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Brenner WG, Leuendorf JE, Cortleven A, Martin LBB, Schaller H, Schmülling T. Analysis of CFB, a cytokinin-responsive gene of Arabidopsis thaliana encoding a novel F-box protein regulating sterol biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2769-2785. [PMID: 28505379 PMCID: PMC5853388 DOI: 10.1093/jxb/erx146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 04/06/2017] [Indexed: 05/29/2023]
Abstract
Protein degradation by the ubiquitin-26S proteasome pathway is important for the regulation of cellular processes, but the function of most F-box proteins relevant to substrate recognition is unknown. We describe the analysis of the gene Cytokinin-induced F-box encoding (CFB, AT3G44326), identified in a meta-analysis of cytokinin-related transcriptome studies as one of the most robust cytokinin response genes. F-box domain-dependent interaction with the E3 ubiquitin ligase complex component ASK1 classifies CFB as a functional F-box protein. Apart from F-box and transmembrane domains, CFB contains no known functional domains. CFB is expressed in all plant tissues, predominantly in root tissue. A ProCFB:GFP-GUS fusion gene showed strongest expression in the lateral root cap and during lateral root formation. CFB-GFP fusion proteins were mainly localized in the nucleus and the cytosol but also at the plasma membrane. cfb mutants had no discernible phenotype, but CFB overexpressing plants showed several defects, such as a white upper inflorescence stem, similar to the hypomorphic cycloartenol synthase mutant cas1-1. Both CFB overexpressing plants and cas1-1 mutants accumulated the CAS1 substrate 2,3-oxidosqualene in the white stem tissue, the latter even more after cytokinin treatment, indicating impairment of CAS1 function. This suggests that CFB may link cytokinin and the sterol biosynthesis pathway.
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Affiliation(s)
- Wolfram G Brenner
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg, Berlin, Germany
| | - Jan Erik Leuendorf
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg, Berlin, Germany
| | - Anne Cortleven
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg, Berlin, Germany
| | - Laetitia B B Martin
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, rue du Général Zimmer, Strasbourg Cedex, France
| | - Hubert Schaller
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, rue du Général Zimmer, Strasbourg Cedex, France
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg, Berlin, Germany
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Reyes-Olalde JI, Zúñiga-Mayo VM, Serwatowska J, Chavez Montes RA, Lozano-Sotomayor P, Herrera-Ubaldo H, Gonzalez-Aguilera KL, Ballester P, Ripoll JJ, Ezquer I, Paolo D, Heyl A, Colombo L, Yanofsky MF, Ferrandiz C, Marsch-Martínez N, de Folter S. The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium. PLoS Genet 2017; 13:e1006726. [PMID: 28388635 PMCID: PMC5400277 DOI: 10.1371/journal.pgen.1006726] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 04/21/2017] [Accepted: 03/30/2017] [Indexed: 11/18/2022] Open
Abstract
Fruits and seeds are the major food source on earth. Both derive from the gynoecium and, therefore, it is crucial to understand the mechanisms that guide the development of this organ of angiosperm species. In Arabidopsis, the gynoecium is composed of two congenitally fused carpels, where two domains: medial and lateral, can be distinguished. The medial domain includes the carpel margin meristem (CMM) that is key for the production of the internal tissues involved in fertilization, such as septum, ovules, and transmitting tract. Interestingly, the medial domain shows a high cytokinin signaling output, in contrast to the lateral domain, where it is hardly detected. While it is known that cytokinin provides meristematic properties, understanding on the mechanisms that underlie the cytokinin signaling pattern in the young gynoecium is lacking. Moreover, in other tissues, the cytokinin pathway is often connected to the auxin pathway, but we also lack knowledge about these connections in the young gynoecium. Our results reveal that cytokinin signaling, that can provide meristematic properties required for CMM activity and growth, is enabled by the transcription factor SPATULA (SPT) in the medial domain. Meanwhile, cytokinin signaling is confined to the medial domain by the cytokinin response repressor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFERASE 6 (AHP6), and perhaps by ARR16 (a type-A ARR) as well, both present in the lateral domains (presumptive valves) of the developing gynoecia. Moreover, SPT and cytokinin, probably together, promote the expression of the auxin biosynthetic gene TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1) and the gene encoding the auxin efflux transporter PIN-FORMED 3 (PIN3), likely creating auxin drainage important for gynoecium growth. This study provides novel insights in the spatiotemporal determination of the cytokinin signaling pattern and its connection to the auxin pathway in the young gynoecium.
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Affiliation(s)
- J. Irepan Reyes-Olalde
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Víctor M. Zúñiga-Mayo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Joanna Serwatowska
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Ricardo A. Chavez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Paulina Lozano-Sotomayor
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Karla L. Gonzalez-Aguilera
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, Spain
| | - Juan José Ripoll
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Dario Paolo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Alexander Heyl
- Biology Department, Adelphi University, Garden City, New York, United States of America
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Martin F. Yanofsky
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Cristina Ferrandiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, Spain
| | | | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
- * E-mail:
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Zeng J, Zhu X, Haider MS, Wang X, Zhang C, Wang C. Genome-Wide Identification and Analysis of the Type-B Authentic Response Regulator Gene Family in Peach (Prunus persica). Cytogenet Genome Res 2017; 151:41-49. [PMID: 28351057 DOI: 10.1159/000458170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2016] [Indexed: 12/15/2022] Open
Abstract
The type-B authentic response regulator (ARR-B) family members serve as DNA-binding transcriptional regulators, whose activities are probably regulated by phosphorylation/dephosphorylation, resulting in the rapid induction of type-A ARR genes. Type-B ARRs are believed to be involved in many biological processes, including cytokinin signaling, plant growth, and stress responses through a chaperone or by isomerization of proline residues during protein folding. The public availability of complete peach genome sequences allows the identification of 23 ARR-B genes by HMMER and blast analysis. Scaffold locations of these genes in the peach genome were determined, and the protein domain and motif organization of peach type-B ARRs were analyzed. The phylogenetic relationships between peach type-B ARRs were also assessed. The expression profiles of peach ARR-B genes revealed that most of the type-B ARRs showed high expression levels in tissues undergoing rapid cell division and may engage more cytokinins, like half-opened flowers, fruits at expansion stages, and young leaves. These findings not only contribute to a better understanding of the complex regulation of the peach ARR-B gene family, but also provide valuable information for future research in peach functional genomics.
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Affiliation(s)
- Jingjue Zeng
- College of Horticulture, Nanjing Agricultural University, Nanjing, PR China
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Raines T, Blakley IC, Tsai YC, Worthen JM, Franco-Zorrilla JM, Solano R, Schaller GE, Loraine AE, Kieber JJ. Characterization of the cytokinin-responsive transcriptome in rice. BMC PLANT BIOLOGY 2016; 16:260. [PMID: 27931185 PMCID: PMC5146874 DOI: 10.1186/s12870-016-0932-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 10/25/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant Arabidopsis thaliana. To expand the understanding of the cytokinin-regulated transcriptome, we employed RNA-Seq to analyze gene expression in response to cytokinin in roots and shoots of the monocotyledonous plant rice. RESULTS We identified over 4,600 and approximately 2,400 genes differentially expressed in response to cytokinin in roots and shoots respectively. There were some similarities in the sets of cytokinin-regulated genes identified in rice and Arabidopsis, including an up-regulation of genes that act to reduce cytokinin function. Consistent with this, we found that the preferred DNA-binding motif of a rice type-B response regulator is similar to those from Arabidopsis. Analysis of the genes regulated by cytokinin in rice revealed a large number of transcription factors, receptor-like kinases, and genes involved in protein degradation, as well as genes involved in development and the response to biotic stress. Consistent with the over-representation of genes involved in biotic stress, there is a substantial overlap in the genes regulated by cytokinin and those differentially expressed in response to pathogen infection, suggesting that cytokinin plays an integral role in the transcriptional response to pathogens in rice, including the induction of a large number of WRKY transcription factors. CONCLUSIONS These results begin to unravel the complex gene regulation after cytokinin perception in a crop of agricultural importance and provide insight into the processes and responses modulated by cytokinin in monocots.
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Affiliation(s)
- Tracy Raines
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280 USA
- Present address: AgBiome, Inc., 104 TW Alexander Drive, Bldg 18, Research Triangle Park, NC 27713 USA
| | - Ivory C. Blakley
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081 USA
| | - Yu-Chang Tsai
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280 USA
- Present address: Department of Agronomy, National Taiwan University, Taipei, 10617 Taiwan
| | | | - José Manuel Franco-Zorrilla
- Genomics Unit, Centro Nacional de Biotecnología (CNB)-Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB)-Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain
| | - G. Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
| | - Ann E. Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, Kannapolis, NC 28081 USA
| | - Joseph J. Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280 USA
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Functional roles of Arabidopsis CKRC2/YUCCA8 gene and the involvement of PIF4 in the regulation of auxin biosynthesis by cytokinin. Sci Rep 2016; 6:36866. [PMID: 27827441 PMCID: PMC5101810 DOI: 10.1038/srep36866] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 10/21/2016] [Indexed: 11/09/2022] Open
Abstract
Auxin and cytokinin (CK) are both important hormones involved in many aspects of plant growth and development. However, the details of auxin biosynthesis and the interaction between auxin and CK are still unclear. Isolation and characterization of an auxin deficient mutant cytokinin induced root curling 2 (ckrc2) in this work reveal that CKRC2 encodes a previously identified member of YUCCA (YUC) flavin monooxygenase-like proteins (YUC8). Our results show that, like other YUCs, CKRC2/YUC8 is a rate-limiting enzyme for catalyzing the conversion of indole-3-pyruvic acid (IPyA) to indole-3-acetic acid (IAA), acting downstream of CKRC1/TAA1 in the IPyA pathway. Here we show that the transcription of both CKRC1/TAA and CKRC2/YUC8 can be induced by CK and that the phytochrome-interacting factor 4 (PIF4) is required for this upregulation. Transcription of PIF4 itself is induced by CK via the AHKs-ARR1/12 signalling pathway. These results indicate that PIF4 plays an essential role in mediating the regulatory effect of CK on the transcriptions of CKRC1 and CKRC2 genes in the IPyA pathway of auxin biosynthesis.
