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Zhang J, Sun T, Zhang W, Chen L. Identification of acidic stress-responsive genes and acid tolerance engineering in Synechococcus elongatus PCC 7942. Appl Microbiol Biotechnol 2024; 108:115. [PMID: 38204133 PMCID: PMC10781874 DOI: 10.1007/s00253-023-12984-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Cyanobacteria are excellent autotrophic photosynthetic chassis employed in synthetic biology, and previous studies have suggested that they have alkaline tolerance but low acid tolerance, significantly limiting their productivity as photosynthetic chassis and necessitating investigations into the acid stress resistance mechanism. In this study, differentially expressed genes were obtained by RNA sequencing-based comparative transcriptomic analysis under long-term acidic stress conditions and acidic shock treatment, in the model cyanobacterium Synechococcus elongatus PCC 7942. A pathway enrichment analysis revealed the upregulated and downregulated pathways during long-term acidic and shock stress treatment. The subsequent single gene knockout and phenotype analysis showed that under acidic stress conditions, the strains with chlL, chlN, pex, synpcc7942_2038, synpcc7942_1890, or synpcc7942_2547 knocked out grew worse than the wild type, suggesting their involvement in acid tolerance. This finding was further confirmed by introducing the corresponding genes back into the knockout mutant individually. Moreover, individual overexpression of the chlL and chlN genes in the wild type successfully improved the tolerance of S. elongatus PCC 7942 to acidic stress. This work successfully identified six genes involved in acidic stress responses, and overexpressing chIL or chIN individually successfully improved acid tolerance in S. elongatus PCC 7942, providing valuable information to better understand the acid resistance mechanism in S. elongatus PCC 7942 and novel insights into the robustness and tolerance engineering of cyanobacterial chassis. KEY POINTS: • DEGs were identified by RNA-seq based transcriptomics analysis in response to acidic stress in S. elongatus PCC 7942. • Six genes were identified to be involved in acid tolerance in S. elongatus PCC 7942. • Overexpression of chIL or chIN individually successfully improved the acid tolerance of S. elongatus PCC 7942.
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Affiliation(s)
- Jie Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300072, People's Republic of China.
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Wen Z, Hu R, Pi Q, Zhang D, Duan J, Li Z, Li Q, Zhao X, Yang M, Zhao X, Liu D, Su Z, Li D, Zhang Y. DEAD-box RNA helicase RH20 positively regulates RNAi-based antiviral immunity in plants by associating with SGS3/RDR6 bodies. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39166471 DOI: 10.1111/pbi.14448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024]
Abstract
RNA silencing plays a crucial role in defending against viral infections in diverse eukaryotic hosts. Despite extensive studies on core components of the antiviral RNAi pathway such as DCLs, AGOs and RDRs proteins, host factors involved in antiviral RNAi remain incompletely understood. In this study, we employed the proximity labelling approach to identify the host factors required for antiviral RNAi in Nicotiana benthamiana. Using the barley stripe mosaic virus (BSMV)-encoded γb, a viral suppressor of RNA silencing (VSR), as the bait protein, we identified the DEAD-box RNA helicase RH20, a broadly conserved protein in plants and animals with a homologous human protein known as DDX5. We demonstrated the interaction between RH20 and BSMV γb. Knockdown or knockout of RH20 attenuates the accumulation of viral small interfering RNAs, leading to increased susceptibility to BSMV, while overexpression of RH20 enhances resistance to BSMV, a process requiring the cytoplasmic localization and RNA-binding activity of RH20. In addition to BSMV, RH20 also negatively regulates the infection of several other positive-sense RNA viruses, suggesting the broad-spectrum antiviral activity of RH20. Mechanistic analysis revealed the colocalization and interaction of RH20 with SGS3/RDR6, and disruption of either SGS3 or RDR6 undermines the antiviral function of RH20, suggesting RH20 as a new component of the SGS3/RDR6 bodies. As a counter-defence, BSMV γb VSR subverts the RH20-mediated antiviral defence by interfering with the RH20-SGS3 interaction. Our results uncover RH20 as a new positive regulator of antiviral RNAi and provide new potential targets for controlling plant viral diseases.
