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Li J, Yang S, Wu Y, Wang R, Liu Y, Liu J, Ye Z, Tang R, Whiteway M, Lv Q, Yan L. Alternative Oxidase: From Molecule and Function to Future Inhibitors. ACS OMEGA 2024; 9:12478-12499. [PMID: 38524433 PMCID: PMC10955580 DOI: 10.1021/acsomega.3c09339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/26/2024]
Abstract
In the respiratory chain of the majority of aerobic organisms, the enzyme alternative oxidase (AOX) functions as the terminal oxidase and has important roles in maintaining metabolic and signaling homeostasis in mitochondria. AOX endows the respiratory system with flexibility in the coupling among the carbon metabolism pathway, electron transport chain (ETC) activity, and ATP turnover. AOX allows electrons to bypass the main cytochrome pathway to restrict the generation of reactive oxygen species (ROS). The inhibition of AOX leads to oxidative damage and contributes to the loss of adaptability and viability in some pathogenic organisms. Although AOXs have recently been identified in several organisms, crystal structures and major functions still need to be explored. Recent work on the trypanosome alternative oxidase has provided a crystal structure of an AOX protein, which contributes to the structure-activity relationship of the inhibitors of AOX. Here, we review the current knowledge on the development, structure, and properties of AOXs, as well as their roles and mechanisms in plants, animals, algae, protists, fungi, and bacteria, with a special emphasis on the development of AOX inhibitors, which will improve the understanding of respiratory regulation in many organisms and provide references for subsequent studies of AOX-targeted inhibitors.
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Affiliation(s)
- Jiye Li
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
- Institute
of Medicinal Biotechnology, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shiyun Yang
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Yujie Wu
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Ruina Wang
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Yu Liu
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Jiacun Liu
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Zi Ye
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Renjie Tang
- Beijing
South Medical District of Chinese PLA General Hospital, Beijing 100072, China
| | - Malcolm Whiteway
- Department
of Biology, Concordia University, Montreal, H4B 1R6 Quebec, Canada
| | - Quanzhen Lv
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
- Basic
Medicine Innovation Center for Fungal Infectious Diseases, (Naval Medical University), Ministry of Education, Shanghai 200433, China
- Key
Laboratory of Biosafety Defense (Naval Medical University), Ministry
of Education, Shanghai 200433, China
- Shanghai
Key Laboratory of Medical Biodefense, Shanghai 200433, China
| | - Lan Yan
- School
of Pharmacy, Naval Medical University, Shanghai 200433, China
- Basic
Medicine Innovation Center for Fungal Infectious Diseases, (Naval Medical University), Ministry of Education, Shanghai 200433, China
- Key
Laboratory of Biosafety Defense (Naval Medical University), Ministry
of Education, Shanghai 200433, China
- Shanghai
Key Laboratory of Medical Biodefense, Shanghai 200433, China
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2
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Cheng Y, Liu Y, Li X, Liu G, Li Z, Liu B, Gao N. Transcriptome analysis of the mechanism of endophytic fungus CHS3 promoting saikosaponin d synthesis in Bupleurum scorzonerifolium Willd. suspension cells. Fitoterapia 2024; 173:105778. [PMID: 38128620 DOI: 10.1016/j.fitote.2023.105778] [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: 06/27/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Saikosaponin d (SSd) is the main component of Bupleuri Radix, a famous traditional Chinese herbal medicine, with high medicinal value. An endophytic fungus (CHS3) was isolated from Bupleurum scorzonerifolium Willd. in the early stage of our research, and we found that CHS3 could promote the accumulation of SSd in Bupleurum scorzonerifolium Willd. suspension cells (BSS cells). It is of practical significance to identify the mechanism that CHS3 promoted the accumulation of SSd and increased the production of SSd in suspension cells. To search the influence of CHS3 on SSd synthesis in the BSS cells, we co-cultured CHS3 with the BSS cells and compared the SSd content in BSS cells before and after co-culture using high-performance liquid chromatography (HPLC). Then the Illumina HiSeq 2500 was performed to detect the transcriptome of the BSS cells before and after co-culture and analyzed for the KEGG enrichment. The expression of genes involved in SSd synthesis was finally corroborated by qPCR analysis. Among which 11 key genes in connection with SSd synthesis were increased in BSS cells of co-cultured group compared with the BSS cells of the control group. In conclusion, CHS3 could promote the accumulation of SSd in BSS cells, and the molecular mechanism was related to its ability to regulate the MVA pathway, the calcium signaling pathway, and the AMPK signaling pathway by upregulating the expressions of ANT, CypD, CaM, AMPK, AATC, HMGS, HMGR, MVK, MVD, SS, and SE.
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Affiliation(s)
- Yupeng Cheng
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Yuanzhen Liu
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Xinhong Li
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Guangjie Liu
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Zhongmeng Li
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China
| | - Bo Liu
- School of Pharmaceutical engineering, Heilongjiang Agricultural Reclamation Vocational College, Harbin 150025, China.
| | - Ning Gao
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin 150040, China.
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3
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Canal MV, Mansilla N, Gras DE, Ibarra A, Figueroa CM, Gonzalez DH, Welchen E. Cytochrome c levels affect the TOR pathway to regulate growth and metabolism under energy-deficient conditions. THE NEW PHYTOLOGIST 2024; 241:2039-2058. [PMID: 38191763 DOI: 10.1111/nph.19506] [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: 12/03/2023] [Indexed: 01/10/2024]
Abstract
Mitochondrial function is essential for plant growth, but the mechanisms involved in adjusting growth and metabolism to changes in mitochondrial energy production are not fully understood. We studied plants with reduced expression of CYTC-1, one of two genes encoding the respiratory chain component cytochrome c (CYTc) in Arabidopsis, to understand how mitochondria communicate their status to coordinate metabolism and growth. Plants with CYTc deficiency show decreased mitochondrial membrane potential and lower ATP content, even when carbon sources are present. They also exhibit higher free amino acid content, induced autophagy, and increased resistance to nutritional stress caused by prolonged darkness, similar to plants with triggered starvation signals. CYTc deficiency affects target of rapamycin (TOR)-pathway activation, reducing S6 kinase (S6K) and RPS6A phosphorylation, as well as total S6K protein levels due to increased protein degradation via proteasome and autophagy. TOR overexpression restores growth and other parameters affected in cytc-1 mutants, even if mitochondrial membrane potential and ATP levels remain low. We propose that CYTc-deficient plants coordinate their metabolism and energy availability by reducing TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion, thus providing a mechanism by which changes in mitochondrial activity are transduced to the rest of the cell.
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Affiliation(s)
- María Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Agustín Ibarra
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
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4
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Khan K, Tran HC, Mansuroglu B, Önsell P, Buratti S, Schwarzländer M, Costa A, Rasmusson AG, Van Aken O. Mitochondria-derived reactive oxygen species are the likely primary trigger of mitochondrial retrograde signaling in Arabidopsis. Curr Biol 2024; 34:327-342.e4. [PMID: 38176418 DOI: 10.1016/j.cub.2023.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/28/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024]
Abstract
Besides their central function in respiration, plant mitochondria play a crucial role in maintaining cellular homeostasis during stress by providing "retrograde" feedback to the nucleus. Despite the growing understanding of this signaling network, the nature of the signals that initiate mitochondrial retrograde regulation (MRR) in plants remains unknown. Here, we investigated the dynamics and causative relationship of a wide range of mitochondria-related parameters for MRR, using a combination of Arabidopsis fluorescent protein biosensor lines, in vitro assays, and genetic and pharmacological approaches. We show that previously linked physiological parameters, including changes in cytosolic ATP, NADH/NAD+ ratio, cytosolic reactive oxygen species (ROS), pH, free Ca2+, and mitochondrial membrane potential, may often be correlated with-but are not the primary drivers of-MRR induction in plants. However, we demonstrate that the induced production of mitochondrial ROS is the likely primary trigger for MRR induction in Arabidopsis. Furthermore, we demonstrate that mitochondrial ROS-mediated signaling uses the ER-localized ANAC017-pathway to induce MRR response. Finally, our data suggest that mitochondrially generated ROS can induce MRR without substantially leaking into other cellular compartments such as the cytosol or ER lumen, as previously proposed. Overall, our results offer compelling evidence that mitochondrial ROS elevation is the likely trigger of MRR.
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Affiliation(s)
- Kasim Khan
- Department of Biology, Lund University, Sölvegatan 35, Lund 223 62, Sweden
| | - Huy Cuong Tran
- Department of Biology, Lund University, Sölvegatan 35, Lund 223 62, Sweden
| | - Berivan Mansuroglu
- Department of Biology, Lund University, Sölvegatan 35, Lund 223 62, Sweden
| | - Pinar Önsell
- Department of Biology, Lund University, Sölvegatan 35, Lund 223 62, Sweden
| | - Stefano Buratti
- Department of Biosciences, University of Milan, Via G. Celoria 26, Milan 20133, Italy
| | - Markus Schwarzländer
- Plant Energy Biology Lab, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | - Alex Costa
- Department of Biosciences, University of Milan, Via G. Celoria 26, Milan 20133, Italy; Institute of Biophysics, Consiglio Nazionale delle Ricerche, Via G. Celoria 26, 20133 Milan, Italy
| | - Allan G Rasmusson
- Department of Biology, Lund University, Sölvegatan 35, Lund 223 62, Sweden
| | - Olivier Van Aken
- Department of Biology, Lund University, Sölvegatan 35, Lund 223 62, Sweden.
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5
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Cadena-Ramos AI, De-la-Peña C. Picky eaters: selective autophagy in plant cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:364-384. [PMID: 37864806 DOI: 10.1111/tpj.16508] [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: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Autophagy, a fundamental cellular process, plays a vital role in maintaining cellular homeostasis by degrading damaged or unnecessary components. While selective autophagy has been extensively studied in animal cells, its significance in plant cells has only recently gained attention. In this review, we delve into the intriguing realm selective autophagy in plants, with specific focus on its involvement in nutrient recycling, organelle turnover, and stress response. Moreover, recent studies have unveiled the interesting interplay between selective autophagy and epigenetic mechanisms in plants, elucidating the significance of epigenetic regulation in modulating autophagy-related gene expression and finely tuning the selective autophagy process in plants. By synthesizing existing knowledge, this review highlights the emerging field of selective autophagy in plant cells, emphasizing its pivotal role in maintaining nutrient homeostasis, facilitating cellular adaptation, and shedding light on the epigenetic regulation that governs these processes. Our comprehensive study provides the way for a deeper understanding of the dynamic control of cellular responses to nutrient availability and stress conditions, opening new avenues for future research in this field of autophagy in plant physiology.
