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Traverse KKF, Breselge S, Trautman JG, Dee A, Wang J, Childs KL, Lee-Parsons CWT. Characterization of the ZCTs, a subgroup of Cys2-His2 zinc finger transcription factors regulating alkaloid biosynthesis in Catharanthus roseus. PLANT CELL REPORTS 2024; 43:209. [PMID: 39115578 PMCID: PMC11310244 DOI: 10.1007/s00299-024-03295-8] [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: 03/11/2024] [Accepted: 07/26/2024] [Indexed: 08/11/2024]
Abstract
KEY MESSAGE The C. roseus ZCTs are jasmonate-responsive, can be induced by CrMYC2a, and can act as significant regulators of the terpenoid indole alkaloid pathway when highly expressed. Catharanthus roseus is the sole known producer of the anti-cancer terpenoid indole alkaloids (TIAs), vinblastine and vincristine. While the enzymatic steps of the pathway have been elucidated, an understanding of its regulation is still emerging. The present study characterizes an important subgroup of Cys2-His2 zinc finger transcription factors known as Zinc finger Catharanthus Transcription factors (ZCTs). We identified three new ZCT members (named ZCT4, ZCT5, and ZCT6) that clustered with the putative repressors of the TIA pathway, ZCT1, ZCT2, and ZCT3. We characterized the role of these six ZCTs as potential redundant regulators of the TIA pathway, and their tissue-specific and jasmonate-responsive expression. These ZCTs share high sequence conservation in their two Cys2-His2 zinc finger domains but differ in the spacer length and sequence between these zinc fingers. The transient overexpression of ZCTs in seedlings significantly repressed the promoters of the terpenoid (pLAMT) and condensation branch (pSTR1) of the TIA pathway, consistent with that previously reported for ZCT1, ZCT2, and ZCT3. In addition, ZCTs significantly repressed and indirectly activated several promoters of the vindoline pathway (not previously studied). The ZCTs differed in their tissue-specific expression but similarly increased with jasmonate in a dosage-dependent manner (except for ZCT5). We showed significant activation of the pZCT1 and pZCT3 promoters by the de-repressed CrMYC2a, suggesting that the jasmonate-responsive expression of the ZCTs can be mediated by CrMYC2a. In summary, the C. roseus ZCTs are jasmonate-responsive, can be induced by CrMYC2a, and can act as significant regulators of the TIA pathway when highly expressed.
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Affiliation(s)
| | - Samuel Breselge
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Juliet G Trautman
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Amanda Dee
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Jie Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Carolyn W T Lee-Parsons
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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Wang D, Qiu Z, Xu T, Yao S, Chen M, Li Q, Agassin RH, Ji K. Transcriptomic Identification of Potential C2H2 Zinc Finger Protein Transcription Factors in Pinus massoniana in Response to Biotic and Abiotic Stresses. Int J Mol Sci 2024; 25:8361. [PMID: 39125930 PMCID: PMC11312842 DOI: 10.3390/ijms25158361] [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: 06/25/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Biotic and abiotic stresses have already seriously restricted the growth and development of Pinus massoniana, thereby influencing the quality and yield of its wood and turpentine. Recent studies have shown that C2H2 zinc finger protein transcription factors play an important role in biotic and abiotic stress response. However, the members and expression patterns of C2H2 TFs in response to stresses in P. massoniana have not been performed. In this paper, 57 C2H2 zinc finger proteins of P. massoniana were identified and divided into five subgroups according to a phylogenetic analysis. In addition, six Q-type PmC2H2-ZFPs containing the plant-specific motif 'QALGGH' were selected for further study under different stresses. The findings demonstrated that PmC2H2-ZFPs exhibit responsiveness towards various abiotic stresses, including drought, NaCl, ABA, PEG, H2O2, etc., as well as biotic stress caused by the pine wood nematode. In addition, PmC2H2-4 and PmC2H2-20 were nuclear localization proteins, and PmC2H2-20 was a transcriptional activator. PmC2H2-20 was selected as a potential transcriptional regulator in response to various stresses in P. massoniana. These findings laid a foundation for further study on the role of PmC2H2-ZFPs in stress tolerance.
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Affiliation(s)
- Dengbao Wang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zimo Qiu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Tao Xu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Meijing Chen
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qianzi Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Romaric Hippolyte Agassin
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (D.W.); (Z.Q.); (T.X.); (S.Y.); (M.C.); (Q.L.); (R.H.A.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland Administration, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Singh J, James D, Das S, Patel MK, Sutar RR, Achary VMM, Goel N, Gupta KJ, Reddy MK, Jha G, Sonti RV, Foyer CH, Thakur JK, Tripathy BC. Co-overexpression of SWEET sucrose transporters modulates sucrose synthesis and defence responses to enhance immunity against bacterial blight in rice. PLANT, CELL & ENVIRONMENT 2024; 47:2578-2596. [PMID: 38533652 DOI: 10.1111/pce.14901] [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: 03/10/2023] [Revised: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024]
Abstract
Enhancing carbohydrate export from source to sink tissues is considered to be a realistic approach for improving photosynthetic efficiency and crop yield. The rice sucrose transporters OsSUT1, OsSWEET11a and OsSWEET14 contribute to sucrose phloem loading and seed filling. Crucially, Xanthomonas oryzae pv. oryzae (Xoo) infection in rice enhances the expression of OsSWEET11a and OsSWEET14 genes, and causes leaf blight. Here we show that co-overexpression of OsSUT1, OsSWEET11a and OsSWEET14 in rice reduced sucrose synthesis and transport leading to lower growth and yield but reduced susceptibility to Xoo relative to controls. The immunity-related hypersensitive response (HR) was enhanced in the transformed lines as indicated by the increased expression of defence genes, higher salicylic acid content and presence of HR lesions on the leaves. The results suggest that the increased expression of OsSWEET11a and OsSWEET14 in rice is perceived as a pathogen (Xoo) attack that triggers HR and results in constitutive activation of plant defences that are related to the signalling pathways of pathogen starvation. These findings provide a mechanistic basis for the trade-off between plant growth and immunity because decreased susceptibility against Xoo compromised plant growth and yield.
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Affiliation(s)
- Jitender Singh
- National Institute of Plant Genome Research, New Delhi, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Donald James
- Forest Biotechnology Department, Kerala Forest Research Institute, Thrissur, Kerala, India
| | - Shubhashis Das
- National Institute of Plant Genome Research, New Delhi, India
| | - Manish Kumar Patel
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion, Israel
| | | | | | - Naveen Goel
- National Institute of Plant Genome Research, New Delhi, India
| | | | - Malireddy K Reddy
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Gopaljee Jha
- National Institute of Plant Genome Research, New Delhi, India
| | - Ramesh V Sonti
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | | | - Jitendra Kumar Thakur
- National Institute of Plant Genome Research, New Delhi, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Baishnab C Tripathy
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India
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Wang Y, Wang H, Zhang L, Wang Y, Wei S, Wang L. Mechanism Analysis of OsZF8-Mediated Regulation of Rice Resistance to Sheath Blight. Int J Mol Sci 2024; 25:5787. [PMID: 38891973 PMCID: PMC11171851 DOI: 10.3390/ijms25115787] [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: 04/10/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Transcription factors are key molecules involved in transcriptional and post-transcriptional regulation in plants and play an important regulatory role in resisting biological stress. In this study, we identified a regulatory factor, OsZF8, mediating rice response to Rhizoctonia solani (R. solani) AG1-IA infection. The expression of OsZF8 affects R. solani rice infection. OsZF8 knockout and overexpressed rice plants were constructed, and the phenotypes of mutant and wild-type (WT) plants showed that OsZF8 negatively regulated rice resistance to rice sheath blight. However, it was speculated that OsZF8 plays a regulatory role at the protein level. The interacting protein PRB1 of OsZF8 was screened using the yeast two-hybrid and bimolecular fluorescence complementation test. The results showed that OsZF8 effectively inhibited PRB1-induced cell death in tobacco cells, and molecular docking results showed that PRB1 had a strong binding effect with OsZF8. Further, the binding ability of OsZF8-PRB1 to ergosterol was significantly reduced when compared with the PRB1 protein. These findings provide new insights into elucidating the mechanism of rice resistance to rice sheath blight.
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Affiliation(s)
- Yan Wang
- College of Plant Protection, Department of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China; (Y.W.); (H.W.); (L.Z.); (Y.W.)
| | - Haining Wang
- College of Plant Protection, Department of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China; (Y.W.); (H.W.); (L.Z.); (Y.W.)
| | - Liangkun Zhang
- College of Plant Protection, Department of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China; (Y.W.); (H.W.); (L.Z.); (Y.W.)
| | - Yiming Wang
- College of Plant Protection, Department of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China; (Y.W.); (H.W.); (L.Z.); (Y.W.)
| | - Songhong Wei
- College of Plant Protection, Department of Plant Pathology, Shenyang Agricultural University, Shenyang 110866, China; (Y.W.); (H.W.); (L.Z.); (Y.W.)
| | - Lili Wang
- Liaoning Academy of Agricultural Sciences, Shenyang 110101, China
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5
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Liu K, Hou Q, Yu R, Deng H, Shen L, Wang Q, Wen X. Genome-wide analysis of C2H2 zinc finger family and their response to abiotic stresses in apple. Gene 2024; 904:148164. [PMID: 38224923 DOI: 10.1016/j.gene.2024.148164] [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: 10/26/2023] [Revised: 12/26/2023] [Accepted: 01/11/2024] [Indexed: 01/17/2024]
Abstract
C2H2-type zinc finger proteins are one of the most widely studied families in plants and play important roles in abiotic stress responses. In the present study, the physicochemical properties, chromosomal locations, evolutionary relationships, and gene structures of 54 C2H2 zinc finger protein (ZFP) family members were analyzed in apple. The MdC2H2-ZFP genes were phylogenetically clustered into seven subfamilies distributed in different densities on 16 chromosomes. The RNA-seq data from various tissues revealed that MdC2H2-ZFPs differentially expressed among root, stem, leaf, flower, and fruits. Quantitative analysis of its expression characteristics showed that the MdC2H2-ZFP genes were rapidly induced as exposure to abiotic stresses such as drought, salt and low temperature etc. Under drought stress, the expression of eight members was significantly up-regulated, and the highest was obtained from MdC2H2-17; as exposure to salt stress, nine MdC2H2-ZFPs was obviously up-regulated, with the highest expression of MdC2H2-13; and under low temperature stress, the expression of seven members was highly up-regulated, and MdC2H2-13 also demonstrated the highest expression which is same as the case under salt stress. Therefore, some members of MdC2H2-ZFP gene family considerably involve in the multiple abiotic stress responses, which may better understand the function of this family and facilitate the breeding of apple for stress tolerance.
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Affiliation(s)
- Ke Liu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Qiandong Hou
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Runrun Yu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Hong Deng
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China
| | - Luonan Shen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Institute for Forest Resources & Environment of Guizhou/ College of Forestry, Guizhou University, Guiyang 550025, China
| | - Qian Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China.
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Key Laboratory of Agro-Bioengineering, Institute of Agro-bioengineering/College of Life Sciences, Guiyang 550025, Guizhou Province, China; National-Local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), Guiyang 550025, Guizhou Province, China.
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Zhou X, Gao T, Zhang Y, Han M, Shen Y, Su Y, Feng X, Wu Q, Sun G, Wang Y. Genome-wide identification, characterization and expression of C2H2 zinc finger gene family in Opisthopappus species under salt stress. BMC Genomics 2024; 25:385. [PMID: 38641598 PMCID: PMC11027532 DOI: 10.1186/s12864-024-10273-7] [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: 02/02/2024] [Accepted: 03/30/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND The C2H2 zinc finger protein family plays important roles in plants. However, precisely how C2H2s function in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear. RESULTS In this study, a total of 69 OpC2H2 zinc finger protein genes were identified and clustered into five Groups. Seven tandem and ten fragment repeats were found in OpC2H2s, which underwent robust purifying selection. Of the identified motifs, motif 1 was present in all OpC2H2s and conserved at important binding sites. Most OpC2H2s possessed few introns and exons that could rapidly activate and react when faced with stress. The OpC2H2 promoter sequences mainly contained diverse regulatory elements, such as ARE, ABRE, and LTR. Under salt stress, two up-regulated OpC2H2s (OpC2H2-1 and OpC2H2-14) genes and one down-regulated OpC2H2 gene (OpC2H2-7) might serve as key transcription factors through the ABA and JA signaling pathways to regulate the growth and development of Opisthopappus species. CONCLUSION The above results not only help to understand the function of C2H2 gene family but also drive progress in genetic improvement for the salt tolerance of Opisthopappus species.