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Singh RK, Jaishankar J, Muthamilarasan M, Shweta S, Dangi A, Prasad M. Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress. Sci Rep 2016; 6:32641. [PMID: 27586959 PMCID: PMC5009299 DOI: 10.1038/srep32641] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/10/2016] [Indexed: 11/12/2022] Open
Abstract
Heat shock proteins (HSPs) perform significant roles in conferring abiotic stress tolerance to crop plants. In view of this, HSPs and their encoding genes were extensively characterized in several plant species; however, understanding their structure, organization, evolution and expression profiling in a naturally stress tolerant crop is necessary to delineate their precise roles in stress-responsive molecular machinery. In this context, the present study has been performed in C4 panicoid model, foxtail millet, which resulted in identification of 20, 9, 27, 20 and 37 genes belonging to SiHSP100, SiHSP90, SiHSP70, SiHSP60 and SisHSP families, respectively. Comprehensive in silico characterization of these genes followed by their expression profiling in response to dehydration, heat, salinity and cold stresses in foxtail millet cultivars contrastingly differing in stress tolerance revealed significant upregulation of several genes in tolerant cultivar. SisHSP-27 showed substantial higher expression in response to heat stress in tolerant cultivar, and its over-expression in yeast system conferred tolerance to several abiotic stresses. Methylation analysis of SiHSP genes suggested that, in susceptible cultivar, higher levels of methylation might be the reason for reduced expression of these genes during stress. Altogether, the study provides novel clues on the role of HSPs in conferring stress tolerance.
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Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Jananee Jaishankar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | | | - Shweta Shweta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Anand Dangi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
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Nguyen TD, Moon S, Nguyen VNT, Gho Y, Chandran AKN, Soh MS, Song JT, An G, Oh SA, Park SK, Jung KH. Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage. PLANT MOLECULAR BIOLOGY 2016; 92:71-88. [PMID: 27356912 DOI: 10.1007/s11103-016-0496-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/23/2016] [Indexed: 06/06/2023]
Abstract
Microspore production using endogenous developmental programs has not been well studied. The main limitation is the difficulty in identifying genes preferentially expressed in pollen grains at early stages. To overcome this limitation, we collected transcriptome data from anthers and microspore/pollen and performed meta-expression analysis. Subsequently, we identified 410 genes showing preferential expression patterns in early developing pollen samples of both japonica and indica cultivars. The expression patterns of these genes are distinguishable from genes showing pollen mother cell or tapetum-preferred expression patterns. Gene Ontology enrichment and MapMan analyses indicated that microspores in rice are closely linked with protein degradation, nucleotide metabolism, and DNA biosynthesis and regulation, while the pollen mother cell or tapetum are strongly associated with cell wall metabolism, lipid metabolism, secondary metabolism, and RNA biosynthesis and regulation. We also generated transgenic lines under the control of the promoters of eight microspore-preferred genes and confirmed the preferred expression patterns in plants using the GUS reporting system. Furthermore, cis-regulatory element analysis revealed that pollen specific elements such as POLLEN1LELAT52, and 5659BOXLELAT5659 were commonly identified in the promoter regions of eight rice genes with more frequency than estimation. Our study will provide new sights on early pollen development in rice, a model crop plant.
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Affiliation(s)
- Tien Dung Nguyen
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Van Ngoc Tuyet Nguyen
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Yunsil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Anil Kumar Nalini Chandran
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Moon-Soo Soh
- Department of Molecular Biology, Sejong University, Seoul, 143-747, Republic of Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Sung Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea.
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
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Cho LH, Yoon J, Pasriga R, An G. Homodimerization of Ehd1 Is Required to Induce Flowering in Rice. PLANT PHYSIOLOGY 2016; 170:2159-71. [PMID: 26864016 PMCID: PMC4825144 DOI: 10.1104/pp.15.01723] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/02/2016] [Indexed: 05/20/2023]
Abstract
In plants, flowering time is elaborately controlled by various environment factors. Ultimately, florigens such as FLOWERING LOCUS T (FT) or FT-like molecules induce flowering. In rice (Oryza sativa), Early heading date 1 (Ehd1) is a major inducer of florigen gene expression. Although Ehd1 is highly homologous to the type-B response regulator (RR) family in the cytokinin signaling pathway, its precise molecular mechanism is not well understood. In this study, we showed that the C-terminal portion of the protein containing the GARP DNA-binding (G) domain can promote flowering when overexpressed. We also observed that the N-terminal portion of Ehd1, carrying the receiver (R) domain, delays flowering by inhibiting endogenous Ehd1 activity. Ehd1 protein forms a homomer via a 16-amino acid region in the inter domain between R and G. From the site-directed mutagenesis analyses, we demonstrated that phosphorylation of the Asp-63 residue within the R domain induces the homomerization of Ehd1, which is crucial for Ehd1 activity. A type-A RR, OsRR1, physically interacts with Ehd1 to form a heterodimer. In addition, OsRR1-overexpressing plants show a late-flowering phenotype. Based on these observations, we conclude that OsRR1 inhibits Ehd1 activity by binding to form an inactive complex.
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Affiliation(s)
- Lae-Hyeon Cho
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea (L.-H.C., J.Y., R.P., G.A.);Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea (L.-H.C., J.Y.); andGraduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea (R.P., G.A.)
| | - Jinmi Yoon
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea (L.-H.C., J.Y., R.P., G.A.);Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea (L.-H.C., J.Y.); andGraduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea (R.P., G.A.)
| | - Richa Pasriga
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea (L.-H.C., J.Y., R.P., G.A.);Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea (L.-H.C., J.Y.); andGraduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea (R.P., G.A.)
| | - Gynheung An
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea (L.-H.C., J.Y., R.P., G.A.);Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea (L.-H.C., J.Y.); andGraduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea (R.P., G.A.)
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Zürcher E, Müller B. Cytokinin Synthesis, Signaling, and Function--Advances and New Insights. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:1-38. [PMID: 27017005 DOI: 10.1016/bs.ircmb.2016.01.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The plant hormones referred to as cytokinins are chemical signals that control numerous developmental processes throughout the plant life cycle, including gametogenesis, root meristem specification, vascular development, shoot and root growth, meristem homeostasis, senescence, and more. In addition, they mediate responses to environmental cues such as light, stress, and nutrient conditions. The core mechanistics of cytokinin metabolism and signaling have been elucidated, but more layers of regulation, additional functions, and interactions with other signals are continuously discovered and described. In this chapter, we recapitulate the highlights of over 100 years of cytokinin research covering its isolation, the elucidation of phosphorelay signaling, and how cytokinin functions in various developmental contexts including its interaction with other pathways. Additionally, given cytokinin's paracrine signaling mechanism, we postulate that cellular exporters for cytokinins exist.
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Affiliation(s)
- E Zürcher
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich Zurich, Switzerland
| | - B Müller
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich Zurich, Switzerland.
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Zhang J, Yu G, Wen W, Ma X, Xu B, Huang B. Functional characterization and hormonal regulation of the PHEOPHYTINASE gene LpPPH controlling leaf senescence in perennial ryegrass. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:935-45. [PMID: 26643195 PMCID: PMC4737083 DOI: 10.1093/jxb/erv509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Chlorophyll (Chl) degradation occurs naturally during leaf maturation and senescence, and can be induced by stresses, both processes involving the regulation of plant hormones. The objective of this study was to determine the functional roles and hormonal regulation of a gene encoding pheophytin pheophorbide hydrolyase (PPH) that catabolizes Chl degradation during leaf senescence in perennial grass species. A PPH gene, LpPPH, was cloned from perennial ryegrass (Lolium perenne L.). LpPPH was localized in the chloroplast. Overexpressing LpPPH accelerated Chl degradation in wild tobacco, and rescued the stay-green phenotype of the Arabidopsis pph null mutant. The expression level of LpPPH was positively related to the extent of leaf senescence. Exogenous application of abscisic acid (ABA) and ethephon (an ethylene-releasing agent) accelerated the decline in Chl content in leaves of perennial ryegrass, whereas cytokinin (CK) and aminoethoxyvinylglycine (AVG; an ethylene biosynthesis inhibitor) treatments suppressed leaf senescence, corresponding to the up- or down-regulation of LpPPH expression. The promoters of five orthologous PPH genes were predicted to share conserved cis-elements potentially recognized by transcription factors in the ABA and CK pathways. Taken together, the results suggested that LpPPH-mediated Chl breakdown could be regulated positively by ABA and ethylene, and negatively by CK, and LpPPH could be a direct downstream target gene of transcription factors in the ABA and CK signaling pathways.
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Affiliation(s)
- Jing Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, PR China Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Guohui Yu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Wuwu Wen
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xiqing Ma
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, PR China Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Bin Xu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
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Larsen PE, Sreedasyam A, Trivedi G, Desai S, Dai Y, Cseke LJ, Collart FR. Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction. FRONTIERS IN PLANT SCIENCE 2016; 6:1061. [PMID: 26834754 PMCID: PMC4717292 DOI: 10.3389/fpls.2015.01061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/16/2015] [Indexed: 05/29/2023]
Abstract
In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root-mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree) and Laccaria bicolor (mycorrhizal fungi) interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with 15 transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.
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Affiliation(s)
- Peter E. Larsen
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
- Department of Bioengineering, University of Illinois at ChicagoChicago IL, USA
| | - Avinash Sreedasyam
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Geetika Trivedi
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Shalaka Desai
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
| | - Yang Dai
- Department of Bioengineering, University of Illinois at ChicagoChicago IL, USA
| | - Leland J. Cseke
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
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Pekárová B, Szmitkowska A, Dopitová R, Degtjarik O, Žídek L, Hejátko J. Structural Aspects of Multistep Phosphorelay-Mediated Signaling in Plants. MOLECULAR PLANT 2016; 9:71-85. [PMID: 26633861 DOI: 10.1016/j.molp.2015.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 05/16/2023]
Abstract
The multistep phosphorelay (MSP) is a central signaling pathway in plants integrating a wide spectrum of hormonal and environmental inputs and controlling numerous developmental adaptations. For the thorough comprehension of the molecular mechanisms underlying the MSP-mediated signal recognition and transduction, the detailed structural characterization of individual members of the pathway is critical. In this review we describe and discuss the recently known crystal and nuclear magnetic resonance structures of proteins acting in MSP signaling in higher plants, focusing particularly on cytokinin and ethylene signaling in Arabidopsis thaliana. We discuss the range of functional aspects of available structural information including determination of ligand specificity, activation of the receptor via its autophosphorylation, and downstream signal transduction through the phosphorelay. We compare the plant structures with their bacterial counterparts and show that although the overall similarity is high, the differences in structural details are frequent and functionally important. Finally, we discuss emerging knowledge on molecular recognition mechanisms in the MSP, and mention the latest findings regarding structural determinants of signaling specificity in the Arabidopsis MSP that could serve as a general model of this pathway in all higher plants.
