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Xie Q, Zhang Y, Wu M, Chen Y, Wang Y, Zeng Q, Han Y, Zhang S, Zhang J, Chen T, Cai M. Identification and Functional Analysis of KH Family Genes Associated with Salt Stress in Rice. Int J Mol Sci 2024; 25:5950. [PMID: 38892138 PMCID: PMC11172612 DOI: 10.3390/ijms25115950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Salinity stress has a great impact on crop growth and productivity and is one of the major factors responsible for crop yield losses. The K-homologous (KH) family proteins play vital roles in regulating plant development and responding to abiotic stress in plants. However, the systematic characterization of the KH family in rice is still lacking. In this study, we performed genome-wide identification and functional analysis of KH family genes and identified a total of 31 KH genes in rice. According to the homologs of KH genes in Arabidopsis thaliana, we constructed a phylogenetic tree with 61 KH genes containing 31 KH genes in Oryza sativa and 30 KH genes in Arabidopsis thaliana and separated them into three major groups. In silico tissue expression analysis showed that the OsKH genes are constitutively expressed. The qRT-PCR results revealed that eight OsKH genes responded strongly to salt stresses, and OsKH12 exhibited the strongest decrease in expression level, which was selected for further study. We generated the Oskh12-knockout mutant via the CRISPR/Cas9 genome-editing method. Further stress treatment and biochemical assays confirmed that Oskh12 mutant was more salt-sensitive than Nip and the expression of several key salt-tolerant genes in Oskh12 was significantly reduced. Taken together, our results shed light on the understanding of the KH family and provide a theoretical basis for future abiotic stress studies in rice.
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Affiliation(s)
- Qinyu Xie
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Yutong Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Mingming Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Youheng Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Yingwei Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Qinzong Zeng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuliang Han
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Siqi Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Juncheng Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Maohong Cai
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
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Dai Y, Gao X, Zhang S, Li F, Zhang H, Li G, Sun R, Zhang S, Hou X. Exploring the Regulatory Dynamics of BrFLC-Associated lncRNA in Modulating the Flowering Response of Chinese Cabbage. Int J Mol Sci 2024; 25:1924. [PMID: 38339202 PMCID: PMC10856242 DOI: 10.3390/ijms25031924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Vernalization plays a crucial role in the flowering and yield of Chinese cabbage, a process intricately influenced by long non-coding RNAs (lncRNAs). Our research focused on lncFLC1, lncFLC2a, and lncFLC2b, which emerged as key players in this process. These lncRNAs exhibited an inverse expression pattern to the flowering repressor genes FLOWERING LOCUS C 1 (BrFLC1) and FLOWERING LOCUS C 2 (BrFLC2) during vernalization, suggesting a complex regulatory mechanism. Notably, their expression in the shoot apex and leaves was confirmed through in fluorescent in situ hybridization (FISH). Furthermore, when these lncRNAs were overexpressed in Arabidopsis, a noticeable acceleration in flowering was observed, unveiling functional similarities to Arabidopsis's COLD ASSISTED INTRONIC NONCODING RNA (COOLAIR). This resemblance suggests a potentially conserved regulatory mechanism across species. This study not only enhances our understanding of lncRNAs in flowering regulation, but also opens up new possibilities for their application in agricultural practices.
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Affiliation(s)
- Yun Dai
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China;
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Xinyu Gao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Shifan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Fei Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Hui Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Guoliang Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Rifei Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Shujiang Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.G.); (S.Z.); (F.L.); (H.Z.); (G.L.); (R.S.)
