1
|
Bahafid E, Bradtmöller I, Thies AM, Nguyen TTON, Gutierrez C, Desvoyes B, Stahl Y, Blilou I, Simon RGW. The Arabidopsis SHORTROOT network coordinates shoot apical meristem development with auxin-dependent lateral organ initiation. eLife 2023; 12:e83334. [PMID: 37862096 PMCID: PMC10642969 DOI: 10.7554/elife.83334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Plants produce new organs post-embryonically throughout their entire life cycle. This is due to stem cells present in the shoot and root apical meristems, the SAM and RAM, respectively. In the SAM, stem cells are located in the central zone where they divide slowly. Stem cell daughters are displaced laterally and enter the peripheral zone, where their mitotic activity increases and lateral organ primordia are formed. How the spatial arrangement of these different domains is initiated and controlled during SAM growth and development, and how sites of lateral organ primordia are determined in the peripheral zone is not yet completely understood. We found that the SHORTROOT (SHR) transcription factor together with its target transcription factors SCARECROW (SCR), SCARECROW-LIKE23 (SCL23) and JACKDAW (JKD), promotes formation of lateral organs and controls shoot meristem size. SHR, SCR, SCL23, and JKD are expressed in distinct, but partially overlapping patterns in the SAM. They can physically interact and activate expression of key cell cycle regulators such as CYCLIND6;1 (CYCD6;1) to promote the formation of new cell layers. In the peripheral zone, auxin accumulates at sites of lateral organ primordia initiation and activates SHR expression via the auxin response factor MONOPTEROS (MP) and auxin response elements in the SHR promoter. In the central zone, the SHR-target SCL23 physically interacts with the key stem cell regulator WUSCHEL (WUS) to promote stem cell fate. Both SCL23 and WUS expression are subject to negative feedback regulation from stem cells through the CLAVATA signaling pathway. Together, our findings illustrate how SHR-dependent transcription factor complexes act in different domains of the shoot meristem to mediate cell division and auxin dependent organ initiation in the peripheral zone, and coordinate this activity with stem cell maintenance in the central zone of the SAM.
Collapse
Affiliation(s)
- Elmehdi Bahafid
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Imke Bradtmöller
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Ann M Thies
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Thi TON Nguyen
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, CantoblancoMadridSpain
| | - Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, CantoblancoMadridSpain
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology, Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Rüdiger GW Simon
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| |
Collapse
|
2
|
Zhang H, Tang Z, Zhang Y, Liu L, Zhao D, Liu X, Guo L, Dong J. TOP1α suppresses lateral root gravitropism in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2022; 17:2098646. [PMID: 35819101 PMCID: PMC9278425 DOI: 10.1080/15592324.2022.2098646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Root gravitropism is important for anchorage and exploration of soil for water and nutrients. It affects root architecture, which is one of the elements that influence crop yield. The mechanism of primary root gravitropism has been widely studied, but it is still not clear how lateral root gravitropism is regulated. Here, in this study, we found that Topoisomerase I α (TOP1α) repressed lateral root gravitropic growth, which was opposite to the previous report that TOP1α maintains primary root gravitropism, revealing a dual function of TOP1α in root gravitropism regulation. Further investigation showed that Target of Rapamycin (TOR) was suppressed in columella cells of lateral root to inhibit columella cell development, especially amyloplast biosynthesis. Our findings uncovered a new mechanism about lateral root gravitropism regulation, which might provide a theoretical support for improving agricultural production.
Collapse
Affiliation(s)
- Hao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ziyan Tang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Ying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Dan Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- College of Life Sciences, Hengshui University, Hengshui, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Lin Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| |
Collapse
|
3
|
Lardon R, Trinh HK, Xu X, Vu LD, Van De Cotte B, Pernisová M, Vanneste S, De Smet I, Geelen D. Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants. FRONTIERS IN PLANT SCIENCE 2022; 13:894208. [PMID: 36684719 PMCID: PMC9847488 DOI: 10.3389/fpls.2022.894208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/27/2022] [Indexed: 06/17/2023]
Abstract
Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.
Collapse
Affiliation(s)
- Robin Lardon
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Hoang Khai Trinh
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Biotechnology Research and Development Institute, Can Tho University, Can Tho, Vietnam
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Brigitte Van De Cotte
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Markéta Pernisová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Steffen Vanneste
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon, South Korea
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| |
Collapse
|
4
|
Abiri N, Sinjushin A, Tekdal D, Cetiner S. Evaluation of the Possible Contribution of Various Regulatory Genes to Determination of Carpel Number as a Potential Mechanism for Optimal Agricultural Yield. Int J Mol Sci 2022; 23:ijms23179723. [PMID: 36077121 PMCID: PMC9456115 DOI: 10.3390/ijms23179723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Various regulatory genes encoding transcription factors and miRNAs regulate carpel number. Multicarpelly is normally associated with increased size of the floral meristem, and several genetic factors have been discovered that influence this characteristic. A fundamental understanding of the regulatory genes affecting carpel number can facilitate strategies for agricultural yield improvement, which is crucial, given that the global population is growing rapidly. A multicarpellate plant may provide a significantly higher yield than a plant bearing fewer carpels. Higher yields can be achieved via various means; in this review, we provide an overview of the current knowledge of the various regulatory factors that contribute to multicarpelly and the potential of increasing carpel number to achieve an increased yield.
Collapse
Affiliation(s)
- Naghmeh Abiri
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
- Correspondence: ; Tel.: +90-5457874622
| | - Andrey Sinjushin
- Department of Genetics, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, 1-12, 119234 Moscow, Russia
| | - Dilek Tekdal
- Faculty of Science and Letters, Department of Biotechnology, Mersin University, 33343 Mersin, Turkey
| | - Selim Cetiner
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| |
Collapse
|
5
|
Chandana BS, Mahto RK, Singh RK, Ford R, Vaghefi N, Gupta SK, Yadav HK, Manohar M, Kumar R. Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea. Front Genet 2022; 13:900253. [PMID: 35937986 PMCID: PMC9355295 DOI: 10.3389/fgene.2022.900253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.
Collapse
Affiliation(s)
- B. S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | | | - Rebecca Ford
- Center for Planetary Health and Food Security, Griffith University, Brisbane, QLD, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | | | | | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
- *Correspondence: Rajendra Kumar,
| |
Collapse
|
6
|
Zhang H, Guo L, Li Y, Zhao D, Liu L, Chang W, Zhang K, Zheng Y, Hou J, Fu C, Zhang Y, Zhang B, Ma Y, Niu Y, Zhang K, Xing J, Cui S, Wang F, Tan K, Zheng S, Tang W, Dong J, Liu X. TOP1α fine-tunes TOR-PLT2 to maintain root tip homeostasis in response to sugars. NATURE PLANTS 2022; 8:792-801. [PMID: 35817819 DOI: 10.1038/s41477-022-01179-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Plant development is highly dependent on energy levels. TARGET OF RAPAMYCIN (TOR) activates the proximal root meristem to promote root development in response to photosynthesis-derived sugars during photomorphogenesis in Arabidopsis thaliana. However, the mechanisms of how root tip homeostasis is maintained to ensure proper root cap structure and gravitropism are unknown. PLETHORA (PLT) transcription factors are pivotal for the root apical meristem (RAM) identity by forming gradients, but how PLT gradients are established and maintained, and their roles in COL development are not well known. We demonstrate that endogenous sucrose induces TOPOISOMERASE1α (TOP1α) expression during the skotomorphogenesis-to-photomorphogenesis transition. TOP1α fine-tunes TOR expression in the root tip columella. TOR maintains columella stem cell identity correlating with reduced quiescent centre cell division in a WUSCHEL RELATED HOMEOBOX5-independent manner. Meanwhile, TOR promotes PLT2 expression and phosphorylates and stabilizes PLT2 to maintain its gradient consistent with TOR expression pattern. PLT2 controls cell division and amyloplast formation to regulate columella development and gravitropism. This elaborate mechanism helps maintain root tip homeostasis and gravitropism in response to energy changes during root development.
Collapse
Affiliation(s)
- Hao Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Lin Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China.
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China.
| | - Yongpeng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Dan Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- College of Life Sciences, Hengshui University, Hengshui, China
| | - Luping Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wenwen Chang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Yichao Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Jiajie Hou
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Chenghao Fu
- Food Science College, Shenyang Agricultural University, ShenYang, China
| | - Ying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Baowen Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Yuru Ma
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Kang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Jihong Xing
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Sujuan Cui
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Fengru Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Ke Tan
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Shuzhi Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Wenqiang Tang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China.