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Affiliation(s)
- Blanka Pekárová
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Agnieszka Szmitkowska
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Radka Dopitová
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Oksana Degtjarik
- Faculty of Science, Institute of Chemistry and Biochemistry, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Lukáš Žídek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jan Hejátko
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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Manimaran P, Raghurami Reddy M, Bhaskar Rao T, Mangrauthia SK, Sundaram RM, Balachandran SM. Identification of cis-elements and evaluation of upstream regulatory region of a rice anther-specific gene, OSIPP3, conferring pollen-specific expression in Oryza sativa (L.) ssp. indica. PLANT REPRODUCTION 2015; 28:133-42. [PMID: 26081459 DOI: 10.1007/s00497-015-0264-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/01/2015] [Indexed: 05/22/2023]
Abstract
Pollen-specific expression. Promoters comprise of various cis-regulatory elements which control development and physiology of plants by regulating gene expression. To understand the promoter specificity and also identification of functional cis-acting elements, progressive 5' deletion analysis of the promoter fragments is widely used. We have evaluated the activity of regulatory elements of 5' promoter deletion sequences of anther-specific gene OSIPP3, viz. OSIPP3-∆1 (1504 bp), OSIPP3-∆2 (968 bp), OSIPP3-∆3 (388 bp) and OSIPP3-∆4 (286 bp) through the expression of transgene GUS in rice. In silico analysis of 1504-bp sequence harboring different copy number of cis-acting regulatory elements such as POLLENLELAT52, GTGANTG10, enhancer element of LAT52 and LAT56 indicated that they were essential for high level of expression in pollen. Histochemical GUS analysis of the transgenic plants revealed that 1504- and 968-bp fragments directed GUS expression in roots and anthers, while the 388- and 286-bp fragments restricted the GUS expression to only pollen, of which 388 bp conferred strong GUS expression. Further, GUS staining analysis of different panicle development stages (P1-P6) confirmed that the GUS gene was preferentially expressed only at P6 stage (late pollen stage). The qRT-PCR analysis of GUS transcript revealed 23-fold higher expression of GUS transcript in OSIPP3-Δ1 followed by OSIPP3-Δ2 (eightfold) and OSIPP3-Δ3 (threefold) when compared to OSIPP3-Δ4. Based on our results, we proposed that among the two smaller fragments, the 388-bp upstream regulatory region could be considered as a promising candidate for pollen-specific expression of agronomically important transgenes in rice.
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Affiliation(s)
- P Manimaran
- Biotechnology Laboratory, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - M Raghurami Reddy
- Biotechnology Laboratory, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - T Bhaskar Rao
- Biotechnology Laboratory, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - Satendra K Mangrauthia
- Biotechnology Laboratory, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - R M Sundaram
- Biotechnology Laboratory, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India
| | - S M Balachandran
- Biotechnology Laboratory, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India.
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64
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Impact of cis-acting elements' frequency in transcription activity in dicot and monocot plants. 3 Biotech 2015; 5:1007-1019. [PMID: 28324408 PMCID: PMC4624133 DOI: 10.1007/s13205-015-0305-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/25/2015] [Indexed: 10/27/2022] Open
Abstract
The production of new cultivars via recombinant DNA technology is important in applied agriculture. Promoters play fundamental roles in successful transformation and gene expression. Fragments of the upstream regulatory region of the movement protein gene of the Tomato yellow leaf curl virus (TYLCV; two fragments) and Watermelon chlorotic stunt virus (WmCSV, two fragments) and one fragment of the coat protein putative promoter of TYLCV (CPTY-pro) were isolated to assess their abilities to drive expression in monocot and dicot plants. We used bioinformatic analyses to identify tentative motifs in the fragments. The five promoter fragments were isolated, fused with the GUS reporter gene, and transformed into tomato, watermelon, and rice plantlets via Agrobacterium infiltration. GUS expression driven by each putative promoter was analysed using histochemical and fluorometric analyses. In both dicots and the monocots, the highest level of GUS expression was obtained using a truncated regulatory region from TYLCV (MMPTY-pro) followed by a truncated regulatory region from WmCSV (MMPWm-pro). However, the corresponding full-length fragments from TYLCV and WmCSV showed essentially equivalent expression levels in the fluorometric GUS assay compared with the enhanced Cauliflower mosaic virus e35S-pro. In addition, CPTY-pro showed no expression in either the dicots or the monocot. This study demonstrated that MMPTY-pro and MMPWm-pro may be useful as plant promoters.
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Park GT, Sundaramoorthy J, Lee JD, Kim JH, Seo HS, Song JT. Elucidation of Molecular Identity of the W3 Locus and Its Implication in Determination of Flower Colors in Soybean. PLoS One 2015; 10:e0142643. [PMID: 26555888 PMCID: PMC4640537 DOI: 10.1371/journal.pone.0142643] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/23/2015] [Indexed: 12/03/2022] Open
Abstract
The wide range of flower colors in soybean is controlled by six independent loci (W1, W2, W3, W4, Wm, and Wp). Among these loci, mutations in the W3 locus under the w4 allelic background (i.e., w3w4) produce near-white flowers, while the W3w4 genotype produces purple throat flowers. Although a gene encoding dihydroflavonol 4-reductase, DFR1, has been known to be closely associated with the W3 locus, its molecular identity has not yet been characterized. In the present study, we aimed to determine whether DFR1 is responsible for allelic variations in the W3 locus. On the basis of the sequence of a DFR probe, Glyma.14G072700 was identified as a candidate gene for DFR1, and nucleotide sequences of Glyma.14G072700 from cultivars with previously validated genotypes for the W3 locus were determined. As a result, a number of nucleotide polymorphisms, mainly single-base substitutions, between both coding and 5'-upstream region sequences of the W3 and w3 alleles were identified. Among them, an indel of 311-bp in the 5'-upstream region was noteworthy, since the Glyma.14G072700 in all the w3 alleles examined contained the indel, whereas that in all the W3 alleles did not; the former was barely expressed, but the latter was well expressed. These results suggest that Glyma.14G072700 is likely to correspond to DFR1 for the W3 locus and that its expression patterns may lead to allelic color phenotypes of W3 and w3 alleles under the w4 allelic background.
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Affiliation(s)
- Gyu Tae Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Korea
| | | | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Korea
| | - Jeong Hoe Kim
- Department of Biology, Kyungpook National University, Daegu, Korea
| | - Hak Soo Seo
- Department of Plant Bioscience, Seoul National University, Seoul, Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu, Korea
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66
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Marín-de la Rosa N, Pfeiffer A, Hill K, Locascio A, Bhalerao RP, Miskolczi P, Grønlund AL, Wanchoo-Kohli A, Thomas SG, Bennett MJ, Lohmann JU, Blázquez MA, Alabadí D. Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins. PLoS Genet 2015; 11:e1005337. [PMID: 26134422 PMCID: PMC4489807 DOI: 10.1371/journal.pgen.1005337] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 06/05/2015] [Indexed: 11/19/2022] Open
Abstract
The ability of plants to provide a plastic response to environmental cues relies on the connectivity between signaling pathways. DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis. Plants respond to environmental cues by modulating transcriptional circuits. One mechanism for such modulation involves DELLA proteins. They are promiscuous interactors of transcription factors and, in most cases, this interaction impairs the recognition of the DNA target sequences. Here we show that DELLA proteins are also recruited to multiple locations of the genome where they act as transcriptional coactivators, and we demonstrate how physical interaction with type-B ARRs is relevant for the regulation of meristem maintenance and photomorphogenesis.
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Affiliation(s)
- Nora Marín-de la Rosa
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Anne Pfeiffer
- Department of Stem Cell Biology, Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Kristine Hill
- School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Nottingham, United Kingdom
| | - Antonella Locascio
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Rishikesh P. Bhalerao
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Sveriges Lantbruksuniversitet, Umeå, Sweden
- College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Pal Miskolczi
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Sveriges Lantbruksuniversitet, Umeå, Sweden
| | | | | | | | - Malcolm J. Bennett
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Sveriges Lantbruksuniversitet, Umeå, Sweden
- College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Jan U. Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Miguel A. Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
- * E-mail:
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
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67
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Müller D, Waldie T, Miyawaki K, To JPC, Melnyk CW, Kieber JJ, Kakimoto T, Leyser O. Cytokinin is required for escape but not release from auxin mediated apical dominance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:874-86. [PMID: 25904120 PMCID: PMC4691322 DOI: 10.1111/tpj.12862] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 04/08/2015] [Accepted: 04/13/2015] [Indexed: 05/18/2023]
Abstract
Auxin produced by an active primary shoot apex is transported down the main stem and inhibits the growth of the axillary buds below it, contributing to apical dominance. Here we use Arabidopsis thaliana cytokinin (CK) biosynthetic and signalling mutants to probe the role of CK in this process. It is well established that bud outgrowth is promoted by CK, and that CK synthesis is inhibited by auxin, leading to the hypothesis that release from apical dominance relies on an increased supply of CK to buds. Our data confirm that decapitation induces the expression of at least one ISOPENTENYLTRANSFERASE (IPT) CK biosynthetic gene in the stem. We further show that transcript abundance of a clade of the CK-responsive type-A Arabidopsis response regulator (ARR) genes increases in buds following CK supply, and that, contrary to their typical action as inhibitors of CK signalling, these genes are required for CK-mediated bud activation. However, analysis of the relevant arr and ipt multiple mutants demonstrates that defects in bud CK response do not affect auxin-mediated bud inhibition, and increased IPT transcript levels are not needed for bud release following decapitation. Instead, our data suggest that CK acts to overcome auxin-mediated bud inhibition, allowing buds to escape apical dominance under favourable conditions, such as high nitrate availability.
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Affiliation(s)
- Dörte Müller
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Tanya Waldie
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Kaori Miyawaki
- Biology Department, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jennifer P C To
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Charles W Melnyk
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Joseph J Kieber
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Tatsuo Kakimoto
- Biology Department, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ottoline Leyser
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
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68
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Zhang D, Ren L, Yue JH, Shi YB, Zhuo LH, Wang L, Shen XH. RNA-Seq-based transcriptome analysis of stem development and dwarfing regulation in Agapanthus praecox ssp. orientalis (Leighton) Leighton. Gene 2015; 565:252-67. [PMID: 25865295 DOI: 10.1016/j.gene.2015.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 03/27/2015] [Accepted: 04/07/2015] [Indexed: 12/29/2022]
Abstract
Agapanthus praecox is a monocotyledonous ornamental bulb plant. Generally, the scape (inflorescence stem) length can develop more than 1m, however application 400 mg·L(-1) paclobutrazol can shorten the length beyond 70%. To get a deeper insight into its dwarfism mechanism, de novo RNA-Seq technology has been employed, for the first time, to describe the scape transcriptome of A. praecox. We got 71,258 assembled unigenes, and 45,597 unigenes obtained protein functional annotation. Take the above sequencing results as a reference gene set, using RNA-seq (quantification) technology analyzed gene expression profiles between the control and paclobutrazol-treated samples, and screened 2838 differentially expressed genes. GO, KEGG and MapMan pathway analyses indicated that these differentially expressed genes were significantly enriched in response to stimulus, hormonal signaling, carbohydrate metabolism, cell wall, cell size, and cell cycle related biological process. To validate the expression profiles obtained by RNA-Seq, real-time qPCR was performed on 24 genes selected from key significantly enriched pathways. Comprehensive analysis suggested that paclobutrazol blocks GA signal that can effectively inhibit scape elongation; the GA signal interact with other hormonal signals including auxin, ethylene, brassinosteroid and cytokinins, and trigger downstream signaling cascades leading to metabolism, cell wall biosynthesis, cell division and the cycle decreased obviously, and finally induced dwarfism trait. Furthermore, AP2/EREBP, bHLH, C2H2, ARR, WRKY and ARF family's transcription factors were involved in the regulation of scape development in A. praecox. This transcriptome dataset will serve as an important public information platform to accelerate research on the gene expression and functional genomics of Agapanthus.
