. munitus 21. The average Ka/Ks value was 0.36, and positive selection was detected in genes of the photosynthetic system (ndhF and rbcL) in Asparagus species. To perform the comparative analysis of plastomes, the two newly sequenced plastomes of the A. meioclados and A. munitus species were compared with that of A. cochinchinensis, and 12 hotspots, including 5 coding regions and 7 inter-genomic regions, were identified. Based on the whole plastome of Asparagus, 2 divergent hotspots (accD and rpl32-trnL-UAG) and 1 international barcode fragment (rbcL) were screened, which may be used as particular molecular markers for the identification of Asparagus species. In addition, we determined the phylogenetic relationship between A. meioclados and A. munitus in the genus Asparagus. This study enriches our knowledge of the molecular evolutionary relationships of the Asparagus genus and provides treasured data records for species identification, molecular breeding, and evolutionary analysis of this genus.
Collapse
Affiliation(s)
- Yulu Tian
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, No. 1166 Liutai Avenue, Wenjiang District, Chengdu, 611137, China
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Xue Liu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
| | - Yuanjiang Xu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Benxia Yu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Le Wang
- College of Life Science and Food Engineering, Chongqing Three Gorges University, 666 Tianxing Road, Wanzhou District, Chongqing, 404100, China
| | - Xianyou Qu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
| |
Collapse
|
5
|
Li C, Liu Y, Lin F, Zheng Y, Huang P. Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae). PeerJ 2022; 10:e13570. [PMID: 35795179 PMCID: PMC9252178 DOI: 10.7717/peerj.13570] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/20/2022] [Indexed: 01/17/2023] Open
Abstract
Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. Moreover, three genera of the Pterocarpus clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of Dalbergia species with their relatives.
Collapse
Affiliation(s)
- Changhong Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Wenzhou, Zhejiang, China
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
6
|
Complete Chloroplast Genome of Cnidium monnieri (Apiaceae) and Comparisons with Other Tribe Selineae Species. DIVERSITY 2022. [DOI: 10.3390/d14050323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cnidium monnieri is an economically important traditional Chinese medicinal plant. In this study, the complete chloroplast (cp) genome of C. monnieri was determined using the Illumina paired-end sequencing, the GetOrganelle de novo assembly strategy, as well as the GeSeq annotation method. Our results showed that the cp genome was 147,371 bp in length with 37.4% GC content and included a large single-copy region (94,361 bp) and a small single-copy region (17,552 bp) separated by a pair of inverted repeat regions (17,729 bp). A total of 129 genes were contained in the cp genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. We also investigated codon usage, RNA editing, repeat sequences, simple sequence repeats (SSRs), IR boundaries, and pairwise Ka/Ks ratios. Four hypervariable regions (trnD-trnY-trnE-trnT, ycf2, ndhF-rpl32-trnL, and ycf1) were identified as candidate molecular markers for species authentication. The phylogenetic analyses supported non-monophyly of Cnidium and C. monnieri located in tribe Selineae based on the cp genome sequences and internal transcribed spacer (ITS) sequences. The incongruence of the phylogenetic position of C. monnieri between ITS and cpDNA phylogenies suggested that C. monnieri might have experienced complex evolutions with hybrid and incomplete lineage sorting. All in all, the results presented herein will provide plentiful chloroplast genomic resources for studies of the taxonomy, phylogeny, and species authentication of C. monnieri. Our study is also conducive to elucidating the phylogenetic relationships and taxonomic position of Cnidium.
Collapse
|
7
|
Zavafer A, Mancilla C. Concepts of photochemical damage of Photosystem II and the role of excessive excitation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2021. [DOI: 10.1016/j.jphotochemrev.2021.100421] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
8
|
Dong PB, Wang RN, Afzal N, Liu ML, Yue M, Liu JN, Tan JL, Li ZH. Phylogenetic relationships and molecular evolution of woody forest tree family Aceraceae based on plastid phylogenomics and nuclear gene variations. Genomics 2021; 113:2365-2376. [PMID: 34051325 DOI: 10.1016/j.ygeno.2021.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/18/2021] [Accepted: 03/25/2021] [Indexed: 11/29/2022]
Abstract
The forest tree family Aceraceae is widespread in the northern hemisphere and it has ecological and economic importance. However, the phylogenetic relationships and classifications within the family are still controversial due to transitional intraspecific morphological characteristics and introgression hybridization among species. In this study, we determined the evolutionary relationships and molecular evolution of Aceraceae based on plastid phylogenomics and two nuclear gene variations. Phylogenetic analysis based on the plastid genomes suggested that Aceraceae species can be divided into two larger sub-clades corresponding to the two genera Acer and Dipteronia. Conjoint analysis of the plastid and nuclear gene sequences supported the classification with two genera in the family. Molecular dating showed that the two genera diverged 60.2 million years ago, which is generally consistently with previously reported results. Divergence hotspots and positively selected genes identified in the plastid genomes could be useful genetic resources in Aceraceae.
Collapse
Affiliation(s)
- Peng-Bin Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ruo-Nan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Nawal Afzal
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jian-Ni Liu
- Early Life Institute, State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an 710069, China
| | - Jiang-Li Tan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| |
Collapse
|
9
|
Wen F, Wu X, Li T, Jia M, Liu X, Liao L. The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China. BMC Genomics 2021; 22:161. [PMID: 33676415 PMCID: PMC7937279 DOI: 10.1186/s12864-021-07484-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. RESULTS A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. CONCLUSIONS This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.
Collapse
Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinsheng Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Liang Liao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| |
Collapse
|
10
|
Xie DF, Tan JB, Yu Y, Gui LJ, Su DM, Zhou SD, He XJ. Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences. ANNALS OF BOTANY 2020; 125:1039-1055. [PMID: 32239179 PMCID: PMC7262478 DOI: 10.1093/aob/mcaa024] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/01/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study. METHODS In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families. RESULTS Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species. CONCLUSIONS Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.
Collapse
Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Jin-Bo Tan
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Lin-Jian Gui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Dan-Mei Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| |
Collapse
|
11
|
Krieger-Liszkay A, Krupinska K, Shimakawa G. The impact of photosynthesis on initiation of leaf senescence. PHYSIOLOGIA PLANTARUM 2019; 166:148-164. [PMID: 30629302 DOI: 10.1111/ppl.12921] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/21/2018] [Accepted: 01/07/2019] [Indexed: 05/20/2023]
Abstract
Senescence is the last stage of leaf development preceding the death of the organ, and it is important for nutrient remobilization and for feeding sink tissues. There are many reports on leaf senescence, but the mechanisms initiating leaf senescence are still poorly understood. Leaf senescence is affected by many environmental factors and seems to vary in different species and even varieties of plants, which makes it difficult to generalize the mechanism. Here, we give an overview on studies reporting about alterations in the composition of the photosynthetic electron transport chain in chloroplasts during senescence. We hypothesize that alternative electron flow and related generation of the proton motive force required for ATP synthesis become increasingly important during progression of senescence. We address the generation of reactive oxygen species (ROS) in chloroplasts in the initiation of senescence, retrograde signaling from the chloroplast to the nucleus and ROS-dependent signaling associated with leaf senescence. Finally, a few ideas for increasing crop yields by increasing the chloroplast lifespan are presented.
Collapse
Affiliation(s)
- Anja Krieger-Liszkay
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Saclay, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette, France
| | - Karin Krupinska
- Institute of Botany, University of Kiel, D-24098, Kiel, Germany
| | - Ginga Shimakawa
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Saclay, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette, France
| |
Collapse
|
12
|
Liu ML, Fan WB, Wang N, Dong PB, Zhang TT, Yue M, Li ZH. Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships. Int J Mol Sci 2018; 19:E4039. [PMID: 30558106 PMCID: PMC6321470 DOI: 10.3390/ijms19124039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 01/08/2023] Open
Abstract
Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.
Collapse
Affiliation(s)
- Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Wei-Bing Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Ning Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Peng-Bin Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Ting-Ting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| |
Collapse
|
13
|
Huang W, Suorsa M, Zhang SB. In vivo regulation of thylakoid proton motive force in immature leaves. PHOTOSYNTHESIS RESEARCH 2018; 138:207-218. [PMID: 30056561 DOI: 10.1007/s11120-018-0565-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
In chloroplast, proton motive force (pmf) is critical for ATP synthesis and photoprotection. To prevent photoinhibition of photosynthetic apparatus, proton gradient (ΔpH) across the thylakoid membranes needs to be built up to minimize the production of reactive oxygen species (ROS) in thylakoid membranes. However, the regulation of thylakoid pmf in immature leaves is little known. In this study, we compared photosynthetic electron sinks, P700 redox state, non-photochemical quenching (NPQ), and electrochromic shift (ECS) signal in immature and mature leaves of a cultivar of Camellia. The immature leaves displayed lower linear electron flow and cyclic electron flow, but higher levels of NPQ and P700 oxidation ratio under high light. Meanwhile, we found that pmf and ΔpH were higher in the immature leaves. Furthermore, the immature leaves showed significantly lower thylakoid proton conductivity than mature leaves. These results strongly indicated that immature leaves can build up enough ΔpH by modulating proton efflux from the lumenal side to the stromal side of thylakoid membranes, which is essential to prevent photoinhibition via thermal energy dissipation and photosynthetic control of electron transfer. This study highlights that the activity of chloroplast ATP synthase is a key safety valve for photoprotection in immature leaves.
