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Zuo W, Li H. Assemble and comparative analysis of the mitochondrial genome of Rhododendron delavayi: Insights into phylogenetic relationships and genomic variations. Gene 2024; 927:148741. [PMID: 38969246 DOI: 10.1016/j.gene.2024.148741] [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: 12/26/2023] [Revised: 04/07/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
Rhododendron delavayi, a notable ornamental plant primarily found in regions of China like Yunnan and Guizhou provinces, holds substantial horticultural value. To elucidate the systematic phylogenetic relationships and organelle genomic differences within R. delavayi and related Rhododendron species, we conducted sequencing and assembly of the complete mitochondrial genome of R. delavayi. The full-length mitochondrial genome of it was a singular circular molecule spanning 1,009,263 bp, comprising 53 protein-coding genes, including 18 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 32 protein-coding genes. A total of 1,182 simple sequence repeats (SSRs) loci were identified in the R. delavayi mitochondrial genome, primarily consisting of single nucleotide, dinucleotide, and trinucleotide repeats. Nucleotide diversity analysis highlighted five genes (atp6, atp9, cox2, nad1, and rpl10) with the highest diversity within the mitochondrial genomes of Rhododendron genus. Comparative analysis of the mitochondrial genome of R. delavayi with those of four other Rhododendron species indicated complex rearrangements in 21 genes, including rps4, nad6, rps3, atp6, cob, atp9, nad7, among others. The mitochondrial phylogenetic tree revealed a close relationship between R. delavayi and R. decorum, forming a sister clade to R. × pulchrum and R. simsii. Furthermore, 126 plastid-to-mitochondrial gene transfers in R. delavayi were identified, ranging from 30 bp to 19,385 bp. These fragments collectively constituted 47.54 % and 9.52 % of the chloroplast and mitochondrial genomes (202,169 bp), respectively. Complex mitochondrial-to-mitochondrial transfers were also observed, with 843 identified fragments totaling 312,036 bp (30.92 % of the mitochondrial genome). Segments exceeding 10 kb may mediate homologous recombination within the mitochondrial molecules. Remarkably, our study underscores that the mitochondrial genome of R. delavayi was the largest reported within the Rhododendron genus to date. The intricate rearrangements observed in the mitochondrial genomes of Rhododendron species, alone with the identification of five potential molecular marker sites, provided valuable insights for species classification and parentage identification within the Rhododendron genus.
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Affiliation(s)
- Weiwei Zuo
- College of Agriculture, Guizhou University, Guiyang 550025, China.
| | - Huie Li
- College of Agriculture, Guizhou University, Guiyang 550025, China.
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Collado-Arenal AM, Exposito-Rodriguez M, Mullineaux PM, Olmedilla A, Romero-Puertas MC, Sandalio LM. Cadmium exposure induced light/dark- and time-dependent redox changes at subcellular level in Arabidopsis plants. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135164. [PMID: 39032180 DOI: 10.1016/j.jhazmat.2024.135164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/21/2024] [Accepted: 07/08/2024] [Indexed: 07/22/2024]
Abstract
Cadmium (Cd) is one of the most toxic heavy metals for plants and humans. Reactive oxygen species (ROS) are some of the primary signaling molecules produced after Cd treatment in plants but the contribution of different organelles and specific cell types, together with the impact of light is unknown. We used Arabidopsis lines expressing GRX1-roGFP2 (glutaredoxin1-roGFP) targeted to different cell compartments and analysed changes in redox state over 24 h light/dark cycle in Cd-treated leaf discs. We imaged redox state changes in peroxisomes and chloroplasts in leaf tissue. Chloroplasts and peroxisomes were the most affected organelles in the dark and blocking the photosynthetic electron transport chain (pETC) by DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea) promotes higher Cd-dependent oxidation in all organelles. Peroxisomes underwent the most rapid changes in redox state in response to Cd and DCMU and silencing chloroplastic NTRC (NADPH thioredoxin reductase C) considerably increases peroxisome oxidation. Total NAD(P)H and cytosolic NADH decreased during exposure to Cd, while Ca+2 content in chloroplasts and cytosol increased in the dark period. Our results demonstrate a Cd-, time- and light-dependent increase of oxidation of all organelles analysed, that could be in part triggered by disturbances in pETC and photorespiration, the decrease of NAD(P)H availability, and differential antioxidants expression at subcellular level.
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Affiliation(s)
- Aurelio M Collado-Arenal
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada 18008, Spain.
| | | | - Philip M Mullineaux
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
| | - Adela Olmedilla
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada 18008, Spain.
| | - María C Romero-Puertas
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada 18008, Spain.
| | - Luisa M Sandalio
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada 18008, Spain.
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Zhang M, Zhang X, Huang Y, Chen Z, Chen B. Comparative mitochondrial genomics of Terniopsis yongtaiensis in Malpighiales: structural, sequential, and phylogenetic perspectives. BMC Genomics 2024; 25:853. [PMID: 39267005 PMCID: PMC11391645 DOI: 10.1186/s12864-024-10765-6] [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: 04/19/2024] [Accepted: 09/03/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Terniopsis yongtaiensis, a member of the Podostemaceae family, is an aquatic flowering plant displaying remarkable adaptive traits that enable survival in submerged, turbulent habitats. Despite the progressive expansion of chloroplast genomic information within this family, mitochondrial genome sequences have yet to be reported. RESULTS In current study, the mitochondrial genome of the T. yongtaiensis was characterized by a circular genome of 426,928 bp encoding 31 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNA genes. Our comprehensive analysis focused on gene content, repeat sequences, RNA editing processes, intracellular gene transfer, phylogeny, and codon usage bias. Numerous repeat sequences were identified, including 130 simple sequence repeats, 22 tandem repeats, and 220 dispersed repeats. Phylogenetic analysis positioned T. yongtaiensis (Podostemaceae) within the Malpighiales order, showing a close relationship with the Calophyllaceae family, which was consistent with the APG IV classification. A comparative analysis with nine other Malpighiales species revealed both variable and conserved regions, providing insights into the genomic evolution within this order. Notably, the GC content of T. yongtaiensis was distinctively lower compared to other Malpighilales, primarily due to variations in non-coding regions and specific protein-coding genes, particularly the nad genes. Remarkably, the number of RNA editing sites was low (276), distributed unevenly across 27 PCGs. The dN/dS analysis showed only the ccmB gene of T. yongtaiensis was positively selected, which plays a crucial role in cytochrome c biosynthesis. Additionally, there were 13 gene-containing homologous regions between the mitochondrial and chloroplast genomes of T. yongtaiensis, suggesting the gene transfer events between these organellar genomes. CONCLUSIONS This study assembled and annotated the first mitochondrial genome of the Podostemaceae family. The comparison results of mitochondrial gene composition, GC content, and RNA editing sites provided novel insights into the adaptive traits and genetic reprogramming of this aquatic eudicot group and offered a foundation for future research on the genomic evolution and adaptive mechanisms of Podostemaceae and related plant families in the Malpighiales order.
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Affiliation(s)
- Miao Zhang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xiaohui Zhang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Normal University, Fuzhou, 350117, China
| | - Yinglin Huang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Normal University, Fuzhou, 350117, China
| | - Zhangxue Chen
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Normal University, Fuzhou, 350117, China
| | - Binghua Chen
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Normal University, Fuzhou, 350117, China.
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Kwasniak-Owczarek M, Janska H. Experimental approaches to studying translation in plant semi-autonomous organelles. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5175-5187. [PMID: 38592734 PMCID: PMC11389837 DOI: 10.1093/jxb/erae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Plant mitochondria and chloroplasts are semi-autonomous organelles originated from free-living bacteria that have retained reduced genomes during evolution. As a consequence, relatively few of the mitochondrial and chloroplast proteins are encoded in the organellar genomes and synthesized by the organellar ribosomes. Since both organellar genomes encode mainly components of the energy transduction systems, oxidative phosphorylation in mitochondria and photosynthetic apparatus in chloroplasts, understanding organellar translation is critical for a thorough comprehension of key aspects of mitochondrial and chloroplast activity affecting plant growth and development. Recent studies have clearly shown that translation is a key regulatory node in the expression of plant organellar genes, underscoring the need for an adequate methodology to study this unique stage of gene expression. The organellar translatome can be analysed by studying newly synthesized proteins or the mRNA pool recruited to the organellar ribosomes. In this review, we present experimental approaches used for studying translation in plant bioenergetic organelles. Their benefits and limitations, as well as the critical steps, are discussed. Additionally, we briefly mention several recently developed strategies to study organellar translation that have not yet been applied to plants.
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Affiliation(s)
- Malgorzata Kwasniak-Owczarek
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, Wroclaw, 50-383, Poland
| | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, Wroclaw, 50-383, Poland
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Zhao S, Shi R, Liang X, Li P, Bai X, Wang Y, Zhang Y. Sulfadiazine degradation by Bjerkandera adusta DH0817 at low temperatures and its cold-adaptation mechanisms. BIORESOURCE TECHNOLOGY 2024; 407:131108. [PMID: 39009046 DOI: 10.1016/j.biortech.2024.131108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/29/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024]
Abstract
The prolonged period of low temperatures in northern China poses a significant challenge to the bioremediation of antibiotic pollution. This study reports that a white-rot fungus Bjerkandera adusta DH0817, isolated from a poultry farm in Liaoning Province, can remove 60 % of SDZ within 20 days at 10°C and reduce the biotoxicity of SDZ. Six degradation pathways were proposed. SDZ biodegradation was primarily driven by cytochrome P450. Transcriptome analysis revealed that DH0817 upregulated genes associated with cell membrane, transcription factors and soluble sugars in response to low temperatures. Subsequently, genes associated with fatty acid, proteins and enzymes were upregulated to remove SDZ at low temperatures. This study provides valuable microbial resources and serves as a theoretical reference for addressing antibiotic pollution in livestock and poultry farms under low temperature conditions.
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Affiliation(s)
- Shuang Zhao
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongjiu Shi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xiaolong Liang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Ping Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Bai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongfeng Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Ying Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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Harshkova D, Zielińska E, Narajczyk M, Kapusta M, Aksmann A. Mitochondria dysfunction is one of the causes of diclofenac toxicity in the green alga Chlamydomonas reinhardtii. PeerJ 2024; 12:e18005. [PMID: 39221263 PMCID: PMC11365475 DOI: 10.7717/peerj.18005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
Background Non-steroidal anti-inflammatory drugs (NSAIDs), such as diclofenac (DCF), form a significant group of environmental contaminants. When the toxic effects of DCF on plants are analyzed, authors often focus on photosynthesis, while mitochondrial respiration is usually overlooked. Therefore, an in vivo investigation of plant mitochondria functioning under DCF treatment is needed. In the present work, we decided to use the green alga Chlamydomonas reinhardtii as a model organism. Methods Synchronous cultures of Chlamydomonas reinhardtii strain CC-1690 were treated with DCF at a concentration of 135.5 mg × L-1, corresponding to the toxicological value EC50/24. To assess the effects of short-term exposure to DCF on mitochondrial activity, oxygen consumption rate, mitochondrial membrane potential (MMP) and mitochondrial reactive oxygen species (mtROS) production were analyzed. To inhibit cytochrome c oxidase or alternative oxidase activity, potassium cyanide (KCN) or salicylhydroxamic acid (SHAM) were used, respectively. Moreover, the cell's structure organization was analyzed using confocal microscopy and transmission electron microscopy. Results The results indicate that short-term exposure to DCF leads to an increase in oxygen consumption rate, accompanied by low MMP and reduced mtROS production by the cells in the treated populations as compared to control ones. These observations suggest an uncoupling of oxidative phosphorylation due to the disruption of mitochondrial membranes, which is consistent with the malformations in mitochondrial structures observed in electron micrographs, such as elongation, irregular forms, and degraded cristae, potentially indicating mitochondrial swelling or hyper-fission. The assumption about non-specific DCF action is further supported by comparing mitochondrial parameters in DCF-treated cells to the same parameters in cells treated with selective respiratory inhibitors: no similarities were found between the experimental variants. Conclusions The results obtained in this work suggest that DCF strongly affects cells that experience mild metabolic or developmental disorders, not revealed under control conditions, while more vital cells are affected only slightly, as it was already indicated in literature. In the cells suffering from DCF treatment, the drug influence on mitochondria functioning in a non-specific way, destroying the structure of mitochondrial membranes. This primary effect probably led to the mitochondrial inner membrane permeability transition and the uncoupling of oxidative phosphorylation. It can be assumed that mitochondrial dysfunction is an important factor in DCF phytotoxicity. Because studies of the effects of NSAIDs on the functioning of plant mitochondria are relatively scarce, the present work is an important contribution to the elucidation of the mechanism of NSAID toxicity toward non-target plant organisms.
