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Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading. Proc Natl Acad Sci U S A 2022; 119:e2001290119. [PMID: 35759655 PMCID: PMC9271158 DOI: 10.1073/pnas.2001290119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of the Arabidopsis thaliana genome are specifically down-regulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some transposable element loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine synthase methionine adenosyl transferase 3 (MAT3), which is required for H3K9me2. A Topoisomerase VI defect affects MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a possible mechanistic explanation to the essential role of Topoisomerase VI in the delimitation of chromatin domains.
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Noryan M, Hervan IM, Sabouri H, Kojouri FD, Mastinu A. Drought Resistance Loci in Recombinant Lines of Iranian Oryza sativa L. in Germination Stage. BIOTECH 2021; 10:biotech10040026. [PMID: 35822800 PMCID: PMC9245469 DOI: 10.3390/biotech10040026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 12/17/2022] Open
Abstract
In order to locate control genes related to Oryza sativa L. traits at the germination stage under normal conditions and at drought stress levels (−4.5 and −9.0 bar), we evaluated 120 F8 generation offspring from the cross between two cultivars Neda × Ahlemitarum in a factorial experiment in a completely randomized block design with three replications in 2013 in the botanical laboratory of Gonbad Kavous University. A linkage map was prepared using 90 Simple Sequence Repeats (SSR) markers and 28 Inter Simple Sequence Repeats (ISSR), and 6 iPBS and 9 IRAP markers (265 polymorphic alleles). The results of the analysis of variance showed that all of the evaluated traits had a significant difference at the probability level of 1%. Hence, it can be noted that the desired genetic diversity can be found between genotypes. The results of the stepwise regression analysis for the germination percentage as a dependent variable and other traits as independent variables in the studied treatments showed that under normal conditions, there was variable coleoptile length, but under drought stress of −4.5 and −9.0 bar, the variable plumule dry weight entered the model. In this study, the markers included in RM1-RM490 and ISSR2-3-RM133 of chromosomes 1 and 6 of Oryza sativa were identified as the main regulators of traits associated with Oryza sativa drought resistance. In particular, they present the quantitative trait loci (QTL) that control the first stages of germination of Oryza sativa in water stress conditions.
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Affiliation(s)
- Morteza Noryan
- Department of Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran; (M.N.); (I.M.H.); (F.D.K.)
| | - Islam Majidi Hervan
- Department of Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran; (M.N.); (I.M.H.); (F.D.K.)
| | - Hossein Sabouri
- Department of Plant Production, Collage of Agricultural Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous 4971799151, Iran
- Correspondence: (H.S.); (A.M.)
| | - Faroukh Darvish Kojouri
- Department of Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran; (M.N.); (I.M.H.); (F.D.K.)
| | - Andrea Mastinu
- Department of Molecular and Translational Medicine, Division of Pharmacology, University of Brescia, 25123 Brescia, Italy
- Correspondence: (H.S.); (A.M.)
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Qi T, Liu J, Zhao P, Ge B, Liu Q, Jiang S, Wang Z, Zhang H, Tang B, Ding G, Zhang D. A novel modulation of physiological regulation in cultured Chinese mitten crab (Eriocheir japonica sinensis) in response to consistent salinity changes. Gene 2020; 756:144914. [PMID: 32574759 DOI: 10.1016/j.gene.2020.144914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/17/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
The life history of the Chinese mitten crab (Eriocheir japonica sinensis) includes two migrations: a feeding migration and a reproductive migration. Ambient salinity is one of the most critical factors during migration. In this study, the salinity adaptation mechanism of Chinese mitten crabs was simulated using continuous salinity changes. The expression of six key genes [Na+/K+-ATPase α subunit (NAK-α), V-type H+-ATPase subunit A (VHA-A), Zinc transporter (ZnT), Cl- channel protein 2 (CLCN2), ubiquitin/ribosomal S27 fusionprotein (S27), and glutathione S-transferase (GST)] and the activities of three enzymes [Na+/K+-ATPase (NAK), V-type H+-ATPase (VHA), and glutathione S-transferase (GST)] were evaluated in ten groups exposed to a range of salinity changes during mariculture based on the transcriptome data obtained from short term salinity-induced crabs (ES) compared to control group in freshwater crabs (EF). The results revealed that different genes exhibited different roles in physiological regulation. In total, 3,599 unigenes were significantly and differentially expressed in a comparison between the EF and ES treatments. A novel modulation of gene expression and the corresponding enzyme activity of NAK and VHA exhibited similar patterns. As genes related to osmoregulation, NAK and VHA showed similar patterns of both gene expression and enzyme activity in mariculture. During the gradual change in salinity from 0‰ to 25‰ and back to 0‰, the gene expression and enzyme activities of NAK and VHA initially increased (0‰ → 10‰), weakened (10‰ → 20‰) and then increased again (20‰ → 25‰ → 0‰). S27 could serve as a reference gene in the expression analysis of Chinese mitten crabs under salinity stress. ZnT and CLCN2 were involved in osmoregulation as functional proteins. Our findings provide insights into the regulation mechanisms employed during the migration of the Chinese mitten crab.