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Affiliation(s)
- Alexis I Cadena-Ramos
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
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6
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Bravo-Vázquez LA, Méndez-García A, Chamu-García V, Rodríguez AL, Bandyopadhyay A, Paul S. The applications of CRISPR/Cas-mediated microRNA and lncRNA editing in plant biology: shaping the future of plant non-coding RNA research. PLANTA 2023; 259:32. [PMID: 38153530 DOI: 10.1007/s00425-023-04303-z] [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: 05/28/2023] [Accepted: 11/25/2023] [Indexed: 12/29/2023]
Abstract
MAIN CONCLUSION CRISPR/Cas technology has greatly facilitated plant non-coding RNA (ncRNA) biology research, establishing itself as a promising tool for ncRNA functional characterization and ncRNA-mediated plant improvement. Throughout the last decade, the promising genome editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated proteins (Cas; CRISPR/Cas) has allowed unprecedented advances in the field of plant functional genomics and crop improvement. Even though CRISPR/Cas-mediated genome editing system has been widely used to elucidate the biological significance of a number of plant protein-coding genes, this technology has been barely applied in the functional analysis of those non-coding RNAs (ncRNAs) that modulate gene expression, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Nevertheless, compelling findings indicate that CRISPR/Cas-based ncRNA editing has remarkable potential for deciphering the biological roles of ncRNAs in plants, as well as for plant breeding. For instance, it has been demonstrated that CRISPR/Cas tool could overcome the challenges associated with other approaches employed in functional genomic studies (e.g., incomplete knockdown and off-target activity). Thus, in this review article, we discuss the current status and progress of CRISPR/Cas-mediated ncRNA editing in plant science in order to provide novel prospects for further assessment and validation of the biological activities of plant ncRNAs and to enhance the development of ncRNA-centered protocols for crop improvement.
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Affiliation(s)
- Luis Alberto Bravo-Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Andrea Méndez-García
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Verenice Chamu-García
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Puebla, Atlixcáyotl 5718, Reserva Territorial Atlixcáyotl, 72453, Puebla, Mexico
| | - Alma L Rodríguez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico
| | - Anindya Bandyopadhyay
- International Rice Research Institute, 4031, Manila, Philippines.
- Reliance Industries Ltd., Navi Mumbai, Maharashtra, 400701, India.
| | - Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Querétaro, Av. Epigmenio González, No. 500 Fracc. San Pablo, 76130, Querétaro, Mexico.
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7
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Zhang Y, Hu Y, Wang Z, Lin X, Li Z, Ren Y, Zhao J. The translocase of the inner mitochondrial membrane 22-2 is required for mitochondrial membrane function during Arabidopsis seed development. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4427-4448. [PMID: 37105529 DOI: 10.1093/jxb/erad141] [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: 09/26/2022] [Accepted: 04/27/2023] [Indexed: 06/19/2023]
Abstract
The carrier translocase (also known as translocase of the inner membrane 22; TIM22 complex) is an important component of the mitochondrial protein import apparatus. However, the biological functions of AtTIM22-2 in Arabidopsis remain poorly defined. Here, we report studies on two tim22-2 mutants that exhibit defects in embryo and endosperm development, leading to seed abortion. AtTIM22-2, which was localized in mitochondria, was widely expressed in embryos and in various seedling organs. Loss of AtTIM22-2 function resulted in irregular mitochondrial cristae, decreased respiratory activity, and a lower membrane potential, together with changes in gene expression and enzyme activity related to reactive oxygen species (ROS) metabolism, leading to increased accumulation of ROS in the embryo. The levels of transcripts encoding mitochondrial protein import components were also altered in the tim22-2 mutants. Furthermore, mass spectrometry, bimolecular fluorescence complementation and co-immunoprecipitation assays revealed that AtTIM22-2 interacted with AtTIM23-2, AtB14.7 (a member of Arabidopsis OEP16 family encoded by At2G42210), and AT5G27395 (mitochondrial inner membrane translocase complex, subunit TIM44-related protein). Taken together, these results demonstrate that AtTIM22-2 is essential for maintaining mitochondrial membrane functions during seed development. These findings lay the foundations for a new model of the composition and functions of the TIM22 complex in higher plants.
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Affiliation(s)
- Yuqin Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yuanyuan Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiqin Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaodi Lin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zihui Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafang Ren
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Szlachtowska Z, Rurek M. Plant dehydrins and dehydrin-like proteins: characterization and participation in abiotic stress response. FRONTIERS IN PLANT SCIENCE 2023; 14:1213188. [PMID: 37484455 PMCID: PMC10358736 DOI: 10.3389/fpls.2023.1213188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023]
Abstract
Abiotic stress has a significant impact on plant growth and development. It causes changes in the subcellular organelles, which, due to their stress sensitivity, can be affected. Cellular components involved in the abiotic stress response include dehydrins, widely distributed proteins forming a class II of late embryogenesis abundant protein family with characteristic properties including the presence of evolutionarily conserved sequence motifs (including lysine-rich K-segment, N-terminal Y-segment, and often phosphorylated S motif) and high hydrophilicity and disordered structure in the unbound state. Selected dehydrins and few poorly characterized dehydrin-like proteins participate in cellular stress acclimation and are also shown to interact with organelles. Through their functioning in stabilizing biological membranes and binding reactive oxygen species, dehydrins and dehydrin-like proteins contribute to the protection of fragile organellar structures under adverse conditions. Our review characterizes the participation of plant dehydrins and dehydrin-like proteins (including some organellar proteins) in plant acclimation to diverse abiotic stress conditions and summarizes recent updates on their structure (the identification of dehydrin less conserved motifs), classification (new proposed subclasses), tissue- and developmentally specific accumulation, and key cellular activities (including organellar protection under stress acclimation). Recent findings on the subcellular localization (with emphasis on the mitochondria and plastids) and prospective applications of dehydrins and dehydrin-like proteins in functional studies to alleviate the harmful stress consequences by means of plant genetic engineering and a genome editing strategy are also discussed.
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9
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Microcystin-LR, a Cyanobacterial Toxin, Induces Changes in the Organization of Membrane Compartments in Arabidopsis. Microorganisms 2023; 11:microorganisms11030586. [PMID: 36985160 PMCID: PMC10051171 DOI: 10.3390/microorganisms11030586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
To evaluate the effects of the cyanobacterial toxin microcystin-LR (MCY-LR, a protein phosphatase inhibitor) and diquat (DQ, an oxidative stress inducer) on the organization of tonoplast, the effect of MCY-LR on plastid stromule formation and on mitochondria was investigated in wild-type Arabidopsis. Tonoplast was also studied in PP2A catalytic (c3c4) and regulatory subunit mutants (fass-5 and fass-15). These novel studies were performed by CLSM microscopy. MCY-LR is produced during cyanobacterial blooms. The organization of tonoplast of PP2A mutants of Arabidopsis is much more sensitive to MCY-LR and DQ treatments than that of wild type. In c3c4, fass-5 and fass-15, control and treated plants showed increased vacuole fragmentation that was the strongest when the fass-5 mutant was treated with MCY-LR. It is assumed that both PP2A/C and B” subunits play an important role in normal formation and function of the tonoplast. In wild-type plants, MCY-LR affects mitochondria. Under the influence of MCY-LR, small, round-shaped mitochondria appeared, while long/fused mitochondria were typical in control plants. Presumably, MCY-LR either inhibits the fusion of mitochondria or induces fission. Consequently, PP2A also plays an important role in the fusion of mitochondria. MCY-LR also increased the frequency of stromules appearing on chloroplasts after 1 h treatments. Along the stromules, signals can be transported between plastids and endoplasmic reticulum. It is probable that they promote a faster response to stress.
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10
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Khan K, Van Aken O. The colonization of land was a likely driving force for the evolution of mitochondrial retrograde signalling in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7182-7197. [PMID: 36055768 PMCID: PMC9675596 DOI: 10.1093/jxb/erac351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Most retrograde signalling research in plants was performed using Arabidopsis, so an evolutionary perspective on mitochondrial retrograde regulation (MRR) is largely missing. Here, we used phylogenetics to track the evolutionary origins of factors involved in plant MRR. In all cases, the gene families can be traced to ancestral green algae or earlier. However, the specific subfamilies containing factors involved in plant MRR in many cases arose during the transition to land. NAC transcription factors with C-terminal transmembrane domains, as observed in the key regulator ANAC017, can first be observed in non-vascular mosses, and close homologs to ANAC017 can be found in seed plants. Cyclin-dependent kinases (CDKs) are common to eukaryotes, but E-type CDKs that control MRR also diverged in conjunction with plant colonization of land. AtWRKY15 can be traced to the earliest land plants, while AtWRKY40 only arose in angiosperms and AtWRKY63 even more recently in Brassicaceae. Apetala 2 (AP2) transcription factors are traceable to algae, but the ABI4 type again only appeared in seed plants. This strongly suggests that the transition to land was a major driver for developing plant MRR pathways, while additional fine-tuning events have appeared in seed plants or later. Finally, we discuss how MRR may have contributed to meeting the specific challenges that early land plants faced during terrestrialization.
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Affiliation(s)
- Kasim Khan
- Department of Biology, Lund University, Lund, Sweden
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11
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Liao WT, Chu PY, Su CC, Wu CC, Li CJ. Mitochondrial AAA protease gene associated with immune infiltration is a prognostic biomarker in human ovarian cancer. Pathol Res Pract 2022; 240:154215. [DOI: 10.1016/j.prp.2022.154215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
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12
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Hemono M, Salinas‐Giegé T, Roignant J, Vingadassalon A, Hammann P, Ubrig E, Ngondo P, Duchêne A. FRIENDLY (FMT) is an RNA binding protein associated with cytosolic ribosomes at the mitochondrial surface. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:309-321. [PMID: 36050837 PMCID: PMC9826127 DOI: 10.1111/tpj.15962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The spatial organization of protein synthesis in the eukaryotic cell is essential for maintaining the integrity of the proteome and the functioning of the cell. Translation on free polysomes or on ribosomes associated with the endoplasmic reticulum has been studied for a long time. More recent data have revealed selective translation of mRNAs in other compartments, in particular at the surface of mitochondria. Although these processes have been described in many organisms, particularky in plants, the mRNA targeting and localized translation mechanisms remain poorly understood. Here, the Arabidopsis thaliana Friendly (FMT) protein is shown to be a cytosolic RNA binding protein that associates with cytosolic ribosomes at the surface of mitochondria. FMT knockout delays seedling development and causes mitochondrial clustering. The mutation also disrupts the mitochondrial proteome, as well as the localization of nuclear transcripts encoding mitochondrial proteins at the surface of mitochondria. These data indicate that FMT participates in the localization of mRNAs and their translation at the surface of mitochondria.
