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Guo Q, Jiang J, Yao W, Li L, Zhao K, Cheng Z, Han L, Wei R, Zhou B, Jiang T. Genome-wide analysis of poplar HD-Zip family and over-expression of PsnHDZ63 confers salt tolerance in transgenic Populus simonii × P.nigra. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 311:111021. [PMID: 34482922 DOI: 10.1016/j.plantsci.2021.111021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
HD-Zip is a plant-specific HB transcription factor, which participates in plant development and stress response. In this study, we identified 63 poplar HD-Zip transcription factors, which were randomly distributed on 19 chromosomes of poplar. Based on the gene structure and phylogenetic relationship, these members are divided into four groups, which have a variety of collinear evolutionary relationships. They also have rich segmental replication events and experienced strong purification selection. Based on RNA-seq analysis, we profiled the expression pattern of the 63 HD-Zip members under salt stress. Subsequently, we carried out in-depth study on the significantly up-regulated PsnHDZ63 in the stems and leaves. The transgenic Populus simonii × P.nigra plants over-expressing PsnHDZ63 displayed better morphological and physiological indexes than WT under salt stress. In addition, PsnHDZ63 enhanced salt stress tolerance of transgenic lines by combining effective stress-resistant elements to improve reactive oxygen species scavenging ability. These studies laid a foundation for a comprehensive understanding of poplar HD-Zip family members, and revealed the important role of PsnHDZ63 in plant salt tolerance.
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Affiliation(s)
- Qing Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Jiahui Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Wenjing Yao
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Li Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Kai Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Zihan Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Lianbin Han
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Ran Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China.
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Mahtha SK, Purama RK, Yadav G. StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication. Front Genet 2021; 12:737194. [PMID: 34567086 PMCID: PMC8455945 DOI: 10.3389/fgene.2021.737194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/16/2021] [Indexed: 02/04/2023] Open
Abstract
The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.
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Affiliation(s)
- Sanjeet Kumar Mahtha
- Computational Biology Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Ravi Kiran Purama
- Computational Biology Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, New Delhi, India
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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Paul P, Dhatt BK, Sandhu J, Hussain W, Irvin L, Morota G, Staswick P, Walia H. Divergent phenotypic response of rice accessions to transient heat stress during early seed development. PLANT DIRECT 2020; 4:e00196. [PMID: 31956854 PMCID: PMC6955394 DOI: 10.1002/pld3.196] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/05/2019] [Accepted: 12/19/2019] [Indexed: 05/03/2023]
Abstract
Increasing global surface temperatures is posing a major food security challenge. Part of the solution to address this problem is to improve crop heat resilience, especially during grain development, along with agronomic decisions such as shift in planting time and increasing crop diversification. Rice is a major food crop consumed by more than 3 billion people. For rice, thermal sensitivity of reproductive development and grain filling is well-documented, while knowledge concerning the impact of heat stress (HS) on early seed development is limited. Here, we aim to study the phenotypic variation in a set of diverse rice accessions for elucidating the HS response during early seed development. To explore the variation in HS sensitivity, we investigated aus (1), indica (2), temperate japonica (2), and tropical japonica (4) accessions for their HS (39/35°C) response during early seed development that accounts for transition of endosperm from syncytial to cellularization, which broadly corresponds to 24 and 96 hr after fertilization (HAF), respectively, in rice. The two indica and one of the tropical japonica accessions exhibited severe heat sensitivity with increased seed abortion; three tropical japonicas and an aus accession showed moderate heat tolerance, while temperate japonicas exhibited strong heat tolerance. The accessions exhibiting extreme heat sensitivity maintain seed size at the expense of number of fully developed mature seeds, while the accessions showing relative resilience to the transient HS maintained number of fully developed seeds but compromised on seed size, especially seed length. Further, histochemical analysis revealed that all the tested accessions have delayed endosperm cellularization upon exposure to the transient HS by 96 HAF; however, the rate of cellularization was different among the accessions. These findings were further corroborated by upregulation of cellularization-associated marker genes in the developing seeds from the heat-stressed samples.