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Affiliation(s)
- Tingting Qi
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China; College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jun Liu
- Key Laboratory of Biotechnology, Lianyungang Normal College, Lianyungang 222006, China
| | - Peisong Zhao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Baoming Ge
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Qiuning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Senhao Jiang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Huabin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China
| | - Ge Ding
- Chemical and Biological Engineering College, Yancheng Institute of Technology, Yancheng 224003, China.
| | - Daizhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224051, China.
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Sexual reproduction potential implied by functional analysis of SPO11 in Phaeodactylum tricornutum. Gene 2020; 757:144929. [PMID: 32622990 DOI: 10.1016/j.gene.2020.144929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/19/2020] [Accepted: 06/27/2020] [Indexed: 01/05/2023]
Abstract
Phaeodactylum tricornutum is a model microalgae that is widely used to study diatom physiology and ecology. Since the meiotic process and sexual cycle have never been observed directly, P. tricornutum has been considered to be an asexual species. However, phylogenetic analysis of the P. tricornutum genome has revealed a series of meiosis-specific gene homologues in this species. We identified two copies of differently transcribed SPO11 homologs that contain the conserved motifs of Winged-helix and Toprim domains. The homolog PtSPO11-3 interacts with TopoVIB in yeast two-hybrid analysis, whereas the homolog PtSPO11-2 could rescue the sporulation defect of a Spo11 yeast mutant strain. PtSPO11-2 was also found to be significantly up-regulated at low temperatures in P. tricornutum and its key catalytic residue was important to the homolog's function in sporulation. The results herein provide positive clue that meiosis and sexual reproduction could exist in this diatom.
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Lang L, Schnittger A. Endoreplication - a means to an end in cell growth and stress response. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:85-92. [PMID: 32217456 DOI: 10.1016/j.pbi.2020.02.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
Endoreplication, also called endoreduplication or endopolyploidization, is a cell cycle variant in which the genome is re-replicated in the absence of mitosis causing cellular polyploidization. Despite the common occurrence of endoreplication in plants and the tremendous extent in specific tissues and cell types such as the endosperm, the underlying molecular regulation and the physiological consequences have only now started to be understood. Endoreplication is often associated with cell differentiation and withdrawal from mitotic cycles. Recent studies have underlined the importance of endoreplication as a stress response and we summarize here this progress with particular focus on future perspectives offered by the recent advances in genomics and biotechnology.
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Affiliation(s)
- Lucas Lang
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Developmental Biology, Ohnhorststr. 18, D-22609 Hamburg, Germany
| | - Arp Schnittger
- University of Hamburg, Institute of Plant Science and Microbiology, Department of Developmental Biology, Ohnhorststr. 18, D-22609 Hamburg, Germany.