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Affiliation(s)
- Zhiyan Wen
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Rujian Hu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qinglin Pi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dingliang Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiangning Duan
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhen Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qian Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiaoyun Zhao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Meng Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiaofei Zhao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Deshui Liu
- Beijing Life Science Academy, Beijing, China
| | - Zhen Su
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
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Mu F, Zheng H, Zhao Q, Zhu M, Dong T, Kai L, Li Z. Genome-wide systematic survey and analysis of the RNA helicase gene family and their response to abiotic stress in sweetpotato. BMC PLANT BIOLOGY 2024; 24:193. [PMID: 38493089 PMCID: PMC10944623 DOI: 10.1186/s12870-024-04824-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/14/2024] [Indexed: 03/18/2024]
Abstract
Sweetpotato (Ipomoea batatas (L.) Lam.) holds a crucial position as one of the staple foods globally, however, its yields are frequently impacted by environmental stresses. In the realm of plant evolution and the response to abiotic stress, the RNA helicase family assumes a significant role. Despite this importance, a comprehensive understanding of the RNA helicase gene family in sweetpotato has been lacking. Therefore, we conducted a comprehensive genome-wide analysis of the sweetpotato RNA helicase family, encompassing aspects such as chromosome distribution, promoter elements, and motif compositions. This study aims to shed light on the intricate mechanisms underlying the stress responses and evolutionary adaptations in sweetpotato, thereby facilitating the development of strategies for enhancing its resilience and productivity. 300 RNA helicase genes were identified in sweetpotato and categorized into three subfamilies, namely IbDEAD, IbDEAH and IbDExDH. The collinearity relationship between the sweetpotato RNA helicase gene and 8 related homologous genes from other species was explored, providing a reliable foundation for further study of the sweetpotato RNA helicase gene family's evolution. Furthermore, through RNA-Seq analysis and qRT-PCR verification, it was observed that the expression of eight RNA helicase genes exhibited significant responsiveness to four abiotic stresses (cold, drought, heat, and salt) across various tissues of ten different sweetpotato varieties. Sweetpotato transgenic lines overexpressing the RNA helicase gene IbDExDH96 were generated using A.rhizogenes-mediated technology. This approach allowed for the preliminary investigation of the role of sweetpotato RNA helicase genes in the response to cold stress. Notably, the promoters of RNA helicase genes contained numerous cis-acting elements associated with temperature, hormone, and light response, highlighting their crucial role in sweetpotato abiotic stress response.
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Affiliation(s)
- Fangfang Mu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Hao Zheng
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Qiaorui Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Lei Kai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China.
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Wu ZH, He LL, Wang CC, Liang C, Li HY, Zhong DW, Dong ZX, Zhang LJ, Zhang XQ, Ge LF, Chen S. Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high-quality reference transcript dataset. PHYSIOLOGIA PLANTARUM 2024; 176:e14280. [PMID: 38644527 DOI: 10.1111/ppl.14280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/29/2024] [Accepted: 03/09/2024] [Indexed: 04/23/2024]
Abstract
Inadequate reference databases in RNA-seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high-quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely-used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low-temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low-temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low-temperature stress, suggesting a unique co-regulatory mechanism governing transcription and splicing in the context of low-temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.
