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Bhattacharya J, Nitnavare RB, Bhatnagar-Mathur P, Reddy PS. Cytoplasmic male sterility-based hybrids: mechanistic insights. PLANTA 2024; 260:100. [PMID: 39302508 DOI: 10.1007/s00425-024-04532-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 09/15/2024] [Indexed: 09/22/2024]
Abstract
MAIN CONCLUSION A comprehensive understanding of the nucleocytoplasmic interactions that occur between genes related to the restoration of fertility and cytoplasmic male sterility (CMS) provides insight into the development of hybrids of important crop species. Modern biotechnological techniques allow this to be achieved in an efficient and quick manner. Heterosis is paramount for increasing the yield and quality of a crop. The development of hybrids for achieving heterosis has been well-studied and proven to be robust and efficient. Cytoplasmic male sterility (CMS) has been explored extensively in the production of hybrids. The underlying mechanisms of CMS include the role of cytotoxic proteins, PCD of tapetal cells, and improper RNA editing of restoration factors. On the other hand, the restoration of fertility is caused by the presence of restorer-of-fertility (Rf) genes or restorer genes, which inhibit the effects of sterility-causing genes. The interaction between mitochondria and the nuclear genome is crucial for several regulatory pathways, as observed in the CMS-Rf system and occurs at the genomic, transcriptional, post-transcriptional, translational, and post-translational levels. These CMS-Rf mechanisms have been validated in several crop systems. This review aims to summarize the nucleo-mitochondrial interaction mechanism of the CMS-Rf system. It also sheds light on biotechnological interventions, such as genetic engineering and genome editing, to achieve CMS-based hybrids.
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Affiliation(s)
- Joorie Bhattacharya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India
- Department of Genetics, Osmania University, Hyderabad, Telangana, 500007, India
| | - Rahul B Nitnavare
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, Nottingham, LE12 5RD, UK
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India.
- Plant Breeding & Genetics Laboratory of United Nation, International Atomic Energy Agency, 1400, Vienna, Austria.
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502324, India.
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Dhillon HK, Sharma M, Dhatt AS, Meena OP, Khosa J, Sidhu MK. Insights into cellular crosstalk regulating cytoplasmic male sterility and fertility restoration. Mol Biol Rep 2024; 51:910. [PMID: 39150575 DOI: 10.1007/s11033-024-09855-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
Cytoplasmic male sterility has been a popular genetic tool in development of hybrids. The molecular mechanism behind maternal sterility varies from crop to crop. An understanding of underlying mechanism can help in development of new functional CMS gene in crops which lack effective and stable CMS systems. In crops where seed or fruit is the commercial product, fertility must be recovered in F1 hybrids so that higher yield gains can be realized. This necessitates the presence of fertility restorer gene (Rf) in nucleus of male parent to overcome the effect of sterile cytoplasm. Fertility restoring genes have been identified in crops like wheat, maize, sunflower, rice, pepper, sugar beet, pigeon pea etc. But in crops like eggplant, bell pepper, barley etc. unstable fertility restorers hamper the use of Cytoplasmic genic male sterility (CGMS) system. Stability of CGMS system is influenced by environment, genetic background or interaction of these factors. This review thus aims to understand the genetic mechanisms controlling mitochondrial-nuclear interactions required to design strong and stable restorers without any pleiotropic effects in F1 hybrids.
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Affiliation(s)
- Harnoor Kaur Dhillon
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004, India
| | - Madhu Sharma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004, India.
| | - A S Dhatt
- Director of Research, Punjab Agricultural University, Ludhiana, 141004, India
| | - O P Meena
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004, India
| | - Jiffinvir Khosa
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004, India
| | - M K Sidhu
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004, India
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Nalini Chandran AK, Paul P, Dhatt BK, Sandhu J, Irvin L, Oguro S, Shi Y, Zhang C, Walia H. Phenotypic and transcriptomic responses of diverse rice accessions to transient heat stress during early grain development. FRONTIERS IN PLANT SCIENCE 2024; 15:1429697. [PMID: 39211842 PMCID: PMC11358087 DOI: 10.3389/fpls.2024.1429697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024]
Abstract
Heat stress (HS) occurring during the grain-filling period has a detrimental effect on grain yield and quality in rice (Oryza sativa). The development of heat-resilient cultivars could partly solve this issue if tolerant alleles can be identified and incorporated into the germplasm. In this study, we posit that some of the phenotypic variations for heat resilience during grain development could be due to variations in gene expression among accessions. To test this, we characterized the HS response of 10 diverse rice accessions from three major sub-populations using physiological and transcriptome analyses. At a single-grain level, grain width and grain thickness emerged as the most heat-sensitive traits. During a transient HS, IND-3 was categorized as highly sensitive, while five accessions exhibited moderate heat sensitivity, and four accessions were tolerant. Only a core set of 29.4% of the differentially expressed genes was common to the three rice sub-populations. Heat-tolerant accession TEJ-5 uniquely triggered an unfolded protein response (UPR) under HS, as evident from the induction of OsbZIP50 and downstream UPR genes. OsbZIP58, a gene that positively regulates grain filling, was more highly induced by HS in IND-2 despite its moderate heat sensitivity. Collectively, our analysis suggests that both unique gene expression responses and variation in the level of responses for a given pathway distinguish diverse accessions. Only some of these responses are associated with single-grain phenotypes in a manner consistent with the known roles of these genes and pathways.
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Affiliation(s)
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Larissa Irvin
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Shohei Oguro
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Yu Shi
- Department of Biological Science, University of Nebraska, Lincoln, NE, United States
| | - Chi Zhang
- Department of Biological Science, University of Nebraska, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, United States
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Li Y, Liu Y, Ran G, Yu Y, Zhou Y, Zhu Y, Du Y, Pi L. The pentatricopeptide repeat protein DG1 promotes the transition to bilateral symmetry during Arabidopsis embryogenesis through GUN1-mediated plastid signals. THE NEW PHYTOLOGIST 2024; 244:542-557. [PMID: 39140987 DOI: 10.1111/nph.20056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024]
Abstract
During Arabidopsis embryogenesis, the transition of the embryo's symmetry from radial to bilateral between the globular and heart stage is a crucial event, involving the formation of cotyledon primordia and concurrently the establishment of a shoot apical meristem (SAM). However, a coherent framework of how this transition is achieved remains to be elucidated. In this study, we investigated the function of DELAYED GREENING 1 (DG1) in Arabidopsis embryogenesis using a newly identified dg1-3 mutant. The absence of chloroplast-localized DG1 in the mutants led to embryos being arrested at the globular or heart stage, accompanied by an expansion of WUSCHEL (WUS) and SHOOT MERISTEMLESS (STM) expression. This finding pinpoints the essential role of DG1 in regulating the transition to bilateral symmetry. Furthermore, we showed that this regulation of DG1 may not depend on its role in plastid RNA editing. Nevertheless, we demonstrated that the DG1 function in establishing bilateral symmetry is genetically mediated by GENOMES UNCOUPLED 1 (GUN1), which represses the transition process in dg1-3 embryos. Collectively, our results reveal that DG1 functionally antagonizes GUN1 to promote the transition of the Arabidopsis embryo's symmetry from radial to bilateral and highlight the role of plastid signals in regulating pattern formation during plant embryogenesis.
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Affiliation(s)
- Yajie Li
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Yiqiong Liu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Guiping Ran
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Yue Yu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Yifan Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuxian Zhu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yujuan Du
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Limin Pi
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
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Jaqueth JS, Li B, Vollbrecht E. Pentatricopeptide repeat 153 (PPR153) restores maize C-type cytoplasmic male sterility in conjunction with RF4. PLoS One 2024; 19:e0303436. [PMID: 38985786 PMCID: PMC11236208 DOI: 10.1371/journal.pone.0303436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/24/2024] [Indexed: 07/12/2024] Open
Abstract
Maize (Zea mays L.) C-type cytoplasmic male sterility (CMS-C) is a highly used CMS system for maize commercial hybrid seed production. Rf4 is the major dominant restorer gene for CMS-C. Inbreds were recently discovered which contain the restoring Rf4 allele yet are unable to restore fertility due to the lack of an additional gene required for Rf4's restoration. To find this additional gene, QTL mapping and positional cloning were performed using an inbred that contained Rf4 but was incapable of restoring CMS-C. The QTL was mapped to a 738-kb interval on chromosome 2, which contains a Pentatricopeptide Repeat (PPR) gene cluster. Allele content comparisons of the inbreds identified three potential candidate genes responsible for fertility restoration in CMS-C. Complementation via transformation of these three candidate genes showed that PPR153 (Zm00001eb114660) is required for Rf4 to restore fertility to tassels. The PPR153 sequence is present in B73 genome, but it is not capable of restoring CMS-C without Rf4. Analysis using NAM lines revealed that Rf4 requires the presence of PPR153 to restore CMS-C in diverse germplasms. This research uncovers a major CMS-C genetic restoration pathway and can be used for identifying inbreds suitable for maize hybrid production with CMS-C cytoplasm.
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Affiliation(s)
| | - Bailin Li
- Corteva Agriscience™, Johnston, IA, United States of America
| | - Erik Vollbrecht
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States of America
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6
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Shi C, Xie Y, Guan D, Qin G. Transcriptomic Analysis Reveals Adaptive Evolution and Conservation Implications for the Endangered Magnolia lotungensis. Genes (Basel) 2024; 15:787. [PMID: 38927723 PMCID: PMC11203017 DOI: 10.3390/genes15060787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Magnolia lotungensis is an extremely endangered endemic tree in China. To elucidate the genetic basis of M. lotungensis, we performed a comprehensive transcriptome analysis using a sample integrating the plant's bark, leaves, and flowers. De novo transcriptome assembly yielded 177,046 transcripts and 42,518 coding sequences. Notably, we identified 796 species-specific genes enriched in organelle gene regulation and defense responses. A codon usage bias analysis revealed that mutation bias appears to be the primary driver of selection in shaping the species' genetic architecture. An evolutionary analysis based on dN/dS values of paralogous and orthologous gene pairs indicated a predominance of purifying selection, suggesting strong evolutionary constraints on most genes. A comparative transcriptomic analysis with Magnolia sinica identified approximately 1000 ultra-conserved genes, enriched in essential cellular processes such as transcriptional regulation, protein synthesis, and genome stability. Interestingly, only a limited number of 511 rapidly evolving genes under positive selection were detected compared to M. sinica and Magnolia kuangsiensis. These genes were enriched in metabolic processes associated with adaptation to specific environments, potentially limiting the species' ability to expand its range. Our findings contribute to understanding the genetic architecture of M. lotungensis and suggest that an insufficient number of adaptive genes contribute to its endangered status.
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Affiliation(s)
- Chenyu Shi
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, Hechi University, Hechi 546300, China; (C.S.); (Y.X.)
- Guangxi Collaborative Innovation Center of Modern Sericulture and Silk, Hechi University, Hechi 546300, China
| | - Yanjun Xie
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, Hechi University, Hechi 546300, China; (C.S.); (Y.X.)
- Guangxi Collaborative Innovation Center of Modern Sericulture and Silk, Hechi University, Hechi 546300, China
| | - Delong Guan
- Guangxi Collaborative Innovation Center of Modern Sericulture and Silk, Hechi University, Hechi 546300, China
- School of Chemistry and Bioengineering, Hechi University, Hechi 546300, China
| | - Guole Qin
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, Hechi University, Hechi 546300, China; (C.S.); (Y.X.)