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Affiliation(s)
- Di Zhang
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Li Ren
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jian-Hua Yue
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yu-Bo Shi
- Department of Ornamental Plants and Horticulture, College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China.
| | - Li-Huan Zhuo
- Department of Ornamental Plants and Horticulture, College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China.
| | - Ling Wang
- Department of Ornamental Plants and Horticulture, College of Landscape Architecture, Northeast Forestry University, Harbin 150040, China.
| | - Xiao-Hui Shen
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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69
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Meena MK, Ghawana S, Sardar A, Dwivedi V, Khandal H, Roy R, Chattopadhyay D. Investigation of genes encoding calcineurin B-like protein family in legumes and their expression analyses in chickpea (Cicer arietinum L.). PLoS One 2015; 10:e0123640. [PMID: 25853855 PMCID: PMC4390317 DOI: 10.1371/journal.pone.0123640] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/20/2015] [Indexed: 11/29/2022] Open
Abstract
Calcium ion (Ca2+) is a ubiquitous second messenger that transmits various internal and external signals including stresses and, therefore, is important for plants’ response process. Calcineurin B-like proteins (CBLs) are one of the plant calcium sensors, which sense and convey the changes in cytosolic Ca2+-concentration for response process. A search in four leguminous plant (soybean, Medicago truncatula, common bean and chickpea) genomes identified 9 to 15 genes in each species that encode CBL proteins. Sequence analyses of CBL peptides and coding sequences (CDS) suggested that there are nine original CBL genes in these legumes and some of them were multiplied during whole genome or local gene duplication. Coding sequences of chickpea CBL genes (CaCBL) were cloned from their cDNAs and sequenced, and their annotations in the genome assemblies were corrected accordingly. Analyses of protein sequences and gene structures of CBL family in plant kingdom indicated its diverse origin but showed a remarkable conservation in overall protein structure with appearance of complex gene structure in the course of evolution. Expression of CaCBL genes in different tissues and in response to different stress and hormone treatment were studied. Most of the CaCBL genes exhibited high expression in flowers. Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA) at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance. These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.
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Affiliation(s)
- Mukesh Kumar Meena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjay Ghawana
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Atish Sardar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vikas Dwivedi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Hitaishi Khandal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Riti Roy
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- * E-mail:
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70
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Functional roles of three cutin biosynthetic acyltransferases in cytokinin responses and skotomorphogenesis. PLoS One 2015; 10:e0121943. [PMID: 25803274 PMCID: PMC4372371 DOI: 10.1371/journal.pone.0121943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/09/2015] [Indexed: 11/24/2022] Open
Abstract
Cytokinins (CKs) regulate plant development and growth via a two-component signaling pathway. By forward genetic screening, we isolated an Arabidopsis mutant named grow fast on cytokinins 1 (gfc1), whose seedlings grew larger aerial parts on MS medium with CK. gfc1 is allelic to a previously reported cutin mutant defective in cuticular ridges (dcr). GFC1/DCR encodes a soluble BAHD acyltransferase (a name based on the first four enzymes characterized in this family: Benzylalcohol O-acetyltransferase, Anthocyanin O-hydroxycinnamoyltransferase, anthranilate N-hydroxycinnamoyl/benzoyltransferase and Deacetylvindoline 4-O-acetyltransferase) with diacylglycerol acyltransferase (DGAT) activity in vitro and is necessary for normal cuticle formation on epidermis in vivo. Here we show that gfc1 was a CK-insensitive mutant, as revealed by its low regeneration frequency in vitro and resistance to CK in adventitious root formation and dark-grown hypocotyl inhibition assays. In addition, gfc1 had de-etiolated phenotypes in darkness and was therefore defective in skotomorphogenesis. The background expression levels of most type-A Arabidopsis Response Regulator (ARR) genes were higher in the gfc1 mutant. The gfc1-associated phenotypes were also observed in the cutin-deficient glycerol-3-phosphate acyltransferase 4/8 (gpat4/8) double mutant [defective in glycerol-3-phosphate (G3P) acyltransferase enzymes GPAT4 and GPAT8, which redundantly catalyze the acylation of G3P by hydroxyl fatty acid (OH-FA)], but not in the cutin-deficient mutant cytochrome p450, family 86, subfamily A, polypeptide 2/aberrant induction of type three 1 (cyp86A2/att1), which affects the biosynthesis of some OH-FAs. Our results indicate that some acyltransferases associated with cutin formation are involved in CK responses and skotomorphogenesis in Arabidopsis.
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71
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Azizi P, Rafii M, Maziah M, Abdullah S, Hanafi M, Latif M, Rashid A, Sahebi M. Understanding the shoot apical meristem regulation: A study of the phytohormones, auxin and cytokinin, in rice. Mech Dev 2015; 135:1-15. [DOI: 10.1016/j.mod.2014.11.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 11/05/2014] [Accepted: 11/14/2014] [Indexed: 11/30/2022]
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72
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Wang Y, Wang L, Zou Y, Chen L, Cai Z, Zhang S, Zhao F, Tian Y, Jiang Q, Ferguson BJ, Gresshoff PM, Li X. Soybean miR172c targets the repressive AP2 transcription factor NNC1 to activate ENOD40 expression and regulate nodule initiation. THE PLANT CELL 2014; 26:4782-801. [PMID: 25549672 PMCID: PMC4311200 DOI: 10.1105/tpc.114.131607] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 11/19/2014] [Accepted: 12/08/2014] [Indexed: 05/18/2023]
Abstract
MicroRNAs are noncoding RNAs that act as master regulators to modulate various biological processes by posttranscriptionally repressing their target genes. Repression of their target mRNA(s) can modulate signaling cascades and subsequent cellular events. Recently, a role for miR172 in soybean (Glycine max) nodulation has been described; however, the molecular mechanism through which miR172 acts to regulate nodulation has yet to be explored. Here, we demonstrate that soybean miR172c modulates both rhizobium infection and nodule organogenesis. miR172c was induced in soybean roots inoculated with either compatible Bradyrhizobium japonicum or lipooligosaccharide Nod factor and was highly upregulated during nodule development. Reduced activity and overexpression of miR172c caused dramatic changes in nodule initiation and nodule number. We show that soybean miR172c regulates nodule formation by repressing its target gene, Nodule Number Control1, which encodes a protein that directly targets the promoter of the early nodulin gene, ENOD40. Interestingly, transcriptional levels of miR172c were regulated by both Nod Factor Receptor1α/5α-mediated activation and by autoregulation of nodulation-mediated inhibition. Thus, we established a direct link between miR172c and the Nod factor signaling pathway in addition to adding a new layer to the precise nodulation regulation mechanism of soybean.
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Affiliation(s)
- Youning Wang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Lixiang Wang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yanmin Zou
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Liang Chen
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Zhaoming Cai
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Senlei Zhang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Zhao
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Yinping Tian
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Qiong Jiang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Brett J Ferguson
- Centre for Integrative Legume Research, University of Queensland, Brisbane St. Lucia, Queensland 4072, Australia
| | - Peter M Gresshoff
- Centre for Integrative Legume Research, University of Queensland, Brisbane St. Lucia, Queensland 4072, Australia
| | - Xia Li
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
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Muthamilarasan M, Khandelwal R, Yadav CB, Bonthala VS, Khan Y, Prasad M. Identification and molecular characterization of MYB Transcription Factor Superfamily in C4 model plant foxtail millet (Setaria italica L.). PLoS One 2014; 9:e109920. [PMID: 25279462 PMCID: PMC4184890 DOI: 10.1371/journal.pone.0109920] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/06/2014] [Indexed: 02/02/2023] Open
Abstract
MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I - X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli.
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Affiliation(s)
| | | | | | | | - Yusuf Khan
- National Institute of Plant Genome Research, New Delhi, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
- * E-mail:
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A multi-step phosphorelay two-component system impacts on tolerance against dehydration stress in common wheat. Funct Integr Genomics 2014; 14:707-16. [PMID: 25228409 DOI: 10.1007/s10142-014-0398-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 08/27/2014] [Accepted: 08/31/2014] [Indexed: 02/02/2023]
Abstract
Wheat is an important staple crop, and its productivity is severely constrained by drought stress (DS). An understanding of the molecular basis of drought tolerance is necessary for genetic improvement of wheat for tolerance to DS. The two-component system (TCS) serves as a common sensor-regulator coupling mechanism implicated in the regulation of diverse biological processes (including response to DS) not only in prokaryotes, but also in higher plants. In the latter, TCS generally consists of two signalling elements, a histidine kinase (HK) and a response regulator (RR) associated with an intermediate element called histidine phosphotransferase (HPT). Keeping in view the possible utility of TCS in developing water use efficient (WUE) wheat cultivars, we identified and characterized 62 wheat genes encoding TCS elements in a silico study; these included 7 HKs, 45 RRs along with 10 HPTs. Twelve of the 62 genes showed relatively higher alterations in the expression under drought. The quantitative RT-PCR (qRT-PCR)-based expression analysis of these 12 TCS genes was carried out in wheat seedlings of a drought sensitive (HD2967) and a tolerant (Dharwar Dry) cultivar subjected to either dehydration stress or cytokinin treatment. The expression of these 12 genes under dehydration stress differed in sensitive and tolerant genotypes, even though for individual genes, both showed either up-regulation or down-regulation. In response to the treatment of cytokinin, the expression of type-A RR genes was higher in the tolerant genotype, relative to that in the sensitive genotype, the situation being reverse for the type-B RRs. These results have been discussed in the context of the role of TCS elements in drought tolerance in wheat.