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China.
| |
Collapse
|
7
|
Gu N, Chen C, Kabeya Y, Hasebe M, Tamada Y. Topoisomerase 1α is required for synchronous spermatogenesis in Physcomitrium patens. THE NEW PHYTOLOGIST 2022; 234:137-148. [PMID: 35067949 DOI: 10.1111/nph.17983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
DNA topoisomerase 1 (TOP1) plays general roles in DNA replication and transcription by regulating DNA topology in land plants and metazoans. TOP1 is also involved in specific developmental events; however, whether TOP1 plays a conserved developmental role among multicellular organisms is unknown. Here, we investigated the developmental roles of TOP1 in the moss Physcomitrium (Physcomitrella) patens with gene targeting, microscopy, 3D image segmentation and crossing experiments. We discovered that the disruption of TOP1α, but not its paralogue TOP1β, leads to a defect in fertilisation and subsequent sporophyte formation in P. patens. In the top1α mutant, the egg cell was functional for fertilisation, while sperm cells were fewer and infertile with disordered structures. We observed that the nuclei volume of wild-type sperm cells synchronously decreases during antheridium development, indicating chromatin condensation towards the compact sperm head. By contrast, the top1α mutant exhibited attenuated cell divisions and asynchronous and defective contraction of the nuclei of sperm cells throughout spermatogenesis. These results indicate that TOP1α is involved in cell division and chromatin condensation during spermatogenesis in P. patens. Our results suggest that the regulation of DNA topology by TOP1 plays a key role in spermatogenesis in both land plants and metazoans.
Collapse
Affiliation(s)
- Nan Gu
- Robotics, Engineering and Agriculture-technology Laboratory (REAL), Utsunomiya University, Utsunomiya, 321-8585, Japan
- School of Engineering, Utsunomiya University, Utsunomiya, 321-8585, Japan
- Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Chunli Chen
- Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang, 550025, China
| | - Yukiko Kabeya
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Mitsuyasu Hasebe
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, 444-8585, Japan
| | - Yosuke Tamada
- Robotics, Engineering and Agriculture-technology Laboratory (REAL), Utsunomiya University, Utsunomiya, 321-8585, Japan
- School of Engineering, Utsunomiya University, Utsunomiya, 321-8585, Japan
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
- School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, 444-8585, Japan
- Center for Optical Research & Education (CORE), Utsunomiya University, Utsunomiya, 321-8585, Japan
| |
Collapse
|
8
|
Schlegel J, Denay G, Wink R, Pinto KG, Stahl Y, Schmid J, Blümke P, Simon RGW. Control of Arabidopsis shoot stem cell homeostasis by two antagonistic CLE peptide signalling pathways. eLife 2021; 10:e70934. [PMID: 34643181 PMCID: PMC8594942 DOI: 10.7554/elife.70934] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022] Open
Abstract
Stem cell homeostasis in plant shoot meristems requires tight coordination between stem cell proliferation and cell differentiation. In Arabidopsis, stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which signals through the leucine-rich repeat (LRR)-receptor kinase CLAVATA1 (CLV1) and related CLV1-family members to downregulate expression of the homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from cells below the stem cell domain to the meristem tip and promotes stem cell identity, together with CLV3 expression, generating a negative feedback loop. How stem cell activity in the meristem centre is coordinated with organ initiation and cell differentiation at the periphery is unknown. We show here that the CLE40 gene, encoding a secreted peptide closely related to CLV3, is expressed in the SAM in differentiating cells in a pattern complementary to that of CLV3. CLE40 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40 expression is in turn repressed in a WUS-dependent manner. Together, CLE40-BAM1-WUS establish a second negative feedback loop. We propose that stem cell homeostasis is achieved through two intertwined pathways that adjust WUS activity and incorporate information on the size of the stem cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.
Collapse
Affiliation(s)
- Jenia Schlegel
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Gregoire Denay
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Rene Wink
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Karine Gustavo Pinto
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Yvonne Stahl
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Julia Schmid
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Patrick Blümke
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| | - Rüdiger GW Simon
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine UniversityDüsseldorfGermany
| |
Collapse
|
9
|
Yin X. Phyllotaxis: from classical knowledge to molecular genetics. JOURNAL OF PLANT RESEARCH 2021; 134:373-401. [PMID: 33550488 DOI: 10.1007/s10265-020-01247-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Plant organs are repetitively generated at the shoot apical meristem (SAM) in recognizable patterns. This phenomenon, known as phyllotaxis, has long fascinated scientists from different disciplines. While we have an enriched body of knowledge on phyllotactic patterns, parameters, and transitions, only in the past 20 years, however, have we started to identify genes and elucidate genetic pathways that involved in phyllotaxis. In this review, I first summarize the classical knowledge of phyllotaxis from a morphological perspective. I then discuss recent advances in the regulation of phyllotaxis, from a molecular genetics perspective. I show that the morphological beauty of phyllotaxis we appreciate is the manifestation of many regulators, in addition to the critical role of auxin as a patterning signal, exerting their respective effects in a coordinated fashion either directly or indirectly in the SAM.
Collapse
Affiliation(s)
- Xiaofeng Yin
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Japan Society for the Promotion of Science, Tokyo, Japan.
| |
Collapse
|
10
|
Geng Y, Zhou Y. HAM Gene Family and Shoot Meristem Development. FRONTIERS IN PLANT SCIENCE 2021; 12:800332. [PMID: 34987539 PMCID: PMC8720772 DOI: 10.3389/fpls.2021.800332] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/19/2021] [Indexed: 05/18/2023]
Abstract
Land plants develop highly diversified shoot architectures, all of which are derived from the pluripotent stem cells in shoot apical meristems (SAMs). As sustainable resources for continuous organ formation in the aboveground tissues, SAMs play an important role in determining plant yield and biomass production. In this review, we summarize recent advances in understanding one group of key regulators - the HAIRY MERISTEM (HAM) family GRAS domain proteins - in shoot meristems. We highlight the functions of HAM family members in dictating shoot stem cell initiation and proliferation, the signaling cascade that shapes HAM expression domains in shoot meristems, and the conservation and diversification of HAM family members in land plants. We also discuss future directions that potentially lead to a more comprehensive view of the HAM gene family and stem cell homeostasis in land plants.
Collapse
Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- *Correspondence: Yun Zhou,
| |
Collapse
|
11
|
Integration of pluripotency pathways regulates stem cell maintenance in the Arabidopsis shoot meristem. Proc Natl Acad Sci U S A 2020; 117:22561-22571. [PMID: 32839309 PMCID: PMC7486707 DOI: 10.1073/pnas.2015248117] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pluripotent stem cells are critical in both animal and plant development. Unlike higher animals, plants have unique postembryonic development, which continuously produce organs depending on shoot and root meristems. In the shoot meristem, division of the stem cells in the outermost layers provides the cells for all shoot structures. How those meristem cells are tightly controlled attracted intense studies. Genetic and molecular analyses in Arabidopsis have identified the key transcription factors WUSCHEL (WUS) and SHOOTMERISTEMLESS (STM) as the major regulators of pluripotency in the shoot meristem. Here, the results provide solid evidence showing how those two pluripotency factors WUS and STM coordinate to control shoot meristem cells strictly in plants. In the shoot meristem, both WUSCHEL (WUS) and SHOOT MERISTEMLESS (STM), two transcription factors with overlapping spatiotemporal expression patterns, are essential for maintaining stem cells in an undifferentiated state. Despite their importance, it remains unclear how these two pathways are integrated to coordinate stem cell development. Here, we show that the WUS and STM pathways in Arabidopsis thaliana converge through direct interaction between the WUS and STM proteins. STM binds to the promoter of CLAVATA3 (CLV3) and enhances the binding of WUS to the same promoter through the WUS–STM interaction. Both the heterodimerization and simultaneous binding of WUS and STM at two sites on the CLV3 promoter are required to regulate CLV3 expression, which in turn maintains a constant number of stem cells. Furthermore, the expression of STM depends on WUS, and this WUS-activated STM expression enhances the WUS-mediated stem cell activity. Our data provide a framework for understanding how spatial expression patterns within the shoot meristem are translated into regulatory units of stem cell homeostasis.
Collapse
|
12
|
Fuchs M, Lohmann JU. Aiming for the top: non-cell autonomous control of shoot stem cells in Arabidopsis. JOURNAL OF PLANT RESEARCH 2020; 133:297-309. [PMID: 32146616 PMCID: PMC7214502 DOI: 10.1007/s10265-020-01174-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/27/2020] [Indexed: 05/13/2023]
Abstract
In multicellular organisms, not all cells are created equal. Instead, organismal complexity is achieved by specialisation and division of labour between distinct cell types. Therefore, the organism depends on the presence, correct proportion and function of all cell types. It follows that early development is geared towards setting up the basic body plan and to specify cell lineages. Since plants employ a post-embryonic mode of development, the continuous growth and addition of new organs require a source of new cells, as well as a strict regulation of cellular composition throughout the entire life-cycle. To meet these demands, evolution has brought about complex regulatory systems to maintain and control continuously active stem cell systems. Here, we review recent work on the mechanisms of non cell-autonomous control of shoot stem cells in the model plant Arabidopsis thaliana with a strong focus on the cell-to-cell mobility and function of the WUSCHEL homeodomain transcription factor.
