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Moy A, Nkongolo K. Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine ( Pinus banksiana) Based on Transcriptomic Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1042. [PMID: 38611570 PMCID: PMC11013723 DOI: 10.3390/plants13071042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding gene expression toward each metal. The objectives of this study were to (1) extend the analysis of the Pinus banksiana transcriptome exposed to nickel and copper, (2) assess the differential gene expression in nickel-resistant compared to copper-resistant genotypes, and (3) identify mechanisms specific to each metal. The Illumina platform was used to sequence RNA that was extracted from seedlings treated with each of the metals. There were 449 differentially expressed genes (DEGs) between copper-resistant genotypes (RGs) and nickel-resistant genotypes (RGs) at a high stringency cut-off, indicating a distinct pattern of gene expression toward each metal. For biological processes, 19.8% of DEGs were associated with the DNA metabolic process, followed by the response to stress (13.15%) and the response to chemicals (8.59%). For metabolic function, 27.9% of DEGs were associated with nuclease activity, followed by nucleotide binding (27.64%) and kinase activity (10.16%). Overall, 21.49% of DEGs were localized to the plasma membrane, followed by the cytosol (16.26%) and chloroplast (12.43%). Annotation of the top upregulated genes in copper RG compared to nickel RG identified genes and mechanisms that were specific to copper and not to nickel. NtPDR, AtHIPP10, and YSL1 were identified as genes associated with copper resistance. Various genes related to cell wall metabolism were identified, and they included genes encoding for HCT, CslE6, MPG, and polygalacturonase. Annotation of the top downregulated genes in copper RG compared to nickel RG revealed genes and mechanisms that were specific to nickel and not copper. Various regulatory and signaling-related genes associated with the stress response were identified. They included UGT, TIFY, ACC, dirigent protein, peroxidase, and glyoxyalase I. Additional research is needed to determine the specific functions of signaling and stress response mechanisms in nickel-resistant plants.
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Affiliation(s)
| | - Kabwe Nkongolo
- Biomolecular Sciences Program, Department of Biology, School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
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Kuntz M, Dimnet L, Pullara S, Moyet L, Rolland N. The Main Functions of Plastids. Methods Mol Biol 2024; 2776:89-106. [PMID: 38502499 DOI: 10.1007/978-1-0716-3726-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Plastids are semi-autonomous organelles like mitochondria and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.
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Affiliation(s)
- Marcel Kuntz
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France.
| | - Laura Dimnet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Sara Pullara
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Lucas Moyet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
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Flores-Iga G, Lopez-Ortiz C, Gracia-Rodriguez C, Almeida A, Nimmakayala P, Reddy UK, Balagurusamy N. A Genome-Wide Identification and Comparative Analysis of the Heavy-Metal-Associated Gene Family in Cucurbitaceae Species and Their Role in Cucurbita pepo under Arsenic Stress. Genes (Basel) 2023; 14:1877. [PMID: 37895226 PMCID: PMC10606463 DOI: 10.3390/genes14101877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The heavy-metal-associated (HMA) proteins are a class of PB1-type ATPases related to the intracellular transport and detoxification of metals. However, due to a lack of information regarding the HMA gene family in the Cucurbitaceae family, a comprehensive genome-wide analysis of the HMA family was performed in ten Cucurbitaceae species: Citrullus amarus, Citrullus colocynthis, Citrullus lanatus, Citrullus mucosospermus, Cucumis melo, Cucumis sativus, Cucurbita maxima, Cucurbita moschata, Cucurbita pepo, and Legenaria siceraria. We identified 103 Cucurbit HMA proteins with various members, ranging from 8 (Legenaria siceraria) to 14 (Cucurbita pepo) across species. The phylogenetic and structural analysis confirmed that the Cucurbitaceae HMA protein family could be further classified into two major clades: Zn/Co/Cd/Pb and Cu/Ag. The GO-annotation-based subcellular localization analysis predicted that all HMA gene family members were localized on membranes. Moreover, the analysis of conserved motifs and gene structure (intron/exon) revealed the functional divergence between clades. The interspecies microsynteny analysis demonstrated that maximum orthologous genes were found between species of the Citrullus genera. Finally, nine candidate HMA genes were selected, and their expression analysis was carried out via qRT-PCR in root, leaf, flower, and fruit tissues of C. pepo under arsenic stress. The expression pattern of the CpeHMA genes showed a distinct pattern of expression in root and shoot tissues, with a remarkable expression of CpeHMA6 and CpeHMA3 genes from the Cu/Ag clade. Overall, this study provides insights into the functional analysis of the HMA gene family in Cucurbitaceae species and lays down the basic knowledge to explore the role and mechanism of the HMA gene family to cope with arsenic stress conditions.