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Affiliation(s)
- Darya Harshkova
- Department of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Elżbieta Zielińska
- Department of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Magdalena Narajczyk
- Bioimaging Laboratory, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Małgorzata Kapusta
- Bioimaging Laboratory, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Anna Aksmann
- Department of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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Zhou F, Feng W, Mou K, Yu Z, Zeng Y, Zhang W, Zhou Y, Li Y, Gao H, Xu K, Feng C, Jing Y, Li H. Genome-Wide Analysis and Expression Profiling of Soybean RbcS Family in Response to Plant Hormones and Functional Identification of GmRbcS8 in Soybean Mosaic Virus. Int J Mol Sci 2024; 25:9231. [PMID: 39273180 PMCID: PMC11395302 DOI: 10.3390/ijms25179231] [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: 07/22/2024] [Revised: 08/19/2024] [Accepted: 08/24/2024] [Indexed: 09/15/2024] Open
Abstract
Rubisco small subunit (RbcS), a core component with crucial effects on the structure and kinetic properties of the Rubisco enzyme, plays an important role in response to plant growth, development, and various stresses. Although Rbcs genes have been characterized in many plants, their muti-functions in soybeans remain elusive. In this study, a total of 11 GmRbcS genes were identified and subsequently divided into three subgroups based on a phylogenetic relationship. The evolutionary analysis revealed that whole-genome duplication has a profound effect on GmRbcSs. The cis-acting elements responsive to plant hormones, development, and stress-related were widely found in the promoter region. Expression patterns based on the RT-qPCR assay exhibited that GmRbcS genes are expressed in multiple tissues, and notably Glyma.19G046600 (GmRbcS8) exhibited the highest expression level compared to other members, especially in leaves. Moreover, differential expressions of GmRbcS genes were found to be significantly regulated by exogenous plant hormones, demonstrating their potential functions in diverse biology processes. Finally, the function of GmRbcS8 in enhancing soybean resistance to soybean mosaic virus (SMV) was further determined through the virus-induced gene silencing (VIGS) assay. All these findings establish a strong basis for further elucidating the biological functions of RbcS genes in soybeans.
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Affiliation(s)
- Fangxue Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Wenmi Feng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Kexin Mou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Zhe Yu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Yicheng Zeng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Wenping Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Yonggang Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Yaxin Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Hongtao Gao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Keheng Xu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Chen Feng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Yan Jing
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Haiyan Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
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Li L, Li X, Liu Y, Li J, Zhen X, Huang Y, Ye J, Fan L. Comparative analysis of the complete mitogenomes of Camellia sinensis var. sinensis and C. sinensis var. assamica provide insights into evolution and phylogeny relationship. FRONTIERS IN PLANT SCIENCE 2024; 15:1396389. [PMID: 39239196 PMCID: PMC11374768 DOI: 10.3389/fpls.2024.1396389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024]
Abstract
Introduction Among cultivated tea plants (Camellia sinensis), only four mitogenomes for C. sinensis var. assamica (CSA) have been reported so far but none for C. sinensis var. sinensis (CSS). Here, two mitogenomes of CSS (CSSDHP and CSSRG) have been sequenced and assembled. Methods Using a combination of Illumina and Nanopore data for the first time. Comparison between CSS and CSA mitogenomes revealed a huge heterogeneity. Results The number of the repetitive sequences was proportional to the mitogenome size and the repetitive sequences dominated the intracellular gene transfer segments (accounting for 88.7%- 92.8% of the total length). Predictive RNA editing analysis revealed that there might be significant editing in NADH dehydrogenase subunit transcripts. Codon preference analysis showed a tendency to favor A/T bases and T was used more frequently at the third base of the codon. ENc plots analysis showed that the natural selection play an important role in shaping the codon usage bias, and Ka/Ks ratios analysis indicated Nad1 and Sdh3 genes may have undergone positive selection. Further, phylogenetic analysis shows that six C. sinensis clustered together, with the CSA and CSS forming two distinct branches, suggesting two different evolutionary pathway. Discussion Altogether, this investigation provided an insight into evolution and phylogeny relationship of C. sinensis mitogenome, thereby enhancing comprehension of the evolutionary patterns within C. sinensis species.
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Affiliation(s)
- Li Li
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Xiangru Li
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Yun Liu
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Junda Li
- College of Tea and Food Science, Wuyi University, Wuyishan, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyun Zhen
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Yu Huang
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Jianghua Ye
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Li Fan
- College of Tea and Food Science, Wuyi University, Wuyishan, China
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Qin N, Yang S, Wang Y, Cheng H, Gao Y, Cheng X, Li S. The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd ( Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination. FRONTIERS IN PLANT SCIENCE 2024; 15:1416913. [PMID: 39188545 PMCID: PMC11345175 DOI: 10.3389/fpls.2024.1416913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024]
Abstract
Introduction Bottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding. Methods A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes. Results The length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing. Conclusion In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.
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Affiliation(s)
- Nannan Qin
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Department of Development Planning & Cooperation, Shanxi Agricultural University, Taiyuan, China
| | - Shanjie Yang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Yunan Wang
- Department of Scientific Research Management, Shanxi Agricultural University, Taiyuan, China
| | - Hui Cheng
- Department of Scientific Research Management, Shanxi Agricultural University, Taiyuan, China
| | - Yang Gao
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Xiaojing Cheng
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
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Zeng Z, Zhang Z, Tso N, Zhang S, Chen Y, Shu Q, Li J, Liang Z, Wang R, Wang J, Qiong L. Complete mitochondrial genome of Hippophae tibetana: insights into adaptation to high-altitude environments. FRONTIERS IN PLANT SCIENCE 2024; 15:1449606. [PMID: 39170791 PMCID: PMC11335646 DOI: 10.3389/fpls.2024.1449606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 07/17/2024] [Indexed: 08/23/2024]
Abstract
Hippophae tibetana, belonging to the Elaeagnaceae family, is an endemic plant species of the Qinghai-Tibet Plateau, valued for its remarkable ecological restoration capabilities, as well as medicinal and edible properties. Despite being acknowledged as a useful species, its mitochondrial genome data and those of other species of the Elaeagnaceae family are lacking to date. In this study, we, for the first time, successfully assembled the mitochondrial genome of H. tibetana, which is 464,208 bp long and comprises 31 tRNA genes, 3 rRNA genes, 37 protein-coding genes, and 3 pseudogenes. Analysis of the genome revealed a high copy number of the trnM-CAT gene and a high prevalence of repetitive sequences, both of which likely contribute to genome rearrangement and adaptive evolution. Through nucleotide diversity and codon usage bias analyses, we identified specific genes that are crucial for adaptation to high-altitude conditions. Notably, genes such as atp6, ccmB, nad4L, and nad7 exhibited signs of positive selection, indicating the presence of unique adaptive traits for survival in extreme environments. Phylogenetic analysis confirmed the close relationship between the Elaeagnaceae family and other related families, whereas intergenomic sequence transfer analysis revealed a substantial presence of homologous fragments among the mitochondrial, chloroplast, and whole genomes, which may be linked to the high-altitude adaptation mechanisms of H. tibetana. The findings of this study not only enrich our knowledge of H. tibetana molecular biology but also advance our understanding of the adaptive evolution of plants on the Qinghai-Tibet Plateau. This study provides a solid scientific foundation for the molecular breeding, conservation, and utilization of H. tibetana genetic resources.
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Affiliation(s)
- Zhefei Zeng
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
- Yani Observation and Research Station for Wetland Ecosystem of the Tibet (Xizang) Autonomous Region, Tibet University, Lhasa, China
| | - Zhengyan Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Norzin Tso
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Shutong Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Yan Chen
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Qi Shu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Junru Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Ziyi Liang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Ruoqiu Wang
- Tech X Academy, Shenzhen Polytechnic University, Shenzhen, China
| | - Junwei Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
- Yani Observation and Research Station for Wetland Ecosystem of the Tibet (Xizang) Autonomous Region, Tibet University, Lhasa, China
| | - La Qiong
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, China
- Yani Observation and Research Station for Wetland Ecosystem of the Tibet (Xizang) Autonomous Region, Tibet University, Lhasa, China
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11
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Ma W, Zhu M, Wan Y, Cai H, Sun Y, Jiao P, Liu Y. Mitochondrial pathway of programmed cell death in Paeonia lactiflora pollen cryopreservation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112107. [PMID: 38685455 DOI: 10.1016/j.plantsci.2024.112107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/01/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
Programmed cell death (PCD) is an important factor to reduces the viability of plant germplasm after cryopreservation. However, the pathways by which PCD occurs is not fully understood. To investigate whether there is a mitochondrial pathway for pollen PCD after cryopreservation, the pollen of Paeonia lactiflora two cultivars with different PCD levels after cryopreservation was used as test material and the changes of mitochondrial calcium ions (Ca2+), structure, function and their relationship with PCD were compared. The results showed that compared with fresh pollen, the PCD of 'Feng Huang Nie Pan' was significantly reduced after cryopreservation. Their mitochondrial Ca2+ content decreased by 74.27%, mitochondrial permeability transition pore (MPTP) opening reduced by 25.41%, mitochondrial membrane potential slightly decreased by 5.02%, cardiolipin oxidation decreased by 65.31%, and oxygen consumption remained stable, with a slightly ATP production increase. On the contrary, compared with fresh pollen, 'Zi Feng Chao Yang' showed severe PCD after cryopreservation. The decline in mitochondrial Ca2+-ATPase activity led to an accumulation of excessive Ca2+ within mitochondria, triggering widespread opening of MPTP, significantly affecting mitochondrial respiration and energy synthesis. These results suggest the mitochondrial pathway of PCD exists in pollen cryopreservation.