Collapse
Affiliation(s)
- Michael Fuchs
- Department of Stem Cell Biology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
| |
Collapse
|
13
|
Singh S, Singh A, Singh A, Yadav S, Bajaj I, Kumar S, Jain A, Sarkar AK. Role of chromatin modification and remodeling in stem cell regulation and meristem maintenance in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:778-792. [PMID: 31793642 DOI: 10.1093/jxb/erz459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
In higher plants, pluripotent stem cells reside in the specialized microenvironment called stem cell niches (SCNs) harbored at the shoot apical meristem (SAM) and root apical meristem (RAM), which give rise to the aerial and underground parts of a plant, respectively. The model plant Arabidopsis thaliana (Arabidopsis) has been extensively studied to decipher the intricate regulatory mechanisms involving some key transcriptions factors and phytohormones that play pivotal roles in stem cell homeostasis, meristem maintenance, and organ formation. However, there is increasing evidence to show the epigenetic regulation of the chromatin architecture, gene expression exerting an influence on an innate balance between the self-renewal of stem cells, and differentiation of the progeny cells to a specific tissue type or organ. Post-translational histone modifications, ATP-dependent chromatin remodeling, and chromatin assembly/disassembly are some of the key features involved in the modulation of chromatin architecture. Here, we discuss the major epigenetic regulators and illustrate their roles in the regulation of stem cell activity, meristem maintenance, and related organ patterning in Arabidopsis.
Collapse
Affiliation(s)
- Sharmila Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Alka Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Archita Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sandeep Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Ishita Bajaj
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shailendra Kumar
- Amity School of Architecture and Planning, Amity University, Kant Kalwar, Rajasthan, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University, Kant Kalwar, Rajasthan, India
| | - Ananda K Sarkar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| |
Collapse
|
14
|
Han H, Geng Y, Guo L, Yan A, Meyerowitz EM, Liu X, Zhou Y. The Overlapping and Distinct Roles of HAM Family Genes in Arabidopsis Shoot Meristems. FRONTIERS IN PLANT SCIENCE 2020; 11:541968. [PMID: 33013964 PMCID: PMC7498855 DOI: 10.3389/fpls.2020.541968] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/19/2020] [Indexed: 05/02/2023]
Abstract
In Arabidopsis shoot apical meristems (SAMs), a well-characterized regulatory loop between WUSCHEL (WUS) and CLAVATA3 (CLV3) maintains stem cell homeostasis by regulating the balance between cell proliferation and cell differentiation. WUS proteins, translated in deep cell layers, move into the overlaying stem cells to activate CLV3. The secreted peptide CLV3 then regulates WUS levels through a ligand-receptor mediated signaling cascade. CLV3 is specifically expressed in the stem cells and repressed in the deep cell layers despite presence of the WUS activator, forming an apical-basal polarity along the axis of the SAM. Previously, we proposed and validated a hypothesis that the HAIRY MERISTEM (HAM) family genes regulate this polarity, keeping the expression of CLV3 off in interior cells of the SAM. However, the specific role of each individual member of the HAM family in this process remains to be elucidated. Combining live imaging and molecular genetics, we have dissected the conserved and distinct functions of different HAM family members in control of CLV3 patterning in the SAMs and in the de novo shoot stem cell niches as well.
Collapse
Affiliation(s)
- Han Han
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Lei Guo
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - An Yan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, United States
| | - Elliot M. Meyerowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, United States
| | - Xing Liu
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- *Correspondence: Yun Zhou,
| |
Collapse
|
15
|
Kitagawa M, Balkunde R, Bui H, Jackson D. An Aminoacyl tRNA Synthetase, OKI1, Is Required for Proper Shoot Meristem Size in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:2597-2608. [PMID: 31393575 DOI: 10.1093/pcp/pcz153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
In plants, the stem cells that form the shoot system reside within the shoot apical meristem (SAM), which is regulated by feedback signaling between the WUSCHEL (WUS) homeobox protein and CLAVATA (CLV) peptides and receptors. WUS-CLV feedback signaling can be modulated by various endogenous or exogenous factors, such as chromatin state, hormone signaling, reactive oxygen species (ROS) signaling and nutrition, leading to a dynamic control of SAM size corresponding to meristem activity. Despite these insights, however, the knowledge of genes that control SAM size is still limited, and in particular, the regulation by ROS signaling is only beginning to be comprehended. In this study, we report a new function in maintenance of SAM size, encoded by the OKINA KUKI1 (OKI1) gene. OKI1 is expressed in the SAM and encodes a mitochondrial aspartyl tRNA synthetase (AspRS). oki1 mutants display enlarged SAMs with abnormal expression of WUS and CLV3 and overaccumulation of ROS in the meristem. Our findings support the importance of normal AspRS function in the maintenance of the WUS-CLV3 feedback loop and SAM size.
Collapse
Affiliation(s)
- Munenori Kitagawa
- Cold Spring Harbor Laboratory, 1 Bungtown road, Cold Spring Harbor, NY, USA
| | - Rachappa Balkunde
- Cold Spring Harbor Laboratory, 1 Bungtown road, Cold Spring Harbor, NY, USA
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO, USA
| | - Huyen Bui
- Cold Spring Harbor Laboratory, 1 Bungtown road, Cold Spring Harbor, NY, USA
- Center of Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, 1 Bungtown road, Cold Spring Harbor, NY, USA
| |
Collapse
|
16
|
Abstract
A fascinating feature of plant growth and development is that plants initiate organs continually throughout their lifespan. The ability to do this relies on specialized groups of pluripotent stem cells termed meristems, which allow for the elaboration of the shoot, root, and vascular systems. We now have a deep understanding of the genetic networks that control meristem initiation and stem cell maintenance, including the roles of receptors and their ligands, transcription factors, and integrated hormonal and chromatin control. This review describes these networks and discusses how this knowledge is being applied to improve crop productivity by increasing fruit size and seed number.
Collapse
Affiliation(s)
- Munenori Kitagawa
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
| |
Collapse
|
17
|
Zhong P, Li J, Luo L, Zhao Z, Tian Z. TOP1α regulates FLOWERING LOCUS C expression by coupling histone modification and transcription machinery. Development 2019; 146:dev.167841. [PMID: 30705075 DOI: 10.1242/dev.167841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 01/22/2019] [Indexed: 11/20/2022]
Abstract
The key steps of transcription are coupled with the opening of the DNA helical structure and establishment of active chromatin to facilitate the movement of the transcription machinery. Type I topoisomerases cleave one DNA strand and relax the supercoiled structure of transcribed templates. How topoisomerase-mediated DNA topological changes promote transcription and establish a permissive histone modification for transcription elongation is largely unknown. Here, we show that TOPOISOMERASE 1α in plants regulates FLOWERING LOCUS C transcription by coupling histone modification and transcription machinery. We demonstrate that TOP1α directly interacts with the methyltransferase SDG8 to establish high levels of H3K36 methylation downstream of FLC transcription start sites and recruits RNA polymerase II to facilitate transcription elongation. Our results provide a mechanistic framework for TOP1α control of the main steps of early transcription and demonstrate how topoisomerases couple RNA polymerase II and permissive histone modifications to initiate transcription elongation.
Collapse
Affiliation(s)
- Peiqiao Zhong
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Jiaojiao Li
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Linjie Luo
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Zhong Zhao
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Zhaoxia Tian
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| |
Collapse
|
18
|
Zhou Y, Yan A, Han H, Li T, Geng Y, Liu X, Meyerowitz EM. HAIRY MERISTEM with WUSCHEL confines CLAVATA3 expression to the outer apical meristem layers. Science 2018; 361:502-506. [PMID: 30072538 PMCID: PMC6095697 DOI: 10.1126/science.aar8638] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 06/19/2018] [Indexed: 12/29/2022]
Abstract
The control of the location and activity of stem cells depends on spatial regulation of gene activities in the stem cell niche. Using computational and experimental approaches, we have tested and found support for a hypothesis for gene interactions that specify the Arabidopsis apical stem cell population. The hypothesis explains how the WUSCHEL gene product, synthesized basally in the meristem, induces CLAVATA3-expressing stem cells in the meristem apex but, paradoxically, not in the basal domain where WUSCHEL itself is expressed. The answer involves the activity of the small family of HAIRY MERISTEM genes, which prevent the activation of CLAVATA3 and which are expressed basally in the shoot meristem.
Collapse
Affiliation(s)
- Yun Zhou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - An Yan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Han
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Ting Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Xing Liu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Elliot M Meyerowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
19
|
Kupriyanova EV, Albert EV, Bliznina AI, Mamoshina PO, Ezhova TA. Arabidopsis DNA topoisomerase I alpha is required for adaptive response to light and flower development. Biol Open 2017; 6:832-843. [PMID: 28495963 PMCID: PMC5483022 DOI: 10.1242/bio.024422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA topoisomerase I alpha (TOP1α) plays a specific role in Arabidopsis thaliana development and is required for stem cell regulation in shoot and floral meristems. Recently, a new role independent of meristem functioning has been described for TOP1α, namely flowering time regulation. The same feature had been detected by us earlier for fas5, a mutant allele of TOP1α. In this study we clarify the effects of fas5 on bolting initiation and analyze the molecular basis of its role on flowering time regulation. We show that fas5 mutation leads to a constitutive shade avoidance syndrome, accompanied by leaf hyponasty, petiole elongation, lighter leaf color and early bolting. Other alleles of TOP1α demonstrate the same shade avoidance response. RNA sequencing confirmed the activation of shade avoidance gene pathways in fas5 mutant plants. It also revealed the repression of many genes controlling floral meristem identity and organ morphogenesis. Our research further expands the knowledge of TOP1α function in plant development and reveals that besides stem cell maintenance TOP1α plays an important new role in regulating the adaptive plant response to light stimulus and flower development. Summary: This study expands upon the existing knowledge of Arabidopsis DNA topoisomerase gene TOP1α function in plant development and demonstrates its important new role in regulating shade response and flower development.