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Affiliation(s)
- Xiaojuan Zhou
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Ting Gao
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Yimeng Zhang
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Mian Han
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Yuexin Shen
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Yu Su
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Xiaolong Feng
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Qi Wu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Genlou Sun
- Department of Botany, Saint Mary's University, Halifax, NS, B3H 3C3, Canada.
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China.
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7
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Nikraftar S, Ebrahimzadegan R, Majdi M, Mirzaghaderi G. Genome-wide analysis of the C2H2-ZFP gene family in Stevia rebaudiana reveals involvement in abiotic stress response. Sci Rep 2024; 14:6164. [PMID: 38486071 PMCID: PMC10940304 DOI: 10.1038/s41598-024-56624-y] [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: 01/26/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Stevia (Stevia rebaudiana Bertoni) is a natural sweetener plant that accumulates highly sweet steviol glycosides (SGs) especially in leaves. Stevia is native to humid areas and does not have a high tolerance to drought which is the most serious abiotic stress restricting its production worldwide. C2H2 zinc finger proteins (C2H2-ZFPs) are a group of well-known transcription factors that involves in various developmental, physiological and biochemical activities as well as in response to abiotic stresses. Here we analyzed C2H2-ZFP gene family in stevia and identified a total of 185 putative SrC2H2-ZF proteins from the genome sequence of S. rebaudiana. We further characterized the identified C2H2-ZF domains and their organization, additional domains and motifs and analyzed their physicochemical properties, localization and gene expression patterns. The cis-element analysis suggested multiple roles of SrC2H2-ZFPs in response to light, phytohormone, and abiotic stresses. In silico analysis revealed that the stevia C2H2-ZFP genes are interactively expressed in different tissues and developmental stages and some C2H2-ZFP genes are involved in response to drought stress. This study provides a background for future exploration of the functional, and regulatory aspects of the C2H2-ZFP gene family in S. rebaudiana.
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Affiliation(s)
- Shahla Nikraftar
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Rahman Ebrahimzadegan
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Mohammad Majdi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Ghader Mirzaghaderi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran.
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Zhang Y, Xiao W, Wang M, Khan M, Liu JH. A C2H2-type zinc finger protein ZAT12 of Poncirus trifoliata acts downstream of CBF1 to regulate cold tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1317-1329. [PMID: 38017362 DOI: 10.1111/tpj.16562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/21/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
The Cys2/His2 (C2H2)-type zinc finger family has been reported to regulate multiple aspects of plant development and abiotic stress response. However, the role of C2H2-type zinc finger proteins in cold tolerance remains largely unclear. Through RNA-sequence analysis, a cold-responsive zinc finger protein, named as PtrZAT12, was identified and isolated from trifoliate orange (Poncirus trifoliata L. Raf.), a cold-hardy plant closely related to citrus. Furthermore, we found that PtrZAT12 was markedly induced by various abiotic stresses, especially cold stress. PtrZAT12 is a nuclear protein, and physiological analysis suggests that overexpression of PtrZAT12 conferred enhanced cold tolerance in transgenic tobacco (Nicotiana tabacum) plants, while knockdown of PtrZAT12 by virus-induced gene silencing (VIGS) increased the cold sensitivity of trifoliate orange and repressed expression of genes involved in stress tolerance. The promoter of PtrZAT12 harbors a DRE/CRT cis-acting element, which was verified to be specifically bound by PtrCBF1 (Poncirus trifoliata C-repeat BINDING FACTOR1). VIGS-mediated silencing of PtrCBF1 reduced the relative expression levels of PtrZAT12 and decreased the cold resistance of trifoliate orange. Based on these results, we propose that PtrZAT12 is a direct target of CBF1 and plays a positive role in modulation of cold stress tolerance. The knowledge gains new insight into a regulatory module composed of CBF1-ZAT12 in response to cold stress and advances our understanding of cold stress response in plants.
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Affiliation(s)
- Yang Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Germplasm Innovation and Utilization of Fruit Trees, Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Wei Xiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Wang
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, China
| | - Madiha Khan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ji-Hong Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
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Qian Z, Shi D, Zhang H, Li Z, Huang L, Yan X, Lin S. Transcription Factors and Their Regulatory Roles in the Male Gametophyte Development of Flowering Plants. Int J Mol Sci 2024; 25:566. [PMID: 38203741 PMCID: PMC10778882 DOI: 10.3390/ijms25010566] [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: 12/07/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
Male gametophyte development in plants relies on the functions of numerous genes, whose expression is regulated by transcription factors (TFs), non-coding RNAs, hormones, and diverse environmental stresses. Several excellent reviews are available that address the genes and enzymes associated with male gametophyte development, especially pollen wall formation. Growing evidence from genetic studies, transcriptome analysis, and gene-by-gene studies suggests that TFs coordinate with epigenetic machinery to regulate the expression of these genes and enzymes for the sequential male gametophyte development. However, very little summarization has been performed to comprehensively review their intricate regulatory roles and discuss their downstream targets and upstream regulators in this unique process. In the present review, we highlight the research progress on the regulatory roles of TF families in the male gametophyte development of flowering plants. The transcriptional regulation, epigenetic control, and other regulators of TFs involved in male gametophyte development are also addressed.
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Affiliation(s)
- Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Hongxia Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Zhenzhen Li
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China;
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; (Z.Q.); (D.S.); (H.Z.); (Z.L.)
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
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10
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Jia HH, Xu YT, Yin ZJ, Qing M, Xie KD, Guo WW, Wu XM. Genome-wide identification of the C2H2-Zinc finger gene family and functional validation of CsZFP7 in citrus nucellar embryogenesis. PLANT REPRODUCTION 2023; 36:287-300. [PMID: 37247027 DOI: 10.1007/s00497-023-00470-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
KEY MESSAGE Genome-wide identification of C2H2-ZF gene family in the poly- and mono-embryonic citrus species and validation of the positive role of CsZFP7 in sporophytic apomixis. The C2H2 zinc finger (C2H2-ZF) gene family is involved in plant vegetative and reproductive development. Although a large number of C2H2 zinc-finger proteins (C2H2-ZFPs) have been well characterized in some horticultural plants, little is known about the C2H2-ZFPs and their function in citrus. In this work, we performed a genome-wide sequence analysis and identified 97 and 101 putative C2H2-ZF gene family members in the genomes of sweet orange (C. sinensis, poly-embryonic) and pummelo (C. grandis, mono-embryonic), respectively. Phylogenetic analysis categorized citrus C2H2-ZF gene family into four clades, and their possible functions were inferred. According to the numerous regulatory elements on promoter, citrus C2H2-ZFPs can be divided into five different regulatory function types that indicate functional differentiation. RNA-seq data revealed 20 differentially expressed C2H2-ZF genes between poly-embryonic and mono-embryonic ovules at two stages of citrus nucellar embryogenesis, among them CsZFP52 specifically expressed in mono-embryonic pummelo ovules, while CsZFP7, 37, 44, 45, 67 and 68 specifically expressed in poly-embryonic sweet orange ovules. RT-qPCR further validated that CsZFP7 specifically expressed at higher levels in poly-embryonic ovules, and down-regulation of CsZFP7 in the poly-embryonic mini citrus (Fortunella hindsii) increased rate of mono-embryonic seeds compared with the wild type, indicating the regulatory potential of CsZFP7 in nucellar embryogenesis of citrus. This work provided a comprehensive analysis of C2H2-ZF gene family in citrus, including genome organization and gene structure, phylogenetic relationships, gene duplications, possible cis-elements on promoter regions and expression profiles, especially in the poly- and mono-embryogenic ovules, and suggested that CsZFP7 is involved in nucellar embryogenesis.
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Affiliation(s)
- Hui-Hui Jia
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan-Tao Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhu-Jun Yin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Qing
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kai-Dong Xie
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wen-Wu Guo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiao-Meng Wu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
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11
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Chu M, Wang T, Li W, Liu Y, Bian Z, Mao J, Chen B. Genome-Wide Identification and Analysis of the Genes Encoding Q-Type C2H2 Zinc Finger Proteins in Grapevine. Int J Mol Sci 2023; 24:15180. [PMID: 37894862 PMCID: PMC10607507 DOI: 10.3390/ijms242015180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Q-type C2H2 zinc finger proteins (ZFPs), the largest family of transcription factors, have been extensively studied in plant genomes. However, the genes encoding this transcription factor family have not been explored in grapevine genomes. Therefore, in this study, we conducted a genome-wide identification of ZFP genes in three species of grapevine, namely Vitis vinifera, Vitis riparia, and Vitis amurensis, based on the sequence databases and phylogenetic and their conserved domains. We identified 52, 54, and 55 members of Q-type C2H2 ZFPs in V. vinifera, V. riparia, and V. amurensis, respectively. The physical and chemical properties of VvZFPs, VrZFPs, and VaZFPs were examined. The results showed that these proteins exhibited differences in the physical and chemical properties and that they all were hydrophobic proteins; the instability index showed that the four proteins were stable. The subcellular location of the ZFPs in the grapevine was predicted mainly in the nucleus. The phylogenetic tree analysis of the amino acid sequences of VvZFP, VaZFP, VrZFP, and AtZFP proteins showed that they were closely related and were divided into six subgroups. Chromosome mapping analysis showed that VvZFPs, VrZFPs, and VaZFPs were unevenly distributed on different chromosomes. The clustered gene analysis showed that the motif distribution was similar and the sequence of genes was highly conserved. Exon and intron structure analysis showed that 118 genes of ZFPs were intron deletion types, and the remaining genes had variable numbers of introns, ranging from 2 to 15. Cis-element analysis showed that the promoter of VvZFPs contained multiple cis-elements related to plant hormone response, stress resistance, and growth, among which the stress resistance elements were the predominant elements. Finally, the expression of VvZFP genes was determined using real-time quantitative PCR, which confirmed that the identified genes were involved in response to methyl jasmonate (MeJA), abscisic acid (ABA), salicylic acid (SA), and low-temperature (4 °C) stress. VvZFP10-GFP and VvZFP46-GFP fusion proteins were localized in the nucleus of tobacco cells, and VvZFP10 is the most responsive gene among all VvZFPs with the highest relative expression level to MeJA, ABA, SA and low-temperature (4 °C) stress. The present study provides a theoretical basis for exploring the mechanism of response to exogenous hormones and low-temperature tolerance in grapes and its molecular breeding in the future.
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Affiliation(s)
| | | | | | | | | | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (M.C.)
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; (M.C.)
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12
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Li M, Dong X, Long G, Zhang Z, Han C, Wang Y. Genome-Wide Analysis of Q-Type C2H2 ZFP Genes in Response to Biotic and Abiotic Stresses in Sugar Beet. BIOLOGY 2023; 12:1309. [PMID: 37887019 PMCID: PMC10604892 DOI: 10.3390/biology12101309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023]
Abstract
A plant's Q-type C2H2-type ZFP plays key roles in plant growth and development and responses to biotic and abiotic stresses. Sugar beet (Beta vulgaris L.) is an important crop for sugar production. Salt stress and viral infection significantly reduce the root yield and sugar content of sugar beet. However, there is a lack of comprehensive genome-wide analyses of Q-type C2H2 ZFPs and their expression patterns in sugar beet under stress. In this study, 35 sugar beet Q-type C2H2 ZFPs (BvZFPs) containing at least one conserved "QALGGH" motif were identified via bioinformatics techniques using TBtools software. According to their evolutionary relationship, the BvZFPs were classified into five subclasses. Within each subclass, the physicochemical properties and motif compositions showed strong similarities. A Ka/Ks analysis indicated that the BvZFPs were conserved during evolution. Promoter cis-element analysis revealed that most BvZFPs are associated with elements related to phytohormone, biotic or abiotic stress, and plant development. The expression data showed that the BvZFPs in sugar beet are predominantly expressed in the root. In addition, BvZFPs are involved in the response to abiotic and biotic stresses, including salt stress and viral infection. Overall, these results will extend our understanding of the Q-type C2H2 gene family and provide valuable information for the biological breeding of sugar beet against abiotic and biotic stresses in the future.