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75
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Characterization of putative cis-regulatory elements in genes preferentially expressed in Arabidopsis male meiocytes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:708364. [PMID: 25250331 PMCID: PMC4163388 DOI: 10.1155/2014/708364] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/19/2014] [Accepted: 07/20/2014] [Indexed: 11/18/2022]
Abstract
Meiosis is essential for plant reproduction because it is the process during which homologous chromosome pairing, synapsis, and meiotic recombination occur. The meiotic transcriptome is difficult to investigate because of the size of meiocytes and the confines of anther lobes. The recent development of isolation techniques has enabled the characterization of transcriptional profiles in male meiocytes of Arabidopsis. Gene expression in male meiocytes shows unique features. The direct interaction of transcription factors (TFs) with DNA regulatory sequences forms the basis for the specificity of transcriptional regulation. Here, we identified putative cis-regulatory elements (CREs) associated with male meiocyte-expressed genes using in silico tools. The upstream regions (1 kb) of the top 50 genes preferentially expressed in Arabidopsis meiocytes possessed conserved motifs. These motifs are putative binding sites of TFs, some of which share common functions, such as roles in cell division. In combination with cell-type-specific analysis, our findings could be a substantial aid for the identification and experimental verification of the protein-DNA interactions for the specific TFs that drive gene expression in meiocytes.
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76
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García JR, Anderson N, Le-Feuvre R, Iturra C, Elissetche J, Chapple C, Valenzuela S. Rescue of syringyl lignin and sinapate ester biosynthesis in Arabidopsis thaliana by a coniferaldehyde 5-hydroxylase from Eucalyptus globulus. PLANT CELL REPORTS 2014; 33:1263-1274. [PMID: 24737414 DOI: 10.1007/s00299-014-1614-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/26/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
The gene coding for F5H from Eucalyptus globulus was cloned and used to transform an f5h -mutant of Arabidopsis thaliana , which was complemented, thus verifying the identity of the cloned gene. Coniferaldehyde 5-hydroxylase (F5H; EC 1.14.13) is a cytochrome P450-dependent monooxygenase that catalyzes the 5-hydroxylation step required for the production of syringyl units in lignin biosynthesis. The Eucalyptus globulus enzyme was characterized in vitro, and results showed that the preferred substrates were coniferaldehyde and coniferyl alcohol. Complementation experiments demonstrated that both cDNA and genomic constructs derived from F5H from E. globulus under the control of the cinnamate 4-hydroxylase promoter from Arabidopsis thaliana, or a partial F5H promoter from E. globulus, can rescue the inability of the A. thaliana fah1-2 mutant to accumulate sinapate esters and syringyl lignin. E. globulus is a species widely used to obtain products that require lignin removal, and the results suggest that EglF5H is a good candidate for engineering efforts aimed at increasing the lignin syringyl unit content, either for kraft pulping or biofuel production.
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Affiliation(s)
- José Renán García
- Centro de Biotecnología y Facultad Ciencias Forestales, Universidad de Concepción, Concepción, Chile
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Zhang C, Gao L, Sun J, Jia J, Ren Z. Haplotype variation of Green Revolution gene Rht-D1 during wheat domestication and improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:774-780. [PMID: 24645900 DOI: 10.1111/jipb.12197] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/18/2014] [Indexed: 06/03/2023]
Abstract
Green Revolution made a substantial contribution to wheat yields worldwide in the 1960s and 1970s. It is of great importance to analyze the haplotype variation of Rht-D1, the Green Revolution gene, during wheat (Triticum aestivum L.) domestication and breeding to understand its evolution and function in wheat breeding history. In this study, the Rht-D1 and its flanking regions were sequenced and single nucleotide polymorphisms were detected based on a panel of 45 accessions of Aegilops tauschii, 51 accessions of landraces and 80 accessions of commercial varieties. Genetic diversity in the wild accessions was much higher than that in the varieties and higher than that reported previously. Seven haplotypes (Hapl I to Hapl VII) of Rht-D1 were identified and their evolutionary relationships were proposed. In addition to the well-known Green Revolution allele Rht-D1b, Hapl VII (an allele Rht-D1k) was identified in early breeding varieties, which reduced plant height by 16%. The results suggested that Rht-D1k had been used in breeding before the Green Revolution and made a great contribution to wheat production worldwide. Based on the breeding history and molecular evidence, we proposed that the wheat Green Revolution in China and International Maize and Wheat Improvement Center (CIMMYT) occurred independently.
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Affiliation(s)
- Chihong Zhang
- Agronomy Department, Sichuan Agricultural University, Chengdu, 611130, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Germplasm and Biotechnology, Ministry of Agriculture, Beijing, 100081, China; Chengdu Institution of Biology, the Chinese Academy of Sciences, Chengdu, 610041, China
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78
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Liu Z, Zhang M, Kong L, Lv Y, Zou M, Lu G, Cao J, Yu X. Genome-wide identification, phylogeny, duplication, and expression analyses of two-component system genes in Chinese cabbage (Brassica rapa ssp. pekinensis). DNA Res 2014; 21:379-96. [PMID: 24585003 PMCID: PMC4131832 DOI: 10.1093/dnares/dsu004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 01/20/2014] [Indexed: 12/27/2022] Open
Abstract
In plants, a two component system (TCS) composed of sensor histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs) has been employed in cytokinin signal transduction. A TCS exhibits important functions in diverse biological processes, including plant growth, development, and response to environmental stimuli. Conducting an exhaustive search of the Chinese cabbage genome, a total of 20 HK(L) (11 HKs and 9 HKLs), 8 HP (7 authentic and 1 pseudo), and 57 RR (21 Type-A, 17 Type-B, 4 Type-C, and 15 pseudo) proteins were identified. The structures, conserved domains, and phylogenetic relationships of these protein-coding genes were analysed in detail. The duplications, evolutionary patterns, and divergence of the TCS genes were investigated. The transcription levels of TCS genes in various tissues, organs, and developmental stages were further analysed to obtain information of the functions of these genes. Cytokinin-related binding elements were found in the putative promoter regions of Type-A BrRR genes. Furthermore, gene expression patterns to adverse environmental stresses (drought and high salinity) and exogenous phytohormones (tZ and ABA) were investigated. Numerous stress-responsive candidate genes were obtained. Our systematic analyses provided insights into the characterization of the TCS genes in Chinese cabbage and basis for further functional studies of such genes.
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Affiliation(s)
- Zhenning Liu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Mei Zhang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Lijun Kong
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Yanxia Lv
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Minghua Zou
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Gang Lu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Xiaolin Yu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China Laboratory of Horticultural Plant Growth and Quality Regulation, Ministry of Agriculture, Hangzhou 310058, PR China
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Herrero J, Esteban Carrasco A, Zapata JM. Arabidopsis thaliana peroxidases involved in lignin biosynthesis: in silico promoter analysis and hormonal regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 80:192-202. [PMID: 24792389 DOI: 10.1016/j.plaphy.2014.03.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/26/2014] [Indexed: 05/08/2023]
Abstract
Phytohormones such as auxins, cytokinins, and brassinosteroids, act by means of a signaling cascade of transcription factors of the families NAC, MYB, AP2 (APETALA2), MADS and class III HD (homeodomain) Zip, regulating secondary growth. When the hormonal regulation of Zinnia elegans peroxidase (ZePrx), an enzyme involved in lignin biosynthesis, was studied, it was found that this peroxidase is sensitive to a plethora of hormones which control xylem lignification. In a previous study we sought Arabidopsis thaliana homologues to ZePrx. Peroxidases 4, 52, 49 and 72 are the four peroxidases that fulfill the restrictive conditions that a peroxidase involved in lignification must have. In the present study, we focus our attention on hormonal regulation in order to establish the minimal structural and regulatory elements contained in the promoter region which an AtPrx involved in lignification must have. The results indicate that of the four peroxidases selected in our previous study, the one most likely to be homologous to ZePrx is AtPrx52. The results suggest that hormones such as auxins, cytokinins and BRs directly regulate AtPrx52, and that the AtPrx52 promoter may be the target of the set of transcription factors (NAC, MYB, AP2 and class I and III HD Zip) which are up-regulated by these hormones during secondary growth. In addition, the AtPrx52 promoter contains multiple copies of all the putative cis-elements (the ACGT box, the OCS box, the OPAQ box, the L1BX, the MYCL box and the W box) known to confer regulation by NO and H2O2.
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Affiliation(s)
- Joaquín Herrero
- Department of Life Sciences, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.
| | | | - José Miguel Zapata
- Department of Life Sciences, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.
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80
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Yamada H, Koizumi N, Nakamichi N, Kiba T, Yamashino T, Mizuno T. Rapid Response ofArabidopsisT87 Cultured Cells to Cytokinin through His-to-Asp Phosphorelay Signal Transduction. Biosci Biotechnol Biochem 2014; 68:1966-76. [PMID: 15388974 DOI: 10.1271/bbb.68.1966] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
According to the current consistent model for the higher plant Arabidopsis thaliana, the scheme for an immediate early response to the plant hormone cytokinin can be formulated as Arabidopsis histidine kinase (AHK) cytokinin receptor-mediated His --> Asp phosphorelay signal transduction. Nonetheless, clarification of the comprehensive picture of cytokinin-mediated signal transduction in this higher plant is at a very early stage. As a new approach to this end, we studied whether or not a certain Arabidopsis cell line (named T87) would be versatile for such work on cytokinin signal transduction. We show that T87 cells had the ability to respond to cytokinin, displaying the immediate early induction of type-A Arabidopsis response regulator (ARR) family genes (e.g., ARR6) at the transcriptional level. This event was further confirmed by employing the stable transgenic lines of T87 cells with a set of ARR::LUC reporter transgenes. We also show that T87 cells had the ability to respond to auxin when the expression of a set of AUX/IAA genes (e.g., IAA5) was examined. As postulated for intact plants, in T87 cells too, the induction of IAA5 by auxin was selectively inhibited in the presence of a proteasome inhibitor, while the induction of ARR6 by cytokinin was not significantly affected under the same conditions. Through transient expression assays with T87 protoplasts, it is shown that the intracellular localization profiles of the phosphorelay intermediate Arabidopsis histidine-containing phosphotransfer factor (AHPs; e.g., AHP1 and AHP4) were markedly affected in response to cytokinin, but those of type-A ARRs were not (e.g., ARR15 and ARR16). Taken together, we conclude that, in T87 cells, the AHK-dependent His --> Asp phosphorelay circuitry appears to be propagated in response to cytokinin, as in the case of plants, as far as the immediate early responses were concerned. This cultured cell system might therefore provide us with an alternative means to further characterize the mechanisms underlying cytokinin (and also auxin) responses at the molecular level.