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Tian Y, Gu H, Fan Z, Shi G, Yuan J, Wei F, Yang Y, Tian B, Cao G, Huang J. Role of a cotton endoreduplication-related gene, GaTOP6B, in response to drought stress. PLANTA 2019; 249:1119-1132. [PMID: 30552583 DOI: 10.1007/s00425-018-3067-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/10/2018] [Indexed: 05/24/2023]
Abstract
Cotton GaTOP6B is involved in cellular endoreduplication and a positive response to drought stress via promoting plant leaf and root growth. Drought is deemed as one of adverse conditions that could cause substantial reductions in crop yields worldwide. Since cotton exhibits a moderate-tolerant phenotype under water-deficit conditions, the plant could therefore be used to characterize potential new genes regulating drought tolerance in crop plants. In this work, GaTOP6B, encoding DNA topoisomerase VI subunit B, was identified in Asian cotton (Gossypium arboreum). Virus-induced gene silencing (VIGS) and overexpression (OE) were used to investigate the biological function of GaTOP6B in G. arboreum and Arabidopsis thaliana under drought stress. The GaTOP6B-silencing plants showed a reduced ploidy level, and displayed a compromised tolerance phenotype including lowered relative water content (RWC), decreased proline content and antioxidative enzyme activity, and an increased malondialdehyde (MDA) content under drought stress. GaTOP6B-overexpressing Arabidopsis lines, however, had increased ploidy levels, and were more tolerant to drought treatment, associated with improved RWC maintenance, higher proline accumulation, and reduced stomatal aperture under drought stress. Transcriptome analysis showed that genes involved in the processes like cell cycle, transcription and signal transduction, were substantially up-regulated in GaTOP6B-overexpressing Arabidopsis, promoting plant growth and development. More specifically, under drought stress, the genes involved in the biosynthesis of secondary metabolites such as phenylpropanoid, starch and sucrose were selectively enhanced to improve tolerance in plants. Taken together, the results demonstrated that GaTOP6B could coordinately regulate plant leaf and root growth via cellular endoreduplication, and positively respond to drought stress. Thus, GaTOP6B could be a competent candidate gene for improvement of drought tolerance in crop species.
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Affiliation(s)
- Yanfei Tian
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Huihui Gu
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Zhuxuan Fan
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Gongyao Shi
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Jiachen Yuan
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Fang Wei
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
| | - Yan Yang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Baoming Tian
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
| | - Gangqiang Cao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Jinyong Huang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
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Li QF, Wang JD, Xiong M, Wei K, Zhou P, Huang LC, Zhang CQ, Fan XL, Liu QQ. iTRAQ-Based Analysis of Proteins Co-Regulated by Brassinosteroids and Gibberellins in Rice Embryos during Seed Germination. Int J Mol Sci 2018; 19:ijms19113460. [PMID: 30400353 PMCID: PMC6274883 DOI: 10.3390/ijms19113460] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/27/2018] [Accepted: 11/01/2018] [Indexed: 11/23/2022] Open
Abstract
Seed germination, a pivotal process in higher plants, is precisely regulated by various external and internal stimuli, including brassinosteroid (BR) and gibberellin (GA) phytohormones. The molecular mechanisms of crosstalk between BRs and GAs in regulating plant growth are well established. However, whether BRs interact with GAs to coordinate seed germination remains unknown, as do their common downstream targets. In the present study, 45 differentially expressed proteins responding to both BR and GA deficiency were identified using isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis during seed germination. The results indicate that crosstalk between BRs and GAs participates in seed germination, at least in part, by modulating the same set of responsive proteins. Moreover, most targets exhibited concordant changes in response to BR and GA deficiency, and gene ontology (GO) indicated that most possess catalytic activity and are involved in various metabolic processes. Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) analysis was used to construct a regulatory network of downstream proteins mediating BR- and GA-regulated seed germination. The mutation of GRP, one representative target, notably suppressed seed germination. Our findings not only provide critical clues for validating BR–GA crosstalk during rice seed germination, but also help to optimise molecular regulatory networks.
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Affiliation(s)
- Qian-Feng Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.
| | - Jin-Dong Wang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
| | - Min Xiong
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
| | - Ke Wei
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
| | - Peng Zhou
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
| | - Li-Chun Huang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
| | - Chang-Quan Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.
| | - Xiao-Lei Fan
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.
| | - Qiao-Quan Liu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.