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Affiliation(s)
- Wenjie Ma
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China; Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China; National Engineering Research Center for Floriculture, Beijing 100083, China
| | - Mengting Zhu
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China; Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China; National Engineering Research Center for Floriculture, Beijing 100083, China
| | - Yingling Wan
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China; Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China; National Engineering Research Center for Floriculture, Beijing 100083, China
| | - Hui Cai
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China; Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China; National Engineering Research Center for Floriculture, Beijing 100083, China
| | - Yue Sun
- Cell Biology Facility, Center of Biomedical Analysis, Tsinghua University, Beijing 100083, China
| | - Pengcheng Jiao
- Core Facility, Center of Biomedical Analysis, Tsinghua University, Beijing 100083, China
| | - Yan Liu
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China; Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China; National Engineering Research Center for Floriculture, Beijing 100083, China.
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12
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Yang Y, Ji Y, Wang K, Li J, Zhu G, Ma L, Ostersetzer-Biran O, Zhu B, Fu D, Qu G, Luo Y, Zhu H. RNA editing factor SlORRM2 regulates the formation of fruit pointed tips in tomato. PLANT PHYSIOLOGY 2024; 195:2757-2771. [PMID: 38668628 DOI: 10.1093/plphys/kiae235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/28/2024] [Indexed: 08/02/2024]
Abstract
Domestication of tomato (Solanum lycopersicum) has led to large variation in fruit size and morphology. The development of the distal end of the fruit is a critical factor in determining its overall shape. However, the intricate mechanisms underlying distal fruit development require further exploration. This study aimed to investigate the regulatory role of an organelle RNA recognition motif (RRM)-containing protein SlORRM2 in tomato fruit morphology development. Mutant plants lacking SlORRM2 exhibited fruits with pointed tips at the distal end. However, this phenotype could be successfully restored through the implementation of a "functional complementation" strategy. Our findings suggest that the formation of pointed tips in the fruits of the CR-slorrm2 mutants is linked to alterations in the development of the ovary and style. We observed a substantial decrease in the levels of indole-3-acetic acid (IAA) and altered expression of IAA-related response genes in the ovary and style tissues of CR-slorrm2. Moreover, our data demonstrated that SlORRM2 plays a role in regulating mitochondrial RNA editing sites, particularly within genes encoding various respiratory chain subunits. Additionally, the CR-slorrm2 mutants exhibited modified organellar morphology and increased levels of reactive oxygen species. These findings provide valuable insights into the mechanisms underlying the formation of fruit pointed tips in tomato and offer genetic resources for tomato breeding.
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Affiliation(s)
- Yongfang Yang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yajing Ji
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Keru Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Guoning Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Guiqin Qu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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13
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Gorbenko IV, Tarasenko VI, Garnik EY, Yakovleva TV, Katyshev AI, Belkov VI, Orlov YL, Konstantinov YM, Koulintchenko MV. Overexpression of RPOTmp Being Targeted to Either Mitochondria or Chloroplasts in Arabidopsis Leads to Overall Transcriptome Changes and Faster Growth. Int J Mol Sci 2024; 25:8164. [PMID: 39125738 PMCID: PMC11312007 DOI: 10.3390/ijms25158164] [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: 06/04/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
The transcription of Arabidopsis organellar genes is performed by three nuclear-encoded RNA polymerases: RPOTm, RPOTmp, and RPOTp. The RPOTmp protein possesses ambiguous transit peptides, allowing participation in gene expression control in both mitochondria and chloroplasts, although its function in plastids is still under discussion. Here, we show that the overexpression of RPOTmp in Arabidopsis, targeted either to mitochondria or chloroplasts, disturbs the dormant seed state, and it causes the following effects: earlier germination, decreased ABA sensitivity, faster seedling growth, and earlier flowering. The germination of RPOTmp overexpressors is less sensitive to NaCl, while rpotmp knockout is highly vulnerable to salt stress. We found that mitochondrial dysfunction in the rpotmp mutant induces an unknown retrograde response pathway that bypasses AOX and ANAC017. Here, we show that RPOTmp transcribes the accD, clpP, and rpoB genes in plastids and up to 22 genes in mitochondria.
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Affiliation(s)
- Igor V. Gorbenko
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Vladislav I. Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Elena Y. Garnik
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Tatiana V. Yakovleva
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Alexander I. Katyshev
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Vadim I. Belkov
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
| | - Yuriy L. Orlov
- The Digital Health Center, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, Moscow 117198, Russia
| | - Yuri M. Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
- Biosoil Department, Irkutsk State University, Irkutsk 664003, Russia
| | - Milana V. Koulintchenko
- Siberian Institute of Plant Physiology and Biochemistry of Siberian Branch of Russian Academy of Sciences, Irkutsk 664033, Russia; (V.I.T.); (T.V.Y.); (A.I.K.); (Y.M.K.); (M.V.K.)
- Kazan Institute of Biochemistry and Biophysics of the Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences” (KIBB FRC KazSC RAS), Kazan 420111, Russia
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14
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Li S, Yang C, Wang Z, Xu C, Zhang G, Huang Y, Zhang B, Zhou S, Gao Y, Zong W, Duan W, Yang X. Assembly and comparative genome analysis of four mitochondrial genomes from Saccharum complex species. FRONTIERS IN PLANT SCIENCE 2024; 15:1421170. [PMID: 39100089 PMCID: PMC11294102 DOI: 10.3389/fpls.2024.1421170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/01/2024] [Indexed: 08/06/2024]
Abstract
Saccharum complex includes genera Saccharum, Miscanthus, Erianthus, Narenga, and Tripidium. Since the Saccharum complex/Saccharinae constitutes the gene pool used by sugarcane breeders to introduce useful traits into sugarcane, studying the genomic characterization of the Saccharum complex has become particularly important. Here, we assembled graph-based mitochondrial genomes (mitogenomes) of four Saccharinae species (T. arundinaceum, E. rockii, M. sinensis, and N. porphyrocoma) using Illumina and PacBio sequencing data. The total lengths of the mitogenomes of T. arundinaceum, M. sinensis, E. rockii and N. porphyrocoma were 549,593 bp, 514,248 bp, 481,576 bp and 513,095 bp, respectively. Then, we performed a comparative mitogenomes analysis of Saccharinae species, including characterization, organelles transfer sequence, collinear sequence, phylogenetics analysis, and gene duplicated/loss. Our results provided the mitogenomes of four species closely related to sugarcane breeding, enriching the mitochondrial genomic resources of the Saccharinae. Additionally, our study offered new insights into the evolution of mitogenomes at the family and genus levels and enhanced our understanding of organelle evolution in the highly polyploid Saccharum genus.
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Affiliation(s)
- Sicheng Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Cuifang Yang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China
| | - Zhen Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Chaohua Xu
- National Key Laboratory for Biological Breeding of Tropical Crops, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Gemin Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China
| | - Yuxin Huang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China
| | - Baoqing Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China
| | - Shan Zhou
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China
| | - Yijing Gao
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China
| | - Wenyi Zong
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China
| | - Weixing Duan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
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15
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Jiang Z, Chen Y, Zhang X, Meng F, Chen J, Cheng X. Assembly and evolutionary analysis of the complete mitochondrial genome of Trichosanthes kirilowii, a traditional Chinese medicinal plant. PeerJ 2024; 12:e17747. [PMID: 39035164 PMCID: PMC11260417 DOI: 10.7717/peerj.17747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Trichosanthes kirilowii (T. kirilowii) is a valuable plant used for both medicinal and edible purposes. It belongs to the Cucurbitaceae family. However, its phylogenetic position and relatives have been difficult to accurately determine due to the lack of mitochondrial genomic information. This limitation has been an obstacle to the potential applications of T. kirilowii in various fields. To address this issue, Illumina and Nanopore HiFi sequencing were used to assemble the mitogenome of T. kirilowii into two circular molecules with sizes of 245,700 bp and 107,049 bp, forming a unique multi-branched structure. The mitogenome contains 61 genes, including 38 protein-coding genes (PCGs), 20 tRNAs, and three rRNAs. Within the 38 PCGs of the T. kirilowii mitochondrial genome, 518 potential RNA editing sites were identified. The study also revealed the presence of 15 homologous fragments that span both the chloroplast and mitochondrial genomes. The phylogenetic analysis strongly supports that T. kirilowii belongs to the Cucurbitaceae family and is closely related to Luffa. Collinearity analysis of five Cucurbitaceae mitogenomes shows a high degree of structural variability. Interestingly, four genes, namely atp1, ccmFC, ccmFN, and matR, played significant roles in the evolution of T. kirilowii through selection pressure analysis. The comparative analysis of the T. kirilowii mitogenome not only sheds light on its functional and structural features but also provides essential information for genetic studies of the genus of Cucurbitaceae.
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Affiliation(s)
- Zhuanzhuan Jiang
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Yuhan Chen
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Xingyu Zhang
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Fansong Meng
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Jinli Chen
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
| | - Xu Cheng
- Anqing Normal University, Anqing, Anhui, China
- Provincial Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui, Anqing, Anhui, China
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16
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Li S, Wang Z, Jing Y, Duan W, Yang X. Graph-based mitochondrial genomes of three foundation species in the Saccharum genus. PLANT CELL REPORTS 2024; 43:191. [PMID: 38977492 DOI: 10.1007/s00299-024-03277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/24/2024] [Indexed: 07/10/2024]
Abstract
KEY MESSAGE We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes.
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Affiliation(s)
- Sicheng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Zhen Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yanfen Jing
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming, 650221, China
| | - Weixing Duan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences /Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China.
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China.
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17
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Zhang X, Chen H, Ni Y, Wu B, Li J, Burzyński A, Liu C. Plant mitochondrial genome map (PMGmap): A software tool for the comprehensive visualization of coding, noncoding and genome features of plant mitochondrial genomes. Mol Ecol Resour 2024; 24:e13952. [PMID: 38523350 DOI: 10.1111/1755-0998.13952] [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: 10/18/2023] [Revised: 12/18/2023] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
Tools for visualizing genomes are essential for investigating genomic features and their interactions. Currently, tools designed originally for animal mitogenomes and plant plastomes are used to visualize the mitogens of plants but cannot accurately display features specific to plant mitogenomes, such as nonlinear exon arrangement for genes, the prevalence of functional noncoding features and complex chromosomal architecture. To address these problems, a software package, plant mitochondrial genome map (PMGmap), was developed using the Python programming language. PMGmap can draw genes at exon levels; draw cis- and trans-splicing gene maps, noncoding features and repetitive sequences; and scale genic regions by using the scaling of the genic regions on the mitogenome (SAGM) algorithm. It can also draw multiple chromosomes simultaneously. Compared with other state-of-the-art tools, PMGmap showed better performance in visualizing 405 plant mitogenomes, showing potential as an invaluable tool for plant mitogenome research. The web and container versions and the source code of PMGmap can be accessed through the following link: http://www.1kmpg.cn/pmgmap.
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Affiliation(s)
- Xinyi Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingling Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Artur Burzyński
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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18
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Wang R, Luo Y, Lan Z, Qiu D. Insights into structure, codon usage, repeats, and RNA editing of the complete mitochondrial genome of Perilla frutescens (Lamiaceae). Sci Rep 2024; 14:13940. [PMID: 38886463 DOI: 10.1038/s41598-024-64509-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Perilla frutescens (L.) Britton, a member of the Lamiaceae family, stands out as a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in Îś-linolenic acid, holding substantial economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. To this end, the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens were hereby conducted using a combination of Illumina and PacBio data. The assembled P. frutescens mitochondrial genome spanned 299,551 bp and exhibited a typical circular structure, involving a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes. Additionally, 18 introns were observed in 8 protein-coding genes. Notably, the codons of the P. frutescens mitochondrial genome displayed a notable A/T bias. The analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Moreover, RNA editing sites preferentially produced leucine at amino acid editing sites. Furthermore, 70 sequence fragments (12,680 bp) having been transferred from the chloroplast to the mitochondrial genome were identified, accounting for 4.23% of the entire mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salvia miltiorrhiza and Platostoma chinense. Meanwhile, inter-species Ka/Ks results suggested that Ka/Ks < 1 for 28 PCGs, indicating that these genes were evolving under purifying selection. Overall, this study enriches the mitochondrial genome data for P. frutescens and forges a theoretical foundation for future molecular breeding research.