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Affiliation(s)
- Zhi-Hao Wu
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Liang-Liang He
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Cong-Cong Wang
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Chen Liang
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Han-Ying Li
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Dan-Wen Zhong
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Zhao-Xia Dong
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Li-Juan Zhang
- Shenzhen Tourism College of Jinan University, Shenzhen, Guangdong, China
| | - Xiang-Qian Zhang
- College of Food Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Liang-Fa Ge
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Shu Chen
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
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Yang Q, Xin C, Xiao QS, Lin YT, Li L, Zhao JL. Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species. FRONTIERS IN PLANT SCIENCE 2023; 14:1304264. [PMID: 38169692 PMCID: PMC10758403 DOI: 10.3389/fpls.2023.1304264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
Codon usage bias (CUB) refers to different codons exhibiting varying frequencies of usage in the genome. Studying CUB is crucial for understanding genome structure, function, and evolutionary processes. Herein, we investigated the codon usage patterns and influencing factors of protein-coding genes in the chloroplast genomes of four sister genera (monophyletic Roscoea and Cautleya, and monophyletic Pommereschea and Rhynchanthus) from the Zingiberaceae family with contrasting habitats in southwestern China. These genera exhibit distinct habitats, providing a unique opportunity to explore the adaptive evolution of codon usage. We conducted a comprehensive analysis of nucleotide composition and codon usage on protein-coding genes in the chloroplast genomes. The study focused on understanding the relationship between codon usage and environmental adaptation, with a particular emphasis on genes associated with photosynthesis. Nucleotide composition analysis revealed that the overall G/C content of the coding genes was ˂ 48%, indicating an enrichment of A/T bases. Additionally, synonymous and optimal codons were biased toward ending with A/U bases. Natural selection is the primary factor influencing CUB characteristics, particularly photosynthesis-associated genes. We observed differential gene expressions related to light adaptation among sister genera inhabiting different environments. Certain codons were favored under specific conditions, possibly contributing to gene expression regulation in particular environments. This study provides insights into the adaptive evolution of these sister genera by analyzing CUB and offers theoretical assistance for understanding gene expression and regulation. In addition, the data support the relationship between RNA editing and CUB, and the findings shed light on potential research directions for investigating adaptive evolution.
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Affiliation(s)
- Qian Yang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Cheng Xin
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qing-Song Xiao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Ya-Ting Lin
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Li Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Jian-Li Zhao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
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Stapley J, McDonald BA. Quantitative trait locus mapping of osmotic stress response in the fungal wheat pathogen Zymoseptoria tritici. G3 (BETHESDA, MD.) 2023; 13:jkad226. [PMID: 37774498 PMCID: PMC10700024 DOI: 10.1093/g3journal/jkad226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Osmotic stress is a ubiquitous and potent stress for all living organisms, but few studies have investigated the genetic basis of salt tolerance in filamentous fungi. The main aim of this study was to identify regions of the genome associated with tolerance to potassium chloride (KCl) in the wheat pathogen Zymoseptoria tritici. A secondary aim was to identify candidate genes affecting salt tolerance within the most promising chromosomal regions. We achieved these aims with a quantitative trait locus (QTL) mapping study using offspring from 2 crosses grown in vitro in the presence or absence of osmotic stress imposed by 0.75 M KCl. We identified significant QTL for most of the traits in both crosses. Several QTLs overlapped with QTL identified in earlier studies for other traits, and some QTL explained trait variation in both the control and salt stress environments. A significant QTL on chromosome 3 explained variation in colony radius at 8-day postinoculation (dpi) in the KCl environment as well as colony radius KCl tolerance at 8 dpi. The QTL peak had a high logarithm of the odds ratio (LOD) and encompassed an interval containing only 36 genes. Six of these genes present promising candidates for functional analyses. A gene ontology (GO) enrichment analysis of QTL unique to the KCl environment found evidence for the enrichment of functions involved in osmotic stress responses.
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Affiliation(s)
- Jessica Stapley
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zürich 8092, Switzerland
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zürich 8092, Switzerland
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Zheng M, Song Y, Wang L, Yang D, Yan J, Sun Y, Hsu YF. CaRH57, a RNA helicase, contributes pepper tolerance to heat stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108202. [PMID: 37995575 DOI: 10.1016/j.plaphy.2023.108202] [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: 08/01/2023] [Revised: 10/19/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
RNA helicases (RHs) are required for most aspects of RNA metabolism and play an important role in plant stress tolerance. Heat stress (HS) causes the deleterious effects on plant cells, such as membrane disruption and protein misfolding, which results in the inhibition of plant growth and development. In this study, CaRH57 was identified from pepper (Capsicum annuum) and encodes a DEAD-box RH. CaRH57 was induced by HS, and overexpression of CaRH57 in Atrh57-1 rescued the glucose-sensitive phenotype of Atrh57-1, suggesting the functional replacement of CaRH57 to AtRH57. The nucleolus-localized CaRH57 possessed a RH activity in vitro. CaRH57 knockdown impaired pepper heat tolerance, showing severe necrosis and enhanced ROS accumulation in the region of the shoot tip. Additionally, accumulation of aberrant-spliced CaHSFA1d and CaHSFA9d was enhanced, and the corresponding mature mRNA levels were reduced in the TRV2 (Tobacco rattle virus)-CaRH57-infected plants compared with the control plants under HS. Overall, these results suggested that CaRH57 acted as a RH to confer pepper heat tolerance and was required for the proper pre-mRNA splicing of some HS-related genes.
