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Zeng J, Wang Y, Wu G, Sun Q, He X, Zhang X, Sun X, Zhao Y, Liu W, Xu D, Dai X, Ma W. Comparative Transcriptome Analysis Reveals the Genes and Pathways Related to Wheat Root Hair Length. Int J Mol Sci 2024; 25:2069. [PMID: 38396749 PMCID: PMC10889798 DOI: 10.3390/ijms25042069] [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: 01/10/2024] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Tube-like outgrowths from root epidermal cells, known as root hairs, enhance water and nutrient absorption, facilitate microbial interactions, and contribute to plant anchorage by expanding the root surface area. Genetically regulated and strongly influenced by environmental conditions, longer root hairs generally enhance water and nutrient absorption, correlating with increased stress resistance. Wheat, a globally predominant crop pivotal for human nutrition, necessitates the identification of long root hair genotypes and their regulatory genes to enhance nutrient capture and yield potential. This study focused on 261 wheat samples of diverse genotypes during germination, revealing noticeable disparities in the length of the root hair among the genotypes. Notably, two long root hair genotypes (W106 and W136) and two short root hair genotypes (W90 and W100) were identified. Transcriptome sequencing resulted in the development of 12 root cDNA libraries, unveiling 1180 shared differentially expressed genes (DEGs). Further analyses, including GO function annotation, KEGG enrichment, MapMan metabolic pathway analysis, and protein-protein interaction (PPI) network prediction, underscored the upregulation of root hair length regulatory genes in the long root hair genotypes. These included genes are associated with GA and BA hormone signaling pathways, FRS/FRF and bHLH transcription factors, phenylpropanoid, lignin, lignan secondary metabolic pathways, the peroxidase gene for maintaining ROS steady state, and the ankyrin gene with diverse biological functions. This study contributes valuable insights into modulating the length of wheat root hair and identifies candidate genes for the genetic improvement of wheat root traits.
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Affiliation(s)
- Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Yongmei Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Gang Wu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Qingyi Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xiaoyan He
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xinyi Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xuelian Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Yan Zhao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Wenxing Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Xuehuan Dai
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (J.Z.); (X.Z.); (X.D.)
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
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Wang J, Liu M, Mao C, Li S, Zhou J, Fan Y, Guo L, Yu H, Yang X. Comparative proteomics reveals the mechanism of cyclosporine production and mycelial growth in Tolypocladium inflatum affected by different carbon sources. Front Microbiol 2023; 14:1259101. [PMID: 38163081 PMCID: PMC10757567 DOI: 10.3389/fmicb.2023.1259101] [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: 07/15/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Cyclosporine A (CsA) is a secondary cyclopeptide metabolite produced by Tolypocladium inflatum that is widely used clinically as an immunosuppressant. CsA production and mycelial growth differed when T. inflatum was cultured in different carbon source media. During early fermentation, CsA was preferred to be produced in fructose medium, while the mycelium preferred to accumulate in sucrose medium. On the sixth day, the difference was most pronounced. In this study, high-throughput comparative proteomics methods were applied to analyze differences in protein expression of mycelial samples on day 6, revealing the proteins and mechanisms that positively regulate CsA production related to carbon metabolism. The differences included small molecule acid metabolism, lipid metabolism, organic catabolism, exocrine secretion, CsA substrate Bmt synthesis, and transcriptional regulation processes. The proteins involved in the regulation of mycelial growth related to carbon metabolism were also revealed and were associated with waste reoxidation processes or coenzyme metabolism, small molecule synthesis or metabolism, the stress response, genetic information or epigenetic changes, cell component assembly, cell wall integrity, membrane metabolism, vesicle transport, intramembrane localization, and the regulation of filamentous growth. This study provides a reliable reference for CsA production from high-efficiency fermentation. This study provides key information for obtaining more CsA high-yielding strains through metabolic engineering strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiuqing Yang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, China
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Jimmy JL, Karn R, Kumari S, Sruthilaxmi CB, Pooja S, Emerson IA, Babu S. Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes. Funct Integr Genomics 2023; 23:249. [PMID: 37474674 DOI: 10.1007/s10142-023-01167-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023]
Abstract
In plants, pathogen resistance is brought about by the binding of certain transcription factor (TF) proteins to the cis-elements of certain target genes. These cis-elements are present upstream in the motif of the promoters of each gene. This ensures the binding of a specific TF to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific TF. Rice 1 kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using Gene Ontology and gene set enrichment analysis. A gene with more than 4 TF bm in their promoter was selected. Ten genes reported to have a role in rice disease resistance were selected for further analysis. Cis-acting regulatory element analysis was carried out to find the cis-elements and confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding ten genes were built, and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY13 was considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected disease resistance-related genes with the WRKY13 TF protein. This study suggests downstream target genes that are regulated by the WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.