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Affiliation(s)
- Hisami Yamada
- Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University, Chikusa-ku, Japan
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81
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Gruhn N, Halawa M, Snel B, Seidl MF, Heyl A. A subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants. PLANT PHYSIOLOGY 2014; 165:227-37. [PMID: 24520157 PMCID: PMC4012582 DOI: 10.1104/pp.113.228080] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 02/07/2014] [Indexed: 05/05/2023]
Abstract
The two-component signaling system--the major signaling pathway of bacteria--is found among higher eukaryotes only in plants, where it regulates diverse processes, such as the signaling of the phytohormone cytokinin. Cytokinin is perceived by a hybrid histidine (His) kinase receptor, and the signal is transduced by a multistep phosphorelay system of His phosphotransfer proteins and different classes of response regulators (RRs). To shed light on the origin and evolution of the two-component signaling system members in plants, we conducted a comprehensive domain-based phylogenetic study across the relevant kingdoms, including Charophyceae algae, the group of green algae giving rise to land plants. Surprisingly, we identified a subfamily of cytokinin receptors with members only from the early diverging land plants Marchantia polymorpha and Physcomitrella patens and then experimentally characterized two members of this subfamily. His phosphotransfer proteins of Charophyceae seemed to be more closely related to land plants than to other groups of green algae. Farther down the signaling pathway, the type-B RRs were found across all plant clades, but many members lack either the canonical Asp residue or the DNA binding domain. In contrast, the type-A RRs seemed to be limited to land plants. Finally, the analysis provided hints that one additional group of RRs, the type-C RRs, might be degenerated receptors and thus, of a different evolutionary origin than bona fide RRs.
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Affiliation(s)
- Nijuscha Gruhn
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität, 14195 Berlin, Germany (N.G., M.H., A.H.)
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands (B.S., M.F.S.); and
- Centre for BioSystems Genomics, 6700 AB, Wageningen, The Netherlands (B.S., M.F.S.)
| | - Mhyeddeen Halawa
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität, 14195 Berlin, Germany (N.G., M.H., A.H.)
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands (B.S., M.F.S.); and
- Centre for BioSystems Genomics, 6700 AB, Wageningen, The Netherlands (B.S., M.F.S.)
| | - Berend Snel
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität, 14195 Berlin, Germany (N.G., M.H., A.H.)
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands (B.S., M.F.S.); and
- Centre for BioSystems Genomics, 6700 AB, Wageningen, The Netherlands (B.S., M.F.S.)
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Zhang L, Yang T, Li X, Hao H, Xu S, Cheng W, Sun Y, Wang C. Cloning and characterization of a novel Athspr promoter specifically active in vascular tissue. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 78:88-96. [PMID: 24675528 DOI: 10.1016/j.plaphy.2014.02.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/22/2014] [Indexed: 06/03/2023]
Abstract
The vascular system--xylem, phloem and the cambium--is essential for water supply, nutrient transport, and physical support in higher plants. Although it is known that vascular-specific gene expression is regulated by cis-acting regulatory sequences in promoters, it is largely unknown how many regulatory elements exist and what their roles are in promoters. To understand the regulatory elements of vascular-specific promoters and their roles in vascular development, a T-DNA insertion mutant showing delayed growth and diminished resistance to environmental stress was isolated using promoter trap strategy. The novel gene, Arabidopsis thaliana heat shock protein-related (Athspr), was cloned from Arabidopsis ecotype C24. Strong GUS (β-glucuronidase) staining in the original promoter trap line was found in the vascular tissues of all organs in the mutant. The Athspr promoter was cloned and fused with GUS and eGFP (enhanced green fluorescent protein) reporter genes to verify its vascular-specific expression in Arabidopsis. Further histochemical analysis in transgenic plants demonstrated a similar GUS expression pattern in the vascular tissues. In addition, ATHSPR-eGFP driven by Athspr promoter was observed in vascular bundles of the transgenic seedling roots. Finally, comparative analysis with promoter motifs from 37 genes involved in vascular development revealed that Athspr and all other promoters active in vascular tissues contained regulatory elements responding to phytohormones, light, biotic and abiotic stresses, as well as those regulating tissue-specific expression. These results demonstrated that the Athspr promoter has a vascular tissue-specific activity and Athspr may have multiple functions in vascular development and resistance against various stresses.
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Affiliation(s)
- Liang Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tao Yang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoying Li
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hongyan Hao
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shengtao Xu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Wei Cheng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yingli Sun
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chongying Wang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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Kurepa J, Li Y, Smalle JA. Cytokinin signaling stabilizes the response activator ARR1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:157-68. [PMID: 24617630 DOI: 10.1111/tpj.12458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 12/18/2013] [Accepted: 01/22/2014] [Indexed: 05/22/2023]
Abstract
The cytokinins play essential roles in the development and environmental responses of higher plants. Cytokinin signaling leads to the phosphorylation-dependent activation of two classes of Arabidopsis response regulators (RRs): the type-B RR (RRB) transcriptional activators that promote the expression of cytokinin response genes and the type-A RRs (RRAs) that are encoded by primary cytokinin response genes and function as response inhibitors. We show that cytokinin signaling increases the abundance of ARR1, a ubiquitously expressed RRB, by preventing its degradation by the 26S proteasome. We also show that the RRAs act to suppress ARR1 accumulation, thus providing an explanation for their inhibitory action in cytokinin signaling. Collectively, our results reveal an additional regulatory mechanism in the cytokinin response pathway that involves the cytokinin-dependent stability control of a major RRB response activator.
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Affiliation(s)
- Jasmina Kurepa
- Plant Physiology, Biochemistry, Molecular Biology Program, Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
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84
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Oo MM, Bae HK, Nguyen TD, Moon S, Oh SA, Kim JH, Soh MS, Song JT, Jung KH, Park SK. Evaluation of rice promoters conferring pollen-specific expression in a heterologous system, Arabidopsis. PLANT REPRODUCTION 2014; 27:47-58. [PMID: 24550073 DOI: 10.1007/s00497-014-0239-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Promoters can direct gene expression specifically to targeted tissues or cells. Effective with both crop species and model plant systems, these tools can help researchers overcome the practical obstacles associated with transgenic protocols. Here, we identified promoters that allow one to target the manipulation of gene expression during pollen development. Utilizing published transcriptomic databases for rice, we investigated the promoter activity of selected genes in Arabidopsis. From various microarray datasets, including those for anthers and pollen grains at different developmental stages, we selected nine candidate genes that showed high levels of expression in the late stages of rice pollen development. We named these Oryza sativa late pollen-specific genes. Their promoter regions contained various cis-acting elements that could be responsible for anther-/pollen-specific expression. Promoter::GUS-GFP reporters were constructed and introduced into Arabidopsis plants. Histochemical GUS staining revealed that six of the nine rice promoters conferred strong GUS expression that was restricted to the anthers in Arabidopsis. Further analysis showed that although the GUS signals were not detected at the unicellular stage, they strengthened in the bicellular or tricellular stages, peaking at the mature pollen stage. This paralleled their transcriptomic profiles in rice. Based on our results, we proposed that these six rice promoters, which are active in the late stages of pollen formation in the dicot Arabidopsis, can aid molecular breeders in generating new varieties of a monocot plant, rice.
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Affiliation(s)
- Moe Moe Oo
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
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85
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Hyun TK, Rim Y, Kim E, Kim JS. Genome-wide and molecular evolution analyses of the KT/HAK/KUP family in tomato (Solanum lycopersicum L.). Genes Genomics 2014. [DOI: 10.1007/s13258-014-0174-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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86
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Abstract
Cytokinins are N (6) substituted adenine derivatives that affect many aspects of plant growth and development, including cell division, shoot initiation and growth, leaf senescence, apical dominance, sink/source relationships, nutrient uptake, phyllotaxis, and vascular, gametophyte, and embryonic development, as well as the response to biotic and abiotic factors. Molecular genetic studies in Arabidopsis have helped elucidate the mechanisms underlying the function of this phytohormone in plants. Here, we review our current understanding of cytokinin biosynthesis and signaling in Arabidopsis, the latter of which is similar to bacterial two-component phosphorelays. We discuss the perception of cytokinin by the ER-localized histidine kinase receptors, the role of the AHPs in mediating the transfer of the phosphoryl group from the receptors to the response regulators (ARRs), and finally the role of the large ARR family in cytokinin function. The identification and genetic manipulation of the genes involved in cytokinin metabolism and signaling have helped illuminate the roles of cytokinins in Arabidopsis. We discuss these diverse roles, and how other signaling pathways influence cytokinin levels and sensitivity though modulation of the expression of cytokinin signaling and metabolic genes.
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Affiliation(s)
- Joseph J Kieber
- University of North Carolina, Biology Department, Chapel Hill, NC 27599-3280
| | - G Eric Schaller
- Dartmouth College, Department of Biological Sciences, Hanover, NH 03755
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87
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Kang NY, Cho C, Kim J. Inducible expression of Arabidopsis response regulator 22 (ARR22), a type-C ARR, in transgenic Arabidopsis enhances drought and freezing tolerance. PLoS One 2013; 8:e79248. [PMID: 24244460 PMCID: PMC3828410 DOI: 10.1371/journal.pone.0079248] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/20/2013] [Indexed: 12/14/2022] Open
Abstract
The Arabidopsis two-component signaling system, which is comprised of sensor histidine kinases, histidine phosphotransfer proteins, and response regulators, mediates cytokinin response as well as various other plant responses including abiotic stress responses. Arabidopsis response regulators (ARRs) are classified into type-A, -B, and -C. Although the roles of type-A and -B ARRs are well established in Arabidopsis plant signaling, roles of type-C ARRs, ARR22 and ARR24, remain elusive. ARR22, a preferentially cytosolic protein, interacts with certain Arabidopsis histidine phosphotransfer proteins (AHPs) and displays phosphatase activity on AHP5. ARR22 is induced by cold and dehydration. Here, we show that inducible overexpression of ARR22 in Arabidopsis enhanced dehydration, drought, and cold tolerance in a dexamethasone-dependent manner, whereas mutation of the putative phospho-accepting Asp to Asn in ARR22 (ARR22D74N) abolished these tolerance phenotypes. Overexpression of ARR22 decreased electrolyte leakage in dehydration-, drought-, or cold-stressed transgenic Arabidopsis plants compared with that of ARR22D74N or compared with wild-type plants. Transpiration rates and stomatal apertures were not affected by ARR22 overexpression. No significant difference in both dehydration and freezing tolerance was observed between wild-type and arr22 mutants with or without cytokinin preincubation, consistent with the lack of phenotypes of arr22 mutants in their vegetative development. Meta-profile analyses of the microarray data on ARR22-responsive genes indicate that ARR22 modulates expression of a variety of abiotic stress-responsive genes, which might contribute to increasing drought and freezing tolerance. Taken together, these results suggest that ARR22 plays a positive role in the stress tolerance response in part via enhancing cell membrane integrity and that phospho-histidine phosphatase activity of ARR22 may be required for this function.