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Affiliation(s)
- Puneet Paul
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Balpreet K. Dhatt
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Jaspreet Sandhu
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Waseem Hussain
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- International Rice Research InstituteLos BanosPhilippines
| | - Larissa Irvin
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Gota Morota
- Department of Animal and Poultry SciencesVirginia Polytechnic Institute and State UniversityBlacksburgVAUSA
| | - Paul Staswick
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Harkamal Walia
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
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Kovalchuk N, Wu W, Bazanova N, Reid N, Singh R, Shirley N, Eini O, Johnson AAT, Langridge P, Hrmova M, Lopato S. Wheat wounding-responsive HD-Zip IV transcription factor GL7 is predominantly expressed in grain and activates genes encoding defensins. PLANT MOLECULAR BIOLOGY 2019; 101:41-61. [PMID: 31183604 DOI: 10.1007/s11103-019-00889-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Several classes of transcription factors are involved in the activation of defensins. A new type of the transcription factor responsible for the regulation of wheat grain specific defensins was characterised in this work. HD-Zip class IV transcription factors constitute a family of multidomain proteins. A full-length cDNA of HD-Zip IV, designated TaGL7 was isolated from the developing grain of bread wheat, using a specific DNA sequence as bait in the Y1H screen. 3D models of TaGL7 HD complexed with DNA cis-elements rationalised differences that underlined accommodations of binding and non-binding DNA, while the START-like domain model predicted binding of lipidic molecules inside a concave hydrophobic cavity. The 3'-untranslated region of TaGL7 was used as a probe to isolate the genomic clone of TdGL7 from a BAC library prepared from durum wheat. The spatial and temporal activity of the TdGL7 promoter was tested in transgenic wheat, barley and rice. TdGL7 was expressed mostly in ovary at fertilisation and its promoter was active in a liquid endosperm during cellularisation and later in the endosperm transfer cells, aleurone, and starchy endosperm. The pattern of TdGL7 expression resembled that of genes that encode grain-specific lipid transfer proteins, particularly defensins. In addition, GL7 expression was upregulated by mechanical wounding, similarly to defensin genes. Co-bombardment of cultured wheat cells with TdGL7 driven by constitutive promoter and seven grain or root specific defensin promoters fused to GUS gene, revealed activation of four promoters. The data confirmed the previously proposed role of HD-Zip IV transcription factors in the regulation of genes that encode lipid transfer proteins involved in lipid transport and defence. The TdGL7 promoter could be used to engineer cereal grains with enhanced resistance to insects and fungal infections.
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Affiliation(s)
- Nataliya Kovalchuk
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Wei Wu
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Agronomy College, Sichuan Agricultural University, Ya'an, 625014, China
| | - Natalia Bazanova
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Commonwealth Scientific and Industrial Research Organisation, Glen Osmond, 5064, SA, Australia
| | - Nicolas Reid
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Rohan Singh
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Neil Shirley
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Omid Eini
- Department of Plant Protection, School of Agriculture, University of Zanjan, Zanjan, Iran
| | | | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Maria Hrmova
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia.
- School of Life Sciences, Huaiyin Normal University, Huai'an, China.
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
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Cao XK, Cheng J, Huang YZ, Wang XG, Ma YL, Peng SJ, Chaogetu B, Zhuoma Z, Chen H. Growth Performance and Meat Quality Evaluations in Three-Way Cross Cattle Developed for the Tibetan Plateau and their Molecular Understanding by Integrative Omics Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:541-550. [PMID: 30596412 DOI: 10.1021/acs.jafc.8b05477] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Despite of favorable characteristics of high protein, low fat, and free-pollution, yak meat has intrinsically poor performance in tenderness and color, which is ever challenging yak sector. To this end, a three-way cross system was first developed for high quality beef of the Tibetan Plateau using Angus cattle ( Bos taurus) as terminal sire to mate with 1/2 yak (F1) generated from♂Qaidam cattle ( Bos taurus) × ♀yak ( Bos grunniens). The withers height, chest girth, and body weight of 1/4 yak (F2) were all great higher than that of yak and 1/2 yak ( P < 0.01), especially at later period, suggesting the faster growth rate of 1/4 yak. Also the dressing percentage was much better in 1/4 yak ( P < 0.01). Tenderness and meat color were both significantly improved in 1/4 yak with some unpleasant sacrifice of PUFAs, such as EPA and DHA, and meat protein, given the significantly lower shear force and higher L* ( P < 0.01). A total of 769 genes, including SREBF1, GHR, and FASN, the widely recognized causal genes of meat quality, were identified from 11947 differently expressed genes by the data integration of transcriptome, GWAS and QTL. These genes were significantly enriched for important pathway and GO terms, such as insulin signaling pathway, fatty acid biosynthesis, calcium signaling pathway, metabolic pathway, and cellular response to stress ( P < 0.01). And 12 promising candidates were exemplified with annotation of H3K4me3 data from divergent meat quality, such as OSTF1, NRAS1, and KCNJ11. Interestingly, 75 high-altitude adaptive candidate genes were also detected in the list. This study is a first step toward high quality beef of the Tibetan Plateau and provides useful information for their molecular understanding.