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Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK. Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. RICE (NEW YORK, N.Y.) 2016; 9:1. [PMID: 26743769 PMCID: PMC4705060 DOI: 10.1186/s12284-015-0073-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/22/2015] [Indexed: 05/05/2023]
Abstract
Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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Robert T, Vrielynck N, Mézard C, de Massy B, Grelon M. A new light on the meiotic DSB catalytic complex. Semin Cell Dev Biol 2016; 54:165-76. [DOI: 10.1016/j.semcdb.2016.02.025] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/22/2016] [Indexed: 11/30/2022]
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Guan QJ, Ma HY, Wang ZJ, Wang ZY, Bu QY, Liu SK. A rice LSD1-like-type ZFP gene OsLOL5 enhances saline-alkaline tolerance in transgenic Arabidopsis thaliana, yeast and rice. BMC Genomics 2016; 17:142. [PMID: 26920613 PMCID: PMC4769587 DOI: 10.1186/s12864-016-2460-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/10/2016] [Indexed: 11/26/2022] Open
Abstract
Background Zinc finger proteins (ZFPs) play an important role in regulating plant responses to abiotic stress. However, little is known about the function of LSD1-like-type ZFP in saline-alkaline (SA) stress resistance of rice. In this study, OsLOL5 (GenBank No. AJ620677), containing two LSD1-like-type C2C2 domains, was isolated and analyzed its protection roles in transgenic plants and yeast. OsLOL5 was located in the nucleus as evidenced by the bombardment of onion epidermal cells. Results OsLOL5 expression significantly increased in rice leaves and roots under 150 mmol L-1 NaCl, 30 mM NaHCO3, and 10 mmol L-1 H2O2 treatment, respectively. Overexpression of OsLOL5 in yeast resulted in SA tolerance at significant level. Transgenic Arabidopsis plants overexpressing OsLOL5 grew well in the presence ofboth NaCl and NaHCO3 treatments, whereas wild-type plants exhibited chlorosis, stunted growth phenotype, and even death. SA stress caused significant changes in the malondialdehyde (MDA) contents in non-transgenic plants compared with those in transgenic lines. Transgenic rice overexpressing OsLOL5 exhibited stronger resistance than NT under NaHCO3 treatment, as demonstrated by its greater shoot length, and fresh weight. The genes associated with oxidative stress, such as OsAPX2, OsCAT, OsCu/Zn-SOD, and OsRGRC2, were significantly upregulated in OsLOL5-overexpressing rice. The results suggested that OsLOL5 improved SA tolerance in plants, and regulated oxidative and salinity stress retardation via the active oxygen detoxification pathway. Conclusions The yeast INVScI bacterium grew significantly better than the control strain under NaCl, NaHCO3, and H2O2 treatments. These findings illustrated that OsLOL5 overexpression enhanced yeast resistance for SA stress through active oxygen species. The present study showed that the OsLOL5 genes involved in the ROS signaling pathways may combine with the model plant Arabidopsis and rice in LDS1-type ZFP by ROS signaling pathways that regulate cell necrosis. We speculated that the OsLOL5 active oxygen scavenging system may have coordinating roles. The present study further revealed that OsLOL5 ZFP could regulate oxidative stress function, but could also provide a basis for salt-resistant rice strains. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2460-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Q J Guan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No.26 Hexing Road, Nangang District, Harbin City, Heilongjiang, 150040, China.
| | - H Y Ma
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No.26 Hexing Road, Nangang District, Harbin City, Heilongjiang, 150040, China.
| | - Z J Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No.26 Hexing Road, Nangang District, Harbin City, Heilongjiang, 150040, China.
| | - Z Y Wang
- Lab of Soybean Molecular Biology and Molecular Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No.138 Haping Road, Nangang District, Harbin City, Heilongjiang, 150081, China.
| | - Q Y Bu
- Lab of Soybean Molecular Biology and Molecular Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, No.138 Haping Road, Nangang District, Harbin City, Heilongjiang, 150081, China.
| | - S K Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, No.26 Hexing Road, Nangang District, Harbin City, Heilongjiang, 150040, China.