| | - Xilin Hou
- National Key Laboratory of Crop Genetics & Germplasm Innovation and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China;
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Li S, Chen H, Hong J, Ye X, Wang J, Chen Y, Zhang L, Su Z, Yang Z. Chlorate-induced molecular floral transition revealed by transcriptomes. Open Life Sci 2023; 18:20220612. [PMID: 37528883 PMCID: PMC10389677 DOI: 10.1515/biol-2022-0612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/25/2023] [Accepted: 04/08/2023] [Indexed: 08/03/2023] Open
Abstract
Flowering in off-season longan (Dimocarpus longan L.) can be induced effectively by the application of potassium chlorate (KClO3), but the mechanism of the physiological induction is largely unknown to decipher its mechanism and identify genes potentially regulating the process, and comparative analysis via RNA-Seq was performed between vegetative and KClO3-induced floral buds. A total of 18,649 differentially expressed genes (DEGs) were identified between control and treated samples. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs related to plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling pathway, starch and sucrose metabolism, and phenylpropanoid biosynthesis were enriched in our data. A total of 29 flowering-related DEGs were identified in our study, such as APETALA1 (AP1), APETALA2 (AP2), AUXIN RESPONSE FACTOR 3/ETTIN (ARF3), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8), AGAMOUS (AG), and others. The upregulation of AP2 and SPL genes indicates that the age-related pathway is activated and influences the floral induction in KClO3-induced longan floral buds by coordinated regulation of genes related to AP1, AG, and ARF3. This study provides a valuable resource for studying molecular mechanisms underlying chlorate-induced floral transition in off-season longan, which may benefit the development and production of off-season tropical/subtropical fruit trees.
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Affiliation(s)
- Songgang Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Houbin Chen
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Jiwang Hong
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Jiabao Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Lei Zhang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Zuanxian Su
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Ziqin Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
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Bobadilla LK, Baek Y, Tranel PJ. Comparative transcriptomic analysis of male and females in the dioecious weeds Amaranthus palmeri and Amaranthus tuberculatus. BMC PLANT BIOLOGY 2023; 23:339. [PMID: 37365527 DOI: 10.1186/s12870-023-04286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and Palmer amaranth (Amaranthus palmeri S. Wats.) are two dioecious and important weed species in the world that can rapidly evolve herbicide-resistance traits. Understanding these two species' dioecious and sex-determination mechanisms could open opportunities for new tools to control them. This study aims to identify the differential expression patterns between males and females in A. tuberculatus and A. palmeri. Multiple analyses, including differential expression, co-expression, and promoter analyses, used RNA-seq data from multiple tissue types to identify putative essential genes for sex determination in both dioecious species. RESULTS Genes were identified as potential key players for sex determination in A. palmeri. Genes PPR247, WEX, and ACD6 were differentially expressed between the sexes and located at scaffold 20 within or near the male-specific Y (MSY) region. Multiple genes involved with flower development were co-expressed with these three genes. For A. tuberculatus, no differentially expressed gene was identified within the MSY region; however, multiple autosomal class B and C genes were identified as differentially expressed and possible candidate genes. CONCLUSIONS This is the first study comparing the global expression profile between males and females in dioecious weedy Amaranthus species. Results narrow down putative essential genes for sex-determination in A. palmeri and A. tuberculatus and also strengthen the hypothesis of two different evolutionary events for dioecy within the genus.
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Affiliation(s)
- Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Yousoon Baek
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
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Fabian M, Gao M, Zhang XN, Shi J, Vrydagh L, Kim SH, Patel P, Hu AR, Lu H. The flowering time regulator FLK controls pathogen defense in Arabidopsis thaliana. PLANT PHYSIOLOGY 2023; 191:2461-2474. [PMID: 36662556 PMCID: PMC10069895 DOI: 10.1093/plphys/kiad021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 05/22/2023]
Abstract
Plant disease resistance is a complex process that is maintained in an intricate balance with development. Increasing evidence indicates the importance of posttranscriptional regulation of plant defense by RNA binding proteins. In a genetic screen for suppressors of Arabidopsis (Arabidopsis thaliana) accelerated cell death 6-1 (acd6-1), a small constitutive defense mutant whose defense level is grossly in a reverse proportion to plant size, we identified an allele of the canonical flowering regulatory gene FLOWERING LOCUS K HOMOLOGY DOMAIN (FLK) encoding a putative protein with triple K homology (KH) repeats. The KH repeat is an ancient RNA binding motif found in proteins from diverse organisms. The relevance of KH-domain proteins in pathogen resistance is largely unexplored. In addition to late flowering, the flk mutants exhibited decreased resistance to the bacterial pathogen Pseudomonas syringae and increased resistance to the necrotrophic fungal pathogen Botrytis cinerea. We further found that the flk mutations compromised basal defense and defense signaling mediated by salicylic acid (SA). Mutant analysis revealed complex genetic interactions between FLK and several major SA pathway genes. RNA-seq data showed that FLK regulates expression abundance of some major defense- and development-related genes as well as alternative splicing of a number of genes. Among the genes affected by FLK is ACD6, whose transcripts had increased intron retentions influenced by the flk mutations. Thus, this study provides mechanistic support for flk suppression of acd6-1 and establishes that FLK is a multifunctional gene involved in regulating pathogen defense and development of plants.