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Affiliation(s)
- John Lilly Jimmy
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India.
| | - Rohit Karn
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Sweta Kumari
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | | | - Singh Pooja
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Isaac Arnold Emerson
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Subramanian Babu
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, India
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Gordon A, McCartney C, Knox RE, Ereful N, Hiebert CW, Konkin DJ, Hsueh YC, Bhadauria V, Sgroi M, O'Sullivan DM, Hadley C, Boyd LA, Menzies JG. Genetic and transcriptional dissection of resistance to Claviceps purpurea in the durum wheat cultivar Greenshank. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1873-1886. [PMID: 32060572 PMCID: PMC7237535 DOI: 10.1007/s00122-020-03561-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 06/02/2023]
Abstract
Four QTL for ergot resistance (causal pathogen Claviceps purpurea) have been identified in the durum wheat cultivar Greenshank. Claviceps purpurea is a pathogen of grasses that infects flowers, replacing the seed with an ergot sclerotium. Ergot presents a significant problem to rye, barley and wheat, in particular hybrid seed production systems. In addition, there is evidence that the highly toxic alkaloids that accumulate within sclerotia can cross-contaminate otherwise healthy grain. Host resistance to C. purpurea is rare, few resistance loci having been identified. In this study, four ergot resistance loci are located on chromosomes 1B, 2A, 5A and 5B in the durum wheat cv. Greenshank. Ergot resistance was assessed through analysis of phenotypes associated with C. purpurea infection, namely the number of inoculated flowers that produced sclerotia, or resulted in ovary death but no sclerotia, the levels of honeydew produced, total sclerotia weight and average sclerotia weight and size per spike. Ergot testing was undertaken in Canada and the UK. A major effect QTL, QCp.aafc.DH-2A, was detected in both the Canadian and UK experiments and had a significant effect on honeydew production levels. QCp.aafc.DH-5B had the biggest influence on total sclerotia weight per spike. QCp.aafc.DH-1B was only detected in the Canadian experiments and QCp.aafc.DH-5A in the UK experiment. An RNASeq analysis, undertaken to identify wheat differentially expressed genes associated with different combinations of the four ergot resistance QTL, revealed a disproportionate number of DEGs locating to the QCp.aafc.DH-1B, QCp.aafc.DH-2A and QCp.aafc.DH-5B QTL intervals.
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Affiliation(s)
- Anna Gordon
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Nelzo Ereful
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Colin W Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - David J Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Ya-Chih Hsueh
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Vijai Bhadauria
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Mara Sgroi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK
| | - Caroline Hadley
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK
| | - Lesley A Boyd
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.
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Jiang N, Yan J, Liang Y, Shi Y, He Z, Wu Y, Zeng Q, Liu X, Peng J. Resistance Genes and their Interactions with Bacterial Blight/Leaf Streak Pathogens (Xanthomonas oryzae) in Rice (Oryza sativa L.)-an Updated Review. RICE (NEW YORK, N.Y.) 2020; 13:3. [PMID: 31915945 PMCID: PMC6949332 DOI: 10.1186/s12284-019-0358-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/18/2019] [Indexed: 05/19/2023]
Abstract
Rice (Oryza sativa L.) is a staple food crop, feeding more than 50% of the world's population. Diseases caused by bacterial, fungal, and viral pathogens constantly threaten the rice production and lead to enormous yield losses. Bacterial blight (BB) and bacterial leaf streak (BLS), caused respectively by gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), are two important diseases affecting rice production worldwide. Due to the economic importance, extensive genetic and genomic studies have been conducted to elucidate the molecular mechanism of rice response to Xoo and Xoc in the last two decades. A series of resistance (R) genes and their cognate avirulence and virulence effector genes have been characterized. Here, we summarize the recent advances in studies on interactions between rice and the two pathogens through these R genes or their products and effectors. Breeding strategies to develop varieties with durable and broad-spectrum resistance to Xanthomonas oryzae based on the published studies are also discussed.