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Affiliation(s)
- Mickaele Hemono
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Thalia Salinas‐Giegé
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Jeanne Roignant
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Audrey Vingadassalon
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
- Université des Antilles, COVACHIM M2E (EA 3592), UFR SEN, Campus de FouilloleF‐97 110Pointe‐à‐PitreFrance
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg‐EsplanadeInstitut de Biologie Moléculaire et CellulaireFR1589 du CNRS, 2 Allée Konrad Roentgen67084Strasbourg CedexFrance
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
| | - Patryk Ngondo
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
- Institut de Biologie Moléculaire et Cellulaire, UPR 9002 du CNRS, Université de Strasbourg2 Allée Konrad Roentgen67 084Strasbourg CedexFrance
| | - Anne‐Marie Duchêne
- Institut de biologie moléculaire des plantes, UPR 2357 du CNRS, Université de Strasbourg12 rue du Général Zimmer67084Strasbourg CedexFrance
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Barreto P, Koltun A, Nonato J, Yassitepe J, Maia IDG, Arruda P. Metabolism and Signaling of Plant Mitochondria in Adaptation to Environmental Stresses. Int J Mol Sci 2022; 23:ijms231911176. [PMID: 36232478 PMCID: PMC9570015 DOI: 10.3390/ijms231911176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
The interaction of mitochondria with cellular components evolved differently in plants and mammals; in plants, the organelle contains proteins such as ALTERNATIVE OXIDASES (AOXs), which, in conjunction with internal and external ALTERNATIVE NAD(P)H DEHYDROGENASES, allow canonical oxidative phosphorylation (OXPHOS) to be bypassed. Plant mitochondria also contain UNCOUPLING PROTEINS (UCPs) that bypass OXPHOS. Recent work revealed that OXPHOS bypass performed by AOXs and UCPs is linked with new mechanisms of mitochondrial retrograde signaling. AOX is functionally associated with the NO APICAL MERISTEM transcription factors, which mediate mitochondrial retrograde signaling, while UCP1 can regulate the plant oxygen-sensing mechanism via the PRT6 N-Degron. Here, we discuss the crosstalk or the independent action of AOXs and UCPs on mitochondrial retrograde signaling associated with abiotic stress responses. We also discuss how mitochondrial function and retrograde signaling mechanisms affect chloroplast function. Additionally, we discuss how mitochondrial inner membrane transporters can mediate mitochondrial communication with other organelles. Lastly, we review how mitochondrial metabolism can be used to improve crop resilience to environmental stresses. In this respect, we particularly focus on the contribution of Brazilian research groups to advances in the topic of mitochondrial metabolism and signaling.
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Affiliation(s)
- Pedro Barreto
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista, Botucatu 18618-970, Brazil
| | - Alessandra Koltun
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, Brazil
| | - Juliana Nonato
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, Brazil
| | - Juliana Yassitepe
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, Brazil
- Embrapa Agricultura Digital, Campinas 13083-886, Brazil
| | - Ivan de Godoy Maia
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista, Botucatu 18618-970, Brazil
| | - Paulo Arruda
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas 13083-875, Brazil
- Correspondence:
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Mdivi-1 Induced Mitochondrial Fusion as a Potential Mechanism to Enhance Stress Tolerance in Wheat. Life (Basel) 2022; 12:life12091386. [PMID: 36143422 PMCID: PMC9503966 DOI: 10.3390/life12091386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Mitochondria play a key role in providing energy to cells. This paper is dedicated to elucidating mitochondria-dependent mechanisms that may enhance abiotic stress tolerance in wheat. Mitochondria are constantly undergoing dynamic processes of fusion and fission. In plants, stressful conditions tend to favor mitochondrial fusion processes. The role of mitochondrial fusion was studied by applying Mdivi-1, an inhibitor of mitochondrial fission, to wheat roots subjected to a wounding stress. Increased mitochondrial functional activity and upregulation of genes involved in energy metabolism suggest that mitochondrial fusion is associated with a general activation of energy metabolism. Controlling mitochondrial fusion rates could change the physiology of wheat plants by altering the energy status of the cell and helping to reduce the effects of stress. Abstract Mitochondria play a key role in providing energy to cells. These organelles are constantly undergoing dynamic processes of fusion and fission that change in stressful conditions. The role of mitochondrial fusion in wheat root cells was studied using Mdivi-1, an inhibitor of the mitochondrial fragmentation protein Drp1. The effect of the inhibitor was studied on mitochondrial dynamics in the roots of wheat seedlings subjected to a wounding stress, simulated by excision. Treatment of the stressed roots with the inhibitor increased the size of the mitochondria, enhanced their functional activity, and elevated their membrane potentials. Mitochondrial fusion was accompanied by a decrease in ROS formation and associated cell damage. Exposure to Mdivi-1 also upregulated genes encoding the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and an energy sensor AMP-dependent protein sucrose non-fermenting-related kinase (SnRK1), suggesting that mitochondrial fusion is associated with a general activation of energy metabolism. Controlling mitochondrial fusion rates could change the physiology of wheat plants by altering the energy status of the cell and helping to mitigate the effects of stress.
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Racca S, Gras DE, Canal MV, Ferrero LV, Rojas BE, Figueroa CM, Ariel FD, Welchen E, Gonzalez DH. Cytochrome c and the transcription factor ABI4 establish a molecular link between mitochondria and ABA-dependent seed germination. THE NEW PHYTOLOGIST 2022; 235:1780-1795. [PMID: 35637555 DOI: 10.1111/nph.18287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
During germination, seed reserves are mobilised to sustain the metabolic and energetic demands of plant growth. Mitochondrial respiration is presumably required to drive germination in several species, but only recently its role in this process has begun to be elucidated. Using Arabidopsis thaliana lines with changes in the levels of the respiratory chain component cytochrome c (CYTc), we investigated the role of this protein in germination and its relationship with hormonal pathways. Cytochrome c deficiency causes delayed seed germination, which correlates with decreased cyanide-sensitive respiration and ATP production at the onset of germination. In addition, CYTc affects the sensitivity of germination to abscisic acid (ABA), which negatively regulates the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts downstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA and regulates its expression. The results show that CYTc is a main player during seed germination through its role in respiratory metabolism and energy production. In addition, the direct regulation of CYTC-2 by ABI4 and its effect on ABA-responsive germination establishes a link between mitochondrial and hormonal functions during this process.
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Affiliation(s)
- Sofía Racca
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - M Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Lucía V Ferrero
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Bruno E Rojas
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
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16
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Tarasenko TA, Koulintchenko MV. Heterogeneity of the Mitochondrial Population in Cells of Plants and Other Organisms. Mol Biol 2022. [DOI: 10.1134/s0026893322020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Welchen E, Gonzalez DH. Breaking boundaries: exploring short- and long-distance mitochondrial signalling in plants. THE NEW PHYTOLOGIST 2021; 232:494-501. [PMID: 34255867 DOI: 10.1111/nph.17614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/29/2021] [Indexed: 05/20/2023]
Abstract
Communication of mitochondria with other cell compartments is essential for the coordination of cellular functions. Mitochondria send retrograde signals through metabolites, redox changes, direct organelle contacts and protein trafficking. Accumulating evidence indicates that, in animal systems, changes in mitochondrial function also trigger responses in other, either neighbouring or distantly located, cells. Although not clearly established, there are indications that this type of communication may also be operative in plants. Grafting experiments suggested that the translocation of entire mitochondria or submitochondrial vesicles between neighbouring cells is possible in plants, as already documented in animals. Changes in mitochondrial function also regulate cell-to-cell communication via plasmodesmata and may be transmitted over long distances through plant hormones acting as mitokines to relay mitochondrial signals to distant tissues. Long-distance movement of transcripts encoding mitochondrial proteins involved in crucial aspects of metabolism and retrograde signalling was also described. Finally, changes in mitochondrial reactive species (ROS) production may affect the 'ROS wave' that triggers systemic acquired acclimation throughout the plant. In this review, we summarise available evidence suggesting that mitochondria establish sophisticated communications not only within the cell but also with neighbouring cells and distant tissues to coordinate plant growth and stress responses in a cell nonautonomous manner.
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Affiliation(s)
- Elina Welchen
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, Santa Fe, 3000, Argentina
| | - Daniel H Gonzalez
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, Santa Fe, 3000, Argentina
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18
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Han T, Wang F, Song Q, Ye W, Liu T, Wang L, Chen ZJ. An epigenetic basis of inbreeding depression in maize. SCIENCE ADVANCES 2021; 7:7/35/eabg5442. [PMID: 34452913 PMCID: PMC8397266 DOI: 10.1126/sciadv.abg5442] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/07/2021] [Indexed: 05/12/2023]
Abstract
Inbreeding depression is widespread across plant and animal kingdoms and may arise from the exposure of deleterious alleles and/or loss of overdominant alleles resulting from increased homozygosity, but these genetic models cannot fully explain the phenomenon. Here, we report epigenetic links to inbreeding depression in maize. Teosinte branched1/cycloidea/proliferating cell factor (TCP) transcription factors control plant development. During successive inbreeding among inbred lines, thousands of genomic regions across TCP-binding sites (TBS) are hypermethylated through the H3K9me2-mediated pathway. These hypermethylated regions are accompanied by decreased chromatin accessibility, increased levels of the repressive histone marks H3K27me2 and H3K27me3, and reduced binding affinity of maize TCP-proteins to TBS. Consequently, hundreds of TCP-target genes involved in mitochondrion, chloroplast, and ribosome functions are down-regulated, leading to reduced growth vigor. Conversely, random mating can reverse corresponding hypermethylation sites and TCP-target gene expression, restoring growth vigor. These results support a unique role of reversible epigenetic modifications in inbreeding depression.
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Affiliation(s)
- Tongwen Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Fang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Tieshan Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liming Wang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.
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Wrzesińska B, Zmienko A, Vu LD, De Smet I, Obrępalska-Stęplowska A. Multiple cellular compartments engagement in Nicotiana benthamiana-peanut stunt virus-satRNA interactions revealed by systems biology approach. PLANT CELL REPORTS 2021; 40:1247-1267. [PMID: 34028582 PMCID: PMC8233301 DOI: 10.1007/s00299-021-02706-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE PSV infection changed the abundance of host plant's transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and cytosol, affecting photosynthesis, translation, transcription, and splicing. Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)-Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The 'omic' results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)-seq data were obtained to provide new insights into PSV-P-satRNA-plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.
