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Liang J, Wu Z, Zhang X, Du X, Wang S, Yang Y, Wang Y, Wang Y, Yang H. Study on the Interactions of Cyclins with CDKs Involved in Auxin Signal during Leaf Development by WGCNA in Populus alba. Int J Mol Sci 2023; 24:13445. [PMID: 37686248 PMCID: PMC10487486 DOI: 10.3390/ijms241713445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Cell division plays an indispensable role in leaf morphogenesis, which is regulated via the complexes formed by cyclin and cyclin-dependent kinase (CDK). In this study, gene family analysis, exogenous auxin stimulation, RNA-seq and WGCNA analysis were all used to investigate the molecular mechanisms by which cell-cycle-related factors participated in the auxin signaling pathway on leaf morphogenesis. Sixty-three cyclin members and seventeen CDK members in Populus alba were identified and systematically analyzed. During the evolution, WGD was the main reason that resulted in the expansion of cyclin and CDK genes. Firstly, after a short time treating with auxin to matured leaves of seedlings, genes related to cell division including GRF and ARGOS were both upregulated to restart the transition of cells from G1-to-S phase. Secondly, with three days of continuous auxin stimulation to leaves at different developmental stages, leaves area variation, transcriptomes and hormones were analyzed. By PCA, PCoA and WGCNA analyses, the turquoise module was both positively related to leaf development and auxin. Based on the co-expression analysis and Y2H experiment, PoalbCYCD1;4, PoalbCYCD3;3 and PoalbCYCD3;5 were supposed to interact with PoalbCDKA;1, which could be the trigger to promote the G1-to-S phase transition. The ARF transcription factor might play the key role of connecting the auxin signaling pathway and cell division in leaf morphogenesis by affecting CYC-CDK complexes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hailing Yang
- State Key Laboratory of Tree Genetics and Breeding, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100107, China; (J.L.); (Z.W.); (X.Z.); (X.D.); (S.W.); (Y.Y.); (Y.W.); (Y.W.)
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Control of vein-forming, striped gene expression by auxin signaling. BMC Biol 2021; 19:213. [PMID: 34556094 PMCID: PMC8461865 DOI: 10.1186/s12915-021-01143-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Activation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals, gene expression is activated in striped domains by the differential affinity of broadly expressed transcription factors for their target genes and the combinatorial interaction between such target genes. In plants, how gene expression is activated in striped domains is instead unknown. We address this question for the broadly expressed MONOPTEROS (MP) transcription factor and its target gene ARABIDOPSIS THALIANA HOMEOBOX FACTOR8 (ATHB8). Results We find that ATHB8 promotes vein formation and that such vein-forming function depends on both levels of ATHB8 expression and width of ATHB8 expression domains. We further find that ATHB8 expression is activated in striped domains by a combination of (1) activation of ATHB8 expression through binding of peak levels of MP to a low-affinity MP-binding site in the ATHB8 promoter and (2) repression of ATHB8 expression by MP target genes of the AUXIN/INDOLE-3-ACETIC-ACID-INDUCIBLE family. Conclusions Our findings suggest that a common regulatory logic controls activation of gene expression in striped domains in both plants and animals despite the independent evolution of their multicellularity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01143-9.
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Govindaraju P, Verna C, Zhu T, Scarpella E. Vein patterning by tissue-specific auxin transport. Development 2020; 147:dev.187666. [PMID: 32493758 DOI: 10.1242/dev.187666] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/27/2020] [Indexed: 11/20/2022]
Abstract
Unlike in animals, in plants, vein patterning does not rely on direct cell-cell interaction and cell migration; instead, it depends on the transport of the plant hormone auxin, which in turn depends on the activity of the PIN-FORMED1 (PIN1) auxin transporter. The current hypotheses of vein patterning by auxin transport propose that, in the epidermis of the developing leaf, PIN1-mediated auxin transport converges to peaks of auxin level. From those convergence points of epidermal PIN1 polarity, auxin would be transported in the inner tissues where it would give rise to major veins. Here, we have tested predictions of this hypothesis and have found them unsupported: epidermal PIN1 expression is neither required nor sufficient for auxin transport-dependent vein patterning, whereas inner-tissue PIN1 expression turns out to be both required and sufficient for auxin transport-dependent vein patterning. Our results refute all vein patterning hypotheses based on auxin transport from the epidermis and suggest alternatives for future tests.