- Guangxi Collaborative Innovation Center of Modern Sericulture and Silk, Hechi University, Hechi 546300, China
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7
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Liu Z, Jin T, Qin B, Li R, Shang J, Huang Y. The deletion of ppr2 interferes iron sensing and leads to oxidative stress response in Schizosaccharomyces pombe. Mitochondrion 2024; 76:101875. [PMID: 38499131 DOI: 10.1016/j.mito.2024.101875] [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: 11/07/2023] [Revised: 03/09/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
Pentatricopeptide repeat proteins are involved in mitochondrial both transcriptional and posttranscriptional regulation. Schizosaccharomyces pombe Ppr2 is a general mitochondrial translation factor that plays a critical role in the synthesis of all mitochondrial DNA-encoded oxidative phosphorylation subunits, which are essential for mitochondrial respiration. Our previous analysis showed that ppr2 deletion resulted in increased expression of iron uptake genes and caused ferroptosis-like cell death in S. pombe. In the present work, we showed that deletion of ppr2 reduced viability on glycerol- and galactose-containing media.Php4 is a transcription repressor that regulates iron homeostasis in fission yeast. We found that in the ppr2 deletion strain, Php4 was constitutively active and accumulated in the nucleus in the stationary phase. We also found that deletion of ppr2 decreased the ferroptosis-related protein Gpx1 in the mitochondria. Overexpression of Gpx1 improves the viability of Δppr2 cells. We showed that the deletion of ppr2 increased the production of ROS, downregulated heme synthesis and iron-sulfur cluster proteins, and induced stress proteins. Finally, we observed the nuclear accumulation of Pap1-GFP and Sty1-GFP, suggesting that Sty1 and Pap1 in response to cellular stress in the ppr2 deletion strain. These results suggest thatppr2 deletion may cause mitochondrial dysfunction, which is likely to lead to iron-sensing defect and iron starvation response, resulting in perturbation of iron homeostasis and increased hydroxyl radical production. The increased hydroxyl radical production triggers cellular responses in theppr2 deletion strain.
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Affiliation(s)
- Zecheng Liu
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; School of Public Health, Hubei University of Medicine, Shiyan 442000, China
| | - Ting Jin
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Bingxin Qin
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Rongrong Li
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jinjie Shang
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Xu M, Zhang X, Cao J, Liu J, He Y, Guan Q, Tian X, Tang J, Li X, Ren D, Bu Q, Wang Z. OsPGL3A encodes a DYW-type pentatricopeptide repeat protein involved in chloroplast RNA processing and regulated chloroplast development. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:29. [PMID: 38549701 PMCID: PMC10965880 DOI: 10.1007/s11032-024-01468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/19/2024] [Indexed: 04/24/2024]
Abstract
The chloroplast serves as the primary site of photosynthesis, and its development plays a crucial role in regulating plant growth and morphogenesis. The Pentatricopeptide Repeat Sequence (PPR) proteins constitute a vast protein family that function in the post-transcriptional modification of RNA within plant organelles. In this study, we characterized mutant of rice with pale green leaves (pgl3a). The chlorophyll content of pgl3a at the seedling stage was significantly reduced compared to the wild type (WT). Transmission electron microscopy (TEM) and quantitative PCR analysis revealed that pgl3a exhibited aberrant chloroplast development compared to the wild type (WT), accompanied by significant alterations in gene expression levels associated with chloroplast development and photosynthesis. The Mutmap analysis revealed that a single base deletionin the coding region of Os03g0136700 in pgl3a. By employing CRISPR/Cas9 mediated gene editing, two homozygous cr-pgl3a mutants were generated and exhibited a similar phenotype to pgl3a, thereby confirming that Os03g0136700 was responsible for pgl3a. Consequently, it was designated as OsPGL3A. OsPGL3A belongs to the DYW-type PPR protein family and is localized in chloroplasts. Furthermore, we demonstrated that the RNA editing efficiency of rps8-182 and rpoC2-4106, and the splicing efficiency of ycf3-1 were significantly decreased in pgl3a mutants compared to WT. Collectively, these results indicate that OsPGL3A plays a crucial role in chloroplast development by regulating the editing and splicing of chloroplast genes in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01468-7.
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Affiliation(s)
- Min Xu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xinying Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
| | - Jinzhe Cao
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Jiali Liu
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Yiyuan He
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qingjie Guan
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Jiaqi Tang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Xiufeng Li
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Deyong Ren
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Zhenyu Wang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
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Wang Y, Jin T, Huang Y. Sls1 and Mtf2 mediate the assembly of the Mrh5C complex required for activation of cox1 mRNA translation. J Biol Chem 2024; 300:107176. [PMID: 38499152 PMCID: PMC11015131 DOI: 10.1016/j.jbc.2024.107176] [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: 01/27/2024] [Revised: 03/06/2024] [Accepted: 03/09/2024] [Indexed: 03/20/2024] Open
Abstract
Mitochondrial translation depends on mRNA-specific activators. In Schizosaccharomyces pombe, DEAD-box protein Mrh5, pentatricopeptide repeat (PPR) protein Ppr4, Mtf2, and Sls1 form a stable complex (designated Mrh5C) required for translation of mitochondrial DNA (mtDNA)-encoded cox1 mRNA, the largest subunit of the cytochrome c oxidase complex. However, how Mrh5C is formed and what role Mrh5C plays in cox1 mRNA translation have not been reported. To address these questions, we investigated the role of individual Mrh5C subunits in the assembly and function of Mrh5C. Our results revealed that Mtf2 and Sls1 form a subcomplex that serves as a scaffold to bring Mrh5 and Ppr4 together. Mrh5C binds to the small subunit of the mitoribosome (mtSSU), but each subunit could not bind to the mtSSU independently. Importantly, Mrh5C is required for the association of cox1 mRNA with the mtSSU. Finally, we investigated the importance of the signature DEAD-box in Mrh5. We found that the DEAD-box of Mrh5 is required for the association of Mrh5C and cox1 mRNA with the mtSSU. Unexpectedly, this motif is also required for the interaction of Mrh5 with other Mrh5C subunits. Altogether, our results suggest that Mrh5 and Ppr4 cooperate in activating the translation of cox1 mRNA. Our results also suggest that Mrh5C activates the translation of cox1 mRNA by promoting the recruitment of cox1 mRNA to the mtSSU.
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Affiliation(s)
- Yirong Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Nanjing Normal University, Nanjing, China
| | - Ting Jin
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Nanjing Normal University, Nanjing, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Nanjing Normal University, Nanjing, China.
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10
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Laube E, Schiller J, Zickermann V, Vonck J. Using cryo-EM to understand the assembly pathway of respiratory complex I. Acta Crystallogr D Struct Biol 2024; 80:159-173. [PMID: 38372588 PMCID: PMC10910544 DOI: 10.1107/s205979832400086x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024] Open
Abstract
Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the first component of the mitochondrial respiratory chain. In recent years, high-resolution cryo-EM studies of complex I from various species have greatly enhanced the understanding of the structure and function of this important membrane-protein complex. Less well studied is the structural basis of complex I biogenesis. The assembly of this complex of more than 40 subunits, encoded by nuclear or mitochondrial DNA, is an intricate process that requires at least 20 different assembly factors in humans. These are proteins that are transiently associated with building blocks of the complex and are involved in the assembly process, but are not part of mature complex I. Although the assembly pathways have been studied extensively, there is limited information on the structure and molecular function of the assembly factors. Here, the insights that have been gained into the assembly process using cryo-EM are reviewed.
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Affiliation(s)
- Eike Laube
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Jonathan Schiller
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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11
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Sridhara S. Multiple structural flavors of RNase P in precursor tRNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1835. [PMID: 38479802 DOI: 10.1002/wrna.1835] [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: 08/28/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 06/06/2024]
Abstract
The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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12
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Qu L, Liu SJ, Zhang L, Liu JF, Zhou YJ, Zeng PH, Jing QC, Yin WJ. The Role of m6A-Mediated DNA Damage Repair in Tumor Development and Chemoradiotherapy Resistance. Cancer Control 2024; 31:10732748241247170. [PMID: 38662732 PMCID: PMC11047261 DOI: 10.1177/10732748241247170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Among the post-transcriptional modifications, m6A RNA methylation has gained significant research interest due to its critical role in regulating transcriptional expression. This modification affects RNA metabolism in several ways, including processing, nuclear export, translation, and decay, making it one of the most abundant transcriptional modifications and a crucial regulator of gene expression. The dysregulation of m6A RNA methylation-related proteins in many tumors has been shown to lead to the upregulation of oncoprotein expression, tumor initiation, proliferation, cancer cell progression, and metastasis.Although the impact of m6A RNA methylation on cancer cell growth and proliferation has been extensively studied, its role in DNA repair processes, which are crucial to the pathogenesis of various diseases, including cancer, remains unclear. However, recent studies have shown accumulating evidence that m6A RNA methylation significantly affects DNA repair processes and may play a role in cancer drug resistance. Therefore, a comprehensive literature review is necessary to explore the potential biological role of m6A-modified DNA repair processes in human cancer and cancer drug resistance.In conclusion, m6A RNA methylation is a crucial regulator of gene expression and a potential player in cancer development and drug resistance. Its dysregulation in many tumors leads to the upregulation of oncoprotein expression and tumor progression. Furthermore, the impact of m6A RNA methylation on DNA repair processes, although unclear, may play a crucial role in cancer drug resistance. Therefore, further studies are warranted to better understand the potential biological role of m6A-modified DNA repair processes in human cancer and cancer drug resistance.
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Affiliation(s)
- Li Qu
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hunan Province Clinical Research Center for Accurate Diagnosis and Treatment of High-incidence Sexually Transmitted Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hunan, China
| | - Si jian Liu
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hunan Province Clinical Research Center for Accurate Diagnosis and Treatment of High-incidence Sexually Transmitted Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hunan, China
| | - Ling Zhang
- Department of Clinical Laboratory Medicine, The Affiliated Changsha Central Hospital, Hengyang Medical school, University of South China, Changsha, China
| | - Jia Feng Liu
- Department of Clinical Laboratory Medicine, The Affiliated Changsha Central Hospital, Hengyang Medical school, University of South China, Changsha, China
| | - Ying Jie Zhou
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hunan Province Clinical Research Center for Accurate Diagnosis and Treatment of High-incidence Sexually Transmitted Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hunan, China
| | - Peng Hui Zeng
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hunan Province Clinical Research Center for Accurate Diagnosis and Treatment of High-incidence Sexually Transmitted Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hunan, China
| | - Qian Cheng Jing
- Department of Otolaryngology Head and Neck Surgery, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
- Institute of Otolaryngology Head and Neck Surgery, Hengyang Medical School, University of South China, Changsha, China
| | - Wen Jun Yin
- Department of Clinical Laboratory Medicine, The Affiliated Changsha Central Hospital, Hengyang Medical school, University of South China, Changsha, China
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Baleva MV, Piunova U, Chicherin I, Vasilev R, Levitskii S, Kamenski P. Mitochondrial Protein SLIRP Affects Biosynthesis of Cytochrome c Oxidase Subunits in HEK293T Cells. Int J Mol Sci 2023; 25:93. [PMID: 38203264 PMCID: PMC10779364 DOI: 10.3390/ijms25010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Mitochondria carry out various vital roles in eukaryotic cells, including ATP energy synthesis, the regulation of apoptosis, Fe-S cluster formation, and the metabolism of fatty acids, amino acids, and nucleotides. Throughout evolution, mitochondria lost most of their ancestor's genome but kept the replication, transcription, and translation machinery. Protein biosynthesis in mitochondria is specialized in the production of highly hydrophobic proteins encoded by mitochondria. These proteins are components of oxidative phosphorylation chain complexes. The coordination of protein synthesis must be precise to ensure the correct assembly of nuclear-encoded subunits for these complexes. However, the regulatory mechanisms of mitochondrial translation in human cells are not yet fully understood. In this study, we examined the contribution of the SLIRP protein in regulating protein biosynthesis in mitochondria. Using a click-chemistry approach, we discovered that deletion of the SLIRP gene disturbs mitochondrial translation, leading to the dysfunction of complexes I and IV, but it has no significant effect on complexes III and V. We have shown that this protein interacts only with the small subunit of the mitochondrial ribosome, which may indicate its involvement in the regulation of the mitochondrial translation initiation stage.