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Affiliation(s)
- Ru Wang
- Hubei Minzu University, School of Forestry and Horticulture, Enshi, 445000, China
| | - Yongjian Luo
- Hubei Minzu University, School of Forestry and Horticulture, Enshi, 445000, China
| | - Zheng Lan
- Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Daoshou Qiu
- Key Laboratory of Crops Genetics and Improvement of Guangdong Province, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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19
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Hörandl E. Apomixis and the paradox of sex in plants. ANNALS OF BOTANY 2024; 134:1-18. [PMID: 38497809 PMCID: PMC11161571 DOI: 10.1093/aob/mcae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/15/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species. SCOPE This review compares the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity in comparison to asexuality are discussed in the light of developmental, evolutionary, genetic and phylogenetic studies. CONCLUSIONS Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms for oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles and prolonged multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is not well understood. In plants in general, the costs of mating are low because of predominant hermaphroditism. Phylogenetic patterns in the archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long-term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), University of Göttingen, Göttingen, Germany
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20
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Rugen N, Senkler M, Braun HP. Deep proteomics reveals incorporation of unedited proteins into mitochondrial protein complexes in Arabidopsis. PLANT PHYSIOLOGY 2024; 195:1180-1199. [PMID: 38060994 PMCID: PMC11142381 DOI: 10.1093/plphys/kiad655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/12/2023] [Indexed: 06/02/2024]
Abstract
The mitochondrial proteome consists of numerous types of proteins which either are encoded and synthesized in the mitochondria, or encoded in the cell nucleus, synthesized in the cytoplasm and imported into the mitochondria. Their synthesis in the mitochondria, but not in the nucleus, relies on the editing of the primary transcripts of their genes at defined sites. Here, we present an in-depth investigation of the mitochondrial proteome of Arabidopsis (Arabidopsis thaliana) and a public online platform for the exploration of the data. For the analysis of our shotgun proteomic data, an Arabidopsis sequence database was created comprising all available protein sequences from the TAIR10 and Araport11 databases, supplemented with sequences of proteins translated from edited and nonedited transcripts of mitochondria. Amino acid sequences derived from partially edited transcripts were also added to analyze proteins encoded by the mitochondrial genome. Proteins were digested in parallel with six different endoproteases to obtain maximum proteome coverage. The resulting peptide fractions were finally analyzed using liquid chromatography coupled to ion mobility spectrometry and tandem mass spectrometry. We generated a "deep mitochondrial proteome" of 4,692 proteins. 1,339 proteins assigned to mitochondria by the SUBA5 database (https://suba.live) accounted for >80% of the total protein mass of our fractions. The coverage of proteins by identified peptides was particularly high compared to single-protease digests, allowing the exploration of differential splicing and RNA editing events at the protein level. We show that proteins translated from nonedited transcripts can be incorporated into native mitoribosomes and the ATP synthase complex. We present a portal for the use of our data, based on "proteomaps" with directly linked protein data. The portal is available at www.proteomeexplorer.de.
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Affiliation(s)
- Nils Rugen
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Michael Senkler
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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21
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Baranova EN, Kononenko NV, Lapshin PV, Nechaeva TL, Khaliluev MR, Zagoskina NV, Smirnova EA, Yuorieva NO, Raldugina GN, Chaban IA, Kurenina LV, Gulevich AA. Superoxide Dismutase Premodulates Oxidative Stress in Plastids for Protection of Tobacco Plants from Cold Damage Ultrastructure Damage. Int J Mol Sci 2024; 25:5544. [PMID: 38791585 PMCID: PMC11122273 DOI: 10.3390/ijms25105544] [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: 04/07/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
ROS-dependent induction of oxidative damage can be used as a trigger initiating genetically determined non-specific protection in plant cells and tissues. Plants are potentially able to withstand various specific (toxic, osmotic) factors of abiotic effects, but do not have sufficient or specific sensitivity to form an adequate effective response. In this work, we demonstrate one of the possible approaches for successful cold acclimation through the formation of effective protection of photosynthetic structures due to the insertion of the heterologous FeSOD gene into the tobacco genome under the control of the constitutive promoter and equipped with a signal sequence targeting the protein to plastid. The increased enzymatic activity of superoxide dismutase in the plastid compartment of transgenic tobacco plants enables them to tolerate the oxidative factor of environmental stresses scavenging ROS. On the other hand, the cost of such resistance is quite high and, when grown under normal conditions, disturbs the arrangement of the intrachloroplastic subdomains leading to the modification of stromal thylakoids, probably significantly affecting the photosynthesis processes that regulate the efficiency of photosystem II. This is partially compensated for by the fact that, at the same time, under normal conditions, the production of peroxide induces the activation of ROS detoxification enzymes. However, a violation of a number of processes, such as the metabolism of accumulation, and utilization and transportation of sugars and starch, is significantly altered, which leads to a shift in metabolic chains. The expected step for further improvement of the applied technology could be both the use of inducible promoters in the expression cassette, and the addition of other genes encoding for hydrogen peroxide-scavenging enzymes in the genetic construct that are downstream in the metabolic chain.
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Affiliation(s)
- Ekaterina N. Baranova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St. 42, 127550 Moscow, Russia (M.R.K.); (E.A.S.); (I.A.C.); (L.V.K.)
- N.V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, 127276 Moscow, Russia
- Moscow K.A. Timiryazev Agricultural Academy (RSAU-MTAA), Russian State Agrarian University, Timiryazevskaya 49, 127434 Moscow, Russia
| | - Neonila V. Kononenko
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St. 42, 127550 Moscow, Russia (M.R.K.); (E.A.S.); (I.A.C.); (L.V.K.)
| | - Pyotr V. Lapshin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St. 35, 127276 Moscow, Russia (T.L.N.); (N.V.Z.)
| | - Tatiana L. Nechaeva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St. 35, 127276 Moscow, Russia (T.L.N.); (N.V.Z.)
| | - Marat R. Khaliluev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St. 42, 127550 Moscow, Russia (M.R.K.); (E.A.S.); (I.A.C.); (L.V.K.)
- Moscow K.A. Timiryazev Agricultural Academy (RSAU-MTAA), Russian State Agrarian University, Timiryazevskaya 49, 127434 Moscow, Russia
| | - Natalia V. Zagoskina
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St. 35, 127276 Moscow, Russia (T.L.N.); (N.V.Z.)
| | - Elena A. Smirnova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St. 42, 127550 Moscow, Russia (M.R.K.); (E.A.S.); (I.A.C.); (L.V.K.)
- Biology Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Building 12, 119991 Moscow, Russia
- Department of Biology, MSU-BIT University, Shenzhen 518172, China
| | - Natalya O. Yuorieva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St. 35, 127276 Moscow, Russia (T.L.N.); (N.V.Z.)
| | - Galina N. Raldugina
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya St. 35, 127276 Moscow, Russia (T.L.N.); (N.V.Z.)
| | - Inna A. Chaban
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St. 42, 127550 Moscow, Russia (M.R.K.); (E.A.S.); (I.A.C.); (L.V.K.)
| | - Ludmila V. Kurenina
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St. 42, 127550 Moscow, Russia (M.R.K.); (E.A.S.); (I.A.C.); (L.V.K.)
| | - Alexander A. Gulevich
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya St. 42, 127550 Moscow, Russia (M.R.K.); (E.A.S.); (I.A.C.); (L.V.K.)
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22
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Mizrahi R, Ostersetzer-Biran O. Mitochondrial RNA Helicases: Key Players in the Regulation of Plant Organellar RNA Splicing and Gene Expression. Int J Mol Sci 2024; 25:5502. [PMID: 38791540 PMCID: PMC11122041 DOI: 10.3390/ijms25105502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial genomes of land plants are large and exhibit a complex mode of gene organization and expression, particularly at the post-transcriptional level. The primary organellar transcripts in plants undergo extensive maturation steps, including endo- and/or exo-nucleolytic cleavage, RNA-base modifications (mostly C-to-U deaminations) and both 'cis'- and 'trans'-splicing events. These essential processing steps rely on the activities of a large set of nuclear-encoded factors. RNA helicases serve as key players in RNA metabolism, participating in the regulation of transcription, mRNA processing and translation. They unwind RNA secondary structures and facilitate the formation of ribonucleoprotein complexes crucial for various stages of gene expression. Furthermore, RNA helicases are involved in RNA metabolism by modulating pre-mRNA maturation, transport and degradation processes. These enzymes are, therefore, pivotal in RNA quality-control mechanisms, ensuring the fidelity and efficiency of RNA processing and turnover in plant mitochondria. This review summarizes the significant roles played by helicases in regulating the highly dynamic processes of mitochondrial transcription, RNA processing and translation in plants. We further discuss recent advancements in understanding how dysregulation of mitochondrial RNA helicases affects the splicing of organellar genes, leading to respiratory dysfunctions, and consequently, altered growth, development and physiology of land plants.
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Affiliation(s)
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus—Givat Ram, Jerusalem 9190401, Israel
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23
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Edris R, Sultan LD, Best C, Mizrahi R, Weinstein O, Chen S, Kamennaya NA, Keren N, Zer H, Zhu H, Ostersetzer-Biran O. Root Primordium Defective 1 Encodes an Essential PORR Protein Required for the Splicing of Mitochondria-Encoded Group II Introns and for Respiratory Complex I Biogenesis. PLANT & CELL PHYSIOLOGY 2024; 65:602-617. [PMID: 37702436 DOI: 10.1093/pcp/pcad101] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023]
Abstract
Cellular respiration involves complex organellar metabolic activities that are pivotal for plant growth and development. Mitochondria contain their own genetic system (mitogenome, mtDNA), which encodes key elements of the respiratory machinery. Plant mtDNAs are notably larger than their counterparts in Animalia, with complex genome organization and gene expression characteristics. The maturation of the plant mitochondrial transcripts involves extensive RNA editing, trimming and splicing events. These essential processing steps rely on the activities of numerous nuclear-encoded cofactors, which may also play key regulatory roles in mitochondrial biogenesis and function and hence in plant physiology. Proteins that harbor the plant organelle RNA recognition (PORR) domain are represented in a small gene family in plants. Several PORR members, including WTF1, WTF9 and LEFKOTHEA, are known to act in the splicing of organellar group II introns in angiosperms. The AT4G33495 gene locus encodes an essential PORR protein in Arabidopsis, termed ROOT PRIMORDIUM DEFECTIVE 1 (RPD1). A null mutation of At.RPD1 causes arrest in early embryogenesis, while the missense mutant lines, rpd1.1 and rpd1.2, exhibit a strong impairment in root development and retarded growth phenotypes, especially under high-temperature conditions. Here, we further show that RPD1 functions in the splicing of introns that reside in the coding regions of various complex I (CI) subunits (i.e. nad2, nad4, nad5 and nad7), as well as in the maturation of the ribosomal rps3 pre-RNA in Arabidopsis mitochondria. The altered growth and developmental phenotypes and modified respiration activities are tightly correlated with respiratory chain CI defects in rpd1 mutants.