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Affiliation(s)
- Xiu-Kai Cao
- College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Jie Cheng
- College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Yong-Zhen Huang
- College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Xiao-Gang Wang
- College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Yu-Lin Ma
- Animal Disease Control Center of Haixi Mongolian and Tibetan Autonomous Prefecture , Delingha , Qinghai 817000 , China
| | - Shu-Jun Peng
- College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Buren Chaogetu
- Animal Disease Control Center of Haixi Mongolian and Tibetan Autonomous Prefecture , Delingha , Qinghai 817000 , China
| | - Zhaxi Zhuoma
- Animal Disease Control Center of Haixi Mongolian and Tibetan Autonomous Prefecture , Delingha , Qinghai 817000 , China
| | - Hong Chen
- College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
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Bang SW, Lee D, Jung H, Chung PJ, Kim YS, Choi YD, Suh J, Kim J. Overexpression of OsTF1L, a rice HD-Zip transcription factor, promotes lignin biosynthesis and stomatal closure that improves drought tolerance. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:118-131. [PMID: 29781573 PMCID: PMC6330637 DOI: 10.1111/pbi.12951] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/08/2018] [Accepted: 05/10/2018] [Indexed: 05/19/2023]
Abstract
Drought stress seriously impacts on plant development and productivity. Improvement of drought tolerance without yield penalty is a great challenge in crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper transcription factor gene, OsTF1L (Oryza sativa transcription factor 1-like), is a key regulator of drought tolerance mechanisms. Overexpression of the OsTF1L in rice significantly increased drought tolerance at the vegetative stages of growth and promoted both effective photosynthesis and a reduction in the water loss rate under drought conditions. Importantly, the OsTF1L overexpressing plants showed a higher drought tolerance at the reproductive stage of growth with a higher grain yield than nontransgenic controls under field-drought conditions. Genomewide analysis of OsTF1L overexpression plants revealed up-regulation of drought-inducible, stomatal movement and lignin biosynthetic genes. Overexpression of OsTF1L promoted accumulation of lignin in shoots, whereas the RNAi lines showed opposite patterns of lignin accumulation. OsTF1L is mainly expressed in outer cell layers including the epidermis, and the vasculature of the shoots, which coincides with areas of lignification. In addition, OsTF1L overexpression enhances stomatal closure under drought conditions resulted in drought tolerance. More importantly, OsTF1L directly bound to the promoters of lignin biosynthesis and drought-related genes involving poxN/PRX38, Nodulin protein, DHHC4, CASPL5B1 and AAA-type ATPase. Collectively, our results provide a new insight into the role of OsTF1L in enhancing drought tolerance through lignin biosynthesis and stomatal closure in rice.
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Affiliation(s)
- Seung Woon Bang
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
- Center for Nutraceutical and Pharmaceutical MaterialsDivision of BioinformaticsMyongji UniversityYongin, GyeonggiKorea
| | - Dong‐Keun Lee
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Harin Jung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
- Present address:
NUS Synthetic Biology for Clinical and Technological InnovationDepartment of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore117596Singapore
| | - Pil Joong Chung
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Youn Shic Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
| | - Yang Do Choi
- Department of Agricultural BiotechnologySeoul National UniversitySeoulKorea
| | - Joo‐Won Suh
- Center for Nutraceutical and Pharmaceutical MaterialsDivision of BioinformaticsMyongji UniversityYongin, GyeonggiKorea
| | - Ju‐Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangKorea
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Huang X, Peng X, Sun MX. OsGCD1 is essential for rice fertility and required for embryo dorsal-ventral pattern formation and endosperm development. THE NEW PHYTOLOGIST 2017; 215:1039-1058. [PMID: 28585692 DOI: 10.1111/nph.14625] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/25/2017] [Indexed: 05/20/2023]
Abstract
Rice fertility is critical for rice reproduction and is thus a focus of interest. Most studies have addressed male sterility and its relation to rice production. The mechanisms of regulation of embryogenesis and endosperm development are essential for rice reproduction, but remain largely unknown. Here, we report a functional analysis of the rice gene OsGCD1, which encodes a highly conserved homolog of Arabidopsis GCD1 (GAMETE CELLS DEFECTIVE1). OsGCD1 mutants were generated using the CRISPR/Cas9 system and subjected to functional analysis. The homozygote mutants cannot be obtained, whereas heterozygotes showed altered phenotypes. In the majority of aborted seeds, the endosperm nucleus divided a limited number of times. The free nuclei were distributed only at the micropylar end of embryo sacs, and their oriented positioning was blocked. In addition, aleurone differentiation was interrupted. The embryo developed slowly, and pattern formation, particularly the dorsal-ventral pattern and symmetry establishment, of embryos was disturbed. Thus, the embryos showed various morphological and structural dysplasias. Our findings reveal that OsGCD1 is essential for rice fertility and is required for dorsal-ventral pattern formation and endosperm free nucleus positioning, suggesting a critical role in sexual reproduction of both monocotyledon and dicotyledon plants.
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Affiliation(s)
- Xiaorong Huang
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, 430072, China
| | - Xiongbo Peng
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, 430072, China
| | - Meng-Xiang Sun
- College of Life Science, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, 430072, China
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Wei J, Choi H, Jin P, Wu Y, Yoon J, Lee YS, Quan T, An G. GL2-type homeobox gene Roc4 in rice promotes flowering time preferentially under long days by repressing Ghd7. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:133-143. [PMID: 27717449 DOI: 10.1016/j.plantsci.2016.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
Under long day (LD) lengths, flowering can be delayed in rice by modulating several regulatory genes. We found activation tagging lines that showed an early flowering phenotype preferentially under LD conditions. Expression of Rice outermost cell-specific gene 4 (Roc4), encoding a homeodomain Leu-zipper class IV family protein, was significantly increased. Transcript levels of Grain number, plant height, and heading date7 (Ghd7) were significantly reduced while those of Ghd7 downstream genes were increased. However, other flowering regulators were unaffected. Whereas constitutive overexpression of Roc4 in 'Dongjin' japonica rice, which carries active Ghd7, also caused LD-preferential early flowering, its overexpression in 'Longjing27' rice, which is defective in functional Ghd7, did not produce the same result. This confirmed that Roc4 regulates flowering time mainly through Ghd7. Phytochromes and O. sativa GIGANTEA (OsGI) function upstream of Roc4. Transgenic plants showed ubiquitous expression of the β-glucuronidase reporter gene under the Roc4 promoter. Furthermore, Roc4 had transcriptional activation activity in the N-terminal region of the StAR-related lipid-transfer domain. All of these findings are evidence that Roc4 is an LD-preferential flowering enhancer that functions downstream of phytochromes and OsGI, but upstream of Ghd7.