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Affiliation(s)
| | | | | | | | | | - Ying Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (M.L.); (X.D.); (G.L.); (Z.Z.); (C.H.)
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13
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Kong Y, Yuan Y, Menghan Y, Yiming L, Liang X, Gleason ML, Rong Z, Sun G. CfCpmd1 Regulates Pathogenicity and Sexual Development of Plus and Minus Strains in Colletotrichum fructicola Causing Glomerella Leaf Spot on Apple in China. PHYTOPATHOLOGY 2023; 113:1985-1993. [PMID: 37129259 DOI: 10.1094/phyto-02-23-0071-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Colletotrichum fructicola is a devastating fungal pathogen of diverse plants. Sexually compatible plus and minus strains occur in the same ascus. However, the differentiation mechanism of plus and minus strains remains poorly understood. Here, we characterized a novel Cys2-His2-containing transcription factor CfCpmd1. The plus CfCpmd1 deletion mutant (Δ+CfCpmd1) resulted in slow hyphal growth and a fluffy cotton-like colony, and the minus deletion mutant (Δ-CfCpmd1) exhibited characters similar to the wild type (WT). Δ+CfCpmd1 led to defective perithecial formation, whereas Δ-CfCpmd1 produced more and smaller perithecia. The normal mating line was developed by pairing cultures of Δ-CfCpmd1 and plus WT, whereas a weak line was observed between Δ+CfCpmd1 and minus WT. Conidial production was completely abolished in both plus and minus mutants. When inoculated on non-wounded apple leaves with mycelial plugs, Δ-CfCpmd1 was nonpathogenic because of failure to develop conidia and appressoria, while Δ+CfCpmd1 could infect apple leaves by appressoria differentiated directly from hyphal tips, even though no conidia formed. Collectively, our results demonstrate that CfCpmd1 of C. fructicola is an important gene related to plus and minus strain differentiation, which also affects hyphal growth, sporulation, appressorium formation, and pathogenicity.
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Affiliation(s)
- Yuanyuan Kong
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yilong Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yang Menghan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Lu Yiming
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, U.S.A
| | - Zhang Rong
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
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14
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Saavedra Núñez G, González-Villanueva E, Ramos P. Floral Development on Vitis vinifera Is Associated with MADS-Box Transcription Factors through the Transcriptional Regulation of VviZIP3. PLANTS (BASEL, SWITZERLAND) 2023; 12:3322. [PMID: 37765487 PMCID: PMC10535425 DOI: 10.3390/plants12183322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
Several grapevine (Vitis vinifera L.) cultivars show a tendency to develop parthenocarpic seedless grapes, affecting fruit yield and quality. This reproductive disorder originates in defective ovule fertilization due to a failure in pollen tube growth. Zinc (Zn) is a crucial trace element, playing a vital role in various physiological and metabolic processes. It is particularly essential for the healthy growth of flowers and fruits. Insufficient zinc has been suggested as a potential reason for issues in this development process. This microelement is taken up through a mechanism that involves transporters, including the ZRT-IRT-like protein (ZIP) gene family, associated with the influx of Zn into the cell. In grapevines, 20 genes for ZIP-type transporters have been described. In this study, we analyzed the expression pattern of VviZIP3 during flower development and employ transgenic methods to assess its transcriptional regulation. Furthermore, through computational examination of the promoter region, we identified two CArG boxes, recognized as responsive elements to MADS transcription factors. These factors play a key role in shaping various components of a flower, such as pollen. Our investigation of the VviZIP3 promoter confirms the functionality of these CArG boxes. Overall, our results suggest that the increased expression of VviZIP3 during flowering is likely under the influence of MADS transcription factors.
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Affiliation(s)
- Germán Saavedra Núñez
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3460787, Chile; (G.S.N.); (E.G.-V.)
| | | | - Patricio Ramos
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca 3460787, Chile; (G.S.N.); (E.G.-V.)
- Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3480112, Chile
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15
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Qi F, Wang F, Xiaoyang C, Wang Z, Lin Y, Peng Z, Zhang J, Wang N, Zhang J. Gene Expression Analysis of Different Organs and Identification of AP2 Transcription Factors in Flax ( Linum usitatissimum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3260. [PMID: 37765422 PMCID: PMC10535939 DOI: 10.3390/plants12183260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023]
Abstract
Flax (Linum usitatissimum L.) is an important oilseed crop widely cultivated for its oil and fiber. This study conducted transcriptome analysis to analyze the gene expression profiles of roots, leaves, stamens, pistils, and fruits in the flax cultivar Longya10. A total of 43,471 genes were detected in the RNA-seq data, with 34,497 genes showing differential expression levels between different organs. Gene expression patterns varied across different organs, with differences observed in expression-regulating genes within specific organs. However, 23,448 genes were found to be commonly expressed across all organs. Further analysis revealed organ-specific gene expressions, with 236, 690, 544, 909, and 1212 genes identified in pistils, fruits, leaves, roots, and stamens, respectively. Gene Ontology (GO) enrichment analysis was performed on these organ-specific genes, and significant enrichment was observed in various biological processes, cellular components, and molecular functions, providing new insights for the specific growth patterns of flax organs. Furthermore, we investigated the expression differences of AP2 transcription factors in various tissues and organs of Longya10. We identified 96 AP2 genes that were differentially expressed in different organs and annotated them into various biological pathways. Our results suggest that AP2 transcription factors may play important roles in regulating the growth and development of flax organs including stress response. In summary, our study provides a comprehensive analysis of gene expression patterns in different organs and tissues of flax plant and identifies potential critical regulators of flax organ growth and development. These findings contribute to a better understanding of the molecular mechanisms underlying flax organ development and may have important implications for the genetic improvement of flax crops.
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Affiliation(s)
- Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Fu Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Chunxiao Xiaoyang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Yujie Lin
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun 130000, China;
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC V1V 1V7, Canada
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16
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Wen J, Deng M, Zhao K, Zhou H, Wu R, Li M, Cheng H, Li P, Zhang R, Lv J. Characterization of Plant Homeodomain Transcription Factor Genes Involved in Flower Development and Multiple Abiotic Stress Response in Pepper. Genes (Basel) 2023; 14:1737. [PMID: 37761877 PMCID: PMC10531376 DOI: 10.3390/genes14091737] [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: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Plant homeodomain (PHD) transcription factor genes are involved in plant development and in a plant's response to stress. However, there are few reports about this gene family in peppers (Capsicum annuum L.). In this study, the pepper inbred line "Zunla-1" was used as the reference genome, and a total of 43 PHD genes were identified, and systematic analysis was performed to study the chromosomal location, evolutionary relationship, gene structure, domains, and upstream cis-regulatory elements of the CaPHD genes. The fewest CaPHD genes were located on chromosome 4, while the most were on chromosome 3. Genes with similar gene structures and domains were clustered together. Expression analysis showed that the expression of CaPHD genes was quite different in different tissues and in response to various stress treatments. The expression of CaPHD17 was different in the early stage of flower bud development in the near-isogenic cytoplasmic male-sterile inbred and the maintainer inbred lines. It is speculated that this gene is involved in the development of male sterility in pepper. CaPHD37 was significantly upregulated in leaves and roots after heat stress, and it is speculated that CaPHD37 plays an important role in tolerating heat stress in pepper; in addition, CaPHD9, CaPHD10, CaPHD11, CaPHD17, CaPHD19, CaPHD20, and CaPHD43 were not sensitive to abiotic stress or hormonal factors. This study will provide the basis for further research into the function of CaPHD genes in plant development and responses to abiotic stresses and hormones.
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Affiliation(s)
- Jinfen Wen
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650500, China;
| | - Minghua Deng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Kai Zhao
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Huidan Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Rui Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Mengjuan Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Hong Cheng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Pingping Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Ruihao Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Junheng Lv
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
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17
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Shao L, Li L, Huang X, Fu Y, Yang D, Li C, Yang J. Identification of C2H2 zinc finger genes through genome-wide association study and functional analyses of LkZFPs in response to stresses in Larix kaempferi. BMC PLANT BIOLOGY 2023; 23:298. [PMID: 37268918 DOI: 10.1186/s12870-023-04298-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/19/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND C2H2 zinc finger proteins (C2H2-ZFPs), one of the largest transcription factors, play a variety of roles in plant development and growth as well as stress response. While, the evolutionary history and expression profile of the C2H2-ZFP genes in Larix kaempferi (LkZFPs) have not been reported so far. RESULTS In this study, the whole genome of the LkZFPs was identified and characterized, including physicochemical properties, phylogenetic relationships, conservative motifs, the promoter cis-elements and Gene Ontology (GO) annotation. We identified 47 LkZFPs and divided them into four subfamilies based on phylogenetic analysis and conserved motifs. Subcellular localization prediction showed that most of the LkZFPs were located in the nucleus. Promoter cis-element analysis suggested that the LkZFPs may be involved in the regulation of stress responses. Moreover, Real-time quantitative PCR (RT-qPCR) results showed that Q-type LkZFP genes were involved in the response to abiotic stress, such as salt, drought and hormone stresses. Subcellular localization results showed that LkZFP7 and LkZFP37 were located in the nucleus, LkZFP32 was located in both cytoplasm and nucleus. CONCLUSION The identification and functional analysis of LkZFPs suggested that some LkZFP genes might play important roles in coping with both biological and abiotic stresses. These results could further increase understanding of the function of the LkZFPs, and provide some research direction and theoretical support.
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Affiliation(s)
- Liying Shao
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Lu Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Xun Huang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yanrui Fu
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Da Yang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Jingli Yang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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Mahto A, Yadav A, P V A, Parida SK, Tyagi AK, Agarwal P. Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size. BMC Biol 2023; 21:91. [PMID: 37076907 PMCID: PMC10116700 DOI: 10.1186/s12915-023-01577-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/27/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Rice grain size (GS) is an essential agronomic trait. Though several genes and miRNA modules influencing GS are known and seed development transcriptomes analyzed, a comprehensive compendium connecting all possible players is lacking. This study utilizes two contrasting GS indica rice genotypes (small-grained SN and large-grained LGR). Rice seed development involves five stages (S1-S5). Comparative transcriptome and miRNome atlases, substantiated with morphological and cytological studies, from S1-S5 stages and flag leaf have been analyzed to identify GS proponents. RESULTS Histology shows prolonged endosperm development and cell enlargement in LGR. Stand-alone and comparative RNAseq analyses manifest S3 (5-10 days after pollination) stage as crucial for GS enhancement, coherently with cell cycle, endoreduplication, and programmed cell death participating genes. Seed storage protein and carbohydrate accumulation, cytologically and by RNAseq, is shown to be delayed in LGR. Fourteen transcription factor families influence GS. Pathway genes for four phytohormones display opposite patterns of higher expression. A total of 186 genes generated from the transcriptome analyses are located within GS trait-related QTLs deciphered by a cross between SN and LGR. Fourteen miRNA families express specifically in SN or LGR seeds. Eight miRNA-target modules display contrasting expressions amongst SN and LGR, while 26 (SN) and 43 (LGR) modules are differentially expressed in all stages. CONCLUSIONS Integration of all analyses concludes in a "Domino effect" model for GS regulation highlighting chronology and fruition of each event. This study delineates the essence of GS regulation, providing scope for future exploits. The rice grain development database (RGDD) ( www.nipgr.ac.in/RGDD/index.php ; https://doi.org/10.5281/zenodo.7762870 ) has been developed for easy access of data generated in this paper.