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Affiliation(s)
| | | | | | | | - Sergey Levitskii
- Faculty of Biology, Lomonosov Moscow State University, 1/12 Leninskie Gory, 119234 Moscow, Russia; (M.V.B.); (U.P.); (I.C.); (R.V.)
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, 1/12 Leninskie Gory, 119234 Moscow, Russia; (M.V.B.); (U.P.); (I.C.); (R.V.)
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14
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Wang X, Choi YM, Jeon YA, Yi J, Shin MJ, Desta KT, Yoon H. Analysis of Genetic Diversity in Adzuki Beans ( Vigna angularis): Insights into Environmental Adaptation and Early Breeding Strategies for Yield Improvement. PLANTS (BASEL, SWITZERLAND) 2023; 12:4154. [PMID: 38140482 PMCID: PMC10747723 DOI: 10.3390/plants12244154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
Adzuki beans are widely cultivated in East Asia and are one of the earliest domesticated crops. In order to gain a deeper understanding of the genetic diversity and domestication history of adzuki beans, we conducted Genotyping by Sequencing (GBS) analysis on 366 landraces originating from Korea, China, and Japan, resulting in 6586 single-nucleotide polymorphisms (SNPs). Population structure analysis divided these 366 landraces into three subpopulations. These three subpopulations exhibited distinctive distributions, suggesting that they underwent extended domestication processes in their respective regions of origin. Phenotypic variance analysis of the three subpopulations indicated that the Korean-domesticated subpopulation exhibited significantly higher 100-seed weights, the Japanese-domesticated subpopulation showed significantly higher numbers of grains per pod, and the Chinese-domesticated subpopulation displayed significantly higher numbers of pods per plant. We speculate that these differences in yield-related traits may be attributed to varying emphases placed by early breeders in these regions on the selection of traits related to yield. A large number of genes related to biotic/abiotic stress resistance and defense were found in most quantitative trait locus (QTL) for yield-related traits using genome-wide association studies (GWAS). Genomic sliding window analysis of Tajima's D and a genetic differentiation coefficient (Fst) revealed distinct domestication selection signatures and genotype variations on these QTLs within each subpopulation. These findings indicate that each subpopulation would have been subjected to varied biotic/abiotic stress events in different origins, of which these stress events have caused balancing selection differences in the QTL of each subpopulation. In these balancing selections, plants tend to select genotypes with strong resistance under biotic/abiotic stress, but reduce the frequency of high-yield genotypes to varying degrees. These biotic/abiotic stressors impact crop yield and may even lead to selection purging, resulting in the loss of several high-yielding genotypes among landraces. However, this also fuels the flow of crop germplasms. Overall, balancing selection appears to have a more significant impact on the three yield-related traits compared to breeder-driven domestication selection. These findings are crucial for understanding the impact of domestication selection history on landraces and yield-related traits, aiding in the improvement of adzuki bean varieties.
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Affiliation(s)
| | | | | | | | | | | | - Hyemyeong Yoon
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (X.W.); (Y.-M.C.); (Y.-a.J.); (J.Y.); (M.-J.S.)
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15
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Feng LY, Lin PF, Xu RJ, Kang HQ, Gao LZ. Comparative Genomic Analysis of Asian Cultivated Rice and Its Wild Progenitor ( Oryza rufipogon) Has Revealed Evolutionary Innovation of the Pentatricopeptide Repeat Gene Family through Gene Duplication. Int J Mol Sci 2023; 24:16313. [PMID: 38003501 PMCID: PMC10671101 DOI: 10.3390/ijms242216313] [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: 09/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in land plants. However, current knowledge about the evolution of the PPR gene family remains largely limited. In this study, we performed a comparative genomic analysis of the PPR gene family in O. sativa and its wild progenitor, O. rufipogon, and outlined a comprehensive landscape of gene duplications. Our findings suggest that the majority of PPR genes originated from dispersed duplications. Although segmental duplications have only expanded approximately 11.30% and 13.57% of the PPR gene families in the O. sativa and O. rufipogon genomes, we interestingly obtained evidence that segmental duplication promotes the structural diversity of PPR genes through incomplete gene duplications. In the O. sativa and O. rufipogon genomes, 10 (~33.33%) and 22 pairs of gene duplications (~45.83%) had non-PPR paralogous genes through incomplete gene duplication. Segmental duplications leading to incomplete gene duplications might result in the acquisition of domains, thus promoting functional innovation and structural diversification of PPR genes. This study offers a unique perspective on the evolution of PPR gene structures and underscores the potential role of segmental duplications in PPR gene structural diversity.
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Affiliation(s)
- Li-Ying Feng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; (L.-Y.F.); (P.-F.L.)
| | - Pei-Fan Lin
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; (L.-Y.F.); (P.-F.L.)
| | - Rong-Jing Xu
- Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China; (R.-J.X.); (H.-Q.K.)
| | - Hai-Qi Kang
- Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China; (R.-J.X.); (H.-Q.K.)
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; (L.-Y.F.); (P.-F.L.)
- Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China; (R.-J.X.); (H.-Q.K.)
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16
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Zu X, Luo L, Wang Z, Gong J, Yang C, Wang Y, Xu C, Qiao X, Deng X, Song X, Chen C, Tan BC, Cao X. A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice. Nat Commun 2023; 14:6789. [PMID: 37880207 PMCID: PMC10600133 DOI: 10.1038/s41467-023-42269-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
Cold stress affects rice growth and productivity. Defects in the plastid-localized pseudouridine synthase OsPUS1 affect chloroplast ribosome biogenesis, leading to low-temperature albino seedlings and accumulation of reactive oxygen species (ROS). Here, we report an ospus1-1 suppressor, sop10. SOP10 encodes a mitochondria-localized pentatricopeptide repeat protein. Mutations in SOP10 impair intron splicing of the nad4 and nad5 transcripts and decrease RNA editing efficiency of the nad2, nad6, and rps4 transcripts, resulting in deficiencies in mitochondrial complex I, thus decrease ROS generation and rescuing the albino phenotype. Overexpression of different compartment-localized superoxide dismutases (SOD) genes in ospus1-1 reverses the ROS over-accumulation and albino phenotypes to various degrees, with Mn-SOD reversing the best. Mutation of SOP10 in indica rice varieties enhances cold tolerance with lower ROS levels. We find that the mitochondrial superoxide plays a key role in rice cold responses, and identify a mitochondrial superoxide modulating factor, informing efforts to improve rice cold tolerance.
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Affiliation(s)
- Xiaofeng Zu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lilan Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Gong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Chao Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chunhui Xu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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17
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Huynh SD, Melonek J, Colas des Francs-Small C, Bond CS, Small I. A unique C-terminal domain contributes to the molecular function of Restorer-of-fertility proteins in plant mitochondria. THE NEW PHYTOLOGIST 2023; 240:830-845. [PMID: 37551058 DOI: 10.1111/nph.19166] [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: 05/09/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD (Restorer-of-fertility C-terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2-nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants.
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Affiliation(s)
- Sang Dang Huynh
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Joanna Melonek
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Catherine Colas des Francs-Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ian Small
- School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
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18
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Liu D, Li ZA, Li Y, Molloy DP, Huang C. The DYW domain of RARE1 plays an indispensable role in regulating accD-C794 RNA editing in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 334:111751. [PMID: 37263527 DOI: 10.1016/j.plantsci.2023.111751] [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: 11/29/2022] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023]
Abstract
The Arabidopsis pentatricopeptide repeat (PPR) proteins, required for accD RNA editing 1 (RARE1) and early chloroplast biogenesis 2 (AtECB2), each contain a DYW domain deemed essential for cytosine deamination at the accD-C794 RNA editing site in chloroplasts. Complementation assays using the rare1 mutant investigate the correlation between these PPRs and their respective DYW domain functions in RNA editing of accD-C794. The results demonstrate that the coding sequence of AtECB2 cannot replace that of RARE1. Moreover, rare1 mutants complemented with DYW-deleted RARE1 failed to recover the RNA editing of accD-C794 even in the presence of the highly similar DYW domain of the AtECB2 protein. These findings indicate that RARE1 and AtECB2 possess divergent roles in RNA editing, with specificity for accD-C794 directly attributable to DYW domain within RARE1. Structural modeling data suggest this functioning pertains to a local α-helical motif that residues slightly N-terminal to the consensus glutamate and CXXCH motif in the DYW domain for cytidine deamination during C-to-U editing by RARE1 that is absent within AtECB2.
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Affiliation(s)
- Dan Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Zi-Ang Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Yi Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - David P Molloy
- Department of Biochemistry and Molecular Biology, Basic Medical College, Chongqing Medical University, Chongqing 400016, China; Center for Molecular Medicine and Cancer Research, Basic Medical College, Chongqing Medical University, Chongqing 400016, China.
| | - Chao Huang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
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19
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Tran HC, Schmitt V, Lama S, Wang C, Launay-Avon A, Bernfur K, Sultan K, Khan K, Brunaud V, Liehrmann A, Castandet B, Levander F, Rasmusson AG, Mireau H, Delannoy E, Van Aken O. An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants. Science 2023; 381:eadg0995. [PMID: 37651534 DOI: 10.1126/science.adg0995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that "mitochondrial translation factors" mTRAN1 and mTRAN2 are land plant-specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)-like RNA binding proteins of the mitoribosomal "small" subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5' regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria.