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Affiliation(s)
- Barbara Wrzesińska
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection, National Research Institute, 20 Władysława Węgorka Street, 60-318, Poznan, Poland
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704, Poznan, Poland
- Faculty of Computing Science, Institute of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965, Poznan, Poland
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Aleksandra Obrępalska-Stęplowska
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection, National Research Institute, 20 Władysława Węgorka Street, 60-318, Poznan, Poland.
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20
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Evaluation of Filter, Paramagnetic, and STAGETips Aided Workflows for Proteome Profiling of Symbiodiniaceae Dinoflagellate. Processes (Basel) 2021. [DOI: 10.3390/pr9060983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The integrity of coral reef ecosystems worldwide rests on a fine-tuned symbiotic interaction between an invertebrate and a dinoflagellate microalga from the family Symbiodiniaceae. Recent advances in bottom-up shotgun proteomic approaches and the availability of vast amounts of genetic information about Symbiodiniaceae have provided a unique opportunity to better understand the molecular mechanisms underpinning the interactions of coral-Symbiodiniaceae. However, the resilience of this dinoflagellate cell wall, as well as the presence of polyanionic and phenolics cell wall components, requires the optimization of sample preparation techniques for successful implementation of bottom-up proteomics. Therefore, in this study we compare three different workflows—filter-aided sample preparation (FASP), single-pot solid-phase-enhanced sample preparation (SP3), and stop-and-go-extraction tips (STAGETips, ST)—to develop a high-throughput proteotyping protocol for Symbiodiniaceae algal research. We used the model isolate Symbiodinium tridacnidorum. We show that SP3 outperformed ST and FASP with regard to robustness, digestion efficiency, and contaminant removal, which led to the highest number of total (3799) and unique proteins detected from 23,593 peptides. Most of these proteins were detected with ≥2 unique peptides (73%), zero missed tryptic peptide cleavages (91%), and hydrophilic peptides (>70%). To demonstrate the functionality of this optimized SP3 sample preparation workflow, we examined the proteome of S. tridacnidorum to better understand the molecular mechanism of peridinin-chlorophyll-protein complex (PCP, light harvesting protein) accumulation under low light (LL, 30 μmol photon m−2 s−1). Cells exposed to LL for 7 days upregulated various light harvesting complex (LHCs) proteins through the mevalonate-independent pathway; proteins of this pathway were at 2- to 6-fold higher levels than the control of 120 μmol photon m−2 s−1. Potentially, LHCs which were maintained in an active phosphorylated state by serine/threonine-protein kinase were also upregulated to 10-fold over control. Collectively, our results show that the SP3 method is an efficient high-throughput proteotyping tool for Symbiodiniaceae algal research.
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Zhao H, Yang A, Kong L, Xie F, Wang H, Ao X. Proteome characterization of two contrasting soybean genotypes in response to different phosphorus treatments. AOB PLANTS 2021; 13:plab019. [PMID: 34150189 PMCID: PMC8209930 DOI: 10.1093/aobpla/plab019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/12/2021] [Indexed: 05/04/2023]
Abstract
Phosphorus (P) is an essential element for the growth and development of plants. Soybean (Glycine max) is an important food crop that is grown worldwide. Soybean yield is significantly affected by P deficiency in the soil. To investigate the molecular factors that determine the response and tolerance at low-P in soybean, we conducted a comparative proteomics study of a genotype with low-P tolerance (Liaodou 13, L13) and a genotype with low-P sensitivity (Tiefeng 3, T3) in a paper culture experiment with three P treatments, i.e. P-free (0 mmol·L-1), low-P (0.05 mmol·L-1) and normal-P (0.5 mmol·L-1). A total of 4126 proteins were identified in roots of the two genotypes. Increased numbers of differentially expressed proteins (DEPs) were obtained from low-P to P-free conditions compared to the normal-P treatment. All DEPs obtained in L13 (660) were upregulated in response to P deficiency, while most DEPs detected in T3 (133) were downregulated under P deficiency. Important metabolic pathways such as oxidative phosphorylation, glutathione metabolism and carbon metabolism were suppressed in T3, which could have affected the survival of the plants in P-limited soil. In contrast, L13 increased the metabolic activity in the 2-oxocarboxylic acid metabolism, carbon metabolism, glycolysis, biosynthesis of amino acids, pentose phosphatase, oxidative phosphorylation, other types of O-glycan biosynthesis and riboflavin metabolic pathways in order to maintain normal plant growth under P deficiency. Three key proteins I1KW20 (prohibitins), I1K3U8 (alpha-amylase inhibitors) and C6SZ93 (alpha-amylase inhibitors) were suggested as potential biomarkers for screening soybean genotypes with low-P tolerance. Overall, this study provides new insights into the response and tolerance to P deficiency in soybean.
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Affiliation(s)
- Hongyu Zhao
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Ahui Yang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Lingjian Kong
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Futi Xie
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiying Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Xue Ao
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
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22
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Dang X, Lei S, Luo S, Hu Y, Wang J, Zhang D, Lu D, Jiang F, Fu L. Design, synthesis and biological evaluation of novel thiazole-derivatives as mitochondrial targeting inhibitors of cancer cells. Bioorg Chem 2021; 114:105015. [PMID: 34139611 DOI: 10.1016/j.bioorg.2021.105015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 01/12/2023]
Abstract
Mitochondria are pivotal energy production sources for cells to maintain necessary metabolism activities. Targeting dysfunctional mitochondrial features has been a hotspot for mitochondrial-related disease researches. Investigation with cancerous mitochondrial metabolism is a continuing concern within tumor therapy. Herein, we set out to assess the anti-cancer activities of a novel family of TPP-thiazole derivatives based on our earlier research on mitochondrial targeting agents. Specifically, we designed and synthesized a series of TPP-thiazole derivatives and revealed by the MTT assay that most synthesized compounds effectively inhibited three cancer cell lines (HeLa, PC3 and MCF-7). After structure modifications, we explored the SAR relationships and identified the most promising compound R13 (IC50 of 5.52 μM) for further investigation. In the meantime, we performed ATP production assay to assess the selected compounds inhibitory effect on HeLa cells energy production. The results displayed the test compounds significantly restrained ATP production of cancer cells. Overall, we have designed and synthesized a series of compounds which exhibited significant cytotoxicity against cancer cells and effectively inhibited mitochondrial energy production.
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Affiliation(s)
- Xin Dang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China
| | - Shuwen Lei
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China
| | - Shuhua Luo
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China
| | - Yixin Hu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China
| | - Juntao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China
| | - Dongdong Zhang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China
| | - Dan Lu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China
| | - Faqin Jiang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China
| | - Lei Fu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China; SJTU-Agilent Technologies Joint Laboratory for Pharmaceutical Analysis, School of Pharmacy, Shanghai Jiao Tong University (SJTU), No. 800 Dongchuan Rd., Minhang District, Shanghai 200240, PR China.
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Welchen E, Canal MV, Gras DE, Gonzalez DH. Cross-talk between mitochondrial function, growth, and stress signalling pathways in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4102-4118. [PMID: 33369668 DOI: 10.1093/jxb/eraa608] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 05/16/2023]
Abstract
Plant mitochondria harbour complex metabolic routes that are interconnected with those of other cell compartments, and changes in mitochondrial function remotely influence processes in different parts of the cell. This implies the existence of signals that convey information about mitochondrial function to the rest of the cell. Increasing evidence indicates that metabolic and redox signals are important for this process, but changes in ion fluxes, protein relocalization, and physical contacts with other organelles are probably also involved. Besides possible direct effects of these signalling molecules on cellular functions, changes in mitochondrial physiology also affect the activity of different signalling pathways that modulate plant growth and stress responses. As a consequence, mitochondria influence the responses to internal and external factors that modify the activity of these pathways and associated biological processes. Acting through the activity of hormonal signalling pathways, mitochondria may also exert remote control over distant organs or plant tissues. In addition, an intimate cross-talk of mitochondria with energy signalling pathways, such as those represented by TARGET OF RAPAMYCIN and SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASE 1, can be envisaged. This review discusses available evidence on the role of mitochondria in shaping plant growth and stress responses through various signalling pathways.
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Affiliation(s)
- Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - María Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
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24
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Chustecki JM, Gibbs DJ, Bassel GW, Johnston IG. Network analysis of Arabidopsis mitochondrial dynamics reveals a resolved tradeoff between physical distribution and social connectivity. Cell Syst 2021; 12:419-431.e4. [PMID: 34015261 PMCID: PMC8136767 DOI: 10.1016/j.cels.2021.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/22/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Mitochondria in plant cells exist largely as individual organelles which move, colocalize, and interact, but the cellular priorities addressed by these dynamics remain incompletely understood. Here, we elucidate these principles by studying the dynamic "social networks" of mitochondria in Arabidopsis thaliana wildtype and mutants, describing the colocalization of individuals over time. We combine single-cell live imaging of hypocotyl mitochondrial dynamics with individual-based modeling and network analysis. We identify an inevitable tradeoff between mitochondrial physical priorities (an even cellular distribution of mitochondria) and “social” priorities (individuals interacting, to facilitate the exchange of chemicals and information). This tradeoff results in a tension between maintaining mitochondrial spacing and facilitating colocalization. We find that plant cells resolve this tension to favor efficient networks with high potential for exchanging contents. We suggest that this combination of physical modeling coupled to experimental data through network analysis can shed light on the fundamental principles underlying these complex organelle dynamics. A record of this paper’s transparent peer review process is included in the supplemental information. Dynamic social networks of plant mitochondria reflect physical organellar encounters Network analysis and modeling show priorities and tradeoffs for mitochondrial motion Mitochondria in plant cells trade off physical spacing against social connectivity Plant cells favor efficient networks with high potential for information exchange
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Affiliation(s)
| | - Daniel J Gibbs
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - George W Bassel
- Department of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Realfagbygget, Bergen 5007, Norway; Computational Biology Unit, University of Bergen, Høyteknologisenteret i Bergen, Bergen 5008, Norway.