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Affiliation(s)
- Matthew Fabian
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
| | - Min Gao
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
- Biochemistry Program, Department of Biology, St Bonaventure University, St Bonaventure, New York 14778, USA
| | - Xiao-Ning Zhang
- Biochemistry Program, Department of Biology, St Bonaventure University, St Bonaventure, New York 14778, USA
| | - Jiangli Shi
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
- Department of Biology Education, Korea National University of Education, Chungbuk 28644, Korea
| | - Leah Vrydagh
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
| | - Sung-Ha Kim
- Department of Biology Education, Korea National University of Education, Chungbuk 28644, Korea
| | - Priyank Patel
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
| | - Anna R Hu
- Biochemistry Program, Department of Biology, St Bonaventure University, St Bonaventure, New York 14778, USA
| | - Hua Lu
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
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Zhang X, Xie Q, Xiang L, Lei Z, Huang Q, Zhang J, Cai M, Chen T. AtSIEK, an EXD1-like protein with KH domain, involves in salt stress response by interacting with FRY2/CPL1. Int J Biol Macromol 2023; 233:123369. [PMID: 36693612 DOI: 10.1016/j.ijbiomac.2023.123369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
Abiotic stress has great impacts on plant germination, growth and development and crop yield. Therefore, it is important to understand the molecular mechanism of plants response to abiotic stress. In this study, we identified a plant specific protein AtSIEK (stress-induced protein with EXD1-like domain and KH domain) response to salt stress. AtSIEK encodes a hnRNP K homology (KH) protein localized in nucleus. Amino acid sequences analysis found that SIEK protein is specific in plants, containing two domains with EXD1-like domain and KH domain, while SIEK homolog in animals only had EXD1-like domain without KH domain. Physiology experiments revealed that AtSIEK was significantly induced under salt stress and the siek mutant shows sensitive to salt stress, indicating that AtSIEK was a positive regulator in stress response. Further, molecular, biochemical, and genetic assays suggested that AtSIEK interacts with FRY2/CPL1, a known regulator in response to abiotic stress, and they function synergistically in response to salt stress. Taken together, these results shed new light on the regulation of plant adaption to abiotic stress, which deepen our understanding of the molecular mechanisms of abiotic stress regulation in plants.
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Affiliation(s)
- Xiangxiang Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Qinyu Xie
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Lijun Xiang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China
| | - Zhonghua Lei
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China
| | - Qixiu Huang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China
| | - Juncheng Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China
| | - Maohong Cai
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China.
| | - Tao Chen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 311121, China.
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Laanen P, Cuypers A, Saenen E, Horemans N. Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:246-259. [PMID: 36731286 DOI: 10.1016/j.plaphy.2023.01.049] [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: 06/27/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.