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Affiliation(s)
| | | | - Sbatie Lama
- Department of Biology, Lund University, Lund, Sweden
| | - Chuande Wang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Katja Bernfur
- Department of Chemistry, Lund University, Lund, Sweden
| | - Kristin Sultan
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Kasim Khan
- Department of Biology, Lund University, Lund, Sweden
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Arnaud Liehrmann
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Université Paris-Saclay, CNRS, Université d'Évry, Laboratoire de Mathématiques et Modélisation d'Évry, 91037 Évry-Courcouronnes, France
| | - Benoît Castandet
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | | | - Hakim Mireau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
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20
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Cabral AL, Ruan Y, Cuthbert RD, Li L, Zhang W, Boyle K, Berraies S, Henriquez MA, Burt A, Kumar S, Fobert P, Piche I, Bokore FE, Meyer B, Sangha J, Knox RE. Multi-locus genome-wide association study of fusarium head blight in relation to days to anthesis and plant height in a spring wheat association panel. FRONTIERS IN PLANT SCIENCE 2023; 14:1166282. [PMID: 37457352 PMCID: PMC10346453 DOI: 10.3389/fpls.2023.1166282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/03/2023] [Indexed: 07/18/2023]
Abstract
Fusarium head blight (FHB) is a highly destructive fungal disease of wheat to which host resistance is quantitatively inherited and largely influenced by the environment. Resistance to FHB has been associated with taller height and later maturity; however, a further understanding of these relationships is needed. An association mapping panel (AMP) of 192 predominantly Canadian spring wheat was genotyped with the wheat 90K single-nucleotide polymorphism (SNP) array. The AMP was assessed for FHB incidence (INC), severity (SEV) and index (IND), days to anthesis (DTA), and plant height (PLHT) between 2015 and 2017 at three Canadian FHB-inoculated nurseries. Seven multi-environment trial (MET) datasets were deployed in a genome-wide association study (GWAS) using a single-locus mixed linear model (MLM) and a multi-locus random SNP-effect mixed linear model (mrMLM). MLM detected four quantitative trait nucleotides (QTNs) for INC on chromosomes 2D and 3D and for SEV and IND on chromosome 3B. Further, mrMLM identified 291 QTNs: 50 (INC), 72 (SEV), 90 (IND), 41 (DTA), and 38 (PLHT). At two or more environments, 17 QTNs for FHB, DTA, and PLHT were detected. Of these 17, 12 QTNs were pleiotropic for FHB traits, DTA, and PLHT on chromosomes 1A, 1D, 2D, 3B, 5A, 6B, 7A, and 7B; two QTNs for DTA were detected on chromosomes 1B and 7A; and three PLHT QTNs were located on chromosomes 4B and 6B. The 1B DTA QTN and the three pleiotropic QTNs on chromosomes 1A, 3B, and 6B are potentially identical to corresponding quantitative trait loci (QTLs) in durum wheat. Further, the 3B pleiotropic QTN for FHB INC, SEV, and IND co-locates with TraesCS3B02G024900 within the Fhb1 region on chromosome 3B and is ~3 Mb from a cloned Fhb1 candidate gene TaHRC. While the PLHT QTN on chromosome 6B is putatively novel, the 1B DTA QTN co-locates with a disease resistance protein located ~10 Mb from a Flowering Locus T1-like gene TaFT3-B1, and the 7A DTA QTN is ~5 Mb away from a maturity QTL QMat.dms-7A.3 of another study. GWAS and QTN candidate genes enabled the characterization of FHB resistance in relation to DTA and PLHT. This approach should eventually generate additional and reliable trait-specific markers for breeding selection, in addition to providing useful information for FHB trait discovery.
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Affiliation(s)
- Adrian L. Cabral
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Richard D. Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Lin Li
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Wentao Zhang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada
| | - Kerry Boyle
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada
| | - Samia Berraies
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Andrew Burt
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Pierre Fobert
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Isabelle Piche
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Firdissa E. Bokore
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Brad Meyer
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Jatinder Sangha
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Ron E. Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
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Hawliczek A, Borzęcka E, Tofil K, Alachiotis N, Bolibok L, Gawroński P, Siekmann D, Hackauf B, Dušinský R, Švec M, Bolibok-Brągoszewska H. Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement. BMC PLANT BIOLOGY 2023; 23:323. [PMID: 37328739 PMCID: PMC10273710 DOI: 10.1186/s12870-023-04337-1] [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: 01/22/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection. RESULTS Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production. CONCLUSIONS Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.
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Affiliation(s)
- Anna Hawliczek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | - Nikolaos Alachiotis
- Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, Enschede, The Netherlands
| | - Leszek Bolibok
- Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland
| | | | | | - Roman Dušinský
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Miroslav Švec
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland.
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22
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Lin R, Chen R, Ye L, Huang Z, Lin X, Chen T. The Role of RNA Methylation Modification Related Genes in Prognosis and Immunotherapy of Colorectal Cancer. Int J Gen Med 2023; 16:2133-2147. [PMID: 37284034 PMCID: PMC10239628 DOI: 10.2147/ijgm.s405419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023] Open
Abstract
Background Researches showed RNA methylation genes can affect the prognosis of tumors. Thus, the study aimed to comprehensively analyze the effects of RNA methylation regulatory genes in prognosis and treatment of colorectal cancer (CRC). Methods Prognostic signature associated with CRCs were constructed by differential expression analysis, Cox and Least Absolute Shrinkage and Selection Operator (LASSO) analyses. Receiver operating characteristic (ROC) and Kaplan-Meier survival analyses were used to validate the reliability of the developed model. Gene Ontology (GO), Gene set variation analysis (GSVA), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for functional annotation. Finally, normal and cancerous tissue were collected to validate gene by quantitative real-time PCR (qRT-PCR). Results A prognostic risk model based on leucine rich pentatricopeptide repeat containing (LRPPRC) and ubiquitin-like with PHD and ring finger domains 2 (UHRF2) was constructed and relevant to the overall survival (OS) of CRC. Functional enrichment analysis revealed that collagen fibrous tissue, ion channel complex and other pathways were significantly enriched, which might help explain the underlying molecular mechanisms. There were significant differences in ImmuneScore, StromalScore, ESTIMATEScore between high- and low-risk groups (p < 0.05). Ultimately, qRT-PCR validation showed that a significant upregulation in the expression of LRPPRC and UHRF2 in cancerous tissue, which verified the effectiveness of our signature. Conclusion In conclusion, 2 prognostic genes (LRPPRC and UHRF2) related to RNA methylation were identified by bioinformatics analysis, which might supply a new insight into the treatment and evaluation of CRC.
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Affiliation(s)
- Ruoyang Lin
- Department of Gastroenterology and Hepatology, the First Affiliated Hospital of Wenzhou, Medical University, Wenzhou, People’s Republic of China
| | - Renpin Chen
- Department of Gastroenterology and Hepatology, the First Affiliated Hospital of Wenzhou, Medical University, Wenzhou, People’s Republic of China
| | - Lechi Ye
- Department of Colorectal and Anal Surgery, the First Affiliated Hospital of Wenzhou, Medical University, Wenzhou, People’s Republic of China
| | - Zhiming Huang
- Department of Gastroenterology and Hepatology, the First Affiliated Hospital of Wenzhou, Medical University, Wenzhou, People’s Republic of China
| | - Xianfan Lin
- Department of Gastroenterology and Hepatology, the First Affiliated Hospital of Wenzhou, Medical University, Wenzhou, People’s Republic of China
| | - Tanzhou Chen
- Department of Gastroenterology and Hepatology, the First Affiliated Hospital of Wenzhou, Medical University, Wenzhou, People’s Republic of China
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Guo J, Zhao Y, Chu Y, Li Y, Song Y, Pan Q, Qiu Z, Yu B, Zhu Y. Screening Candidate Genes at the Co Locus Conferring to the Columnar Growth Habit in Apple ( Malus × Domestica Borkh.). Genes (Basel) 2023; 14:genes14050964. [PMID: 37239324 DOI: 10.3390/genes14050964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023] Open
Abstract
The columnar growth trait of apple (Malus × domestica Borkh.) is genetically controlled by the Columnar (Co) locus on 10 chromosomes, including several candidate genes. Except for MdCo31, other candidate genes at the Co locus are less elucidated. In this study, a strategy of step-by-step screening was adopted to select 11 candidate genes by experimental cloning, transient expression, and genetic transformation. There existed several SNPs in four genes by sequence alignment in columnar and non-columnar apples. Two genes were detected in the nucleus and three genes in the cell membrane, other genes were located in multiple cellular structures by subcellular location. Ectopic expression demonstrated that more branching occurred in MdCo38-OE by upregulating NtPIN1 and NtGA2ox and enlarged leaves in MdCo41-OE tobaccos by upregulating NtCCDs. Transcripts of MdCo38 and MdCo41 were associated with the Co genotypes in apples. The results indicate that MdCo38 and MdCo41 are involved in the columnar growth phenotype in apple, probably through altering polar auxin transport, active gibberellin levels, and strigolactone biosynthesis.
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Affiliation(s)
- Jing Guo
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yuan Zhao
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yu Chu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yuru Li
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yuqi Song
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Qi Pan
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Zhannan Qiu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Boyang Yu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yuandi Zhu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
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Sushmita K, Sharma S, Singh Kaushik M, Kateriya S. Algal rhodopsins encoding diverse signal sequence holds potential for expansion of organelle optogenetics. Biophys Physicobiol 2023; 20:e201008. [PMID: 38362319 PMCID: PMC10865886 DOI: 10.2142/biophysico.bppb-v20.s008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Rhodopsins have been extensively employed for optogenetic regulation of bioelectrical activity of excitable cells and other cellular processes across biological systems. Various strategies have been adopted to attune the cellular processes at the desired subcellular compartment (plasma membrane, endoplasmic reticulum, Golgi, mitochondria, lysosome) within the cell. These strategies include-adding signal sequences, tethering peptides, specific interaction sites, or mRNA elements at different sites in the optogenetic proteins for plasma membrane integration and subcellular targeting. However, a single approach for organelle optogenetics was not suitable for the relevant optogenetic proteins and often led to the poor expression, mislocalization, or altered physical and functional properties. Therefore, the current study is focused on the native subcellular targeting machinery of algal rhodopsins. The N- and C-terminus signal prediction led to the identification of rhodopsins with diverse organelle targeting signal sequences for the nucleus, mitochondria, lysosome, endosome, vacuole, and cilia. Several identified channelrhodopsins and ion-pumping rhodopsins possess effector domains associated with DNA metabolism (repair, replication, and recombination) and gene regulation. The identified algal rhodopsins with diverse effector domains and encoded native subcellular targeting sequences hold immense potential to establish expanded organelle optogenetic regulation and associated cellular signaling.
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Affiliation(s)
- Kumari Sushmita
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sunita Sharma
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manish Singh Kaushik
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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Hooker JC, Nissan N, Luckert D, Charette M, Zapata G, Lefebvre F, Mohr RM, Daba KA, Warkentin TD, Hadinezhad M, Barlow B, Hou A, Golshani A, Cober ER, Samanfar B. A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean ( Glycine max). Int J Mol Sci 2022; 24:ijms24010222. [PMID: 36613666 PMCID: PMC9820483 DOI: 10.3390/ijms24010222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help uncover the underlying differences between high and low protein soybean varieties, we performed differential expression analysis on high and low total protein soybean varieties and high and low 11S soybean varieties grown in four locations across Eastern and Western Canada over three years (2018-2020). Simultaneously, ten individual differential expression datasets for high vs. low total protein soybeans and ten individual differential expression datasets for high vs. low 11S soybeans were assessed, for a total of 20 datasets. The top 15 most upregulated and the 15 most downregulated genes were extracted from each differential expression dataset and cross-examination was conducted to create shortlists of the most consistently differentially expressed genes. Shortlisted genes were assessed for gene ontology to gain a global appreciation of the commonly differentially expressed genes. Genes with roles in the lipid metabolic pathway and carbohydrate metabolic pathway were differentially expressed in high total protein and high 11S soybeans in comparison to their low total protein and low 11S counterparts. Expression differences were consistent between East and West locations with the exception of one, Glyma.03G054100. These data are important for uncovering the genes and biological pathways responsible for the difference in seed protein between high and low total protein or 11S cultivars.
