1
|
Jiang H, Zhang Y, Li J, Tang R, Liang F, Tang R, Zhou Y, Zhang C. Genome-wide identification of SIMILAR to RCD ONE (SRO) gene family in rapeseed ( Brassica napus L.) reveals their role in drought stress response. PLANT SIGNALING & BEHAVIOR 2024; 19:2379128. [PMID: 39003725 PMCID: PMC11249032 DOI: 10.1080/15592324.2024.2379128] [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: 04/03/2024] [Accepted: 05/22/2024] [Indexed: 07/16/2024]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop widely cultivated worldwide, and drought is the main environmental factor limiting its yield enhancement and the expansion of planted areas. SIMILAR TO RCD ONE (SRO) is a plant-specific small gene family that plays a crucial role in plant growth, development, and responses to abiotic stresses such as drought. However, the functional role of SROs in rapeseed remains poorly understood. In this study, 19 BnaSROs were identified from the rapeseed genome, with 9, 10, 10, 18, and 20 members identified from the genomes of Brassica rapa, Brassica nigra, Brassica oleracea, Brassica juncea, and Brassica carinata, respectively. We then analyzed their sequence characteristics, phylogenetic relationships, gene structures, and conserved domains, and explored the collinearity relationships of the SRO members in Brassica napus and Brassica juncea. Next, we focused on the analysis of tissue expression and stress-responsive expression patterns of rapeseed SRO members and examined their expression profiles under ABA, MeJA and water-deficit drought treatments using qPCR. Transcriptome data analysis and qPCR detection indicated that BnaSROs exhibit multiple stress-responsive expression patterns. BnaSRO1 and BnaSRO11, which are likely to function through interactions with NAC transcription factors, were screened as major drought-regulated members. Our results provide a solid foundation for functional analysis of the role of the SRO gene family in abiotic stress responses, especially drought stress responses, in rapeseed.
Collapse
Affiliation(s)
- Huanhuan Jiang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yuling Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Jia Li
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Rongzi Tang
- Qianxi'nan Academy of Agricultural and Forestry Sciences, Xingyi, Guizhou, China
| | - Fenghao Liang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Rong Tang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yuyu Zhou
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Chao Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| |
Collapse
|
2
|
Liu S, Li L, Wang W, Xia G, Liu S. TaSRO1 interacts with TaVP1 to modulate seed dormancy and pre-harvest sprouting resistance in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:36-53. [PMID: 38108123 DOI: 10.1111/jipb.13600] [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: 10/14/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Dormancy is an adaptive trait which prevents seeds from germinating under unfavorable environmental conditions. Seeds with weak dormancy undergo pre-harvest sprouting (PHS) which decreases grain yield and quality. Understanding the genetic mechanisms that regulate seed dormancy and resistance to PHS is crucial for ensuring global food security. In this study, we illustrated the function and molecular mechanism of TaSRO1 in the regulation of seed dormancy and PHS resistance by suppressing TaVP1. The tasro1 mutants exhibited strong seed dormancy and enhanced resistance to PHS, whereas the mutants of tavp1 displayed weak dormancy. Genetic evidence has shown that TaVP1 is epistatic to TaSRO1. Biochemical evidence has shown that TaSRO1 interacts with TaVP1 and represses the transcriptional activation of the PHS resistance genes TaPHS1 and TaSdr. Furthermore, TaSRO1 undermines the synergistic activation of TaVP1 and TaABI5 in PHS resistance genes. Finally, we highlight the great potential of tasro1 alleles for breeding elite wheat cultivars that are resistant to PHS.
Collapse
Affiliation(s)
- Shupeng Liu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Li Li
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Wenlong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Guangmin Xia
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Shuwei Liu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| |
Collapse
|
3
|
Hermawaty D, Cahn J, Lister R, Considine MJ. Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds. TREE PHYSIOLOGY 2023; 43:675-689. [PMID: 36637421 PMCID: PMC10094961 DOI: 10.1093/treephys/tpac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 11/17/2022] [Accepted: 12/21/2022] [Indexed: 05/03/2023]
Abstract
The regulation of DNA accessibility by histone modification has emerged as a paradigm of developmental and environmental programming. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a versatile tool to investigate in vivo protein-DNA interaction and has enabled advances in mechanistic understanding of physiologies. The technique has been successfully demonstrated in several plant species and tissues; however, it has remained challenging in woody tissues, in particular complex structures such as perennating buds. Here we developed a ChIP method specifically for mature dormant buds of grapevine (Vitis vinifera cv. Cabernet Sauvignon). Each step of the protocol was systematically optimized, including crosslinking, chromatin extraction, sonication and antibody validation. Analysis of histone H3-enriched DNA was performed to evaluate the success of the protocol and identify occupancy of histone H3 along grapevine bud chromatin. To our best knowledge, this is the first ChIP experiment protocol optimized for the grapevine bud system.
Collapse
Affiliation(s)
- Dina Hermawaty
- The UWA Institute of Agriculture, The University of Western Australia, M082/35 Striling Hwy, Perth, WA 6009, Australia
| | - Jonathan Cahn
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M310/35 Striling Hwy, Perth, WA 6009, Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M310/35 Striling Hwy, Perth, WA 6009, Australia
| | - Michael J Considine
- The UWA Institute of Agriculture, The University of Western Australia, M082/35 Striling Hwy, Perth, WA 6009, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M310/35 Striling Hwy, Perth, WA 6009, Australia
- Horticulture and Irrigated Agriculture, Department of Primary Industries and Regional Development, 1 Nash St, Perth, 6000, Australia
| |
Collapse
|
4
|
Wang Y, Wang R, Yu Y, Gu Y, Wang S, Liao S, Xu X, Jiang T, Yao W. Genome-Wide Analysis of SIMILAR TO RCD ONE (SRO) Family Revealed Their Roles in Abiotic Stress in Poplar. Int J Mol Sci 2023; 24:ijms24044146. [PMID: 36835559 PMCID: PMC9961671 DOI: 10.3390/ijms24044146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
SIMILAR TO RCD ONE (SRO) gene family is a small plant-specific gene family responsible for growth, development, and stress responses. In particular, it plays a vital role in responding to abiotic stresses such as salt, drought, and heavy metals. Poplar SROs are rarely reported to date. In this study, a total of nine SRO genes were identified from Populus simonii × Populus nigra, which are more similar to dicotyledon SRO members. According to phylogenetic analysis, the nine PtSROs can be divided into two groups, and the members in the same cluster have a similar structure. There were some cis-regulatory elements related to abiotic stress response and hormone-induced factors identified in the promoter regions of PtSROs members. Subcellular localization and transcriptional activation activity of PtSRO members revealed a consistent expression profile of the genes with similar structural profiles. In addition, both RT-qPCR and RNA-Seq results indicated that PtSRO members responded to PEG-6000, NaCl, and ABA stress in the roots and leaves of Populus simonii × Populus nigra. The PtSRO genes displayed different expression patterns and peaked at different time points in the two tissues, which was more significant in the leaves. Among them, PtSRO1c and PtSRO2c were more prominent in response to abiotic stress. Furthermore, protein interaction prediction showed that the nine PtSROs might interact with a broad range of transcription factors (TFs) involved in stress responses. In conclusion, the study provides a solid basis for functional analysis of the SRO gene family in abiotic stress responses in poplar.
Collapse
Affiliation(s)
- Yuting Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yue Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yongmei Gu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shixian Liao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiaoya Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Correspondence: (T.J.); (W.Y.)
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
- Correspondence: (T.J.); (W.Y.)
| |
Collapse
|
5
|
Sipari N, Lihavainen J, Keinänen M. Metabolite Profiling of Paraquat Tolerant Arabidopsis thaliana Radical-induced Cell Death1 ( rcd1)-A Mediator of Antioxidant Defence Mechanisms. Antioxidants (Basel) 2022; 11:antiox11102034. [PMID: 36290757 PMCID: PMC9598866 DOI: 10.3390/antiox11102034] [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: 09/09/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
RADICAL-INDUCED CELL DEATH1 (RCD1) is an Arabidopsis thaliana nuclear protein that is disrupted during oxidative stress. RCD1 is considered an important integrative node in development and stress responses, and the rcd1 plants have several phenotypes and altered resistance to a variety of abiotic and biotic stresses. One of the phenotypes of rcd1 is resistance to the herbicide paraquat, but the mechanisms behind it are unknown. Paraquat causes a rapid burst of reactive oxygen species (ROS) initially in the chloroplast. We performed multi-platform metabolomic analyses in wild type Col-0 and paraquat resistant rcd1 plants to identify pathways conveying resistance and the function of RCD1 in this respect. Wild type and rcd1 plants were clearly distinguished by their abundance of antioxidants and specialized metabolites and their responses to paraquat. The lack of response in rcd1 suggested constitutively active defense against ROS via elevated flavonoid, glutathione, β-carotene, and tocopherol levels, whereas its ascorbic acid levels were compromised under non-stressed control conditions when compared to Col-0. We propose that RCD1 acts as a hub that maintains basal antioxidant system, and its inactivation induces defense responses by enhancing the biosynthesis and redox cycling of low molecular weight antioxidants and specialized metabolites with profound antioxidant activities alleviating oxidative stress.