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Wu Z, Ji J, Tang D, Wang H, Shen Y, Shi W, Li Y, Tan X, Cheng Z, Luo Q. OsSDS is essential for DSB formation in rice meiosis. FRONTIERS IN PLANT SCIENCE 2015; 6:21. [PMID: 25691887 PMCID: PMC4315026 DOI: 10.3389/fpls.2015.00021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/10/2015] [Indexed: 05/18/2023]
Abstract
SDS is a meiosis specific cyclin-like protein and required for DMC1 mediated double-strand break (DSB) repairing in Arabidopsis. Here, we found its rice homolog, OsSDS, is essential for meiotic DSB formation. The Ossds mutant is normal in vegetative growth but both male and female gametes are inviable. The Ossds meiocytes exhibit severe defects in homologous pairing and synapsis. No γH2AX immunosignals in Ossds meiocytes together with the suppression of chromosome fragmentation in Ossds-1 Osrad51c, both provide strong evidences that OsSDS is essential for meiotic DSB formation. Immunostaining investigations revealed that meiotic chromosome axes are normally formed but both SC installation and localization of recombination elements are failed in Ossds. We suspected that this cyclin protein has been differentiated pretty much between monocots and dicots on its function in meiosis.
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Affiliation(s)
- Zhigang Wu
- Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural UniversityKunming, China
| | - Jianhui Ji
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- School of Life Sciences, Huaiyin Normal UniversityHuaian, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Hongjun Wang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Wenqing Shi
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Xuelin Tan
- Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural UniversityKunming, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- *Correspondence: Zhukuan Cheng, State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China e-mail:
| | - Qiong Luo
- Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural UniversityKunming, China
- Qiong Luo, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Heilongtan, Guandu District, Kunming 650201, China e-mail:
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12
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Characterization of putative cis-regulatory elements in genes preferentially expressed in Arabidopsis male meiocytes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:708364. [PMID: 25250331 PMCID: PMC4163388 DOI: 10.1155/2014/708364] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/19/2014] [Accepted: 07/20/2014] [Indexed: 11/18/2022]
Abstract
Meiosis is essential for plant reproduction because it is the process during which homologous chromosome pairing, synapsis, and meiotic recombination occur. The meiotic transcriptome is difficult to investigate because of the size of meiocytes and the confines of anther lobes. The recent development of isolation techniques has enabled the characterization of transcriptional profiles in male meiocytes of Arabidopsis. Gene expression in male meiocytes shows unique features. The direct interaction of transcription factors (TFs) with DNA regulatory sequences forms the basis for the specificity of transcriptional regulation. Here, we identified putative cis-regulatory elements (CREs) associated with male meiocyte-expressed genes using in silico tools. The upstream regions (1 kb) of the top 50 genes preferentially expressed in Arabidopsis meiocytes possessed conserved motifs. These motifs are putative binding sites of TFs, some of which share common functions, such as roles in cell division. In combination with cell-type-specific analysis, our findings could be a substantial aid for the identification and experimental verification of the protein-DNA interactions for the specific TFs that drive gene expression in meiocytes.
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13
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Mittal A, Balasubramanian R, Cao J, Singh P, Subramanian S, Hicks G, Nothnagel EA, Abidi N, Janda J, Galbraith DW, Rock CD. TOPOISOMERASE 6B is involved in chromatin remodelling associated with control of carbon partitioning into secondary metabolites and cell walls, and epidermal morphogenesis in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4217-39. [PMID: 24821950 PMCID: PMC4112631 DOI: 10.1093/jxb/eru198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant growth is continuous and modular, a combination that allows morphogenesis by cell division and elongation and serves to facilitate adaptation to changing environments. The pleiotropic phenotypes of the harlequin (hlq) mutant, isolated on the basis of ectopic expression of the abscisic acid (ABA)- and auxin-inducible proDc3:GUS reporter gene, were previously characterized. Mutants are skotomorphogenic, have deformed and collapsed epidermal cells which accumulate callose and starch, cell walls abundant in pectins and cell wall proteins, and abnormal and reduced root hairs and leaf trichomes. hlq and two additional alleles that vary in their phenotypic severity of starch accumulation in the light and dark have been isolated, and it is shown that they are alleles of bin3/hyp6/rhl3/Topoisomerase6B. Mutants and inhibitors affecting the cell wall phenocopy several of the traits displayed in hlq. A microarray analysis was performed, and coordinated expression of physically adjacent pairs/sets of genes was observed in hlq, suggesting a direct effect on chromatin. Histones, WRKY and IAA/AUX transcription factors, aquaporins, and components of ubiquitin-E3-ligase-mediated proteolysis, and ABA or biotic stress response markers as well as proteins involved in cellular processes affecting carbon partitioning into secondary metabolites were also identified. A comparative analysis was performed of the hlq transcriptome with other previously published TopoVI mutant transcriptomes, namely bin3, bin5, and caa39 mutants, and limited concordance between data sets was found, suggesting indirect or genotype-specific effects. The results shed light on the molecular mechanisms underlying the det/cop/fus-like pleiotropic phenotypes of hlq and support a broader role for TopoVI regulation of chromatin remodelling to mediate development in response to environmental and hormonal signals.