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Affiliation(s)
- Priyanka Govindaraju
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB T6G 2E9, Canada
| | - Carla Verna
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB T6G 2E9, Canada
| | - Tongbo Zhu
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB T6G 2E9, Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB T6G 2E9, Canada
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Kim S, Nie H, Jun B, Kim J, Lee J, Kim S, Kim E, Kim S. Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation. Genes Genomics 2020; 42:581-596. [PMID: 32240514 DOI: 10.1007/s13258-020-00927-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/26/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Sweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear. OBJECTIVE To understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato. METHODS RNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression. RESULTS 42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation. CONCLUSIONS The detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.
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Affiliation(s)
- Sujung Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Hualin Nie
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Byungki Jun
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.,NH Seed Research Development Center, Nonghyup Agribusiness Group Incorporation, Anseong, 17558, Korea
| | - Jiseong Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Jeongeun Lee
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Ekyune Kim
- College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk, 38430, Korea
| | - Sunhyung Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
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Cheng H, Liang Q, Chen X, Zhang Y, Qiao F, Guo D. Hydrogen peroxide facilitates Arabidopsis seedling establishment by interacting with light signalling pathway in the dark. PLANT, CELL & ENVIRONMENT 2019; 42:1302-1317. [PMID: 30474863 DOI: 10.1111/pce.13482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
Light is essential for the plant establishment. Arabidopsis seedlings germinated in the dark cannot grow leaf and only have closed cotyledons. However, exogenous application of H2 O2 can induce leaves (establishment) in the dark. Comparative transcriptomic analysis revealed that light-responsive genes were activated by H2 O2 treatment. These genes are functionally correlated with photosynthesis, photorespiration, and components of photosystem, such as antenna proteins and light-harvesting chlorophyll proteins. We further found that application of H2 O2 facilitates cell cycle by accelerating G2 -M checkpoint transition in shoot apical meristem. Phytochrome-mediated light signalling pathway was also involved in the H2 O2 -facilitated establishment process. The constitutive photomorphogenesis 1 and phytochrome interacting factor 3 proteins were shown to be down-regulated by H2 O2 treatment and accordingly removed their inhibitory effects on photomorphogenesis in the dark. The crosstalk between oxidation and light signal pathways explains the mechanism that H2 O2 regulates plant dark establishment. The endogenous photorespiratory H2 O2 production was mimicked by overexpression of glycolate oxidase genes and supplement of substrate glycolate. As expected, seedling establishment was also induced by the endogenously produced H2 O2 under dark condition. These findings also suggest that photorespiratory H2 O2 production is at least partially involved in postgermination establishment.
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Affiliation(s)
- Han Cheng
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, Hainan, China
- School of Life Science and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Qun Liang
- School of Agricultural Science, Hainan University, Haikou, Hainan, China
| | - Xiang Chen
- School of Agricultural Science, Hainan University, Haikou, Hainan, China
| | - Yuanyuan Zhang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, Hainan, China
| | - Fei Qiao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, Hainan, China
| | - Dianjing Guo
- School of Life Science and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
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Olszak M, Truman W, Stefanowicz K, Sliwinska E, Ito M, Walerowski P, Rolfe S, Malinowski R. Transcriptional profiling identifies critical steps of cell cycle reprogramming necessary for Plasmodiophora brassicae-driven gall formation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:715-729. [PMID: 30431210 PMCID: PMC6850046 DOI: 10.1111/tpj.14156] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/31/2018] [Accepted: 11/06/2018] [Indexed: 05/08/2023]
Abstract
Plasmodiophora brassicae is a soil-borne biotroph whose life cycle involves reprogramming host developmental processes leading to the formation of galls on its underground parts. Formation of such structures involves modification of the host cell cycle leading initially to hyperplasia, increasing the number of cells to be invaded, followed by overgrowth of cells colonised by the pathogen. Here we show that P. brassicae infection stimulates formation of the E2Fa/RBR1 complex and upregulation of MYB3R1, MYB3R4 and A- and B-type cyclin expression. These factors were previously described as important regulators of the G2-M cell cycle checkpoint. As a consequence of this manipulation, a large population of host hypocotyl cells are delayed in cell cycle exit and maintained in the proliferative state. We also report that, during further maturation of galls, enlargement of host cells invaded by the pathogen involves endoreduplication leading to increased ploidy levels. This study characterises two aspects of the cell cycle reprogramming efforts of P. brassicae: systemic, related to the disturbance of host hypocotyl developmental programs by preventing cell cycle exit; and local, related to the stimulation of cell enlargement via increased endocycle activity.