Collapse
Affiliation(s)
- Evgenia V Kupriyanova
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Evgeniy V Albert
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Aleksandra I Bliznina
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Polina O Mamoshina
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Tatiana A Ezhova
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| |
Collapse
|
20
|
Zhao X, Bramsiepe J, Van Durme M, Komaki S, Prusicki MA, Maruyama D, Forner J, Medzihradszky A, Wijnker E, Harashima H, Lu Y, Schmidt A, Guthörl D, Logroño RS, Guan Y, Pochon G, Grossniklaus U, Laux T, Higashiyama T, Lohmann JU, Nowack MK, Schnittger A. RETINOBLASTOMA RELATED1 mediates germline entry in
Arabidopsis. Science 2017; 356:356/6336/eaaf6532. [DOI: 10.1126/science.aaf6532] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 02/06/2017] [Accepted: 03/14/2017] [Indexed: 01/10/2023]
|
21
|
Gong X, Shen L, Peng YZ, Gan Y, Yu H. DNA Topoisomerase Iα Affects the Floral Transition. PLANT PHYSIOLOGY 2017; 173:642-654. [PMID: 27837087 PMCID: PMC5210759 DOI: 10.1104/pp.16.01603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/08/2016] [Indexed: 05/16/2023]
Abstract
DNA topoisomerases modulate DNA topology to maintain chromosome superstructure and genome integrity, which is indispensable for DNA replication and RNA transcription. Their function in plant development still remains largely unknown. Here, we report a hitherto unidentified role of Topoisomerase Iα (TOP1α) in controlling flowering time in Arabidopsis (Arabidopsis thaliana). Loss of function of TOP1α results in early flowering under both long and short days. This is attributed mainly to a decrease in the expression of a central flowering repressor, FLOWERING LOCUS C (FLC), and its close homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, during the floral transition. TOP1α physically binds to the genomic regions of FLC, MAF4, and MAF5 and promotes the association of RNA polymerase II complexes to their transcriptional start sites. These correlate with the changes in histone modifications but do not directly affect nucleosome occupancy at these loci. Our results suggest that TOP1α mediates DNA topology to facilitate the recruitment of RNA polymerase II at FLC, MAF4, and MAF5 in conjunction with histone modifications, thus facilitating the expression of these key flowering repressors to prevent precocious flowering in Arabidopsis.
Collapse
Affiliation(s)
- Ximing Gong
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Lisha Shen
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Ya Zhi Peng
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Yinbo Gan
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| |
Collapse
|
22
|
Threshold-dependent transcriptional discrimination underlies stem cell homeostasis. Proc Natl Acad Sci U S A 2016; 113:E6298-E6306. [PMID: 27671653 DOI: 10.1073/pnas.1607669113] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcriptional mechanisms that underlie the dose-dependent regulation of gene expression in animal development have been studied extensively. However, the mechanisms of dose-dependent transcriptional regulation in plant development have not been understood. In Arabidopsis shoot apical meristems, WUSCHEL (WUS), a stem cell-promoting transcription factor, accumulates at a higher level in the rib meristem and at a lower level in the central zone where it activates its own negative regulator, CLAVATA3 (CLV3). How WUS regulates CLV3 levels has not been understood. Here we show that WUS binds a group of cis-elements, cis- regulatory module, in the CLV3-regulatory region, with different affinities and conformations, consisting of monomers at lower concentration and as dimers at a higher level. By deleting cis elements, manipulating the WUS-binding affinity and the homodimerization threshold of cis elements, and manipulating WUS levels, we show that the same cis elements mediate both the activation and repression of CLV3 at lower and higher WUS levels, respectively. The concentration-dependent transcriptional discrimination provides a mechanistic framework to explain the regulation of CLV3 levels that is critical for stem cell homeostasis.
Collapse
|
23
|
DNA-dependent homodimerization, sub-cellular partitioning, and protein destabilization control WUSCHEL levels and spatial patterning. Proc Natl Acad Sci U S A 2016; 113:E6307-E6315. [PMID: 27671631 DOI: 10.1073/pnas.1607673113] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The homeodomain transcription factor WUSCHEL (WUS) promotes stem cell maintenance in inflorescence meristems of Arabidopsis thaliana WUS, which is synthesized in the rib meristem, migrates and accumulates at lower levels in adjacent cells. Maintenance of WUS protein levels and spatial patterning distribution is not well-understood. Here, we show that the last 63-aa stretch of WUS is necessary for maintaining different levels of WUS protein in the rib meristem and adjacent cells. The 63-aa region contains the following transcriptional regulatory domains: the acidic region, the WUS-box, which is conserved in WUS-related HOMEOBOX family members, and the ethylene-responsive element binding factor-associated amphiphilic repression (EAR-like) domain. Our analysis reveals that the opposing functions of WUS-box, which is required for nuclear retention, and EAR-like domain, which participates in nuclear export, are necessary to maintain higher nuclear levels of WUS in cells of the rib meristem and lower nuclear levels in adjacent cells. We also show that the N-terminal DNA binding domain, which is required for both DNA binding and homodimerization, along with the homodimerization sequence located in the central part of the protein, restricts WUS from spreading excessively and show that the homodimerization is critical for WUS function. Our analysis also reveals that a higher level of WUS outside the rib meristem leads to protein destabilization, suggesting a new tier of regulation in WUS protein regulation. Taken together our data show that processes that influence WUS protein levels and spatial distribution are highly coupled to its transcriptional activity.
Collapse
|
24
|
Dolzblasz A, Nardmann J, Clerici E, Causier B, van der Graaff E, Chen J, Davies B, Werr W, Laux T. Stem Cell Regulation by Arabidopsis WOX Genes. MOLECULAR PLANT 2016; 9:1028-39. [PMID: 27109605 DOI: 10.1016/j.molp.2016.04.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/08/2016] [Accepted: 04/10/2016] [Indexed: 05/05/2023]
Abstract
Gene amplification followed by functional diversification is a major force in evolution. A typical example of this is seen in the WUSCHEL-RELATED HOMEOBOX (WOX) gene family, named after the Arabidopsis stem cell regulator WUSCHEL. Here we analyze functional divergence in the WOX gene family. Members of the WUS clade, except the cambium stem cell regulator WOX4, can substitute for WUS function in shoot and floral stem cell maintenance to different degrees. Stem cell function of WUS requires a canonical WUS-box, essential for interaction with TPL/TPR co-repressors, whereas the repressive EAR domain is dispensable and the acidic domain seems only to be required for female fertility. In contrast to the WUS clade, members of the ancient WOX13 and the WOX9 clades cannot support stem cell maintenance. Although the homeodomains are interchangeable between WUS and WOX9 clade members, a WUS-compatible homeodomain together with canonical WUS-box is not sufficient for stem cell maintenance. Our results suggest that WOX function in shoot and floral meristems of Arabidopsis is restricted to the modern WUS clade, suggesting that stem cell control is a derived function. Yet undiscovered functional domains in addition to the homeodomain and the WUS-box are necessary for this function.
Collapse
Affiliation(s)
- Alicja Dolzblasz
- BIOSS Centre for Biological Signalling Studies, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.
| | - Judith Nardmann
- Institute of Developmental Biology, Biocenter Cologne, Universität zu Köln, Zülpicher Street 47b, 50674 Köln, Germany
| | - Elena Clerici
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Barry Causier
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Eric van der Graaff
- BIOSS Centre for Biological Signalling Studies, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Jinhui Chen
- BIOSS Centre for Biological Signalling Studies, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Brendan Davies
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Wolfgang Werr
- Institute of Developmental Biology, Biocenter Cologne, Universität zu Köln, Zülpicher Street 47b, 50674 Köln, Germany
| | - Thomas Laux
- BIOSS Centre for Biological Signalling Studies, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.
| |
Collapse
|
25
|
Lin TF, Saiga S, Abe M, Laux T. OBE3 and WUS Interaction in Shoot Meristem Stem Cell Regulation. PLoS One 2016; 11:e0155657. [PMID: 27196372 PMCID: PMC4873020 DOI: 10.1371/journal.pone.0155657] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/02/2016] [Indexed: 11/18/2022] Open
Abstract
The stem cells in the shoot apical meristem (SAM) are the origin of all above ground tissues in plants. In Arabidopsis thaliana, shoot meristem stem cells are maintained by the homeobox transcription factor gene WUS (WUSCHEL) that is expressed in cells of the organizing center underneath the stem cells. In order to identify factors that operate together with WUS in stem cell maintenance, we performed an EMS mutant screen for modifiers of the hypomorphic wus-6 allele. We isolated the oberon3-2 (obe3-2) mutant that enhances stem cell defects in wus-6, but does not affect the putative null allele wus-1. The OBE3 gene encodes a PHD (Plant Homeo Domain) protein that is thought to function in chromatin regulation. Single mutants of OBE3 or its closest homolog OBE4 do not display any defects, whereas the obe3-2 obe4-2 double mutant displays broad growth defects and developmental arrest of seedlings. Transcript levels of WUS and its target gene in the stem cells, CLAVATA3, are reduced in obe3-2. On the other hand, OBE3 and OBE4 transcripts are both indirectly upregulated by ectopic WUS expression. Our results suggest a positive feedback regulation between WUS and OBE3 that contributes to shoot meristem homeostasis.