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Affiliation(s)
- Gerardo Flores-Iga
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Carlos Lopez-Ortiz
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Celeste Gracia-Rodriguez
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Aldo Almeida
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark;
| | - Padma Nimmakayala
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Umesh K. Reddy
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA; (C.L.-O.); (P.N.)
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón 27275, Coahuila, México; (G.F.-I.); (C.G.-R.)
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Yang L, Wu X, Liu S, Zhang L, Li T, Cao Y, Duan Q. Comprehensive Analysis of BrHMPs Reveals Potential Roles in Abiotic Stress Tolerance and Pollen–Stigma Interaction in Brassica rapa. Cells 2023; 12:cells12071096. [PMID: 37048168 PMCID: PMC10093364 DOI: 10.3390/cells12071096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/28/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023] Open
Abstract
Heavy metal-associated proteins (HMPs) participate in heavy metal detoxification. Although HMPs have been identified in several plants, no studies to date have identified the HMPs in Brassica rapa (B. rapa). Here, we identified 85 potential HMPs in B. rapa by bioinformatic methods. The promoters of the identified genes contain many elements associated with stress responses, including response to abscisic acid, low-temperature, and methyl jasmonate. The expression levels of BrHMP14, BrHMP16, BrHMP32, BrHMP41, and BrHMP42 were upregulated under Cu2+, Cd2+, Zn2+, and Pb2+ stresses. BrHMP06, BrHMP30, and BrHMP41 were also significantly upregulated after drought treatment. The transcripts of BrHMP06 and BrHMP11 increased mostly under cold stress. After applying salt stress, the expression of BrHMP02, BrHMP16, and BrHMP78 was induced. We observed increased BrHMP36 expression during the self-incompatibility (SI) response and decreased expression in the compatible pollination (CP) response during pollen–stigma interactions. These changes in expression suggest functions for these genes in HMPs include participating in heavy metal transport, detoxification, and response to abiotic stresses, with the potential for functions in sexual reproduction. We found potential co-functional partners of these key players by protein–protein interaction (PPI) analysis and found that some of the predicted protein partners are known to be involved in corresponding stress responses. Finally, phosphorylation investigation revealed many phosphorylation sites in BrHMPs, suggesting post-translational modification may occur during the BrHMP-mediated stress response. This comprehensive analysis provides important clues for the study of the molecular mechanisms of BrHMP genes in B. rapa, especially for abiotic stress and pollen–stigma interactions.