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Affiliation(s)
- Julia C. Hooker
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Nour Nissan
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Doris Luckert
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Martin Charette
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, 740 Dr. Penfield Ave, Montréal, QC H3A 0G1, Canada
| | - François Lefebvre
- Canadian Centre for Computational Genomics, 740 Dr. Penfield Ave, Montréal, QC H3A 0G1, Canada
| | - Ramona M. Mohr
- Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB R7A 5Y3, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Thomas D. Warkentin
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Mehri Hadinezhad
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Anfu Hou
- Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
- Correspondence:
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McDowell R, Small I, Bond CS. Synthetic PPR proteins as tools for sequence-specific targeting of RNA. Methods 2022; 208:19-26. [DOI: 10.1016/j.ymeth.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
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Mechanisms and players of mitoribosomal biogenesis revealed in trypanosomatids. Trends Parasitol 2022; 38:1053-1067. [PMID: 36075844 DOI: 10.1016/j.pt.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 01/13/2023]
Abstract
Translation in mitochondria is mediated by mitochondrial ribosomes, or mitoribosomes, complex ribonucleoprotein machines with dual genetic origin. Mitoribosomes in trypanosomatid parasites diverged markedly from their bacterial ancestors and other eukaryotic lineages in terms of protein composition, rRNA content, and overall architecture, yet their core functional elements remained conserved. Recent cryo-electron microscopy studies provided atomic models of trypanosomatid large and small mitoribosomal subunits and their precursors, making these parasites the organisms with the best-understood biogenesis of mitoribosomes. The structures revealed molecular mechanisms and players involved in the assembly of mitoribosomes not only in the parasites, but also in eukaryotes in general.
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Gomes-Messias LM, Vianello RP, Marinho GR, Rodrigues LA, Coelho AG, Pereira HS, Melo LC, de Souza TLPO. Genetic mapping of the Andean anthracnose resistance gene present in the common bean cultivar BRSMG Realce. FRONTIERS IN PLANT SCIENCE 2022; 13:1033687. [PMID: 36507385 PMCID: PMC9728541 DOI: 10.3389/fpls.2022.1033687] [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: 08/31/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
The rajado seeded Andean bean (Phaseolus vulgaris L.) cultivar BRSMG Realce (striped seed coat) developed by Embrapa expressed a high level of anthracnose resistance, caused by Colletotrichum lindemuthianum, in field and greenhouse screenings. The main goal of this study was to evaluate the inheritance of anthracnose resistance in BRSMG Realce, map the resistance locus or major gene cluster previously named as Co-Realce, identify resistance-related positional genes, and analyze potential markers linked to the resistance allele. F2 plants derived from the cross BRSMG Realce × BRS FC104 (Mesoamerican) and from the cross BRSMG Realce × BRS Notável (Mesoamerican) were inoculated with the C. lindemuthianum races 475 and 81, respectively. The BRSMG Realce × BRS FC104 F2 population was also genotyped using the DArTseq technology. Crosses between BRSMG Realce and BAT 93 (Mesoamerican) were also conducted and resulting F2 plants were inoculated with the C. lindemuthianum races 65 and 1609, individually. The results shown that anthracnose resistance in BRSMG Realce is controlled by a single locus with complete dominance. A genetic map including 1,118 SNP markers was built and shown 78% of the markers mapped at a distances less than 5.0 cM, with a total genetic length of 4,473.4 cM. A major locus (Co-Realce) explaining 54.6% of the phenotypic variation of symptoms caused by the race 475 was identified in Pv04, flanked by the markers snp1327 and snp12782 and 4.48 cM apart each other. These SNPs are useful for marker-assisted selection, due to an estimated selection efficiency of 99.2%. The identified resistance allele segregates independently of the resistance allele Co-33 (Pv04) present in BAT 93. The mapped genomic region with 704,867 bp comprising 63 putative genes, 44 of which were related to the pathogen-host interaction. Based on all these results and evidence, anthracnose resistance in BRSMG Realce should be considered as monogenic, useful for breeding purpose. It is proposed that locus Co-Realce is unique and be provisionally designated as CoPv04R until be officially nominated in accordance with the rules established by the Bean Improvement Cooperative Genetics Committee.
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Holušová K, Čmejlová J, Suran P, Čmejla R, Sedlák J, Zelený L, Bartoš J. High-resolution genome-wide association study of a large Czech collection of sweet cherry ( Prunus avium L.) on fruit maturity and quality traits. HORTICULTURE RESEARCH 2022; 10:uhac233. [PMID: 36643756 PMCID: PMC9832837 DOI: 10.1093/hr/uhac233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/10/2022] [Indexed: 06/17/2023]
Abstract
In sweet cherry (Prunus avium L.), quantitative trait loci have been identified for fruit maturity, colour, firmness, and size to develop markers for marker-assisted selection. However, resolution is usually too low in those analyses to directly target candidate genes, and some associations are missed. In contrast, genome-wide association studies are performed on broad collections of accessions, and assemblies of reference sequences from Tieton and Satonishiki cultivars enable identification of single nucleotide polymorphisms after whole-genome sequencing, providing high marker density. Two hundred and thirty-five sweet cherry accessions were sequenced and phenotyped for harvest time and fruit colour, firmness, and size. Genome-wide association studies were used to identify single nucleotide polymorphisms associated with each trait, which were verified in breeding material consisting of 64 additional accessions. A total of 1 767 106 single nucleotide polymorphisms were identified. At that density, significant single nucleotide polymorphisms could be linked to co-inherited haplotype blocks (median size ~10 kb). Thus, markers were tightly associated with respective phenotypes, and individual allelic combinations of particular single nucleotide polymorphisms provided links to distinct phenotypes. In addition, yellow-fruit accessions were sequenced, and a ~ 90-kb-deletion on chromosome 3 that included five MYB10 transcription factors was associated with the phenotype. Overall, the study confirmed numerous quantitative trait loci from bi-parental populations using high-diversity accession populations, identified novel associations, and genome-wide association studies reduced the size of trait-associated loci from megabases to kilobases and to a few candidate genes per locus. Thus, a framework is provided to develop molecular markers and evaluate and characterize genes underlying important agronomic traits.
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Affiliation(s)
- Kateřina Holušová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 779 00, Czech Republic
| | - Jana Čmejlová
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
| | - Pavol Suran
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
| | - Radek Čmejla
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
| | - Jiří Sedlák
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
| | - Lubor Zelený
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, Holovousy, 508 01, Czech Republic
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Huang D, Huang D. Relationship between M6A methylation regulator and prognosis in patients with hepatocellular carcinoma after transcatheter arterial chemoembolization. Heliyon 2022; 8:e10931. [PMID: 36262291 PMCID: PMC9573888 DOI: 10.1016/j.heliyon.2022.e10931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/02/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Background Patients with mid-stage HCC (hepatocellular carcinoma) may benefit from transcatheter arterial chemoembolization (TACE). However, patient efficacy varies widely, and the detailed assessment index is unknown. The most general methylation alteration in mRNA (Messenger RNA), N6-methyladenosine (m6A), is controlled by the m6A regulator, which is associated with the emergence of tumors. To include the molecular causes of cancer, competition with ceRNA (endogenous RNA) networks is crucial. However, the exact processes they contribute to TACE HCC remain uncertain. The purpose of this study was tantamount to investigating the possible function of ceRNA networks and m6A regulators in patients with TACE HCC. Methods Genes Associated with m6A were discovered using the TACE GEO (Gene Expression Omnibus) dataset. An additional estimate of M6A-associated DEGs (differentially expressed genes) was used to create a predictive response model, which is required. LncRNA-miRNA and miRNA-mRNA interactions were then predicted, the regulatory ceRNA network was set up using Cytoscape software, and target genes were identified using GEPIA online analysis. The connection between immunological checkpoints, immune cell marker genes, and target genes for immune cells was also examined. Results The detection of 4 m6A-associated DEGs, the development and evaluation of 2 Machine learning models, and the development of risk models that accurately predicted the response rate of specific patients. Additionally, we obtained two miRNAs (micro RNAs)and six lncRNAs (Long non-coding RNAs), forming an 8-pair ceRNA network, and the target gene LRPPRC deletion of one copy number and gene expression was highly correlated with the amount of Tregs immune cells. LRPPRC was related positively with NRP1, IRF5, and ITGAM and negatively with CCR7 and CD8B among immune cell marker genes. We also discovered that LRPPRC correlates positively with immune checkpoint CD274 cells. Conclusion The response of HCC patients to TACE therapy may be predicted using a model based on four gene expression data. We also developed a ceRNA network for TACE HCC related to m6A, which offered suggestions for more research into its molecular processes and possible prognostic indicators.
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Affiliation(s)
- Deliang Huang
- Department of Interventional Medicine, Yellow River Central Hospital, Zhengzhou, Henan Province, China
| | - Dejing Huang
- Department of Thoracic Surgery, The Second Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China,Corresponding author.
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Che L, Lu S, Liang G, Gou H, Li M, Chen B, Mao J. Identification and expression analysis of the grape pentatricopeptide repeat (PPR) gene family in abiotic stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1849-1874. [PMID: 36484031 PMCID: PMC9723081 DOI: 10.1007/s12298-022-01252-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The pentatricopeptide repeat (PPR) is one of the largest gene family in plants, and play important role in regulating plant growth, development and abiotic stress response. However, PPR genes have been poorly studied in grapes. In this study, based on the grape genome database, bioinformatics methods and quantitative real-time PCR (qRT-PCR) were used to identify the VvPPR family and the response to abiotic stress. A total of 181 PPR genes were identified in grape and divided into two subfamilies. Subcellular localization predicted that this gene family mainly functions in chloroplasts, nucleus, and mitochondria. Protein-protein interaction prediction indicated that there may be interaction between VvPPR44,53 and VvPPR44. The promoter region of VvPPR gene family contained various cis-acting elements, which were related to light and hormone. Expression pattern analysis showed that the VvPPR gene family was highly expressed in grape leaves, buds and carpel tissues. qRT-PCR results showed that the expression of VvPPR genes in roots was higher than stems and leaves under NAA, SA, ABA, MeJA and GA3 treatments. VvPPR8 was significantly up-regulated after GA3 and MeJA treatment for 24 h, VvPPR53 was significantly up-regulated after SA, NAA, ABA and MeJA treatment. In addition, In grape leaves, VvPPR53 was up-regulated under PEG, Nacl and 4 ℃ treatments. These data indicate that VvPPR gene family members are responsive to hormones and abiotic stresses, and that there are some differences in the degree of response and expression in different grape tissues. This study provides a certain theoretical basis for grape resistance breeding.