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Affiliation(s)
- Rana Edris
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Laure D Sultan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Corinne Best
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Ron Mizrahi
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Ofir Weinstein
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Stav Chen
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Nina A Kamennaya
- The French Associates Institute for Agriculture and Biotechnology of Drylands, Bluestein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Sede Boqer 8499000, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Hagit Zer
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Hongliang Zhu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
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24
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Waters ER, Bezanilla M, Vierling E. ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages. PLANT & CELL PHYSIOLOGY 2024; 65:493-502. [PMID: 37859594 DOI: 10.1093/pcp/pcad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
ATPase family AAA domain-containing 3 (ATAD3) proteins are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent in Fungi and Amoebozoa. These ∼600-amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal ATPases Associated with a variety of cellular Activities (AAA+) matrix domain and an ATAD3_N domain, which is located primarily in the inner membrane space but potentially extends to the cytosol to interact with the ER. Sequence and structural alignments indicate that ATAD3 proteins are most similar to classic chaperone unfoldases in the AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here, we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants and the challenges in determining their essential roles in mitochondria.
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Affiliation(s)
- Elizabeth R Waters
- Department of Biology, San Diego State University, 5500 Campanille Dr., San Diego, CA 92182, USA
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, 78 College St., Hanover, NH 03755, USA
| | - Elizabeth Vierling
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003, USA
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25
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Li Z, Liu J, Liang M, Guo Y, Chen X, Wu H, Jin S. De novo assembly of the complete mitochondrial genome of pepino (Solanum muricatum) using PacBio HiFi sequencing: insights into structure, phylogenetic implications, and RNA editing. BMC PLANT BIOLOGY 2024; 24:361. [PMID: 38702620 PMCID: PMC11069145 DOI: 10.1186/s12870-024-04978-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/02/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Solanum muricatum is an emerging horticultural fruit crop with rich nutritional and antioxidant properties. Although the chromosome-scale genome of this species has been sequenced, its mitochondrial genome sequence has not been reported to date. RESULTS PacBio HiFi sequencing was used to assemble the circular mitogenome of S. muricatum, which was 433,466 bp in length. In total, 38 protein-coding, 19 tRNA, and 3 rRNA genes were annotated. The reticulate mitochondrial conformations with multiple junctions were verified by polymerase chain reaction, and codon usage, sequence repeats, and gene migration from chloroplast to mitochondrial genome were determined. A collinearity analysis of eight Solanum mitogenomes revealed high structural variability. Overall, 585 RNA editing sites in protein coding genes were identified based on RNA-seq data. Among them, mttB was the most frequently edited (52 times), followed by ccmB (46 times). A phylogenetic analysis based on the S. muricatum mitogenome and those of 39 other taxa (including 25 Solanaceae species) revealed the evolutionary and taxonomic status of S. muricatum. CONCLUSIONS We provide the first report of the assembled and annotated S. muricatum mitogenome. This information will help to lay the groundwork for future research on the evolutionary biology of Solanaceae species. Furthermore, the results will assist the development of molecular breeding strategies for S. muricatum based on the most beneficial agronomic traits of this species.
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Affiliation(s)
- Ziwei Li
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jiaxun Liu
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Mingtai Liang
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Yanbing Guo
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xia Chen
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Hongzhi Wu
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Shoulin Jin
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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26
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Demircan N, Sonmez MC, Akyol TY, Ozgur R, Turkan I, Dietz KJ, Uzilday B. Alternative electron sinks in chloroplasts and mitochondria of halophytes as a safety valve for controlling ROS production during salinity. PHYSIOLOGIA PLANTARUM 2024; 176:e14397. [PMID: 38894507 DOI: 10.1111/ppl.14397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/07/2024] [Accepted: 05/12/2024] [Indexed: 06/21/2024]
Abstract
Electron flow through the electron transport chain (ETC) is essential for oxidative phosphorylation in mitochondria and photosynthesis in chloroplasts. Electron fluxes depend on environmental parameters, e.g., ionic and osmotic conditions and endogenous factors, and this may cause severe imbalances. Plants have evolved alternative sinks to balance the reductive load on the electron transport chains in order to avoid overreduction, generation of reactive oxygen species (ROS), and to cope with environmental stresses. These sinks act primarily as valves for electron drainage and secondarily as regulators of tolerance-related metabolism, utilizing the excess reductive energy. High salinity is an environmental stressor that stimulates the generation of ROS and oxidative stress, which affects growth and development by disrupting the redox homeostasis of plants. While glycophytic plants are sensitive to high salinity, halophytic plants tolerate, grow, and reproduce at high salinity. Various studies have examined the ETC systems of glycophytic plants, however, information about the state and regulation of ETCs in halophytes under non-saline and saline conditions is scarce. This review focuses on alternative electron sinks in chloroplasts and mitochondria of halophytic plants. In cases where information on halophytes is lacking, we examined the available knowledge on the relationship between alternative sinks and gradual salinity resilience of glycophytes. To this end, transcriptional responses of involved components of photosynthetic and respiratory ETCs were compared between the glycophyte Arabidopsis thaliana and the halophyte Schrenkiella parvula, and the time-courses of these transcripts were examined in A. thaliana. The observed regulatory patterns are discussed in the context of reactive molecular species formation in halophytes and glycophytes.
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Affiliation(s)
- Nil Demircan
- Department of Biology, Faculty of Science, Ege University, Izmir, Türkiye
| | | | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Rengin Ozgur
- Department of Biology, Faculty of Science, Ege University, Izmir, Türkiye
| | - Ismail Turkan
- Department of Soil and Plant Nutrition, Faculty of Agricultural Sciences and Technologies, Yasar University, İzmir, Türkiye
| | - Karl-Josef Dietz
- Faculty of Biology, Department of Biochemistry and Physiology of Plants, University of Bielefeld, Bielefeld, Germany
| | - Baris Uzilday
- Department of Biology, Faculty of Science, Ege University, Izmir, Türkiye
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27
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K. Raval P, MacLeod AI, Gould SB. A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms. PLoS Biol 2024; 22:e3002608. [PMID: 38713727 PMCID: PMC11135702 DOI: 10.1371/journal.pbio.3002608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 05/29/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.
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Affiliation(s)
- Parth K. Raval
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander I. MacLeod
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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28
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Xiao J, Zhou Y, Xie Y, Li T, Su X, He J, Jiang Y, Zhu H, Qu H. ATP homeostasis and signaling in plants. PLANT COMMUNICATIONS 2024; 5:100834. [PMID: 38327057 PMCID: PMC11009363 DOI: 10.1016/j.xplc.2024.100834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/14/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
ATP is the primary form of energy for plants, and a shortage of cellular ATP is generally acknowledged to pose a threat to plant growth and development, stress resistance, and crop quality. The overall metabolic processes that contribute to the ATP pool, from production, dissipation, and transport to elimination, have been studied extensively. Considerable evidence has revealed that in addition to its role in energy supply, ATP also acts as a regulatory signaling molecule to activate global metabolic responses. Identification of the eATP receptor DORN1 contributed to a better understanding of how plants cope with disruption of ATP homeostasis and of the key points at which ATP signaling pathways intersect in cells or whole organisms. The functions of SnRK1α, the master regulator of the energy management network, in restoring the equilibrium of the ATP pool have been demonstrated, and the vast and complex metabolic network mediated by SnRK1α to adapt to fluctuating environments has been characterized. This paper reviews recent advances in understanding the regulatory control of the cellular ATP pool and discusses possible interactions among key regulators of ATP-pool homeostasis and crosstalk between iATP/eATP signaling pathways. Perception of ATP deficit and modulation of cellular ATP homeostasis mediated by SnRK1α in plants are discussed at the physiological and molecular levels. Finally, we suggest future research directions for modulation of plant cellular ATP homeostasis.
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Affiliation(s)
- Jiaqi Xiao
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijie Zhou
- Guangdong AIB Polytechnic, Guangzhou 510507, China
| | - Yunyun Xie
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Taotao Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinguo Su
- Guangdong AIB Polytechnic, Guangzhou 510507, China
| | - Junxian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zhu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hongxia Qu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Chustecki JM, Johnston IG. Collective mitochondrial dynamics resolve conflicting cellular tensions: From plants to general principles. Semin Cell Dev Biol 2024; 156:253-265. [PMID: 38043948 DOI: 10.1016/j.semcdb.2023.09.005] [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: 06/05/2023] [Revised: 08/18/2023] [Accepted: 09/15/2023] [Indexed: 12/05/2023]
Abstract
Mitochondria play diverse and essential roles in eukaryotic cells, and plants are no exception. Plant mitochondria have several differences from their metazoan and fungal cousins: they often exist in a fragmented state, move rapidly on actin rather than microtubules, have many plant-specific metabolic features and roles, and usually contain only a subset of the complete mtDNA genome, which itself undergoes frequent recombination. This arrangement means that exchange and complementation is essential for plant mitochondria, and recent work has begun to reveal how their collective dynamics and resultant "social networks" of encounters support this exchange, connecting plant mitochondria in time rather than in space. This review will argue that this social network perspective can be extended to a "societal network", where mitochondrial dynamics are an essential part of the interacting cellular society of organelles and biomolecules. Evidence is emerging that mitochondrial dynamics allow optimal resolutions to competing cellular priorities; we will survey this evidence and review potential future research directions, highlighting that plant mitochondria can help reveal and test principles that apply across other kingdoms of life. In parallel with this fundamental cell biology, we also highlight the translational "One Health" importance of plant mitochondrial behaviour - which is exploited in the production of a vast amount of crops consumed worldwide - and the potential for multi-objective optimisation to understand and rationally re-engineer the evolved resolutions to these tensions.
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Affiliation(s)
- Joanna M Chustecki
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway; Computational Biology Unit, University of Bergen, Bergen, Norway.
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30
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Liu J, Feng Y, Chen C, Yan J, Bai X, Li H, Lin C, Xiang Y, Tian W, Qi Z, Yu J, Yan X. Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications. FRONTIERS IN PLANT SCIENCE 2024; 15:1347945. [PMID: 38516667 PMCID: PMC10954886 DOI: 10.3389/fpls.2024.1347945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024]
Abstract
Background The cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for Opuntia species hinders these efforts. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments. Results We sequenced the total DNA of the O. cochenillifera using DNBSEQ and Nanopore platforms. The mitochondrial genome was then assembled using a hybrid assembly strategy using Unicycler software. We found that the mitochondrial genome of O. cochenillifera has a length of 1,156,235 bp, a GC content of 43.06%, and contains 54 unique protein-coding genes and 346 simple repeats. Comparative genomic analysis revealed 48 homologous fragments shared between mitochondrial and chloroplast genomes, with a total length of 47,935 bp. Additionally, the comparison of mitochondrial genomes from four Cactaceae species highlighted their dynamic nature and frequent mitogenomic reorganizations. Conclusion Our study provides a new perspective on the evolution of the organelle genome and its potential application in genetic breeding. These findings offer valuable insights into the mitochondrial genetics of Cactaceae, potentially facilitating future research and breeding programs aimed at enhancing the genetic diversity and adaptability of O. cochenillifera by leveraging its unique mitochondrial genome characteristics.