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Affiliation(s)
- Lin Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Xiaoyu Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Shangjia Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Lina Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Ting Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Yunyun Cao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
| | - Qiaohong Duan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China
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Liu Y, Jing X, Zhang H, Xiong J, Qiao Y. Identification of Imprinted Genes Based on Homology: An Example of Fragaria vesca. Genes (Basel) 2021; 12:genes12030380. [PMID: 33800118 PMCID: PMC7999015 DOI: 10.3390/genes12030380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 01/04/2023] Open
Abstract
Genomic imprinting has drawn increasing attention in plant biology in recent years. At present, hundreds of imprinted genes have been identified in various plants, and some of them have been reported to be evolutionarily conserved in plant species. In this research, 17 candidate genes in Fragaria vesca were obtained based on the homologous imprinted genes in Arabidopsis thaliana and other species. We further constructed reciprocal crosses of diploid strawberry (F. vesca) using the varieties 10-41 and 18-86 as the parents to investigate the conservation of these imprinted genes. Potentially informative single nucleotide polymorphisms (SNPs) were used as molecular markers of two parents obtained from candidate imprinted genes which have been cloned and sequenced. Meanwhile, we analyzed the SNP site variation ratios and parent-of-origin expression patterns of candidate imprinted genes at 10 days after pollination (DAP) endosperm and embryo for the hybrids of reciprocal cross, respectively. A total of five maternally expressed genes (MEGs), i.e., FvARI8, FvKHDP-2, FvDRIP2, FvBRO1, and FvLTP3, were identified in the endosperm, which did not show imprinting in the embryo. Finally, tissues expression analysis indicated that the five imprinted genes excluding FvDRIP2 mainly expressed in the endosperm. This is the first report on imprinted genes of Fragaria, and we provide a simple and rapid method based on homologous conservation to screen imprinted genes. The present study will provide a basis for further study of function and mechanism of genomic imprinting in F. vesca.
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Lim SD, Mayer JA, Yim WC, Cushman JC. Plant tissue succulence engineering improves water-use efficiency, water-deficit stress attenuation and salinity tolerance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1049-1072. [PMID: 32338788 DOI: 10.1111/tpj.14783] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/01/2020] [Accepted: 04/14/2020] [Indexed: 05/25/2023]
Abstract
Tissue succulence (ratio of tissue water/leaf area or dry mass) or the ability to store water within living tissues is among the most successful adaptations to drought in the plant kingdom. This taxonomically widespread adaptation helps plants avoid the damaging effects of drought, and is often associated with the occupancy of epiphytic, epilithic, semi-arid and arid environments. Tissue succulence was engineered in Arabidopsis thaliana by overexpression of a codon-optimized helix-loop-helix transcription factor (VvCEB1opt ) from wine grape involved in the cell expansion phase of berry development. VvCEB1opt -overexpressing lines displayed significant increases in cell size, succulence and decreased intercellular air space. VvCEB1opt -overexpressing lines showed increased instantaneous and integrated water-use efficiency (WUE) due to reduced stomatal conductance caused by reduced stomatal aperture and density resulting in increased attenuation of water-deficit stress. VvCEB1opt -overexpressing lines also showed increased salinity tolerance due to reduced salinity uptake and dilution of internal Na+ and Cl- as well as other ions. Alterations in transporter activities were further suggested by media and apoplastic acidification, hygromycin B tolerance and changes in relative transcript abundance patterns of various transporters with known functions in salinity tolerance. Engineered tissue succulence might provide an effective strategy for improving WUE, drought avoidance or attenuation, salinity tolerance, and for crassulacean acid metabolism biodesign.
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Affiliation(s)
- Sung Don Lim
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | | | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557-0330, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557-0330, USA
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Schmidt SB, Eisenhut M, Schneider A. Chloroplast Transition Metal Regulation for Efficient Photosynthesis. TRENDS IN PLANT SCIENCE 2020; 25:817-828. [PMID: 32673582 DOI: 10.1016/j.tplants.2020.03.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/14/2020] [Accepted: 03/04/2020] [Indexed: 05/24/2023]
Abstract
Plants require sunlight, water, CO2, and essential nutrients to drive photosynthesis and fulfill their life cycle. The photosynthetic apparatus resides in chloroplasts and fundamentally relies on transition metals as catalysts and cofactors. Accordingly, chloroplasts are particularly rich in iron (Fe), manganese (Mn), and copper (Cu). Owing to their redox properties, those metals need to be carefully balanced within the cell. However, the regulation of transition metal homeostasis in chloroplasts is poorly understood. With the availability of the arabidopsis genome information and membrane protein databases, a wider catalogue for searching chloroplast metal transporters has considerably advanced the study of transition metal regulation. This review provides an updated overview of the chloroplast transition metal requirements and the transporters involved for efficient photosynthesis in higher plants.