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Affiliation(s)
- Arunima Mahto
- National Institute of Plant Genome Research, New Delhi, India
| | - Antima Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Aswathi P V
- National Institute of Plant Genome Research, New Delhi, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, New Delhi, India
| | - Akhilesh K Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, India.
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19
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Thapa R, Tabien RE, Johnson CD, Septiningsih EM. Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress. BMC Genomics 2023; 24:185. [PMID: 37024819 PMCID: PMC10080786 DOI: 10.1186/s12864-023-09262-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Rice is one of the most important cereals consumed worldwide. Two major abiotic factors affecting rice plants in different growth stages are flooding stress and cold stress. These abiotic stresses can take place independently or simultaneously and significantly affect rice plants during germination and seedling growth. Fortunately, a wide array of phenotypic responses conferring flooding stress and chilling stress tolerance exist within the rice germplasm, indicating the presence of different molecular mechanisms underlying tolerance to these stresses. Understanding these differences may assist in developing improved rice cultivars having higher tolerance to both stresses. In this study, we conducted a comparative global gene expression analysis of two rice genotypes with contrasting phenotypes under cold stress, anaerobic stress, and combined cold and anaerobic stress during germination. RESULTS The differential gene expression analysis revealed that 5571 differentially expressed genes (DEGs), 7206 DEGs, and 13279 DEGs were identified under anaerobic stress, cold stress, and combined stress, respectively. Genes involved in the carbohydrate metabolic process, glucosyltransferase activity, regulation of nitrogen compound metabolic process, protein metabolic process, lipid metabolic process, cellular nitrogen compound biosynthetic process, lipid biosynthetic process, and a microtubule-based process were enriched across all stresses. Notably, the common Gene Ontology (GO) analysis identified three hub genes, namely Os08g0176800 (similar to mRNA-associated protein mrnp 41), Os11g0454200 (dehydrin), and OS10g0505900 (expressed protein). CONCLUSION A large number of differentially expressed genes were identified under anaerobic, cold conditions during germination and the combination of the two stress conditions in rice. These results will assist in the identification of promising candidate genes for possible manipulation toward rice crops that are more tolerant under flooding and cold during germination, both independently and concurrently.
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Affiliation(s)
- Ranjita Thapa
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
- Present address: Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | | | - Charles D Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | - Endang M Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.
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20
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Moulick D, Bhutia KL, Sarkar S, Roy A, Mishra UN, Pramanick B, Maitra S, Shankar T, Hazra S, Skalicky M, Brestic M, Barek V, Hossain A. The intertwining of Zn-finger motifs and abiotic stress tolerance in plants: Current status and future prospects. FRONTIERS IN PLANT SCIENCE 2023; 13:1083960. [PMID: 36684752 PMCID: PMC9846276 DOI: 10.3389/fpls.2022.1083960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Environmental stresses such as drought, high salinity, and low temperature can adversely modulate the field crop's ability by altering the morphological, physiological, and biochemical processes of the plants. It is estimated that about 50% + of the productivity of several crops is limited due to various types of abiotic stresses either presence alone or in combination (s). However, there are two ways plants can survive against these abiotic stresses; a) through management practices and b) through adaptive mechanisms to tolerate plants. These adaptive mechanisms of tolerant plants are mostly linked to their signalling transduction pathway, triggering the action of plant transcription factors and controlling the expression of various stress-regulated genes. In recent times, several studies found that Zn-finger motifs have a significant function during abiotic stress response in plants. In the first report, a wide range of Zn-binding motifs has been recognized and termed Zn-fingers. Since the zinc finger motifs regulate the function of stress-responsive genes. The Zn-finger was first reported as a repeated Zn-binding motif, comprising conserved cysteine (Cys) and histidine (His) ligands, in Xenopus laevis oocytes as a transcription factor (TF) IIIA (or TFIIIA). In the proteins where Zn2+ is mainly attached to amino acid residues and thus espousing a tetrahedral coordination geometry. The physical nature of Zn-proteins, defining the attraction of Zn-proteins for Zn2+, is crucial for having an in-depth knowledge of how a Zn2+ facilitates their characteristic function and how proteins control its mobility (intra and intercellular) as well as cellular availability. The current review summarized the concept, importance and mechanisms of Zn-finger motifs during abiotic stress response in plants.
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Affiliation(s)
- Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal, India
| | - Karma Landup Bhutia
- Department of Agricultural Biotechnology & Molecular Breeding, College of Basic Science and Humanities, Dr. Rajendra Prasad Central Agricultural University, Samastipur, India
| | - Sukamal Sarkar
- School of Agriculture and Rural Development, Faculty Centre for Integrated Rural Development and Management (IRDM), Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, India
| | - Anirban Roy
- School of Agriculture and Rural Development, Faculty Centre for Integrated Rural Development and Management (IRDM), Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, India
| | - Udit Nandan Mishra
- Department of Crop Physiology and Biochemistry, Sri University, Cuttack, Odisha, India
| | - Biswajit Pramanick
- Department of Agronomy, Dr. Rajendra Prasad Central Agricultural University, PUSA, Samastipur, Bihar, India
- Department of Agronomy and Horticulture, University of Nebraska Lincoln, Scottsbluff, NE, United States
| | - Sagar Maitra
- Department of Agronomy and Agroforestry, Centurion University of Technology and Management, Paralakhemundi, Odisha, India
| | - Tanmoy Shankar
- Department of Agronomy and Agroforestry, Centurion University of Technology and Management, Paralakhemundi, Odisha, India
| | - Swati Hazra
- School of Agricultural Sciences, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Institute of Plant and Environmental Sciences, Slovak University of Agriculture, Nitra, Slovakia
| | - Viliam Barek
- Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Nitra, Slovakia
| | - Akbar Hossain
- Division of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, Bangladesh
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21
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Analysis of the C2H2 Gene Family in Maize ( Zea mays L.) under Cold Stress: Identification and Expression. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010122. [PMID: 36676071 PMCID: PMC9863836 DOI: 10.3390/life13010122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023]
Abstract
The C2H2 zinc finger protein is one of the most common zinc finger proteins, widely exists in eukaryotes, and plays an important role in plant growth and development, as well as in salt, low-temperature, and drought stress and other abiotic stress responses. In this study, C2H2 members were identified and analyzed from the low-temperature tolerant transcriptome sequencing data of maize seedlings. The chromosome position, physical and chemical properties, evolution analysis, gene structure, conservative motifs, promoter cis elements and collinearity relationships of gene the family members were analyzed using bioinformatics, and the expression of the ZmC2H2 gene family under cold stress was analyzed by fluorescent quantitative PCR. The results showed that 150 members of the C2H2 zinc finger protein family were identified, and their protein lengths ranged from 102 to 1223 bp. The maximum molecular weight of the ZmC2H2s was 135,196.34, and the minimum was 10,823.86. The isoelectric point of the ZmC2H2s was between 33.21 and 94.1, and the aliphatic index was 42.07-87.62. The promoter cis element analysis showed that the ZmC2H2 family contains many light-response elements, plant hormone-response elements, and stress-response elements. The analysis of the transcriptome data showed that most of the ZmC2H2 genes responded to cold stress, and most of the ZmC2H2 genes were highly expressed in cold-tolerant materials and lowly expressed in cold-sensitive materials. The real-time quantitative PCR (qRT-PCR) analysis showed that ZmC2H2-69, ZmC2H2-130, and ZmC2H2-76 were significantly upregulated, and that ZmC2H2-149, ZmC2H2-33, and ZmC2H2-38 were significantly downregulated. It is hypothesized that these genes, which function in different metabolic pathways, may play a key role in the maize cold response. These genes could be further studied as candidate genes. This study provides a theoretical reference for further study on the function analysis of the maize C2H2 gene family.
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22
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Zhi Y, Li X, Lian F, Wang C, White JC, Wang Z, Xing B. Nanoscale Iron trioxide catalyzes the synthesis of auxins analogs in artificial humic acids to enhance rice growth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157536. [PMID: 35878859 DOI: 10.1016/j.scitotenv.2022.157536] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/13/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Humic acids (HAs), kinds of valuable active carbon, are critical for improving soil fertility. However, the majority of soils are poor in HAs, arousing the development of artificial HAs. In this study, two iron-based catalysts (nanoscale iron trioxide (nFe2O3) and FeCl3) were used to catalyze the hydrothermal humification of waste corn straw. With the help of ultra-performance liquid chromatography-mass spectrometry, we proposed the specific humification process with the action of catalysis for the first time, which is of great significance for the design, synthesis and application of artificial HAs in the future. Moreover, the growth-promoting effect and mechanisms of the artificial HAs were determined by rice planting in a greenhouse. Results showed that compared to no catalyst treatment, the FeCl3 and nFe2O3 catalysts increased the decomposition rate of macromolecular biomass by 39 and 14 %, respectively, increasing the yield of artificial HAs. During the humification process, nFe2O3 catalysts benefit the formation of many aromatic structure monomers including furfural and hydroxycaproic acids. These monomers were condensed into growth hormone analogs such as vanillin and methionine sulfoxide and were further built in the artificial HAs. Therefore, the artificial HAs from nFe2O3 catalytic treatment promoted the rice growth the best, showing that the resultant germination rate, root activity, and photosynthetic rate of rice increased by 50, 167, and 72 %, respectively; moreover, the uptake and accumulation of water and nutrient by roots as well as the contents of soluble protein and sugar of rice are also significantly increased. This could be ascribed to the upregulated expression of functional genes including OsRHL1, OsZPT5-07, OsSHR2 and OsDCL. Considering both the economic and environmental benefits, we suggested that the artificial HAs, especially that produced with the action of nFe2O3 catalysis, are promising in alleviating environmental stress from waste biomass and sustainably improving agricultural production.
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Affiliation(s)
- Yancai Zhi
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaona Li
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fei Lian
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT 06504, United States
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
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23
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Genome-Wide Identification of Strawberry C2H2-ZFP C1-2i Subclass and the Potential Function of FaZAT10 in Abiotic Stress. Int J Mol Sci 2022; 23:ijms232113079. [PMID: 36361867 PMCID: PMC9654774 DOI: 10.3390/ijms232113079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022] Open
Abstract
C2H2-type zinc finger proteins (C2H2-ZFPs) play a key role in various plant biological processes and responses to environmental stresses. In Arabidopsisthaliana, C2H2-ZFP members with two zinc finger domains have been well-characterized in response to abiotic stresses. To date, the functions of these genes in strawberries are still uncharacterized. Here, 126 C2H2-ZFPs in cultivated strawberry were firstly identified using the recently sequenced Fragaria × ananassa genome. Among these C2H2-ZFPs, 46 members containing two zinc finger domains in cultivated strawberry were further identified as the C1-2i subclass. These genes were unevenly distributed on 21 chromosomes and classified into five groups according to the phylogenetic relationship, with similar physicochemical properties and motif compositions in the same group. Analyses of conserved domains and gene structures indicated the evolutionary conservation of the C1-2i subclass. A Ka/Ks analysis indicated that the C1-2i members were subjected to purifying selection during evolution. Furthermore, FaZAT10, a typical C2H2-ZFP, was isolated. FaZAT10 was expressed the highest in roots, and it was induced by drought, salt, low-temperature, ABA, and MeJA treatments. It was localized in the nucleus and showed no transactivation activity in yeast cells. Overall, these results provide useful information for enriching the analysis of the ZFPs gene family in strawberry, and they provide support for revealing the mechanism of FaZAT10 in the regulatory network of abiotic stress.