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Affiliation(s)
- Jing Liu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yuqing Feng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Cheng Chen
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Jing Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xinyu Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Huiru Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Chen Lin
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yinan Xiang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Wen Tian
- Animal Plant and Food Inspection Center of Nanjing Customs District, Nanjing, China
| | - Zhechen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jing Yu
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Xiaoling Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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Li L, Lu X, Dai P, Ma H. DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages. Int J Mol Sci 2024; 25:2964. [PMID: 38474210 DOI: 10.3390/ijms25052964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.
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Affiliation(s)
- Lijie Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaochen Lu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Ping Dai
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Huaiyu Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
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32
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Kant K, Rigó G, Faragó D, Benyó D, Tengölics R, Szabados L, Zsigmond L. Mutation in Arabidopsis mitochondrial Pentatricopeptide repeat 40 gene affects tolerance to water deficit. PLANTA 2024; 259:78. [PMID: 38427069 PMCID: PMC10907415 DOI: 10.1007/s00425-024-04354-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024]
Abstract
MAIN CONCLUSION The Arabidopsis Pentatricopeptide repeat 40 (PPR40) insertion mutants have increased tolerance to water deficit compared to wild-type plants. Tolerance is likely the consequence of ABA hypersensitivity of the mutants. Plant growth and development depend on multiple environmental factors whose alterations can disrupt plant homeostasis and trigger complex molecular and physiological responses. Water deficit is one of the factors which can seriously restrict plant growth and viability. Mitochondria play an important role in cellular metabolism, energy production, and redox homeostasis. During drought and salinity stress, mitochondrial dysfunction can lead to ROS overproduction and oxidative stress, affecting plant growth and survival. Alternative oxidases (AOXs) and stabilization of mitochondrial electron transport chain help mitigate ROS damage. The mitochondrial Pentatricopeptide repeat 40 (PPR40) protein was implicated in stress regulation as ppr40 mutants were found to be hypersensitive to ABA and high salinity during germination. This study investigated the tolerance of the knockout ppr40-1 and knockdown ppr40-2 mutants to water deprivation. Our results show that these mutants display an enhanced tolerance to water deficit. The mutants had higher relative water content, reduced level of oxidative damage, and better photosynthetic parameters in water-limited conditions compared to wild-type plants. ppr40 mutants had considerable differences in metabolic profiles and expression of a number of stress-related genes, suggesting important metabolic reprogramming. Tolerance to water deficit was also manifested in higher survival rates and alleviated growth reduction when watering was suspended. Enhanced sensitivity to ABA and fast stomata closure was suggested to lead to improved capacity for water conservation in such environment. Overall, this study highlights the importance of mitochondrial functions and in particular PPR40 in plant responses to abiotic stress, particularly drought.
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Affiliation(s)
- Kamal Kant
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Gábor Rigó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Dóra Faragó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Dániel Benyó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Roland Tengölics
- Institute of Biochemistry, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - László Szabados
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary.
| | - Laura Zsigmond
- Institute of Plant Biology, HUN-REN Biological Research Centre, Temesvári Krt. 62, 6726, Szeged, Hungary
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Bi C, Shen F, Han F, Qu Y, Hou J, Xu K, Xu LA, He W, Wu Z, Yin T. PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data. HORTICULTURE RESEARCH 2024; 11:uhae023. [PMID: 38469379 PMCID: PMC10925850 DOI: 10.1093/hr/uhae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/14/2024] [Indexed: 03/13/2024]
Abstract
Complete mitochondrial genomes (mitogenomes) of plants are valuable resources for nucleocytoplasmic interactions, plant evolution, and plant cytoplasmic male sterile line breeding. However, the complete assembly of plant mitogenomes is challenging due to frequent recombination events and horizontal gene transfers. Previous studies have adopted Illumina, PacBio, and Nanopore sequencing data to assemble plant mitogenomes, but the poor assembly completeness, low sequencing accuracy, and high cost limit the sampling capacity. Here, we present an efficient assembly toolkit (PMAT) for de novo assembly of plant mitogenomes using low-coverage HiFi sequencing data. PMAT has been applied to the de novo assembly of 13 broadly representative plant mitogenomes, outperforming existing organelle genome assemblers in terms of assembly accuracy and completeness. By evaluating the assembly of plant mitogenomes from different sequencing data, it was confirmed that PMAT only requires 1× HiFi sequencing data to obtain a complete plant mitogenome. The source code for PMAT is available at https://github.com/bichangwei/PMAT. The developed PMAT toolkit will indeed accelerate the understanding of evolutionary variation and breeding application of plant mitogenomes.
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Affiliation(s)
- Changwei Bi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
- Department of artificial intelligence, College of Information Science and Technology, College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fuchuan Han
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yanshu Qu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Jing Hou
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Kewang Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Li-an Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Tongming Yin
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China
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Cadorna CAE, Pahayo DG, Rey JD. The first mitochondrial genome of Calophyllum soulattri Burm.f. Sci Rep 2024; 14:5112. [PMID: 38429360 PMCID: PMC10907642 DOI: 10.1038/s41598-024-55016-6] [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: 09/28/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
Calophyllum soulattri Burm.f. is traditionally used to treat skin infections and reduce rheumatic pain, yet genetic and genomic studies are still limited. Here, we present the first complete mitochondrial genome of C. soulattri. It is 378,262 bp long with 43.97% GC content, containing 55 genes (30 protein-coding, 5 rRNA, and 20 tRNA). Repeat analysis of the mitochondrial genome revealed 194 SSRs, mostly mononucleotides, and 266 pairs of dispersed repeats ( ≥ 30 bp) that were predominantly palindromic. There were 23 homologous fragments found between the mitochondrial and plastome genomes. We also predicted 345 C-to-U RNA editing sites from 30 protein-coding genes (PCGs) of the C. soulatrii mitochondrial genome. These RNA editing events created the start codon of nad1 and the stop codon of ccmFc. Most PCGs of the C. soulattri mitochondrial genome underwent negative selection, but atp4 and ccmB experienced positive selection. Phylogenetic analyses showed C. soulattri is a sister taxon of Garcinia mangostana. This study has shed light on C. soulattri's evolution and Malpighiales' phylogeny. As the first complete mitochondrial genome in Calophyllaceae, it can be used as a reference genome for other medicinal plant species within the family for future genetic studies.
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Affiliation(s)
- Charles Anthon E Cadorna
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Dexter G Pahayo
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Jessica D Rey
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines.
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35
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Zsigmond L, Juhász-Erdélyi A, Valkai I, Aleksza D, Rigó G, Kant K, Szepesi Á, Fiorani F, Körber N, Kovács L, Szabados L. Mitochondrial complex I subunit NDUFS8.2 modulates responses to stresses associated with reduced water availability. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108466. [PMID: 38428158 DOI: 10.1016/j.plaphy.2024.108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Mitochondria are important sources of energy in plants and are implicated in coordination of a number of metabolic and physiological processes including stabilization of redox balance, synthesis and turnover of a number of metabolites, and control of programmed cell death. Mitochondrial electron transport chain (mETC) is the backbone of the energy producing process which can influence other processes as well. Accumulating evidence suggests that mETC can affect responses to environmental stimuli and modulate tolerance to extreme conditions such as drought or salinity. Screening for stress responses of 13 Arabidopsis mitochondria-related T-DNA insertion mutants, we identified ndufs8.2-1 which has an increased ability to withstand osmotic and oxidative stresses compared to wild type plants. Insertion in ndufs8.2-1 disrupted the gene that encodes the NADH dehydrogenase [ubiquinone] fragment S subunit 8 (NDUFS8) a component of Complex I of mETC. ndufs8.2-1 tolerated reduced water availability, retained photosynthetic activity and recovered from severe water stress with higher efficiency compared to wild type plants. Several mitochondrial functions were altered in the mutant including oxygen consumption, ROS production, ATP and ADP content as well as activities of genes encoding alternative oxidase 1A (AOX1A) and various alternative NAD(P)H dehydrogenases (ND). Our results suggest that in the absence of NDUFS8.2 stress-induced ROS generation is restrained leading to reduced oxidative damage and improved tolerance to water deficiency. mETC components can be implicated in redox and energy homeostasis and modulate responses to stresses associated with reduced water availability.
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Affiliation(s)
- Laura Zsigmond
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary.
| | - Annabella Juhász-Erdélyi
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Ildikó Valkai
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Dávid Aleksza
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Gábor Rigó
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Kamal Kant
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Ágnes Szepesi
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Fabio Fiorani
- Institute of Bio- and Geo-Sciences, IBG2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Niklas Körber
- Nunhems - BASF Vegetable Seeds, Department of Data Science and Technology, Roermond, Netherlands
| | - László Kovács
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - László Szabados
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
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36
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van Wijk KJ, Bentolila S, Leppert T, Sun Q, Sun Z, Mendoza L, Li M, Deutsch EW. Detection and editing of the updated Arabidopsis plastid- and mitochondrial-encoded proteomes through PeptideAtlas. PLANT PHYSIOLOGY 2024; 194:1411-1430. [PMID: 37879112 DOI: 10.1093/plphys/kiad572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/12/2023] [Accepted: 09/23/2023] [Indexed: 10/27/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) ecotype Col-0 has plastid and mitochondrial genomes encoding over 100 proteins. Public databases (e.g. Araport11) have redundancy and discrepancies in gene identifiers for these organelle-encoded proteins. RNA editing results in changes to specific amino acid residues or creation of start and stop codons for many of these proteins, but the impact of RNA editing at the protein level is largely unexplored due to the complexities of detection. Here, we assembled the nonredundant set of identifiers, their correct protein sequences, and 452 predicted nonsynonymous editing sites of which 56 are edited at lower frequency. We then determined accumulation of edited and/or unedited proteoforms by searching ∼259 million raw tandem MS spectra from ProteomeXchange, which is part of PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/). We identified all mitochondrial proteins and all except 3 plastid-encoded proteins (NdhG/Ndh6, PsbM, and Rps16), but no proteins predicted from the 4 ORFs were identified. We suggest that Rps16 and 3 of the ORFs are pseudogenes. Detection frequencies for each edit site and type of edit (e.g. S to L/F) were determined at the protein level, cross-referenced against the metadata (e.g. tissue), and evaluated for technical detection challenges. We detected 167 predicted edit sites at the proteome level. Minor frequency sites were edited at low frequency at the protein level except for cytochrome C biogenesis 382 at residue 124 (Ccb382-124). Major frequency sites (>50% editing of RNA) only accumulated in edited form (>98% to 100% edited) at the protein level, with the exception of Rpl5-22. We conclude that RNA editing for major editing sites is required for stable protein accumulation.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA
| | - Stephane Bentolila
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, NY 14853, USA
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
| | - Margaret Li
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, WA 98109, USA
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37
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Zhang Y, Li H, Wang Y, Nie M, Zhang K, Pan J, Zhang Y, Ye Z, Zufall RA, Lynch M, Long H. Mitogenomic architecture and evolution of the soil ciliates Colpoda. mSystems 2024; 9:e0116123. [PMID: 38259100 PMCID: PMC10878089 DOI: 10.1128/msystems.01161-23] [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: 11/01/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Colpoda are cosmopolitan unicellular eukaryotes primarily inhabiting soil and benefiting plant growth, but they remain one of the least understood taxa in genetics and genomics within the realm of ciliated protozoa. Here, we investigate the architecture of de novo assembled mitogenomes of six Colpoda species, using long-read sequencing and involving 36 newly isolated natural strains in total. The mitogenome sizes span from 43 to 63 kbp and typically contain 28-33 protein-coding genes. They possess a linear structure with variable telomeres and central repeats, with one Colpoda elliotti strain isolated from Tibet harboring the longest telomeres among all studied ciliates. Phylogenomic analyses reveal that Colpoda species started to diverge more than 326 million years ago, eventually evolving into two distinct groups. Collinearity analyses also reveal significant genomic divergences and a lack of long collinear blocks. One of the most notable features is the exceptionally high level of gene rearrangements between mitochondrial genomes of different Colpoda species, dominated by gene loss events. Population-level mitogenomic analysis on natural strains also demonstrates high sequence divergence, regardless of geographic distance, but the gene order remains highly conserved within species, offering a new species identification criterion for Colpoda species. Furthermore, we identified underlying heteroplasmic sites in the majority of strains of three Colpoda species, albeit without a discernible recombination signal to account for this heteroplasmy. This comprehensive study systematically unveils the mitogenomic structure and evolution of these ancient and ecologically significant Colpoda ciliates, thus laying the groundwork for a deeper understanding of the evolution of unicellular eukaryotes.IMPORTANCEColpoda, one of the most widespread ciliated protozoa in soil, are poorly understood in regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by gene loss events, potentially leading to the streamlining of Colpoda mitogenomes. Surprisingly, while interspecific rearrangements abound, our population-level mitogenomic study revealed a conserved gene order within species, offering a potential new identification criterion. Phylogenomic analysis traced their lineage over 326 million years, revealing two distinct groups. Substantial genomic divergence might be associated with the lack of extended collinear blocks and relaxed purifying selection. This study systematically reveals Colpoda ciliate mitogenome structures and evolution, providing insights into the survival and evolution of these vital soil microorganisms.