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25
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Steiner P, Buchner O, Andosch A, Wanner G, Neuner G, Lütz-Meindl U. Fusion of Mitochondria to 3-D Networks, Autophagy and Increased Organelle Contacts are Important Subcellular Hallmarks during Cold Stress in Plants. Int J Mol Sci 2020; 21:E8753. [PMID: 33228190 PMCID: PMC7699614 DOI: 10.3390/ijms21228753] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/25/2022] Open
Abstract
Low temperature stress has a severe impact on the distribution, physiology, and survival of plants in their natural habitats. While numerous studies have focused on the physiological and molecular adjustments to low temperatures, this study provides evidence that cold induced physiological responses coincide with distinct ultrastructural alterations. Three plants from different evolutionary levels and habitats were investigated: The freshwater alga Micrasterias denticulata, the aquatic plant Lemna sp., and the nival plant Ranunculus glacialis. Ultrastructural alterations during low temperature stress were determined by the employment of 2-D transmission electron microscopy and 3-D reconstructions from focused ion beam-scanning electron microscopic series. With decreasing temperatures, increasing numbers of organelle contacts and particularly the fusion of mitochondria to 3-dimensional networks were observed. We assume that the increase or at least maintenance of respiration during low temperature stress is likely to be based on these mitochondrial interconnections. Moreover, it is shown that autophagy and degeneration processes accompany freezing stress in Lemna and R. glacialis. This might be an essential mechanism to recycle damaged cytoplasmic constituents to maintain the cellular metabolism during freezing stress.
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Affiliation(s)
- Philip Steiner
- Department of Biosciences, Faculty of Natural Sciences, University of Salzburg, Hellbrunnerstraße 34, A-5020 Salzburg, Austria; (O.B.); (A.A.); (U.L.-M.)
| | - Othmar Buchner
- Department of Biosciences, Faculty of Natural Sciences, University of Salzburg, Hellbrunnerstraße 34, A-5020 Salzburg, Austria; (O.B.); (A.A.); (U.L.-M.)
| | - Ancuela Andosch
- Department of Biosciences, Faculty of Natural Sciences, University of Salzburg, Hellbrunnerstraße 34, A-5020 Salzburg, Austria; (O.B.); (A.A.); (U.L.-M.)
| | - Gerhard Wanner
- Ultrastructural Research, Department Biology I, Faculty of Biology, Ludwig-Maximilians-University, Großhadernerstraße 2−4, Planegg-Martinsried, D-82152 Munich, Germany;
| | - Gilbert Neuner
- Department of Botany, Functional Plant Biology, Faculty of Biology, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria;
| | - Ursula Lütz-Meindl
- Department of Biosciences, Faculty of Natural Sciences, University of Salzburg, Hellbrunnerstraße 34, A-5020 Salzburg, Austria; (O.B.); (A.A.); (U.L.-M.)
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26
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Almikhlafi MA, Stauch KL, Villeneuve LM, Purnell PR, Lamberty BG, Fox HS. Deletion of DJ-1 in rats affects protein abundance and mitochondrial function at the synapse. Sci Rep 2020; 10:13719. [PMID: 32792613 PMCID: PMC7426919 DOI: 10.1038/s41598-020-70486-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/30/2020] [Indexed: 02/08/2023] Open
Abstract
DJ-1 is a multifunctional protein affecting different biological and cellular processes. In addition, DJ-1 has roles in regulating mitochondrial function. Loss-of-function mutations in DJ-1 were found to cause an autosomal recessive form of Parkinson's disease. One of the main pathological features of PD is loss of dopamine neurons in the nigrostriatal pathway. DJ-1 knockout (KO) rats exhibit progressive nigral neurodegeneration with about 50% dopaminergic cell loss at 8 months of age. In order to assess the effects of DJ-1 deficiency on neuronal mitochondria prior to neuron loss, we performed proteomic analysis of synaptic mitochondria isolated from the striatum, the location of nigrostriatal pathway nerve terminals, of 3-month-old DJ-1 KO rats. In total, 371 mitochondrial proteins were quantified, and of these 76 were differentially expressed in DJ-1 KO rats. Proteins perturbed by the loss of DJ-1 were involved in several mitochondrial functional pathways, including the tricarboxylic acid cycle and electron transport chain. Thus, synaptic mitochondrial respiration was measured and showed a significant change due to DJ-1 deficiency. The dataset generated here highlights the role of synaptic mitochondria in PD associated with DJ-1. This study improves our understanding of DJ-1 effects in a complex tissue environment and the synaptic mitochondrial changes that accompany its loss.
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Affiliation(s)
- Mohannad A Almikhlafi
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Pharmacology and Toxicology, Collage of Pharmacy, Taibah University, Medina, Saudi Arabia
| | - Kelly L Stauch
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Lance M Villeneuve
- Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Neurosurgery, Collage of Medicine, University of Oklahoma, Oklahoma City, OK, USA
| | - Phillip R Purnell
- Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Otolaryngology/Head and Neck Surgery, School of Medicine, West Virginia University, Morgantown, WV, USA
| | - Benjamin G Lamberty
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA. .,Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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27
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Lu C, Xie Z, Yu F, Tian L, Hao X, Wang X, Chen L, Li D. Mitochondrial ribosomal protein S9M is involved in male gametogenesis and seed development in Arabidopsis. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:655-667. [PMID: 32141186 DOI: 10.1111/plb.13108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Mitochondrial function is critical for cell vitality in all eukaryotes including plants. Although plant mitochondria contain many proteins, few have been studied in the context of plant development and physiology. We used knock-down mutant RPS9M to study its important role in male gametogenesis and seed development in Arabidopsis thaliana. Knock-down of RPS9M in the rps9m-3 mutant led to abnormal pollen development and impaired pollen tube growth. In addition, both embryo and endosperm development were affected. Phenotype analysis revealed that the rps9m-3 mutant contained a lower amount of endosperm and nuclear proteins, and both embryo cell division and embryo pattern were affected, resulting in an abnormal and defective embryo. Lowering the level of RPS9M in rps9m-3 affects mitochondrial ribosome biogenesis, energy metabolism and production of ROS. Our data revealed that RPS9M plays important roles in normal gametophyte development and seed formation, possibly by sustaining mitochondrial function.
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Affiliation(s)
- C Lu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Z Xie
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - F Yu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - L Tian
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - X Hao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - X Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - L Chen
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
| | - D Li
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, China
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28
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What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply? PLANTS 2020; 9:plants9030361. [PMID: 32182978 PMCID: PMC7154926 DOI: 10.3390/plants9030361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022]
Abstract
Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production. Although male sterility is caused by S cytoplasm (male-sterility inducing mitochondria), the action of S cytoplasm is suppressed by restorer-of-fertility (Rf), a nuclear gene. Hence, the genetics of Rf has attained particular interest among plant breeders. The genetic model posits Rf diversity in which an Rf specifically suppresses the cognate S cytoplasm. Molecular analysis of Rf loci in plants has identified various genes; however, pentatricopeptide repeat (PPR) protein (a specific type of RNA-binding protein) is so prominent as the Rf-gene product that Rfs have been categorized into two classes, PPR and non-PPR. In contrast, several shared features between PPR- and some non-PPR Rfs are apparent, suggesting the possibility of another grouping. Our present focus is to group Rfs by molecular genetic classes other than the presence of PPRs. We propose three categories that define partially overlapping groups of Rfs: association with post-transcriptional regulation of mitochondrial gene expression, resistance gene-like copy number variation at the locus, and lack of a direct link to S-orf (a mitochondrial ORF associated with CMS). These groups appear to reflect their own evolutionary background and their mechanism of conferring S cytoplasm specificity.
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29
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Poór P. Effects of Salicylic Acid on the Metabolism of Mitochondrial Reactive Oxygen Species in Plants. Biomolecules 2020; 10:E341. [PMID: 32098073 PMCID: PMC7072379 DOI: 10.3390/biom10020341] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 01/16/2023] Open
Abstract
Different abiotic and biotic stresses lead to the production and accumulation of reactive oxygen species (ROS) in various cell organelles such as in mitochondria, resulting in oxidative stress, inducing defense responses or programmed cell death (PCD) in plants. In response to oxidative stress, cells activate various cytoprotective responses, enhancing the antioxidant system, increasing the activity of alternative oxidase and degrading the oxidized proteins. Oxidative stress responses are orchestrated by several phytohormones such as salicylic acid (SA). The biomolecule SA is a key regulator in mitochondria-mediated defense signaling and PCD, but the mode of its action is not known in full detail. In this review, the current knowledge on the multifaceted role of SA in mitochondrial ROS metabolism is summarized to gain a better understanding of SA-regulated processes at the subcellular level in plant defense responses.
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Affiliation(s)
- Péter Poór
- Department of Plant Biology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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30
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Zhai XT, Wei SS, Liang WQ, Bai JT, Jia N, Li B. Arabidopsis mtHSC70-1 physically interacts with the Cox2 subunit of cytochrome c oxidase. PLANT SIGNALING & BEHAVIOR 2020; 15:1714189. [PMID: 31933409 PMCID: PMC7053962 DOI: 10.1080/15592324.2020.1714189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/04/2020] [Accepted: 01/07/2020] [Indexed: 06/03/2023]
Abstract
The 70-kD heat shock proteins (HSP70s or HSC70s) function as molecular chaperones and are involved in diverse cellular processes. We recently demonstrated the roles of mitochondrial HSC70-1 (mtHSC70-1) in the establishment of cytochrome c oxidase (COX)-dependent respiration and redox homeostasis in Arabidopsis thaliana. Defects in COX assembly were observed in the mtHSC70-1 knockout lines. The levels of Cox2 (COX subunit 2) proteins in COX complex were markedly lower in the mutants than in wild-type plants; however, the levels of total Cox2 proteins in the mutants were not obviously different from those in wild-type plants, suggesting that the stability of COX or the availability of Cox2 was impaired in the mtHSC70-1 mutants. Here, we further detected the interaction between mtHSC70-1 and Cox2 proteins through co-immunoprecipitation, pull-down and firefly luciferase complementation imaging assays. The results showed that mtHSC70-1 could directly combine Cox2 in vivo and in vitro, providing supporting evidence for the role of mtHSC70-1 in COX assembly.