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Affiliation(s)
- Amandeep Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Rajagopal Balasubramanian
- Tamil Nadu Agricultural University, Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Madurai-625 104, India
| | - Jin Cao
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143 005, Punjab, India
| | - Senthil Subramanian
- South Dakota State University, Department of Plant Science, Brookings, SD 57007, USA
| | - Glenn Hicks
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA Department of Botany and Plant Sciences, University of California, Riverside CA 92521-0124, USA
| | - Eugene A Nothnagel
- Department of Botany and Plant Sciences, University of California, Riverside CA 92521-0124, USA
| | - Noureddine Abidi
- Texas Tech University, Department of Plant and Soil Science and Fiber and Biopolymer Research Institute, 1001 East Loop 289, Lubbock, TX 79409-5019, USA
| | - Jaroslav Janda
- University of Arizona, Department of Plant Sciences and BIO5 Institute, 341 Keating Bldg, Tucson, AZ 85721, USA
| | - David W Galbraith
- University of Arizona, Department of Plant Sciences and BIO5 Institute, 341 Keating Bldg, Tucson, AZ 85721, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
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de Massy B. Initiation of meiotic recombination: how and where? Conservation and specificities among eukaryotes. Annu Rev Genet 2014; 47:563-99. [PMID: 24050176 DOI: 10.1146/annurev-genet-110711-155423] [Citation(s) in RCA: 241] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Meiotic recombination is essential for fertility in most sexually reproducing species. This process also creates new combinations of alleles and has important consequences for genome evolution. Meiotic recombination is initiated by the formation of DNA double-strand breaks (DSBs), which are repaired by homologous recombination. DSBs are catalyzed by the evolutionarily conserved SPO11 protein, assisted by several other factors. Some of them are absolutely required, whereas others are needed only for full levels of DSB formation and may participate in the regulation of DSB timing and frequency as well as the coordination between DSB formation and repair. The sites where DSBs occur are not randomly distributed in the genome, and remarkably distinct strategies have emerged to control their localization in different species. Here, I review the recent advances in the components required for DSB formation and localization in the various model organisms in which these studies have been performed.
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Affiliation(s)
- Bernard de Massy
- Institute of Human Genetics, Centre National de la Recherché Scientifique, UPR1142, 34396 Montpellier, France;
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15
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Checker VG, Khurana P. Molecular and functional characterization of mulberry EST encoding remorin (MiREM) involved in abiotic stress. PLANT CELL REPORTS 2013; 32:1729-41. [PMID: 23942844 DOI: 10.1007/s00299-013-1483-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 05/08/2023]
Abstract
KEY MESSAGE Group1 remorins may help the plants to optimize their growth under adverse conditions by their involvement in mediating osmotic stress responses in plants. ABSTRACT Mulberry (Morus indica), a deciduous woody tree, serves as the cardinal component of the sericulture industry. Genomic endeavors in sequencing of mulberry ESTs provided clues to stress-specific clones, but their functional relevance remains fragmentary. Therefore in this study, we assessed the functional significance of a remorin gene family member that was identified in leaf ESTs. Remorins represent a large, plant-specific multigene family gaining importance in recent times with respect to their role in plant-microbe interactions, although their role in response to environmental stresses remains speculative as in vivo functions of remorin genes are limited. Mulberry remorin (MiREM) localizes to plasma membrane and is ubiquitously present in all plant organs. Expression analysis of MiREM by northern analysis reveals that its transcript increases under different abiotic stress conditions especially during dehydration and salt stress, implicating it in regulation of stress signaling pathways. Concomitantly, transgenic Arabidopsis plants overexpressing heterologous remorin show tolerance to dehydration and salinity at the germination and seedling stages as revealed by percentage germination, root inhibition assays, fresh weight and activity of photosystem II. This study predicts the possible function of group 1 remorin gene in mediating osmotic stress thus bringing novel perspectives in understanding the function of remorins in plant abiotic stress responses.