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Affiliation(s)
- Lili Che
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu Province People’s Republic of China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu Province People’s Republic of China
| | - Guoping Liang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu Province People’s Republic of China
| | - Huimin Gou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu Province People’s Republic of China
| | - Min Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu Province People’s Republic of China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu Province People’s Republic of China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 Gansu Province People’s Republic of China
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32
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Wu C, Chaw S. Evolution of mitochondrial RNA editing in extant gymnosperms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1676-1687. [PMID: 35877596 PMCID: PMC9545813 DOI: 10.1111/tpj.15916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 06/01/2023]
Abstract
To unveil the evolution of mitochondrial RNA editing in gymnosperms, we characterized mitochondrial genomes (mitogenomes), plastid genomes, RNA editing sites, and pentatricopeptide repeat (PPR) proteins from 10 key taxa representing four of the five extant gymnosperm clades. The assembled mitogenomes vary in gene content due to massive gene losses in Gnetum and Conifer II clades. Mitochondrial gene expression levels also vary according to protein function, with the most highly expressed genes involved in the respiratory complex. We identified 9132 mitochondrial C-to-U editing sites, as well as 2846 P-class and 8530 PLS-class PPR proteins. Regains of editing sites were demonstrated in Conifer II rps3 transcripts whose corresponding mitogenomic sequences lack introns due to retroprocessing. Our analyses reveal that non-synonymous editing is efficient and results in more codons encoding hydrophobic amino acids. In contrast, synonymous editing, although performed with variable efficiency, can increase the number of U-ending codons that are preferentially utilized in gymnosperm mitochondria. The inferred loss-to-gain ratio of mitochondrial editing sites in gymnosperms is 2.1:1, of which losses of non-synonymous editing are mainly due to genomic C-to-T substitutions. However, such substitutions only explain a small fraction of synonymous editing site losses, indicating distinct evolutionary mechanisms. We show that gymnosperms have experienced multiple lineage-specific duplications in PLS-class PPR proteins. These duplications likely contribute to accumulated RNA editing sites, as a mechanistic correlation between RNA editing and PLS-class PPR proteins is statistically supported.
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Affiliation(s)
- Chung‐Shien Wu
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
| | - Shu‐Miaw Chaw
- Biodiversity Research CenterAcademia SinicaTaipei11529Taiwan
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Histological characterization of anther structure in Tetep-cytoplasmic male sterility and fine mapping of restorer-of-fertility gene in rice. PLoS One 2022; 17:e0268174. [PMID: 35980881 PMCID: PMC9387866 DOI: 10.1371/journal.pone.0268174] [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: 01/25/2022] [Accepted: 04/25/2022] [Indexed: 11/19/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait that inhibits plants from producing or releasing viable pollen. CMS is caused by mitochondrial–nuclear interaction, and can be rescued by introducing functional nuclear restorer-of-fertility (Rf) gene. The Tetep-CMS/Rf lines were developed through successive inter-subspecific backcrosses between indica and japonica rice accessions. Phenotypic characterization of Tetep-CMS lines revealed abnormal anther dehiscence and the inability to release, while possessing functional pollen. Transverse sections of developing anthers collected from CMS plants showed connective tissue deformities and aberrant dehydration of endothecium and epidermis. Fine mapping of Rf-Tetep using a series of segregating populations, delimited the candidate region to an approximately 109 kb genomic interval between M2099 and FM07 flanking markers. Nanopore long-read sequencing and genome assembly, proceeded by gene prediction and annotation revealed 11 open reading frames (ORFs) within the candidate region, and suggest ORF6 annotated as pentatricopeptide repeat motif containing gene 1 (PPR1), as a possible candidate gene responsible for fertility restoration. This study suggests that tissue-specific abnormalities in anthers are responsible for indehiscence-based sterility, and propose that the functional Rf gene is derived from allelic variation between inter-subspecies in rice.
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Wang S, Gao J, Chao H, Li Z, Pu W, Wang Y, Chen M. Comparative Chloroplast Genomes of Nicotiana Species (Solanaceae): Insights Into the Genetic Variation, Phylogenetic Relationship, and Polyploid Speciation. FRONTIERS IN PLANT SCIENCE 2022; 13:899252. [PMID: 35865282 PMCID: PMC9295722 DOI: 10.3389/fpls.2022.899252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/26/2022] [Indexed: 05/25/2023]
Abstract
Nicotiana L. is a genus rich in polyploidy, which represents an ideal natural system for investigating speciation, biodiversity, and phytogeography. Despite a wealth of phylogenetic work on this genus, a robust evolutionary framework with a dated molecular phylogeny for the genus is still lacking. In this study, the 19 complete chloroplast genomes of Nicotiana species were assembled, and five published chloroplast genomes of Nicotiana were retrieved for comparative analyses. The results showed that the 24 chloroplast genomes of Nicotiana, ranging from 155,327 bp (N. paniculata) to 156,142 bp (N. heterantha) in size, exhibited typical quadripartite structure. The chloroplast genomes were rather conserved in genome structure, GC content, RNA editing sites, and gene content and order. The higher GC content observed in the IR regions could be a result of the presence of abundant rRNA and tRNA genes, which contained a relatively higher GC content. A total of seven hypervariable regions, as new molecular markers for phylogenetic analysis, were uncovered. Based on 78 protein-coding genes, we constructed a well-supported phylogenetic tree, which was largely in agreement with previous studies, except for a slight conflict in several sections. Chloroplast phylogenetic results indicated that the progenitors of diploid N. sylvestris, N. knightiana, and the common ancestor of N. sylvestris and N. glauca might have donated the maternal genomes of allopolyploid N. tabacum, N. rustica, and section Repandae, respectively. Meanwhile, the diploid section Noctiflorae lineages (N. glauca) acted as the most likely maternal progenitor of section Suaveolentes. Molecular dating results show that the polyploid events range considerably in ~0.12 million (section Nicotiana) to ~5.77 million (section Repandae) years ago. The younger polyploids (N. tabacum and N. rustica) were estimated to have arisen ~0.120 and ~0.186 Mya, respectively. The older polyploids (section Repandae and Suaveolentes) were considered to have originated from a single polyploid event at ~5.77 and ~4.49 Mya, respectively. In summary, the comparative analysis of chloroplast genomes of Nicotiana species has not only revealed a series of new insights into the genetic variation and phylogenetic relationships in Nicotiana but also provided rich genetic resources for speciation and biodiversity research in the future.
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Affiliation(s)
- Shuaibin Wang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Junping Gao
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Haoyu Chao
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhaowu Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Wenxuan Pu
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Yaofu Wang
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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Rehman O, Uzair M, Chao H, Khan MR, Chen M. Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:892729. [PMID: 35812946 PMCID: PMC9260663 DOI: 10.3389/fpls.2022.892729] [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: 03/09/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Ribonucleic acid editing (RE) is a post-transcriptional process that altered the genetics of RNA which provide the extra level of gene expression through insertion, deletions, and substitutions. In animals, it converts nucleotide residues C-U. Similarly in plants, the role of RNA editing sites (RES) in rice under alkaline stress is not fully studied. Rice is a staple food for most of the world population. Alkaline stress cause reduction in yield. Here, we explored the effect of alkaline stress on RES in the whole mRNA from rice chloroplast and mitochondria. Ribonucleic acid editing sites in both genomes (3336 RESs) including chloroplast (345 RESs) and mitochondria (2991 RESs) with average RES efficiency ∼55% were predicted. Our findings showed that majority of editing events found in non-synonymous codon changes and change trend in amino acids was hydrophobic. Four types of RNA editing A-G (A-I), C-T (C-U), G-A, and T-C were identified in treated and untreated samples. Overall, RNA editing efficiency was increased in the treated samples. Analysis of Gene Ontology revealed that mapped genes were engaged in many biological functions and molecular processes. We also checked the expression of pentatricopeptide repeat (PPR), organelle zinc-finger (OZI), and multiple organellar RNA editing factors/RNA editing factor interacting proteins genes in control and treatment, results revealed upregulation of PPR and OZ1 genes in treated samples. This induction showed the role of these genes in RNA editing. The current findings report that RNA editing increased under alkaline stress which may contribute in adaptation for rice by changing amino acids in edited genes (88 genes). These findings will provide basis for identification of RES in other crops and also will be useful in alkaline tolerance development in rice.
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Affiliation(s)
- Obaid Rehman
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
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Kang MC, Kang HJ, Jung SY, Lee HY, Kang MY, Jo YD, Kang BC. The Unstable Restorer-of-fertility locus in pepper (Capsicum annuum. L) is delimited to a genomic region containing PPR genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1923-1937. [PMID: 35357525 DOI: 10.1007/s00122-022-04084-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Unstable Restorer-of-fertility (Rfu), conferring unstable fertility restoration in the pepper CGMS system, was delimited to a genomic region near Rf and is syntenic to the PPR-like gene-rich region in tomato. The use of cytoplasmic-genic male sterility (CGMS) systems greatly increases the efficiency of hybrid seed production. Although marker development and candidate gene isolation have been performed for the Restorer-of-fertility (Rf) gene in pepper (Capsicum annuum L.), the broad use of CGMS systems has been hampered by the instability of fertility restoration among pepper accessions, especially sweet peppers, due to the widespread presence of the Unstable Restorer-of-fertility (Rfu) locus. Therefore, to investigate the genetic factors controlling unstable fertility restoration in sweet peppers, we developed a segregation population (BC4F5) from crosses using a male-sterile line and an Rfu-containing line. Segregation did not significantly deviate from a 3:1 ratio for unstable fertility restoration to sterility, indicating single dominant locus control for unstable fertility restoration in this population. Genetic mapping delimited the Rfu locus to a 398 kb genomic region on chromosome 6, which is close to but different from the previously identified Rf-containing region. The Rfu-containing region harbors a pentatricopeptide repeat (PPR) gene, along with 10 other candidate genes. In addition, this region is syntenic to the genomic region containing the largest number of Rf-like PPR genes in tomato. Therefore, the dynamic evolution of PPR genes might be responsible for both the restoration and instability of fertility in pepper. During genetic mapping, we developed various molecular markers, including one that co-segregated with Rfu. These markers showed higher accuracy for genotyping than previously developed markers, pointing to their possible use in marker-assisted breeding of sweet peppers.
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Affiliation(s)
- Moo Chan Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hwa-Jeong Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - So-Young Jung
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hae-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Min-Young Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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The Rice Serine/Arginine Splicing Factor RS33 Regulates Pre-mRNA Splicing during Abiotic Stress Responses. Cells 2022; 11:cells11111796. [PMID: 35681491 PMCID: PMC9180459 DOI: 10.3390/cells11111796] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 05/07/2022] [Indexed: 02/06/2023] Open
Abstract
Abiotic stresses profoundly affect plant growth and development and limit crop productivity. Pre-mRNA splicing is a major form of gene regulation that helps plants cope with various stresses. Serine/arginine (SR)-rich splicing factors play a key role in pre-mRNA splicing to regulate different biological processes under stress conditions. Alternative splicing (AS) of SR transcripts and other transcripts of stress-responsive genes generates multiple splice isoforms that contribute to protein diversity, modulate gene expression, and affect plant stress tolerance. Here, we investigated the function of the plant-specific SR protein RS33 in regulating pre-mRNA splicing and abiotic stress responses in rice. The loss-of-function mutant rs33 showed increased sensitivity to salt and low-temperature stresses. Genome-wide analyses of gene expression and splicing in wild-type and rs33 seedlings subjected to these stresses identified multiple splice isoforms of stress-responsive genes whose AS are regulated by RS33. The number of RS33-regulated genes was much higher under low-temperature stress than under salt stress. Our results suggest that the plant-specific splicing factor RS33 plays a crucial role during plant responses to abiotic stresses.