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Affiliation(s)
- Min Zheng
- School of Life Sciences, Southwest University, Chongqing, China.
| | - Yu Song
- School of Life Sciences, Southwest University, Chongqing, China
| | - Lingyu Wang
- School of Life Sciences, Southwest University, Chongqing, China
| | - Dandan Yang
- School of Life Sciences, Southwest University, Chongqing, China
| | - Jiawen Yan
- School of Life Sciences, Southwest University, Chongqing, China
| | - Yutao Sun
- School of Life Sciences, Southwest University, Chongqing, China
| | - Yi-Feng Hsu
- School of Life Sciences, Southwest University, Chongqing, China.
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Zhang XD, Han Y, Yang ZM, Sun D. DEAD-box RNA helicase 6 regulates drought and abscisic acid stress responses in rapeseed (Brassica napus). Gene 2023; 886:147717. [PMID: 37595852 DOI: 10.1016/j.gene.2023.147717] [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: 05/10/2023] [Revised: 08/05/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
DEAD-box RNA helicase is a major subfamily of RNA helicases with vital roles played in plant growth, development, and plant-environment interactions. RNA helicase 6 in rapeseed (Brassica napus) (BnRH6) is a member of DEAD-box RNA helicase. While previous research has demonstrated the role of BnRH6 in salt stress regulation, the involvement of BnRH6 in drought stress adaptation remains unknown. This report described a function of BnRH6 in drought stress response. BnRH6 was sufficiently induced by osmotic stress. Transgenic Brassica napus and Arabidopsis thaliana (Arabidopsis) overexpressing BnRH6 (OE) showed a drought tolerance phenotype, characterized by improved plant growth, increased survival rates, reduced water loss, leaf chlorosis and oxidative stress. Furthermore, BnRH6 was also induced by exogenous abscisic acid (ABA). BnRH6 overexpression plants exhibited ABA hypersensitivity with lagging seed germination, growth stunt and diminished stomatal opening in the presence of ABA, suggesting the involvement of ABA signal. Assessment of several well-identified drought stress responsive genes such as Calcium-dependent Protein Kinase 14 (BnCDPK14), Enhanced Response to ABA1 (BnERA1) and ABA Insensitive 1 (BnABI1) revealed that their expressions were accordingly changed in BnOE plants, possibly with interplays between BnRH6 and those genes. Our data highlighted the functional role of BnRH6, which plays a positive role in active regulation of drought stress response likely through an ABA-dependent manner in rapeseed plants.
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Affiliation(s)
- Xian Duo Zhang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuxiang Han
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Di Sun
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Mihailova G, Solti Á, Sárvári É, Hunyadi-Gulyás É, Georgieva K. Protein Changes in Shade and Sun Haberlea rhodopensis Leaves during Dehydration at Optimal and Low Temperatures. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020401. [PMID: 36679114 PMCID: PMC9861795 DOI: 10.3390/plants12020401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 05/27/2023]
Abstract
Haberlea rhodopensis is a unique resurrection plant of high phenotypic plasticity, colonizing both shady habitats and sun-exposed rock clefts. H. rhodopensis also survives freezing winter temperatures in temperate climates. Although survival in conditions of desiccation and survival in conditions of frost share high morphological and physiological similarities, proteomic changes lying behind these mechanisms are hardly studied. Thus, we aimed to reveal ecotype-level and temperature-dependent variations in the protective mechanisms by applying both targeted and untargeted proteomic approaches. Drought-induced desiccation enhanced superoxide dismutase (SOD) activity, but FeSOD and Cu/ZnSOD-III were significantly better triggered in sun plants. Desiccation resulted in the accumulation of enzymes involved in carbohydrate/phenylpropanoid metabolism (enolase, triosephosphate isomerase, UDP-D-apiose/UDP-D-xylose synthase 2, 81E8-like cytochrome P450 monooxygenase) and protective proteins such as vicinal oxygen chelate metalloenzyme superfamily and early light-induced proteins, dehydrins, and small heat shock proteins, the latter two typically being found in the latest phases of dehydration and being more pronounced in sun plants. Although low temperature and drought stress-induced desiccation trigger similar responses, the natural variation of these responses in shade and sun plants calls for attention to the pre-conditioning/priming effects that have high importance both in the desiccation responses and successful stress recovery.