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Affiliation(s)
- Sidsel Birkelund Schmidt
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Marion Eisenhut
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Anja Schneider
- Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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Marchand J, Heydarizadeh P, Schoefs B, Spetea C. Ion and metabolite transport in the chloroplast of algae: lessons from land plants. Cell Mol Life Sci 2018; 75:2153-2176. [PMID: 29541792 PMCID: PMC5948301 DOI: 10.1007/s00018-018-2793-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 03/01/2018] [Accepted: 03/07/2018] [Indexed: 12/28/2022]
Abstract
Chloroplasts are endosymbiotic organelles and play crucial roles in energy supply and metabolism of eukaryotic photosynthetic organisms (algae and land plants). They harbor channels and transporters in the envelope and thylakoid membranes, mediating the exchange of ions and metabolites with the cytosol and the chloroplast stroma and between the different chloroplast subcompartments. In secondarily evolved algae, three or four envelope membranes surround the chloroplast, making more complex the exchange of ions and metabolites. Despite the importance of transport proteins for the optimal functioning of the chloroplast in algae, and that many land plant homologues have been predicted, experimental evidence and molecular characterization are missing in most cases. Here, we provide an overview of the current knowledge about ion and metabolite transport in the chloroplast from algae. The main aspects reviewed are localization and activity of the transport proteins from algae and/or of homologues from other organisms including land plants. Most chloroplast transporters were identified in the green alga Chlamydomonas reinhardtii, reside in the envelope and participate in carbon acquisition and metabolism. Only a few identified algal transporters are located in the thylakoid membrane and play role in ion transport. The presence of genes for putative transporters in green algae, red algae, diatoms, glaucophytes and cryptophytes is discussed, and roles in the chloroplast are suggested. A deep knowledge in this field is required because algae represent a potential source of biomass and valuable metabolites for industry, medicine and agriculture.
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Affiliation(s)
- Justine Marchand
- Metabolism, Bioengineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML, FR 3473 CNRS, Le Mans University, 72000, Le Mans, France
| | - Parisa Heydarizadeh
- Metabolism, Bioengineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML, FR 3473 CNRS, Le Mans University, 72000, Le Mans, France
| | - Benoît Schoefs
- Metabolism, Bioengineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML, FR 3473 CNRS, Le Mans University, 72000, Le Mans, France.
| | - Cornelia Spetea
- Department of Biological and Environmental Sciences, University of Gothenburg, 40530, Göteborg, Sweden.
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Abstract
Plastids are semiautonomous organelles like mitochondria, and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.
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Affiliation(s)
- Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France.
| | - Imen Bouchnak
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
| | - Lucas Moyet
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
| | - Daniel Salvi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
| | - Marcel Kuntz
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France
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Wang B, Guo X, Zhao P, Ruan M, Yu X, Zou L, Yang Y, Li X, Deng D, Xiao J, Xiao Y, Hu C, Wang X, Wang X, Wang W, Peng M. Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100-day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz). PLoS One 2017; 12:e0177456. [PMID: 28493955 PMCID: PMC5426748 DOI: 10.1371/journal.pone.0177456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/27/2017] [Indexed: 11/19/2022] Open
Abstract
Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags-simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2.87 alleles per locus, gene diversity of 0.48 and polymorphic information content (PIC) of 0.41 on average. The genetic coefficient between every two lines was 0.37 on average, ranging from 0.21 to 0.82. According to our population structure analysis, these samples could be divided into three sub-populations showing obvious gene flow between them. We also performed water stress experiments using 100-day old cassava plants in two years and calculated the drought tolerance coefficients (DTCs) and used them as phenotypes for marker-trait association mapping. We found that 53 markers were significantly associated with these drought-related traits, with a contribution rate for trait variation of 8.60% on average, ranging between 2.66 and 28.09%. Twenty-four of these 53 associated genes showed differential transcription or protein levels which were confirmed by qRT-PCR under drought stress when compared to the control conditions in cassava. Twelve of twenty-four genes were the same differential expression patterns in omics data and results of qRT-PCR. Out of 33 marker-traits combinations on 24 loci, 34 were positive and 53 negative alleles according to their phenotypic effects and we also obtained the typical materials which carried these elite alleles. We also found 23 positive average allele effects while 10 loci were negative according to their allele effects (AAEs). Our results on molecular diversity, locus association and differential expression under drought can prove beneficial to select excellent materials through marker assisted selection and for functional genes research in the future.