Collapse
Affiliation(s)
- Wei Huang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | | | - Shi-Bao Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| |
Collapse
|
14
|
Huang W, Tikkanen M, Cai YF, Wang JH, Zhang SB. Chloroplastic ATP synthase optimizes the trade-off between photosynthetic CO2 assimilation and photoprotection during leaf maturation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1067-1074. [DOI: 10.1016/j.bbabio.2018.06.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/03/2018] [Accepted: 06/08/2018] [Indexed: 11/24/2022]
|
15
|
Huang W, Tikkanen M, Zhang SB. Photoinhibition of photosystem I in Nephrolepis falciformis depends on reactive oxygen species generated in the chloroplast stroma. PHOTOSYNTHESIS RESEARCH 2018; 137:129-140. [PMID: 29357086 DOI: 10.1007/s11120-018-0484-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/17/2018] [Indexed: 05/26/2023]
Abstract
We studied how high light causes photoinhibition of photosystem I (PSI) in the shade-demanding fern Nephrolepis falciformis, in an attempt to understand the mechanism of PSI photoinhibition under natural field conditions. Intact leaves were treated with constant high light and fluctuating light. Detached leaves were treated with constant high light in the presence and absence of methyl viologen (MV). Chlorophyll fluorescence and P700 signal were determined to estimate photoinhibition. PSI was highly oxidized under high light before treatments. N. falciformis showed significantly stronger photoinhibition of PSI and PSII under constant high light than fluctuating light. These results suggest that high levels of P700 oxidation ratio cannot prevent PSI photoinhibition under high light in N. falciformis. Furthermore, photoinhibition of PSI in N. falciformis was largely accelerated in the presence of MV that promotes the production of superoxide anion radicals in the chloroplast stroma by accepting electrons from PSI. From these results, we propose that photoinhibition of PSI in N. falciformis is mainly caused by superoxide radicals generated in the chloroplast stroma, which is different from the mechanism of PSI photoinhibition in Arabidopsis thaliana and spinach. Here, we provide some new insights into the PSI photoinhibition under natural field conditions.
Collapse
Affiliation(s)
- Wei Huang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Mikko Tikkanen
- Department of Biochemistry, Molecular Plant Biology, University of Turku, 20014, Turku, Finland
| | - Shi-Bao Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| |
Collapse
|
16
|
Xie DF, Yu Y, Deng YQ, Li J, Liu HY, Zhou SD, He XJ. Comparative Analysis of the Chloroplast Genomes of the Chinese Endemic Genus Urophysa and Their Contribution to Chloroplast Phylogeny and Adaptive Evolution. Int J Mol Sci 2018; 19:ijms19071847. [PMID: 29932433 PMCID: PMC6073864 DOI: 10.3390/ijms19071847] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 11/16/2022] Open
Abstract
Urophysa is a Chinese endemic genus comprising two species, Urophysa rockii and Urophysa henryi. In this study, we sequenced the complete chloroplast (cp) genomes of these two species and of their relative Semiquilegia adoxoides. Illumina sequencing technology was used to compare sequences, elucidate the intra- and interspecies variations, and infer the phylogeny relationship with other Ranunculaceae family species. A typical quadripartite structure was detected, with a genome size from 158,473 to 158,512 bp, consisting of a pair of inverted repeats separated by a small single-copy region and a large single-copy region. We analyzed the nucleotide diversity and repeated sequences components and conducted a positive selection analysis by the codon-based substitution on single-copy coding sequence (CDS). Seven regions were found to possess relatively high nucleotide diversity, and numerous variable repeats and simple sequence repeats (SSR) markers were detected. Six single-copy genes (atpA, rpl20, psaA, atpB, ndhI, and rbcL) resulted to have high posterior probabilities of codon sites in the positive selection analysis, which means that the six genes may be under a great selection pressure. The visualization results of the six genes showed that the amino acid properties across each column of all species are variable in different genera. All these regions with high nucleotide diversity, abundant repeats, and under positive selection will provide potential plastid markers for further taxonomic, phylogenetic, and population genetics studies in Urophysa and its relatives. Phylogenetic analyses based on the 79 single-copy genes, the whole complete genome sequences, and all CDS sequences showed same topologies with high support, and U. rockii was closely clustered with U. henryi within the Urophysa genus, with S. adoxoides as their closest relative. Therefore, the complete cp genomes in Urophysa species provide interesting insights and valuable information that can be used to identify related species and reconstruct their phylogeny.
Collapse
Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Yi-Qi Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Hai-Ying Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| |
Collapse
|
17
|
Abstract
Bisphenol A (BPA), a widely distributed pollutant, suppresses photosynthesis in leaves. In previous studies on higher plants, the plants were treated by BPA through irrigation to root. This method cannot distinguish whether the BPA directly suppresses photosynthesis in leaves, or indirectly influences photosynthesis through affecting the function of root. Here, only the leaves but not the roots of cucumber were infiltrated with BPA solution. The photosystem II and I (PSII, PSI) were insensitive to BPA under darkness. BPA aggravated the PSII but not the PSI photoinhibition under light. BPA also inhibited CO2 assimilation, and the effect of BPA on PSII photoinhibition disappeared when the CO2 assimilation was blocked. The H2O2 accumulated in BPA-treated leaves under light. And the BPA-caused PSII photoinhibition was prevented under low (2%) O2. We also proved that the BPA-caused PSII photoinhibition depend on the turnover of D1 protein. In conclusion, this study proved that BPA could directly suppress photosynthesis in leaves, however, BPA does not damage PSII directly, but inhibits CO2 assimilation and over-reduces the electron transport chain under light, which increases the production of reactive oxygen species (H2O2), the over-accumulated ROS inhibits the turnover of D1 protein and consequently aggravates PSII photoinhibition.
Collapse
|
18
|
Li YT, Liang Y, Li YN, Che XK, Zhao SJ, Zhang ZS, Gao HY. Mechanisms by which Bisphenol A affect the photosynthetic apparatus in cucumber (Cucumis sativus L.) leaves. Sci Rep 2018. [PMID: 29523804 DOI: 10.1038/s41598-018-22486-22484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Bisphenol A (BPA), a widely distributed pollutant, suppresses photosynthesis in leaves. In previous studies on higher plants, the plants were treated by BPA through irrigation to root. This method cannot distinguish whether the BPA directly suppresses photosynthesis in leaves, or indirectly influences photosynthesis through affecting the function of root. Here, only the leaves but not the roots of cucumber were infiltrated with BPA solution. The photosystem II and I (PSII, PSI) were insensitive to BPA under darkness. BPA aggravated the PSII but not the PSI photoinhibition under light. BPA also inhibited CO2 assimilation, and the effect of BPA on PSII photoinhibition disappeared when the CO2 assimilation was blocked. The H2O2 accumulated in BPA-treated leaves under light. And the BPA-caused PSII photoinhibition was prevented under low (2%) O2. We also proved that the BPA-caused PSII photoinhibition depend on the turnover of D1 protein. In conclusion, this study proved that BPA could directly suppress photosynthesis in leaves, however, BPA does not damage PSII directly, but inhibits CO2 assimilation and over-reduces the electron transport chain under light, which increases the production of reactive oxygen species (H2O2), the over-accumulated ROS inhibits the turnover of D1 protein and consequently aggravates PSII photoinhibition.