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Affiliation(s)
- Yuanyuan Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
| | - Haichao Li
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Yaohai Wang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Mu Nie
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Kexin Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Jiao Pan
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Yu Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
- School of Mathematics Science, Ocean University of China, Qingdao, Shandong Province, China
| | - Zhiqiang Ye
- School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Rebecca A. Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Hongan Long
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
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Lin JY, Liu YC, Tseng YH, Chan MT, Chang CC. TALE-based organellar genome editing and gene expression in plants. PLANT CELL REPORTS 2024; 43:61. [PMID: 38336900 DOI: 10.1007/s00299-024-03150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
KEY MESSAGE TALE-based editors provide an alternative way to engineer the organellar genomes in plants. We update and discuss the most recent developments of TALE-based organellar genome editing in plants. Gene editing tools have been widely used to modify the nuclear genomes of plants for various basic research and biotechnological applications. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 editing platform is the most commonly used technique because of its ease of use, fast speed, and low cost; however, it encounters difficulty when being delivered to plant organelles for gene editing. In contrast, protein-based editing technologies, such as transcription activator-like effector (TALE)-based tools, could be easily delivered, expressed, and targeted to organelles in plants via Agrobacteria-mediated nuclear transformation. Therefore, TALE-based editors provide an alternative way to engineer the organellar genomes in plants since the conventional chloroplast transformation method encounters technical challenges and is limited to certain species, and the direct transformation of mitochondria in higher plants is not yet possible. In this review, we update and discuss the most recent developments of TALE-based organellar genome editing in plants.
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Affiliation(s)
- Jer-Young Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yu-Chang Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan
| | - Yan-Hao Tseng
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 71150, Taiwan.
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Ching-Chun Chang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
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Li C, Liu H, Qin M, Tan YJ, Ou XL, Chen XY, Wei Y, Zhang ZJ, Lei M. RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola. FRONTIERS IN PLANT SCIENCE 2024; 15:1332460. [PMID: 38379941 PMCID: PMC10876856 DOI: 10.3389/fpls.2024.1332460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.
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Affiliation(s)
- Cui Li
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Han Liu
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Mei Qin
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yao-jing Tan
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Xia-lian Ou
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Xiao-ying Chen
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ying Wei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhan-jiang Zhang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ming Lei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Guangxi Engineering Research Center of Traditional Chinese Medicine (TCM) Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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Sankar TV, Saharay M, Santhosh D, Menon S, Raran-Kurussi S, Padmasree K. Biomolecular interaction of purified recombinant Arabidopsis thaliana's alternative oxidase 1A with TCA cycle metabolites: Biophysical and molecular docking studies. Int J Biol Macromol 2024; 258:128814. [PMID: 38114006 DOI: 10.1016/j.ijbiomac.2023.128814] [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: 04/14/2023] [Revised: 11/08/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
In higher plants, the mitochondrial alternative oxidase (AOX) pathway plays an essential role in maintaining the TCA cycle/cellular carbon and energy balance under various physiological and stress conditions. Though the activation of AOX pathway upon exogenous addition of α-ketoacids/TCA cycle metabolites [pyruvate, α-ketoglutarate (α-KG), oxaloacetic acid (OAA), succinate and malic acid] to isolated mitochondria is known, the molecular mechanism of interaction of these metabolites with AOX protein is limited. The present study is designed to understand the biomolecular interaction of pure recombinant Arabidopsis thaliana AOX1A with TCA cycle metabolites under in vitro conditions using various biophysical and molecular docking studies. The binding of α-KG, fumaric acid and OAA to rAtAOX1A caused conformational change in the microenvironment of tryptophan residues as evidenced by red shift in the synchronous fluorescence spectra (∆λ = 60 nm). Besides, a decrease in conventional fluorescence emission spectra, tyrosine specific synchronous fluorescence spectra (∆λ = 15 nm) and α-helical content of CD spectra revealed the conformation changes in rAtAOX1A structure associated with binding of various TCA cycle metabolites. Further, surface plasmon resonance (SPR) and microscale thermophoresis (MST) studies revealed the binding affinity, while docking studies identified binding pocket residues, respectively, for these metabolites on rAtAOX1A.
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Affiliation(s)
- Tadiboina Veera Sankar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Moumita Saharay
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Dharawath Santhosh
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Saji Menon
- Senior Field Application Scientist, Nanotemper Technologies GmbH, India
| | - Sreejith Raran-Kurussi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 500107, India
| | - Kollipara Padmasree
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India.
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41
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Lima RPM, Oliveira JS, do Nascimento LC, Labate MTV, Labate CA, Barreto P, Maia IDG. High-throughput analysis reveals disturbances throughout the cell caused by Arabidopsis UCP1 and UCP3 double knockdown. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108324. [PMID: 38183903 DOI: 10.1016/j.plaphy.2023.108324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/12/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024]
Abstract
Three genes encoding mitochondrial uncoupling proteins (UCPs) have been described in Arabidopsis thaliana (UCP1 to UCP3). In plants, UCPs may act as an uncoupler or as an aspartate/glutamate exchanger. For instance, much of the data regarding UCP functionality were obtained for the UCP1 and UCP2 isoforms compared with UCP3. Here, to get a better understanding about the concerted action of UCP1 and UCP3 in planta, we investigated the transcriptome and metabolome profiles of ucp1 ucp3 double mutant plants during the vegetative phase. For that, 21-day-old mutant plants, which displayed the most evident phenotypic alterations compared to wild type (WT) plants, were employed. The double knockdown of UCP1 and UCP3, isoforms unequivocally present inside the mitochondria, promoted important transcriptional reprogramming with alterations in the expression of genes related to mitochondrial and chloroplast function as well as those responsive to abiotic stress, suggesting disturbances throughout the cell. The observed transcriptional changes were well integrated with the metabolomic data of ucp1 ucp3 plants. Alterations in metabolites related to primary and secondary metabolism, particularly enriched in the Alanine, Aspartate and Glutamate metabolism, were detected. These findings extend our knowledge of the underlying roles played by UCP3 in concert with UCP1 at the whole plant level.
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Affiliation(s)
- Rômulo Pedro Macêdo Lima
- Departamento de Ciências Químicas e Biológicas (Setor Genética), Instituto de Biociências, UNESP, CEP 18618-689, Botucatu, SP, Brazil
| | - Jakeline Santos Oliveira
- Departamento de Biologia Estrutural e Funcional (Setor Fisiologia), Instituto de Biociências, UNESP, CEP 18618-689, Botucatu, SP, Brazil
| | | | | | - Carlos Alberto Labate
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", USP, CEP 13418-260, Piracicaba, SP, Brazil
| | - Pedro Barreto
- Departamento de Ciências Químicas e Biológicas (Setor Genética), Instituto de Biociências, UNESP, CEP 18618-689, Botucatu, SP, Brazil
| | - Ivan de Godoy Maia
- Departamento de Ciências Químicas e Biológicas (Setor Genética), Instituto de Biociências, UNESP, CEP 18618-689, Botucatu, SP, Brazil.
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Fuchs P, Feixes-Prats E, Arruda P, Feitosa-Araújo E, Fernie AR, Grefen C, Lichtenauer S, Linka N, de Godoy Maia I, Meyer AJ, Schilasky S, Sweetlove LJ, Wege S, Weber APM, Millar AH, Keech O, Florez-Sarasa I, Barreto P, Schwarzländer M. PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 2 localizes to the Golgi. PLANT PHYSIOLOGY 2024; 194:623-628. [PMID: 37820040 DOI: 10.1093/plphys/kiad540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 10/13/2023]
Abstract
In contrast to its close homolog PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 1 (UCP1), which is an abundant carrier protein in the mitochondria, UCP2 localizes to the Golgi.
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Affiliation(s)
- Philippe Fuchs
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Elisenda Feixes-Prats
- Centre for Research in Agricultural Genomics (CRAG), Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Paulo Arruda
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875 Campinas, Brazil
| | - Elias Feitosa-Araújo
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, D-14476 Postdam-Golm, Germany
| | - Christopher Grefen
- Institute of Molecular and Cellular Botany, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Sophie Lichtenauer
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Ivan de Godoy Maia
- Institute of Biosciences, São Paulo State University (UNESP), 18618-970 Botucatu, Brazil
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Sören Schilasky
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Lee J Sweetlove
- Department of Biology, South Parks Road, University of Oxford, OX1 3RB Oxford, UK
| | - Stefanie Wege
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 6009 Perth, Western Australia, Australia
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden
| | - Igor Florez-Sarasa
- Centre for Research in Agricultural Genomics (CRAG), Campus UAB Bellaterra, 08193 Barcelona, Spain
- Institut de Recerca i Tecnología Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Pedro Barreto
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
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Liu D, Zhang Z, Hao Y, Li M, Yu H, Zhang X, Mi H, Cheng L, Zhao Y. Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae. BMC Genomics 2024; 25:114. [PMID: 38273225 PMCID: PMC10811901 DOI: 10.1186/s12864-024-10016-8] [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: 09/02/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history. RESULT We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203 bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae. CONCLUSIONS We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.
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Affiliation(s)
- Daliang Liu
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
| | - Zhihan Zhang
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China
- College of Engineering and Technology, Northeast Forestry University, Harbin, 150040, China
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
- Present address: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Xingruo Zhang
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Haoyang Mi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Lin Cheng
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High-Value Utilization, College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
| | - Yiyong Zhao
- Key Laboratory of Functional Agriculture in Higher Education of Guizhou Province, College of Agriculture, Guizhou University, Guiyang, 550025, China.