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Affiliation(s)
- Gergana Mihailova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Ádám Solti
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary
| | - Éva Sárvári
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Eötvös Loránd Research Network, Temesvári Krt. 62., H-6726 Szeged, Hungary
| | - Katya Georgieva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
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Yang S, Li G, Li H. Molecular characterizations of genes in chloroplast genomes of the genus Arachis L. (Fabaceae) based on the codon usage divergence. PLoS One 2023; 18:e0281843. [PMID: 36917565 PMCID: PMC10013919 DOI: 10.1371/journal.pone.0281843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/01/2023] [Indexed: 03/16/2023] Open
Abstract
Studies on the molecular characteristics of chloroplast genome are generally important for clarifying the evolutionary processes of plant species. The base composition, the effective number of codons, the relative synonymous codon usage, the codon bias index, and their correlation coefficients of a total of 41 genes in 21 chloroplast genomes of the genus Arachis were investigated to further perform the correspondence and clustering analyses, revealing significantly higher variations in genomes of wild species than those of the cultivated taxa. The codon usage patterns of all 41 genes in the genus Arachis were AT-rich, suggesting that the natural selection was the main factor affecting the evolutionary history of these genomes. Five genes (i.e., ndhC, petD, atpF, rpl14, and rps11) and five genes (i.e., atpE, psbD, psaB, ycf2, and rps12) showed higher and lower base usage divergences, respectively. This study provided novel insights into our understanding of the molecular evolution of chloroplast genomes in the genus Arachis.
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Affiliation(s)
- Shuwei Yang
- School of Intelligent Science and Information Engineering, Xi’an Peihua University, Xi’An, Shaanxi, China
| | - Gun Li
- Department of Biomedical Engineering, Laboratory for Biodiversity Science, School of Electronic Information Engineering, Xi’An Technological University, Xi’An, Shaanxi, China
- * E-mail: (GL); (HL)
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, Jilin, China
- * E-mail: (GL); (HL)
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11
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Parakkunnel R, Naik K B, Vanishree G, C S, Purru S, Bhaskar K U, Bhat KV, Kumar S. Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome. FRONTIERS IN PLANT SCIENCE 2022; 13:1076229. [PMID: 36618639 PMCID: PMC9817154 DOI: 10.3389/fpls.2022.1076229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Susmita C
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
| | - Supriya Purru
- ICAR- National Academy of Agricultural Research Management, Hyderabad, Telengana, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - KV. Bhat
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
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12
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Identification of a DEAD-box RNA Helicase BnRH6 Reveals Its Involvement in Salt Stress Response in Rapeseed ( Brassica napus). Int J Mol Sci 2022; 24:ijms24010002. [PMID: 36613447 PMCID: PMC9819673 DOI: 10.3390/ijms24010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Rapeseed (Brassica napus) is one of the most important vegetable oil crops worldwide. Abiotic stresses such as salinity are great challenges for its growth and productivity. DEAD-box RNA helicase 6 (RH6) is a subfamily member of superfamily 2 (SF2), which plays crucial roles in plant growth and development. However, no report is available on RH6 in regulating plant abiotic stress response. This study investigated the function and regulatory mechanism for BnRH6. BnRH6 was targeted to the nucleus and cytoplasmic processing body (P-body), constitutively expressed throughout the lifespan, and induced by salt stress. Transgenic overexpressing BnRH6 in Brassica and Arabidopsis displayed salt hypersensitivity, manifested by lagging seed germination (decreased to 55−85% of wild-type), growth stunt, leaf chlorosis, oxidative stress, and over-accumulation of Na ions with the K+/Na+ ratio being decreased by 18.3−28.6%. Given the undesirable quality of knockout Brassica plants, we utilized an Arabidopsis T-DNA insertion mutant rh6-1 to investigate downstream genes by transcriptomics. We constructed four libraries with three biological replicates to investigate global downstream genes by RNA sequencing. Genome-wide analysis of differentially expressed genes (DEGs) (2-fold, p < 0.05) showed that 41 genes were upregulated and 66 genes were downregulated in rh6-1 relative to wild-type under salt stress. Most of them are well-identified and involved in transcription factors, ABA-responsive genes, and detoxified components or antioxidants. Our research suggests that BnRH6 can regulate a group of salt-tolerance genes to negatively promote Brassica adaptation to salt stress.