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Affiliation(s)
- Jinhuan Wei
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Heebak Choi
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea; Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Ping Jin
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Yunfei Wu
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Jinmi Yoon
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Yang-Seok Lee
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Taiyong Quan
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, College of Life Science, Shandong University, Jinan 250100, People's Republic of China
| | - Gynheung An
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea.
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Zhang H, Wang L, Zheng S, Liu Z, Wu X, Gao Z, Cao C, Li Q, Ren Z. A fragment substitution in the promoter of CsHDZIV11/CsGL3 is responsible for fruit spine density in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1289-1301. [PMID: 27015676 DOI: 10.1007/s00122-016-2703-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/05/2016] [Indexed: 05/25/2023]
Abstract
The indel in the promoter of CsHDZIV11 co-segregates with fruit spine density and could be used for molecular breeding in cucumber. Fruit spine density is an important quality trait for marketing in cucumber (Cucumis sativus L.). However, the molecular basis of fruit spine density in cucumber remains unclear. In this study, we isolated a mutant, few spines 1 (fs1), from CNS2 (wild type, WT), a North China-type cucumber with a high density of fruit spines. Genetic analysis showed that fs1 was controlled by a single recessive Mendelian factor. Bulked segregant analysis combined with genome resequencing were used for mapping fs1 in the F2 population derived from a cross between the fs1 mutant and WT, and it was located on chromosome 6 through association analysis. To develop more polymorphic markers to locate fs1, another F2 population was constructed from the cross between fs1 and 'Chinese long' 9930. Then, fs1 was narrowed down to a 110.4-kb genomic region containing 25 annotated genes. A fragment substitution was identified in the promoter region of Csa6M514870 between fs1 and WT. This fragment in fs1 was also present in wild cucumber. Csa6M514870 encodes a PDF2-related protein, a homeodomain-leucine zipper IV transcription factor (CsHDZIV11/CsGL3) sharing high identity and similarity with proteins related to trichome formation or epidermal cell differentiation. Quantitative reverse-transcription PCR revealed a higher expression level of CsHDZIV11 in young fruits from fs1 compared to WT. A molecular marker based on this indel co-segregated with the spine density. This work provides a solid foundation not only for understanding the molecular mechanism of fruit spine density, but also for molecular breeding in cucumber.
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Affiliation(s)
- Haiyang Zhang
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Lina Wang
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Shuangshuang Zheng
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Zezhou Liu
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Xiaoqin Wu
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Zhihui Gao
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Chenxing Cao
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Qiang Li
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Zhonghai Ren
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
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Khosla A, Paper JM, Boehler AP, Bradley AM, Neumann TR, Schrick K. HD-Zip Proteins GL2 and HDG11 Have Redundant Functions in Arabidopsis Trichomes, and GL2 Activates a Positive Feedback Loop via MYB23. THE PLANT CELL 2014; 26:2184-2200. [PMID: 24824485 PMCID: PMC4079377 DOI: 10.1105/tpc.113.120360] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 04/18/2014] [Accepted: 04/28/2014] [Indexed: 05/20/2023]
Abstract
The class IV homeodomain leucine zipper transcription factor GLABRA2 (GL2) acts in a complex regulatory circuit that regulates the differentiation of trichomes in Arabidopsis thaliana. We describe a genetic interaction with HOMEODOMAIN GLABROUS11 (HDG11), previously identified as a negative regulator of trichome branching. gl2 hdg11 double mutants display enhanced trichome cell-type differentiation defects. Transgenic expression of HDG11 using the GL2 promoter partially suppresses gl2 trichome phenotypes. Vice versa, expression of GL2 under the control of its native promoter partially complements hdg11 ectopic branching. Since gl2 hdg11 and gl2 myb23 double mutants and the triple mutant display similar trichome differentiation defects, we investigated a connection to the R2R3-MYB transcription factor MYB23. We show that MYB23 transcript levels are significantly reduced in shoots from gl2 mutants and that GL2 can drive the expression of a MYB23-promoter fusion to green fluorescent protein. Yeast one-hybrid, chromatin immunoprecipitation, and in planta reporter gene experiments indicate that an L1-box in the MYB23 promoter acts as a GL2 binding site. Taken together, our findings reveal a functional redundancy between GL2 and HDG11, two homeodomain leucine zipper transcription factors previously thought to mediate opposing functions in trichome morphogenesis. A model is proposed in which GL2 transcript levels are maintained through a positive feedback loop involving GL2 activation of MYB23.