Collapse
Affiliation(s)
- Yu-Ting Li
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Ying Liang
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Yue-Nan Li
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Xing-Kai Che
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Shi-Jie Zhao
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Zi-Shan Zhang
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China.
| | - Hui-Yuan Gao
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| |
Collapse
|
19
|
Dong WL, Wang RN, Zhang NY, Fan WB, Fang MF, Li ZH. Molecular Evolution of Chloroplast Genomes of Orchid Species: Insights into Phylogenetic Relationship and Adaptive Evolution. Int J Mol Sci 2018; 19:ijms19030716. [PMID: 29498674 PMCID: PMC5877577 DOI: 10.3390/ijms19030716] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 01/08/2023] Open
Abstract
Orchidaceae is the 3rd largest family of angiosperms, an evolved young branch of monocotyledons. This family contains a number of economically-important horticulture and flowering plants. However, the limited availability of genomic information largely hindered the study of molecular evolution and phylogeny of Orchidaceae. In this study, we determined the evolutionary characteristics of whole chloroplast (cp) genomes and the phylogenetic relationships of the family Orchidaceae. We firstly characterized the cp genomes of four orchid species: Cremastra appendiculata, Calanthe davidii, Epipactis mairei, and Platanthera japonica. The size of the chloroplast genome ranged from 153,629 bp (C. davidi) to 160,427 bp (E. mairei). The gene order, GC content, and gene compositions are similar to those of other previously-reported angiosperms. We identified that the genes of ndhC, ndhI, and ndhK were lost in C. appendiculata, in that the ndh I gene was lost in P. japonica and E. mairei. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in orchid species. E. mairei had the highest number of repeats (81), while C. davidii had the lowest number (57). The total number of Simple Sequence Repeats is at least 50 in C. davidii, and, at most, 78 in P. japonica. Interestingly, we identified 16 genes with positive selection sites (the psbH, petD, petL, rpl22, rpl32, rpoC1, rpoC2, rps12, rps15, rps16, accD, ccsA, rbcL, ycf1, ycf2, and ycf4 genes), which might play an important role in the orchid species’ adaptation to diverse environments. Additionally, 11 mutational hotspot regions were determined, including five non-coding regions (ndhB intron, ccsA-ndhD, rpl33-rps18, ndhE-ndhG, and ndhF-rpl32) and six coding regions (rps16, ndhC, rpl32, ndhI, ndhK, and ndhF). The phylogenetic analysis based on whole cp genomes showed that C. appendiculata was closely related to C. striata var. vreelandii, while C. davidii and C. triplicate formed a small monophyletic evolutionary clade with a high bootstrap support. In addition, five subfamilies of Orchidaceae, Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae, formed a nested evolutionary relationship in the phylogenetic tree. These results provide important insights into the adaptive evolution and phylogeny of Orchidaceae.
Collapse
Affiliation(s)
- Wan-Lin Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Ruo-Nan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Na-Yao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Wei-Bing Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Min-Feng Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| |
Collapse
|
20
|
Fan WB, Wu Y, Yang J, Shahzad K, Li ZH. Comparative Chloroplast Genomics of Dipsacales Species: Insights Into Sequence Variation, Adaptive Evolution, and Phylogenetic Relationships. FRONTIERS IN PLANT SCIENCE 2018; 9:689. [PMID: 29875791 PMCID: PMC5974163 DOI: 10.3389/fpls.2018.00689] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/04/2018] [Indexed: 05/19/2023]
Abstract
In general, the chloroplast genomes of angiosperms are considered to be highly conserved and affected little by adaptive evolution. In this study, we tested this hypothesis based on sequence differentiation and adaptive variation in the plastid genomes in the order Dipsacales. We sequenced the plastid genomes of one Adoxaceae species and six Caprifoliaceae species, and together with seven previously released Dipsacales chloroplasts, we determined the sequence variations, evolutionary divergence of the plastid genomes, and phylogeny of Dipsacales species. The chloroplast genomes of Adoxaceae species ranged in size from 157,074 bp (Sinadoxa corydalifolia) to 158,305 bp (Sambucus williamsii), and the plastid genomes of Caprifoliaceae varied from 154,732 bp (Lonicera fragrantissima var. lancifolia) to 156,874 bp (Weigela florida). The differences in the number of genes in Caprifoliaceae and Adoxaceae species were largely due to the expansion and contraction of inverted repeat regions. In addition, we found that the number of dispersed repeats (Adoxaceae = 37; Caprifoliaceae = 384) was much higher than that of tandem repeats (Adoxaceae = 34; Caprifoliaceae = 291) in Dipsacales species. Interestingly, we determined 19 genes with positive selection sites, including three genes encoding ATP protein subunits (atpA, atpB, and atpI), four genes for ribosome protein small subunits (rps3, rps7, rps14, and rps15), four genes for photosystem protein subunits (psaA, psaJ, psbC, and pabK), two genes for ribosome protein large subunits (rpl22 and rpl32), and the clpP, infA, matK, rbcL, ycf1, and ycf2 genes. These gene regions may have played key roles in the adaptation of Dipsacales to diverse environments. In addition, phylogenetic analysis based on the plastid genomes strongly supported the division of 14 Dipsacales species into two previously recognized sections. The diversification of Adoxaceae and Caprifoliaceae was dated to the late Cretaceous and Tertiary periods. The availability of these chloroplast genomes provides useful genetic information for studying taxonomy, phylogeny, and species evolution in Dipsacales.
Collapse
|
21
|
Wu Y, Liu F, Yang DG, Li W, Zhou XJ, Pei XY, Liu YG, He KL, Zhang WS, Ren ZY, Zhou KH, Ma XF, Li ZH. Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny. FRONTIERS IN PLANT SCIENCE 2018; 9:376. [PMID: 29619041 PMCID: PMC5871733 DOI: 10.3389/fpls.2018.00376] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/06/2018] [Indexed: 05/10/2023]
Abstract
Cotton is one of the most economically important fiber crop plants worldwide. The genus Gossypium contains a single allotetraploid group (AD) and eight diploid genome groups (A-G and K). However, the evolution of repeat sequences in the chloroplast genomes and the phylogenetic relationships of Gossypium species are unclear. Thus, we determined the variations in the repeat sequences and the evolutionary relationships of 40 cotton chloroplast genomes, which represented the most diverse in the genus, including five newly sequenced diploid species, i.e., G. nandewarense (C1-n), G. armourianum (D2-1), G. lobatum (D7), G. trilobum (D8), and G. schwendimanii (D11), and an important semi-wild race of upland cotton, G. hirsutum race latifolium (AD1). The genome structure, gene order, and GC content of cotton species were similar to those of other higher plant plastid genomes. In total, 2860 long sequence repeats (>10 bp in length) were identified, where the F-genome species had the largest number of repeats (G. longicalyx F1: 108) and E-genome species had the lowest (G. stocksii E1: 53). Large-scale repeat sequences possibly enrich the genetic information and maintain genome stability in cotton species. We also identified 10 divergence hotspot regions, i.e., rpl33-rps18, psbZ-trnG (GCC), rps4-trnT (UGU), trnL (UAG)-rpl32, trnE (UUC)-trnT (GGU), atpE, ndhI, rps2, ycf1, and ndhF, which could be useful molecular genetic markers for future population genetics and phylogenetic studies. Site-specific selection analysis showed that some of the coding sites of 10 chloroplast genes (atpB, atpE, rps2, rps3, petB, petD, ccsA, cemA, ycf1, and rbcL) were under protein sequence evolution. Phylogenetic analysis based on the whole plastomes suggested that the Gossypium species grouped into six previously identified genetic clades. Interestingly, all 13 D-genome species clustered into a strong monophyletic clade. Unexpectedly, the cotton species with C, G, and K-genomes were admixed and nested in a large clade, which could have been due to their recent radiation, incomplete lineage sorting, and introgression hybridization among different cotton lineages. In conclusion, the results of this study provide new insights into the evolution of repeat sequences in chloroplast genomes and interspecific relationships in the genus Gossypium.
Collapse
Affiliation(s)
- Ying Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Dai-Gang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiao-Jian Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiao-Yu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yan-Gai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kun-Lun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wen-Sheng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhong-Ying Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Ke-Hai Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Zhong-Hu Li, Xiong-Feng Ma,
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
- *Correspondence: Zhong-Hu Li, Xiong-Feng Ma,
| |
Collapse
|
22
|
Giovanardi M, Poggioli M, Ferroni L, Lespinasse M, Baldisserotto C, Aro EM, Pancaldi S. Higher packing of thylakoid complexes ensures a preserved Photosystem II activity in mixotrophic Neochloris oleoabundans. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.05.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
23
|
Huang W, Yang YJ, Zhang JL, Hu H, Zhang SB. Superoxide generated in the chloroplast stroma causes photoinhibition of photosystem I in the shade-establishing tree species Psychotria henryi. PHOTOSYNTHESIS RESEARCH 2017; 132:293-303. [PMID: 28432538 DOI: 10.1007/s11120-017-0389-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/15/2017] [Indexed: 05/07/2023]
Abstract
Our previous studies indicated that high light induced significant photoinhibition of photosystem I (PSI) in the shade-establishing tree species Psychotria henryi. However, the underlying mechanism has not been fully clarified. In the present study, in order to investigate the mechanism of PSI photoinhibition in P. henryi, we treated detached leaves with constant high light in the presence of methyl viologen (MV) or a soluble α-tocopherol analog, 2,2,5,7,8-pentamethyl-6-chromanol (PMC). We found that MV significantly depressed photochemical quantum yields in PSI and PSII when compared to PMC. On condition that no PSI photoinhibition happened, although cyclic electron flow (CEF) was abolished in the MV-treated samples, P700 oxidation ratio was maintain at higher levels than the PMC-treated samples. In the presence of PMC, PSI photoinhibition little changed but PSII photoinhibition was significantly alleviated. Importantly, PSI photoinhibition was largely accelerated in the presence of MV, which stimulates the production of superoxide and subsequently other reactive oxygen species at the chloroplast stroma by accepting electrons from PSI. Furthermore, MV largely aggravated PSII photoinhibition when compared to control. These results suggest that high P700 oxidation ratio cannot prevent PSI photoinhibition in P. henryi. Furthermore, the superoxide produced in the chloroplast stroma is critical for PSI photoinhibition in the higher plant P. henryi, which is opposite to the mechanism underlying PSI photoinhibition in Arabidopsis thaliana and spinach. These findings highlight a new mechanism of PSI photoinhibition in higher plants.