Collapse
Affiliation(s)
- Ta-Fang Lin
- BIOSS Centre for Biological Signalling Studies, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Shunsuke Saiga
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA, Wageningen, The Netherlands
| | - Mitsutomo Abe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113–0033, Japan
| | - Thomas Laux
- BIOSS Centre for Biological Signalling Studies, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- * E-mail:
| |
Collapse
|
26
|
Jia N, Liu X, Gao H. A DNA2 Homolog Is Required for DNA Damage Repair, Cell Cycle Regulation, and Meristem Maintenance in Plants. PLANT PHYSIOLOGY 2016; 171:318-33. [PMID: 26951435 PMCID: PMC4854720 DOI: 10.1104/pp.16.00312] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 03/04/2016] [Indexed: 05/18/2023]
Abstract
Plant meristem cells divide and differentiate in a spatially and temporally regulated manner, ultimately giving rise to organs. In this study, we isolated the Arabidopsis jing he sheng 1 (jhs1) mutant, which exhibited retarded growth, an abnormal pattern of meristem cell division and differentiation, and morphological defects such as fasciation, an irregular arrangement of siliques, and short roots. We identified JHS1 as a homolog of human and yeast DNA Replication Helicase/Nuclease2, which is known to be involved in DNA replication and damage repair. JHS1 is strongly expressed in the meristem of Arabidopsis. The jhs1 mutant was sensitive to DNA damage stress and had an increased DNA damage response, including increased expression of genes involved in DNA damage repair and cell cycle regulation, and a higher frequency of homologous recombination. In the meristem of the mutant plants, cell cycle progression was delayed at the G2 or late S phase and genes essential for meristem maintenance were misregulated. These results suggest that JHS1 plays an important role in DNA replication and damage repair, meristem maintenance, and development in plants.
Collapse
Affiliation(s)
- Ning Jia
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China (N.J., X.L., H.G.)
| | - Xiaomin Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China (N.J., X.L., H.G.)
| | - Hongbo Gao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China (N.J., X.L., H.G.)
| |
Collapse
|
27
|
Zhang Y, Zheng L, Hong JH, Gong X, Zhou C, Pérez-Pérez JM, Xu J. TOPOISOMERASE1α Acts through Two Distinct Mechanisms to Regulate Stele and Columella Stem Cell Maintenance. PLANT PHYSIOLOGY 2016; 171:483-93. [PMID: 26969721 PMCID: PMC4854680 DOI: 10.1104/pp.15.01754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/10/2016] [Indexed: 05/11/2023]
Abstract
TOPOISOMERASE1 (TOP1), which releases DNA torsional stress generated during replication through its DNA relaxation activity, plays vital roles in animal and plant development. In Arabidopsis (Arabidopsis thaliana), TOP1 is encoded by two paralogous genes (TOP1α and TOP1β), of which TOP1α displays specific developmental functions that are critical for the maintenance of shoot and floral stem cells. Here, we show that maintenance of two different populations of root stem cells is also dependent on TOP1α-specific developmental functions, which are exerted through two distinct novel mechanisms. In the proximal root meristem, the DNA relaxation activity of TOP1α is critical to ensure genome integrity and survival of stele stem cells (SSCs). Loss of TOP1α function triggers DNA double-strand breaks in S-phase SSCs and results in their death, which can be partially reversed by the replenishment of SSCs mediated by ETHYLENE RESPONSE FACTOR115 In the quiescent center and root cap meristem, TOP1α is epistatic to RETINOBLASTOMA-RELATED (RBR) in the maintenance of undifferentiated state and the number of columella stem cells (CSCs). Loss of TOP1α function in either wild-type or RBR RNAi plants leads to differentiation of CSCs, whereas overexpression of TOP1α mimics and further enhances the effect of RBR reduction that increases the number of CSCs Taken together, these findings provide important mechanistic insights into understanding stem cell maintenance in plants.
Collapse
Affiliation(s)
- Yonghong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Lanlan Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Jing Han Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Ximing Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Chun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - José Manuel Pérez-Pérez
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Jian Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| |
Collapse
|
28
|
Adibi M, Yoshida S, Weijers D, Fleck C. Centering the Organizing Center in the Arabidopsis thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization. PLoS One 2016; 11:e0147830. [PMID: 26872130 PMCID: PMC4752473 DOI: 10.1371/journal.pone.0147830] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 01/08/2016] [Indexed: 12/15/2022] Open
Abstract
Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation.
Collapse
Affiliation(s)
- Milad Adibi
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
- * E-mail: (MA); (CF)
| | - Saiko Yoshida
- Laboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands
| | - Christian Fleck
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
- * E-mail: (MA); (CF)
| |
Collapse
|
29
|
Iglesias FM, Cerdán PD. Maintaining Epigenetic Inheritance During DNA Replication in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:38. [PMID: 26870059 PMCID: PMC4735446 DOI: 10.3389/fpls.2016.00038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/11/2016] [Indexed: 05/18/2023]
Abstract
Biotic and abiotic stresses alter the pattern of gene expression in plants. Depending on the frequency and duration of stress events, the effects on the transcriptional state of genes are "remembered" temporally or transmitted to daughter cells and, in some instances, even to offspring (transgenerational epigenetic inheritance). This "memory" effect, which can be found even in the absence of the original stress, has an epigenetic basis, through molecular mechanisms that take place at the chromatin and DNA level but do not imply changes in the DNA sequence. Many epigenetic mechanisms have been described and involve covalent modifications on the DNA and histones, such as DNA methylation, histone acetylation and methylation, and RNAi dependent silencing mechanisms. Some of these chromatin modifications need to be stable through cell division in order to be truly epigenetic. During DNA replication, histones are recycled during the formation of the new nucleosomes and this process is tightly regulated. Perturbations to the DNA replication process and/or the recycling of histones lead to epigenetic changes. In this mini-review, we discuss recent evidence aimed at linking DNA replication process to epigenetic inheritance in plants.
Collapse
Affiliation(s)
| | - Pablo D. Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Buenos Aires, Argentina
- *Correspondence: Pablo D. Cerdán,
| |
Collapse
|
30
|
Gaillochet C, Lohmann JU. The never-ending story: from pluripotency to plant developmental plasticity. Development 2015; 142:2237-49. [PMID: 26130755 PMCID: PMC4510588 DOI: 10.1242/dev.117614] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Plants are sessile organisms, some of which can live for over a thousand years. Unlike most animals, plants employ a post-embryonic mode of development driven by the continuous activity of pluripotent stem cells. Consequently, plants are able to initiate new organs over extended periods of time, and many species can readily replace lost body structures by de novo organogenesis. Classical studies have also shown that plant tissues have a remarkable capacity to undergo de-differentiation and proliferation in vitro, highlighting the fact that plant cell fate is highly plastic. This suggests that the mechanisms regulating fate transitions must be continuously active in most plant cells and that the control of cellular pluripotency lies at the core of diverse developmental programs. Here, we review how pluripotency is established in plant stem cell systems, how it is maintained during development and growth and re-initiated during regeneration, and how these mechanisms eventually contribute to the amazing developmental plasticity of plants.
Collapse
Affiliation(s)
- Christophe Gaillochet
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| |
Collapse
|
31
|
Cao X, He Z, Guo L, Liu X. Epigenetic Mechanisms Are Critical for the Regulation of WUSCHEL Expression in Floral Meristems. PLANT PHYSIOLOGY 2015; 168:1189-96. [PMID: 25829464 PMCID: PMC4528737 DOI: 10.1104/pp.15.00230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/25/2015] [Indexed: 05/04/2023]
Abstract
The floral meristem (FM), which develops from the inflorescence meristem upon completion of the floral transition, terminates after producing a defined number of floral organs. This is in contrast to the shoot apical meristem, which is active throughout the entire life span of plants. WUSCHEL (WUS) encodes a homeodomain-containing protein and plays a critical role in shoot apical meristem, inflorescence meristem, and FM establishment and maintenance as well as FM determinacy. Although many genes have been implicated in FM determinacy through the regulation of WUS expression, precisely how these genes are coordinated to regulate WUS and consequently dictate FM fate remains unclear. Emerging lines of evidence indicate that epigenetic mechanisms, such as histone modification, chromatin remodeling, noncoding RNAs, and DNA methylation, play vital roles in meristem maintenance and termination. Here, recent findings demonstrating the involvement of the epigenetic network in the regulation of WUS expression in the context of FM determinacy are summarized and discussed.