Collapse
Affiliation(s)
- Nina Sipari
- Viikki Metabolomics Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, FI-00014 Helsinki, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Correspondence: (N.S.); (M.K.)
| | - Jenna Lihavainen
- Umeå Plant Science Center, Department of Plant Physiology, Umeå Universitet, 90 187 Umeå, Sweden
| | - Markku Keinänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Institute of Photonics, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Correspondence: (N.S.); (M.K.)
| |
Collapse
|
6
|
Yang T, He Y, Niu S, Zhang Y. A YABBY gene CRABS CLAW a (CRCa) negatively regulates flower and fruit sizes in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111285. [PMID: 35643610 DOI: 10.1016/j.plantsci.2022.111285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 06/15/2023]
Abstract
CRABS CLAW (CRC) is a YABBY transcription factor that plays a pivotal role in carpel development and flower meristem determinacy. Here, we characterized a CRC homolog SlCRCa and elucidated its specific roles in tomato (Solanum lycopersicum). SlCRCa is highly expressed in the petals and stamens, and is responsive to gibberellin (GA) treatment. Overexpression of SlCRCa in tomato reduces the sizes of petals, stamens, and fruits, while the inverse phenotypes are induced by knockdown of SlCRCa. Furthermore, histological investigation suggests that the smaller or larger fruits in SlCRCa-overexpressing or SlCRCa-RNAi plants are mainly determined by the decreases or increases in cell layers and cell sizes in pericarp, respectively. Through transcriptome and qRT-PCR analyses, we speculate that SlCRCa inhibits cell division by regulating the transcription of cell division-related genes, and also suppresses cell expansion by modulating the expansin genes and GA pathway in tomato fruits. Besides, SlCRCa is involved in the feedback regulation of GA biosynthesis. Our findings reveal that SlCRCa negatively regulates fruit size by affecting cell division and cell expansion, and it is also an inhibitor of floral organ sizes in tomato.
Collapse
Affiliation(s)
- Tongwen Yang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center for Vegetables, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
| | - Yu He
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center for Vegetables, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
| | - Shaobo Niu
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center for Vegetables, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
| | - Yan Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center for Vegetables, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
| |
Collapse
|
7
|
Wittmer J, Heidstra R. A dialogue between generations. NATURE PLANTS 2022; 8:607-608. [PMID: 35710884 DOI: 10.1038/s41477-022-01174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Jana Wittmer
- Plant Science Department, Plant Developmental Biology Group, Wageningen University Research, Wageningen, the Netherlands.
| | - Renze Heidstra
- Plant Science Department, Plant Developmental Biology Group, Wageningen University Research, Wageningen, the Netherlands.
| |
Collapse
|
8
|
Du Y, Roldan MVG, Haraghi A, Haili N, Izhaq F, Verdenaud M, Boualem A, Bendahmane A. Spatially expressed WIP genes control Arabidopsis embryonic root development. NATURE PLANTS 2022; 8:635-645. [PMID: 35710883 DOI: 10.1038/s41477-022-01172-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Development of plant organs is a highly organized process. In Arabidopsis, proper root development requires that distinct cell types and tissue layers are specified and formed in a restricted manner in space and over time. Despite its importance, genetic controls underlying such regularity remain elusive. Here we found that WIP genes expressed in the embryo and suspensor functionally oppose those expressed in the surrounding maternal tissues to orchestrate cell division orientation and cell fate specification in the embryonic root, thereby promoting regular root formation. The maternal WIPs act non-cell autonomously to repress root cell fate specification through SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) family members. When losing all WIPs, root cells divide irregularly in the early embryo, but this barely alters their fate specification and the morphology of post-embryonic roots. Our results reveal cross-communication between the embryonic and maternal WIPs in controlling root development.
Collapse
Affiliation(s)
- Yujuan Du
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris Cité, Gif sur Yvette, France.
| | - Maria Victoria Gomez Roldan
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris Cité, Gif sur Yvette, France
| | - Aimen Haraghi
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris Cité, Gif sur Yvette, France
| | - Nawel Haili
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris Cité, Gif sur Yvette, France
| | - Farhaj Izhaq
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris Cité, Gif sur Yvette, France
| | - Marion Verdenaud
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris Cité, Gif sur Yvette, France
| | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris Cité, Gif sur Yvette, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris Cité, Gif sur Yvette, France.
| |
Collapse
|
9
|
Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses. Int J Mol Sci 2021; 22:ijms222313048. [PMID: 34884850 PMCID: PMC8657681 DOI: 10.3390/ijms222313048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 01/12/2023] Open
Abstract
SIMILAR TO RCD-ONEs (SROs) comprise a small plant-specific gene family which play important roles in regulating numerous growth and developmental processes and responses to environmental stresses. However, knowledge of SROs in sesame (Sesamum indicum L.) is limited. In this study, four SRO genes were identified in the sesame genome. Phylogenetic analysis showed that 64 SROs from 10 plant species were divided into two groups (Group I and II). Transcriptome data revealed different expression patterns of SiSROs over various tissues. Expression analysis showed that Group II SROs, especially SiSRO2b, exhibited a stronger response to various abiotic stresses and phytohormones than those in Group I, implying their crucial roles in response to environmental stimulus and hormone signals. In addition, the co-expression network and protein-protein interaction network indicated that SiSROs are associated with a wide range of stress responses. Moreover, transgenic yeast harboring SiSRO2b showed improved tolerance to salt, osmotic and oxidative stress, indicating SiSRO2b could confer multiple tolerances to transgenic yeast. Taken together, this study not only lays a foundation for further functional dissection of the SiSRO gene family, but also provides valuable gene candidates for genetic improvement of abiotic stress tolerance in sesame.
Collapse
|
10
|
Bacher H, Zhu F, Gao T, Liu K, Dhatt BK, Awada T, Zhang C, Distelfeld A, Yu H, Peleg Z, Walia H. Wild emmer introgression alters root-to-shoot growth dynamics in durum wheat in response to water stress. PLANT PHYSIOLOGY 2021; 187:1149-1162. [PMID: 34618034 PMCID: PMC8566259 DOI: 10.1093/plphys/kiab292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Water deficit during the early vegetative growth stages of wheat (Triticum) can limit shoot growth and ultimately impact grain productivity. Introducing diversity in wheat cultivars to enhance the range of phenotypic responses to water limitations during vegetative growth can provide potential avenues for mitigating subsequent yield losses. We tested this hypothesis in an elite durum wheat background by introducing a series of introgressions from a wild emmer (Triticum turgidum ssp. dicoccoides) wheat. Wild emmer populations harbor rich phenotypic diversity for drought-adaptive traits. To determine the effect of these introgressions on vegetative growth under water-limited conditions, we used image-based phenotyping to catalog divergent growth responses to water stress ranging from high plasticity to high stability. One of the introgression lines exhibited a significant shift in root-to-shoot ratio in response to water stress. We characterized this shift by combining genetic analysis and root transcriptome profiling to identify candidate genes (including a root-specific kinase) that may be linked to the root-to-shoot carbon reallocation under water stress. Our results highlight the potential of introducing functional diversity into elite durum wheat for enhancing the range of water stress adaptation.
Collapse
Affiliation(s)
- Harel Bacher
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Feiyu Zhu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Tian Gao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kan Liu
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Balpreet K Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Tala Awada
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Hongfeng Yu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| |
Collapse
|
11
|
Li N, Xu R, Wang B, Wang J, Huang S, Yu Q, Gao J. Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato. Front Genet 2021; 12:753638. [PMID: 34621298 PMCID: PMC8490783 DOI: 10.3389/fgene.2021.753638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
SRO (SIMILAR TO RCD ONE) is a family of plant-specific small molecule proteins that play an important role in plant growth and development and environmental responses. However, SROs still lack systematic characterization in tomato. Based on bioinformatics methods, SRO family genes were identified and characterized from cultivated tomatoes and several wild tomatoes. qRT-PCR was used to study the expression of SRO gene in cultivated tomatoes. Phylogenetic and evolutionary analyses showed that SRO genes in angiosperms share a common ancestor and that the number of SRO family members changed as plants diverged and evolved. Cultivated tomato had six SRO members, five of which still shared some degree of identity with the ancestral SRO genes. Genetic structure and physicochemical properties showed that tomato SRO genes were highly conserved with chromosomal distribution. They could be divided into three groups based on exon-intron structure, and cultivated tomato contained only two of these subclades. A number of hormonal, light and abiotic stress-responsive cis-regulatory elements were identified from the promoter of the tomato SRO gene, and they also interacted with a variety of stress-responsive proteins and microRNAs. RNA-seq analysis showed that SRO genes were widely expressed in different tissues and developmental stages of tomato, with significant tissue-specific features. Expression analysis also showed that SRO genes respond significantly to high temperature and salt stress and mediate the tomato hormone regulatory network. These results provide a theoretical basis for further investigation of the functional expression of tomato SRO genes and provide potential genetic resources for tomato resistance breeding.