Collapse
Affiliation(s)
- Wei Huang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Ying-Jie Yang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jiao-Lin Zhang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Hong Hu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Shi-Bao Zhang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| |
Collapse
|
24
|
Jin L, Che X, Zhang Z, Li Y, Gao H, Zhao S. The mechanisms by which phenanthrene affects the photosynthetic apparatus of cucumber leaves. CHEMOSPHERE 2017; 168:1498-1505. [PMID: 27939666 DOI: 10.1016/j.chemosphere.2016.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/01/2016] [Accepted: 12/01/2016] [Indexed: 05/28/2023]
Abstract
Phenanthrene is a polycyclic aromatic hydrocarbon (PAH) that is widely distributed in the environment and seriously affects the growth and development of plants. To clarify the mechanisms of the direct effects of phenanthrene on the plant photosynthetic apparatus, we measured short-term phenanthrene-treated cucumber leaves. Phenanthrene inhibited Rubisco carboxylation activity, decreasing photosynthesis rates (Pn). And phenanthrene inhibited photosystem II (PSII) activity, thereby blocking photosynthetic electron transport. The inhibition of the light and dark reactions decreased the photosynthetic electron transport rate (ETR) and increased the excitation pressure (1-qP). Under high light, the maximum photochemical efficiency of photosystem II (Fv/Fm) in phenanthrene-treated cucumber leaves decreased significantly, but photosystem I (PSI) activity (Δ I/Io) did not. Phenanthrene also caused a J-point rise in the OJIP curve under high light, which indicated that the acceptor side of PSII QA to QB electron transfer was restricted. This was primarily due to the net degradation of D1 protein, which is caused by the accumulation of reactive oxygen species (ROS) in phenanthrene-treated cucumber leaves under high light. This study demonstrated that phenanthrene could directly inhibit photosynthetic electron transport and Rubisco carboxylation activity to decrease net Pn. Under high light, phenanthrene caused the accumulation of ROS, resulting in net increases in D1 protein degradation and consequently causing PSII photoinhibition.
Collapse
Affiliation(s)
- Liqiao Jin
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xingkai Che
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Zishan Zhang
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Yuting Li
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Huiyuan Gao
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Shijie Zhao
- State Key Lab of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| |
Collapse
|
25
|
Ivanova Z, Sablok G, Daskalova E, Zahmanova G, Apostolova E, Yahubyan G, Baev V. Chloroplast Genome Analysis of Resurrection Tertiary Relict Haberlea rhodopensis Highlights Genes Important for Desiccation Stress Response. FRONTIERS IN PLANT SCIENCE 2017; 8:204. [PMID: 28265281 PMCID: PMC5316520 DOI: 10.3389/fpls.2017.00204] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/03/2017] [Indexed: 05/20/2023]
Abstract
Haberlea rhodopensis is a paleolithic tertiary relict species, best known as a resurrection plant with remarkable tolerance to desiccation. When exposed to severe drought stress, H. rhodopensis shows an ability to maintain the structural integrity of its photosynthetic apparatus, which re-activates easily upon rehydration. We present here the results from the assembly and annotation of the chloroplast (cp) genome of H. rhodopensis, which was further subjected to comparative analysis with the cp genomes of closely related species. H. rhodopensis showed a cp genome size of 153,099 bp, harboring a pair of inverted repeats (IR) of 25,415 bp separated by small and large copy regions (SSC and LSC) of 17,826 and 84,443 bp. The genome structure, gene order, GC content and codon usage are similar to those of the typical angiosperm cp genomes. The genome hosts 137 genes representing 70.66% of the plastome, which includes 86 protein-coding genes, 36 tRNAs, and 4 rRNAs. A comparative plastome analysis with other closely related Lamiales members revealed conserved gene order in the IR and LSC/SSC regions. A phylogenetic analysis based on protein-coding genes from 33 species defines this species as belonging to the Gesneriaceae family. From an evolutionary point of view, a site-specific selection analysis detected positively selected sites in 17 genes, most of which are involved in photosynthesis (e.g., rbcL, ndhF, accD, atpE, etc.). The observed codon substitutions may be interpreted as being a consequence of molecular adaptation to drought stress, which ensures an evolutionary advantage to H. rhodopensis.
Collapse
Affiliation(s)
- Zdravka Ivanova
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster, University of Technology at Sydney, SydneyNSW, Australia
| | - Evelina Daskalova
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Gergana Zahmanova
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Elena Apostolova
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Galina Yahubyan
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
- *Correspondence: Vesselin Baev,
| |
Collapse
|
26
|
Tan S, Hu X, Yin P, Zhao L. Photosynthetic inhibition and oxidative stress to the toxic Phaeocystis globosa caused by a diketopiperazine isolated from products of algicidal bacterium metabolism. J Microbiol 2016; 54:364-75. [PMID: 27095455 DOI: 10.1007/s12275-016-6012-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/05/2016] [Accepted: 04/04/2016] [Indexed: 11/24/2022]
Abstract
Algicidal bacteria have been turned out to be available for inhibiting Phaeocystis globosa which frequently caused harmful algal blooms and threatened to economic development and ecological balance. A marine bacterium Bacillus sp. Ts-12 exhibited significant algicidal activity against P. globosa by indirect attack. In present study, an algicidal compound was isolated by silica gel column, Sephadex G-15 column and HPLC, further identified as hexahydropyrrolo[1,2-a]pyrazine-1,4-dione, cyclo-(Pro-Gly), by GC-MS and (1)H-NMR. Cyclo-(Pro-Gly) significantly increased the level of reactive oxygen species (ROS) within P. globosa cells, further activating the enzymatic and non-enzymatic antioxidant systems, including superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) and ascorbic acid (AsA). The increase in methane dicarboxylic aldehyde (MDA) content showed that the surplus ROS induced lipid peroxidation on membrane system. Transmission electron microscope (TEM) and flow cytometry (FCM) analysis revealed that cyclo-(Pro-Gly) caused reduction of Chl-a content, destruction of cell membrane integrity, chloroplasts and nuclear structure. Real-time PCR assay showed that the transcriptions of photosynthesis related genes (psbA, psbD, rbcL) were significantly inhibited. This study indicated that cyclo-(Pro-Gly) from marine Bacillus sp. Ts-12 exerted photosynthetic inhibition and oxidative stress to P. globosa and eventually led to the algal cells lysis. This algicidal compound might be potential bio-agent for controlling P. globosa red tide.
Collapse
Affiliation(s)
- Shuo Tan
- Department of Chemistry, School of Life Science and technology, Jinan University, Guangzhou, 510632, P. R. China
| | - Xiaoli Hu
- Department of Chemistry, School of Life Science and technology, Jinan University, Guangzhou, 510632, P. R. China
| | - Pinghe Yin
- Department of Chemistry, School of Life Science and technology, Jinan University, Guangzhou, 510632, P. R. China.
| | - Ling Zhao
- Key Laboratory of Water/Soil Toxic Pollutants Control and Bioremediation of Guangdong Higher Education Institutes, School of Environment, Jinan University, Guangzhou, 510632, P. R. China.
| |
Collapse
|
27
|
Dahro B, Wang F, Peng T, Liu JH. PtrA/NINV, an alkaline/neutral invertase gene of Poncirus trifoliata, confers enhanced tolerance to multiple abiotic stresses by modulating ROS levels and maintaining photosynthetic efficiency. BMC PLANT BIOLOGY 2016. [PMID: 27025596 DOI: 10.1016/j.envexpbot.2018.12.009] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND Alkaline/neutral invertase (A/N-INV), an enzyme that hydrolyzes sucrose irreversibly into glucose and fructose, is essential for normal plant growth,development, and stress tolerance. However, the physiological and/or molecular mechanism underpinning the role of A/N-INV in abiotic stress tolerance is poorly understood. RESULTS In this report, an A/N-INV gene (PtrA/NINV) was isolated from Poncirus trifoliata, a cold-hardy relative of citrus, and functionally characterized. PtrA/NINV expression levels were induced by cold, salt, dehydration, sucrose, and ABA, but decreased by glucose. PtrA/NINV was found to localize in both chloroplasts and mitochondria. Overexpression of PtrA/NINV conferred enhanced tolerance to multiple stresses, including cold, high salinity, and drought, as supported by lower levels of reactive oxygen species (ROS), reduced oxidative damages, decreased water loss rate, and increased photosynthesis efficiency, relative to wild-type (WT). The transgenic plants exhibited higher A/N-INV activity and greater reducing sugar content under normal and stress conditions. CONCLUSIONS PtrA/NINV is an important gene implicated in sucrose decomposition, and plays a positive role in abiotic stress tolerance by promoting osmotic adjustment, ROS detoxification and photosynthesis efficiency. Thus, PtrA/NINV has great potential to be used in transgenic breeding for improvement of stress tolerance.