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Affiliation(s)
- Pol Laanen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Ann Cuypers
- Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Eline Saenen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium.
| | - Nele Horemans
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
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Wang W, Wang S, Gong W, Lv L, Xu L, Nie J, Huang L. Valsa mali secretes an effector protein VmEP1 to target a K homology domain-containing protein for virulence in apple. MOLECULAR PLANT PATHOLOGY 2022; 23:1577-1591. [PMID: 35851537 PMCID: PMC9562843 DOI: 10.1111/mpp.13248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The K homology (KH) repeat is an RNA-binding motif that exists in various proteins, some of which participate in plant growth. However, the function of KH domain-containing proteins in plant defence is still unclear. In this study, we found that a KH domain-containing protein in apple (Malus domestica), HEN4-like (MdKRBP4), is involved in the plant immune response. Silencing of MdKRBP4 compromised reactive oxygen species (ROS) production and enhanced the susceptibility of apple to Valsa mali, whereas transient overexpression of MdKRBP4 stimulated ROS accumulation in apple leaves, indicating that MdKRBP4 is a positive immune regulator. Additionally, MdKRBP4 was proven to interact with the VmEP1 effector secreted by V. mali, which led to decreased accumulation of MdKRBP4. Coexpression of MdKRBP4 with VmEP1 inhibited cell death and ROS production induced by MdKRBP4 in Nicotiana benthamiana. These results indicate that MdKRBP4 functions as a novel positive regulatory factor in plant immunity in M. domestica and is a virulence target of the V. mali effector VmEP1.
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Affiliation(s)
- Weidong Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Shuaile Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Wan Gong
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Luqiong Lv
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Liangsheng Xu
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jiajun Nie
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid AreasYanglingChina
- College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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Genome-Wide Characterization and Expression Analysis of KH Family Genes Response to ABA and SA in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23010511. [PMID: 35008936 PMCID: PMC8745409 DOI: 10.3390/ijms23010511] [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: 11/08/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
K-homologous (KH) family is a type of nucleic acid-binding protein containing the KH domain and has been found to affect splicing and transcriptional regulation. However, KH family genes haven’t been investigated in plant species systematically. In this study, we identified 30 genes that belonged to the KH family based on HMM of the KH domain in Arabidopsis thaliana. Phylogenetic tree analysis showed that the KH family is grouped into three subgroups. Synteny analysis showed that AtKH9 and AtKH29 have the conserved synteny relationship between A. thaliana and the other five species. The AtKH9 and AtKH29 were located in the cytoplasm and nucleus. The seed germination rates of the mutants atkh9 and atkh29 were higher than wild-type after abscisic acid (ABA) and salicylic acid (SA) treatments. In addition, the expression of ABA-related genes, such as ABRE-binding factor 2 (ABF2), ABRE-binding factor 4 (ABF4), and delta 1-pyrroline-5-carboxylate synthase (P5CS), and an SA-related gene pathogenesis-related proteins b (PR1b) were downregulated after ABA and SA treatments, respectively. These results suggested that atkh9 and atkh29 mutants inhibit the effect of ABA and SA on seed germination. In conclusion, our results provide valuable information for further exploration of the function of KH family genes and propose directions and ideas for the identification and characterization of KH family genes in other plants.
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Yu YH, Li XF, Yang SD, Li SQ, Meng XX, Liu HN, Pei MS, Wei TL, Zhang YJ, Guo DL. Overexpression of VvPPR1, a DYW-type PPR protein in grape, affects the phenotype of Arabidopsis thaliana leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 164:195-204. [PMID: 34004557 DOI: 10.1016/j.plaphy.2021.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins play important roles in plant growth and development. However, little is known about their functions in the leaf morphogenesis of Jingxiu grape (Vitis vinifera L.). Here, we explored the function of VvPPR1, which encodes a DYW-type PPR protein in grape. We showed that VvPPR1 is involved in the regulation of leaf rolling, anthocyanin accumulation, and trichome formation in Arabidopsis thaliana. Analysis of structural characteristics showed that VvPPR1 is a DYW-type PPR gene in the PLS subfamily consisting of 15 PPR motifs. The N-terminal had a targeted chloroplast site, and the C-terminal had a DYW domain. Quantitative PCR analysis revealed that the expression level of VvPPR1 was highest in grape leaves. Subcellular localization revealed that VvPPR1 is localized in the cytoplasm and chloroplast. VvPPR1-overexpressing plants had rolled leaves, high degrees of anthocyanin accumulation, and longer trichomes. The expression levels of genes related to these phenotypes were either significantly up-regulated or down-regulated. These results demonstrate that VvPPR1 is involved in leaf rolling, anthocyanin accumulation, and trichome formation in Arabidopsis; more generally, our findings indicate that VvPPR1 could be a target for improving the cultivation of horticultural crops.