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24
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Li X, Cao X, Li J, Niu Q, Mo Y, Xiao L. Genome-wide characterization of C2H2 zinc-finger gene family provides insight into the mechanisms and evolution of the dehydration-rehydration responses in Physcomitrium and Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:953459. [PMID: 36262662 PMCID: PMC9574186 DOI: 10.3389/fpls.2022.953459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Dehydration tolerance is a vital factor for land plant evolution and world agricultural production. Numerous studies enlightened that the plant-specific C2H2-type zinc-finger proteins (C2H2-ZFPs) as master regulators played pivotal roles in the abiotic stress responses of plants. However, a comprehensive understanding of the evolution of C2H2-ZFPs in terrestrial plants and its regulatory mechanism in dehydration and rehydration response remains a mystery. In this study, the genome-wide identification of C2H2-ZFP genes revealed 549 homologs in the representatives of terrestrial plant lineages from liverwort to angiosperms. Based on the characteristics of the conserved C2H2-ZF domains, four major C2H2-ZF types (M-, Z-, Q-, and D-type) were identified in the C2H2-ZFPs, with the dominants of M-type in all selected species and followed by Z-type in non-seed plants and Q-type in seed plants, respectively. Phylogenetic analyses of the identified C2H2-ZFPs supported four major groups in the land plant representatives, among which the members from the desiccation-tolerant Physcomitrium patens and the dehydration-sensitive Arabidopsis thaliana displayed different topological relationships in the phylogenies reconstructed for a single species. C2H2-ZFPs clustered in the same subclades shared similar features in their conserved domains and gene structures. Approximately, 81% of the C2H2-ZFP promoters of all 549 identified C2H2-ZFPs harbored the conserved ABA-responsive elements (ABREs) and/or dehydration-responsive elements (DREs). Comparative transcriptomic analyses showed that 50 PpZFPs and 56 AtZFPs significantly changed their transcripts abundance. Interestingly, most of the dehydration- and rehydration-responsive PpZPFs and AtZFPs had been predicted to contain the ABRE and DRE elements in their promoter regions and with over half of which phylogenetically belonging to group III. The differences in the expression patterns of C2H2-ZFPs in responses to dehydration and rehydration between P. patens and A. thaliana reflected their different strategies to adapt to dehydration. The identified candidate PpZFPs were specifically induced by moderate dehydration and reached the peak transcript abundance in severe dehydration. Our study lays the foundations for further functional investigation of C2H2-ZFPs in dehydration responses from an evolutionary perspective in land plants. The findings will provide us with genetic resources and potential targets for drought tolerance breeding in crops and beyond.
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25
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Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum. PLANTS 2022; 11:plants11192511. [PMID: 36235376 PMCID: PMC9572532 DOI: 10.3390/plants11192511] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022]
Abstract
The zinc finger protein (ZFP) family is one of plants’ most diverse family of transcription factors. These proteins with finger-like structural domains have been shown to play a critical role in plant responses to abiotic stresses such as drought. This study aimed to systematically characterize Triticum aestivum ZFPs (TaZFPs) and understand their roles under drought stress. A total of 9 TaC2H2, 38 TaC3HC4, 79 TaCCCH, and 143 TaPHD were identified, which were divided into 4, 7, 12, and 14 distinct subgroups based on their phylogenetic relationships, respectively. Segmental duplication dominated the evolution of four subfamilies and made important contributions to the large-scale amplification of gene families. Syntenic relationships, gene duplications, and Ka/Ks result consistently indicate a potential strong purifying selection on TaZFPs. Additionally, TaZFPs have various abiotic stress-associated cis-acting regulatory elements and have tissue-specific expression patterns showing different responses to drought and heat stress. Therefore, these genes may play multiple functions in plant growth and stress resistance responses. This is the first comprehensive genome-wide analysis of ZFP gene families in T. aestivum to elucidate the basis of their function and resistance mechanisms, providing a reference for precise manipulation of genetic engineering for drought resistance in T. aestivum.
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Affortit P, Effa-Effa B, Ndoye MS, Moukouanga D, Luchaire N, Cabrera-Bosquet L, Perálvarez M, Pilloni R, Welcker C, Champion A, Gantet P, Diedhiou AG, Manneh B, Aroca R, Vadez V, Laplaze L, Cubry P, Grondin A. Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5279-5293. [PMID: 35429274 DOI: 10.1093/jxb/erac156] [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: 11/28/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Improving crop water use efficiency, the amount of carbon assimilated as biomass per unit of water used by a plant, is of major importance as water for agriculture becomes scarcer. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand remain unknown. These traits were measured in 2019 in a panel of 147 African rice (Oryza glaberrima) genotypes known to be potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly contrasted genotypes in terms of biomass accumulation and transpiration confirmed these associations and suggested that root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency, and its residuals, with links to genes involved in water transport and cell wall patterning. Our data suggest that root-shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.
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Affiliation(s)
- Pablo Affortit
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Branly Effa-Effa
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CENAREST, Libreville, Gabon
| | - Mame Sokhatil Ndoye
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CERAAS, Thiès, Senegal
| | | | - Nathalie Luchaire
- LEPSE, Université de Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | | | - Raphaël Pilloni
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Claude Welcker
- LEPSE, Université de Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Antony Champion
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Pascal Gantet
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | | | | | | | - Vincent Vadez
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CERAAS, Thiès, Senegal
- LMI LAPSE, Dakar, Senegal
- ICRISAT, Patancheru, India
| | - Laurent Laplaze
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LMI LAPSE, Dakar, Senegal
| | - Philippe Cubry
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Alexandre Grondin
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CERAAS, Thiès, Senegal
- LMI LAPSE, Dakar, Senegal
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27
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Puentes-Romero AC, González SA, González-Villanueva E, Figueroa CR, Ruiz-Lara S. AtZAT4, a C 2H 2-Type Zinc Finger Transcription Factor from Arabidopsis thaliana, Is Involved in Pollen and Seed Development. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11151974. [PMID: 35956451 PMCID: PMC9370812 DOI: 10.3390/plants11151974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/16/2022] [Accepted: 07/27/2022] [Indexed: 06/01/2023]
Abstract
Pollen plays an essential role in plant fertility by delivering the male gametes to the embryo sac before double fertilization. In several plant species, including Arabidopsis, C2H2-type zinc-finger transcription factors (TFs) have been involved in different stages of pollen development and maturation. ZINC FINGER of Arabidopsis thaliana 4 (AtZAT4) is homologous to such TFs and subcellular localization analysis has revealed that AtZAT4 is located in the nucleus. Moreover, analysis of AtZAT4 expression revealed strong levels of it in flowers and siliques, suggesting a role of the encoded protein in the regulation of genes that are associated with reproductive development. We characterized a T-DNA insertional heterozygous mutant Atzat4 (+/−). The relative gene expression analysis of Atzat4 (+/−) showed significant transcript reductions in flowers and siliques. Furthermore, the Atzat4 (+/−) phenotypic characterization revealed defects in the male germline, showing a reduction in pollen tube germination and elongation. Atzat4 (+/−) presented reduced fertility, characterized by a smaller silique size compared to the wild type (WT), and a lower number of seeds per silique. Additionally, seeds displayed lower viability and germination. Altogether, our data suggest a role for AtZAT4 in fertilization and seed viability, through the regulation of gene expression associated with reproductive development.
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Affiliation(s)
- A. Carolina Puentes-Romero
- Laboratorio de Genómica Funcional, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile; (A.C.P.-R.); (S.A.G.); (E.G.-V.)
- Millenium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8340755, Chile;
| | - Sebastián A. González
- Laboratorio de Genómica Funcional, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile; (A.C.P.-R.); (S.A.G.); (E.G.-V.)
| | - Enrique González-Villanueva
- Laboratorio de Genómica Funcional, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile; (A.C.P.-R.); (S.A.G.); (E.G.-V.)
| | - Carlos R. Figueroa
- Millenium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8340755, Chile;
- Laboratory of Plant Molecular Physiology, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile
| | - Simón Ruiz-Lara
- Laboratorio de Genómica Funcional, Institute of Biological Sciences, Universidad de Talca, Talca 3460000, Chile; (A.C.P.-R.); (S.A.G.); (E.G.-V.)
- Millenium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8340755, Chile;
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28
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Huang Y, Du L, Wang M, Ren M, Yu S, Yang Q. Multifaceted roles of zinc finger proteins in regulating various agronomic traits in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:974396. [PMID: 35958192 PMCID: PMC9359907 DOI: 10.3389/fpls.2022.974396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Rice is an important cereal crop, which provides staple food for more than half of the world's population. To meet the demand of the ever-growing population in the next few decades, an extra increase in rice yield is an urgent need. Given that various agronomic traits contribute to the yield of rice, deciphering the key regulators involved in multiple agronomic trait formation is particularly important. As a superfamily of transcription factors, zinc finger proteins participate in regulating multiple genes in almost every stage of rice growth and development. Therefore, understanding zinc finger proteins underlying regulatory network would provide insights into the regulation of agronomic traits in rice. To this end, we intend to summarize the current advances in zinc finger proteins, with emphasis on C2H2 and CCCH proteins, and then discuss their potential in improving rice yield.
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Affiliation(s)
- Yifeng Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
- Guangdong Province Key Laboratory of Plant Molecular Breeding, Guangzhou, China
| | - Longgang Du
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Meixi Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Mengyun Ren
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Shouwu Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Qianying Yang
- Division of Integrative Bioscience and Biotechnology, Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang-si, South Korea
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29
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Jiang Y, Liu L, Pan Z, Zhao M, Zhu L, Han Y, Li L, Wang Y, Wang K, Liu S, Wang Y, Zhang M. Genome-wide analysis of the C2H2 zinc finger protein gene family and its response to salt stress in ginseng, Panax ginseng Meyer. Sci Rep 2022; 12:10165. [PMID: 35715520 PMCID: PMC9206012 DOI: 10.1038/s41598-022-14357-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 12/12/2022] Open
Abstract
The C2H2 zinc finger protein (C2H2-ZFP) gene family plays important roles in response to environmental stresses and several other biological processes in plants. Ginseng is a precious medicinal herb cultivated in Asia and North America. However, little is known about the C2H2-ZFP gene family and its functions in ginseng. Here, we identified 115 C2H2-ZFP genes from ginseng, defined as the PgZFP gene family. It was clustered into five groups and featured with eight conserved motifs, with each gene containing one to six of them. The family genes are categorized into 17 gene ontology subcategories and have numerous regulatory elements responsive to a variety of biological process, suggesting their functional differentiation. The 115 PgZFP genes were spliced into 228 transcripts at seed setting stage and varied dramatically in expression across tissues, developmental stages, and genotypes, but they form a co-expression network, suggesting their functional correlation. Furthermore, four genes, PgZFP31, PgZFP78-01, PgZFP38, and PgZFP39-01, were identified from the gene family that were actively involved in plant response to salt stress. These results provide new knowledge on origin, differentiation, evolution, and function of the PgZFP gene family and new gene resources for C2H2-ZFP gene research and application in ginseng and other plant species.
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Affiliation(s)
- Yue Jiang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Lingyu Liu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Zhaoxi Pan
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China.,Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Lei Zhu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yilai Han
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Li Li
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yanfang Wang
- Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, 130118, Jilin, China.,College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China.,Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Sizhang Liu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China. .,Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China. .,Jilin Engineering Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, 130118, Jilin, China.
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30
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Zhou K, Chen Z, Du X, Huang Y, Qin J, Wen L, Pan X, Lin Y. SMRT Sequencing Reveals Candidate Genes and Pathways With Medicinal Value in Cipangopaludina chinensis. Front Genet 2022; 13:881952. [PMID: 35783279 PMCID: PMC9243326 DOI: 10.3389/fgene.2022.881952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/26/2022] [Indexed: 12/03/2022] Open
Abstract
Cipangopaludina chinensis is an economically important aquatic snail with high medicinal value. However, molecular biology research on C. chinensis is limited by the lack of a reference genome, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. chinensis. Herein, we conducted the first full-length transcriptome analysis of C. chinensis using PacBio single-molecule real-time (SMRT) sequencing technology. We identified a total of 26,312 unigenes with an average length of 2,572 bp, of which the largest number of zf-c2h2 transcription factor families (120,18.24%) were found, and also observed that the majority of the 8,058 SSRs contained 4-7 repeat units, which provided data for subsequent work on snail genetics Subsequently, 91.86% (24,169) of the genes were successfully annotated to the four major databases, while the highest homology was observed with Pomacea canaliculata. Functional annotation revealed that the majority of transcripts were enriched in metabolism, signal transduction and Immune-related pathways, and several candidate genes involved in drug metabolism and immune response were identified (e.g., CYP1A1, CYP2J, CYP2U1, GST, ,PIK3, PDE3A, PRKAG). This study lays a foundation for future molecular biology research and provides a reference for studying genes associated with the medicinal value of C. chinensis.