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Affiliation(s)
- Vibha G Checker
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, 110021, India
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16
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Integration of stress-related and reactive oxygen species-mediated signals by Topoisomerase VI in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2012; 109:16360-5. [PMID: 22988090 DOI: 10.1073/pnas.1202041109] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Environmental stress often leads to an increased production of reactive oxygen species that are involved in plastid-to-nucleus retrograde signaling. Soon after the release of singlet oxygen ((1)O(2)) in chloroplasts of the flu mutant of Arabidopsis, reprogramming of nuclear gene expression reveals a rapid transfer of signals from the plastid to the nucleus. We have identified extraplastidic signaling constituents involved in (1)O(2)-initiated plastid-to-nucleus signaling and nuclear gene activation after mutagenizing a flu line expressing the luciferase reporter gene under the control of the promoter of a (1)O(2)-responsive AAA-ATPase gene (At3g28580) and isolating second-site mutations that lead to a constitutive up-regulation of the reporter gene or abrogate its (1)O(2)-dependent up-regulation. One of these mutants, caa39, turned out to be a weak mutant allele of the Topoisomerase VI (Topo VI) A-subunit gene with a single amino acid substitution. Transcript profile analysis of flu and flu caa39 mutants revealed that Topo VI is necessary for the full activation of AAA-ATPase and a set of (1)O(2)-responsive transcripts in response to (1)O(2). Topo VI binds to the promoter of the AAA-ATPase and other (1)O(2)-responsive genes, and hence could directly regulate their expression. Under photoinhibitory stress conditions, which enhance the production of (1)O(2) and H(2)O(2), Topo VI regulates (1)O(2)-responsive and H(2)O(2)-responsive genes in a distinct manner. These results suggest that Topo VI acts as an integrator of multiple signals generated by reactive oxygen species formed in plants under adverse environmental conditions.
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17
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Jia Y, Jia MH, Wang X, Liu G. Indica and japonica crosses resulting in linkage block and recombination suppression on rice chromosome 12. PLoS One 2012; 7:e43066. [PMID: 22912788 PMCID: PMC3422337 DOI: 10.1371/journal.pone.0043066] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/16/2012] [Indexed: 11/23/2022] Open
Abstract
Understanding linkage block size and molecular mechanisms of recombination suppression is important for plant breeding. Previously large linkage blocks ranging from 14 megabases to 27 megabases were observed around the rice blast resistance gene Pi-ta in rice cultivars and backcross progeny involving an indica and japonica cross. In the present study, the same linkage block was further examined in 456 random recombinant individuals of rice involving 5 crosses ranging from F(2) to F(10) generation, with and without Pi-ta containing genomic indica regions with both indica and japonica germplasm. Simple sequence repeat markers spanning the entire chromosome 12 were used to detect recombination break points and to delimit physical size of linkage blocks. Large linkage blocks ranging from 4.1 megabases to 10 megabases were predicted from recombinant individuals involving genomic regions of indica and japonica. However, a significantly reduced block from less than 800 kb to 2.1megabases was identified from crosses of indica with indica rice regardless of the existence of Pi-ta. These findings suggest that crosses of indica and japonica rice have significant recombination suppression near the centromere on chromosome 12.
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Affiliation(s)
- Yulin Jia
- Dale Bumpers National Rice Research Center, Agricultural Research Service, United States Department of Agriculture, Stuttgart, Arkansas, United States of America.