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Affiliation(s)
- Yi-He Yu
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Xu-Fei Li
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Sheng-Di Yang
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Song-Qi Li
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Xiang-Xuan Meng
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Hai-Nan Liu
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Mao-Song Pei
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Tong-Lu Wei
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Yu-Jie Zhang
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
| | - Da-Long Guo
- College of Horticulure and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.
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11
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Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22115716. [PMID: 34071961 PMCID: PMC8198774 DOI: 10.3390/ijms22115716] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Flowering is one of the most critical developmental transitions in plants’ life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny’s success. In Arabidopsis thaliana, seven flowering genetic pathways have been described under specific growth conditions. However, the evidence condensed here suggest that these pathways are tightly interconnected in a complex multilevel regulatory network. In this review, we pursue an integrative approach emphasizing the molecular interactions among the flowering regulatory network components. We also consider that the same regulatory network prevents or induces flowering phase change in response to internal cues modulated by environmental signals. In this sense, we describe how during the vegetative phase of development it is essential to prevent the expression of flowering promoting genes until they are required. Then, we mention flowering regulation under suboptimal growing temperatures, such as those in autumn and winter. We next expose the requirement of endogenous signals in flowering, and finally, the acceleration of this transition by long-day photoperiod and temperature rise signals allowing A. thaliana to bloom in spring and summer seasons. With this approach, we aim to provide an initial systemic view to help the reader integrate this complex developmental process.
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Kumar K, Srivastava H, Das A, Tribhuvan KU, Durgesh K, Joshi R, Sevanthi AM, Jain PK, Singh NK, Gaikwad K. Identification and characterization of MADS box gene family in pigeonpea for their role during floral transition. 3 Biotech 2021; 11:108. [PMID: 33569264 DOI: 10.1007/s13205-020-02605-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022] Open
Abstract
MADS box genes are class of transcription factors involved in various physiological and developmental processes in plants. To understand their role in floral transition-related pathways, a genome-wide identification was done in Cajanus cajan, identifying 102 members which were classified into two different groups based on their gene structure. The status of all these genes was further analyzed in three wild species i.e. C. scarabaeoides, C. platycarpus and C. cajanifolius which revealed absence of 31-34 MADS box genes in them hinting towards their role in domestication and evolution. We could locate only a single copy of both FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) genes, while three paralogs of SUPPRESSOR OF ACTIVATION OF CONSTANS 1 (SOC1) were found in C. cajan genome. One of those SOC1 paralogs i.e. CcMADS1.5 was found to be missing in all three wild relatives, also forming separate clade in phylogeny. This SOC1 gene was also lacking the characteristic MADS box domain in it. Expression profiling of major MADS box genes involved in flowering was done in different tissues viz shoot apical meristem, vegetative leaf, reproductive meristem, and reproductive bud. Gene-based time tree of FLC and SOC1 gene dictates their divergence from Arabidopsis before 71 and 23 million year ago (mya), respectively. This study provides valuable insights into the functional characteristics, expression pattern, and evolution of MADS box proteins in grain legumes with emphasis on C. cajan, which may help in further characterizing these genes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02605-7.