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Freitas AV, Herb JT, Pan M, Chen Y, Gucek M, Jin T, Xu H. Generation of a mitochondrial protein compendium in Dictyostelium discoideum. iScience 2022; 25:104332. [PMID: 35602934 PMCID: PMC9118663 DOI: 10.1016/j.isci.2022.104332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/29/2022] [Accepted: 04/26/2022] [Indexed: 11/20/2022] Open
Abstract
The social ameba Dictyostelium discoideum has emerged as a powerful model to study mitochondrial genetics and bioenergetics. However, a comprehensive inventory of mitochondrial proteins that is critical to understanding mitochondrial processes has yet to be curated. Here, we utilized high-throughput multiplexed protein quantitation and homology analyses to generate a high-confidence mitochondrial protein compendium consisting of 936 proteins. Our proteomic approach, which utilizes mass spectrometry in combination with mathematical modeling, was validated through mitochondrial targeting sequence prediction and live-cell imaging. Our final compendium consists of 936 proteins. Nearly, a third of D. discoideum mitochondrial proteins do not have homologs in humans, budding yeasts, or an ancestral alphaproteobacteria. Additionally, we leverage our compendium to highlight the complexity of metabolic reprogramming during starvation-induced development. Our compendium lays a foundation to investigate mitochondrial processes that are unique in ameba and to understand the functions of conserved mitochondrial proteins in D. discoideum.
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Affiliation(s)
- Anna V. Freitas
- National Heart, Lung and Blood Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Jake T. Herb
- National Heart, Lung and Blood Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Miao Pan
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Rockville, MD 20852, USA
| | - Yong Chen
- National Heart, Lung and Blood Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Marjan Gucek
- National Heart, Lung and Blood Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Tian Jin
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Rockville, MD 20852, USA
| | - Hong Xu
- National Heart, Lung and Blood Institute, National Institute of Health, Bethesda, MD 20892, USA
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Identification, Characterization and Comparison of the Genome-Scale UTR Introns from Six Citrus Species. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ever since their discovery, introns within the coding sequence (CDS) of transcripts have been paid great attention. However, the introns located in the untranslated regions (UTRs) are often ignored. Here, we identified, characterized and compared the UTR introns (UIs) from six citrus species. Results showed that the average intron number of UTRs is greatly lower than that of CDSs. Among all six citrus species, the number and density of 5′UTR introns (5UIs) are higher than those of 3′UTR introns (3UIs). The UI densities varied greatly among different citrus species. There are 11 and 9 types of splice site (SS) pairs for the UIs of C. sinensis and C. medica, respectively. However, the UIs of the other four citrus species all own only three kinds of SS pairs. The ‘GT-AG’, accounting for more than 95% of both 5UIs and 3UIs SS pairs for all the six species, is the most popular type. Moreover, 81 5UIs and 26 3UIs were identified as common UIs among the six citrus species, and the transcripts containing these common UIs were mostly involved in gene expression or gene expression regulation. Our study revealed that the UIs’ length, abundance, density and SS pair types varied among different citrus species and that many UI-containing genes play important roles in gene expression regulation. Our findings have great implications for future citrus UI function research.
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Jyothsna S, Alagu M. Role of phasiRNAs in plant-pathogen interactions: molecular perspectives and bioinformatics tools. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:947-961. [PMID: 35722509 PMCID: PMC9203634 DOI: 10.1007/s12298-022-01189-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/01/2022] [Accepted: 05/18/2022] [Indexed: 05/03/2023]
Abstract
The genome of an organism is regulated in concert with the organized action of various genetic regulators at different hierarchical levels. Small non-coding RNAs are one of these regulators, among which microRNAs (miRNAs), a distinguished sRNA group with decisive functions in the development, growth and stress-responsive activities of both plants as well as animals, are keenly explored over a good number of years. Recent studies in plants revealed that apart from the silencing activity exhibited by miRNAs on their targets, miRNAs of specific size and structural features can direct the phasing pattern of their target loci to form phased secondary small interfering RNAs (phasiRNAs). These trigger-miRNAs were identified to target both coding and long non-coding RNAs that act as potent phasiRNA precursors or PHAS loci. The phasiRNAs produced thereby exhibit a role in enhancing further downstream regulation either on their own precursors or on those transcripts that are distinct from their genetic source of origin. Hence, these tiny regulators can stimulate an elaborative cascade of interacting RNA networks via cis and trans-regulatory mechanisms. Our review focuses on the comprehensive understanding of phasiRNAs and their trigger miRNAs, by giving much emphasis on their role in the regulation of plant defense responses, together with a summary of the computational tools available for the prediction of the same.
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Affiliation(s)
- S. Jyothsna
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala 671316 India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala 671316 India
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Liu Y, Chen Z, Wang ZH, Delaney KM, Tang J, Pirooznia M, Lee DY, Tunc I, Li Y, Xu H. The PPR domain of mitochondrial RNA polymerase is an exoribonuclease required for mtDNA replication in Drosophila melanogaster. Nat Cell Biol 2022; 24:757-765. [PMID: 35449456 DOI: 10.1038/s41556-022-00887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 03/08/2022] [Indexed: 11/09/2022]
Abstract
Mitochondrial DNA (mtDNA) replication and transcription are of paramount importance to cellular energy metabolism. Mitochondrial RNA polymerase is thought to be the primase for mtDNA replication. However, it is unclear how this enzyme, which normally transcribes long polycistronic RNAs, can produce short RNA oligonucleotides to initiate mtDNA replication. We show that the PPR domain of Drosophila mitochondrial RNA polymerase (PolrMT) has 3'-to-5' exoribonuclease activity, which is indispensable for PolrMT to synthesize short RNA oligonucleotides and prime DNA replication in vitro. An exoribonuclease-deficient mutant, PolrMTE423P, partially restores mitochondrial transcription but fails to support mtDNA replication when expressed in PolrMT-mutant flies, indicating that the exoribonuclease activity is necessary for mtDNA replication. In addition, overexpression of PolrMTE423P in adult flies leads to severe neuromuscular defects and a marked increase in mtDNA transcript errors, suggesting that exoribonuclease activity may contribute to the proofreading of mtDNA transcription.
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Affiliation(s)
- Yi Liu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhe Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zong-Heng Wang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katherine M Delaney
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Juanjie Tang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mehdi Pirooznia
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Duck-Yeon Lee
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ilker Tunc
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yuesheng Li
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hong Xu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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Kiyosawa A, Yonemaru JI, Mizuno H, Kanamori H, Wu J, Kawahigashi H, Goto K. Fine mapping of Rf5 region for a sorghum fertility restorer gene and microsynteny analysis across grass species. BREEDING SCIENCE 2022; 72:141-149. [PMID: 36275935 PMCID: PMC9522528 DOI: 10.1270/jsbbs.21057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/20/2021] [Indexed: 06/16/2023]
Abstract
Cytoplasmic male sterility (CMS) is widely used to control pollination in the production of commercial F1 hybrid seed in sorghum. So far, 6 major fertility restorer genes, Rf1 to Rf6, have been reported in sorghum. Here, we fine-mapped the Rf5 locus on sorghum chromosome 5 using descendant populations of a 'Nakei MS-3A' × 'JN43' cross. The Rf5 locus was narrowed to a 140-kb region in BTx623 genome (161-kb in JN43) with 16 predicted genes, including 6 homologous to the rice fertility restorer Rf1 (PPR.1 to PPR.6). These 6 homologs have tandem pentatricopeptide repeat (PPR) motifs. Many Rf genes encode PPR proteins, which bind RNA transcripts and modulate gene expression at the RNA level. No PPR genes were detected at the Rf5 locus on the corresponding homologous chromosome of rice, foxtail millet, or maize, so this gene cluster may have originated by chromosome translocation and duplication after the divergence of sorghum from these species. Comparison of the sequences of these genes between fertile and CMS lines identified PPR.4 as the most plausible candidate gene for Rf5.
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Affiliation(s)
- Atsushi Kiyosawa
- Nagano Animal Industry Experiment Station, 10931-1 Kataoka, Shiojiri, Nagano 399-0711, Japan
| | - Jun-ichi Yonemaru
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Kawahigashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kazumi Goto
- Nagano Animal Industry Experiment Station, 10931-1 Kataoka, Shiojiri, Nagano 399-0711, Japan
- Nagano Agricultural Development Public Corporation, Kami-Ina Branch, 3497 Arai, Ina, Nagano 396-8666, Japan
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Hollin T, Abel S, Falla A, Pasaje CFA, Bhatia A, Hur M, Kirkwood JS, Saraf A, Prudhomme J, De Souza A, Florens L, Niles JC, Le Roch KG. Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum. Nat Commun 2022; 13:1275. [PMID: 35277503 PMCID: PMC8917122 DOI: 10.1038/s41467-022-28981-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
The RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their main biological functions remain unknown. In this study, we use inducible knockdown studies in the human malaria parasite, Plasmodium falciparum, to show that two RAP proteins, PF3D7_0105200 (PfRAP01) and PF3D7_1470600 (PfRAP21), are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrate that these RAP proteins are involved in mitochondrial RNA metabolism. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validate that PfRAP01 and PfRAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs. Finally, mitochondrial enrichment experiments followed by deep sequencing of small RNAs demonstrate that PfRAP21 controls mitochondrial rRNA expression. Collectively, our results establish the role of these RAP proteins in mitoribosome activity and contribute to further understanding this protein family in malaria parasites.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Alejandra Falla
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Anil Bhatia
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Manhoi Hur
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Jay S Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Amancio De Souza
- Metabolomics Core Facility, University of California, Riverside, CA, 92521, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.
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Arif MAR, Waheed MQ, Lohwasser U, Shokat S, Alqudah AM, Volkmar C, Börner A. Genetic Insight Into the Insect Resistance in Bread Wheat Exploiting the Untapped Natural Diversity. Front Genet 2022; 13:828905. [PMID: 35222543 PMCID: PMC8874221 DOI: 10.3389/fgene.2022.828905] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change is an undeniable threat to sustainable wheat production in the future as an increased temperature will significantly increase grain loss due to the increased number of generations per season of multivoltine species that are detrimental to plants. Among insects, orange wheat blossom midge (OWBM), yellow wheat blossom midge (YWBM), saddle gall midge (SGM), thrips, and frit fly (FF) are important wheat pests in the European environments, which can be managed by the development of resistant cultivars. This involves the identification, confirmation, and incorporation of insect resistance sources into new high-yielding cultivars. We used two diverse and unrelated wheat [winter wheat (WW) and spring wheat (SW)] panels to associate single-nucleotide polymorphism (SNP) markers with the mentioned pests using the tools of association mapping. All in all, a total of 645 and 123 significant associations were detected in WW and SW, respectively, which were confined to 246 quantitative trait loci. Many candidate genes were identified using the BLAST analysis of the sequences of associated SNPs. Some of them are involved in controlling the physical structures of plants such as stomatal immunity and closure, cuticular wax in leaf blade, whereas others are involved in the production of certain enzymes in response to biotic and abiotic stresses. To our knowledge, this is the first detailed investigation that deals with YWBM, SGM, thrips, and FF resistance genetics using the natural variation in wheat. The reported germplasm is also readily available to breeders across the world that can make rational decisions to breed for the pest resilience of their interest by including the resistant genotypes being reported.