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18
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Li J, Farmer AD, Lindquist IE, Dukowic-Schulze S, Mudge J, Li T, Retzel EF, Chen C. Characterization of a set of novel meiotically-active promoters in Arabidopsis. BMC PLANT BIOLOGY 2012; 12:104. [PMID: 22776406 PMCID: PMC3462685 DOI: 10.1186/1471-2229-12-104] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/13/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND Homologous recombination, together with selection, laid the foundation for traditional plant breeding. The recombination process that takes place during meiotic cell division is crucial for the creation of novel variations of highly desired traits by breeders. Gaining control over this process is important for molecular breeding to achieve more precise, large-scale and quicker plant improvement. As conventional ubiquitous promoters are neither tissue-specific nor efficient in driving gene expression in meiocytes, promoters with high meiotic activities are potential candidates for manipulating the recombination process. So far, only a few meiotically-active promoters have been reported. Recently developed techniques to profile the transcriptome landscape of isolated meiocytes provided the means to discover promoters from genes that are actively expressed in meiosis. RESULTS In a screen for meiotically-active promoters, we examined ten promoter sequences that are associated with novel meiotic candidate genes. Each promoter was tested by expressing a GFP reporter gene in Arabidopsis. Characterization of regulatory regions revealed that these meiotically-active promoters possessed conserved motifs and motif arrangement. Some of the promoters unite optimal properties which are invaluable for meiosis-directed studies such as delivering specific gene expression in early meiosis I and/or meiosis II. Furthermore, the examination of homologs of the corresponding genes within green plants points to a great potential of applying the information from Arabidopsis to other species, especially crop plants. CONCLUSIONS We identified ten novel meiotically-active promoters; which, along with their homologs, are prime candidates to specifically drive gene expression during meiosis in plants and can thus provide important tools for meiosis study and crop breeding.
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Affiliation(s)
- Junhua Li
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN, 55108, USA
- College of Life Sciences, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Andrew D Farmer
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Ingrid E Lindquist
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Stefanie Dukowic-Schulze
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN, 55108, USA
| | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Tao Li
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN, 55108, USA
| | - Ernest F Retzel
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN, 55108, USA
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An XJ, Deng ZY, Wang T. OsSpo11-4, a rice homologue of the archaeal TopVIA protein, mediates double-strand DNA cleavage and interacts with OsTopVIB. PLoS One 2011; 6:e20327. [PMID: 21637817 PMCID: PMC3102714 DOI: 10.1371/journal.pone.0020327] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 04/21/2011] [Indexed: 11/17/2022] Open
Abstract
DNA topoisomerase VI from Archaea, a heterotetrameric complex composed of two TopVIA and two TopVIB subunits, is involved in altering DNA topology during replication, transcription and chromosome segregation by catalyzing DNA strand transfer through transient double-strand breaks. The sequenced yeast and animal genomes encode only one homologue of the archaeal TopVIA subunit, namely Spo11, and no homologue of the archaeal TopVIB subunit. In yeast, Spo11 is essential for initiating meiotic recombination and this function appears conserved among other eukaryotes. In contrast to yeast and animals, studies in Arabidopsis and rice have identified three Spo11/TopVIA homologues and one TopVIB homologue in plants. Here, we further identified two novel Spo11/TopVIA homologues (named OsSpo11-4 and OsSpo11-5, respectively) that exist just in the monocot model plant Oryza sativa, indicating that at least five Spo11/TopVIA homologues are present in the rice genome. To reveal the biochemical function of the two novel Spo11/TopVIA homologues, we first examined the interactions among OsSpo11-1, OsSpo11-4, OsSpo11-5, and OsTopVIB by yeast two-hybrid assay. The results showed that OsSpo11-4 and OsTopVIB can self-interact strongly and among the 3 examined OsSpo11 proteins, only OsSpo11-4 interacted with OsTopVIB. Pull-down assay confirmed the interaction between OsSpo11-4 and OsTopVIB, which indicates that OsSpo11-4 may interact with OsTopVIB in vivo. Further in vitro enzymatic analysis revealed that among the above 4 proteins, only OsSpo11-4 exhibited double-strand DNA cleavage activity and its enzymatic activity appears dependent on Mg2+ and independent of OsTopVIB, despite its interaction with OsTopVIB. We further analyzed the biological function of OsSpo11-4 by RNA interference and found that down-regulated expression of OsSpo11-4 led to defects in male meiosis, indicating OsSpo11-4 is required for meiosis.
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Affiliation(s)
- Xiao Jing An
- Research Center of Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Jia Y. Artificial introgression of a large chromosome fragment around the rice blast resistance gene Pi-ta in backcross progeny and several elite rice cultivars. Heredity (Edinb) 2009; 103:333-9. [DOI: 10.1038/hdy.2009.95] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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