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Affiliation(s)
- Aashima Khosla
- Division of Biology, Kansas State University, Manhattan, Kansas 66506-4901 Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506-3702
| | - Janet M Paper
- Division of Biology, Kansas State University, Manhattan, Kansas 66506-4901
| | - Allison P Boehler
- Division of Biology, Kansas State University, Manhattan, Kansas 66506-4901
| | - Amanda M Bradley
- Division of Biology, Kansas State University, Manhattan, Kansas 66506-4901
| | - Titus R Neumann
- Division of Biology, Kansas State University, Manhattan, Kansas 66506-4901
| | - Kathrin Schrick
- Division of Biology, Kansas State University, Manhattan, Kansas 66506-4901 Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506-3702 Molecular, Cellular, and Developmental Biology, Kansas State University, Manhattan, Kansas 66506-4901
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Lopato S, Borisjuk N, Langridge P, Hrmova M. Endosperm transfer cell-specific genes and proteins: structure, function and applications in biotechnology. FRONTIERS IN PLANT SCIENCE 2014; 5:64. [PMID: 24578704 PMCID: PMC3936200 DOI: 10.3389/fpls.2014.00064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/07/2014] [Indexed: 05/21/2023]
Abstract
Endosperm transfer cells (ETC) are one of four main types of cells in endosperm. A characteristic feature of ETC is the presence of cell wall in-growths that create an enlarged plasma membrane surface area. This specialized cell structure is important for the specific function of ETC, which is to transfer nutrients from maternal vascular tissue to endosperm. ETC-specific genes are of particular interest to plant biotechnologists, who use genetic engineering to improve grain quality and yield characteristics of important field crops. The success of molecular biology-based approaches to manipulating ETC function is dependent on a thorough understanding of the functions of ETC-specific genes and ETC-specific promoters. The aim of this review is to summarize the existing data on structure and function of ETC-specific genes and their products. Potential applications of ETC-specific genes, and in particular their promoters for biotechnology will be discussed.
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Affiliation(s)
- Sergiy Lopato
- *Correspondence: Sergiy Lopato, Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia e-mail:
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12
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Chew W, Hrmova M, Lopato S. Role of Homeodomain leucine zipper (HD-Zip) IV transcription factors in plant development and plant protection from deleterious environmental factors. Int J Mol Sci 2013; 14:8122-47. [PMID: 23584027 PMCID: PMC3645734 DOI: 10.3390/ijms14048122] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/26/2013] [Accepted: 04/03/2013] [Indexed: 01/11/2023] Open
Abstract
Homeobox genes comprise an important group of genes that are responsible for regulation of developmental processes. These genes determine cell differentiation and cell fate in all eukaryotic organisms, starting from the early stages of embryo development. Homeodomain leucine zipper (HD-Zip) transcription factors are unique to the plant kingdom. Members of the HD-Zip IV subfamily have a complex domain topology and can bind several cis-elements with overlapping sequences. Many of the reported HD-Zip IV genes were shown to be specifically or preferentially expressed in plant epidermal or sub-epidermal cells. HD-Zip IV TFs were found to be associated with differentiation and maintenance of outer cell layers, and regulation of lipid biosynthesis and transport. Insights about the role of these proteins in plant cuticle formation, and hence their possible involvement in plant protection from pathogens and abiotic stresses has just started to emerge. These roles make HD-Zip IV proteins an attractive tool for genetic engineering of crop plants. To this end, there is a need for in-depth studies to further clarify the function of each HD-Zip IV subfamily member in commercially important plant species.
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Affiliation(s)
- William Chew
- Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia.
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Lau S, Slane D, Herud O, Kong J, Jürgens G. Early embryogenesis in flowering plants: setting up the basic body pattern. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:483-506. [PMID: 22224452 DOI: 10.1146/annurev-arplant-042811-105507] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Early embryogenesis is the critical developmental phase during which the basic features of the plant body are established: the apical-basal axis of polarity, different tissue layers, and both the root pole and the shoot pole. Polarization of the zygote correlates with the generation of apical and basal (embryonic and extraembryonic) cell fates. Whereas mechanisms of zygote polarization are still largely unknown, distinct expression domains of WOX family transcription factors as well as directional auxin transport and local auxin response are known to be involved in early apical-basal patterning. Radial patterning of tissue layers appears to be mediated by cell-cell communication involving both peptide signaling and transcription factor movement. Although the initiation of the shoot pole is still unclear, the apical organization of the embryo depends on both the proper establishment of transcription factor expression domains and, for cotyledon initiation, upward auxin flow in the protoderm. Here we focus on the essential patterning processes, drawing mainly on data from Arabidopsis thaliana and also including relevant data from other species if available.