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Affiliation(s)
- Marcin Olszak
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
| | - William Truman
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
| | - Karolina Stefanowicz
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and CytometryDepartment of Plant Genetics, Physiology and BiotechnologyUTP University of Science and TechnologyKaliskiego Ave. 785‐789BydgoszczPoland
| | - Masaki Ito
- Graduate School of Bioagricultural SciencesNagoya UniversityChikusaNagoya464‐8601Japan
| | - Piotr Walerowski
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
| | - Stephen Rolfe
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldS10 2TNUK
| | - Robert Malinowski
- Department of Integrative Plant BiologyInstitute of Plant Genetics of the Polish Academy of Sciencesul. Strzeszyńska 3460‐479PoznańPoland
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Jha AK, Wang Y, Hercyk BS, Shin HS, Chen R, Yang M. The role for CYCLIN A1;2/TARDY ASYNCHRONOUS MEIOSIS in differentiated cells in Arabidopsis. PLANT MOLECULAR BIOLOGY 2014; 85:81-94. [PMID: 24430502 DOI: 10.1007/s11103-013-0170-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/24/2013] [Indexed: 05/10/2023]
Abstract
The Arabidopsis A1-type cyclin, CYCA1;2, also named TARDY ASYNCHRONOUS MEIOSIS (TAM), is known for its positive role in meiotic cell cycle progression, but its function in other cells has not been characterized. This paper reports the role of CYCA1;2/TAM in differentiated cells in vegetative organs. The pattern of CYCA1;2/TAM expression was investigated by promoter and protein fusions using the β-glucuronidase and the green fluorescent protein, respectively. The relevance of the promoter region used in these gene fusion constructs was verified by the effective complementation of the phenotype of the diploid null allele, tam-2 2C by a genomic fragment containing the wild-type coding region of CYCA1;2/TAM and the promoter region. CYCA1;2/TAM expression was found primarily in non-proliferating cells such as guard cells, trichomes, and mesophyll cells, and in vascular tissue. In two types of overexpression lines, one containing the CYCA1;2/TAM transgene driven by the ARABIDOPSIS SKP1-LIKE1 (ASK1) promoter and the other CYCA1;2/TAM-GFP driven by the cauliflower mosaic virus 35S promoter, the largest differences between the transgene transcript levels were approximately 72- and 45-folds, respectively, but the TAM-GFP signal levels in the mesophyll and stomata in the 35S:TAM-GFP lines only differ slightly. Furthermore, the GFP signals in the mesophyll and stomata in the TAM:TAM-GFP and 35S:TAM-GFP lines were all at similarly low levels. These results indicate that the CYCA1;2/TAM protein is likely maintained at low levels in these cells through post-transcriptional regulation. Loss of function in CYCA1;2/TAM resulted in increases in the nuclear size in both trichomes and guard cells. Surprisingly, overexpression of CYCA1;2/TAM led to similar increases. The large increases in trichome nuclear size likely reflected ploidy increases while the moderate increases in guard cell nuclear size did not justify for a ploidy increase. These nuclear size increases were not clearly correlated with trichome branch number increases and guard cell size increases, respectively. These results suggest that cellular homeostasis of the CYCA1;2/TAM protein is linked to the control of nuclear sizes in trichomes and guard cells.
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Affiliation(s)
- Ajay K Jha
- 301 Physical Science, Department of Botany, Oklahoma State University, Stillwater, OK, 74078, USA
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Hehl R, Bülow L. AthaMap web tools for the analysis of transcriptional and posttranscriptional regulation of gene expression in Arabidopsis thaliana. Methods Mol Biol 2014; 1158:139-56. [PMID: 24792049 DOI: 10.1007/978-1-4939-0700-7_9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The AthaMap database provides a map of verified and predicted transcription factor (TF) and small RNA-binding sites for the A. thaliana genome. The database can be used for bioinformatic predictions of putative regulatory sites. Several online web tools are available that address specific questions. Starting with the identification of transcription factor-binding sites (TFBS) in any gene of interest, colocalizing TFBS can be identified as well as common TFBS in a set of user-provided genes. Furthermore, genes can be identified that are potentially targeted by specific transcription factors or small inhibitory RNAs. This chapter provides detailed information on how each AthaMap web tool can be used online. Examples on how this database is used to address questions in circadian and diurnal regulation are given. Furthermore, complementary databases and databases that go beyond questions addressed with AthaMap are discussed.
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Affiliation(s)
- Reinhard Hehl
- Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany,
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