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Affiliation(s)
- Bin Wang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xin Guo
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Pingjuan Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Mengbin Ruan
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaoling Yu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Liangping Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiling Yang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiao Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Deli Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Jixiang Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiwei Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Chunji Hu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xue Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaolin Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
- * E-mail:
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11
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Mayerhofer H, Sautron E, Rolland N, Catty P, Seigneurin-Berny D, Pebay-Peyroula E, Ravaud S. Structural Insights into the Nucleotide-Binding Domains of the P1B-type ATPases HMA6 and HMA8 from Arabidopsis thaliana. PLoS One 2016; 11:e0165666. [PMID: 27802305 PMCID: PMC5089723 DOI: 10.1371/journal.pone.0165666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/14/2016] [Indexed: 01/24/2023] Open
Abstract
Copper is a crucial ion in cells, but needs to be closely controlled due to its toxic potential and ability to catalyse the formation of radicals. In chloroplasts, an important step for the proper functioning of the photosynthetic electron transfer chain is the delivery of copper to plastocyanin in the thylakoid lumen. The main route for copper transport to the thylakoid lumen is driven by two PIB-type ATPases, Heavy Metal ATPase 6 (HMA6) and HMA8, located in the inner membrane of the chloroplast envelope and in the thylakoid membrane, respectively. Here, the crystal structures of the nucleotide binding domain of HMA6 and HMA8 from Arabidopsis thaliana are reported at 1.5Å and 1.75Å resolution, respectively, providing the first structural information on plants Cu+-ATPases. The structures reveal a compact domain, with two short helices on both sides of a twisted beta-sheet. A double mutant, aiding in the crystallization, provides a new crystal contact, but also avoids an internal clash highlighting the benefits of construct modifications. Finally, the histidine in the HP motif of the isolated domains, unable to bind ATP, shows a side chain conformation distinct from nucleotide bound structures.
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Affiliation(s)
- Hubert Mayerhofer
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Emeline Sautron
- Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Patrice Catty
- Laboratoire de Chimie et Biologie des Métaux (LCBM), BIG, Université Grenoble Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Daphné Seigneurin-Berny
- Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Eva Pebay-Peyroula
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Stéphanie Ravaud
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- * E-mail:
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12
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Sautron E, Giustini C, Dang T, Moyet L, Salvi D, Crouzy S, Rolland N, Catty P, Seigneurin-Berny D. Identification of Two Conserved Residues Involved in Copper Release from Chloroplast PIB-1-ATPases. J Biol Chem 2016; 291:20136-48. [PMID: 27493208 PMCID: PMC5025697 DOI: 10.1074/jbc.m115.706978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/04/2016] [Indexed: 01/12/2023] Open
Abstract
Copper is an essential transition metal for living organisms. In the plant model Arabidopsis thaliana, half of the copper content is localized in the chloroplast, and as a cofactor of plastocyanin, copper is essential for photosynthesis. Within the chloroplast, copper delivery to plastocyanin involves two transporters of the PIB-1-ATPases subfamily: HMA6 at the chloroplast envelope and HMA8 in the thylakoid membranes. Both proteins are high affinity copper transporters but share distinct enzymatic properties. In the present work, the comparison of 140 sequences of PIB-1-ATPases revealed a conserved region unusually rich in histidine and cysteine residues in the TMA-L1 region of eukaryotic chloroplast copper ATPases. To evaluate the role of these residues, we mutated them in HMA6 and HMA8. Mutants of interest were selected from phenotypic tests in yeast and produced in Lactococcus lactis for further biochemical characterizations using phosphorylation assays from ATP and Pi Combining functional and structural data, we highlight the importance of the cysteine and the first histidine of the CX3HX2H motif in the process of copper release from HMA6 and HMA8 and propose a copper pathway through the membrane domain of these transporters. Finally, our work suggests a more general role of the histidine residue in the transport of copper by PIB-1-ATPases.