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Affiliation(s)
| | | | | | | | | | | | | | - Yong Lin
- *Correspondence: Xianhui Pan, ; Yong Lin,
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31
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Han J, Ma Z, Chen L, Wang Z, Wang C, Wang L, Chen C, Ren Z, Cao C. Morphological Characterization and Integrated Transcriptome and Proteome Analysis of Organ Development Defective 1 ( odd1) Mutant in Cucumis sativus L. Int J Mol Sci 2022; 23:ijms23105843. [PMID: 35628653 PMCID: PMC9145247 DOI: 10.3390/ijms23105843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/09/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Cucumber (Cucumis sativus L.) is an economically important vegetable crop with the unique growth habit and typical trailing shoot architecture of Cucurbitaceae. Elucidating the regulatory mechanisms of growth and development is significant for improving quality and productivity in cucumber. Here we isolated a spontaneous cucumber mutant organ development defective 1 (odd1) with multiple morphological changes including root, plant stature, stem, leaf, male and female flowers, as well as fruit. Anatomical and cytological analyses demonstrated that both cell size and number decreased, and the shoot apical meristem (SAM) was smaller in odd1 compared with WT. Pollen vigor and germination assays and cross tests revealed that odd1 is female sterile, which may be caused by the absence of ovules. Genetic analysis showed that odd1 is a recessive single gene mutant. Using the MutMap strategy, the odd1 gene was found to be located on chromosome 5. Integrated profiling of transcriptome and proteome indicated that the different expression genes related to hormones and SAM maintenance might be the reason for the phenotypic changes of odd1. These results expanded the insight into the molecular regulation of organ growth and development and provided a comprehensive reference map for further studies in cucumber.
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32
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Cui H, Chen J, Liu M, Zhang H, Zhang S, Liu D, Chen S. Genome-Wide Analysis of C2H2 Zinc Finger Gene Family and Its Response to Cold and Drought Stress in Sorghum [ Sorghum bicolor (L.) Moench]. Int J Mol Sci 2022; 23:ijms23105571. [PMID: 35628380 PMCID: PMC9146226 DOI: 10.3390/ijms23105571] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
C2H2 zinc finger protein (C2H2-ZFP) is one of the most important transcription factor families in higher plants. In this study, a total of 145 C2H2-ZFPs was identified in Sorghum bicolor and randomly distributed on 10 chromosomes. Based on the phylogenetic tree, these zinc finger gene family members were divided into 11 clades, and the gene structure and motif composition of SbC2H2-ZFPs in the same clade were similar. SbC2H2-ZFP members located in the same clade contained similar intron/exon and motif patterns. Thirty-three tandem duplicated SbC2H2-ZFPs and 24 pairs of segmental duplicated genes were identified. Moreover, synteny analysis showed that sorghum had more collinear regions with monocotyledonous plants such as maize and rice than did dicotyledons such as soybean and Arabidopsis. Furthermore, we used quantitative RT-PCR (qRT-PCR) to analyze the expression of C2H2-ZFPs in different organs and demonstrated that the genes responded to cold and drought. For example, Sobic.008G088842 might be activated by cold but is inhibited in drought in the stems and leaves. This work not only revealed an important expanded C2H2-ZFP gene family in Sorghum bicolor but also provides a research basis for determining the role of C2H2-ZFPs in sorghum development and abiotic stress resistance.
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Affiliation(s)
- Huiying Cui
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
- Correspondence: (H.C.); (S.C.)
| | - Jiaqi Chen
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Mengjiao Liu
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Hongzhi Zhang
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Shuangxi Zhang
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Dan Liu
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
| | - Shaolin Chen
- College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (J.C.); (M.L.); (H.Z.); (S.Z.); (D.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Xianyang 712100, China
- Correspondence: (H.C.); (S.C.)
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33
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Tiwari S, Nutan KK, Deshmukh R, Sarsu F, Gupta KJ, Singh AK, Singla-Pareek SL, Pareek A. Seedling-stage salinity tolerance in rice: Decoding the role of transcription factors. PHYSIOLOGIA PLANTARUM 2022; 174:e13685. [PMID: 35419814 DOI: 10.1111/ppl.13685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/10/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Rice is an important staple food crop that feeds over half of the human population, particularly in developing countries. Increasing salinity is a major challenge for continuing rice production. Though rice is affected by salinity at all the developmental stages, it is most sensitive at the early seedling stage. The yield thus depends on how many seedlings can withstand saline water at the stage of transplantation, especially in coastal farms. The rapid development of "omics" approaches has assisted researchers in identifying biological molecules that are responsive to salt stress. Several salinity-responsive quantitative trait loci (QTL) contributing to salinity tolerance have been identified and validated, making it essential to narrow down the search for the key genes within QTLs. Owing to the impressive progress of molecular tools, it is now clear that the response of plants toward salinity is highly complex, involving multiple genes, with a specific role assigned to the repertoire of transcription factors (TF). Targeting the TFs for improving salinity tolerance can have an inbuilt advantage of influencing multiple downstream genes, which in turn can contribute toward tolerance to multiple stresses. This is the first comparative study for TF-driven salinity tolerance in contrasting rice cultivars at the seedling stage that shows how tolerant genotypes behave differently than sensitive ones in terms of stress tolerance. Understanding the complexity of salt-responsive TF networks at the seedling stage will be helpful to alleviate crop resilience and prevent crop damage at an early growth stage in rice.
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Affiliation(s)
- Shalini Tiwari
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Kamlesh Kant Nutan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Sahibzada Ajit Singh Nagar, Punjab, India
| | - Fatma Sarsu
- General Directorate of Agricultural Research and Policies, Ministry of Agriculture and Forestry, Ankara, Turkey
| | | | - Anil K Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, Delhi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
- National Agri-Food Biotechnology Institute, Sahibzada Ajit Singh Nagar, Punjab, India
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34
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Liu Y, Khan AR, Gan Y. C2H2 Zinc Finger Proteins Response to Abiotic Stress in Plants. Int J Mol Sci 2022; 23:ijms23052730. [PMID: 35269875 PMCID: PMC8911255 DOI: 10.3390/ijms23052730] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 12/14/2022] Open
Abstract
Abiotic stresses have already exhibited the negative effects on crop growth and development, thereby influencing crop quality and yield. Therefore, plants have developed regulatory mechanisms to adopt against such harsh changing environmental conditions. Recent studies have shown that zinc finger protein transcription factors play a crucial role in plant growth and development as well as in stress response. C2H2 zinc finger proteins are one of the best-studied types and have been shown to play diverse roles in the plant abiotic stress responses. However, the C2H2 zinc finger network in plants is complex and needs to be further studied in abiotic stress responses. Here in this review, we mainly focus on recent findings on the regulatory mechanisms, summarize the structural and functional characterization of C2H2 zinc finger proteins, and discuss the C2H2 zinc finger proteins involved in the different signal pathways in plant responses to abiotic stress.
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Affiliation(s)
- Yihua Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China
- Correspondence: (Y.L.); (Y.G.)
| | - Ali Raza Khan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Yinbo Gan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
- Correspondence: (Y.L.); (Y.G.)
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35
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Li C, Xia P, Ma Y, Zhang X, Liu Y. Expression pattern of ZNF33B in bovine ovaries and the effect of its polymorphism on superovulation traits. Arch Anim Breed 2022; 65:69-77. [PMID: 35252544 PMCID: PMC8889308 DOI: 10.5194/aab-65-69-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/24/2022] [Indexed: 11/11/2022] Open
Abstract
ZNF33B belongs to recently duplicated Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs), which
is widely present in various organs, and some evidence showed that its
expression is altered in the ovary undergoing superovulation. In this study,
the expression of ZNF33B in ovary and early embryo was determined by
immunohistochemistry and immunofluorescence techniques. Results showed that
the expression of ZNF33B in the ovary was mainly in the cytoplasm of oocytes
and granulosa luteal cells of ovarian corpus luteum and significantly
reduced during follicular ovulation to luteal degeneration. The expression
of ZNF33B in the early embryo transferred from the nucleus to the whole
cell, suggesting that the expression of ZNF33B is spatiotemporally specific.
Then, in combination with the single nucleotide polymorphism (SNP) database, the g.-61G>T mutant
of the 5′-untranslated region (5′ UTR) of the ZNF33B gene was screened out from 556
Changbaishan black cattle, and the frequency of the mutant gene was counted.
The statistics of superovulation and superovulation traits confirmed
significant differences between the two genotypes in the quantity and
quality of oocytes obtained after superovulation. This study confirmed, for
the first time, the effect of ZNF33B gene polymorphism on superovulation
traits and suggested that the mutation could provide a basis for cattle
breeding and improving animal fertility.
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Affiliation(s)
- Changhong Li
- College of Life Sciences, Baicheng Normal University, Baicheng, Jilin,
China
| | - Peijun Xia
- College of Animal Science, Jilin University, Changchun, Jilin, China
| | - Yijuan Ma
- College of Life Sciences, Baicheng Normal University, Baicheng, Jilin,
China
| | - Xinyue Zhang
- College of Life Sciences, Baicheng Normal University, Baicheng, Jilin,
China
| | - Yijia Liu
- College of Life Sciences, Baicheng Normal University, Baicheng, Jilin,
China
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36
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Shuai Y, Feng G, Yang Z, Liu Q, Han J, Xu X, Nie G, Huang L, Zhang X. Genome-wide identification of C2H2-type zinc finger gene family members and their expression during abiotic stress responses in orchardgrass ( Dactylis glomerata). Genome 2022; 65:189-203. [PMID: 35104149 DOI: 10.1139/gen-2020-0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The C2H2-type zinc finger protein (ZFP) family is one of the largest transcription factor families in the plant kingdom and its members are involved in plant growth, development, and stress responses. As an economically valuable perennial graminaceous forage crop, orchardgrass (Dactylis glomerata) is an important feedstuff resource owing to its high yield and quality. In this study, 125 C2H2-type ZFPs in orchardgrass (Dg-ZFPs) were identified and further classified by phylogenetic analysis. The members with similar gene structures were generally clustered into the same groups, with proteins containing the conserved QALGGH motif being concentrated in groups VIII and IX. Gene ontology and miRNA target analyses indicated that Dg-ZFPs likely perform diverse biological functions through their gene interactions. The RNA-seq data revealed differentially expressed genes across tissues and development phases, suggesting that some Dg-ZFPs might participate in growth and development regulation. Abiotic stress responses of Dg-ZFP genes were verified by qPCR and Saccharomyces cerevisiae transformation, revealing that Dg-ZFP125 could enhance the tolerance of yeasts to osmotic and salt stresses. Our study performed a novel systematic analysis of Dg-ZFPs in orchardgrass, providing a reference for this gene family in other grasses and revealing new insights for enhancing gene utilization.
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Affiliation(s)
- Yang Shuai
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiuxu Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiating Han
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
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37
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Zheng F, Cui L, Li C, Xie Q, Ai G, Wang J, Yu H, Wang T, Zhang J, Ye Z, Yang C. Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:228-244. [PMID: 34499170 DOI: 10.1093/jxb/erab417] [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: 05/02/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Trichomes are specialized glandular or non-glandular structures that provide physical or chemical protection against insect and pathogen attack. Trichomes in Arabidopsis have been extensively studied as typical non-glandular structures. By contrast, the molecular mechanism underlying glandular trichome formation and elongation remains largely unknown. We previously demonstrated that Hair is essential for the formation of type I and type VI trichomes. Here, we found that overexpression of Hair increased the density and length of tomato trichomes. Biochemical assays revealed that Hair physically interacts with its close homolog SlZFP8-like (SlZFP8L), and SlZFP8L also directly interacts with Woolly. SlZFP8L-overexpressing plants showed increased trichome density and length. We further found that the expression of SlZFP6, which encodes a C2H2 zinc finger protein, is positively regulated by Hair. Using chromatin immunoprecipitation, yeast one-hybrid, and dual-luciferase assays we identified that SlZFP6 is a direct target of Hair. Similar to Hair and SlZFP8L, the overexpression of SlZFP6 also increased the density and length of tomato trichomes. Taken together, our results suggest that Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato.