Collapse
Affiliation(s)
- Ning Li
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, China.,Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Ruiqiang Xu
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, China.,Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Baike Wang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Juan Wang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Shaoyong Huang
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, China.,Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Qinghui Yu
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China.,Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi, China
| | - Jie Gao
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, China
| |
Collapse
|
12
|
Yin X, He T, Yi K, Zhao Y, Hu Y, Liu J, Zhang X, Meng L, Wang L, Liu H, Li Y, Cui G. Comprehensive evaluation of candidate reference genes for quantitative real-time PCR-based analysis in Caucasian clover. Sci Rep 2021; 11:3269. [PMID: 33558610 PMCID: PMC7870939 DOI: 10.1038/s41598-021-82633-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 01/19/2021] [Indexed: 11/08/2022] Open
Abstract
The forage species Caucasian clover (Trifolium ambiguum M. Bieb.), a groundcover plant, is resistant to both cold and drought. However, reference genes for qRT-PCR-based analysis of Caucasian clover are lacking. In this study, 12 reference genes were selected on the basis of transcriptomic data. These genes were used to determine the most stably expressed genes in various organs of Caucasian clover under cold, salt and drought stress for qRT-PCR-based analysis. Reference gene stability was analyzed by geNorm, NormFinder, BestKeeper, the ∆Ct method and RefFinder. Under salt stress, RCD1 and PPIL3 were the most stable reference genes in the leaves, and NLI1 and RCD1 were the most stable references genes in the roots. Under low-temperature stress, APA and EFTu-GTP were the most stable reference genes in the leaves, and the RCD1 and NLI2 genes were highly stable in the roots. Under 10% PEG-6000 stress, NLI1 and NLI2 were highly stable in the leaves, and RCD1 and PPIL3 were the most stable in the roots. Overall, RCD1 and NLI2 were the most stable reference genes in organs under normal conditions and across all samples. The most and least stable reference genes were validated by assessing their appropriateness for normalization via WRKY genes.
Collapse
Affiliation(s)
- Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Taotao He
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Kun Yi
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yihang Zhao
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yao Hu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Jiaxue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Xiaomeng Zhang
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Lingdong Meng
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Lina Wang
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Haoyue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yonggang Li
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China.
| |
Collapse
|
13
|
Taipakova S, Kuanbay A, Saint-Pierre C, Gasparutto D, Baiken Y, Groisman R, Ishchenko AA, Saparbaev M, Bissenbaev AK. The Arabidopsis thaliana Poly(ADP-Ribose) Polymerases 1 and 2 Modify DNA by ADP-Ribosylating Terminal Phosphate Residues. Front Cell Dev Biol 2020; 8:606596. [PMID: 33324653 PMCID: PMC7726343 DOI: 10.3389/fcell.2020.606596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/22/2020] [Indexed: 12/20/2022] Open
Abstract
Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyze the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are viewed as DNA damage sensors that, upon binding to strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. The flowering plant Arabidopsis thaliana contains three genes encoding homologs of mammalian PARPs: atPARP1, atPARP2, and atPARP3. Both atPARP1 and atPARP2 contain poly(ADP-ribosyl)ating activity; however, it is unknown whether they could covalently modify DNA by ADP-ribosylating the strand break termini. Here, we report that similar to their mammalian counterparts, the plant atPARP1 and atPARP2 proteins ADP-ribosylate 5′-terminal phosphate residues in duplex DNA oligonucleotides and plasmid containing at least two closely spaced DNA strand breaks. AtPARP1 preferentially catalyzes covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 5′-phosphate, whereas atPARP2 preferentially ADP-ribosylates the nicked and gapped DNA duplexes containing the terminal 5′-phosphate. Similar to their mammalian counterparts, the plant PARP-catalyzed DNA ADP-ribosylation is particularly sensitive to the distance that separates two strand breaks in the same DNA molecule, 1.5 and 1 or 2 turns of helix for atPARP1 and atPARP2, respectively. PAR glycohydrolase (PARG) restored native DNA structure by hydrolyzing the PAR–DNA adducts generated by atPARPs. Biochemical and mass spectrometry analyses of the PAR–DNA adducts showed that atPARPs utilize phosphorylated DNA termini as an alternative to protein acceptor residues to catalyze PAR chain synthesis via phosphodiester bond formation between C1′ of ADP-ribose and a phosphate residue of the terminal nucleotide in DNA fragment. Taken together, these data establish the presence of a new type of DNA-modifying activity in Arabidopsis PARPs, suggesting a possible role of DNA ADP-ribosylation in DNA damage signaling and repair of terrestrial plants.
Collapse
Affiliation(s)
- Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aigerim Kuanbay
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | | | - Didier Gasparutto
- CEA, CNRS, IRIG/SyMMES-UMR 5819/CREAB, Université Grenoble Alpes, Grenoble, France
| | - Yeldar Baiken
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Regina Groisman
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Alexander A Ishchenko
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Murat Saparbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Amangeldy K Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| |
Collapse
|
14
|
Jiang W, Geng Y, Liu Y, Chen S, Cao S, Li W, Chen H, Ma D, Yin J. Genome-wide identification and characterization of SRO gene family in wheat: Molecular evolution and expression profiles during different stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:590-611. [PMID: 32912491 DOI: 10.1016/j.plaphy.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
SRO (SIMILAR TO RCD ONE), a type of plant-specific small protein family, play important roles in plant growth and development, as well as in response to biotic/abiotic stresses. Although characterization of SROs have been performed in model plants, little is known about their function in wheat, especially under stress conditions. In this study, 30 SRO genes were identified from the wheat genome (TaSRO). They were phylogenetically separated into two groups with distinct structures. The cis-regulatory elements in the promoter region of TaSROs were analyzed and numerous elements functionally associated with stress responding and hormones were interpreted, implying the reason for induction expression patterns of TaSROs during abiotic and biotic stresses in wheat. Whole-genome replication events in the SRO gene family of wheat and seven other species (Arabidopsis thaliana, rice, maize, barley, soybean, upland cotton, and cucumber) were analyzed, resulting in 1, 12, 9, 23, 6, 5, and 3 of gene pairs, respectively. The tissue-specific expression pattern profiling revealed that most TaSROs are highly expressed in one or more tissues and may play an important role in wheat growth and development. In addition, qRT-PCR results further confirmed that these TaSRO genes are involved in wheat stress response. In summary, our study laid a theoretical basis for molecular function deciphering of TaSROs, especially in plant hormones and biotic/abiotic stress responses.
Collapse
Affiliation(s)
- Wenqiang Jiang
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China; Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210014, Jiangsu, China
| | - Yike Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Shuhui Chen
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China
| | - Shulin Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Wei Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China.
| | - Junliang Yin
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China; Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| |
Collapse
|
15
|
Isolation and Identification of Ipomoea cairica (L.) Sweet Gene IcSRO1 Encoding a SIMILAR TO RCD-ONE Protein, Which Improves Salt and Drought Tolerance in Transgenic Arabidopsis. Int J Mol Sci 2020; 21:ijms21031017. [PMID: 32033046 PMCID: PMC7036886 DOI: 10.3390/ijms21031017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/19/2020] [Accepted: 01/28/2020] [Indexed: 11/17/2022] Open
Abstract
Ipomoea cairica is a tropical plant and a wild relative of the food plant sweet potato (Ipomoea batatas), listed as one of the most invasive alien species in China. Recently, it has been reported that I. cairica had successfully invaded mangrove wetlands, indicating its high salt tolerance. Based on previous genetic studies, I. cairica offers a good model for characterizing stress-resistant genes. It has recently been identified that the SRO proteins (SIMILAR TO RCD-ONE) play important roles in a variety of stress and developmental responses. Radical-Induced Cell Death1 (RCD1) was the first identified plant SRO protein from Arabidopsis thaliana. As a typical SRO protein, IcSRO1 had a highly conservative WWE domain, a conserved PARP fold and protein C in the RST function area. The expression of IcSRO1 was induced by salt, drought, and the plant hormone ABA. The transgenic Arabidopsis overexpressing IcSRO1 showed higher tolerance against salt and drought stress along with lower accumulation of hydrogen peroxide (H2O2) and superoxide (O2-) than the wild type. The IcSRO1 protein was localized in the nucleus after cultivation in the buffer. Our results indicated it could interact with Arabidopsis SALT OVERLY SENSITIVE 1 (AtSOS1), suggesting IcSRO1 may have similar functions. The pleiotropic effect of IcSRO1 on physiological processes contributes to the improvement of plant tolerance against diverse abiotic stresses, and may be associated with the adaptation of I. cairica to those environments with extreme saline and drought conditions. It therefore provides valuable gene resources for crop breeding enhancement.
Collapse
|
16
|
Zhao X, Gao L, Ren J, Pan F. Arabidopsis SIMILAR TO RCD-ONE genes are ubiquitous and respond to multiple abiotic stresses through diverse signaling pathways. J Biosci 2019; 44:129. [PMID: 31894110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The SIMILAR TO RCD-ONE (SROs) have been characterized as a group of plant-specific proteins which play important functions in stress responses and development. Here, we analyze the expression profiles of six SRO genes under different stress treatments in Arabidopsis. Our results revealed that RCD1 play an essential role in plant responses to various environmental stresses. SRO1 has partially overlapping functions with RCD1 in plant response to HgCl2 and H2O2 stress. Analysis of the transcriptional expression of SROs indicated that both of the RCD1 and SRO1 transcripts were up-regulated by HgCl2 and light, not by other stresses, and that of SRO5 was induced by salt. Expression of SRO3 and SRO4 were not influenced by stresses. The different effects of these stresses on the expression of the SRO genes indicate that the SRO family is regulated by multiple signaling pathways. Sequence analyses of the SRO proteins implicate a highly preserved protein structure and are specific to plants, which might have implications for functional conservation. The ubiquitous expression and nuclear localization of SRO family suggested that their function might be related to transcription factor regulation and complex formation. Taken together, SRO family is critical for proper plant development and multiple stress responses.