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Affiliation(s)
- Na Young Kang
- Department of Bioenergy Science and Technology and Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju, Korea
| | - Chuloh Cho
- Department of Bioenergy Science and Technology and Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology and Kumho Life Science Laboratory, Chonnam National University, Buk-Gu, Gwangju, Korea
- * E-mail:
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88
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Takahashi N, Kajihara T, Okamura C, Kim Y, Katagiri Y, Okushima Y, Matsunaga S, Hwang I, Umeda M. Cytokinins Control Endocycle Onset by Promoting the Expression of an APC/C Activator in Arabidopsis Roots. Curr Biol 2013; 23:1812-7. [DOI: 10.1016/j.cub.2013.07.051] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/16/2013] [Accepted: 07/16/2013] [Indexed: 01/31/2023]
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89
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Bai H, Euring D, Volmer K, Janz D, Polle A. The nitrate transporter (NRT) gene family in poplar. PLoS One 2013; 8:e72126. [PMID: 23977227 PMCID: PMC3747271 DOI: 10.1371/journal.pone.0072126] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/03/2013] [Indexed: 11/29/2022] Open
Abstract
Nitrate is an important nutrient required for plant growth. It also acts as a signal regulating plant development. Nitrate is actively taken up and transported by nitrate transporters (NRT), which form a large family with many members and distinct functions. In contrast to Arabidopsis and rice there is little information about the NRT family in woody plants such as Populus. In this study, a comprehensive analysis of the Populus NRT family was performed. Sixty-eight PtNRT1/PTR, 6 PtNRT2, and 5 PtNRT3 genes were identified in the P. trichocarpa genome. Phylogenetic analysis confirmed that the genes of the NRT family are divided into three clades: NRT1/PTR with four subclades, NRT2, and NRT3. Topological analysis indicated that all members of PtNRT1/PTR and PtNRT2 have 8 to 12 trans-membrane domains, whereas the PtNRT3 proteins have no or up to two trans-membrane domains. Four PtNRT3 members were predicted as secreted proteins. Microarray analyses revealed tissue-specific expression patterns of PtNRT genes with distinct clusters of NRTs for roots, for the elongation zone of the apical stem segment and the developing xylem and a further cluster for leaves, bark and wood. A comparison of different poplar species (P. trichocarpa, P. tremula, P. euphratica, P. fremontii x P. angustifolia, and P. x canescens) showed that the tissue-specific patterns of the NRT genes varied to some extent with species. Bioinformatic analysis of putative cis-regulatory elements in the promoter regions of PtNRT family retrieved motifs suggesting the regulation of the NRT genes by N metabolism, by energy and carbon metabolism, and by phytohormones and stress. Multivariate analysis suggested that the combination and abundance of motifs in distinct promoters may lead to tissue-specificity. Our genome wide analysis of the PtNRT genes provides a valuable basis for functional analysis towards understanding the role of nitrate transporters for tree growth.
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Affiliation(s)
- Hua Bai
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Dejuan Euring
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Katharina Volmer
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Dennis Janz
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Andrea Polle
- Forstbotanik und Baumphysiologie, Georg-August Universität Göttingen, Göttingen, Germany
- * E-mail:
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90
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Philip A, Syamaladevi DP, Chakravarthi M, Gopinath K, Subramonian N. 5' Regulatory region of ubiquitin 2 gene from Porteresia coarctata makes efficient promoters for transgene expression in monocots and dicots. PLANT CELL REPORTS 2013; 32:1199-210. [PMID: 23508257 DOI: 10.1007/s00299-013-1416-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 01/30/2013] [Accepted: 03/04/2013] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE Porteresia ubiquitin 5' regulatory region drives transgene expression in monocots and dicots. Ubiquitin promoters are promising candidates for constitutive transgene expression in plants. In this study, we isolated and characterized a novel 5' regulatory sequence of a ubiquitin gene from Porteresia coarctata, a stress-tolerant wild grass species. Through functional analysis in heterologous plant systems, we have demonstrated that full length (Port Ubi2.3) or truncated sequence (PD2) of the isolated regulatory fragment can drive constitutive expression of GUS in monocots and/or dicots. In silico analysis of Port Ubi2.3 has revealed the presence of a 640 bp core promoter region followed by two exons and two introns with numerous putative cis-acting sites scattered throughout the regulatory region. Transformation and expression studies of six different deletion constructs in rice, tobacco and sugarcane revealed that the proximal intron has an enhancing effect on the activity of the core promoter in both monocots and dicots, whereas, Port Ubi2.3 was able to render strong expression only in monocots. This regulatory sequence is quite distinct from the other reported ubiquitin promoters in structure and performs better in monocots compared to other commonly used promoters-maize Ubi1 and Cauliflower Mosaic Virus 35S.
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Affiliation(s)
- Anna Philip
- Sugarcane Breeding Institute, Indian Council of Agriculture Research, Coimbatore, 641 007, Tamilnadu, India
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91
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Ramireddy E, Brenner WG, Pfeifer A, Heyl A, Schmülling T. In planta analysis of a cis-regulatory cytokinin response motif in Arabidopsis and identification of a novel enhancer sequence. PLANT & CELL PHYSIOLOGY 2013; 54:1079-92. [PMID: 23620480 DOI: 10.1093/pcp/pct060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The phytohormone cytokinin plays a key role in regulating plant growth and development, and is involved in numerous physiological responses to environmental changes. The type-B response regulators, which regulate the transcription of cytokinin response genes, are a part of the cytokinin signaling system. Arabidopsis thaliana encodes 11 type-B response regulators (type-B ARRs), and some of them were shown to bind in vitro to the core cytokinin response motif (CRM) 5'-(A/G)GAT(T/C)-3' or, in the case of ARR1, to an extended motif (ECRM), 5'-AAGAT(T/C)TT-3'. Here we obtained in planta proof for the functionality of the latter motif. Promoter deletion analysis of the primary cytokinin response gene ARR6 showed that a combination of two extended motifs within the promoter is required to mediate the full transcriptional activation by ARR1 and other type-B ARRs. CRMs were found to be over-represented in the vicinity of ECRMs in the promoters of cytokinin-regulated genes, suggesting their functional relevance. Moreover, an evolutionarily conserved 27 bp long T-rich region between -220 and -193 bp was identified and shown to be required for the full activation by type-B ARRs and the response to cytokinin. This novel enhancer is not bound by the DNA-binding domain of ARR1, indicating that additional proteins might be involved in mediating the transcriptional cytokinin response. Furthermore, genome-wide expression profiling identified genes, among them ARR16, whose induction by cytokinin depends on both ARR1 and other specific type-B ARRs. This together with the ECRM/CRM sequence clustering indicates cooperative action of different type-B ARRs for the activation of particular target genes.
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Affiliation(s)
- Eswarayya Ramireddy
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Germany
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92
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Chai C, Lin Y, Shen D, Wu Y, Li H, Dou D. Identification and functional characterization of the soybean GmaPPO12 promoter conferring Phytophthora sojae induced expression. PLoS One 2013; 8:e67670. [PMID: 23840763 PMCID: PMC3695865 DOI: 10.1371/journal.pone.0067670] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/26/2013] [Indexed: 01/13/2023] Open
Abstract
Identification of pathogen-inducible promoters largely lags behind cloning of the genes for disease resistance. Here, we cloned the soybean GmaPPO12 gene and found that it was rapidly and strongly induced by Phytophthorasojae infection. Computational analysis revealed that its promoter contained many known cis-elements, including several defense related transcriptional factor-binding boxes. We showed that the promoter could mediate induction of GUS expression upon infection in both transient expression assays in Nicotianabenthamiana and stable transgenic soybean hairy roots. Importantly, we demonstrated that pathogen-induced expression of the GmaPPO12 promoter was higher than that of the soybean GmaPR1a promoter. A progressive 5' and 3' deletion analysis revealed two fragments that were essential for promoter activity. Thus, the cloned promoter could be used in transgenic plants to enhance resistance to phytophthora pathogens, and the identified fragment could serve as a candidate to produce synthetic pathogen-induced promoters.
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Affiliation(s)
- Chunyue Chai
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- College of Life Science and Technology, Nanyang Normal University, Nanyang, China
| | - Yanling Lin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yuren Wu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Hongjuan Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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93
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Yang CQ, Liu YZ, An JC, Li S, Jin LF, Zhou GF, Wei QJ, Yan HQ, Wang NN, Fu LN, Liu X, Hu XM, Yan TS, Peng SA. Digital gene expression analysis of corky split vein caused by boron deficiency in 'Newhall' Navel Orange (Citrus sinensis Osbeck) for selecting differentially expressed genes related to vascular hypertrophy. PLoS One 2013; 8:e65737. [PMID: 23755275 PMCID: PMC3673917 DOI: 10.1371/journal.pone.0065737] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/26/2013] [Indexed: 01/01/2023] Open
Abstract
Corky split vein caused by boron (B) deficiency in 'Newhall' Navel Orange was studied in the present research. The boron-deficient citrus exhibited a symptom of corky split vein in mature leaves. Morphologic and anatomical surveys at four representative phases of corky split veins showed that the symptom was the result of vascular hypertrophy. Digital gene expression (DGE) analysis was performed based on the Illumina HiSeq™ 2000 platform, which was applied to analyze the gene expression profilings of corky split veins at four morphologic phases. Over 5.3 million clean reads per library were successfully mapped to the reference database and more than 22897 mapped genes per library were simultaneously obtained. Analysis of the differentially expressed genes (DEGs) revealed that the expressions of genes associated with cytokinin signal transduction, cell division, vascular development, lignin biosynthesis and photosynthesis in corky split veins were all affected. The expressions of WOL and ARR12 involved in the cytokinin signal transduction pathway were up-regulated at 1(st) phase of corky split vein development. Furthermore, the expressions of some cell cycle genes, CYCs and CDKB, and vascular development genes, WOX4 and VND7, were up-regulated at the following 2(nd) and 3(rd) phases. These findings indicated that the cytokinin signal transduction pathway may play a role in initiating symptom observed in our study.