Collapse
Affiliation(s)
- Xiuwei Cao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| | - Zishan He
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| | - Lin Guo
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| | - Xigang Liu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| |
Collapse
|
32
|
Huang W, Pitorre D, Poretska O, Marizzi C, Winter N, Poppenberger B, Sieberer T. ALTERED MERISTEM PROGRAM1 suppresses ectopic stem cell niche formation in the shoot apical meristem in a largely cytokinin-independent manner. PLANT PHYSIOLOGY 2015; 167:1471-86. [PMID: 25673776 PMCID: PMC4378165 DOI: 10.1104/pp.114.254623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 02/09/2015] [Indexed: 05/03/2023]
Abstract
Plants are able to reiteratively form new organs in an environmentally adaptive manner during postembryonic development. Organ formation in plants is dependent on stem cell niches (SCNs), which are located in the so-called meristems. Meristems show a functional zonation along the apical-basal axis and the radial axis. Shoot apical meristems of higher plants are dome-like structures, which contain a central SCN that consists of an apical stem cell pool and an underlying organizing center. Organ primordia are formed in the circular peripheral zone (PZ) from stem cell descendants in which differentiation programs are activated. One mechanism to keep this radial symmetry integrated is that the existing SCN actively suppresses stem cell identity in the PZ. However, how this lateral inhibition system works at the molecular level is far from understood. Here, we show that a defect in the putative carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) causes the formation of extra SCNs in the presence of an intact primary shoot apical meristem, which at least partially contributes to the enhanced shoot meristem size and leaf initiation rate found in the mutant. This defect appears to be neither a specific consequence of the altered cytokinin levels in amp1 nor directly mediated by the WUSCHEL/CLAVATA feedback loop. De novo formation of supernumerary stem cell pools was further enhanced in plants mutated in both AMP1 and its paralog LIKE AMP1, indicating that they exhibit partially overlapping roles to suppress SCN respecification in the PZ.
Collapse
Affiliation(s)
- Wenwen Huang
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria (W.H., D.P., O.P., C.M., N.W., B.P., T.S.); andResearch Unit Plant Growth Regulation (O.P., T.S.) and Biotechnology of Horticultural Crops (B.P.), TUM School of Life Sciences Weihenstephan, Technische Universität München, D-85354 Freising, Germany
| | - Delphine Pitorre
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria (W.H., D.P., O.P., C.M., N.W., B.P., T.S.); andResearch Unit Plant Growth Regulation (O.P., T.S.) and Biotechnology of Horticultural Crops (B.P.), TUM School of Life Sciences Weihenstephan, Technische Universität München, D-85354 Freising, Germany
| | - Olena Poretska
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria (W.H., D.P., O.P., C.M., N.W., B.P., T.S.); andResearch Unit Plant Growth Regulation (O.P., T.S.) and Biotechnology of Horticultural Crops (B.P.), TUM School of Life Sciences Weihenstephan, Technische Universität München, D-85354 Freising, Germany
| | - Christine Marizzi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria (W.H., D.P., O.P., C.M., N.W., B.P., T.S.); andResearch Unit Plant Growth Regulation (O.P., T.S.) and Biotechnology of Horticultural Crops (B.P.), TUM School of Life Sciences Weihenstephan, Technische Universität München, D-85354 Freising, Germany
| | - Nikola Winter
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria (W.H., D.P., O.P., C.M., N.W., B.P., T.S.); andResearch Unit Plant Growth Regulation (O.P., T.S.) and Biotechnology of Horticultural Crops (B.P.), TUM School of Life Sciences Weihenstephan, Technische Universität München, D-85354 Freising, Germany
| | - Brigitte Poppenberger
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria (W.H., D.P., O.P., C.M., N.W., B.P., T.S.); andResearch Unit Plant Growth Regulation (O.P., T.S.) and Biotechnology of Horticultural Crops (B.P.), TUM School of Life Sciences Weihenstephan, Technische Universität München, D-85354 Freising, Germany
| | - Tobias Sieberer
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria (W.H., D.P., O.P., C.M., N.W., B.P., T.S.); andResearch Unit Plant Growth Regulation (O.P., T.S.) and Biotechnology of Horticultural Crops (B.P.), TUM School of Life Sciences Weihenstephan, Technische Universität München, D-85354 Freising, Germany
| |
Collapse
|
33
|
Zhou Y, Liu X, Engstrom EM, Nimchuk ZL, Pruneda-Paz JL, Tarr PT, Yan A, Kay SA, Meyerowitz EM. Control of plant stem cell function by conserved interacting transcriptional regulators. Nature 2015; 517:377-80. [PMID: 25363783 PMCID: PMC4297503 DOI: 10.1038/nature13853] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 09/10/2014] [Indexed: 11/08/2022]
Abstract
Plant stem cells in the shoot apical meristem (SAM) and root apical meristem are necessary for postembryonic development of aboveground tissues and roots, respectively, while secondary vascular stem cells sustain vascular development. WUSCHEL (WUS), a homeodomain transcription factor expressed in the rib meristem of the Arabidopsis SAM, is a key regulatory factor controlling SAM stem cell populations, and is thought to establish the shoot stem cell niche through a feedback circuit involving the CLAVATA3 (CLV3) peptide signalling pathway. WUSCHEL-RELATED HOMEOBOX 5 (WOX5), which is specifically expressed in the root quiescent centre, defines quiescent centre identity and functions interchangeably with WUS in the control of shoot and root stem cell niches. WOX4, expressed in Arabidopsis procambial cells, defines the vascular stem cell niche. WUS/WOX family proteins are evolutionarily and functionally conserved throughout the plant kingdom and emerge as key actors in the specification and maintenance of stem cells within all meristems. However, the nature of the genetic regime in stem cell niches that centre on WOX gene function has been elusive, and molecular links underlying conserved WUS/WOX function in stem cell niches remain unknown. Here we demonstrate that the Arabidopsis HAIRY MERISTEM (HAM) family of transcription regulators act as conserved interacting cofactors with WUS/WOX proteins. HAM and WUS share common targets in vivo and their physical interaction is important in driving downstream transcriptional programs and in promoting shoot stem cell proliferation. Differences in the overlapping expression patterns of WOX and HAM family members underlie the formation of diverse stem cell niche locations, and the HAM family is essential for all of these stem cell niches. These findings establish a new framework for the control of stem cell production during plant development.
Collapse
Affiliation(s)
- Yun Zhou
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - Xing Liu
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - Eric M. Engstrom
- Biology Department, College of William and Mary, Williamsburg, Virginia 23187–8795, United States
| | - Zachary L. Nimchuk
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - Jose L. Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Paul T. Tarr
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - An Yan
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| | - Steve A. Kay
- University of Southern California, Molecular and Computational Biology, Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Science, Los Angeles, CA 90089, United States
| | - Elliot M. Meyerowitz
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
- Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, United States
| |
Collapse
|
34
|
Abstract
The study of epigenetics in plants has a long and rich history, from initial descriptions of non-Mendelian gene behaviors to seminal discoveries of chromatin-modifying proteins and RNAs that mediate gene silencing in most eukaryotes, including humans. Genetic screens in the model plant Arabidopsis have been particularly rewarding, identifying more than 130 epigenetic regulators thus far. The diversity of epigenetic pathways in plants is remarkable, presumably contributing to the phenotypic plasticity of plant postembryonic development and the ability to survive and reproduce in unpredictable environments.
Collapse
Affiliation(s)
- Craig S Pikaard
- Department of Biology, Department of Molecular and Cellular Biochemistry, and Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405
| | - Ortrun Mittelsten Scheid
- Gregor Mendel-Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| |
Collapse
|
35
|
Abstract
The study of epigenetics in plants has a long and rich history, from initial descriptions of non-Mendelian gene behaviors to seminal discoveries of chromatin-modifying proteins and RNAs that mediate gene silencing in most eukaryotes, including humans. Genetic screens in the model plant Arabidopsis have been particularly rewarding, identifying more than 130 epigenetic regulators thus far. The diversity of epigenetic pathways in plants is remarkable, presumably contributing to the phenotypic plasticity of plant postembryonic development and the ability to survive and reproduce in unpredictable environments.