Collapse
Affiliation(s)
- Xiaoliang Zhao
- School of Basic Medicine, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | | | | | | |
Collapse
|
17
|
Zhao X, Gao L, Ren J, Pan F. Arabidopsis SIMILAR TO RCD-ONE genes are ubiquitous and respond to multiple abiotic stresses through diverse signaling pathways. J Biosci 2019. [DOI: 10.1007/s12038-019-9946-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
18
|
Zhang L, Zhou D, Hu H, Li W, Hu Y, Xie J, Huang S, Wang W. Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.). BMC PLANT BIOLOGY 2019; 19:211. [PMID: 31113386 PMCID: PMC6530135 DOI: 10.1186/s12870-019-1807-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/26/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Banana (Musa spp.) is one of the world's most important fruits and its production is largely limited by diverse stress conditions. SROs (SIMILAR TO RCD-ONE) have important functions in abiotic stress resistance and development of plants. They contain a catalytic core of the poly(ADP-ribose) polymerase (PARP) domain and a C-terminal RST (RCD-SRO-TAF4) domain. In addition, partial SROs also include an N-terminal WWE domain. Although a few of SROs have been characterized in some model plants, little is known about their functions in banana, especially in response to biotic stress. RESULTS Six MaSRO genes in banana genome were identified using the PARP and RST models as a query. Phylogenetic analysis showed that 77 SROs from 15 species were divided into two structurally distinct groups. The SROs in the group I possessed three central regions of the WWE, PARP and RST domains. The WWE domain was lacking in the group II SROs. In the selected monocots, only MaSROs of banana were present in the group II. Most of MaSROs expressed in more than one banana tissue. The stress- and hormone-related cis-regulatory elements (CREs) in the promoter regions of MaSROs supported differential transcripts of MaSROs in banana roots treated with abiotic and biotic stresses. Moreover, expression profiles of MaSROs in the group I were clearly distinct with those observed in the group II after hormone treatment. Notably, the expression of MaSRO4 was significantly upregulated by the multiple stresses and hormones. The MaSRO4 protein could directly interact with MaNAC6 and MaMYB4, and the PARP domain was required for the protein-protein interaction. CONCLUSIONS Six MaSROs in banana genome were divided into two main groups based on the characteristics of conserved domains. Comprehensive expression analysis indicated that MaSROs had positive responses to biotic and abiotic stresses via a complex interaction network with hormones. MaSRO4 could interact directly with MaNAC6 and MaMYB4 through the PARP domain to regulate downstream signaling pathway.
Collapse
Affiliation(s)
- Lu Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Dengbo Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Huigang Hu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of China Southern Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Weiming Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of China Southern Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Yulin Hu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of China Southern Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Jianghui Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of China Southern Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 Guangdong China
| | - Wei Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| |
Collapse
|
19
|
Rissel D, Peiter E. Poly(ADP-Ribose) Polymerases in Plants and Their Human Counterparts: Parallels and Peculiarities. Int J Mol Sci 2019; 20:E1638. [PMID: 30986964 PMCID: PMC6479469 DOI: 10.3390/ijms20071638] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/25/2022] Open
Abstract
Poly(ADP-ribosyl)ation is a rapid and transient post-translational protein modification that was described first in mammalian cells. Activated by the sensing of DNA strand breaks, poly(ADP-ribose)polymerase1 (PARP1) transfers ADP-ribose units onto itself and other target proteins using NAD⁺ as a substrate. Subsequently, DNA damage responses and other cellular responses are initiated. In plants, poly(ADP-ribose) polymerases (PARPs) have also been implicated in responses to DNA damage. The Arabidopsis genome contains three canonical PARP genes, the nomenclature of which has been uncoordinated in the past. Albeit assumptions concerning the function and roles of PARP proteins in planta have often been inferred from homology and structural conservation between plant PARPs and their mammalian counterparts, plant-specific roles have become apparent. In particular, PARPs have been linked to stress responses of plants. A negative role under abiotic stress has been inferred from studies in which a genetic or, more commonly, pharmacological inhibition of PARP activity improved the performance of stressed plants; in response to pathogen-associated molecular patterns, a positive role has been suggested. However, reports have been inconsistent, and the effects of PARP inhibitors appear to be more robust than the genetic abolition of PARP gene expression, indicating the presence of alternative targets of those drugs. Collectively, recent evidence suggests a conditionality of stress-related phenotypes of parp mutants and calls for a reconsideration of PARP inhibitor studies on plants. This review critically summarizes our current understanding of poly(ADP-ribosylation) and PARP proteins in plants, highlighting similarities and differences to human PARPs, areas of controversy, and requirements for future studies.
Collapse
Affiliation(s)
- Dagmar Rissel
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany.
- Agrochemisches Institut Piesteritz e.V. (AIP), Möllensdorfer Strasse 13, 06886 Lutherstadt Wittenberg, Germany.
- Institute for Plant Protection in Field Crops and Grassland, Julius Kühn-Institut (JKI), 38104 Braunschweig, Germany.
| | - Edgar Peiter
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany.
- Agrochemisches Institut Piesteritz e.V. (AIP), Möllensdorfer Strasse 13, 06886 Lutherstadt Wittenberg, Germany.
| |
Collapse
|
20
|
Huertas R, Catalá R, Jiménez-Gómez JM, Mar Castellano M, Crevillén P, Piñeiro M, Jarillo JA, Salinas J. Arabidopsis SME1 Regulates Plant Development and Response to Abiotic Stress by Determining Spliceosome Activity Specificity. THE PLANT CELL 2019; 31:537-554. [PMID: 30696706 PMCID: PMC6447010 DOI: 10.1105/tpc.18.00689] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/14/2018] [Accepted: 01/25/2019] [Indexed: 05/19/2023]
Abstract
The control of precursor-messenger RNA (pre-mRNA) splicing is emerging as an important layer of regulation in plant responses to endogenous and external cues. In eukaryotes, pre-mRNA splicing is governed by the activity of a large ribonucleoprotein machinery, the spliceosome, whose protein core is composed of the Sm ring and the related Sm-like 2-8 complex. Recently, the Arabidopsis (Arabidopsis thaliana) Sm-like 2-8 complex has been characterized. However, the role of plant Sm proteins in pre-mRNA splicing remains largely unknown. Here, we present the functional characterization of Sm protein E1 (SME1), an Arabidopsis homolog of the SME subunit of the eukaryotic Sm ring. Our results demonstrate that SME1 regulates the spliceosome activity and that this regulation is controlled by the environmental conditions. Indeed, depending on the conditions, SME1 ensures the efficiency of constitutive and alternative splicing of selected pre-mRNAs. Moreover, missplicing of most targeted pre-mRNAs leads to the generation of nonsense-mediated decay signatures, indicating that SME1 also guarantees adequate levels of the corresponding functional transcripts. In addition, we show that the selective function of SME1 in ensuring appropriate gene expression patterns through the regulation of specific pre-mRNA splicing is essential for adequate plant development and adaptation to freezing temperatures. These findings reveal that SME1 plays a critical role in plant development and interaction with the environment by providing spliceosome activity specificity.
Collapse
Affiliation(s)
- Raul Huertas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain
| | - Rafael Catalá
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain
| | | | - M Mar Castellano
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain
| | - Pedro Crevillén
- Centro de Biotecnología y Genómica de Plantas, UPM/INIA, 28223 Pozuelo de Alarcón, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, UPM/INIA, 28223 Pozuelo de Alarcón, Spain
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas, UPM/INIA, 28223 Pozuelo de Alarcón, Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain
| |
Collapse
|
21
|
Rubio-Cabetas MJ, Pons C, Bielsa B, Amador ML, Marti C, Granell A. Preformed and induced mechanisms underlies the differential responses of Prunus rootstock to hypoxia. JOURNAL OF PLANT PHYSIOLOGY 2018; 228:134-149. [PMID: 29913428 DOI: 10.1016/j.jplph.2018.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/01/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Analysis of the transcriptomic changes produced in response to hypoxia in root tissues from two rootstock Prunus genotypes differing in their sensitivity to waterlogging: resistant Myrobalan 'P.2175' (P. cerasifera Erhr.), and sensitive 'Felinem' hybrid [P. amygdalus Batsch × P. persica (L.) Batsch] revealed alterations in both metabolism and regulatory processes. Early hypoxia response in both genotypes is characterized by a molecular program aimed to adapt the cell metabolism to the new conditions. Upon hypoxia conditions, tolerant Myrobalan represses first secondary metabolism gene expression as a strategy to prevent the waste of resources/energy, and by the up-regulation of protein degradation genes probably leading to structural adaptations to long-term response to hypoxia. In response to the same conditions, sensitive 'Felinem' up-regulates a core of signal transduction and transcription factor genes. A combination of PLS-DA and qRT-PCR approaches revealed a set of transcription factors and signalling molecules as differentially regulated in the sensitive and tolerant genotypes including the peach orthologs for oxygen sensors. Apart from providing insights into the molecular processes underlying the differential response to waterlogging of two Prunus rootstocks, our approach reveals a set of candidate genes to be used expression biomarkers for biotech or breeding approaches to waterlogging tolerance.