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Affiliation(s)
- Steffen Lau
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Kovalchuk N, Wu W, Eini O, Bazanova N, Pallotta M, Shirley N, Singh R, Ismagul A, Eliby S, Johnson A, Langridge P, Lopato S. The scutellar vascular bundle-specific promoter of the wheat HD-Zip IV transcription factor shows similar spatial and temporal activity in transgenic wheat, barley and rice. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:43-53. [PMID: 21689369 DOI: 10.1111/j.1467-7652.2011.00633.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
An HD-Zip IV gene from wheat, TaGL9, was isolated using a Y1H screen of a cDNA library prepared from developing wheat grain. TaGL9 has an amino acid sequence distinct from other reported members of the HD-Zip IV family. The 3' untranslated region of TaGL9 was used as a probe to isolate a genomic clone of the TaGL9 homologue from a BAC library prepared from Triticum durum L. cv. Langdon. The full-length gene containing a 3-kb-long promoter region was designated TdGL9H1. Spatial and temporal activity of TdGL9H1 was examined using promoter-GUS fusion constructs in transgenic wheat, barley and rice plants. Whole-mount and histochemical GUS staining patterns revealed grain-specific expression of TdGL9H1. GUS expression was initially observed between 3 and 8 days after pollination (DAP) in embryos at the globular stage and adjacent to the embryo fraction of the endosperm. Expression was strongest in the outer cell layer of the embryo. In developed wheat and barley embryos, strong activity of the promoter was only detected in the main vascular bundle of the scutellum, which is known to be responsible for the uptake of nutrients from the endosperm during germination and the endosperm-dependent phase of seedling development. Furthermore, this pattern of GUS staining was observed in dry seeds several weeks after harvesting but quickly disappeared during imbibition. The promoter of this gene could be a useful tool for engineering of early seedling vigour and protecting the endosperm to embryo axis pathway from pathogens during grain desiccation and storage.
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Affiliation(s)
- Nataliya Kovalchuk
- Australian Centre for Plant Functional Genomics, University of Adelaide, Hartley Grove, Urrbrae, South Australia, Australia
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Sakuma S, Salomon B, Komatsuda T. The domestication syndrome genes responsible for the major changes in plant form in the Triticeae crops. PLANT & CELL PHYSIOLOGY 2011; 52:738-49. [PMID: 21389058 PMCID: PMC3093126 DOI: 10.1093/pcp/pcr025] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The process of crop domestication began 10,000 years ago in the transition of early humans from hunter/gatherers to pastoralists/farmers. Recent research has revealed the identity of some of the main genes responsible for domestication. Two of the major domestication events in barley were (i) the failure of the spike to disarticulate and (ii) the six-rowed spike. The former mutation increased grain yield by preventing grain loss after maturity, while the latter resulted in an up to 3-fold increase in yield potential. Here we provide an overview of the disarticulation systems and inflorescence characteristics, along with the genes underlying these traits, occurring in the Triticeae tribe.
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Affiliation(s)
- Shun Sakuma
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, 2-1-2 Kan-non-dai, Tsukuba, Ibaraki, 305-8602 Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510 Japan
| | - Björn Salomon
- Swedish University of Agricultural Sciences, Department of Plant Breeding and Biotechnology, PO Box 101, SE-23053 Alnarp, Sweden
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, 2-1-2 Kan-non-dai, Tsukuba, Ibaraki, 305-8602 Japan
- *Corresponding author: E-mail, ; Fax, +81-29-838-7408
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Agarwal P, Kapoor S, Tyagi AK. Transcription factors regulating the progression of monocot and dicot seed development. Bioessays 2011; 33:189-202. [PMID: 21319185 DOI: 10.1002/bies.201000107] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Seed development in this paper has been classified into the three landmark stages of cell division, organ initiation and maturation, based on morphological changes, and the available literature. The entire process proceeds at the behest of an interplay of various specific and general transcription factors (TFs). Monocots and dicots utilize overlapping, as well as distinct, TF networks during the process of seed development. The known TFs in rice and Arabidopsis have been chronologically categorized into the three stages. The main regulators of seed development contain B3 or HAP3 domains. These interact with bZIP and AP2 TFs. Other TFs that play an indispensable role during the process contain homeobox-, NAC-, MYB-, or ARF-domains. This paper is a comprehensive analysis of the TFs essential for seed development and their interactions. An understanding of this interplay will not only help unravel an integrated developmental process, but will also pave the way for biotechnological applications.