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Affiliation(s)
- Nan Jiang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agronomy, Hunan Agricultural University, Changsha, 410128 Hunan China
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture Rural Affairs, School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106 Sichuan China
| | - Yi Liang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agronomy, Hunan Agricultural University, Changsha, 410128 Hunan China
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Yanlong Shi
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Zhizhou He
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Yuntian Wu
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Qin Zeng
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
| | - Xionglun Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agronomy, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Junhua Peng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agronomy, Hunan Agricultural University, Changsha, 410128 Hunan China
- Huazhi Rice Bio-tech Company Ltd., Changsha, 410125 Hunan China
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Singh P, Mazumdar P, Harikrishna JA, Babu S. Sheath blight of rice: a review and identification of priorities for future research. PLANTA 2019; 250:1387-1407. [PMID: 31346804 DOI: 10.1007/s00425-019-03246-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/20/2019] [Indexed: 05/04/2023]
Abstract
Rice sheath blight research should prioritise optimising biological control approaches, identification of resistance gene mechanisms and application in genetic improvement and smart farming for early disease detection. Rice sheath blight, caused by Rhizoctonia solani AG1-1A, is one of the most devasting diseases of the crop. To move forward with effective crop protection against sheath blight, it is important to review the published information related to pathogenicity and disease management and to determine areas of research that require deeper study. While progress has been made in the identification of pathogenesis-related genes both in rice and in the pathogen, the mechanisms remain unclear. Research related to disease management practices has addressed the use of agronomic practices, chemical control, biological control and genetic improvement: Optimising nitrogen fertiliser use in conjunction with plant spacing can reduce spread of infection while smart agriculture technologies such as crop monitoring with Unmanned Aerial Systems assist in early detection and management of sheath blight disease. Replacing older fungicides with natural fungicides and use of biological agents can provide effective sheath blight control, also minimising environmental impact. Genetic approaches that show promise for the control of sheath blight include treatment with exogenous dsRNA to silence pathogen gene expression, genome editing to develop rice lines with lower susceptibility to sheath blight and development of transgenic rice lines overexpressing or silencing pathogenesis related genes. The main challenges that were identified for effective crop protection against sheath blight are the adaptive flexibility of the pathogen, lack of resistant rice varieties, abscence of single resistance genes for use in breeding and low access of farmers to awareness programmes for optimal management practices.
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Affiliation(s)
- Pooja Singh
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Purabi Mazumdar
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Faculty of Science, Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Subramanian Babu
- VIT School of Agricultural Innovations and Advanced Learning, VIT University, Vellore, Tamil Nadu, 632014, India
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Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses. Sci Rep 2018; 8:6505. [PMID: 29695843 PMCID: PMC5916932 DOI: 10.1038/s41598-018-24946-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 04/13/2018] [Indexed: 12/31/2022] Open
Abstract
To facilitate developing rice varieties tolerant to salt stress, a panel of 208 rice mini-core accessions collected from 25 countries were evaluated for 13 traits associated with salt tolerance (ST) at the germination and seedling stages. The rice panel showed tremendous variation for all measured ST traits and eight accessions showing high levels of ST at either and/or both the germination and seedling stages. Using 395,553 SNP markers covering ~372 Mb of the rice genome and multi-locus mixed linear models, 20 QTN associated with 11 ST traits were identified by GWAS, including 6 QTN affecting ST at the germination stage and 14 QTN for ST at the seedling stage. The integration of bioinformatic with haplotype analyses for the ST QTN lets us identify 22 candidate genes for nine important ST QTN (qGR3, qSNK1, qSNK12, qSNC1, qSNC6, qRNK2, qSDW9a, qSST5 and qSST9). These candidate genes included three known ST genes (SKC1, OsTZF1 and OsEATB) for QTN qSNK1 qSST5 and qSST9. Candidate genes showed significant phenotypic differences in ST traits were detected between or among 2-4 major haplotypes. Thus, our results provided useful materials and genetic information for improving rice ST in future breeding and for molecular dissection of ST in rice.
