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Zhen Z, Dongying F, Yue S, Lipeng Z, Jingjing L, Minying L, Yuanyuan X, Juan H, Shiren S, Yi R, Bin H, Chao M. Translational profile of coding and non-coding RNAs revealed by genome wide profiling of ribosome footprints in grapevine. FRONTIERS IN PLANT SCIENCE 2023; 14:1097846. [PMID: 36844052 PMCID: PMC9944039 DOI: 10.3389/fpls.2023.1097846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Translation is a crucial process during plant growth and morphogenesis. In grapevine (Vitis vinifera L.), many transcripts can be detected by RNA sequencing; however, their translational regulation is still largely unknown, and a great number of translation products have not yet been identified. Here, ribosome footprint sequencing was carried out to reveal the translational profile of RNAs in grapevine. A total of 8291 detected transcripts were divided into four parts, including the coding, untranslated regions (UTR), intron, and intergenic regions, and the 26 nt ribosome-protected fragments (RPFs) showed a 3 nt periodic distribution. Furthermore, the predicted proteins were identified and classified by GO analysis. More importantly, 7 heat shock-binding proteins were found to be involved in molecular chaperone DNA J families participating in abiotic stress responses. These 7 proteins have different expression patterns in grape tissues; one of them was significantly upregulated by heat stress according to bioinformatics research and was identified as DNA JA6. The subcellular localization results showed that VvDNA JA6 and VvHSP70 were both localized on the cell membrane. Therefore, we speculate that DNA JA6 may interact with HSP70. In addition, overexpression of VvDNA JA6 and VvHSP70, reduced the malondialdehyde (MDA) content, improved the antioxidant enzyme activity of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD), increased the content of proline, an osmolyte substance, and affected the expression of the high-temperature marker genes VvHsfB1, VvHsfB2A, VvHsfC and VvHSP100. In summary, our study proved that VvDNA JA6 and the heat shock protein VvHSP70 play a positive role in the response to heat stress. This study lays a foundation for further exploring the balance between gene expression and protein translation in grapevine under heat stress.
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Affiliation(s)
- Zhang Zhen
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Dongying
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Song Yue
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhang Lipeng
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Liu Jingjing
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Liu Minying
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Yuanyuan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - He Juan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Song Shiren
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ren Yi
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Han Bin
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli, Hebei, China
| | - Ma Chao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Gill-Hille M, Wang A, Murcha MW. Presequence translocase-associated motor subunits of the mitochondrial protein import apparatus are dual-targeted to mitochondria and plastids. FRONTIERS IN PLANT SCIENCE 2022; 13:981552. [PMID: 36438081 PMCID: PMC9695410 DOI: 10.3389/fpls.2022.981552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The import and assembly of most of the mitochondrial proteome is regulated by protein translocases located within the mitochondrial membranes. The Presequence Translocase-Associated Motor (PAM) complex powers the translocation of proteins across the inner membrane and consists of Hsp70, the J-domain containing co-chaperones, Pam16 and Pam18, and their associated proteins Tim15 and Mge1. In Arabidopsis, multiple orthologues of Pam16, Pam18, Tim15 and Mge1 have been identified and a mitochondrial localization has been confirmed for most. As the localization of Pam18-1 has yet to be determined and a plastid localization has been observed for homologues of Tim15 and Mge1, we carried out a comprehensive targeting analysis of all PAM complex orthologues using multiple in vitro and in vivo methods. We found that, Pam16 was exclusively targeted to the mitochondria, but Pam18 orthologues could be targeted to both the mitochondria and plastids, as observed for the PAM complex interacting partner proteins Tim15 and Mge1.
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Affiliation(s)
- Mabel Gill-Hille
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
| | - Andre Wang
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
| | - Monika W. Murcha
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia
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Tamadaddi C, Verma AK, Zambare V, Vairagkar A, Diwan D, Sahi C. J-like protein family of Arabidopsis thaliana: the enigmatic cousins of J-domain proteins. PLANT CELL REPORTS 2022; 41:1343-1355. [PMID: 35290497 DOI: 10.1007/s00299-022-02857-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
J-like proteins (JLPs) are emerging as ancillaries to the cellular chaperone network. They modulate functions of Hsp70:J-domain protein (JDP) systems in novel ways thereby having key roles in diverse plant processes. J-domain proteins (JDPs) form an obligate co-chaperone partnership with Hsp70s with their highly conserved J-domain to steer protein quality control processes in the cell. The HPD motif between helix II and helix III of the J-domain is crucial for JDP's interaction with Hsp70s. According to the most recent classification, J-like proteins (JLPs) form an extended class of the JDP family possessing a degenerate J-domain with the HPD motif non-conservatively replaced by other amino acid residues and hence are not able to interact with Hsp70s. Considering this most updated and acceptable JLP classification, we identified 21 JLPs in Arabidopsis thaliana that share a structurally conserved J-like domain (JLD), but lack the HPD motif. Analysis of publicly available gene expression data as well as real-time quantitative PCR performed for a few selected JLPs implicated some of these proteins in growth, development and stress response. Here, we summarize the current state of knowledge on plant JLPs and their involvement in vital plant cellular/metabolic processes, including chloroplast division, mitochondrial protein import and flowering. Finally, we propose possible modes of action for these highly elusive proteins and other DnaJ-related proteins (DNAJRs) in regulating the Hsp70 chaperone network.