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13
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Comparative Analysis on the Codon Usage Pattern of the Chloroplast Genomes in Malus Species. Biochem Genet 2022; 61:1050-1064. [DOI: 10.1007/s10528-022-10302-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
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14
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Amoroso CG, Andolfo G, Capuozzo C, Di Donato A, Martinez C, Tomassoli L, Ercolano MR. Transcriptomic and genomic analysis provides new insights in molecular and genetic processes involved in zucchini ZYMV tolerance. BMC Genomics 2022; 23:371. [PMID: 35578183 PMCID: PMC9109310 DOI: 10.1186/s12864-022-08596-4] [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: 12/22/2020] [Accepted: 04/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cucurbita pepo is highly susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species cannot be considered as complete or broad-spectrum resistance. In this study, a source of tolerance introgressed in C. pepo (381e) from C. moschata, in True French (TF) background, was investigated 12 days post-inoculation (DPI) at transcriptomic and genomic levels. RESULTS The comparative RNA-sequencing (RNA-Seq) of TF (susceptible to ZYMV) and 381e (tolerant to ZYMV) allowed the evaluation of about 33,000 expressed transcripts and the identification of 146 differentially expressed genes (DEGs) in 381e, mainly involved in photosynthesis, transcription, cytoskeleton organization and callose synthesis. By contrast, the susceptible cultivar TF triggered oxidative processes related to response to biotic stimulus and activated key regulators of plant virus intercellular movement. In addition, the discovery of variants located in transcripts allowed the identification of two chromosome regions rich in Single Nucleotide Polymorphisms (SNPs), putatively introgressed from C. moschata, containing genes exclusively expressed in 381e. CONCLUSION 381e transcriptome analysis confirmed a global improvement of plant fitness by reducing the virus titer and movement. Furthermore, genes implicated in ZYMV tolerance in C. moschata introgressed regions were detected. Our work provides new insight into the plant virus recovery process and a better understanding of the molecular basis of 381e tolerance.
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Affiliation(s)
- C G Amoroso
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy
| | - G Andolfo
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy
| | - C Capuozzo
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy
| | - A Di Donato
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy
| | - C Martinez
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, 04120, Almería, Spain
| | - L Tomassoli
- Consiglio Per La Ricerca in Agricoltura e l'Analisi Dell'Economia Agraria, Research Centre of Plant Control and Certification, Rome, Italy
| | - M R Ercolano
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy.
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15
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Becskei A, Rahaman S. The life and death of RNA across temperatures. Comput Struct Biotechnol J 2022; 20:4325-4336. [PMID: 36051884 PMCID: PMC9411577 DOI: 10.1016/j.csbj.2022.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/05/2022] Open
Abstract
Temperature is an environmental condition that has a pervasive effect on cells along with all the molecules and reactions in them. The mechanisms by which prototypical RNA molecules sense and withstand heat have been identified mostly in bacteria and archaea. The relevance of these phenomena is, however, broader, and similar mechanisms have been recently found throughout the tree of life, from sex determination in reptiles to adaptation of viral RNA polymerases, to genetic disorders in humans. We illustrate the temperature dependence of RNA metabolism with examples from the synthesis to the degradation of mRNAs, and review recently emerged questions. Are cells exposed to greater temperature variations and gradients than previously surmised? How do cells reconcile the conflicting thermal stability requirements of primary and tertiary structures of RNAs? To what extent do enzymes contribute to the temperature compensation of the reaction rates in mRNA turnover by lowering the energy barrier of the catalyzed reactions? We conclude with the ecological, forensic applications of the temperature-dependence of RNA degradation and the biotechnological aspects of mRNA vaccine production.