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Affiliation(s)
- Xiao-Ting Zhai
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Shan-Shan Wei
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Wei-Qian Liang
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jiao-Teng Bai
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Ning Jia
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bing Li
- College of Life Science, Hebei Normal University, Shijiazhuang, China
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31
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Steiner P, Obwegeser S, Wanner G, Buchner O, Lütz-Meindl U, Holzinger A. Cell Wall Reinforcements Accompany Chilling and Freezing Stress in the Streptophyte Green Alga Klebsormidium crenulatum. FRONTIERS IN PLANT SCIENCE 2020; 11:873. [PMID: 32714344 PMCID: PMC7344194 DOI: 10.3389/fpls.2020.00873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/28/2020] [Indexed: 05/15/2023]
Abstract
Adaptation strategies in freezing resistance were investigated in Klebsormidium crenulatum, an early branching streptophyte green alga related to higher plants. Klebsormidium grows naturally in unfavorable environments like alpine biological soil crusts, exposed to desiccation, high irradiation and cold stress. Here, chilling and freezing induced alterations of the ultrastructure were investigated. Control samples (kept at 20°C) were compared to chilled (4°C) as well as extracellularly frozen algae (-2 and -4°C). A software-controlled laboratory freezer (AFU, automatic freezing unit) was used for algal exposure to various temperatures and freezing was manually induced. Samples were then high pressure frozen and cryo-substituted for electron microscopy. Control cells had a similar appearance in size and ultrastructure as previously reported. While chilling stressed algae only showed minor ultrastructural alterations, such as small inward facing cell wall plugs and minor alterations of organelles, drastic changes of the cell wall and in organelle distribution were found in extracellularly frozen samples (-2°C and -4°C). In frozen samples, the cytoplasm was not retracted from the cell wall, but extensive three-dimensional cell wall layers were formed, most prominently in the corners of the cells, as determined by FIB-SEM and TEM tomography. Similar alterations/adaptations of the cell wall were not reported or visualized in Klebsormidium before, neither in controls, nor during other stress scenarios. This indicates that the cell wall is reinforced by these additional wall layers during freezing stress. Cells allowed to recover from freezing stress (-2°C) for 5 h at 20°C lost these additional cell wall layers, suggesting their dynamic formation. The composition of these cell wall reinforcement areas was investigated by immuno-TEM. In addition, alterations of structure and distribution of mitochondria, dictyosomes and a drastically increased endoplasmic reticulum were observed in frozen cells by TEM and TEM tomography. Measurements of the photosynthetic oxygen production showed an acclimation of Klebsormidium to chilling stress, which correlates with our findings on ultrastructural alterations of morphology and distribution of organelles. The cell wall reinforcement areas, together with the observed changes in organelle structure and distribution, are likely to contribute to maintenance of an undisturbed cell physiology and to adaptation to chilling and freezing stress.
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Affiliation(s)
- Philip Steiner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Sabrina Obwegeser
- Department of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, Austria
| | - Gerhard Wanner
- Ultrastructural Research, Department Biology I, Ludwig-Maximilians-University, Munich, Germany
| | - Othmar Buchner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Andreas Holzinger
- Department of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, Austria
- *Correspondence: Andreas Holzinger,
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32
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Mansilla N, Welchen E, Gonzalez DH. Arabidopsis SCO Proteins Oppositely Influence Cytochrome c Oxidase Levels and Gene Expression during Salinity Stress. PLANT & CELL PHYSIOLOGY 2019; 60:2769-2784. [PMID: 31418792 DOI: 10.1093/pcp/pcz166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
SCO (synthesis of cytochrome c oxidase) proteins are involved in the insertion of copper during the assembly of cytochrome c oxidase (COX), the final enzyme of the mitochondrial respiratory chain. Two SCO proteins, namely, homolog of copper chaperone 1 and 2 (HCC1 and HCC2) are present in seed plants, but HCC2 lacks the residues involved in copper binding, leading to uncertainties about its function. In this study, we performed a transcriptomic and phenotypic analysis of Arabidopsis thaliana plants with reduced expression of HCC1 or HCC2. We observed that a deficiency in HCC1 causes a decrease in the expression of several stress-responsive genes, both under basal growth conditions and after applying a short-term high salinity treatment. In addition, HCC1 deficient plants show a faster decrease in chlorophyll content, photosystem II quantum efficiency and COX levels after salinity stress, as well as a faster increase in alternative oxidase capacity. Notably, HCC2 deficiency causes opposite changes in most of these parameters. Bimolecular fluorescence complementation analysis indicated that both proteins are able to interact. We postulate that HCC1 is a limiting factor for COX assembly during high salinity conditions and that HCC2 probably acts as a negative modulator of HCC1 activity through protein-protein interactions. In addition, a direct or indirect role of HCC1 and HCC2 in the gene expression response to stress is proposed.
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Affiliation(s)
- Natanael Mansilla
- Instituto de Agrobiotecnolog�a del Litoral (CONICET-UNL), C�tedra de Biolog�a Celular y Molecular, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnolog�a del Litoral (CONICET-UNL), C�tedra de Biolog�a Celular y Molecular, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnolog�a del Litoral (CONICET-UNL), C�tedra de Biolog�a Celular y Molecular, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
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33
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Dos Santos RC, Nietsche S, Pereira MCT, Ribeiro LM, Mercadante-Simões MO, Carneiro Dos Santos BH. Atemoya fruit development and cytological aspects of GA 3-induced growth and parthenocarpy. PROTOPLASMA 2019; 256:1345-1360. [PMID: 31065805 DOI: 10.1007/s00709-019-01382-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
The exogenous application of GA3 to atemoya tree flowers induces parthenocarpy, and in association with artificial pollination, it increases the fruit size. Morphological, anatomical, ultrastructural, and chemical aspects were evaluated during development of (1) fruit produced by artificial pollination (AP), (2) fruit from AP followed by the application of 250 ppm GA3, and (3) parthenocarpic fruit induced by the application of 1000 ppm GA3. Fruit growth showed a sigmoidal pattern, with development occurring in three phases: (I) cell division, (II) cell differentiation, and (III) maturation. Phase I presented cells with large nuclear volumes and a large population of organelles, phase II presented cells with a reduction in cytoplasm and an increase in vacuole volume, and phase III presented cells with an increase in plastids with reserve compounds. The application of GA3, in association with pollination, precedes cytological events and delays when applied exclusively. GA3 promotes the growth of pollinated fruits by stimulating cell division and expansion, which occur in association with reduced seed production, and the GA3 induces parthenocarpy by maintaining division and stimulating cell expansion. The absence of seeds accounts for the smaller size of the parthenocarpic fruits, and the lower accumulation of calcium accounts for less firm fruit.
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Affiliation(s)
- Rayane Carneiro Dos Santos
- Programa de Pós-Graduação em Produção Vegetal no Semiárido, Universidade Estadual de Montes Claros, Reinaldo Viana 2650, Janaúba, Minas Gerais, CEP-39400-000, Brazil
| | - Silvia Nietsche
- Instituto de Ciências Agrárias, Universidade Federal de Minas Gerais, Avenida Universitária, 1000, Bairro Universitário, Montes Claros, CEP 39.404-547, Brazil.
| | - Marlon Cristian Toledo Pereira
- Programa de Pós-Graduação em Produção Vegetal no Semiárido, Universidade Estadual de Montes Claros, Reinaldo Viana 2650, Janaúba, Minas Gerais, CEP-39400-000, Brazil
| | - Leonardo Monteiro Ribeiro
- Programa de Pós-Graduação em Biotecnologia, Universidade Estadual de Montes Claros, Campus professor Darcy Ribeiro, Montes Claros, Minas Gerais, CEP 39.401-089, Brazil
| | - Maria Olívia Mercadante-Simões
- Programa de Pós-Graduação em Biotecnologia, Universidade Estadual de Montes Claros, Campus professor Darcy Ribeiro, Montes Claros, Minas Gerais, CEP 39.401-089, Brazil
| | - Bruna H Carneiro Dos Santos
- Programa de Pós-Graduação em Produção Vegetal no Semiárido, Universidade Estadual de Montes Claros, Reinaldo Viana 2650, Janaúba, Minas Gerais, CEP-39400-000, Brazil
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34
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Farooq MA, Niazi AK, Akhtar J, Farooq M, Souri Z, Karimi N, Rengel Z. Acquiring control: The evolution of ROS-Induced oxidative stress and redox signaling pathways in plant stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:353-369. [PMID: 31207496 DOI: 10.1016/j.plaphy.2019.04.039] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 05/18/2023]
Abstract
Reactive oxygen species (ROS) - the byproducts of aerobic metabolism - influence numerous aspects of the plant life cycle and environmental response mechanisms. In plants, ROS act like a double-edged sword; they play multiple beneficial roles at low concentrations, whereas at high concentrations ROS and related redox-active compounds cause cellular damage through oxidative stress. To examine the dual role of ROS as harmful oxidants and/or crucial cellular signals, this review elaborates that (i) how plants sense and respond to ROS in various subcellular organelles and (ii) the dynamics of subsequent ROS-induced signaling processes. The recent understanding of crosstalk between various cellular compartments in mediating their redox state spatially and temporally is discussed. Emphasis on the beneficial effects of ROS in maintaining cellular energy homeostasis, regulating diverse cellular functions, and activating acclimation responses in plants exposed to abiotic and biotic stresses are described. The comprehensive view of cellular ROS dynamics covering the breadth and versatility of ROS will contribute to understanding the complexity of apparently contradictory ROS roles in plant physiological responses in less than optimum environments.
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Affiliation(s)
- Muhammad Ansar Farooq
- Institute of Soil & Environmental Sciences, University of Agriculture, Faisalabad, Pakistan.
| | - Adnan Khan Niazi
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Javaid Akhtar
- Institute of Soil & Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Farooq
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Oman
| | - Zahra Souri
- Laboratory of Plant Physiology, Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Naser Karimi
- Laboratory of Plant Physiology, Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Zed Rengel
- School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
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Wang W, Zhang X, Niittylä T. OPENER Is a Nuclear Envelope and Mitochondria Localized Protein Required for Cell Cycle Progression in Arabidopsis. THE PLANT CELL 2019; 31:1446-1465. [PMID: 31023726 PMCID: PMC6635878 DOI: 10.1105/tpc.19.00033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/01/2019] [Accepted: 04/23/2019] [Indexed: 05/19/2023]
Abstract
Currently one-third of the proteins encoded by the Arabidopsis (Arabidopsis thaliana) genome are of unknown function. Some of these unknown proteins are likely to be involved in uncharacterized vital biological processes. Evolutionarily conserved single copy genes in flowering plants have been shown to be enriched in essential housekeeping functions. This together with publicly available gene expression data allows for a focused search for uncharacterized essential genes. Here we identify an essential single copy gene called OPENER (OPNR) in Arabidopsis. We show that OPNR is predominantly expressed in actively dividing cells and performs essential functions in seed development and root meristem maintenance. Cell cycle tracking using 5-ethynyl-2'-deoxyuridine staining and fluorescent cell cycle markers together with the increased size of nucleolus and nucleus in opnr mutants indicate that OPNR is required for cell cycle progression through the S or G2 phases. Intriguingly, OPNR localizes to the nuclear envelope and mitochondria. Furthermore, the nuclear envelope localization of OPNR is dependent on its interaction with nuclear inner membrane Sad1/UNC-84 (SUN) domain proteins SUN1 and SUN2. Taken together our results open a line of investigation into an evolutionarily conserved essential cellular process occurring in both the nuclear envelopes and mitochondria of dividing cells.