- State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China.
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Bruni F. Human mtDNA-Encoded Long ncRNAs: Knotty Molecules and Complex Functions. Int J Mol Sci 2024; 25:1502. [PMID: 38338781 PMCID: PMC10855489 DOI: 10.3390/ijms25031502] [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: 12/20/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Until a few decades ago, most of our knowledge of RNA transcription products was focused on protein-coding sequences, which were later determined to make up the smallest portion of the mammalian genome. Since 2002, we have learnt a great deal about the intriguing world of non-coding RNAs (ncRNAs), mainly due to the rapid development of bioinformatic tools and next-generation sequencing (NGS) platforms. Moreover, interest in non-human ncRNAs and their functions has increased as a result of these technologies and the accessibility of complete genome sequences of species ranging from Archaea to primates. Despite not producing proteins, ncRNAs constitute a vast family of RNA molecules that serve a number of regulatory roles and are essential for cellular physiology and pathology. This review focuses on a subgroup of human ncRNAs, namely mtDNA-encoded long non-coding RNAs (mt-lncRNAs), which are transcribed from the mitochondrial genome and whose disparate localisations and functions are linked as much to mitochondrial metabolism as to cellular physiology and pathology.
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Affiliation(s)
- Francesco Bruni
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
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Tang J, Luo Z, Zhang J, Chen L, Li L. Multi-Chromosomal mitochondrial genome of medicinal plant Acorus tatarinowii (Acoraceae): Firstly reported from Acorales Order. Gene 2024; 892:147847. [PMID: 37774807 DOI: 10.1016/j.gene.2023.147847] [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: 06/20/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Acorus tatarinowii Schott (A. tatarinowii), a well-known traditional Chinese medicinal plant renowned for its high medicinal value, but its mitochondrial genome (mitogenome) is still unexplored. In this study, we meticulously assembled the complete mitochondrial genome of A. tatarinowii using a combination of Illumina short reads and Oxford Nanopore long reads. Our findings revealed that A. tatarinowii possesses a complex chromosomal structural mitogenome, comprising two linear chromosomes and seven circular chromosomes. This mitogenome spans 1.81 Mb in length with a GC content of 38.29 %. Notably, it contained 24 unique mitochondrial core genes, seven unique variable genes, 17 tRNA genes, and three rRNA genes. Analyses of codon usage, most protein-coding genes (PCGs) exhibited a common codon usage preference, with RSCU values greater than 1, and the codon with the highest RSCU value was UAA(End, 1.90). We conducted a thorough analysis of repeat sequences, the distribution of repetitive sequences in nine mitochondrial chromosomes showed distinct patterns. Moreover, we identified 82 and 12 homologous fragments by comparing the sequences of chloroplast and nuclear genomes to the A. tatarinowii mitogenome, respectively. Lastly, We predicted a total of 234 potential RNA editing sites in 28 unique PCGs and discovered that the nad4 gene has been edited the most often, at 26 times. Our results contribute to the enrichment of mitochondrial genome resources for Acoraceae, and the mitogenome also can be used as a reference for other species.
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Affiliation(s)
- Jianfeng Tang
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological and Environment, Wuhan 430010, Hubei, China
| | - Zongkai Luo
- Eco-Environmental Monitoring Station of Pu'er City, Yunnan Provincial Department of Ecology and Environment, Pu'er 665000, Yunnan, China
| | - Jing Zhang
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological and Environment, Wuhan 430010, Hubei, China
| | - Liwen Chen
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological and Environment, Wuhan 430010, Hubei, China
| | - Li Li
- Qiandongnan Ecological Environment Monitoring Center, Kaili 557314, Guizhou, China.
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Liu X, Zhang D, Yu Z, Zeng B. Assembly and analysis of the complete mitochondrial genome of the Chinese wild dwarf almond ( Prunus tenella). Front Genet 2024; 14:1329060. [PMID: 38283144 PMCID: PMC10811783 DOI: 10.3389/fgene.2023.1329060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
Background: The wild dwarf almond (Prunus tenella) is one of the national key grade II-protected wild plants in China. It is a relic deciduous forest species from the middle Eocene of the ancient Mediterranean Sea and is also known as a "living fossil of plants." It is distributed in Southeast Europe, West Asia, Central Asia, Siberia, and Xinjiang (Tacheng) and other areas of China. The plant grows on arid slopes, steppes, depressions, and valleys at an altitude of 1,200 m. The seeds of wild dwarf almonds are frost resistant and contain oil and bitter lentil glycosides, which possess medicinal value. Additionally, the seeds of wild dwarf almonds can be used as the original material for breeding new varieties of almonds and obtain ornamental flowers and trees. Results: The complete mitochondrial genome of P. tenella was sequenced and assembled using two sequencing platforms, namely, Illumina Novaseq6000 and Oxford Nanopore PromethION. The assembled genome was 452,158-bp long with a typical loop structure. The total number of A, T, C, and G bases in the genome was 122,066 (26.99%), 124,114 (27.45%), 103,285 (22.84%), and 102,693 (22.71%), respectively, with a GC content of 45.55%. A total of 63 unique genes, including 36 protein-coding genes, 24 tRNA genes, and 3 rRNA genes, were identified in the genome. Furthermore, codon usage, sequence duplication, RNA editing, and mitochondrial and chloroplast DNA fragment transfer events in the genome were analyzed. A phylogenetic tree was also constructed using 30 protein-coding genes that are common to the mitochondrial genomes of 24 species, which indicated that the genome of wild lentils is highly conserved with those of apples and pears belonging to Rosaceae. Conclusion: Assembly and annotation of the P. tenella mitochondrial genome provided comprehensive information about the mitochondrial genome of wild dwarf almonds, This study provides information on the mitochondrial genome of Prunus species and serves as a reference for further evolutionary studies on wild dwarf almonds.
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Affiliation(s)
| | | | | | - Bin Zeng
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
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Lu G, Li Q. Complete mitochondrial genome of Syzygium samarangense reveals genomic recombination, gene transfer, and RNA editing events. FRONTIERS IN PLANT SCIENCE 2024; 14:1301164. [PMID: 38264024 PMCID: PMC10803518 DOI: 10.3389/fpls.2023.1301164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024]
Abstract
Wax apple (Syzygium samarangense) is a commercial fruit that belongs to one of the most species-rich tree genera in the world. We report here the first complete S. samarangense mitogenome obtained using a hybrid assembly strategy. The mitogenome was a 530,242 bp circular molecule encoding 61 unique genes accounting for 7.99% of the full-length genome. Additionally, 167 simple sequence repeats, 19 tandem repeats, and 529 pairs of interspersed repeats were identified. Long read mapping and Sanger sequencing revealed the involvement of two forward repeats (35,843 bp and 22,925 bp) in mediating recombination. Thirteen homologous fragments in the chloroplast genome were identified, accounting for 1.53% of the mitogenome, and the longest fragment was 2,432 bp. An evolutionary analysis showed that S. samarangense underwent multiple genomic reorganization events and lost at least four protein-coding genes (PCGs) (rps2, rps7, rps11, and rps19). A total of 591 RNA editing sites were predicted in 37 PCGs, of which nad1-2, nad4L-2, and rps10-2 led to the gain of new start codons, while atp6-1156, ccmFC-1315 and rps10-331 created new stop codons. This study reveals the genetic features of the S. samarangense mitogenome and provides a scientific basis for further studies of traits with an epistatic basis and for germplasm identification.
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Affiliation(s)
- Guilong Lu
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- College of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Qing Li
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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Dimnet L, Salinas-Giegé T, Pullara S, Moyet L, Genevey C, Kuntz M, Duchêne AM, Rolland N. Isolation of Cytosolic Ribosomes Associated with Plant Mitochondria and Chloroplasts. Methods Mol Biol 2024; 2776:289-302. [PMID: 38502512 DOI: 10.1007/978-1-0716-3726-5_18] [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] [Indexed: 03/21/2024]
Abstract
Excluding the few dozen proteins encoded by the chloroplast and mitochondrial genomes, the majority of plant cell proteins are synthesized by cytosolic ribosomes. Most of these nuclear-encoded proteins are then targeted to specific cell compartments thanks to localization signals present in their amino acid sequence. These signals can be specific amino acid sequences known as transit peptides, or post-translational modifications, ability to interact with specific proteins or other more complex regulatory processes. Furthermore, in eukaryotic cells, protein synthesis can be regulated so that certain proteins are synthesized close to their destination site, thus enabling local protein synthesis in specific compartments of the cell. Previous studies have revealed that such locally translating cytosolic ribosomes are present in the vicinity of mitochondria and emerging views suggest that localized translation near chloroplasts could also occur. However, in higher plants, very little information is available on molecular mechanisms controlling these processes and there is a need to characterize cytosolic ribosomes associated with organelles membranes. To this goal, this protocol describes the purification of higher plant chloroplast and mitochondria and the organelle-associated cytosolic ribosomes.
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Affiliation(s)
- Laura Dimnet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg Cedex, France
| | - Sara Pullara
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Lucas Moyet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Chloé Genevey
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Marcel Kuntz
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Anne-Marie Duchêne
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg Cedex, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France.
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Koenig AM, Liu B, Hu J. Visualizing the dynamics of plant energy organelles. Biochem Soc Trans 2023; 51:2029-2040. [PMID: 37975429 PMCID: PMC10754284 DOI: 10.1042/bst20221093] [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: 09/28/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
Plant organelles predominantly rely on the actin cytoskeleton and the myosin motors for long-distance trafficking, while using microtubules and the kinesin motors mostly for short-range movement. The distribution and motility of organelles in the plant cell are fundamentally important to robust plant growth and defense. Chloroplasts, mitochondria, and peroxisomes are essential organelles in plants that function independently and coordinately during energy metabolism and other key metabolic processes. In response to developmental and environmental stimuli, these energy organelles modulate their metabolism, morphology, abundance, distribution and motility in the cell to meet the need of the plant. Consistent with their metabolic links in processes like photorespiration and fatty acid mobilization is the frequently observed inter-organellar physical interaction, sometimes through organelle membranous protrusions. The development of various organelle-specific fluorescent protein tags has allowed the simultaneous visualization of organelle movement in living plant cells by confocal microscopy. These energy organelles display an array of morphology and movement patterns and redistribute within the cell in response to changes such as varying light conditions, temperature fluctuations, ROS-inducible treatments, and during pollen tube development and immune response, independently or in association with one another. Although there are more reports on the mechanism of chloroplast movement than that of peroxisomes and mitochondria, our knowledge of how and why these three energy organelles move and distribute in the plant cell is still scarce at the functional and mechanistic level. It is critical to identify factors that control organelle motility coupled with plant growth, development, and stress response.
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Affiliation(s)
- Amanda M. Koenig
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
| | - Bo Liu
- Department of Plant Biology, University of California, Davis, CA, U.S.A
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
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Yao L, Wu X, Jiang X, Shan M, Zhang Z, Li Y, Yang A, Li Y, Yang C. Subcellular compartmentalization in the biosynthesis and engineering of plant natural products. Biotechnol Adv 2023; 69:108258. [PMID: 37722606 DOI: 10.1016/j.biotechadv.2023.108258] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.
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Affiliation(s)
- Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xiuming Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xun Jiang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Muhammad Shan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Zhuoxiang Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yiting Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Changqing Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China.
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