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Affiliation(s)
- Cheng-Quan Yang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Yong-Zhong Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Ji-Cui An
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Shuang Li
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Long-Fei Jin
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Gao-Feng Zhou
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Qing-Jiang Wei
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Hui-Qing Yan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Nan-Nan Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Li-Na Fu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Xiao Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Xiao-Mei Hu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Ting-Shuai Yan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
| | - Shu-Ang Peng
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, China
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94
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Verma V, Sivaraman J, Kumar PP. Expression, purification, and characterization of cytokinin signaling intermediates: Arabidopsis histidine phosphotransfer protein 1 (AHP1) and AHP2. PLANT CELL REPORTS 2013; 32:795-805. [PMID: 23525762 DOI: 10.1007/s00299-013-1424-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/05/2013] [Accepted: 03/10/2013] [Indexed: 06/02/2023]
Abstract
We have expressed, purified, and biophysically characterized recombinant AHP1 and AHP2. Also, using computational homology models for AHP1, ARR7, and AHP1–ARR7 complex, we identified threedimensional positioning of key amino acids. Cytokinin signaling involves activation of Arabidopsis Response Regulators (ARRs) by Arabidopsis Histidine Phosphotransfer Proteins (AHPs) by phosphorylation. Type-A ARRs are key regulators of several developmental pathways, but the mechanism underlying this phosphorylation and activation is not known in plants. In this study, we report the successful expression and purification of recombinant AHP1 and AHP2. Biophysical characterization shows that these two recombinant proteins were purified to homogeneity and possess well-defined secondary structures. Brief attempts to purify recombinant ARR7 posed problems during size-exclusion chromatography. Nevertheless, we generated computational homology models for AHP1, ARR7, and AHP1-ARR7 complex using crystal structures of homologous proteins from other organisms. The homology models helped to identify the three-dimensional positioning of the key conserved residues of AHP1 and ARR7 involved in phosphorylation. The similarity in positioning of these residues to other homologous proteins suggests that AHPs and type-A ARRs could be structurally conserved across kingdoms. Thus, our homology models can serve as valuable tools to gain structural insights into the phosphorylation and activation of cytokinin response regulators in plants.
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Affiliation(s)
- Vivek Verma
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
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95
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El-Showk S, Ruonala R, Helariutta Y. Crossing paths: cytokinin signalling and crosstalk. Development 2013; 140:1373-83. [PMID: 23482484 DOI: 10.1242/dev.086371] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cytokinins are a major class of plant hormones that are involved in various aspects of plant development, ranging from organ formation and apical dominance to leaf senescence. Cytokinin and auxin have long been known to interact antagonistically, and more recent studies have shown that cytokinins also interact with other plant hormones to regulate plant development. A growing body of research has begun to elucidate the molecular and genetic underpinnings of this extensive crosstalk. The rich interconnections between the synthesis, perception and transport networks of these plant hormones provide a wide range of opportunities for them to modulate, amplify or buffer one another. Here, we review this exciting and rapidly growing area of cytokinin research.
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Affiliation(s)
- Sedeer El-Showk
- Institute of Biotechnology/Department of Biosciences, University of Helsinki, Helsinki FI-00014, Finland
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96
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Liao SC, Lin CS, Wang AY, Sung HY. Differential expression of genes encoding acid invertases in multiple shoots of bamboo in response to various phytohormones and environmental factors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:4396-4405. [PMID: 23586540 DOI: 10.1021/jf400776m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The promoter regions of two cell wall invertase genes, Boβfruct1 and Boβfruct2, and a vacuolar invertase gene, Boβfruct3, in Bambusa oldhamii were cloned, and putative regulatory cis-elements were identified. The expression of these three genes in multiple shoots of bamboo that were cultured in vitro under different conditions was analyzed by real-time PCR. The two cell wall invertase genes were upregulated by indole-3-acetic acid and cytokinins but responded differently to other phytohormones and different temperatures. Boβfruct1 was also upregulated by sucrose and glucose. In contrast, the Boβfruct2 expression was induced by the depletion of sucrose, and this induction could be suppressed by glucose and sucrose. The expression of Boβfruct3 was light-dependent; however, abscisic acid (ABA) could induce its expression in the dark. ABA and light exhibited an additive effect on the expression of Boβfruct3. Our results suggest that these three Boβfruct genes have individual roles in the adaption of the plant to environmental changes. Boβfruct2 might also have an essential role in the immediate response of cells to sucrose availability and in the maintenance of sink activity. Moreover, Boβfruct3 might be one of the interacting nodes of the light and ABA signaling pathways.
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Affiliation(s)
- Shu-Chien Liao
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 106, Taiwan
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97
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Hill K, Mathews DE, Kim HJ, Street IH, Wildes SL, Chiang YH, Mason MG, Alonso JM, Ecker JR, Kieber JJ, Schaller GE. Functional characterization of type-B response regulators in the Arabidopsis cytokinin response. PLANT PHYSIOLOGY 2013; 162:212-24. [PMID: 23482873 PMCID: PMC3641203 DOI: 10.1104/pp.112.208736] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 03/10/2013] [Indexed: 05/20/2023]
Abstract
Cytokinins play critical roles in plant growth and development, with the transcriptional response to cytokinin being mediated by the type-B response regulators. In Arabidopsis (Arabidopsis thaliana), type-B response regulators (ARABIDOPSIS RESPONSE REGULATORS [ARRs]) form three subfamilies based on phylogenic analysis, with subfamily 1 having seven members and subfamilies 2 and 3 each having two members. Cytokinin responses are predominantly mediated by subfamily 1 members, with cytokinin-mediated effects on root growth and root meristem size correlating with type-B ARR expression levels. To determine which type-B ARRs can functionally substitute for the subfamily 1 members ARR1 or ARR12, we expressed different type-B ARRs from the ARR1 promoter and assayed their ability to rescue arr1 arr12 double mutant phenotypes. ARR1, as well as a subset of other subfamily 1 type-B ARRs, restore the cytokinin sensitivity to arr1 arr12. Expression of ARR10 from the ARR1 promoter results in cytokinin hypersensitivity and enhances shoot regeneration from callus tissue, correlating with enhanced stability of the ARR10 protein compared with the ARR1 protein. Examination of transfer DNA insertion mutants in subfamilies 2 and 3 revealed little effect on several well-characterized cytokinin responses. However, a member of subfamily 2, ARR21, restores cytokinin sensitivity to arr1 arr12 roots when expressed from the ARR1 promoter, indicating functional conservation of this divergent family member. Our results indicate that the type-B ARRs have diverged in function, such that some, but not all, can complement the arr1 arr12 mutant. In addition, our results indicate that type-B ARR expression profiles in the plant, along with posttranscriptional regulation, play significant roles in modulating their contribution to cytokinin signaling.
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98
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Bhargava A, Clabaugh I, To JP, Maxwell BB, Chiang YH, Schaller GE, Loraine A, Kieber JJ. Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis. PLANT PHYSIOLOGY 2013; 162:272-94. [PMID: 23524861 PMCID: PMC3641208 DOI: 10.1104/pp.113.217026] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 03/21/2013] [Indexed: 05/17/2023]
Abstract
Cytokinins are N(6)-substituted adenine derivatives that play diverse roles in plant growth and development. We sought to define a robust set of genes regulated by cytokinin as well as to query the response of genes not represented on microarrays. To this end, we performed a meta-analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokinin-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Microarray meta-analysis using 13 microarray experiments combined with empirically defined filtering criteria identified a set of 226 genes differentially regulated by cytokinin, a subset of which has previously been validated by other methods. RNA-seq validated about 73% of the up-regulated genes identified by this meta-analysis. In silico promoter analysis indicated an overrepresentation of type-B Arabidopsis response regulator binding elements, consistent with the role of type-B Arabidopsis response regulators as primary mediators of cytokinin-responsive gene expression. RNA-seq analysis identified 73 cytokinin-regulated genes that were not represented on the ATH1 microarray. Representative genes were verified using quantitative reverse transcription-polymerase chain reaction and NanoString analysis. Analysis of the genes identified reveals a substantial effect of cytokinin on genes encoding proteins involved in secondary metabolism, particularly those acting in flavonoid and phenylpropanoid biosynthesis, as well as in the regulation of redox state of the cell, particularly a set of glutaredoxin genes. Novel splicing events were found in members of some gene families that are known to play a role in cytokinin signaling or metabolism. The genes identified in this analysis represent a robust set of cytokinin-responsive genes that are useful in the analysis of cytokinin function in plants.
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Li Y, Kurepa J, Smalle J. AXR1 promotes the Arabidopsis cytokinin response by facilitating ARR5 proteolysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:13-24. [PMID: 23279608 DOI: 10.1111/tpj.12098] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 12/07/2012] [Accepted: 12/11/2012] [Indexed: 05/26/2023]
Abstract
The plant hormone cytokinin plays essential roles in many aspects of growth and development. The cytokinin signal is transmitted by a multi-step phosphorelay to the members of two functionally antagonistic classes of Arabidopsis response regulators (ARRs): type B ARRs (response activators) and type A ARRs (negative-feedback regulators). Previous studies have shown that mutations in AXR1, encoding a subunit of the E1 enzyme in the RUB (related to ubiquitin) modification pathway, lead to decreased cytokinin sensitivity. Here we show that the cytokinin resistance of axr1 seedlings is suppressed by loss of function of the type A ARR family member ARR5. Based on the established role of the RUB pathway in ubiquitin-dependent proteolysis, these data suggest that AXR1 promotes the cytokinin response by facilitating type A ARR degradation. Indeed, both genetic (axr1 mutants) and chemical (MLN4924) suppression of RUB E1 increased ARR5 stability, suggesting that the ubiquitin ligase that promotes ARR5 proteolysis requires RUB modification for optimal activity.
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Affiliation(s)
- Yan Li
- Plant Physiology, Biochemistry and Molecular Biology Program, Department of Plant and Soil Science, University of Kentucky, Lexington, KY 40546, USA
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100
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Zürcher E, Tavor-Deslex D, Lituiev D, Enkerli K, Tarr PT, Müller B. A robust and sensitive synthetic sensor to monitor the transcriptional output of the cytokinin signaling network in planta. PLANT PHYSIOLOGY 2013; 161:1066-75. [PMID: 23355633 PMCID: PMC3585579 DOI: 10.1104/pp.112.211763] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 01/24/2013] [Indexed: 05/17/2023]
Abstract
Cytokinins are classic plant hormones that orchestrate plant growth, development, and physiology. They affect gene expression in target cells by activating a multistep phosphorelay network. Type-B response regulators, acting as transcriptional activators, mediate the final step in the signaling cascade. Previously, we have introduced a synthetic reporter, Two Component signaling Sensor (TCS)::green fluorescent protein (GFP), which reflects the transcriptional activity of type-B response regulators. TCS::GFP was instrumental in uncovering roles of cytokinin and deepening our understanding of existing functions. However, TCS-mediated expression of reporters is weak in some developmental contexts where cytokinin signaling has a documented role, such as in the shoot apical meristem or in the vasculature of Arabidopsis (Arabidopsis thaliana). We also observed that GFP expression becomes rapidly silenced in TCS::GFP transgenic plants. Here, we present an improved version of the reporter, TCS new (TCSn), which, compared with TCS, is more sensitive to phosphorelay signaling in Arabidopsis and maize (Zea mays) cellular assays while retaining its specificity. Transgenic Arabidopsis TCSn::GFP plants exhibit strong and dynamic GFP expression patterns consistent with known cytokinin functions. In addition, GFP expression has been stable over generations, allowing for crosses with different genetic backgrounds. Thus, TCSn represents a significant improvement to report the transcriptional output profile of phosphorelay signaling networks in Arabidopsis, maize, and likely other plants that display common response regulator DNA-binding specificities.
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