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Affiliation(s)
- Fangyan Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Long Cui
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Changxing Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Qingmin Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Guo Ai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Junqiang Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Taotao Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Kaur A, Nijhawan A, Yadav M, Khurana JP. OsbZIP62/OsFD7, a functional ortholog of FLOWERING LOCUS D, regulates floral transition and panicle development in rice. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7826-7845. [PMID: 34459895 DOI: 10.1093/jxb/erab396] [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: 03/13/2021] [Accepted: 08/30/2021] [Indexed: 05/04/2023]
Abstract
We have characterized a rice bZIP protein-coding gene OsbZIP62/OsFD7 that is expressed preferentially in the shoot apical meristem and during early panicle developmental stages in comparison with other OsFD genes characterized to date. Surprisingly, unlike OsFD1, OsFD7 interacts directly and more efficiently with OsFTLs; the interaction is strongest with OsFTL1 followed by Hd3a and RFT1, as confirmed by fluorescence lifetime imaging-Förster resonant energy transfer (FLIM-FRET) analysis. In addition, OsFD7 is phosphorylated at its C-terminal end by OsCDPK41 and OsCDPK49 in vitro, and this phosphorylated moiety is recognized by OsGF14 proteins. OsFD7 RNAi transgenics were late flowering; the transcript levels of some floral meristem identity genes (e.g. OsMADS14, OsMADS15, and OsMADS18) were also down-regulated. RNAi lines also exhibited dense panicle morphology with an increase in the number of primary and secondary branches resulting in longer panicles and more seeds, probably due to down-regulation of SEPALLATA family genes. In comparison with other FD-like proteins previously characterized in rice, it appears that OsFD7 may have undergone diversification during evolution, resulting in the acquisition of newer functions and thus playing a dual role in floral transition and panicle development in rice.
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Affiliation(s)
- Amarjot Kaur
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi-110021, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi-110021, India
| | - Aashima Nijhawan
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi-110021, India
| | - Mahesh Yadav
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi-110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi-110021, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi-110021, India
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Genome-Wide Identification of the Q-type C2H2 Transcription Factor Family in Alfalfa ( Medicago sativa) and Expression Analysis under Different Abiotic Stresses. Genes (Basel) 2021; 12:genes12121906. [PMID: 34946855 PMCID: PMC8701282 DOI: 10.3390/genes12121906] [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: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 02/02/2023] Open
Abstract
Q-type C2H2 zinc-finger protein (C2H2-ZFP) transcription factors are associated with many plant growth development and environmental stress responses. To date, there have been few analyses of the Q-type C2H2-ZFP gene family in alfalfa (Medicago sativa subsp. sativa). In this study, we identified 58 Q-type C2H2-ZFPs across the entire alfalfa genome, and the gene structure, motif composition, chromosomal mapping, and cis-regulatory elements were explored, as well as the expression profiles of specific tissues and the response under different abiotic stresses. According to their phylogenetic features, these 58 MsZFPs were divided into 12 subgroups. Synteny analysis showed that duplication events play a vital role in the expansion of the MsZFP gene family. The collinearity results showed that a total of 26 and 42 of the 58 MsZFP genes were homologous with Arabidopsis and M. truncatula, respectively. The expression profiles showed that C2H2-ZFP genes played various roles in different tissues and abiotic stresses. The results of subsequent quantitative real-time polymerase chain reaction (qRT-PCR) showed that the nine selected MsZFP genes were rapidly induced under different abiotic stresses, indicating that C2H2-ZFP genes are closely related to abiotic stress. This study provides results on MsZFP genes, their response to various abiotic stresses, and new information on the C2H2 family in alfalfa.
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Inagaki N, Asami H, Hirabayashi H, Uchino A, Imaizumi T, Ishimaru K. A Rice Ancestral Genetic Resource Conferring Ideal Plant Shapes for Vegetative Growth and Weed Suppression. FRONTIERS IN PLANT SCIENCE 2021; 12:748531. [PMID: 34899776 PMCID: PMC8664436 DOI: 10.3389/fpls.2021.748531] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/28/2021] [Indexed: 06/02/2023]
Abstract
To maximize crop growth, crops need to capture sunlight efficiently. This property is primarily influenced by the shape of the crops such as the angle, area, and arrangement of leaves. We constructed a rice (Oryza sativa L.) inbred line that displayed an ideal transition of plant shapes in terms of sunlight receiving efficiency. During vegetative growth, this line exhibited tiller spreading with increased tiller number, which formed a parabolic antenna-like structure. The architecture probably improved light reception efficiency of individuals compared with the recurrent parent. The line achieved not only acceleration of the vegetative growth, but also significant suppression of weed growth under the canopy. The increased light reception efficiency of the line has consequently reduced the amount of incident light to the ground and supplied significant competitiveness against weeds. The spread tillers became erect from the entry of the reproductive growth phase, adaptively sustaining light reception efficiency in thicker stands. The line carries a small chromosomal segment from Oryza rufipogon Griff., a putative progenitor of Asian cultivated rice. The introduced chromosome segment had little effect on grain yield and quality. Our results shed light on potentials hidden in the wild rice chromosome segment to achieve the valuable traits.
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Affiliation(s)
- Noritoshi Inagaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hidenori Asami
- Western Region Agricultural Research Center (Kinki, Chugoku, and Shikoku Regions), National Agriculture and Food Research Organization (NARO), Fukuyama, Japan
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hideyuki Hirabayashi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Akira Uchino
- Central Region Agricultural Research Center (Kanto, Tokai, and Hokuriku Regions), National Agriculture and Food Research Organization (NARO), Tsu, Japan
| | - Toshiyuki Imaizumi
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Ken Ishimaru
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
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Li J, Zhang L, Yuan Y, Wang Q, Elbaiomy RG, Zhou W, Wu H, Soaud SA, Abbas M, Chen B, Zhao D, El-Sappah AH. In Silico Functional Prediction and Expression Analysis of C2H2 Zinc-Finger Family Transcription Factor Revealed Regulatory Role of ZmZFP126 in Maize Growth. Front Genet 2021; 12:770427. [PMID: 34804129 PMCID: PMC8602080 DOI: 10.3389/fgene.2021.770427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The C2H2-zinc finger proteins (ZFP) comprise a large family of transcription factors with various functions in biological processes. In maize, the function regulation of C2H2- zine finger (ZF) genes are poorly understood. We conducted an evolution analysis and functional prediction of the maize C2H2-ZF gene family. Furthermore, the ZmZFP126 gene has been cloned and sequenced for further favorable allelic variation discovery. The phylogenetic analysis of the C2H2-ZF domain indicated that the position and sequence of the C2H2-ZF domain of the poly-zinc finger gene are relatively conserved during evolution, and the C2H2-ZF domain with the same position is highly conserved. The expression analysis of the C2H2-ZF gene family in 11 tissues at different growth stages of B73 inbred lines showed that genes with multiple transcripts were endowed with more functions. The expression analysis of the C2H2-ZF gene in P1 and P2 inbred lines under drought conditions showed that the C2H2-ZF genes were mainly subjected to negative regulation under drought stress. Functional prediction indicated that the maize C2H2-ZF gene is mainly involved in reproduction and development, especially concerning the formation of important agronomic traits in maize yield. Furthermore, sequencing and correlation analysis of the ZmZFP126 gene indicated that this gene was significantly associated with the SDW-NAP and TDW-NAP. The analysis of the relationship between maize C2H2-ZF genes and C2H2-ZF genes with known functions indicated that the functions of some C2H2-ZF genes are relatively conservative, and the functions of homologous genes in different species are similar.
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Affiliation(s)
- Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Litian Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Academy of Animal Science and Veterinary Medicine of Qinghai University, Xining, China
| | - Yibing Yuan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | | | - Wanhai Zhou
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Hui Wu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Bo Chen
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Deming Zhao
- Yibin Academy of Agricultural Sciences, Yibin, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
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Targeting the B1 Gene and Analysis of Its Polymorphism Associated with Awned/Awnless Trait in Russian Germplasm Collections of Common Wheat. PLANTS 2021; 10:plants10112285. [PMID: 34834646 PMCID: PMC8621087 DOI: 10.3390/plants10112285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/06/2021] [Accepted: 10/21/2021] [Indexed: 11/25/2022]
Abstract
The presence of awns on the ear is associated with a number of important plant properties, such as drought resistance, quality of the grain mass during processing, etc. The main manifestations of this trait are controlled by the B1 gene, which has recently been identified and encodes the C2H2 zinc finger transcription factor. Based on the previously identified SNPs in the promoter region of this gene, we constructed markers for dominant and recessive alleles which determine awnless and awned phenotypes, respectively. The markers were successful for use in targeting the respective alleles of the B1 gene in 176 varieties of common wheat, accessions of T. spelta L., as well as on F2/F3 hybrids from crosses between awned and awnless forms of T. aestivum. We first identified a new allele, b1mite, which has both an insert of a miniature Stowaway-like transposon, 261 bp in length, and 33 novel SNPs in the promoter region. Despite these changes, this allele had no effect on the awned phenotype. The possible mechanisms of the influence of the analyzed gene on phenotype are discussed.
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A C2H2-Type Zinc-Finger Protein from Millettia pinnata, MpZFP1, Enhances Salt Tolerance in Transgenic Arabidopsis. Int J Mol Sci 2021; 22:ijms221910832. [PMID: 34639173 PMCID: PMC8509772 DOI: 10.3390/ijms221910832] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 01/03/2023] Open
Abstract
C2H2 zinc finger proteins (ZFPs) play important roles in plant development and response to abiotic stresses, and have been studied extensively. However, there are few studies on ZFPs in mangroves and mangrove associates, which represent a unique plant community with robust stress tolerance. MpZFP1, which is highly induced by salt stress in the mangrove associate Millettia pinnata, was cloned and functionally characterized in this study. MpZFP1 protein contains two zinc finger domains with conserved QALGGH motifs and targets to the nucleus. The heterologous expression of MpZFP1 in Arabidopsis increased the seeds' germination rate, seedling survival rate, and biomass accumulation under salt stress. The transgenic plants also increased the expression of stress-responsive genes, including RD22 and RD29A, and reduced the accumulation of reactive oxygen species (ROS). These results indicate that MpZFP1 is a positive regulator of plant responses to salt stress due to its activation of gene expression and efficient scavenging of ROS.
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Li Y, Sun A, Wu Q, Zou X, Chen F, Cai R, Xie H, Zhang M, Guo X. Comprehensive genomic survey, structural classification and expression analysis of C 2H 2-type zinc finger factor in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2021; 21:380. [PMID: 34407757 PMCID: PMC8375173 DOI: 10.1186/s12870-021-03016-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/06/2021] [Indexed: 06/04/2023]
Abstract
BACKGROUND The C2H2-type zinc finger proteins (C2H2-ZFPs) are one of major classes of transcription factors that play important roles in plant growth, development and stress responses. Limit information about the C2H2-ZF genes hinders the molecular breeding in bread wheat (Triticum aestivum). RESULTS In this study, 457 C2H2-ZFP proteins (including 253 splice variants), which contain four types of conserved domain (named Q, M, Z, and D), could be further classified into ten subsets. They were identified to be distributed in 21 chromosomes in T. aestivum. Subset-specific motifs, like NPL-, SFP1-, DL- (EAR-like-motif), R-, PL-, L- and EK-, might make C2H2-ZFP diverse multifunction. Interestingly, NPL- and SFP1-box were firstly found to be located in C2H2-ZFP proteins. Synteny analyses showed that only 4 pairs of C2H2 family genes in T. aestivum, 65 genes in B. distachyon, 66 genes in A. tauschii, 68 genes in rice, 9 genes in Arabidopsis, were syntenic relationships respectively. It indicated that TaZFPs were closely related to genes in Poaceae. From the published transcriptome data, totally 198 of 204 TaC2H2-ZF genes have expression data. Among them, 25 TaC2H2-ZF genes were certificated to be significantly differentially expressed in 5 different organs and 15 different development stages by quantitative RT-PCR. The 18 TaC2H2-ZF genes were verified in response to heat, drought, and heat & drought stresses. According to expression pattern analysis, several TaZFPs, like Traes_5BL_D53A846BE.1, were not only highly expressed in L2DAAs, RTLS, RMS, but also endowed tolerance to drought and heat stresses, making them good candidates for molecular breeding. CONCLUSIONS This study systematically characterized the TaC2H2-ZFPs and their potential roles in T. aestivum. Our findings provide new insights into the C2H2-ZF genes in T. aestivum as well as a foundation for further studies on the roles of TaC2H2-ZF genes in T. aestivum molecular breeding.