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Analyses of Physcomitrella patens Ankyrin Repeat Proteins by Computational Approach. Mol Biol Int 2016; 2016:9156735. [PMID: 27429806 PMCID: PMC4939350 DOI: 10.1155/2016/9156735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 11/22/2022] Open
Abstract
Ankyrin (ANK) repeat containing proteins are evolutionary conserved and have functions in crucial cellular processes like cell cycle regulation and signal transduction. In this study, through an entirely in silico approach using the first release of the moss genome annotation, we found that at least 54 ANK proteins are present in P. patens. Based on their differential domain composition, the identified ANK proteins were classified into nine subfamilies. Comparative analysis of the different subfamilies of ANK proteins revealed that P. patens contains almost all the known subgroups of ANK proteins found in the other angiosperm species except for the ones having the TPR domain. Phylogenetic analysis using full length protein sequences supported the subfamily classification where the members of the same subfamily almost always clustered together. Synonymous divergence (dS) and nonsynonymous divergence (dN) ratios showed positive selection for the ANK genes of P. patens which probably helped them to attain significant functional diversity during the course of evolution. Taken together, the data provided here can provide useful insights for future functional studies of the proteins from this superfamily as well as comparative studies of ANK proteins.
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Deng S, Wang CY, Zhang X, Wang Q, Lin L. VdNUC-2, the Key Regulator of Phosphate Responsive Signaling Pathway, Is Required for Verticillium dahliae Infection. PLoS One 2015; 10:e0145190. [PMID: 26670613 PMCID: PMC4682923 DOI: 10.1371/journal.pone.0145190] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/01/2015] [Indexed: 02/07/2023] Open
Abstract
In fungal cells, a phosphate (Pi) responsive signaling and metabolism (PHO) pathway regulates Pi-homeostasis. NUC-2/PHO81 and its homologs are one of the most important components in the regulation pathway. In soil-borne phytopathogenic fungus Verticillium dahliae, we identified a Neurospora crassa nuc-2 homolog gene VdNUC-2. VdNUC-2 is composed of 1,018 amino acids, and is highly conserved in tested filamentous fungi. Under conditions of Pi-starvation, compared with the wild-type strain and ectopic complementation strains, the VdNUC-2 knocked out mutants exhibited reduced radial growth, decreased production of conidia and microsclerotia, and were more sensitive to hydrogen peroxide stress. The virulence of VdNUC-2 defective mutants was significantly compromised, and that was unable to be restored by exogenous application of extra Pi. Additionally, the deletion mutants of VdNUC-1, a key transcription factor gene positively controlled by VdNUC-2 in the PHO pathway, showed the similar cultural phenotypes as VdNUC-2 mutants when both of them grew in Pi-limited conditions. However, the virulence of VdNUC-1 mutants was comparable to the wild-type strain. These evidences indicated that the virulence reduction in VdNUC-2 mutants is not due to the interruptions in the PHO pathway or the disturbance of Pi-homeostasis in V. dahliae cytoplasm. VdNUC-2 is not only a crucial gene in the PHO pathway in V. dahliae, but also is required for the full virulence during host-infection.
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Affiliation(s)
- Sheng Deng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Cai-yue Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xin Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qing Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ling Lin
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail:
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Homotypic clustering of OsMYB4 binding site motifs in promoters of the rice genome and cellular-level implications on sheath blight disease resistance. Gene 2015; 561:209-18. [DOI: 10.1016/j.gene.2015.02.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 02/08/2015] [Accepted: 02/12/2015] [Indexed: 11/18/2022]
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Luo Q, Li Y, Wang W, Fei X, Deng X. Genome-wide survey and expression analysis of Chlamydomonas reinhardtii U-box E3 ubiquitin ligases (CrPUBs) reveal a functional lipid metabolism module. PLoS One 2015; 10:e0122600. [PMID: 25822994 PMCID: PMC4378952 DOI: 10.1371/journal.pone.0122600] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/11/2015] [Indexed: 11/18/2022] Open
Abstract
E3 ubiquitin ligases determine the substrate specificity of ubiquitination. Plant U-box (PUB) E3 ligases, with a typical 70-amino acid U-box domain, participate in plant developmental processes and environmental responses. Thus far, 64 PUB proteins have been identified in Arabidopsis and 77 PUB proteins have been identified in Oryza. However, detailed studies on U-box genes in the model microalgae Chlamydomonas reinhardtii are lacking. Here, we present a comprehensive analysis of the genes encoding U-box family proteins in C. reinhardtii. Following BLASTP analysis, 30 full-length U-box genes were identified in the C. reinhardtii genome sequence. Bioinformatics analyses of CrPUB genes were performed to characterize the phylogenetic relationships, chromosomal locations and gene structures of each member. The 30 identified CrPUB proteins are clustered into 3 distinct subfamilies, and the genes for these proteins are unevenly distributed among 14 chromosomes. Furthermore, the quantitative real-time RT-PCR or semi-quantitative RT-PCR analysis of 30 CrPUB mRNA abundances under nitrogen starvation showed that 18 CrPUB genes were induced by N starvation and that 7 genes were repressed in the N-poor environment. We selected five CrPUB genes exhibiting marked changes in expression under N-free conditions for further analysis in RNAi experiments and examined the oil content of these gene-silenced transgenic strains. The silencing of CrPUB5 and CrPUB14, which are typically down-regulated under N starvation, induced 9.8%-45.0% and 14.4%-61.8% lipid accumulation, respectively. In contrast, the silencing of CrPUB11, CrPUB23 and CrPUB28, which are markedly up-regulated under N-free conditions, decreased the lipid content by 5.5%-27.8%, 8.1%-27.3% and 6.6%-27.9%, respectively. These results provide a useful reference for the identification and functional analysis of this gene family and fundamental information for microalgae lipid metabolism research.