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Affiliation(s)
- Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 India
- ICAR-Indian Institute of Pulses Research, Kanpur, 208024 Uttar Pradesh India
| | - Harsha Srivastava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 India
| | - Antara Das
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 India
| | - Kishor U Tribhuvan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 India
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 Jharkhand India
| | - Kumar Durgesh
- Division of Genetics, ICAR-Indian Agricultural Reserch Institute, New Delhi, 110012 India
| | - Rekha Joshi
- Division of Genetics, ICAR-Indian Agricultural Reserch Institute, New Delhi, 110012 India
| | | | - Pradeep Kumar Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 India
| | | | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 India
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13
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Dai GY, Chen DK, Sun YP, Liang WY, Liu Y, Huang LQ, Li YK, He JF, Yao N. The Arabidopsis KH-domain protein FLOWERING LOCUS Y delays flowering by upregulating FLOWERING LOCUS C family members. PLANT CELL REPORTS 2020; 39:1705-1717. [PMID: 32948902 DOI: 10.1007/s00299-020-02598-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
We identified FLY as a previously uncharacterized RNA-binding-family protein that controls flowering time by positively regulating the expression of FLC clade members. The ability of flowering plants to adjust the timing of the floral transition based on endogenous and environmental signals contributes to their adaptive success. In Arabidopsis thaliana, the MADS-domain protein FLOWERING LOCUS C (FLC) and the FLC clade members FLOWERING LOCUS M/MADS AFFECTING FLOWERING1 (FLM/MAF1), MAF2, MAF3, MAF4, and MAF5 form nuclear complexes that repress flowering under noninductive conditions. However, how FLM/MAF genes are regulated requires further study. Using a genetic strategy, we showed that the previously uncharacterized K-homology (KH) domain protein FLOWERING LOCUS Y (FLY) modulates flowering time. The fly-1 knockout mutant and FLY artificial microRNA knockdown line flowered earlier than the wild type under long- and short-day conditions. The knockout fly-1 allele, a SALK T-DNA insertion mutant, contains an ~ 110-kb genomic deletion induced by T-DNA integration. FLC clade members were downregulated in the fly-1 mutants and FLY artificial microRNA knockdown line, whereas the level of the FLC antisense transcript COOLAIR was similar to that of the wild type. Our results identify FLY as a regulator that affects flowering time through upregulation of FLC clade members.
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Affiliation(s)
- Guang-Yi Dai
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ding-Kang Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yun-Peng Sun
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wei-Yi Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Li-Qun Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong-Kang Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Fan He
- School of Agriculture, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Nan Yao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Rahmati Ishka M, Vatamaniuk OK. Copper deficiency alters shoot architecture and reduces fertility of both gynoecium and androecium in Arabidopsis thaliana. PLANT DIRECT 2020; 4:e00288. [PMID: 33283140 PMCID: PMC7700745 DOI: 10.1002/pld3.288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/21/2020] [Accepted: 10/25/2020] [Indexed: 05/05/2023]
Abstract
Copper deficiency reduces plant growth, male fertility, and seed set. The contribution of copper to female fertility and the underlying molecular aspects of copper deficiency-caused phenotypes are not well known. We show that among copper deficiency-caused defects in Arabidopsis thaliana were also the increased shoot branching, delayed flowering and senescence, and entirely abolished gynoecium fertility. The increased shoot branching of copper-deficient plants was rescued by the exogenous application of auxin or copper. The delayed flowering was associated with the decreased expression of the floral activator, FT. Copper deficiency also decreased the expression of senescence-associated genes, WRKY53 and SAG13, but increased the expression of SAG12. The reduced fertility of copper-deficient plants stemmed from multiple factors including the abnormal stigma papillae development, the abolished gynoecium fertility, and the failure of anthers to dehisce. The latter defect was associated with reduced lignification, the upregulation of copper microRNAs and the downregulation of their targets, laccases, implicated in lignin synthesis. Copper-deficient plants accumulated ROS in pollen and had reduced cytochrome c oxidase activity in both leaves and floral buds. This study opens new avenues for the investigation into the relationship between copper homeostasis, hormone-mediated shoot architecture, gynoecium fertility, and copper deficiency-derived nutritional signals leading to the delay in flowering and senescence.
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Affiliation(s)
- Maryam Rahmati Ishka
- Soil and Crop Sciences SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Olena K. Vatamaniuk
- Soil and Crop Sciences SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
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