Collapse
Affiliation(s)
- Craig S Pikaard
- Department of Biology, Department of Molecular and Cellular Biochemistry, and Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405
| | - Ortrun Mittelsten Scheid
- Gregor Mendel-Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria
| |
Collapse
|
36
|
Waidmann S, Kusenda B, Mayerhofer J, Mechtler K, Jonak C. A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis. THE PLANT CELL 2014; 26:4328-44. [PMID: 25387881 PMCID: PMC4277211 DOI: 10.1105/tpc.114.129254] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/01/2014] [Accepted: 10/22/2014] [Indexed: 05/19/2023]
Abstract
Chromatin is a major determinant in the regulation of virtually all DNA-dependent processes. Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. The evolutionarily conserved DEK domain-containing protein is implicated in important chromatin-related processes in animals, but little is known about its DNA targets and protein interaction partners. In plants, the role of DEK has remained elusive. In this work, we identified DEK3 as a chromatin-associated protein in Arabidopsis thaliana. DEK3 specifically binds histones H3 and H4. Purification of other proteins associated with nuclear DEK3 also established DNA topoisomerase 1α and proteins of the cohesion complex as in vivo interaction partners. Genome-wide mapping of DEK3 binding sites by chromatin immunoprecipitation followed by deep sequencing revealed enrichment of DEK3 at protein-coding genes throughout the genome. Using DEK3 knockout and overexpressor lines, we show that DEK3 affects nucleosome occupancy and chromatin accessibility and modulates the expression of DEK3 target genes. Furthermore, functional levels of DEK3 are crucial for stress tolerance. Overall, data indicate that DEK3 contributes to modulation of Arabidopsis chromatin structure and function.
Collapse
Affiliation(s)
- Sascha Waidmann
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Branislav Kusenda
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Juliane Mayerhofer
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Claudia Jonak
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| |
Collapse
|
37
|
Stress induces cell dedifferentiation in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:378-84. [PMID: 25086338 DOI: 10.1016/j.bbagrm.2014.07.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/20/2014] [Accepted: 07/22/2014] [Indexed: 12/14/2022]
Abstract
Accumulating evidence lends support to the proposal that a major theme in plant responses to stresses is dedifferentiation, whereby mature cells acquire stem cell features (e.g. open chromatin conformation) prior to acquisition of a new cell fate. In this review, we discuss data addressing plant cell plasticity and provide evidence linking stress, dedifferentiation and a switch in cell fate. We emphasize the epigenetic modifications associated with stress-induced global changes in chromatin structure and conclude with the implications for genetic variation and for induced pluripotent stem cells in animals. It appears that stress is perceived as a signal that directs plant cells to undergo reprogramming (dedifferentiation) as a means for adaptation and in preparation for a stimulus-based acquisition of a new cell fate. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
Collapse
|
38
|
Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella P, Li S, Weigel D, Pontes O, Ecker JR, Chen X. DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. PLoS Genet 2014; 10:e1004446. [PMID: 24992598 PMCID: PMC4080997 DOI: 10.1371/journal.pgen.1004446] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 05/05/2014] [Indexed: 11/18/2022] Open
Abstract
RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9me2 levels. Further studies with Arabidopsis top1α mutants showed that TOP1α silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats. This study assigned a new role in epigenetic silencing to an enzyme that affects DNA topology. DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription. Here, we uncovered an unexpected role of DNA topoisomerase 1α (TOP1α) in the maintenance of genome stability. Eukaryotic genomes are usually littered with transposable elements (TEs) and repeats, which pose threats to genome stability due to their tendency to move or recombine. Mechanisms are in place to silence these elements, such as RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) in plants. Two plant-specific RNA polymerases, Pol IV and Pol V, generate small and long noncoding RNAs, respectively, from TEs and repeats. These RNAs then recruit protein factors to deposit DNA methylation or H3K9me2 to silence the loci. In this study, we found that treatment of plants with camptothecin, a TOP1α inhibitor, or loss of function in TOP1α, led to the de-repression of RdDM target loci, which was accompanied by loss of H3K9me2 or DNA methylation. The role of TOP1α in RdDM could be attributed to its promotion of Pol V, but not Pol IV, transcription to generate long noncoding RNAs.
Collapse
Affiliation(s)
- Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- ChemGen IGERT program, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Lei Gao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Xigang Liu
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Dongming Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shengben Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Michael O'Leary
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Brandon Le
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert J. Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Pablo Manavella
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shaofang Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Olga Pontes
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- Howard Hughes Medical Institute, University of California Riverside, Riverside, California, United States of America
- * E-mail:
| |
Collapse
|
39
|
Liu X, Gao L, Dinh TT, Shi T, Li D, Wang R, Guo L, Xiao L, Chen X. DNA topoisomerase I affects polycomb group protein-mediated epigenetic regulation and plant development by altering nucleosome distribution in Arabidopsis. THE PLANT CELL 2014; 26:2803-17. [PMID: 25070639 PMCID: PMC4145115 DOI: 10.1105/tpc.114.124941] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
It has been perplexing that DNA topoisomerases, enzymes that release DNA supercoils, play specific roles in development. In this study, using a floral stem cell model in Arabidopsis thaliana, we uncovered a role for TOPOISOMERASE1α (TOP1α) in Polycomb Group (PcG) protein-mediated histone 3 lysine 27 trimethylation (H3K27me3) at, and transcriptional repression of, the stem cell maintenance gene WUSCHEL (WUS). We demonstrated that H3K27me3 deposition at other PcG targets also requires TOP1α. Intriguingly, the repression of some, as well as the expression of many, PcG target genes requires TOP1α. The mechanism that unifies the opposing effects of TOP1α appears to lie in its role in decreasing nucleosome density, which probably allows the binding of factors that either recruit PcG, as we demonstrated for AGAMOUS at the WUS locus, or counteract PcG-mediated regulation. Although TOP1α reduces nucleosome density at all genes, the lack of a 5' nucleosome-free region is a feature that distinguishes PcG targets from nontargets and may condition the requirement for TOP1α for their expression. This study uncovers a connection between TOP1α and PcG, which explains the specific developmental functions of TOP1α.
Collapse
Affiliation(s)
- Xigang Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 Key Laboratory of Agricultural Water Resource, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Ting Shi
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongming Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 Key Laboratory of Agricultural Water Resource, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Ruozhong Wang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Lin Guo
- Key Laboratory of Agricultural Water Resource, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Langtao Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521 Howard Hughes Medical Institute, University of California, Riverside, California 92521
| |
Collapse
|
40
|
Abstract
The astonishingly long lives of plants and their regeneration capacity depend on the activity of plant stem cells. As in animals, stem cells reside in stem cell niches, which produce signals that regulate the balance between self-renewal and the generation of daughter cells that differentiate into new tissues. Plant stem cell niches are located within the meristems, which are organized structures that are responsible for most post-embryonic development. The continuous organ production that is characteristic of plant growth requires a robust regulatory network to keep the balance between pluripotent stem cells and differentiating progeny. Components of this network have now been elucidated and provide a unique opportunity for comparing strategies that were developed in the animal and plant kingdoms, which underlie the logic of stem cell behaviour.
Collapse
|
41
|
Sakakibara K, Reisewitz P, Aoyama T, Friedrich T, Ando S, Sato Y, Tamada Y, Nishiyama T, Hiwatashi Y, Kurata T, Ishikawa M, Deguchi H, Rensing SA, Werr W, Murata T, Hasebe M, Laux T. WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens. Development 2014; 141:1660-70. [PMID: 24715456 DOI: 10.1242/dev.097444] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many differentiated plant cells can dedifferentiate into stem cells, reflecting the remarkable developmental plasticity of plants. In the moss Physcomitrella patens, cells at the wound margin of detached leaves become reprogrammed into stem cells. Here, we report that two paralogous P. patens WUSCHEL-related homeobox 13-like (PpWOX13L) genes, homologs of stem cell regulators in flowering plants, are transiently upregulated and required for the initiation of cell growth during stem cell formation. Concordantly, Δppwox13l deletion mutants fail to upregulate genes encoding homologs of cell wall loosening factors during this process. During the moss life cycle, most of the Δppwox13l mutant zygotes fail to expand and initiate an apical stem cell to form the embryo. Our data show that PpWOX13L genes are required for the initiation of cell growth specifically during stem cell formation, in analogy to WOX stem cell functions in seed plants, but using a different cellular mechanism.
Collapse
|
42
|
Ühlken C, Horvath B, Stadler R, Sauer N, Weingartner M. MAIN-LIKE1 is a crucial factor for correct cell division and differentiation in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:107-20. [PMID: 24635680 DOI: 10.1111/tpj.12455] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/04/2013] [Accepted: 01/17/2014] [Indexed: 05/10/2023]
Abstract
Plant development requires accurate coordination of gene expression, both in actively dividing meristematic cells and differentiated cells. Cell fate establishment and maintenance, among others, are mediated by chromatin organization complexes that determine the stable transcriptional states of specific cell types. Here, we focus on MAIN-LIKE1 (MAIL1), one of three homologs of MAINTENANCE OF MERISTEMS (MAIN), which form a plant-specific gene family in Arabidopsis thaliana. We show that MAIL1 encodes a ubiquitously expressed nuclear protein. A mail1 loss-of-function mutant developed short primary roots, in which the meristematic cells accumulated DNA double-strand breaks and underwent massive cell death. In addition, mail1 mutant showed also cell differentiation defects in root and shoot tissues, and developed disorganized callus-like structures. The genetic interaction between main and mail1 mutants suggests that they act in the same pathway, and that both are essential for maintaining correct cell division acitivity in meristematic cells, while MAIL1 has an additional function in differentiating cells.