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Affiliation(s)
- Wei Wang
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
| | - Xueyang Zhang
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
| | - Totte Niittylä
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
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Meyer EH, Welchen E, Carrie C. Assembly of the Complexes of the Oxidative Phosphorylation System in Land Plant Mitochondria. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:23-50. [PMID: 30822116 DOI: 10.1146/annurev-arplant-050718-100412] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant mitochondria play a major role during respiration by producing the ATP required for metabolism and growth. ATP is produced during oxidative phosphorylation (OXPHOS), a metabolic pathway coupling electron transfer with ADP phosphorylation via the formation and release of a proton gradient across the inner mitochondrial membrane. The OXPHOS system is composed of large, multiprotein complexes coordinating metal-containing cofactors for the transfer of electrons. In this review, we summarize the current state of knowledge about assembly of the OXPHOS complexes in land plants. We present the different steps involved in the formation of functional complexes and the regulatory mechanisms controlling the assembly pathways. Because several assembly steps have been found to be ancestral in plants-compared with those described in fungal and animal models-we discuss the evolutionary dynamics that lead to the conservation of ancestral pathways in land plant mitochondria.
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Affiliation(s)
- Etienne H Meyer
- Organelle Biology and Biotechnology Research Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Current affiliation: Institute of Plant Physiology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany;
| | - Elina Welchen
- Cátedra de Biología Celular y Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Chris Carrie
- Plant Sciences Research Group, Department Biologie I, Ludwig-Maximilians-Universität, 82152 Planegg-Martinsried, Germany
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Heidorn-Czarna M, Domanski D, Kwasniak-Owczarek M, Janska H. Targeted Proteomics Approach Toward Understanding the Role of the Mitochondrial Protease FTSH4 in the Biogenesis of OXPHOS During Arabidopsis Seed Germination. FRONTIERS IN PLANT SCIENCE 2018; 9:821. [PMID: 29963070 PMCID: PMC6014109 DOI: 10.3389/fpls.2018.00821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/28/2018] [Indexed: 05/23/2023]
Abstract
Seed germination provides an excellent model to study the process of mitochondrial biogenesis. It is a complex and strictly regulated process which requires a proper biogenesis of fully active organelles from existing promitochondrial structures. We have previously reported that the lack of the inner mitochondrial membrane protease FTSH4 delayed Arabidopsis seed germination. Here, we implemented a targeted mass spectrometry-based approach, Multiple Reaction Monitoring (MRM), with stable-isotope-labeled standard peptides for increased sensitivity, to quantify mitochondrial proteins in dry and germinating wild-type and ftsh4 mutant seeds, lacking the FTSH4 protease. Using total seed protein extracts we measured the abundance of the peptide targets belonging to the OXPHOS complexes, AOX1A, transport, and inner membrane scaffold as well as mitochondrial proteins that are highly specific to dry and germinating seeds. The MRM assay showed that the abundance of these proteins in ftsh4 did not differ substantially from that observed in wild-type at the level of dry seed and after stratification, but we observed a reduction in protein abundance in most of the examined OXPHOS subunits in the later stages of germination. These changes in OXPHOS protein levels in ftsh4 mutants were accompanied by a lower cytochrome pathway activity as well as an increased AOX1A amount at the transcript and protein level and alternative pathway activity. The analyses of the steady-state transcript levels of mitochondrial and nuclear genes encoding OXPHOS subunits did not show significant difference in their amount, indicating that the observed changes in the OXPHOS occurred at the post-transcriptional level. At the time when ftsh4 seeds were fully germinated, the abundance of the OXPHOS proteins in the mutant was either slightly lowered or comparable to these amounts in wild-type seeds at the similar developmental stage. By the implementation of an integrative approach combining targeted proteomics, quantitative transcriptomics, and physiological studies we have shown that the FTSH4 protease has an important role in the biogenesis of OXPHOS and thus biogenesis of mitochondria during germination of Arabidopsis seeds.
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Affiliation(s)
- Malgorzata Heidorn-Czarna
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Dominik Domanski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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Mansilla N, Racca S, Gras DE, Gonzalez DH, Welchen E. The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants. Int J Mol Sci 2018; 19:ijms19030662. [PMID: 29495437 PMCID: PMC5877523 DOI: 10.3390/ijms19030662] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial respiration is an energy producing process that involves the coordinated action of several protein complexes embedded in the inner membrane to finally produce ATP. Complex IV or Cytochrome c Oxidase (COX) is the last electron acceptor of the respiratory chain, involved in the reduction of O2 to H2O. COX is a multimeric complex formed by multiple structural subunits encoded in two different genomes, prosthetic groups (heme a and heme a3), and metallic centers (CuA and CuB). Tens of accessory proteins are required for mitochondrial RNA processing, synthesis and delivery of prosthetic groups and metallic centers, and for the final assembly of subunits to build a functional complex. In this review, we perform a comparative analysis of COX composition and biogenesis factors in yeast, mammals and plants. We also describe possible external and internal factors controlling the expression of structural proteins and assembly factors at the transcriptional and post-translational levels, and the effect of deficiencies in different steps of COX biogenesis to infer the role of COX in different aspects of plant development. We conclude that COX assembly in plants has conserved and specific features, probably due to the incorporation of a different set of subunits during evolution.
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Affiliation(s)
- Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Sofia Racca
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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Zhang N, Rao RSP, Salvato F, Havelund JF, Møller IM, Thelen JJ, Xu D. MU-LOC: A Machine-Learning Method for Predicting Mitochondrially Localized Proteins in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:634. [PMID: 29875778 PMCID: PMC5974146 DOI: 10.3389/fpls.2018.00634] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/23/2018] [Indexed: 05/19/2023]
Abstract
Targeting and translocation of proteins to the appropriate subcellular compartments are crucial for cell organization and function. Newly synthesized proteins are transported to mitochondria with the assistance of complex targeting sequences containing either an N-terminal pre-sequence or a multitude of internal signals. Compared with experimental approaches, computational predictions provide an efficient way to infer subcellular localization of a protein. However, it is still challenging to predict plant mitochondrially localized proteins accurately due to various limitations. Consequently, the performance of current tools can be improved with new data and new machine-learning methods. We present MU-LOC, a novel computational approach for large-scale prediction of plant mitochondrial proteins. We collected a comprehensive dataset of plant subcellular localization, extracted features including amino acid composition, protein position weight matrix, and gene co-expression information, and trained predictors using deep neural network and support vector machine. Benchmarked on two independent datasets, MU-LOC achieved substantial improvements over six state-of-the-art tools for plant mitochondrial targeting prediction. In addition, MU-LOC has the advantage of predicting plant mitochondrial proteins either possessing or lacking N-terminal pre-sequences. We applied MU-LOC to predict candidate mitochondrial proteins for the whole proteome of Arabidopsis and potato. MU-LOC is publicly available at http://mu-loc.org.
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Affiliation(s)
- Ning Zhang
- Informatics Institute, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - R. S. P. Rao
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Fernanda Salvato
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Jesper F. Havelund
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Ian M. Møller
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jay J. Thelen
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Informatics Institute, University of Missouri, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
- *Correspondence: Dong Xu,
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Majsec K, Bhuiyan NH, Sun Q, Kumari S, Kumar V, Ware D, van Wijk KJ. The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis. THE PLANT CELL 2017; 29:2687-2710. [PMID: 28947489 PMCID: PMC5728138 DOI: 10.1105/tpc.17.00481] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/29/2017] [Accepted: 09/21/2017] [Indexed: 05/17/2023]
Abstract
Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.
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Affiliation(s)
- Kristina Majsec
- Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Nazmul H Bhuiyan
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853
| | - Sunita Kumari
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Vivek Kumar
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Doreen Ware
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Klaas J van Wijk
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
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Systems Phytohormone Responses to Mitochondrial Proteotoxic Stress. Mol Cell 2017; 68:540-551.e5. [DOI: 10.1016/j.molcel.2017.10.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 08/07/2017] [Accepted: 10/05/2017] [Indexed: 02/06/2023]
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Samad AFA, Sajad M, Nazaruddin N, Fauzi IA, Murad AMA, Zainal Z, Ismail I. MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network. FRONTIERS IN PLANT SCIENCE 2017; 8:565. [PMID: 28446918 PMCID: PMC5388764 DOI: 10.3389/fpls.2017.00565] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/29/2017] [Indexed: 05/14/2023]
Abstract
Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions. This present review focuses on the regulatory relationships between miRNAs and different families of TFs like; NF-Y, MYB, AP2, TCP, WRKY, NAC, GRF, and SPL. For instance NF-Y play important role during drought tolerance and flower development, MYB are involved in signal transduction and biosynthesis of secondary metabolites, AP2 regulate the floral development and nodule formation, TCP direct leaf development and growth hormones signaling. WRKY have known roles in multiple stress tolerances, NAC regulate lateral root formation, GRF are involved in root growth, flower, and seed development, and SPL regulate plant transition from juvenile to adult. We also studied the relation between miRNAs and TFs by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.
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Affiliation(s)
- Abdul F. A. Samad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Muhammad Sajad
- Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, PunjabPakistan
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Nazaruddin Nazaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Darussalam, Banda AcehIndonesia
| | - Izzat A. Fauzi
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Abdul M. A. Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Zamri Zainal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
- *Correspondence: Ismanizan Ismail,
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Boonrueng C, Tangpranomkorn S, Yazhisai U, Sirikantaramas S. Molecular cloning, subcellular localization and characterization of two adenylate kinases from cassava, Manihot esculenta Crantz cv. KU50. JOURNAL OF PLANT PHYSIOLOGY 2016; 204:66-73. [PMID: 27518222 DOI: 10.1016/j.jplph.2016.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/03/2016] [Accepted: 08/03/2016] [Indexed: 06/06/2023]
Abstract
Adenylate kinase (ADK) is a phosphotransferase that plays an important role in cellular energy homeostasis. Many isozymes located in different subcellular compartments have been reported. In this study, we focus on the characterization of cassava (Manihot esculenta) ADKs. We found 15 ADKs that are publicly available in the African cassava genome database. We cloned two ADKs, namely MeADK1 and MeADK2, which are phylogenetically grouped together with the plastidial ADK in potato. Both MeADK1 and MeADK2 showed 66% identity in the amino acid sequences with plastidial ADK in potato. However, we demonstrated that they are localized to mitochondria using GFP fusions of MeADK1 and MeADK2. The Escherichia coli-produced recombinant MeADK1 and MeADK2 preferred forward reactions that produce ATP. They exhibited similar specific activities. The semi-quantitative RT-PCR analysis showed that MeADK1 and MeADK2 in 2-month-old leaves have similar expression patterns under a diurnal light-dark cycle. However, MeADK2 transcripts were expressed at much higher levels than MeADK1 in 5-month-old leaves and roots. Thus, we conclude that MeADK2 might play a vital role in energy homeostasis in cassava mitochondria.