Collapse
Affiliation(s)
- Bachar Dahro
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Horticulture, Faculty of Agriculture, Tishreen University, Lattakia, Syria
| | - Fei Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ting Peng
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ji-Hong Liu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
28
|
Dahro B, Wang F, Peng T, Liu JH. PtrA/NINV, an alkaline/neutral invertase gene of Poncirus trifoliata, confers enhanced tolerance to multiple abiotic stresses by modulating ROS levels and maintaining photosynthetic efficiency. BMC PLANT BIOLOGY 2016; 16:76. [PMID: 27025596 PMCID: PMC4812658 DOI: 10.1186/s12870-016-0761-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/15/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Alkaline/neutral invertase (A/N-INV), an enzyme that hydrolyzes sucrose irreversibly into glucose and fructose, is essential for normal plant growth,development, and stress tolerance. However, the physiological and/or molecular mechanism underpinning the role of A/N-INV in abiotic stress tolerance is poorly understood. RESULTS In this report, an A/N-INV gene (PtrA/NINV) was isolated from Poncirus trifoliata, a cold-hardy relative of citrus, and functionally characterized. PtrA/NINV expression levels were induced by cold, salt, dehydration, sucrose, and ABA, but decreased by glucose. PtrA/NINV was found to localize in both chloroplasts and mitochondria. Overexpression of PtrA/NINV conferred enhanced tolerance to multiple stresses, including cold, high salinity, and drought, as supported by lower levels of reactive oxygen species (ROS), reduced oxidative damages, decreased water loss rate, and increased photosynthesis efficiency, relative to wild-type (WT). The transgenic plants exhibited higher A/N-INV activity and greater reducing sugar content under normal and stress conditions. CONCLUSIONS PtrA/NINV is an important gene implicated in sucrose decomposition, and plays a positive role in abiotic stress tolerance by promoting osmotic adjustment, ROS detoxification and photosynthesis efficiency. Thus, PtrA/NINV has great potential to be used in transgenic breeding for improvement of stress tolerance.
Collapse
Affiliation(s)
- Bachar Dahro
- />Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
- />Department of Horticulture, Faculty of Agriculture, Tishreen University, Lattakia, Syria
| | - Fei Wang
- />Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ting Peng
- />Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ji-Hong Liu
- />Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070 China
| |
Collapse
|
29
|
Espinas NA, Kobayashi K, Sato Y, Mochizuki N, Takahashi K, Tanaka R, Masuda T. Allocation of Heme Is Differentially Regulated by Ferrochelatase Isoforms in Arabidopsis Cells. FRONTIERS IN PLANT SCIENCE 2016; 7:1326. [PMID: 27630653 PMCID: PMC5005420 DOI: 10.3389/fpls.2016.01326] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/18/2016] [Indexed: 05/03/2023]
Abstract
Heme is involved in various biological processes as a cofactor of hemoproteins located in various organelles. In plant cells, heme is synthesized by two isoforms of plastid-localized ferrochelatase, FC1 and FC2. In this study, by characterizing Arabidopsis T-DNA insertional mutants, we showed that the allocation of heme is differentially regulated by ferrochelatase isoforms in plant cells. Analyses of weak (fc1-1) and null (fc1-2) mutants suggest that FC1-producing heme is required for initial growth of seedling development. In contrast, weak (fc2-1) and null (fc2-2) mutants of FC2 showed pale green leaves and retarded growth, indicating that FC2-producing heme is necessary for chloroplast development. During the initial growth stage, FC2 deficiency caused reduction of plastid cytochromes. In addition, although FC2 deficiency marginally affected the assembly of photosynthetic reaction center complexes, it caused relatively larger but insufficient light-harvesting antenna to reaction centers, resulting in lower efficiency of photosynthesis. In the later vegetative growth, however, fc2-2 recovered photosynthetic growth, showing that FC1-producing heme may complement the FC2 deficiency. On the other hand, reduced level of cytochromes in microsomal fraction was discovered in fc1-1, suggesting that FC1-producing heme is mainly allocated to extraplastidic organelles. Furthermore, the expression of FC1 is induced by the treatment of an elicitor flg22 while that of FC2 was reduced, and fc1-1 abolished the flg22-dependent induction of FC1 expression and peroxidase activity. Consequently, our results clarified that FC2 produces heme for the photosynthetic machinery in the chloroplast, while FC1 is the housekeeping enzyme providing heme cofactor to the entire cell. In addition, FC1 can partly complement FC2 deficiency and is also involved in defense against stressful conditions.
Collapse
Affiliation(s)
- Nino A. Espinas
- Graduate School of Science, The University of TokyoTokyo, Japan
| | - Koichi Kobayashi
- Graduate School of Arts and Sciences, The University of TokyoTokyo, Japan
| | - Yasushi Sato
- Graduate School of Science and Engineering, Ehime UniversityEhime, Japan
| | | | - Kaori Takahashi
- Institute of Low Temperature Science, Hokkaido UniversitySapporo, Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido UniversitySapporo, Japan
| | - Tatsuru Masuda
- Graduate School of Science, The University of TokyoTokyo, Japan
- Graduate School of Arts and Sciences, The University of TokyoTokyo, Japan
- *Correspondence: Tatsuru Masuda,
| |
Collapse
|
30
|
Laisk A, Eichelmann H, Oja V. Oxidation of plastohydroquinone by photosystem II and by dioxygen in leaves. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:565-75. [PMID: 25800682 DOI: 10.1016/j.bbabio.2015.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/16/2015] [Accepted: 03/15/2015] [Indexed: 10/23/2022]
Abstract
In sunflower leaves linear electron flow LEF=4O2 evolution rate was measured at 20 ppm O2 in N2. PSII charge separation rate CSRII=aII∙PAD∙(Fm-F)/Fm, where aII is excitation partitioning to PSII, PAD is photon absorption density, Fm and F are maximum and actual fluorescence yields. Under 630 nm LED+720 nm far-red light (FRL), LEF was equal to CSRII with aII=0.51 to 0.58. After FRL was turned off, plastoquinol (PQH2) accumulated, but LEF decreased more than accountable by F increase, indicating PQH2-oxidizing cyclic electron flow in PSII (CEFII). CEFII was faster under conditions requiring more ATP, consistent with CEFII being coupled with proton translocation. We propose that PQH2 bound to the QC site is oxidized, one e- moving to P680+, the other e- to Cyt b559. From Cyt b559 the e- reduces QB- at the QB site, forming PQH2. About 10-15% electrons may cycle, causing misses in the period-4 flash O2 evolution and lower quantum yield of photosynthesis under stress. We also measured concentration dependence of PQH2 oxidation by dioxygen, as indicated by post-illumination decrease of Chl fluorescence yield. After light was turned off, F rapidly decreased from Fm to 0.2 Fv, but further decrease to F0 was slow and O2 concentration dependent. The rate constant of PQH2 oxidation, determined from this slow phase, was 0.054 s(-1) at 270 μM (21%) O2, decreasing with Km(O2) of 60 μM (4.6%) O2. This eliminates the interference of O2 in the measurements of CEFII.
Collapse
Affiliation(s)
- Agu Laisk
- Tartu Ülikooli Tehnoloogia Instituut, Nooruse tn. 1, Tartu 50411, Estonia.
| | - Hillar Eichelmann
- Tartu Ülikooli Tehnoloogia Instituut, Nooruse tn. 1, Tartu 50411, Estonia
| | - Vello Oja
- Tartu Ülikooli Tehnoloogia Instituut, Nooruse tn. 1, Tartu 50411, Estonia
| |
Collapse
|
31
|
Scharfenberg M, Mittermayr L, VON Roepenack-Lahaye E, Schlicke H, Grimm B, Leister D, Kleine T. Functional characterization of the two ferrochelatases in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2015; 38:280-98. [PMID: 24329537 DOI: 10.1111/pce.12248] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 05/03/2023]
Abstract
The enzyme ferrochelatase catalyses the formation of protoheme by inserting Fe(2+) into protoporphyrin IX. Although most organisms express only one ferrochelatase, all land plants analysed so far possess at least two ferrochelatase proteins. Analysis of publicly available expression data suggests that the two Arabidopsis thaliana ferrochelatases, FC1 and FC2, serve different functions, corroborating previous assumptions. Co-expression analysis of FC1 and FC2, together with microarray analyses, implies that fc1 and fc2 trigger different modes of plastid signalling in roots and leaves, respectively, and indicates that FC2 might be involved in stress responses. Thus, loss of FC2 increases resistance to salt and flagellin treatment. Whereas fc1 plants showed no obvious mutant phenotype, fc2 mutants formed abnormally small, pale green rosette leaves; were low in chlorophylls, carotenoids and several photosynthetic proteins; and their photosynthetic performance was impaired. These phenotypes are attenuated by growth in continuous light, in agreement with the finding that fc2 plants accumulate protochlorophyllide and display a fluorescent (flu) phenotype in the dark. In consequence we show that, contrary to earlier suggestions, FC2 produces heme not only for photosynthetic cytochromes, but also for proteins involved in stress responses, whereas the impairment of FC1 apparently interferes only marginally with stress responses.