Collapse
Affiliation(s)
- María J Rubio-Cabetas
- Hortofruticulture Department, Agrifood Research and Technology Centre of Aragon (CITA), Av. Montañana 930, 50059, Zaragoza, Spain
| | - Clara Pons
- Department of Fruit Quality and Biotechnology, Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Ingeniero Fausto Elio, s/n 46022 Valencia, Spain
| | - Beatriz Bielsa
- Hortofruticulture Department, Agrifood Research and Technology Centre of Aragon (CITA), Av. Montañana 930, 50059, Zaragoza, Spain
| | - María L Amador
- Hortofruticulture Department, Agrifood Research and Technology Centre of Aragon (CITA), Av. Montañana 930, 50059, Zaragoza, Spain
| | - Cristina Marti
- Department of Fruit Quality and Biotechnology, Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Ingeniero Fausto Elio, s/n 46022 Valencia, Spain
| | - Antonio Granell
- Department of Fruit Quality and Biotechnology, Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Ingeniero Fausto Elio, s/n 46022 Valencia, Spain.
| |
Collapse
|
22
|
Maize similar to RCD1 gene induced by salt enhances Arabidopsis thaliana abiotic stress resistance. Biochem Biophys Res Commun 2018; 503:2625-2632. [PMID: 30097269 DOI: 10.1016/j.bbrc.2018.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 12/18/2022]
Abstract
Plant SRO (SIMILAR TO RCD-ONE) proteins play important roles in regulating oxidation and metal ion metabolism. Numbers of SRO proteins have been functional identified in Arabidopsis and rice, but little is known in maize. In this study, we identified a salt induced SRO gene, ZmSRO1b, from maize and analyzed its characteristics. ZmSRO1b expressed mainly in leaf tissues. The ZmSRO1b is encoded by 595 amino acid residues and shared conserved protein models with AtRCD1 and AtSRO1 from Arabidopsis. Promoter-elements analysis showed ZmSRO1b promoter harbored salt and metal stress responsive elements, DRE, GT-like and MRE. Further promoter inductive analysis by GUS staining and quantification confirmed that ZmSRO1b promoter was induced by salt and cadmium (Cd). Methylviologen (MV) simulated oxidative stress showed ZmSRO1b promoter was also induced by MV. Overexpression of ZmSRO1b in Arabidopsis plants showed increased resistance to salt, Cd and oxidative stress. Our results for the first time experimentally validate the function of ZmSRO1b and contribute to the better understanding of SRO genes across different plant species.
Collapse
|
23
|
Seesangboon A, Gruneck L, Pokawattana T, Eungwanichayapant PD, Tovaranonte J, Popluechai S. Transcriptome analysis of Jatropha curcas L. flower buds responded to the paclobutrazol treatment. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:276-286. [PMID: 29631212 DOI: 10.1016/j.plaphy.2018.03.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 03/30/2018] [Accepted: 03/30/2018] [Indexed: 05/15/2023]
Abstract
Jatropha seeds can be used to produce high-quality biodiesel due to their high oil content. However, Jatropha produces low numbers of female flowers, which limits seed yield. Paclobutrazol (PCB), a plant growth retardant, can increase number of Jatropha female flowers and seed yield. However, the underlying mechanisms of flower development after PCB treatment are not well understood. To identify the critical genes associated with flower development, the transcriptome of flower buds following PCB treatment was analyzed. Scanning Electron Microscope (SEM) analysis revealed that the flower developmental stage between PCB-treated and control flower buds was similar. Based on the presence of sex organs, flower buds at 0, 4, and 24 h after treatment were chosen for global transcriptome analysis. In total, 100,597 unigenes were obtained, 174 of which were deemed as interesting based on their response to PCB treatment. Our analysis showed that the JcCKX5 and JcTSO1 genes were up-regulated at 4 h, suggesting roles in promoting organogenic capacity and ovule primordia formation in Jatropha. The JcNPGR2, JcMGP2-3, and JcHUA1 genes were down-regulated indicating that they may contribute to increased number of female flowers and amount of seed yield. Expression of cell division and cellulose biosynthesis-related genes, including JcGASA3, JcCycB3;1, JcCycP2;1, JcKNAT7, and JcCSLG3 was decreased, which might have caused the compacted inflorescences. This study represents the first report combining SEM-based morphology, qRT-PCR and transcriptome analysis of PCB-treated Jatropha flower buds at different stages of flower development.
Collapse
Affiliation(s)
- Anupharb Seesangboon
- School of Science, Mae Fah Luang University, 333 moo 1, Thasud, Muang, ChiangRai, 57100, Thailand.
| | - Lucsame Gruneck
- School of Science, Mae Fah Luang University, 333 moo 1, Thasud, Muang, ChiangRai, 57100, Thailand.
| | - Tittinat Pokawattana
- School of Science, Mae Fah Luang University, 333 moo 1, Thasud, Muang, ChiangRai, 57100, Thailand.
| | | | - Jantrararuk Tovaranonte
- School of Science, Mae Fah Luang University, 333 moo 1, Thasud, Muang, ChiangRai, 57100, Thailand.
| | - Siam Popluechai
- School of Science, Mae Fah Luang University, 333 moo 1, Thasud, Muang, ChiangRai, 57100, Thailand.
| |
Collapse
|
24
|
Agarwal PK, Gupta K, Lopato S, Agarwal P. Dehydration responsive element binding transcription factors and their applications for the engineering of stress tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2135-2148. [PMID: 28419345 DOI: 10.1093/jxb/erx118] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Dehydration responsive element binding (DREB) factors or CRT element binding factors (CBFs) are members of the AP2/ERF family, which comprises a large number of stress-responsive regulatory genes. This review traverses almost two decades of research, from the discovery of DREB/CBF factors to their optimization for application in plant biotechnology. In this review, we describe (i) the discovery, classification, structure, and evolution of DREB genes and proteins; (ii) induction of DREB genes by abiotic stresses and involvement of their products in stress responses; (iii) protein structure and DNA binding selectivity of different groups of DREB proteins; (iv) post-transcriptional and post-translational mechanisms of DREB transcription factor (TF) regulation; and (v) physical and/or functional interaction of DREB TFs with other proteins during plant stress responses. We also discuss existing issues in applications of DREB TFs for engineering of enhanced stress tolerance and improved performance under stress of transgenic crop plants.
Collapse
Affiliation(s)
- Pradeep K Agarwal
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific & Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar-364 002, (Gujarat), India
| | - Kapil Gupta
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific & Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar-364 002, (Gujarat), India
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Parinita Agarwal
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific & Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar-364 002, (Gujarat), India
| |
Collapse
|
25
|
Gul IS, Hulpiau P, Saeys Y, van Roy F. Metazoan evolution of the armadillo repeat superfamily. Cell Mol Life Sci 2017; 74:525-541. [PMID: 27497926 PMCID: PMC11107757 DOI: 10.1007/s00018-016-2319-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/05/2016] [Accepted: 07/25/2016] [Indexed: 02/08/2023]
Abstract
The superfamily of armadillo repeat proteins is a fascinating archetype of modular-binding proteins involved in various fundamental cellular processes, including cell-cell adhesion, cytoskeletal organization, nuclear import, and molecular signaling. Despite their diverse functions, they all share tandem armadillo (ARM) repeats, which stack together to form a conserved three-dimensional structure. This superhelical armadillo structure enables them to interact with distinct partners by wrapping around them. Despite the important functional roles of this superfamily, a comprehensive analysis of the composition, classification, and phylogeny of this protein superfamily has not been reported. Furthermore, relatively little is known about a subset of ARM proteins, and some of the current annotations of armadillo repeats are incomplete or incorrect, often due to high similarity with HEAT repeats. We identified the entire armadillo repeat superfamily repertoire in the human genome, annotated each armadillo repeat, and performed an extensive evolutionary analysis of the armadillo repeat proteins in both metazoan and premetazoan species. Phylogenetic analyses of the superfamily classified them into several discrete branches with members showing significant sequence homology, and often also related functions. Interestingly, the phylogenetic structure of the superfamily revealed that about 30 % of the members predate metazoans and represent an ancient subset, which is gradually evolving to acquire complex and highly diverse functions.