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Affiliation(s)
- Qiulan Luo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
| | - Yajun Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
| | - Wenquan Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
| | - Xiaowen Fei
- School of Science, Hainan Medical College, Haikou, 571101, China
| | - Xiaodong Deng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, 571101, China
- * E-mail:
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12
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Ficklin SP, Feltus FA. A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa. PLoS One 2013; 8:e68551. [PMID: 23874666 PMCID: PMC3713027 DOI: 10.1371/journal.pone.0068551] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/30/2013] [Indexed: 12/13/2022] Open
Abstract
Many traits of biological and agronomic significance in plants are controlled in a complex manner where multiple genes and environmental signals affect the expression of the phenotype. In Oryza sativa (rice), thousands of quantitative genetic signals have been mapped to the rice genome. In parallel, thousands of gene expression profiles have been generated across many experimental conditions. Through the discovery of networks with real gene co-expression relationships, it is possible to identify co-localized genetic and gene expression signals that implicate complex genotype-phenotype relationships. In this work, we used a knowledge-independent, systems genetics approach, to discover a high-quality set of co-expression networks, termed Gene Interaction Layers (GILs). Twenty-two GILs were constructed from 1,306 Affymetrix microarray rice expression profiles that were pre-clustered to allow for improved capture of gene co-expression relationships. Functional genomic and genetic data, including over 8,000 QTLs and 766 phenotype-tagged SNPs (p-value < = 0.001) from genome-wide association studies, both covering over 230 different rice traits were integrated with the GILs. An online systems genetics data-mining resource, the GeneNet Engine, was constructed to enable dynamic discovery of gene sets (i.e. network modules) that overlap with genetic traits. GeneNet Engine does not provide the exact set of genes underlying a given complex trait, but through the evidence of gene-marker correspondence, co-expression, and functional enrichment, site visitors can identify genes with potential shared causality for a trait which could then be used for experimental validation. A set of 2 million SNPs was incorporated into the database and serve as a potential set of testable biomarkers for genes in modules that overlap with genetic traits. Herein, we describe two modules found using GeneNet Engine, one with significant overlap with the trait amylose content and another with significant overlap with blast disease resistance.
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Affiliation(s)
- Stephen P Ficklin
- Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
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Jiang H, Wu Q, Jin J, Sheng L, Yan H, Cheng B, Zhu S. Genome-wide identification and expression profiling of ankyrin-repeat gene family in maize. Dev Genes Evol 2013; 223:303-18. [PMID: 23839078 DOI: 10.1007/s00427-013-0447-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/08/2013] [Indexed: 01/10/2023]
Abstract
Members of the ankyrin repeats (ANK) gene family encode ANK domain that are common in diverse organisms and play important roles in cell growth and development, such as cell-cell signal transduction and cell cycle regulation. Recently, genome-wide identification and evolutionary analyses of the ANK gene family have been carried out in Arabidopsis and rice. However, little is known regarding the ANK genes in the entire maize genome. In this study, we described the identification and structural characterization of 71 ANK genes in maize (ZmANK). Then, comprehensive bioinformatics analyses of ZmANK genes family were performed including phylogenetic, domain and motif analysis, chromosomal localization, intron/exon structural patterns, gene duplications and expression profiling. Domain composition analyses showed that ZmANK genes formed ten subfamilies. Five tandem duplications and 14 segmental duplications were identified in ZmANK genes. Furthermore, we took comparative analysis of the total ANK gene family in Arabidopsis, rice and maize, ZmANKs were more closely paired with OsANKs than with AtANKs. At last, expression profile analyses were performed. Forty-one members of ZmANK genes held EST sequences records. Semi-quantitative expression and microarray data analysis of these 41 ZmANK genes demonstrated that ZmANK genes exhibit a various expression pattern, suggesting that functional diversification of ZmANK genes family. The results will present significant insights to explore ANK genes expression and function in future studies in maize.