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Affiliation(s)
- Chetana Tamadaddi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
- Department of Biology, Eberly College of Science, The Pennsylvania State University, University Park, PA, USA
| | - Amit K Verma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Vyankatesh Zambare
- School of Biotechnology and Bioinformatics, D Y Patil Deemed to be University, Navi Mumbai, India
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Avanti Vairagkar
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Danish Diwan
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
- Department of Biology, University of Alabama, Birmingham, AL, USA
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India.
- IISER Bhopal, Room Number 117, AB3, Bhopal Bypass Road, Bhopal, 462066, MP, India.
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Bahr T, Katuri J, Liang T, Bai Y. Mitochondrial chaperones in human health and disease. Free Radic Biol Med 2022; 179:363-374. [PMID: 34780988 PMCID: PMC8893670 DOI: 10.1016/j.freeradbiomed.2021.11.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 02/03/2023]
Abstract
Molecular chaperones are a family of proteins that maintain cellular protein homeostasis through non-covalent peptide folding and quality control mechanisms. The chaperone proteins found within mitochondria play significant protective roles in mitochondrial biogenesis, quality control, and stress response mechanisms. Defective mitochondrial chaperones have been implicated in aging, neurodegeneration, and cancer. In this review, we focus on the two most prominent mitochondrial chaperones: mtHsp60 and mtHsp70. These proteins demonstrate different cellular localization patterns, interact with different targets, and have different functional activities. We discuss the structure and function of these prominent mitochondrial chaperone proteins and give an update on newly discovered regulatory mechanisms and disease implications.
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Affiliation(s)
- Tyler Bahr
- Department of Cell Systems & Anatomy University of Texas Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Joshua Katuri
- Department of Cell Systems & Anatomy University of Texas Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Ting Liang
- Department of Cell Systems & Anatomy University of Texas Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Yidong Bai
- Department of Cell Systems & Anatomy University of Texas Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA.
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Genome-Wide Identification and Characterization of DnaJ Gene Family in Grape (Vitis vinifera L.). HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Grape production in southern China suffers great loss due to various environmental stresses. To understand the mechanism of how the grape plants respond to these stresses is an active area of research in developing cultivation techniques. Plant stress resistance is known to rely on special proteins. Amongst them, DnaJ protein (HSP40) serves as co-chaperones of HSP70, playing crucial roles in various stress response. However, the DnaJ proteins encoded by the DnaJ gene family in Vitis vinifera L. have not been fully described yet. In this study, we identified 78 VvDnaJs in the grape genome that can be classified into three groups—namely, DJA, DJB, and DJC. To reveal the evolutionary and stress response mechanisms for the VvDnaJ gene family, their evolutionary and expression patterns were analyzed using the bioinformatic approach and qRT-PCR. We found that the members in the same group exhibited a similar gene structure and protein domain organization. Gene duplication analysis demonstrated that segmental and tandem duplication may not be the dominant pathway of gene expansion in the VvDnaJ gene family. Codon usage pattern analysis showed that the codon usage pattern of VvDnaJs differs obviously from the monocotyledon counterparts. Tissue-specific analysis revealed that 12 VvDnaJs present a distinct expression profile, implying their distinct roles in various tissues. Cis-acting element analysis showed that almost all VvDnaJs contained the elements responsive to either hormones or stresses. Therefore, the expression levels of VvDnaJs subjected to exogenous hormone applications and stress treatments were determined, and we found that VvDnaJs were sensitive to hormone treatments and shade, salt, and heat stresses, especially VIT_00s0324g00040. The findings of this study could provide comprehensive information for the further investigation on the genetics and protein functions of the DnaJ gene family in grape.
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Waingankar TP, D'Silva P. Multiple variants of the human presequence translocase motor subunit Magmas govern the mitochondrial import. J Biol Chem 2021; 297:101349. [PMID: 34715125 PMCID: PMC8605242 DOI: 10.1016/j.jbc.2021.101349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/16/2021] [Accepted: 10/22/2021] [Indexed: 11/22/2022] Open
Abstract
Mitochondrial protein translocation is an intricately regulated process that requires dedicated translocases at the outer and inner membranes. The presequence translocase complex, translocase of the inner membrane 23, facilitates most of the import of preproteins containing presequences into the mitochondria, and its primary structural organization is highly conserved. As part of the translocase motor, two J-proteins, DnaJC15 and DnaJC19, are recruited to form two independent translocation machineries (translocase A and translocase B, respectively). On the other hand, the J-like protein subunit of translocase of the inner membrane 23, Mitochondria-associated granulocyte-macrophage colony-stimulating factor signaling molecule (Magmas) (orthologous to the yeast subunit Pam16), can regulate human import-motor activity by forming a heterodimer with DnaJC19 and DnaJC15. However, the precise coordinated regulation of two human import motors by a single Magmas protein is poorly understood. Here, we report two additional Magmas variants (Magmas-1 and Magmas-2) constitutively expressed in the mammalian system. Both the Magmas variants are functional orthologs of Pam16 with an evolutionarily conserved J-like domain critical for cell survival. Moreover, the Magmas variants are peripherally associated with the inner membrane as part of the human import motor for translocation. Our results demonstrate that Magmas-1 is predominantly recruited to translocase B, whereas Magmas-2 is majorly associated with translocase A. Strikingly, both the variants exhibit differential J-protein inhibitory activity in modulating import motor, thereby regulating overall translocase function. Based on our findings, we hypothesize that additional Magmas variants are of evolutionary significance in humans to maximize protein import in familial-linked pathological conditions.
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Affiliation(s)
| | - Patrick D'Silva
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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