Collapse
Affiliation(s)
- Ismail Sahin Gul
- Inflammation Research Center (IRC), VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, FSVM Building, Technologiepark 927, 9052, Ghent, Belgium
| | - Paco Hulpiau
- Inflammation Research Center (IRC), VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, FSVM Building, Technologiepark 927, 9052, Ghent, Belgium
| | - Yvan Saeys
- Inflammation Research Center (IRC), VIB, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University, Ghent, Belgium
| | - Frans van Roy
- Inflammation Research Center (IRC), VIB, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, FSVM Building, Technologiepark 927, 9052, Ghent, Belgium.
| |
Collapse
|
26
|
Anjum S, Raza S, Azhar A, Qamarunnisa S. Bnsro1: A new homologue of Arabidopsis thaliana rcd1 from Brassica napus. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
27
|
Cui H, Kong D, Wei P, Hao Y, Torii KU, Lee JS, Li J. SPINDLY, ERECTA, and its ligand STOMAGEN have a role in redox-mediated cortex proliferation in the Arabidopsis root. MOLECULAR PLANT 2014; 7:1727-39. [PMID: 25267734 PMCID: PMC4261839 DOI: 10.1093/mp/ssu106] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Reactive oxygen species (ROS) are harmful to all living organisms and therefore they must be removed to ensure normal growth and development. ROS are also signaling molecules, but so far little is known about the mechanisms of ROS perception and developmental response in plants. We here report that hydrogen peroxide induces cortex proliferation in the Arabidopsis root and that SPINDLY (SPY), an O-linked glucosamine acetyltransferase, regulates cortex proliferation by maintaining cellular redox homeostasis. We also found that mutation in the leucine-rich receptor kinase ERECTA and its putative peptide ligand STOMAGEN block the effect of hydrogen peroxide on root cortex proliferation. However, ERECTA and STOMAGEN are expressed in the vascular tissue, whereas extra cortex cells are produced from the endodermis, suggesting the involvement of intercellular signaling. SPY appears to act downstream of ERECTA, because the spy mutation still caused cortex proliferation in the erecta mutant background. We therefore have not only gained insight into the mechanism by which SPY regulates root development but also uncovered a novel pathway for ROS signaling in plants. The importance of redox-mediated cortex proliferation as a protective mechanism against oxidative stress is also discussed.
Collapse
Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Danyu Kong
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Pengcheng Wei
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA Present address: Biotechnical Group, Institute of Rice Research, Anhui Agricultural Academy of Science, 40#, Nongke South Road, Hefei, Anhui, 230031, China
| | - Yueling Hao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Keiko U Torii
- Howard Hughes Medical Institute, Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Jin Suk Lee
- Howard Hughes Medical Institute, Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Jie Li
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| |
Collapse
|
28
|
Sanz L, Fernández-Marcos M, Modrego A, Lewis DR, Muday GK, Pollmann S, Dueñas M, Santos-Buelga C, Lorenzo O. Nitric oxide plays a role in stem cell niche homeostasis through its interaction with auxin. PLANT PHYSIOLOGY 2014; 166:1972-84. [PMID: 25315603 PMCID: PMC4256006 DOI: 10.1104/pp.114.247445] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 10/09/2014] [Indexed: 05/18/2023]
Abstract
Nitric oxide (NO) is a unique reactive nitrogen molecule with an array of signaling functions that modulates plant developmental processes and stress responses. To explore the mechanisms by which NO modulates root development, we used a pharmacological approach and NO-deficient mutants to unravel the role of NO in establishing auxin distribution patterns necessary for stem cell niche homeostasis. Using the NO synthase inhibitor and Arabidopsis (Arabidopsis thaliana) NO biosynthesis mutants (nitric oxide-associated1 [noa1], nitrate reductase1 [nia1] and nia2, and nia1 nia2 noa1), we show that depletion of NO in noa1 reduces primary root elongation and increases flavonol accumulation consistent with elevated reactive oxygen species levels. The elevated flavonols are required for the growth effect, because the transparent testa4 mutation reverses the noa1 mutant root elongation phenotype. In addition, noa1 and nia1 nia2 noa1 NO-deficient mutant roots display small root meristems with abnormal divisions. Concomitantly, auxin biosynthesis, transport, and signaling are perturbed. We further show that NO accumulates in cortex/endodermis stem cells and their precursor cells. In endodermal and cortical cells, the noa1 mutant acts synergistically to the effect of the wuschel-related homeobox5 mutation on the proximal meristem, suggesting that NO could play an important role in regulating stem cell decisions, which has been reported in animals.
Collapse
Affiliation(s)
- Luis Sanz
- Departamento de Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain (L.S., M.F.-M., A.M., O.L.);Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106 (D.R.L., G.K.M.);Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain (S.P.); andGrupo de Investigación en Polifenoles, Unidad de Nutrición y Bromatología, Universidad de Salamanca, 37007 Salamanca, Spain (M.D., C.S.-B.)
| | - María Fernández-Marcos
- Departamento de Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain (L.S., M.F.-M., A.M., O.L.);Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106 (D.R.L., G.K.M.);Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain (S.P.); andGrupo de Investigación en Polifenoles, Unidad de Nutrición y Bromatología, Universidad de Salamanca, 37007 Salamanca, Spain (M.D., C.S.-B.)
| | - Abelardo Modrego
- Departamento de Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain (L.S., M.F.-M., A.M., O.L.);Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106 (D.R.L., G.K.M.);Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain (S.P.); andGrupo de Investigación en Polifenoles, Unidad de Nutrición y Bromatología, Universidad de Salamanca, 37007 Salamanca, Spain (M.D., C.S.-B.)
| | - Daniel R Lewis
- Departamento de Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain (L.S., M.F.-M., A.M., O.L.);Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106 (D.R.L., G.K.M.);Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain (S.P.); andGrupo de Investigación en Polifenoles, Unidad de Nutrición y Bromatología, Universidad de Salamanca, 37007 Salamanca, Spain (M.D., C.S.-B.)
| | - Gloria K Muday
- Departamento de Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain (L.S., M.F.-M., A.M., O.L.);Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106 (D.R.L., G.K.M.);Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain (S.P.); andGrupo de Investigación en Polifenoles, Unidad de Nutrición y Bromatología, Universidad de Salamanca, 37007 Salamanca, Spain (M.D., C.S.-B.)
| | - Stephan Pollmann
- Departamento de Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain (L.S., M.F.-M., A.M., O.L.);Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106 (D.R.L., G.K.M.);Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain (S.P.); andGrupo de Investigación en Polifenoles, Unidad de Nutrición y Bromatología, Universidad de Salamanca, 37007 Salamanca, Spain (M.D., C.S.-B.)
| | - Montserrat Dueñas
- Departamento de Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain (L.S., M.F.-M., A.M., O.L.);Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106 (D.R.L., G.K.M.);Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain (S.P.); andGrupo de Investigación en Polifenoles, Unidad de Nutrición y Bromatología, Universidad de Salamanca, 37007 Salamanca, Spain (M.D., C.S.-B.)
| | - Celestino Santos-Buelga
- Departamento de Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain (L.S., M.F.-M., A.M., O.L.);Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106 (D.R.L., G.K.M.);Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain (S.P.); andGrupo de Investigación en Polifenoles, Unidad de Nutrición y Bromatología, Universidad de Salamanca, 37007 Salamanca, Spain (M.D., C.S.-B.)
| | - Oscar Lorenzo
- Departamento de Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, 37185 Salamanca, Spain (L.S., M.F.-M., A.M., O.L.);Department of Biology and Center for Molecular Communication and Signaling, Wake Forest University, Winston-Salem, North Carolina 27106 (D.R.L., G.K.M.);Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Pozuelo de Alarcón, Madrid, Spain (S.P.); andGrupo de Investigación en Polifenoles, Unidad de Nutrición y Bromatología, Universidad de Salamanca, 37007 Salamanca, Spain (M.D., C.S.-B.)
| |
Collapse
|
29
|
Stage-specific reprogramming of gene expression characterizes Lr48-mediated adult plant leaf rust resistance in wheat. Funct Integr Genomics 2014; 15:233-45. [DOI: 10.1007/s10142-014-0416-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 11/09/2014] [Accepted: 11/17/2014] [Indexed: 12/13/2022]
|
30
|
Hollmann J, Gregersen PL, Krupinska K. Identification of predominant genes involved in regulation and execution of senescence-associated nitrogen remobilization in flag leaves of field grown barley. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3963-73. [PMID: 24700620 PMCID: PMC4106439 DOI: 10.1093/jxb/eru094] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The transcriptomes of senescing flag leaves collected from barley field plots with standard or high nitrogen supply were compared to identify genes specifically associated with nitrogen remobilization during leaf senescence under agronomically relevant conditions. In flag leaves collected in field plots with high nitrogen supply, the decline in chlorophyll content was delayed. By comparing changes in gene expression for the two nitrogen levels, it was possible to discriminate genes related to nitrogen remobilization during senescence and genes involved in other processes associated with the late development of leaves under field conditions. Predominant genes that were more strongly upregulated during senescence of flag leaves from plants with standard nitrogen supply included genes encoding the transcription factor HvNAC026, serine type protease SCPL51, and the autophagy factors APG7 and ATG18F. Elevated expression of these genes in senescing leaves from plants with standard nitrogen supply indicates important roles of the corresponding proteins in nitrogen remobilization. In comparison, the genes upregulated in both flag leaf samples might have roles in general senescence processes associated with late leaf development. Among these genes were the transcription factor genes HvNAC001, HvNAC005, HvNAC013, HvWRKY12 and MYB, genes encoding the papain-like cysteine peptidases HvPAP14 and HvPAP20, as well as a subtilase gene.