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Affiliation(s)
- Haiyang Jiang
- Key Laboratory of Crop Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
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Mou S, Liu Z, Guan D, Qiu A, Lai Y, He S. Functional analysis and expressional characterization of rice ankyrin repeat-containing protein, OsPIANK1, in basal defense against Magnaporthe oryzae attack. PLoS One 2013; 8:e59699. [PMID: 23555750 PMCID: PMC3608567 DOI: 10.1371/journal.pone.0059699] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 02/17/2013] [Indexed: 11/18/2022] Open
Abstract
The ankyrin repeat-containing protein gene OsPIANK1 (AK068021) in rice (Oryza sativa L.) was previously shown to be upregulated following infection with the rice leaf blight pathogen Xanthomonas oryzae pv oryzae (Xoo). In this study, we further characterized the role of OsPIANK1 in basal defense against Magnaporthe oryzae (M.oryzae) by 5' deletion analysis of its promoter and overexpression of the gene. The promoter of OsPIANK1 with 1,985 bps in length was sufficient to induce the OsPIANK1 response to inoculation with M.oryzae and to exogenous application of methyl jasmonate (MeJA) or salicylic acid (SA), but not to exogenous application of abscisic acid (ABA). A TCA-element present in the region between -563 bp and -249 bp may be responsible for the OsPIANK1 response to both M.oryzae infection and exogenous SA application. The JERE box, CGTCA-box, and two MYB binding sites locating in the region between -1985 bp and -907 bp may be responsible for the response of OsPIANK1 to exogenous MeJA. OsPIANK1 expression was upregulated after inoculation with M.oryzae and after treatment with exogenous SA and MeJA. Overexpression of OsPIANK1 enhanced resistance of rice to M.oryzae, although it did not confer complete resistance. The enhanced resistance to M.oryzae was accompanied by enhanced transcriptional expression of SA- and JA-dependent genes such as NH1, WKRY13, PAL, AOS2, PR1b, and PR5. This evidence suggests that OsPIANK1 acted as a positive regulator in rice basal defense mediated by SA- and JA-signaling pathways.
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Affiliation(s)
- Shaoliang Mou
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhiqin Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Deyi Guan
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ailian Qiu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yan Lai
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shuilin He
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail:
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Jiang Y, Chen X, Ding X, Wang Y, Chen Q, Song WY. The XA21 binding protein XB25 is required for maintaining XA21-mediated disease resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013. [PMID: 23206229 DOI: 10.1111/tpj.12076] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Plant genomes encode a large number of proteins that potentially function as immune receptors in the defense against pathogen invasion. As a well-characterized receptor kinase consisting of 23 tandem leucine-rich repeats, a transmembrane domain and a serine/threonine kinase, the rice (Oryza sativa) protein XA21 confers resistance to a broad spectrum of Xanthomonas oryzae pv. oryzae (Xoo) races that cause bacterial blight disease. We report here that XA21 binding protein 25 (XB25) belongs to the plant-specific ankyrin-repeat (PANK) family. XB25 physically interacts, in vitro, with the transmembrane domain of XA21 through its N-terminal binding to transmembrane and positively charged domain (BTMP) repeats. In addition, XB25 associates with XA21 in planta. The downregulation of Xb25 results in reduced levels of XA21 and compromised XA21-mediated disease resistance at the adult stage. Moreover, the accumulation of XB25 is induced by Xoo infection. Taken together, these results indicate that XB25 is required for maintaining XA21-mediated disease resistance.
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Affiliation(s)
- Yingnan Jiang
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
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