Collapse
Affiliation(s)
- Michael Scharfenberg
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
| | | | | | | | | | | | | |
Collapse
|
32
|
Li Y, Zhu H, Guan C, Zhang H, Guo J, Chen Z, Cai G, Lei X, Zheng W, Tian Y, Xiong X, Zheng T. Towards molecular, physiological, and biochemical understanding of photosynthetic inhibition and oxidative stress in the toxic Alexandrium tamarense induced by a marine bacterium. Appl Microbiol Biotechnol 2014; 98:4637-52. [DOI: 10.1007/s00253-014-5578-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/17/2014] [Accepted: 01/26/2014] [Indexed: 11/29/2022]
|
33
|
Tikkanen M, Mekala NR, Aro EM. Photosystem II photoinhibition-repair cycle protects Photosystem I from irreversible damage. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:210-5. [DOI: 10.1016/j.bbabio.2013.10.001] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 10/02/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
|
34
|
Putarjunan A, Liu X, Nolan T, Yu F, Rodermel S. Understanding chloroplast biogenesis using second-site suppressors of immutans and var2. PHOTOSYNTHESIS RESEARCH 2013; 116:437-53. [PMID: 23703455 DOI: 10.1007/s11120-013-9855-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/15/2013] [Indexed: 05/07/2023]
Abstract
Chloroplast biogenesis is an essential light-dependent process involving the differentiation of photosynthetically competent chloroplasts from precursors that include undifferentiated proplastids in leaf meristems, as well as etioplasts in dark-grown seedlings. The mechanisms that govern these developmental processes are poorly understood, but entail the coordinated expression of nuclear and plastid genes. This coordination is achieved, in part, by signals generated in response to the metabolic and developmental state of the plastid that regulate the transcription of nuclear genes for photosynthetic proteins (retrograde signaling). Variegation mutants are powerful tools to understand pathways of chloroplast biogenesis, and over the years our lab has focused on immutans (im) and variegated2 (var2), two nuclear gene-induced variegations of Arabidopsis. im and var2 are among the best-characterized chloroplast biogenesis mutants, and they define the genes for plastid terminal oxidase (PTOX) and the AtFtsH2 subunit of the thylakoid FtsH metalloprotease complex, respectively. To gain insight into the function of these proteins, forward and reverse genetic approaches have been used to identify second-site suppressors of im and var2 that replace or bypass the need for PTOX and AtFtsH2 during chloroplast development. In this review, we provide a brief update of im and var2 and the functions of PTOX and AtFtsH2. We then summarize information about second-site suppressors of im and var2 that have been identified to date, and describe how they have provided insight into mechanisms of photosynthesis and pathways of chloroplast development.
Collapse
Affiliation(s)
- Aarthi Putarjunan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | | | | | | | | |
Collapse
|
35
|
Foudree A, Putarjunan A, Kambakam S, Nolan T, Fussell J, Pogorelko G, Rodermel S. The Mechanism of Variegation in immutans Provides Insight into Chloroplast Biogenesis. FRONTIERS IN PLANT SCIENCE 2012; 3:260. [PMID: 23205022 PMCID: PMC3506963 DOI: 10.3389/fpls.2012.00260] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/06/2012] [Indexed: 05/19/2023]
Abstract
The immutans (im) variegation mutant of Arabidopsis has green and white-sectored leaves due to the absence of fully functional plastid terminal oxidase (PTOX), a plastoquinol oxidase in thylakoid membranes. PTOX appears to be at the nexus of a growing number of biochemical pathways in the plastid, including carotenoid biosynthesis, PSI cyclic electron flow, and chlororespiration. During the early steps of chloroplast biogenesis, PTOX serves as an alternate electron sink and is a prime determinant of the redox poise of the developing photosynthetic apparatus. Whereas a lack of PTOX causes the formation of photooxidized plastids in the white sectors of im, compensating mechanisms allow the green sectors to escape the effects of the mutation. This manuscript provides an update on PTOX, the mechanism of im variegation, and findings about im compensatory mechanisms.
Collapse
Affiliation(s)
- Andrew Foudree
- Department of Genetics, Development, and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Aarthi Putarjunan
- Department of Genetics, Development, and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Sekhar Kambakam
- Department of Genetics, Development, and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Trevor Nolan
- Department of Genetics, Development, and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Jenna Fussell
- Department of Genetics, Development, and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Gennady Pogorelko
- Department of Genetics, Development, and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Steve Rodermel
- Department of Genetics, Development, and Cell Biology, Iowa State UniversityAmes, IA, USA
| |
Collapse
|
36
|
Photosynthetic Responses of Plants to Excess Light: Mechanisms and Conditions for Photoinhibition, Excess Energy Dissipation and Repair. PHOTOSYNTHESIS 2012. [DOI: 10.1007/978-94-007-1579-0_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
37
|
Sun X, Wen T. Physiological roles of plastid terminal oxidase in plant stress responses. J Biosci 2011; 36:951-6. [DOI: 10.1007/s12038-011-9161-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
38
|
Vass I. Molecular mechanisms of photodamage in the Photosystem II complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:209-17. [PMID: 21565163 DOI: 10.1016/j.bbabio.2011.04.014] [Citation(s) in RCA: 230] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 04/06/2011] [Accepted: 04/18/2011] [Indexed: 11/26/2022]
Abstract
Light induced damage of the photosynthetic apparatus is an important and highly complex phenomenon, which affects primarily the Photosystem II complex. Here the author summarizes the current state of understanding of the molecular mechanisms, which are involved in the light induced inactivation of Photosystem II electron transport together with the relevant mechanisms of photoprotection. Short wavelength ultraviolet radiation impairs primarily the Mn₄Ca catalytic site of the water oxidizing complex with additional effects on the quinone electron acceptors and tyrosine donors of PSII. The main mechanism of photodamage by visible light appears to be mediated by acceptor side modifications, which develop under conditions of excess excitation in which the capacity of light-independent photosynthetic processes limits the utilization of electrons produced in the initial photoreactions. This situation of excess excitation facilitates the reduction of intersystem electron carriers and Photosystem II acceptors, and thereby induces the formation of reactive oxygen species, especially singlet oxygen whose production is sensitized by triplet chlorophyll formation in the reaction center of Photosystem II. The highly reactive singlet oxygen and other reactive oxygen species, such as H₂O₂ and O₂⁻, which can also be formed in Photosystem II initiate damage of electron transport components and protein structure. In parallel with the excess excitation dependent mechanism of photodamage inactivation of the Mn₄Ca cluster by visible light may also occur, which impairs electron transfer through the Photosystem II complex and initiates further functional and structural damage of the reaction center via formation of highly oxidizing radicals, such as P 680(+) and Tyr-Z(+). However, the available data do not support the hypothesis that the Mn-dependent mechanism would be the exclusive or dominating pathway of photodamage in the visible spectral range. This article is part of a Special Issue entitled: Photosystem II.
Collapse
Affiliation(s)
- Imre Vass
- Institute of Plant Biology, Biology Research Center, Szeged, Hungary.
| |
Collapse
|
39
|
Essemine J, Govindachary S, Ammar S, Bouzid S, Carpentier R. Abolition of photosystem I cyclic electron flow in Arabidopsis thaliana following thermal-stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:235-43. [PMID: 21256041 DOI: 10.1016/j.plaphy.2010.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/29/2010] [Accepted: 11/02/2010] [Indexed: 05/09/2023]
Abstract
Heat tolerance of Arabidopsis thaliana (WT) and its mutants, crr2-2, lacking NADPH-dehydrogenase (Ndh-pathway), and pgr5, deficient in proton gradient regulation and/or ferredoxin-quinone-reductase (FQR-pathway), was studied from 30 to 46°C. Chlorophyll fluorescence revealed that thermal damage to photosystem II (PSII) was maximal in WT plants following short-term exposure of leaves to moderate or high temperature stress. Thermal stress impaired the photosynthetic electron flow at oxidizing and reducing sides of PSII. This was deduced from the transformation of temperature dependent OJIP to OKP patterns, changes in the relative amplitudes of K-step fluorescence rise and F(v)/F(o) ratio. The amplitude of the K-peak that corresponds to the magnitude of damage to the oxygen evolving complex (OEC) in crr2-2 mutants was about 50% of that observed in WT plants exposed to 46°C. The damage to OEC in pgr5 mutants was relatively smaller and thus their PSII complexes were more heat tolerant. P700 oxidation-reduction kinetics following heat-stress revealed that photosystem I (PSI) complexes remained oxidizable either with 10-ms multiple turn-over flashes or far-red illumination but the complementary cyclic electron flow around PSI (CEF) was abolished in both mutants. With further increase in incubation temperature, CEF was fully suppressed even in WT. Thus, P700 turn-over was not enhanced following thermal stress. Furthermore, the experimental data predicts the onset of pseudocyclic electron transport with molecular oxygen as terminal acceptor in crr2-2 and pgr5 mutants but not in wild type Arabidopsis subjected to severe thermal-stress.