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Affiliation(s)
- Emeline Sautron
- From the CNRS, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, F-38054 Grenoble, France, the Université Grenoble Alpes, F-38054 Grenoble, France, the CEA, DSV, BIG, F-38054 Grenoble, France, the INRA, LPCV, UMR 1417, F-38054 Grenoble, France, and
| | - Cécile Giustini
- From the CNRS, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, F-38054 Grenoble, France, the Université Grenoble Alpes, F-38054 Grenoble, France, the CEA, DSV, BIG, F-38054 Grenoble, France, the INRA, LPCV, UMR 1417, F-38054 Grenoble, France, and
| | - ThuyVan Dang
- From the CNRS, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, F-38054 Grenoble, France, the Université Grenoble Alpes, F-38054 Grenoble, France, the CEA, DSV, BIG, F-38054 Grenoble, France, the INRA, LPCV, UMR 1417, F-38054 Grenoble, France, and
| | - Lucas Moyet
- From the CNRS, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, F-38054 Grenoble, France, the Université Grenoble Alpes, F-38054 Grenoble, France, the CEA, DSV, BIG, F-38054 Grenoble, France, the INRA, LPCV, UMR 1417, F-38054 Grenoble, France, and
| | - Daniel Salvi
- From the CNRS, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, F-38054 Grenoble, France, the Université Grenoble Alpes, F-38054 Grenoble, France, the CEA, DSV, BIG, F-38054 Grenoble, France, the INRA, LPCV, UMR 1417, F-38054 Grenoble, France, and
| | - Serge Crouzy
- the Université Grenoble Alpes, F-38054 Grenoble, France, the CEA, DSV, BIG, F-38054 Grenoble, France, the CNRS, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, F-38054 Grenoble, France
| | - Norbert Rolland
- From the CNRS, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, F-38054 Grenoble, France, the Université Grenoble Alpes, F-38054 Grenoble, France, the CEA, DSV, BIG, F-38054 Grenoble, France, the INRA, LPCV, UMR 1417, F-38054 Grenoble, France, and
| | - Patrice Catty
- the Université Grenoble Alpes, F-38054 Grenoble, France, the CEA, DSV, BIG, F-38054 Grenoble, France, the CNRS, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, F-38054 Grenoble, France
| | - Daphné Seigneurin-Berny
- From the CNRS, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, F-38054 Grenoble, France, the Université Grenoble Alpes, F-38054 Grenoble, France, the CEA, DSV, BIG, F-38054 Grenoble, France, the INRA, LPCV, UMR 1417, F-38054 Grenoble, France, and
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13
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Seigneurin-Berny D, King MS, Sautron E, Moyet L, Catty P, André F, Rolland N, Kunji ERS, Frelet-Barrand A. Membrane Protein Production in Lactococcus lactis for Functional Studies. Methods Mol Biol 2016; 1432:79-101. [PMID: 27485331 DOI: 10.1007/978-1-4939-3637-3_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Due to their unique properties, expression and study of membrane proteins in heterologous systems remains difficult. Among the bacterial systems available, the Gram-positive lactic bacterium, Lactococcus lactis, traditionally used in food fermentations, is nowadays widely used for large-scale production and functional characterization of bacterial and eukaryotic membrane proteins. The aim of this chapter is to describe the different possibilities for the functional characterization of peripheral or intrinsic membrane proteins expressed in Lactococcus lactis.