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Affiliation(s)
- Pinky Agarwal
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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17
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Chai G, Bai Z, Wei F, King GJ, Wang C, Shi L, Dong C, Chen H, Liu S. Brassica GLABRA2 genes: analysis of function related to seed oil content and development of functional markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:1597-1610. [PMID: 20162256 DOI: 10.1007/s00122-010-1279-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 01/19/2010] [Indexed: 05/28/2023]
Abstract
Regulation of seed oil accumulation in oilseed rape (Brassica napus) has important economic significance. However, few genes have been characterized that affect final seed oil content. Through a mutant identification, the class IV homeodomain-ZIP transcription factor GLABRA2 (GL2) has been found to regulate seed oil accumulation in Arabidopsis, in addition to its role in trichome development. In this study, we isolated four distinct orthologues of GL2 from B. napus (AC-genome), B. rapa (A) and B. oleracea (C), using an overlapping-PCR strategy. The four GL2 orthologues were very similar, with 96.10-99.69% identity in exon regions, 75.45-93.84% in intron regions, 97.34-99.87% in amino acid sequences. Alignments of the four genes revealed that the A-genome sequences of BnaA.GL2.a from B. napus and BraA.GL2.a from B. rapa are more similar than the others, and likewise the C-genome sequences of BnaC.GL2.b from B. napus and BolC.GL2.a from B. oleracea are more similar. BnaA.GL2.a and BraA.GL2.a from the A-genome are highly expressed in roots, whilst BnaC.GL2.b and BolC.GL2.a from the C-genome are preferentially expressed in seeds. Transgenic ectopic overexpression and suppression of BnaC.GL2.b in Arabidopsis allowed further investigation of the effect on seed oil content. Overexpression generated two phenotypes: the wild-type-like and the gl2-mutant-like (an Arabidopsis glabrous mutant of gl2-2), with increases in seed oil content of 3.5-5.0% in the gl2-mutant-like transgenic plants. Suppression resulted in increases of 2.5-6.1% in seed oil content, and reduced trichome number at the leaf margins. These results suggest that BnaC.GL2.b can negatively regulate oil accumulation in Arabidopsis seeds. As a result of comparing the four GL2 genes, three A/C-genome-specific primer sets were developed and a C-genome-specific EcoRV cleavage site was identified, which can be used as functional markers to distinguish these orthologues within Brassica species. The genes identified and their molecular markers developed in this study will be valuable both for oilseed rape breeding focusing on improvement of seed oil content, and for detecting gene flow between populations.
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Affiliation(s)
- Guohua Chai
- The Key Lab of Oil Crops Biology, The Ministry of Agriculture of the People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan, 430062, Hubei, People's Republic of China
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18
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Agalou A, Purwantomo S, Overnäs E, Johannesson H, Zhu X, Estiati A, de Kam RJ, Engström P, Slamet-Loedin IH, Zhu Z, Wang M, Xiong L, Meijer AH, Ouwerkerk PBF. A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. PLANT MOLECULAR BIOLOGY 2008; 66:87-103. [PMID: 17999151 DOI: 10.1007/s11103-007-9255-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2007] [Accepted: 10/25/2007] [Indexed: 05/20/2023]
Abstract
The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.
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Affiliation(s)
- Adamantia Agalou
- Institute of Biology, Clusius Laboratory, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
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Nakamura M, Katsumata H, Abe M, Yabe N, Komeda Y, Yamamoto KT, Takahashi T. Characterization of the class IV homeodomain-Leucine Zipper gene family in Arabidopsis. PLANT PHYSIOLOGY 2006; 141:1363-75. [PMID: 16778018 PMCID: PMC1533922 DOI: 10.1104/pp.106.077388] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) genome contains 16 genes belonging to the class IV homeodomain-Leucine zipper gene family. These include GLABRA2, ANTHOCYANINLESS2, FWA, ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1), and PROTODERMAL FACTOR2 (PDF2). Our previous study revealed that atml1 pdf2 double mutants have severe defects in the shoot epidermal cell differentiation. Here, we have characterized additional members of this gene family, which we designated HOMEODOMAIN GLABROUS1 (HDG1) through HDG12. Analyses of transgenic Arabidopsis plants carrying the gene-specific promoter fused to the bacterial beta-glucuronidase reporter gene revealed that some of the promoters have high activities in the epidermal layer of the shoot apical meristem and developing shoot organs, while others are temporarily active during reproductive organ development. Expression profiles of highly conserved paralogous gene pairs within the family were found to be not necessarily overlapping. Analyses of T-DNA insertion mutants of these HDG genes revealed that all mutants except hdg11 alleles exhibit no abnormal phenotypes. hdg11 mutants show excess branching of the trichome. This phenotype is enhanced in hdg11 hdg12 double mutants. Double mutants were constructed for other paralogous gene pairs and genes within the same subfamily. However, novel phenotypes were observed only for hdg3 atml1 and hdg3 pdf2 mutants that both exhibited defects in cotyledon development. These observations suggest that some of the class IV homeodomain-Leucine zipper members act redundantly with other members of the family during various aspects of cell differentiation. DNA-binding sites were determined for two of the family members using polymerase chain reaction-assisted DNA selection from random oligonucleotides with their recombinant proteins. The binding sites were found to be similar to those previously identified for ATML1 and PDF2, which correspond to the pseudopalindromic sequence 5'-GCATTAAATGC-3' as the preferential binding site.