Collapse
Affiliation(s)
- Jemâa Essemine
- Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | | | | | | | | |
Collapse
|
40
|
McDonald AE, Ivanov AG, Bode R, Maxwell DP, Rodermel SR, Hüner NPA. Flexibility in photosynthetic electron transport: the physiological role of plastoquinol terminal oxidase (PTOX). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:954-67. [PMID: 21056542 DOI: 10.1016/j.bbabio.2010.10.024] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 11/27/2022]
Abstract
Oxygenic photosynthesis depends on a highly conserved electron transport system, which must be particularly dynamic in its response to environmental and physiological changes, in order to avoid an excess of excitation energy and subsequent oxidative damage. Apart from cyclic electron flow around PSII and around PSI, several alternative electron transport pathways exist including a plastoquinol terminal oxidase (PTOX) that mediates electron flow from plastoquinol to O(2). The existence of PTOX was first hypothesized in 1982 and this was verified years later based on the discovery of a non-heme, di-iron carboxylate protein localized to thylakoid membranes that displayed sequence similarity to the mitochondrial alternative oxidase. The absence of this protein renders higher plants susceptible to excitation pressure dependant variegation combined with impaired carotenoid synthesis. Chloroplasts, as well as other plastids (i.e. etioplasts, amyloplasts and chromoplasts), fail to assemble organized internal membrane structures correctly, when exposed to high excitation pressure early in development. While the role of PTOX in plastid development is established, its physiological role under stress conditions remains equivocal and we postulate that it serves as an alternative electron sink under conditions where the acceptor side of PSI is limited. The aim of this review is to provide an overview of the past achievements in this field and to offer directions for future investigative efforts. Plastoquinol terminal oxidase (PTOX) is involved in an alternative electron transport pathway that mediates electron flow from plastoquinol to O(2). This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.
Collapse
Affiliation(s)
- Allison E McDonald
- Department of Biology, Wilfrid Laurier University, Science Building, 75 University Avenue West, Waterloo, Ontario, Canada N2L 3C5.
| | | | | | | | | | | |
Collapse
|
41
|
Suorsa M, Sirpiö S, Paakkarinen V, Kumari N, Holmström M, Aro EM. Two proteins homologous to PsbQ are novel subunits of the chloroplast NAD(P)H dehydrogenase. PLANT & CELL PHYSIOLOGY 2010; 51:877-83. [PMID: 20460499 DOI: 10.1093/pcp/pcq070] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The PsbQ-like (PQL) proteins 1 and 2, previously shown to be located in the thylakoid lumen of Arabidopsis thaliana, are homologous to PSII oxygen-evolving complex protein PsbQ. Nevertheless, pql mutants showed no defects in PSII but instead the activity of the chloroplast NAD(P)H dehydrogenease (NDH) complex was severely impaired. In line with this observation, the NDH subunits were low in abundance in pql mutants, and, conversely, ndh mutants strongly down-regulated the accumulation of the PQL proteins. In addition, the PQL2 protein was up-regulated in mutant plants deficient in the PSI complex or the thylakoid membrane-bound ferredoxin-NADP(+) oxidoreductase, whereas in pql mutants the PSI complex was slightly up-regulated. Taken together, the two PQL proteins are shown to be novel subunits of the lumenal protuberance of the NDH complex.
Collapse
Affiliation(s)
- Marjaana Suorsa
- Department of Biochemistry and Food Chemistry, Molecular Plant Biology, FI-20014 University of Turku, Finland
| | | | | | | | | | | |
Collapse
|
42
|
Benz J, Stengel A, Lintala M, Lee YH, Weber A, Philippar K, Gügel I, Kaieda S, Ikegami T, Mulo P, Soll J, Bölter B. Arabidopsis Tic62 and ferredoxin-NADP(H) oxidoreductase form light-regulated complexes that are integrated into the chloroplast redox poise. THE PLANT CELL 2009; 21:3965-83. [PMID: 20040542 PMCID: PMC2814497 DOI: 10.1105/tpc.109.069815] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 10/29/2009] [Accepted: 12/14/2009] [Indexed: 05/18/2023]
Abstract
Translocation of nuclear-encoded preproteins across the inner envelope of chloroplasts is catalyzed by the Tic translocon, consisting of Tic110, Tic40, Tic62, Tic55, Tic32, Tic20, and Tic22. Tic62 was proposed to act as a redox sensor of the complex because of its redox-dependent shuttling between envelope and stroma and its specific interaction with the photosynthetic protein ferredoxin-NADP(H) oxidoreductase (FNR). However, the nature of this close relationship so far remained enigmatic. A putative additional localization of Tic62 at the thylakoids mandated further studies examining how this feature might be involved in the respective redox sensing pathway and the interaction with its partner protein. Therefore, both the association with FNR and the physiological role of the third, thylakoid-bound pool of Tic62 were investigated in detail. Coexpression analysis indicates that Tic62 has similar expression patterns as genes involved in photosynthetic functions and protein turnover. At the thylakoids, Tic62 and FNR form high molecular weight complexes that are not involved in photosynthetic electron transfer but are dynamically regulated by light signals and the stromal pH. Structural analyses reveal that Tic62 binds to FNR in a novel binding mode for flavoproteins, with a major contribution from hydrophobic interactions. Moreover, in absence of Tic62, membrane binding and stability of FNR are drastically reduced. We conclude that Tic62 represents a major FNR interaction partner not only at the envelope and in the stroma, but also at the thylakoids of Arabidopsis thaliana and perhaps all flowering plants. Association with Tic62 stabilizes FNR and is involved in its dynamic and light-dependent membrane tethering.
Collapse
Affiliation(s)
- J.P. Benz
- Munich Center for Integrated Protein Science CiPS, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
| | - A. Stengel
- Munich Center for Integrated Protein Science CiPS, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
| | - M. Lintala
- Laboratory of Plant Physiology and Molecular Biology, Department of Biology, University of Turku, FIN-20014 Turku, Finland
| | - Y.-H. Lee
- Institute for Protein Research, Osaka University and CREST, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan
| | - A. Weber
- Institut für Biochemie der Pflanzen, Heinrich-Heine-Universität, 40225 Duesseldorf, Germany
| | - K. Philippar
- Munich Center for Integrated Protein Science CiPS, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
| | - I.L. Gügel
- Munich Center for Integrated Protein Science CiPS, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
| | - S. Kaieda
- Institute for Protein Research, Osaka University and CREST, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan
| | - T. Ikegami
- Institute for Protein Research, Osaka University and CREST, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan
| | - P. Mulo
- Laboratory of Plant Physiology and Molecular Biology, Department of Biology, University of Turku, FIN-20014 Turku, Finland
| | - J. Soll
- Munich Center for Integrated Protein Science CiPS, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
| | - B. Bölter
- Munich Center for Integrated Protein Science CiPS, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
- Address correspondence to
| |
Collapse
|
43
|
Ogawa T, Nishimura K, Aoki T, Takase H, Tomizawa KI, Ashida H, Yokota A. A phosphofructokinase B-type carbohydrate kinase family protein, NARA5, for massive expressions of plastid-encoded photosynthetic genes in Arabidopsis. PLANT PHYSIOLOGY 2009; 151:114-28. [PMID: 19587101 PMCID: PMC2736000 DOI: 10.1104/pp.109.139683] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
To date, there have been no reports on screening for mutants defective in the massive accumulation of Rubisco in higher plants. Here, we describe a screening method based on the toxic accumulation of ammonia in the presence of methionine sulfoximine, a specific inhibitor of glutamine synthetase, during photorespiration initiated by the oxygenase reaction of Rubisco in Arabidopsis (Arabidopsis thaliana). Five recessive mutants with decreased amounts of Rubisco were identified and designated as nara mutants, as they contained a mutation in genes necessary for the achievement of Rubisco accumulation. The nara5-1 mutant showed markedly lower levels of plastid-encoded photosynthetic proteins, including Rubisco. Map-based cloning revealed that NARA5 encoded a chloroplast phosphofructokinase B-type carbohydrate kinase family protein of unknown function. The NARA5 protein fused to green fluorescent protein localized in chloroplasts. We conducted expression analyses of photosynthetic genes during light-induced greening of etiolated seedlings of nara5-1 and the T-DNA insertion mutant, nara5-2. Our results strongly suggest that NARA5 is indispensable for hyperexpression of photosynthetic genes encoded in the plastid genome, particularly rbcL.