Collapse
Affiliation(s)
- Julien Hollmann
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Per L Gregersen
- Department of Molecular Biology and Genetics, Aarhus University, AU-Flakkebjerg, DK-4200 Slagelse, Denmark
| | - Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| |
Collapse
|
31
|
You J, Zong W, Du H, Hu H, Xiong L. A special member of the rice SRO family, OsSRO1c, mediates responses to multiple abiotic stresses through interaction with various transcription factors. PLANT MOLECULAR BIOLOGY 2014; 84:693-705. [PMID: 24337801 DOI: 10.1007/s11103-013-0163-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/05/2013] [Indexed: 05/09/2023]
Abstract
SIMILAR TO RCD ONE (SRO) is a plant-specific gene family involved in development and abiotic stress responses. SRO proteins are characterized by containing poly (ADP-ribose) polymerase catalytic (PARP) and C-terminal RCD1-SRO-TAF4 domains, and can be classified into two groups and five subgroups on the basis of their PARP domain. Expression analysis of rice SRO genes in response to various abiotic stresses showed that OsSRO1c, a rice SRO gene which functions downstream of the stress-responsive transcription factor SNAC1, is the major stress-responsive gene in the rice SRO family. The ossro1c-1 mutant showed resistance not only to chloroplastic oxidative stress, but also to apoplastic oxidative stress. However, the ossro1c-1 mutant and artificial microRNA-OsSRO1c transgenic rice were significantly impaired in cold tolerance. When compared with the well-characterized Arabidopsis SRO protein radical-induced cell death 1 (RCD1), OsSRO1c has considerable variation in the protein sequence, and the two genes exhibit different expression profiles under abiotic stresses. Furthermore, ossro1c-1 and rcd1 showed different responses to multiple abiotic stresses. By screening an Arabidopsis transcription factor library, 29 transcription factors interacted with OsSRO1c in yeast, but only two of these transcription factors were reported to interact with RCD1, which may partly explain the different responses of the two mutants under various stresses. The data presented in this report provide important clues for further elucidating the molecular and biochemical mechanisms of OsSRO1c in mediating responses to multiple abiotic stresses.
Collapse
Affiliation(s)
- Jun You
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | | | | | | | | |
Collapse
|
32
|
Brosché M, Blomster T, Salojärvi J, Cui F, Sipari N, Leppälä J, Lamminmäki A, Tomai G, Narayanasamy S, Reddy RA, Keinänen M, Overmyer K, Kangasjärvi J. Transcriptomics and functional genomics of ROS-induced cell death regulation by RADICAL-INDUCED CELL DEATH1. PLoS Genet 2014; 10:e1004112. [PMID: 24550736 PMCID: PMC3923667 DOI: 10.1371/journal.pgen.1004112] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 12/02/2013] [Indexed: 11/18/2022] Open
Abstract
Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS). Combining transcriptomic and functional genomics approaches we first used microarray analysis in a time series to study changes in gene expression after apoplastic ROS treatment in rcd1. To identify a core set of cell death regulated genes, RCD1-regulated genes were clustered together with other array experiments from plants undergoing cell death or treated with various pathogens, plant hormones or other chemicals. Subsequently, selected rcd1 double mutants were constructed to further define the genetic requirements for the execution of apoplastic ROS induced cell death. Through the genetic analysis we identified WRKY70 and SGT1b as cell death regulators functioning downstream of RCD1 and show that quantitative rather than qualitative differences in gene expression related to cell death appeared to better explain the outcome. Allocation of plant energy to defenses diverts resources from growth. Recently, a plant response termed stress-induced morphogenic response (SIMR) was proposed to regulate the balance between defense and growth. Using a rcd1 double mutant collection we show that SIMR is mostly independent of the classical plant defense signaling pathways and that the redox balance is involved in development of SIMR. Reactive oxygen species (ROS) are utilized in plants as signaling molecules to regulate development, stress responses and cell death. One extreme form of defense uses programmed cell death (PCD) in a scorched earth strategy to deliberately kill off cells invaded by a pathogen. Compared to animals, the regulation of plant PCD remains largely uncharacterized, particularly with regard to how ROS regulate changes in gene expression leading to PCD. Using comparative transcriptome analysis of mutants deficient in PCD regulation and publicly available cell death microarray data, we show that quantitative rather than qualitative differences in cell death gene expression appear to better explain the cell death response. In a genetic analysis with double mutants we also found the transcription factor WRKY70 and a component of ubiquitin mediated protein degradation, SGT1b, to be involved in regulation of ROS induced PCD.
Collapse
Affiliation(s)
- Mikael Brosché
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Institute of Technology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Tiina Blomster
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jarkko Salojärvi
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Fuqiang Cui
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Nina Sipari
- Department of Biology, University of Eastern Finland, Joensuu, Finland
| | - Johanna Leppälä
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Airi Lamminmäki
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Gloria Tomai
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Shaman Narayanasamy
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Ramesha A. Reddy
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Markku Keinänen
- Department of Biology, University of Eastern Finland, Joensuu, Finland
| | - Kirk Overmyer
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jaakko Kangasjärvi
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
33
|
Hiltscher H, Rudnik R, Shaikhali J, Heiber I, Mellenthin M, Meirelles Duarte I, Schuster G, Kahmann U, Baier M. The radical induced cell death protein 1 (RCD1) supports transcriptional activation of genes for chloroplast antioxidant enzymes. FRONTIERS IN PLANT SCIENCE 2014; 5:475. [PMID: 25295044 PMCID: PMC4172000 DOI: 10.3389/fpls.2014.00475] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 08/28/2014] [Indexed: 05/21/2023]
Abstract
The rimb1 (redox imbalanced 1) mutation was mapped to the RCD1 locus (radical-induced cell death 1; At1g32230) demonstrating that a major factor involved in redox-regulation genes for chloroplast antioxidant enzymes and protection against photooxidative stress, RIMB1, is identical to the regulator of disease response reactions and cell death, RCD1. Discovering this link let to our investigation of its regulatory mechanism. We show in yeast that RCD1 can physically interact with the transcription factor Rap2.4a which provides redox-sensitivity to nuclear expression of genes for chloroplast antioxidant enzymes. In the rimb1 (rcd1-6) mutant, a single nucleotide exchange results in a truncated RCD1 protein lacking the transcription factor binding site. Protein-protein interaction between full-length RCD1 and Rap2.4a is supported by H2O2, but not sensitive to the antioxidants dithiotreitol and ascorbate. In combination with transcript abundance analysis in Arabidopsis, it is concluded that RCD1 stabilizes the Rap2.4-dependent redox-regulation of the genes encoding chloroplast antioxidant enzymes in a widely redox-independent manner. Over the years, rcd1-mutant alleles have been described to develop symptoms like chlorosis, lesions along the leaf rims and in the mesophyll and (secondary) induction of extra- and intra-plastidic antioxidant defense mechanisms. All these rcd1 mutant characteristics were observed in rcd1-6 to succeed low activation of the chloroplast antioxidant system and glutathione biosynthesis. We conclude that RCD1 protects plant cells from running into reactive oxygen species (ROS)-triggered programs, such as cell death and activation of pathogen-responsive genes (PR genes) and extra-plastidic antioxidant enzymes, by supporting the induction of the chloroplast antioxidant system.
Collapse
Affiliation(s)
- Heiko Hiltscher
- Plant Science, Heinrich-Heine-University DüsseldorfDüsseldorf, Germany
| | | | - Jehad Shaikhali
- Plant Biochemistry and Physiology, Bielefeld UniversityBielefeld, Germany
- Department of Forest Genetics and Plant Physiology, Umea Plant Science Center, Swedish University of Agricultural SciencesUmea, Sweden
| | - Isabelle Heiber
- Plant Biochemistry and Physiology, Bielefeld UniversityBielefeld, Germany
| | - Marina Mellenthin
- Plant Science, Heinrich-Heine-University DüsseldorfDüsseldorf, Germany
| | | | - Günter Schuster
- Plant Science, Heinrich-Heine-University DüsseldorfDüsseldorf, Germany
| | - Uwe Kahmann
- Molecular Cell Physiology, Bielefeld UniversityBielefeld, Germany
| | - Margarete Baier
- Plant Science, Heinrich-Heine-University DüsseldorfDüsseldorf, Germany
- Plant Physiology, Freie Universität BerlinBerlin, Germany
- Plant Biochemistry and Physiology, Bielefeld UniversityBielefeld, Germany
- *Correspondence: Margarete Baier, Plant Physiology, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195 Berlin, Germany e-mail:
| |
Collapse
|
34
|
De Clercq I, Vermeirssen V, Van Aken O, Vandepoele K, Murcha MW, Law SR, Inzé A, Ng S, Ivanova A, Rombaut D, van de Cotte B, Jaspers P, Van de Peer Y, Kangasjärvi J, Whelan J, Van Breusegem F. The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. THE PLANT CELL 2013; 25:3472-90. [PMID: 24045019 PMCID: PMC3809544 DOI: 10.1105/tpc.113.117168] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 08/06/2013] [Accepted: 08/26/2013] [Indexed: 05/18/2023]
Abstract
Upon disturbance of their function by stress, mitochondria can signal to the nucleus to steer the expression of responsive genes. This mitochondria-to-nucleus communication is often referred to as mitochondrial retrograde regulation (MRR). Although reactive oxygen species and calcium are likely candidate signaling molecules for MRR, the protein signaling components in plants remain largely unknown. Through meta-analysis of transcriptome data, we detected a set of genes that are common and robust targets of MRR and used them as a bait to identify its transcriptional regulators. In the upstream regions of these mitochondrial dysfunction stimulon (MDS) genes, we found a cis-regulatory element, the mitochondrial dysfunction motif (MDM), which is necessary and sufficient for gene expression under various mitochondrial perturbation conditions. Yeast one-hybrid analysis and electrophoretic mobility shift assays revealed that the transmembrane domain-containing no apical meristem/Arabidopsis transcription activation factor/cup-shaped cotyledon transcription factors (ANAC013, ANAC016, ANAC017, ANAC053, and ANAC078) bound to the MDM cis-regulatory element. We demonstrate that ANAC013 mediates MRR-induced expression of the MDS genes by direct interaction with the MDM cis-regulatory element and triggers increased oxidative stress tolerance. In conclusion, we characterized ANAC013 as a regulator of MRR upon stress in Arabidopsis thaliana.