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Affiliation(s)
- Yongliang Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Aolong Sun
- College of Biology, Hunan University, Changsha, 410082, China
| | - Qun Wu
- College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaoxiao Zou
- College of Biology, Hunan University, Changsha, 410082, China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082, China
| | - Ruqiong Cai
- College of Biology, Hunan University, Changsha, 410082, China
| | - Hai Xie
- College of Biology, Hunan University, Changsha, 410082, China
| | - Meng Zhang
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082, China.
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Khan MIR, Palakolanu SR, Chopra P, Rajurkar AB, Gupta R, Iqbal N, Maheshwari C. Improving drought tolerance in rice: Ensuring food security through multi-dimensional approaches. PHYSIOLOGIA PLANTARUM 2021; 172:645-668. [PMID: 33006143 DOI: 10.1111/ppl.13223] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 05/27/2023]
Abstract
Drought has been highly prevalent around the world especially in Sub-Saharan Africa and South-East Asian countries. Consistent climatic instabilities and unpredictable rainfall patterns are further worsening the situation. Rice is a C3 staple cereal and an important food crop for the majority of the world's population and drought stress is one of the major growth retarding threats for rice that slashes down grain quality and yield. Drought deteriorates rice productivity and induces various acclimation responses that aids in stress mitigation. However, the complexity of traits associated with drought tolerance has made the understanding of drought stress-induced responses in rice a challenging process. An integrative understanding based on physiological adaptations, omics, transgenic and molecular breeding approaches successively backed up to developing drought stress-tolerant rice. The review represents a step forward to develop drought-resilient rice plants by exploiting the knowledge that collaborates with omics-based developments with integrative efforts to ensure the compilation of all the possible strategies undertaken to develop drought stress-tolerant rice.
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Affiliation(s)
| | - Sudhakar R Palakolanu
- Cell, Molecular Biology and Genetic Engineering Group, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Ashish B Rajurkar
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Ravi Gupta
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Chirag Maheshwari
- Agricultural Energy and Power Division, ICAR-Central Institute of Agricultural Engineering, Bhopal, India
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Shehzad M, Zhou Z, Ditta A, Khan M, Cai X, Xu Y, Maqbool A, Khalofah A, Shaban M, Naeem M, Ansari MJ, Wang K, Liu F. Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton. PLoS One 2021; 16:e0247593. [PMID: 33770112 PMCID: PMC7997035 DOI: 10.1371/journal.pone.0247593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.
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Affiliation(s)
- Muhammad Shehzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Allah Ditta
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- Plant Breeding, and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Punjab, Pakistan
| | - Majid Khan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Amir Maqbool
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Ahlam Khalofah
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Muhammad Shaban
- Department of Plant Breeding and Genetics, Faculty of Agricultural Science & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Naeem
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Bareilly, India
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- * E-mail: (KW); (FL)
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- * E-mail: (KW); (FL)
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Sharma R, Mahanty B, Mishra R, Joshi RK. Genome wide identification and expression analysis of pepper C 2H 2 zinc finger transcription factors in response to anthracnose pathogen Colletotrichum truncatum. 3 Biotech 2021; 11:118. [PMID: 33747699 PMCID: PMC7933328 DOI: 10.1007/s13205-020-02601-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022] Open
Abstract
Although, the C2H2 zinc finger (ZF) family of plant transcription factors have been implicated in multiple biological processes, they are yet to be characterized in the economically important chilli pepper (Capsicum annuum). In this study, a total of 79 C2H2 ZF genes were identified in the pepper genome. Phylogenetic analysis categorized the pepper C2H2 ZF (CaZF) members into five subfamilies each with unique conserved domains and functions. Genomic organization revealed that CaZF genes have variable number of introns consistent with the characteristics defined by the evolutionary analysis. Segmental duplication-based purifying selection contributed to the expansion of CaZF genes in pepper. Additionally, 11 CaZF genes were identified as targets for 38 miRNAs indicating their role in post-transcriptional silencing-mediated genetic regulation. Gene expression analysis revealed that 18 CaZF genes were differentially expressed post-infection with the anthrocnose pathogen Colletotrichum truncatum, uncovering their potential function in pepper response to biotic stresses. Moreover, CaZFs were significantly induced post-treatment with methyl jasmonate and ethylene indicating their role in defense signaling. Notably, the MeJA responsive cis-elements were detected in the promoter regions of majority of CaZF genes, suggesting that CaZFs may be implicated in defense-responsive signal cross talking. Additionally, 18 CaZF genes were differentially expressed under drought and heat treatment, indicating their involvement in plant response to abiotic stresses. Overall, a comprehensive analysis of CaZF gene family in pepper provided significant insights into the understanding of C2H2 ZF-mediated stress regulation network, which would benefit the genetic improvement of pepper and other allied plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02601-x.
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Affiliation(s)
- Richa Sharma
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
| | - Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha India
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha 751022 India
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Arrey-Salas O, Caris-Maldonado JC, Hernández-Rojas B, Gonzalez E. Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine ( Vitis vinifera L.): Insights into the Roles in the Pollen Development Regulation. Genes (Basel) 2021; 12:302. [PMID: 33672655 PMCID: PMC7924211 DOI: 10.3390/genes12020302] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/02/2023] Open
Abstract
Some C2H2 zinc-finger proteins (ZFP) transcription factors are involved in the development of pollen in plants. In grapevine (Vitis vinifera L.), it has been suggested that abnormalities in pollen development lead to the phenomenon called parthenocarpy that occurs in some varieties of this cultivar. At present, a network involving several transcription factors types has been revealed and key roles have been assigned to members of the C2H2 zinc-finger proteins (ZFP) family in model plants. However, particularities of the regulatory mechanisms controlling pollen formation in grapevine remain unknown. In order to gain insight into the participation of ZFPs in grapevine gametophyte development, we performed a genome-wide identification and characterization of genes encoding ZFP (VviZFP family). A total of 98 genes were identified and renamed based on the gene distribution into grapevine genome. The analysis performed indicate significant changes throughout VviZFP genes evolution explained by high heterogeneity in sequence, length, number of ZF and presence of another conserved domains. Moreover, segmental duplication participated in the gene family expansion in grapevine. The VviZFPs were classified based on domain and phylogenetic analysis into three sets and different groups. Heat-map demonstrated differential and tissue-specific expression patterns of these genes and k-means clustering allowed to identify a group of putative orthologs to some ZFPs related to pollen development. In transgenic plants carrying the promVviZFP13::GUS and promVviZFP68::GUS constructs, GUS signals were detectable in the anther and mature pollen grains. Expression profiling of selected VviZFP genes showed differential expression pattern during flower development and provides a basis for deepening in the understanding of VviZFPs role on grapevine reproductive development.
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Affiliation(s)
- Oscar Arrey-Salas
- Laboratorio de Genómica Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile;
| | | | - Bairon Hernández-Rojas
- Ph.D Program in Sciences Mention in Modeling of Chemical and Biological Systems, Faculty of Engineering, University of Talca, Calle 1 Poniente, 1141, 3462227 Talca, Chile;
| | - Enrique Gonzalez
- Laboratorio de Genómica Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile;
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Verma A, Prakash G, Ranjan R, Tyagi AK, Agarwal P. Silencing of an Ubiquitin Ligase Increases Grain Width and Weight in indica Rice. Front Genet 2021; 11:600378. [PMID: 33510769 PMCID: PMC7835794 DOI: 10.3389/fgene.2020.600378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
Many quantitative trait loci (QTLs) have been identified by molecular genetic studies which control grain size by regulating grain width, length, and/or thickness. Grain width 2 (GW2) is one such QTL that codes for a RING-type E3 ubiquitin ligase and increases grain size by regulating grain width through ubiquitin-mediated degradation of unknown substrates. A natural variation (single-nucleotide polymorphism at the 346th position) in the functional domain-coding region of OsGW2 in japonica rice genotypes has been shown to cause an increase in grain width/weight in rice. However, this variation is absent in indica rice genotypes. In this study, we report that reduced expression of OsGW2 can alter grain size, even though natural sequence variation is not responsible for increased grain size in indica rice genotypes. OsGW2 shows high expression in seed development stages and the protein localizes to the nucleus and cytoplasm. Downregulation of OsGW2 by RNAi technology results in wider and heavier grains. Microscopic observation of grain morphology suggests that OsGW2 determines grain size by influencing both cell expansion and cell proliferation in spikelet hull. Using transcriptome analysis, upregulated genes related to grain size regulation have been identified among 1,426 differentially expressed genes in an OsGW2_RNAi transgenic line. These results reveal that OsGW2 is a negative regulator of grain size in indica rice and affects both cell number and cell size in spikelet hull.
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Affiliation(s)
- Ankit Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Geeta Prakash
- National Institute of Plant Genome Research, New Delhi, India.,Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Rajeev Ranjan
- National Institute of Plant Genome Research, New Delhi, India.,Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, New Delhi, India.,Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, India
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Liao X, Wang L, Zhu S, Zheng F, Yang C. Identification, genomic organization, and expression profiles of single C2H2 zinc finger transcription factors in tomato (Solanum lycopersicum). J Appl Genet 2020; 62:1-15. [PMID: 33034011 DOI: 10.1007/s13353-020-00587-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/20/2020] [Accepted: 09/09/2020] [Indexed: 01/22/2023]
Abstract
C2H2 zinc finger proteins (ZFPs) play essential roles in leaf morphogenesis and floral development, as well as heat stress response and trichome formation, which activate or inhibit gene transcription mainly through interactions with nucleic acids, such as single-strand DNA, RNA binding or RNA/DNA bidirectional binding, and protein interaction. Single C2H2 ZFPs is the subfamily of ZFPs, but little of single C2H2 ZFP family is known in tomato. In this study, we identified 30 single ZFP genes in tomato using bioinformatics-based methods. Gene structures, phylogeny, conserved motifs, cis-element of promoter, chromosomal localization, gene duplication, and expression patterns of these single C2H2 ZFP genes were analyzed. Sequence analysis showed that most single C2H2 ZFP genes possessed only one exon, except for SlC1-liZFP1 and SlC1-liZFP2. These single C2H2 ZFP genes were asymmetrically distributed on 10 chromosomes, excluding 2 and 12 chromosomes. In addition, 24 of these genes were predicated to have experienced segmental duplication. Cis-element prediction indicated that many important elements were located in the putative promoter regions, like light and gibberellic acid (GA)-responsive elements. The expression profiles of these genes in different tissues and various hormones and stress treatment were further analyzed. Many genes were lowly expressed in all tissues, whereas some were specifically expressed in certain tissues, like SlC1-liZFP2 in young leaves, and SlC1-liZFP15 in fruits. Furthermore, these genes could also be induced by several hormones and stresses, including IAA, ETH, GA, cold, and drought. This study sets a good foundation for further characterizing the biological roles of single C2H2 ZFP genes in tomato.
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Affiliation(s)
- Xiaoli Liao
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Wang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shunhua Zhu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangyan Zheng
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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