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16
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Zhou YF, Zhang YC, Sun YM, Yu Y, Lei MQ, Yang YW, Lian JP, Feng YZ, Zhang Z, Yang L, He RR, Huang JH, Cheng Y, Liu YW, Chen YQ. The parent-of-origin lncRNA MISSEN regulates rice endosperm development. Nat Commun 2021; 12:6525. [PMID: 34764271 PMCID: PMC8585977 DOI: 10.1038/s41467-021-26795-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/22/2021] [Indexed: 11/09/2022] Open
Abstract
The cereal endosperm is a major factor determining seed size and shape. However, the molecular mechanisms of endosperm development are not fully understood. Long noncoding RNAs (lncRNAs) function in various biological processes. Here we show a lncRNA, MISSEN, that plays an essential role in early endosperm development in rice (Oryza sativa). MISSEN is a parent-of-origin lncRNA expressed in endosperm, and negatively regulates endosperm development, leading to a prominent dent and bulge in the seed. Mechanistically, MISSEN functions through hijacking a helicase family protein (HeFP) to regulate tubulin function during endosperm nucleus division and endosperm cellularization, resulting in abnormal cytoskeletal polymerization. Finally, we revealed that the expression of MISSEN is inhibited by histone H3 lysine 27 trimethylation (H3K27me3) modification after pollination. Therefore, MISSEN is the first lncRNA identified as a regulator in endosperm development, highlighting the potential applications in rice breeding.
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Affiliation(s)
- Yan-Fei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Meng Sun
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Meng-Qi Lei
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Wei Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jian-Ping Lian
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Zhao Feng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Zhi Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Lu Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jia-Hui Huang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu Cheng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Wei Liu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China. .,MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen University, 510275, Guangzhou, China.
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17
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Gahlaut V, Jaiswal V, Balyan HS, Joshi AK, Gupta PK. Multi-Locus GWAS for Grain Weight-Related Traits Under Rain-Fed Conditions in Common Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:758631. [PMID: 34745191 PMCID: PMC8568012 DOI: 10.3389/fpls.2021.758631] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
In wheat, a multi-locus genome-wide association study (ML-GWAS) was conducted for the four grain weight-related traits (days to anthesis, grain filling duration, grain number per ear, and grain weight per ear) using data recorded under irrigated (IR) and rain-fed (RF) conditions. Seven stress-related indices were estimated for these four traits: (i) drought resistance index (DI), (ii) geometric mean productivity (GMP), (iii) mean productivity index (MPI), (iv) relative drought index (RDI), (v) stress tolerance index (STI), (vi) yield index, and (vii) yield stability index (YSI). The association panel consisted of a core collection of 320 spring wheat accessions representing 28 countries. The panel was genotyped using 9,627 single nucleotide polymorphisms (SNPs). The genome-wide association (GWA) analysis provided 30 significant marker-trait associations (MTAs), distributed as follows: (i) IR (15 MTAs), (ii) RF (14 MTAs), and (iii) IR+RF (1 MTA). In addition, 153 MTAs were available for the seven stress-related indices. Five MTAs co-localized with previously reported QTLs/MTAs. Candidate genes (CGs) associated with different MTAs were also worked out. Gene ontology (GO) analysis and expression analysis together allowed the selection of the two CGs, which may be involved in response to drought stress. These two CGs included: TraesCS1A02G331000 encoding RNA helicase and TraesCS4B02G051200 encoding microtubule-associated protein 65. The results supplemented the current knowledge on genetics for drought tolerance in wheat. The results may also be used for future wheat breeding programs to develop drought-tolerant wheat cultivars.