Collapse
Affiliation(s)
- Inge De Clercq
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Vanessa Vermeirssen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Olivier Van Aken
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Monika W. Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Simon R. Law
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Annelies Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sophia Ng
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Aneta Ivanova
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Debbie Rombaut
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Brigitte van de Cotte
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Pinja Jaspers
- Plant Biology, Department of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jaakko Kangasjärvi
- Plant Biology, Department of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
- Department of Botany, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| |
Collapse
|
35
|
Makkena S, Lamb RS. The bHLH transcription factor SPATULA regulates root growth by controlling the size of the root meristem. BMC PLANT BIOLOGY 2013; 13:1. [PMID: 23924433 PMCID: PMC3583232 DOI: 10.1186/1471-2229-13-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 12/12/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND The Arabidopsis thaliana gene SPATULA (SPT), encoding a bHLH transcription factor, was originally identified for its role in pistil development. SPT is necessary for the growth and development of all carpel margin tissues including the style, stigma, septum and transmitting tract. Since then, it has been shown to have pleiotropic roles during development, including restricting the meristematic region of the leaf primordia and cotyledon expansion. Although SPT is expressed in roots, its role in this organ has not been investigated. RESULTS An analysis of embryo and root development showed that loss of SPT function causes an increase in quiescent center size in both the embryonic and postembryonic stem cell niches. In addition, root meristem size is larger due to increased division, which leads to a longer primary root. spt mutants exhibit other pleiotropic developmental phenotypes, including more flowers, shorter internodes and an extended flowering period. Genetic and molecular analysis suggests that SPT regulates cell proliferation in parallel to gibberellic acid as well as affecting auxin accumulation or transport. CONCLUSIONS Our data suggest that SPT functions in growth control throughout sporophytic growth of Arabidopsis, but is not necessary for cell fate decisions except during carpel development. SPT functions independently of gibberellic acid during root development, but may play a role in regulating auxin transport or accumulation. Our data suggests that SPT plays a role in control of root growth, similar to its roles in above ground tissues.
Collapse
Affiliation(s)
- Srilakshmi Makkena
- Plant Cellular and Molecular Biology Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Rebecca S Lamb
- Plant Cellular and Molecular Biology Graduate Program, The Ohio State University, Columbus, OH, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
36
|
Lamb RS, Citarelli M, Teotia S. Functions of the poly(ADP-ribose) polymerase superfamily in plants. Cell Mol Life Sci 2012; 69:175-89. [PMID: 21861184 PMCID: PMC11114847 DOI: 10.1007/s00018-011-0793-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 08/02/2011] [Accepted: 08/04/2011] [Indexed: 01/09/2023]
Abstract
Poly(ADP-ribosyl)ation is the covalent attachment of ADP-ribose subunits from NAD(+) to target proteins and was first described in plants in the 1970s. This post-translational modification is mediated by poly(ADP-ribose) polymerases (PARPs) and removed by poly(ADP-ribose) glycohydrolases (PARGs). PARPs have important functions in many biological processes including DNA repair, epigenetic regulation and transcription. However, these roles are not always associated with enzymatic activity. The PARP superfamily has been well studied in animals, but remains under-investigated in plants. Although plants lack the variety of PARP superfamily members found in mammals, they do encode three different types of PARP superfamily proteins, including a group of PARP-like proteins, the SRO family, that are plant specific. In plants, members of the PARP family and/or poly(ADP-ribosyl)ation have been linked to DNA repair, mitosis, innate immunity and stress responses. In addition, members of the SRO family have been shown to be necessary for normal sporophytic development. In this review, we summarize the current state of plant research into poly(ADP-ribosyl)ation and the PARP superfamily in plants.
Collapse
Affiliation(s)
- Rebecca S Lamb
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA.
| | | | | |
Collapse
|
37
|
Kjaersgaard T, Jensen MK, Christiansen MW, Gregersen P, Kragelund BB, Skriver K. Senescence-associated barley NAC (NAM, ATAF1,2, CUC) transcription factor interacts with radical-induced cell death 1 through a disordered regulatory domain. J Biol Chem 2011; 286:35418-35429. [PMID: 21856750 DOI: 10.1074/jbc.m111.247221] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Senescence in plants involves massive nutrient relocation and age-related cell death. Characterization of the molecular components, such as transcription factors (TFs), involved in these processes is required to understand senescence. We found that HvNAC005 and HvNAC013 of the plant-specific NAC (NAM, ATAF1,2, CUC) TF family are up-regulated during senescence in barley (Hordeum vulgare). Both HvNAC005 and HvNAC013 bound the conserved NAC DNA target sequence. Computational and biophysical analyses showed that both proteins are intrinsically disordered in their large C-terminal domains, which are transcription regulatory domains (TRDs) in many NAC TFs. Using motif searches and interaction studies in yeast we identified an evolutionarily conserved sequence, the LP motif, in the TRD of HvNAC013. This motif was sufficient for transcriptional activity. In contrast, HvNAC005 did not function as a transcriptional activator suggesting that an involvement of HvNAC013 and HvNAC005 in senescence will be different. HvNAC013 interacted with barley radical-induced cell death 1 (RCD1) via the very C-terminal part of its TRD, outside of the region containing the LP motif. No significant secondary structure was induced in the HvNAC013 TRD upon interaction with RCD1. RCD1 also interacted with regions dominated by intrinsic disorder in TFs of the MYB and basic helix-loop-helix families. We propose that RCD1 is a regulatory protein capable of interacting with many different TFs by exploiting their intrinsic disorder. In addition, we present the first structural characterization of NAC C-terminal domains and relate intrinsic disorder and sequence motifs to activity and protein-protein interactions.
Collapse
Affiliation(s)
- Trine Kjaersgaard
- Department of Biology, University of Copenhagen, Ole Maaloesvej 5, Copenhagen DK-2200
| | - Michael K Jensen
- Department of Biology, University of Copenhagen, Ole Maaloesvej 5, Copenhagen DK-2200
| | - Michael W Christiansen
- Department of Genetics and Biotechnology, University of Aarhus, Research Center Flakkebjerg, 4200 Slagelse, Denmark
| | - Per Gregersen
- Department of Genetics and Biotechnology, University of Aarhus, Research Center Flakkebjerg, 4200 Slagelse, Denmark
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaloesvej 5, Copenhagen DK-2200
| | - Karen Skriver
- Department of Biology, University of Copenhagen, Ole Maaloesvej 5, Copenhagen DK-2200.
| |
Collapse
|
38
|
Costa CT, Strieder ML, Abel S, Delatorre CA. Phosphorus and nitrogen interaction: loss of QC identity in response to P or N limitation is antecipated in pdr23 mutant. ACTA ACUST UNITED AC 2011. [DOI: 10.1590/s1677-04202011000300006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Changes in root architecture are an important adaptive strategy used by plants in response to limited nutrient availability to increase the odds of acquiring them. The quiescent center (QC) plays an important role by altering the meristem activity causing differentiation and therefore, inducing a determinate growth program. The arabidopsis mutant pdr23 presents primary short root in the presence of nitrate and is inefficient in the use of nucleic acids as a source of phosphorus. In this study the effect of the pdr23 mutation on the QC maintenance under low phosphorus (P) and/or nitrogen is evaluated. QC identity is maintained in wild-type in the absence of nitrate and/or phosphate if nucleic acids can be used as an alternative source of these nutrients, but not in pdr23. The mutant is not able to use nucleic acids efficiently for substitute Pi, determinate growth is observed, similar to wild-type in the total absence of P. In the absence of N pdr23 loses the expression of QC identity marker earlier than wild-type, indicating that not only the response to P is altered, but also to N. The data suggest that the mutation affects a gene involved either in the crosstalk between these nutrients or in a pathway shared by both nutrients limitation response. Moreover loss of QC identity is also observed in wild-type in the absence of N at longer limitation. Less drastic symptoms are observed in lateral roots of both genotypes.
Collapse
Affiliation(s)
| | - Mércio L. Strieder
- Federal University of Rio Grande do Sul, Brazil; Empresa Brasileira de Pesquisa Agropecuária, Brazil
| | - Stephen Abel
- Leibniz Institute of Plant Biochemistry, Germany
| | | |
Collapse
|