Collapse
Affiliation(s)
- Taro Ogawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | | | | | | | | | | | | |
Collapse
|
44
|
Ferroni L, Baldisserotto C, Pantaleoni L, Fasulo MP, Fagioli P, Pancaldi S. Degreening of the unicellular alga Euglena gracilis: thylakoid composition, room temperature fluorescence spectra and chloroplast morphology. PLANT BIOLOGY (STUTTGART, GERMANY) 2009; 11:631-41. [PMID: 19538401 DOI: 10.1111/j.1438-8677.2008.00152.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Thylakoid dismantling is one of the most relevant processes occurring when chloroplasts are converted to non-photosynthetically active plastids. The process is well characterised in senescing leaves, but other systems could present different features. In this study, thylakoid dismantling has been analysed in dividing cells of the unicellular alga, Euglena gracilis, cultured in darkness. Changes in photosynthetic pigments and in the abundance of LHC and PSII core proteins (D2 and CP43) showed that: (i) during the 0-24 h interval, the decline in LHCII was faster than that in the PSII core; (ii) during the 24-48 h interval, PSII and LHCII were strongly degraded to nearly the same extent; (iii) in the 48-72 h interval, the PSII core proteins declined markedly, while LHCII was maintained. These changes were accompanied by variations in room temperature fluorescence emission spectra recorded from single living cells with a microspectrofluorimeter (excitation, 436 nm; range 620-780 nm). Emission in the 700-715 nm range was proposed to derive from LHCI-II assemblages; changes in emission at 678 nm relative to PSII matched PSII core degradation phases. Overall, the results suggest that, in degreening E. gracilis, thylakoid dismantling is somewhat different from that associated with senescence, because of the early loss of LHCII. Moreover, it is proposed that, in this alga, disruption of the correct LHCI-II stoichiometry alters the energy transfer to photosystems and destabilises membrane appression leading to the thylakoid destacking observed using transmission electron microscopy.
Collapse
Affiliation(s)
- L Ferroni
- Laboratory of Plant Cytophysiology, Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | | | | | | | | | | |
Collapse
|
45
|
Sirpiö S, Holmström M, Battchikova N, Aro EM. AtCYP20-2 is an auxiliary protein of the chloroplast NAD(P)H dehydrogenase complex. FEBS Lett 2009; 583:2355-8. [PMID: 19549520 DOI: 10.1016/j.febslet.2009.06.031] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 05/28/2009] [Accepted: 06/17/2009] [Indexed: 11/17/2022]
Abstract
AtCYP20-2 is one of 16 immunophilins in thylakoid lumen. The presence of the isomerase domain in AtCYP20-2, an enrichment of AtCYP20-2 in the stroma membranes and it's co-migration with NAD(P)H dehydrogenase (NDH) in native gels provide evidence that AtCYP20-2 is an auxiliary protein of NDH. When different NDH mutants were studied, AtCYP20-2 was found to be strongly reduced especially in mutants deficient in the membrane domain of NDH, thus suggesting a role in the assembly of NDH hydrophobic domain. Lack of AtCYP20-2, however, did not lead to severe malfunction of NDH, indicating redundancy in the function of lumenal immunophilins.
Collapse
Affiliation(s)
- Sari Sirpiö
- Department of Biology, Plant Physiology and Molecular Biology, University of Turku, FI-20014 Turku, Finland
| | | | | | | |
Collapse
|
46
|
Wang J, Sommerfeld M, Hu Q. Occurrence and environmental stress responses of two plastid terminal oxidases in Haematococcus pluvialis (Chlorophyceae). PLANTA 2009; 230:191-203. [PMID: 19408010 DOI: 10.1007/s00425-009-0932-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 04/13/2009] [Indexed: 05/06/2023]
Abstract
The plastid terminal oxidase (PTOX) is a plastoquinol oxidase involved in carotenoid biosynthesis in higher plants, and may also represent the elusive oxidase in chlororespiration. Haematococcus pluvialis is a green alga that has the ability to synthesize and accumulate large amounts of the red carotenoid astaxanthin (ca. 2% of dry weight) under various stress conditions. However, the occurrence and function of PTOX in astaxanthin synthesis and the stress response in this organism is unknown. In this study, two ptox cDNAs were cloned and sequenced from H. pluvialis and were designated as ptox1 and ptox2. Genome sequence analysis and database searching revealed that duplication of PTOX gene occurred in certain eukaryotic algae, but not in cyanobacteria and higher plants. The physiological and biochemical evidence indicated that PTOX is involved in astaxanthin synthesis and plays a critical protective role against stress. Analysis of the transcriptional expression of the PTOXs and phytoene desaturase gene further suggests that it may be PTOX1 rather than PTOX2 that is co-regulated with astaxanthin synthesis. The fact that the changes in transcripts of ptoxs in response to high light and other stressors and the differential expression of ptox1 and ptox2, suggests that PTOX, coupled with astaxanthin synthesis pathway, exerts broad, yet undefined functions in addition to those identified in higher plants.
Collapse
Affiliation(s)
- Jiangxin Wang
- Department of Applied Biological Sciences, Arizona State University, Polytechnic Campus, 7001 E. Williams Field Road, Mesa, AZ 85212, USA
| | | | | |
Collapse
|
47
|
Lintala M, Allahverdiyeva Y, Kangasjärvi S, Lehtimäki N, Keränen M, Rintamäki E, Aro EM, Mulo P. Comparative analysis of leaf-type ferredoxin-NADP oxidoreductase isoforms in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 57:1103-15. [PMID: 19054362 DOI: 10.1111/j.1365-313x.2008.03753.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Physiological roles of the two distinct chloroplast-targeted ferredoxin-NADP(+) oxidoreductase (FNR) isoforms in Arabidopsis thaliana were studied using T-DNA insertion line fnr1 and RNAi line fnr2. In fnr2 FNR1 was present both as a thylakoid membrane-bound form and as a soluble protein, whereas in fnr1 the FNR2 protein existed solely in soluble form in the stroma. The fnr2 plants resembled fnr1 in having downregulated photosynthetic properties, expressed as low chlorophyll content, low accumulation of photosynthetic thylakoid proteins and reduced carbon fixation rate when compared with wild type (WT). Under standard growth conditions the level of F(0)'rise' and the amplitude of the thermoluminescence afterglow (AG) band, shown to correlate with cyclic electron transfer (CET), were reduced in both fnr mutants. In contrast, when plants were grown under low temperatures, both fnr mutants showed an enhanced rate of CET when compared with the WT. These data exclude the possibility that distinct FNR isoforms feed electrons to specific CET pathways. Nevertheless, the fnr2 mutants had a distinct phenotype upon growth at low temperature. The fnr2 plants grown at low temperature were more tolerant against methyl viologen (MV)-induced cell death than fnr1 and WT. The unique tolerance of fnr2 plants grown at low temperature to oxidative stress correlated with an increased level of reduced ascorbate and reactive oxygen species (ROS) scavenging enzymes, as well as with a scarcity in the accumulation of thylakoid membrane protein complexes, as compared with fnr1 and WT. These results emphasize a critical role for FNR2 in the redistribution of electrons to various reducing pathways, upon conditions that modify the photosynthetic capacity of the plant.
Collapse
Affiliation(s)
- Minna Lintala
- Laboratory of Plant Physiology and Molecular Biology, Department of Biology, University of Turku, Turku, Finland
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Sirpiö S, Allahverdiyeva Y, Holmström M, Khrouchtchova A, Haldrup A, Battchikova N, Aro EM. Novel Nuclear-encoded Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex. J Biol Chem 2009; 284:905-12. [DOI: 10.1074/jbc.m805404200] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
49
|
Tikkanen M, Nurmi M, Kangasjärvi S, Aro EM. Core protein phosphorylation facilitates the repair of photodamaged photosystem II at high light. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1432-7. [PMID: 18774768 DOI: 10.1016/j.bbabio.2008.08.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 07/30/2008] [Accepted: 08/07/2008] [Indexed: 11/18/2022]
Abstract
Phosphorylation of photosystem II (PSII) reaction center protein D1 has been hypothesised to function as a signal for the migration of photodamaged PSII core complex from grana membranes to stroma lamellae for concerted degradation and replacement of the photodamaged D1 protein. Here, by using the mutants with impaired capacity (stn8) or complete lack (stn7 stn8) in phosphorylation of PSII core proteins, the role of phosphorylation in PSII photodamage and repair was investigated. We show that the lack of PSII core protein phosphorylation disturbs the disassembly of PSII supercomplexes at high light, which is a prerequisite for efficient migration of damaged PSII complexes from grana to stroma lamellae for repair. This results in accumulation of photodamaged PSII complexes, which in turn results, upon prolonged exposure to high light (HL), in general oxidative damage of photosynthetic proteins in the thylakoid membrane.
Collapse
Affiliation(s)
- Mikko Tikkanen
- Plant Physiology and Molecular Biology, Department of Biology, University of Turku, FIN-20014 Turku, Finland
| | | | | | | |
Collapse
|
50
|
Eisenstadt D, Ohad I, Keren N, Kaplan A. Changes in the photosynthetic reaction centre II in the diatomPhaeodactylum tricornutumresult in non-photochemical fluorescence quenching. Environ Microbiol 2008; 10:1997-2007. [DOI: 10.1111/j.1462-2920.2008.01616.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|