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Affiliation(s)
- Channarong Boonrueng
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Surachat Tangpranomkorn
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Uthaman Yazhisai
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Supaart Sirikantaramas
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand.
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Rao RSP, Salvato F, Thal B, Eubel H, Thelen JJ, Møller IM. The proteome of higher plant mitochondria. Mitochondrion 2016; 33:22-37. [PMID: 27405097 DOI: 10.1016/j.mito.2016.07.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 11/26/2022]
Abstract
Plant mitochondria perform a wide range of functions in the plant cell ranging from providing energy and metabolic intermediates, via coenzyme biosynthesis and their own biogenesis to retrograde signaling and programmed cell death. To perform these functions, they contain a proteome of >2000 different proteins expressed in some cells under some conditions. The vast majority of these proteins are imported, in many cases by a dedicated protein import machinery. Recent proteomic studies have identified about 1000 different proteins in both Arabidopsis and potato mitochondria, but even for energy-related proteins, the most well-studied functional protein group in mitochondria, <75% of the proteins are recognized as mitochondrial by even one of six of the most widely used prediction algorithms. The mitochondrial proteomes contain proteins representing a wide range of different functions. Some protein groups, like energy-related proteins, membrane transporters, and de novo fatty acid synthesis, appear to be well covered by the proteome, while others like RNA metabolism appear to be poorly covered possibly because of low abundance. The proteomic studies have improved our understanding of basic mitochondrial functions, have led to the discovery of new mitochondrial metabolic pathways and are helping us towards appreciating the dynamic role of the mitochondria in the responses of the plant cell to biotic and abiotic stress.
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Affiliation(s)
- R S P Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangalore 575018, India
| | - F Salvato
- Institute of Biology, Department of Plant Biology, University of Campinas, Cidade Universitária Zeferino Vaz - Barão Geraldo, Campinas CEP: 13083-970, São Paulo, Brazil
| | - B Thal
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, DE-30419 Hannover, Germany
| | - H Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, DE-30419 Hannover, Germany
| | - J J Thelen
- Department of Biochemistry, University of Missouri-Columbia, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - I M Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark.
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Welchen E, Gonzalez DH. Cytochrome c, a hub linking energy, redox, stress and signaling pathways in mitochondria and other cell compartments. PHYSIOLOGIA PLANTARUM 2016; 157:310-321. [PMID: 27080474 DOI: 10.1111/ppl.12449] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/04/2016] [Accepted: 02/26/2016] [Indexed: 06/05/2023]
Abstract
Cytochrome c (CYTc) is a soluble redox-active heme protein that transfers electrons from complex III to complex IV in the cyanide-sensitive mitochondrial respiratory pathway. CYTc biogenesis is a complex process that requires multiple steps until the mature active protein is obtained. CYTc levels and activity are finely regulated, revealing the importance of this protein not only as electron carrier but also in many other processes. In this article, we describe the role of CYTc in mitochondrial respiration, from its canonical role as electron carrier for ATP production to its involvement in protein import and the stabilization of respiratory complexes and supercomplexes. In plants, CYTc is connected to the synthesis of the antioxidant ascorbate and the detoxification of toxic compounds. Finally, CYTc is also a multi-functional signaling molecule that influences the balance between life and death, acting in energy provision for cellular functions or triggering programmed cell death. The confluence of several metabolic routes into a single protein that links redox reactions with energy producing pathways seems logical from the point of view of cellular economy, control and organization.
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Affiliation(s)
- Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, 3000, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, 3000, Argentina
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46
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Kmiecik P, Leonardelli M, Teige M. Novel connections in plant organellar signalling link different stress responses and signalling pathways. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3793-807. [PMID: 27053718 DOI: 10.1093/jxb/erw136] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To coordinate growth, development and responses to environmental stimuli, plant cells need to communicate the metabolic state between different sub-compartments of the cell. This requires signalling pathways, including protein kinases, secondary messengers such as Ca(2+) ions or reactive oxygen species (ROS) as well as metabolites and plant hormones. The signalling networks involved have been intensively studied over recent decades and have been elaborated more or less in detail. However, it has become evident that these signalling networks are also tightly interconnected and often merge at common targets such as a distinct group of transcription factors, most prominently ABI4, which are amenable to regulation by phosphorylation, potentially also in a Ca(2+)- or ROS-dependent fashion. Moreover, the signalling pathways connect several organelles or subcellular compartments, not only in functional but also in physical terms, linking for example chloroplasts to the nucleus or peroxisomes to chloroplasts thereby enabling physical routes for signalling by metabolite exchange or even protein translocation. Here we briefly discuss these novel findings and try to connect them in order to point out the remaining questions and emerging developments in plant organellar signalling.
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Affiliation(s)
- Przemyslaw Kmiecik
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Manuela Leonardelli
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Markus Teige
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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Berkowitz O, De Clercq I, Van Breusegem F, Whelan J. Interaction between hormonal and mitochondrial signalling during growth, development and in plant defence responses. PLANT, CELL & ENVIRONMENT 2016; 39:1127-39. [PMID: 26763171 DOI: 10.1111/pce.12712] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/22/2015] [Accepted: 12/30/2015] [Indexed: 05/23/2023]
Abstract
Mitochondria play a central role in plant metabolism as they are a major source of ATP through synthesis by the oxidative phosphorylation pathway and harbour key metabolic reactions such as the TCA cycle. The energy and building blocks produced by mitochondria are essential to drive plant growth and development as well as to provide fuel for responses to abiotic and biotic stresses. The majority of mitochondrial proteins are encoded in the nuclear genome and have to be imported into the organelle. For the regulation of the corresponding genes intricate signalling pathways exist to adjust their expression. Signals directly regulate nuclear gene expression (anterograde signalling) to adjust the protein composition of the mitochondria to the needs of the cell. In parallel, mitochondria communicate back their functional status to the nucleus (retrograde signalling) to prompt transcriptional regulation of responsive genes via largely unknown signalling mechanisms. Plant hormones are the major signalling components regulating all layers of plant development and cellular functions. Increasing evidence is now becoming available that plant hormones are also part of signalling networks controlling mitochondrial function and their biogenesis. This review summarizes recent advances in understanding the interaction of mitochondrial and hormonal signalling pathways.
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Affiliation(s)
- Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Inge De Clercq
- Department of Animal, Plant and Soil Sciences, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
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Garcia L, Welchen E, Gey U, Arce AL, Steinebrunner I, Gonzalez DH. The cytochrome c oxidase biogenesis factor AtCOX17 modulates stress responses in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:628-44. [PMID: 26436309 DOI: 10.1111/pce.12647] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/22/2015] [Indexed: 05/03/2023]
Abstract
COX17 is a soluble protein from the mitochondrial intermembrane space that participates in the transfer of copper for cytochrome c oxidase (COX) assembly in eukaryotic organisms. In this work, we studied the function of both Arabidopsis thaliana AtCOX17 genes using plants with altered expression levels of these genes. Silencing of AtCOX17-1 in a cox17-2 knockout background generates plants with smaller rosettes and decreased expression of genes involved in the response of plants to different stress conditions, including several genes that are induced by mitochondrial dysfunctions. Silencing of either of the AtCOX17 genes does not affect plant development or COX activity but causes a decrease in the response of genes to salt stress. In addition, these plants contain higher reactive oxygen and lipid peroxidation levels after irrigation with high NaCl concentrations and are less sensitive to abscisic acid. In agreement with a role of AtCOX17 in stress and abscisic acid responses, both AtCOX17 genes are induced by several stress conditions, abscisic acid and mutation of the transcription factor ABI4. The results indicate that AtCOX17 is required for optimal expression of a group of stress-responsive genes, probably as a component of signalling pathways that link stress conditions to gene expression responses.
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Affiliation(s)
- Lucila Garcia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Uta Gey
- Technische Universität Dresden, Department of Biology, 01062, Dresden, Germany
| | - Agustín L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Iris Steinebrunner
- Technische Universität Dresden, Department of Biology, 01062, Dresden, Germany
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
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Narsai R. Databases and informatics resources for analysis of plant mitochondria. Methods Mol Biol 2016; 1305:263-79. [PMID: 25910741 DOI: 10.1007/978-1-4939-2639-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
As more omics data is generated from various plant species, it is becoming increasingly possible to carry out a range of in silico analyses to gain insight into mitochondrial function in plants. From the use of software tools for DNA motif analyses and transcript expression visualization to proteomic and subcellular localization resources, it is possible to carry out significant in silico analyses that are highly informative to researchers and can help to guide experimental design for further mitochondrial study. Databases specific to plant mitochondrial analyses have been developed in recent years, revealing mitochondria-specific information. This chapter outlines the databases and informatics resources that are useful for plant mitochondrial studies, with specific examples presented to indicate how these resources can be used to gain insight into plant mitochondrial function(s).
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Affiliation(s)
- Reena Narsai
- Department of Botany, Australian Research Council Centre of Excellence Plant Energy Biology, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, VIC, 3086, Australia,
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Arnholdt-Schmitt B, Ragonezi C, Cardoso H. Do Mitochondria Play a Central Role in Stress-Induced Somatic Embryogenesis? Methods Mol Biol 2016; 1359:87-100. [PMID: 26619859 DOI: 10.1007/978-1-4939-3061-6_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This review highlights a four-step rational for the hypothesis that mitochondria play an upstream central role for stress-induced somatic embryogenesis (SE): (1) Initiation of SE is linked to programmed cell death (PCD) (2) Mitochondria are crucially connected to cell death (3) SE is challenged by stress per se (4) Mitochondria are centrally linked to plant stress response and its management. Additionally the review provides a rough perspective for the use of mitochondrial-derived functional marker (FM) candidates to improve SE efficiency. It is proposed to apply SE systems as phenotyping tool for identifying superior genotypes with high general plasticity under severe plant stress conditions.
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Affiliation(s)
- Birgit Arnholdt-Schmitt
- EU Marie Curie Chair, ICAAM, IIFA, Universidade de Évora, Núcleo da Mitra, Ap. 94, Évora, 7002-554, Portugal.
| | - Carla Ragonezi
- EU Marie Curie Chair, ICAAM, IIFA, Universidade de Évora, Núcleo da Mitra, Ap. 94, Évora, 7002-554, Portugal
| | - Hélia Cardoso
- EU Marie Curie Chair, ICAAM, IIFA, Universidade de Évora, Núcleo da Mitra, Ap. 94, Évora, 7002-554, Portugal
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