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Affiliation(s)
- Miyuki Nakamura
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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Ageez A, Matsunaga S, Uchida W, Sugiyama R, Kazama Y, Kawano S. Isolation and characterization of two homeodomain leucine zipper genes from the dioecious plant Silene latifolia. Genes Genet Syst 2004; 78:353-61. [PMID: 14676426 DOI: 10.1266/ggs.78.353] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Homeodomain leucine zipper (HD-Zip) genes encode transcription factors that are characterized by both a homeodomain and a leucine zipper motif. Two HD-Zip genes were isolated from cDNA of the male flower bud of the dioecious plant Silene latifolia. The two isolated genes, SlHDL1 and SlHDL2, encode proteins with the characteristics of HD-Zip transcription factors belonging to HD-Zip classes I and II, respectively. The expression patterns of SlHDL1 and SlHDL2 throughout the floral developmental stages were studied using real-time PCR and in situ hybridization. SlHDL1 is specifically expressed in the outermost layer of the anthers and gynoeciums with a patchy pattern in the inner layers, suggesting that the product of SlHDL1 plays a role in the early developmental stage of the epidermal tissues of these floral organs. Its expression pattern in the anthers and gynoeciums suggests an involvement in differentiation of the reproductive organs. On the other hand, real-time PCR revealed accumulation of SlHDL2 transcripts in the anther and pollen grains of the male flower. These results suggest that SlHDL1 and SlHDL2 regulate specific targets in restricted regions leading to floral organ differentiation in S. latifolia.
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Affiliation(s)
- Amr Ageez
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.
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21
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Ingram GC. Between the sheets: inter-cell-layer communication in plant development. Philos Trans R Soc Lond B Biol Sci 2004; 359:891-906. [PMID: 15306405 PMCID: PMC1693377 DOI: 10.1098/rstb.2003.1356] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The cells of plant meristems and embryos are arranged in an organized, and sometimes extremely beautiful, layered pattern. This pattern is maintained by the controlled orientation of cell divisions within layers. However, despite this layered structure, cell behaviour during plant development is not lineage dependent, and does not occur in a mosaic fashion. Many studies, both classical and recent, have shown that plant cell identity can be re-specified according to position, allowing plants to show remarkable developmental plasticity. However, the layered structure of meristems and the implications of this during plant development, remain subjects of some speculation. Of particular interest is the question of how cell layers communicate, and how communication between cell layers could allow coordinated developmental processes to take place. Recent research has uncovered several examples both of the molecular mechanisms by which cell layers can communicate, and of how this communication can infringe on developmental processes. A range of examples is used to illustrate the diversity of mechanisms potentially implicated in cell-layer communication during plant development.
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Affiliation(s)
- Gwyneth C Ingram
- Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, Scotland, UK.
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Schrick K, Nguyen D, Karlowski WM, Mayer KFX. START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors. Genome Biol 2004; 5:R41. [PMID: 15186492 PMCID: PMC463074 DOI: 10.1186/gb-2004-5-6-r41] [Citation(s) in RCA: 196] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Revised: 04/08/2004] [Accepted: 04/30/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In animals, steroid hormones regulate gene expression by binding to nuclear receptors. Plants lack genes for nuclear receptors, yet genetic evidence from Arabidopsis suggests developmental roles for lipids/sterols analogous to those in animals. In contrast to nuclear receptors, the lipid/sterol-binding StAR-related lipid transfer (START) protein domains are conserved, making them candidates for involvement in both animal and plant lipid/sterol signal transduction. RESULTS We surveyed putative START domains from the genomes of Arabidopsis, rice, animals, protists and bacteria. START domains are more common in plants than in animals and in plants are primarily found within homeodomain (HD) transcription factors. The largest subfamily of HD-START proteins is characterized by an HD amino-terminal to a plant-specific leucine zipper with an internal loop, whereas in a smaller subfamily the HD precedes a classic leucine zipper. The START domains in plant HD-START proteins are not closely related to those of animals, implying collateral evolution to accommodate organism-specific lipids/sterols. Using crystal structures of mammalian START proteins, we show structural conservation of the mammalian phosphatidylcholine transfer protein (PCTP) START domain in plants, consistent with a common role in lipid transport and metabolism. We also describe putative START-domain proteins from bacteria and unicellular protists. CONCLUSIONS The majority of START domains in plants belong to a novel class of putative lipid/sterol-binding transcription factors, the HD-START family, which is conserved across the plant kingdom. HD-START proteins are confined to plants, suggesting a mechanism by which lipid/sterol ligands can directly modulate transcription in plants.
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Affiliation(s)
- Kathrin Schrick
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA.
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Abe M, Katsumata H, Komeda Y, Takahashi T. Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis. Development 2003; 130:635-43. [PMID: 12505995 DOI: 10.1242/dev.00292] [Citation(s) in RCA: 251] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In higher plants, the outermost cell layer (L1) of the shoot apex gives rise to the epidermis of shoot organs. Our previous study demonstrated that an 8-bp motif named the L1 box functions as a cis-regulatory element for L1-specific gene expression in the shoot system of Arabidopsis: We show here that PROTODERMAL FACTOR2 (PDF2), a member of the HD-GL2 class of homeobox genes, is expressed exclusively in the L1 of shoot meristems and that recombinant PDF2 protein specifically binds to the L1 box in vitro. Although knockout mutants of PDF2 and ATML1, another L1-specific HD-GL2 class gene sharing the highest homology with PDF2, display normal shoot development, the double mutant results in severe defects in shoot epidermal cell differentiation. This suggests that PDF2 and ATML1 are functionally interchangeable and play a critical role in maintaining the identity of L1 cells, possibly by interacting with their L1 box and those of downstream target-gene promoters.
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Affiliation(s)
- Mitsutomo Abe
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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