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Affiliation(s)
- Vijay Gahlaut
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Council of Scientific & Industrial Research-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vandana Jaiswal
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Council of Scientific & Industrial Research-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Harindra S. Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Arun Kumar Joshi
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Pushpendra K. Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
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18
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Cheng J, Zhou S, Yang K, Yu H, Chen R, Zeng L, Li H, Wang Y, Song J. Identification of RNA helicases in Medicago truncatula and their expression patterns under abiotic stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2283-2296. [PMID: 34744366 PMCID: PMC8526662 DOI: 10.1007/s12298-021-01087-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/12/2021] [Accepted: 10/04/2021] [Indexed: 05/29/2023]
Abstract
UNLABELLED RNA helicase catalyzes the denaturation of DNA or the unwinding of double-stranded RNA. It is vital to RNA splicing, transport, editing, degradation and the initiation of protein translation. However, the function of RNA helicase in Medicago truncatula has rarely been reported. In this study, 170 putative RNA helicase genes were identified in the M. truncatula genome, and classified into three subfamilies based on the presence of either a DEAD-box (52 genes), DEAH-box (38 genes), or DExD/H-box (80 genes) in their coding regions. Additionally, conserved helicase_C domains and other functional domains (e.g., the HA2, DUF, and ZnF domains) were also present in these genes. Chromosomal mapping and synteny analyses showed that there were tandem and segment duplications of RNA helicase genes. Furthermore, transcriptome and real-time PCR analysis showed that the expression of 35 RNA helicase genes was affected by abiotic stress. To be specific, 17, 12 and 19 genes were regulated by salt, drought and cold stress, respectively. It is worth noting that MtDEAD8, MtDEAH3, MtDExD/H18 and MtDExD/H23 responded to all three types of stress. These results provide valuable information for understanding the RNA helicase genes in M. truncatula and their abiotic stress-related functions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01087-y.
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Affiliation(s)
- Jie Cheng
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Songsong Zhou
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
- Camphor Engineering Technology Research Center for State Forestry Administration, Jiangxi Academy of Forestry, Nanchang, 330032 People’s Republic of China
| | - Kun Yang
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Hongyang Yu
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Rongrong Chen
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Liming Zeng
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Hua Li
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002 People’s Republic of China
| | - Yihua Wang
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
- College of Science, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Jianbo Song
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
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19
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Li G, Zhang L, Xue P. Codon usage pattern and genetic diversity in chloroplast genomes of Panicum species. Gene 2021; 802:145866. [PMID: 34352297 DOI: 10.1016/j.gene.2021.145866] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022]
Abstract
Exploring the molecular identities and the genetic diversity of a plant species is crucial in figuring out the evolutionary pressure of genes as well as in molecular breeding application. Nineteen chloroplast genomes of Panicum species in the National Center for Biotechnology Information database were downloaded and analyzed. The base composition, the effective number of codons, the relative synonymous codon usage, the codon bias index and the codon adaptation index of all genes in all chloroplast genomes, as well as the correlation coefficient among them, were calculated and discussed. The correspondence analysis and the clustering characteristics among nineteen genomes base on the relative synonymous codon usage values of nineteen chloroplast genomes were calculated and analyzed. In order to figuring out the evolutionary diversity of certain genes, the codon usage pattern of forty-one typical genes were separately counted and compared. Summations of their standard deviations were considered to evaluate their genetic diversities. The results of codon usage pattern showed that all genes were obvious AU-rich ones in chloroplast genomes of Panicum species, revealing that the natural selection was the main factor that influenced their evolutionary process. The correspondence and clustering analysis among nineteen chloroplast genomes showed that the overall evolutionary differences among them were not significant. However, the analysis on the genetic diversity of tyical genes showed that the degrees of diversity are different, and that the shorter sequences are more prone to instability. These findings would improve our understanding on the evolution of chloroplast genomes of Panicum species and be useful for further study on their evolutionary phenomenon.
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Affiliation(s)
- Gun Li
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronics Information Engineering, Xi'An Technological University, Xi'An, China.
| | - Liang Zhang
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronics Information Engineering, Xi'An Technological University, Xi'An, China
| | - Pei Xue
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronics Information Engineering, Xi'An Technological University, Xi'An, China
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Singh RK, Prasad A, Muthamilarasan M, Parida SK, Prasad M. Breeding and biotechnological interventions for trait improvement: status and prospects. PLANTA 2020; 252:54. [PMID: 32948920 PMCID: PMC7500504 DOI: 10.1007/s00425-020-03465-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/12/2020] [Indexed: 05/06/2023]
Abstract
Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.
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Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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