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Affiliation(s)
- Mian Abdur Rehman Arif
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
- *Correspondence: Mian Abdur Rehman Arif, ; Andreas Börner,
| | - Muhammad Qandeel Waheed
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Ulrike Lohwasser
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Sajid Shokat
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Ahmad M. Alqudah
- Department of Agroecology, Aarhus University at Flakkebjerg, Slagelse, Denmark
| | - Christa Volkmar
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- *Correspondence: Mian Abdur Rehman Arif, ; Andreas Börner,
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Hong Y, Wang Z, Li M, Su Y, Wang T. First Multi-Organ Full-Length Transcriptome of Tree Fern Alsophila spinulosa Highlights the Stress-Resistant and Light-Adapted Genes. Front Genet 2022; 12:784546. [PMID: 35186007 PMCID: PMC8854977 DOI: 10.3389/fgene.2021.784546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alsophila spinulosa, a relict tree fern, is a valuable plant for investigating environmental adaptations. Its genetic resources, however, are scarce. We used the PacBio and Illumina platforms to sequence the polyadenylated RNA of A. spinulosa root, rachis, and pinna, yielding 125,758, 89,107, and 89,332 unigenes, respectively. Combining the unigenes from three organs yielded a non-redundant reference transcriptome with 278,357 unigenes and N50 of 4141 bp, which were further reconstructed into 38,470 UniTransModels. According to functional annotation, pentatricopeptide repeat genes and retrotransposon-encoded polyprotein genes are the most abundant unigenes. Clean reads mapping to the full-length transcriptome is used to assess the expression of unigenes. The stress-induced ASR genes are highly expressed in all three organs, which is validated by qRT-PCR. The organ-specific upregulated genes are enriched for pathways involved in stress response, secondary metabolites, and photosynthesis. Genes for five types of photoreceptors, CRY signaling pathway, ABA biosynthesis and transduction pathway, and stomatal movement-related ion channel/transporter are profiled using the high-quality unigenes. The gene expression pattern coincides with the previously identified stomatal characteristics of fern. This study is the first multi-organ full-length transcriptome report of a tree fern species, the abundant genetic resources and comprehensive analysis of A. spinulosa, which provides the groundwork for future tree fern research.
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Affiliation(s)
- Yongfeng Hong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
| | - Ting Wang
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
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46
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Xu F, Yang X, Zhao N, Hu Z, Mackenzie SA, Zhang M, Yang J. Exploiting sterility and fertility variation in cytoplasmic male sterile vegetable crops. HORTICULTURE RESEARCH 2022; 9:uhab039. [PMID: 35039865 PMCID: PMC8807945 DOI: 10.1093/hr/uhab039] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/18/2022] [Accepted: 10/15/2021] [Indexed: 05/04/2023]
Abstract
Cytoplasmic male sterility (CMS) has long been used to economically produce hybrids that harness growth vigor through heterosis. Yet, how CMS systems operate within commercially viable seed production strategies in various economically important vegetable crops, and their underlying molecular mechanisms, are often overlooked details that could expand the utility of CMS as a cost-effective and stable system. We provide here an update on the nature of cytoplasmic-nuclear interplay for pollen sterility and fertility transitions in vegetable crops, based on the discovery of components of nuclear fertility restoration and reversion determinants. Within plant CMS systems, pollen fertility can be rescued by the introduction of nuclear fertility restorer genes (Rfs), which operate by varied mechanisms to countermand the sterility phenotype. By understanding these systems, it is now becoming feasible to achieve fertility restoration with Rfs designed for programmable CMS-associated open reading frames (ORFs). Likewise, new opportunities exist for targeted disruption of CMS-associated ORFs by mito-TALENs in crops where natural Rfs have not been readily identified, providing an alternative approach to recovering fertility of cytoplasmic male sterile lines in crops. Recent findings show that facultative gynodioecy, as a reproductive strategy, can coordinate the sterility and fertility transition in response to environmental cues and/or metabolic signals that reflect ecological conditions of reproductive isolation. This information is important to devising future systems that are more inherently stable.
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Affiliation(s)
- Fengyuan Xu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xiaodong Yang
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Na Zhao
- College of Grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou,
Zhejiang, 310058, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou,
Zhejiang, 310058, China
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47
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Jing XQ, Li WQ, Zhou MR, Shi PT, Zhang R, Shalmani A, Muhammad I, Wang GF, Liu WT, Chen KM. Rice Carbohydrate-Binding Malectin-Like Protein, OsCBM1, Contributes to Drought-Stress Tolerance by Participating in NADPH Oxidase-Mediated ROS Production. RICE (NEW YORK, N.Y.) 2021; 14:100. [PMID: 34874506 PMCID: PMC8651890 DOI: 10.1186/s12284-021-00541-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 11/28/2021] [Indexed: 05/13/2023]
Abstract
Carbohydrate-binding malectin/malectin-like domain-containing proteins (CBMs) are a recently identified protein subfamily of lectins that participates various functional bioprocesses in the animal, bacterial, and plant kingdoms. However, little is known the roles of CBMs in rice development and stress response. In this study, OsCBM1, which encodes a protein containing only one malectin-like domain, was cloned and characterized. OsCBM1 is localized in both the endoplasmic reticulum and plasma membrane. Its transcripts are dominantly expressed in leaves and could be significantly stimulated by a number of phytohormone applications and abiotic stress treatments. Overexpression of OsCBM1 increased drought tolerance and reactive oxygen species production in rice, whereas the knockdown of the gene decreased them. OsCBM1 physically interacts with OsRbohA, a NADPH oxidase, and the expression of OsCBM1 in osrbohA, an OsRbohA-knockout mutant, is significantly downregulated under both normal growth and drought stress conditions. Meanwhile, OsCBM1 can also physically interacts with OsRacGEF1, a specific guanine nucleotide exchange factor for the Rop/Rac GTPase OsRac1, and transient coexpression of OsCBM1 with OaRacGEF1 significantly enhanced ROS production. Further transcriptome analysis showed that multiple signaling regulatory mechanisms are involved in the OsCBM1-mediated processes. All these results suggest that OsCBM1 participates in NADPH oxidase-mediated ROS production by interacting with OsRbohA and OsRacGEF1, contributing to drought stress tolerance of rice. Multiple signaling pathways are likely involved in the OsCBM1-mediated stress tolerance in rice.
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Affiliation(s)
- Xiu-Qing Jing
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
- Department of Biology, Taiyuan Normal University, Taiyuan, 030619 Shanxi China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Meng-Ru Zhou
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Peng-Tao Shi
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ran Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Gang-Feng Wang
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100 Shaanxi China
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Tyrka M, Bakera B, Szeliga M, Święcicka M, Krajewski P, Mokrzycka M, Rakoczy-Trojanowska M. Identification of Rf Genes in Hexaploid Wheat ( Triticumaestivum L.) by RNA-Seq and Paralog Analyses. Int J Mol Sci 2021; 22:ijms22179146. [PMID: 34502055 PMCID: PMC8431562 DOI: 10.3390/ijms22179146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022] Open
Abstract
Among the natural mechanisms used for wheat hybrid breeding, the most desirable is the system combining the cytoplasmic male sterility (cms) of the female parent with the fertility-restoring genes (Rf) of the male parent. The objective of this study was to identify Rf candidate genes in the wheat genome on the basis of transcriptome sequencing (RNA-seq) and paralog analysis data. Total RNA was isolated from the anthers of two fertility-restorer (Primépi and Patras) and two non-restorer (Astoria and Grana) varieties at the tetrad and late uninucleate microspore stages. Of 36,912 differentially expressed genes (DEGs), 21 encoding domains in known fertility-restoring proteins were selected. To enrich the pool of Rf candidates, 52 paralogs (PAGs) of the 21 selected DEGs were included in the analyses. The expression profiles of most of the DEGs and PAGs determined bioinformatically were as expected (i.e., they were overexpressed in at least one fertility-restorer variety). However, these results were only partially consistent with the quantitative real-time PCR data. The DEG and PAG promoters included cis-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as Rf candidate genes, six of which were identified for the first time in this study.
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Affiliation(s)
- Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Rzeszów University of Technology, Powstańców Warszawy 12, 35-959 Rzeszów, Poland; (M.T.); (M.S.)
| | - Beata Bakera
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, Poland; (B.B.); (M.Ś.)
| | - Magdalena Szeliga
- Department of Biotechnology and Bioinformatics, Rzeszów University of Technology, Powstańców Warszawy 12, 35-959 Rzeszów, Poland; (M.T.); (M.S.)
| | - Magdalena Święcicka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, Poland; (B.B.); (M.Ś.)
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland; (P.K.); (M.M.)
| | - Monika Mokrzycka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland; (P.K.); (M.M.)
| | - Monika Rakoczy-Trojanowska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, Poland; (B.B.); (M.Ś.)
- Correspondence: ; Tel./Fax: +48-22-59-32152
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49
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Hilander T, Jackson CB, Robciuc M, Bashir T, Zhao H. The roles of assembly factors in mammalian mitoribosome biogenesis. Mitochondrion 2021; 60:70-84. [PMID: 34339868 DOI: 10.1016/j.mito.2021.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
As ancient bacterial endosymbionts of eukaryotic cells, mitochondria have retained their own circular DNA as well as protein translation system including mitochondrial ribosomes (mitoribosomes). In recent years, methodological advancements in cryoelectron microscopy and mass spectrometry have revealed the extent of the evolutionary divergence of mitoribosomes from their bacterial ancestors and their adaptation to the synthesis of 13 mitochondrial DNA encoded oxidative phosphorylation complex subunits. In addition to the structural data, the first assembly pathway maps of mitoribosomes have started to emerge and concomitantly also the assembly factors involved in this process to achieve fully translational competent particles. These transiently associated factors assist in the intricate assembly process of mitoribosomes by enhancing protein incorporation, ribosomal RNA folding and modification, and by blocking premature or non-native protein binding, for example. This review focuses on summarizing the current understanding of the known mammalian mitoribosome assembly factors and discussing their possible roles in the assembly of small or large mitoribosomal subunits.
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Affiliation(s)
- Taru Hilander
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland.
| | - Christopher B Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Finland.
| | - Marius Robciuc
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Tanzeela Bashir
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland; Key Laboratory of Stem Cell and Biopharmaceutical Technology, School of Life Sciences, Guangxi Normal University, Guangxi, China.
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50
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Butković A, González R, Rivarez MPS, Elena SF. A genome-wide association study identifies Arabidopsis thaliana genes that contribute to differences in the outcome of infection with two Turnip mosaic potyvirus strains that differ in their evolutionary history and degree of host specialization. Virus Evol 2021; 7:veab063. [PMID: 34532063 PMCID: PMC8438913 DOI: 10.1093/ve/veab063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 01/14/2023] Open
Abstract
Viruses lie in a continuum between generalism and specialism depending on their ability to infect more or less hosts. While generalists are able to successfully infect a wide variety of hosts, specialists are limited to one or a few. Even though generalists seem to gain an advantage due to their wide host range, they usually pay a pleiotropic fitness cost within each host. On the contrary, a specialist has maximal fitness within its own host. A relevant yet poorly explored question is whether viruses differ in the way they interact with their hosts' gene expression depending on their degree of specialization. Using a genome-wide association study approach, we have identified host genes whose expression depends on whether hosts were infected with more or less specialized viral strains. Four hundred fifty natural accessions of Arabidopsis thaliana were inoculated with Turnip mosaic potyvirus strains with different past evolutionary histories and that shown different degrees of specialization. Three disease-related traits were measured and associated with different sets of host genes for each strain. The genetic architectures of these traits differed among viral strains and, in the case of the more specialized virus, also varied along the duration of infection. While most of the mapped loci were strain specific, one shared locus was mapped for both strains, a disease-resistance TIR-NBS-LRR class protein. Likewise, only putative cysteine-rich receptor-like protein kinases were involved in all three traits. The impact on disease progress of 10 selected genes was validated by studying the infection phenotypes of loss-of-function mutant plants. Nine of these mutants have altered the disease progress and/or symptoms intensity between both strains. Compared to wild-type plants six had an effect on both viral strains, three had an effect only on the more specialized, and two were significant during infection with the less specialized.
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