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Affiliation(s)
- Daphne Seigneurin-Berny
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS (UMR-5168)/CEA/INRA (UMR1417)/Université Grenoble Alpes, BIG, CEA, Grenoble, France
| | - Martin S King
- Medical Research Council, Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 2XY, UK
| | - Emiline Sautron
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS (UMR-5168)/CEA/INRA (UMR1417)/Université Grenoble Alpes, BIG, CEA, Grenoble, France
| | - Lucas Moyet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS (UMR-5168)/CEA/INRA (UMR1417)/Université Grenoble Alpes, BIG, CEA, Grenoble, France
| | - Patrice Catty
- Laboratoire de Chimie et Biologie des Métaux, CNRS (UMR-5249)/CEA/Université Grenoble Alpes, BIG, CEA, Grenoble, France
| | - François André
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris Saclay, Gif-sur-Yvette, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS (UMR-5168)/CEA/INRA (UMR1417)/Université Grenoble Alpes, BIG, CEA, Grenoble, France
| | - Edmund R S Kunji
- Medical Research Council, Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 2XY, UK
| | - Annie Frelet-Barrand
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris Saclay, Gif-sur-Yvette, France. .,FEMTO-ST Institute, UMR CNRS 6174, University of Bourgogne Franche-Comte, Besançon, France.
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14
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Migocka M. Copper-transporting ATPases: The evolutionarily conserved machineries for balancing copper in living systems. IUBMB Life 2015; 67:737-45. [PMID: 26422816 DOI: 10.1002/iub.1437] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 09/14/2015] [Indexed: 12/29/2022]
Abstract
Copper ATPases (Cu-ATPases) are ubiquitous transmembrane proteins using energy from ATP to transport copper across different biological membranes of prokaryotic and eukaryotic cells. As they belong to the P-ATPase family, Cu-ATPases contain a characteristic catalytic domain with an evolutionarily conserved aspartate residue phosphorylated by ATP to form a phosphoenzyme intermediate, as well as transmembrane helices containing a cation-binding cysteine-proline-cysteine/histidine/serine (CPx) motif for catalytic activation and cation translocation. In addition, most Cu-ATPases possess the N-terminal Cu-binding CxxC motif required for regulation of enzyme activity. In cells, the Cu-ATPases receive copper from soluble chaperones and maintain intracellular copper homeostasis by efflux of copper from the cell or transport of the metal into the intracellular compartments. In addition, copper pumps play an essential role in cuproprotein biosynthesis by the uptake of copper into the cell or delivery of the metal into the chloroplasts and thylakoid lumen or into the lumen of the secretory pathway, where the metal ion is incorporated into copper-dependent enzymes. In the recent years, significant progress has been made toward understanding the function and regulation of Cu-transporting ATPases in archaea, bacteria, yeast, humans, and plants, providing new insights into the specific physiological roles of these essential proteins in various organisms and revealing some conservative regulatory mechanisms of Cu-ATPase activity. In this review, the structural, biochemical, and functional properties of Cu-ATPases from phylogenetically different organisms are summarized and discussed, with particular attention given to the recent insights into the molecular biology of copper pumps in plants.
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Affiliation(s)
- Magdalena Migocka
- Department of Plant Molecular Physiology, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
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15
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Aguirre G, Pilon M. Copper Delivery to Chloroplast Proteins and its Regulation. FRONTIERS IN PLANT SCIENCE 2015; 6:1250. [PMID: 26793223 PMCID: PMC4709454 DOI: 10.3389/fpls.2015.01250] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/21/2015] [Indexed: 05/18/2023]
Abstract
Copper is required for photosynthesis in chloroplasts of plants because it is a cofactor of plastocyanin, an essential electron carrier in the thylakoid lumen. Other chloroplast copper proteins are copper/zinc superoxide dismutase and polyphenol oxidase, but these proteins seem to be dispensable under conditions of low copper supply when transcripts for these proteins undergo microRNA-mediated down regulation. Two ATP-driven copper transporters function in tandem to deliver copper to chloroplast compartments. This review seeks to summarize the mechanisms of copper delivery to chloroplast proteins and its regulation. We also delineate some of the unanswered questions that still remain in this field.
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