Collapse
Affiliation(s)
- Christine Ühlken
- Molekulare Pflanzenphysiologie and Erlangen Center of Plant Science, Friedrich-Alexander Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | | | | | | | | |
Collapse
|
43
|
Wenig U, Meyer S, Stadler R, Fischer S, Werner D, Lauter A, Melzer M, Hoth S, Weingartner M, Sauer N. Identification of MAIN, a factor involved in genome stability in the meristems of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:469-83. [PMID: 23607329 DOI: 10.1111/tpj.12215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 05/17/2023]
Abstract
Stem cells in the root and shoot apical meristem provide the descendant cells required for growth and development throughout the lifecycle of a plant. We found that mutations in the Arabidopsis MAINTENANCE OF MERISTEMS (MAIN) gene led to plants with distorted stem cell niches in which stem cells are not maintained and undergo premature differentiation or cell death. The malfunction of main meristems leads to short roots, mis-shaped leaves, reduced fertility and partial fasciation of stems. MAIN encodes a nuclear-localized protein and is a member of a so far uncharacterized plant-specific gene family. As main mutant plants are hypersensitive to DNA-damaging agents, expression of genes involved in DNA repair is induced and dead cells with damaged DNA accumulate in the mutant meristems, we propose that MAIN is required for meristem maintenance by sustaining genome integrity in stem cells and their descendants cells.
Collapse
Affiliation(s)
- Ulrich Wenig
- Molekulare Pflanzenphysiologie, Friedrich Alexander Universität Erlangen-Nürnberg, Staudtstraße 5, D-91058 Erlangen, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
Cancer stem cells (CSCs) are a subpopulation generally thought to be responsible for cancer initiation and progression. Because CSCs are often rare in the total tumor cell population and differentiate rapidly when grown in culture, it has been challenging to uncover compounds that selectively target CSCs. We previously described CSC-emulating cells derived from breast cancer cell lines that maintained a stable undifferentiated state. We optimized a phenotypic assay with these cells and screened 1,280-bioactive compounds, identifying five that preferentially inhibited CSC-like cell proliferation. Using a compound-guided target identification approach, we found high topoisomerase I (Topo I) expression levels in breast CSC-like cells and primary breast CSCs. Structurally unrelated small molecules targeting Topo I preferentially inhibited CSC-like cells. These results illustrate the substantial power of this CSC phenotypic screening platform and promote Topo I as a potential molecular therapeutic target for therapies aimed at expunging CSCs.
Collapse
|
45
|
Lee C, Clark SE. Core pathways controlling shoot meristem maintenance. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2013; 2:671-84. [PMID: 24014453 DOI: 10.1002/wdev.110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Essential to the function of shoot meristems in plants to act as sites of continuous organ and tissue formation is the ability of cells within the meristem to remain undifferentiated and proliferate indefinitely. These are characteristics of the stem cells within meristems that are critical for their growth properties. Stem cells are found in tight association with the stem cell niche-those cells that signal to maintain stem cells. Shoot meristems are unique among stem cell systems in that the stem cell niche is a constantly changing population of recent daughter stem cells. Recent progress from Arabidopsis and other systems have uncovered a large number of genes with defined roles in meristem structure and maintenance. This review will focus on well-studied pathways that represent signaling between the stem cells and the niche, that prevent ectopic differentiation of stem cells, that regulate the chromatin status of stem cell factors, and that reveal intersection of hormone signaling and meristem maintenance.
Collapse
Affiliation(s)
- Chunghee Lee
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | |
Collapse
|
46
|
Sang Y, Silva-Ortega CO, Wu S, Yamaguchi N, Wu MF, Pfluger J, Gillmor CS, Gallagher KL, Wagner D. Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:1000-14. [PMID: 23062007 PMCID: PMC3561502 DOI: 10.1111/tpj.12009] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
SWI2/SNF2 chromatin remodeling ATPases play important roles in plant and metazoan development. Whereas metazoans generally encode one or two SWI2/SNF2 ATPase genes, Arabidopsis encodes four such chromatin regulators: the well-studied BRAHMA and SPLAYED ATPases, as well as two closely related non-canonical SWI2/SNF2 ATPases, CHR12 and CHR23. No developmental role has as yet been described for CHR12 and CHR23. Here, we show that although strong single chr12 or chr23 mutants are morphologically indistinguishable from the wild type, chr12 chr23 double mutants cause embryonic lethality. The double mutant embryos fail to initiate root and shoot meristems, and display few and aberrant cell divisions. Weak double mutant embryos give rise to viable seedlings with dramatic defects in the maintenance of both the shoot and the root stem cell populations. Paradoxically, the stem cell defects are correlated with increased expression of the stem cell markers WUSCHEL and WOX5. During subsequent development, the meristem defects are partially overcome to allow for the formation of very small, bushy adult plants. Based on the observed morphological defects, we named the two chromatin remodelers MINUSCULE 1 and 2. Possible links between minu1 minu2 defects and defects in hormone signaling and replication-coupled chromatin assembly are discussed.
Collapse
Affiliation(s)
- Yi Sang
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - Claudia O. Silva-Ortega
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV-IPN, Irapuato, Guanajuato, C.P 36821, MEXICO
| | - Shuang Wu
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - Jennifer Pfluger
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), CINVESTAV-IPN, Irapuato, Guanajuato, C.P 36821, MEXICO
| | - Kimberly L. Gallagher
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
- authors for correspondence: Doris Wagner, tel: 215-898-0483, fax: 215 898-8780, ; Kimberly L. Gallagher, tel: 215 746-3605, fax: 215 898-8780,
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104
- authors for correspondence: Doris Wagner, tel: 215-898-0483, fax: 215 898-8780, ; Kimberly L. Gallagher, tel: 215 746-3605, fax: 215 898-8780,
| |
Collapse
|
47
|
Liu Y, Ye W, Li B, Zhou X, Cui Y, Running MP, Liu K. CCS52A2/FZR1, a cell cycle regulator, is an essential factor for shoot apical meristem maintenance in Arabidopsis thaliana. BMC PLANT BIOLOGY 2012; 12:135. [PMID: 22873486 PMCID: PMC3534500 DOI: 10.1186/1471-2229-12-135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/03/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND Cell division and cell fate decisions regulate organ formation and function in plant growth and development. It is still unclear how specific meristematic regulatory networks operate with the cell cycle machinery to translate stem cell identity and maintenance into cellular behavior. In this study, we address these questions by analysis of a shoot apex defective mutant, namely xcm9. RESULTS Phenotypic analysis of the xcm9 mutant reveals concomitant premature termination of floral shoots with frequent bifurcation of the shoot apices, stems, and flowers. Microscopic observations show irregular cell organization in shoot apical meristems of xcm9. Positional cloning revealed that xcm9 is a loss of function allele of the CCS52A2/FZR1 gene, which has previously been implicated in root development. Expression analysis demonstrated that CCS52A2 maintains a higher transcriptional expression level in actively dividing tissue. Genetic studies indicated that the CCS52A2 gene functions together with WUSCHEL (WUS) and CLAVATA3 (CLV3) in regulating the development of the shoot meristem, and also contributes to this regulation together with the chromatin remodeling pathway. In addition, fewer xcm9 cells express CYCLIN B1:1, showing that cell cycle progression is disrupted in the mutant. CONCLUSION We propose that the CCS52A2 gene is a mediator that functions together with meristematic genes to regulate meristem organization, and cross-functions with chromatin regulators in cell cycle progression during shoot apical meristem development.
Collapse
Affiliation(s)
- Yajie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Wei Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Beibei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Xiaojing Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, P. R. China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, ON, N5V 4 T3, Canada
| | | | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| |
Collapse
|
48
|
Cytokinin signaling as a positional cue for patterning the apical-basal axis of the growing Arabidopsis shoot meristem. Proc Natl Acad Sci U S A 2012; 109:4002-7. [PMID: 22345559 DOI: 10.1073/pnas.1200636109] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The transcription factor WUSCHEL (WUS) acts from a well-defined domain within the Arabidopsis thaliana shoot apical meristem (SAM) to maintain a stem cell niche. A negative-feedback loop involving the CLAVATA (CLV) signaling pathway regulates the number of WUS-expressing cells and provides the current paradigm for the homeostatic maintenance of stem cell numbers. Despite the continual turnover of cells in the SAM during development, the WUS domain remains patterned at a fixed distance below the shoot apex. Recent work has uncovered a positive-feedback loop between WUS function and the plant hormone cytokinin. Furthermore, loss of function of the cytokinin biosynthetic gene, LONELY GUY (LOG), results in a wus-like phenotype in rice. Herein, we find the Arabidopsis LOG4 gene is expressed in the SAM epidermis. We use this to develop a computational model representing a growing SAM to suggest the plausibility that apically derived cytokinin and CLV signaling, together, act as positional cues for patterning the WUS domain within the stem cell niche. Furthermore, model simulations backed by experimental data suggest a previously unknown negative feedback between WUS function and cytokinin biosynthesis in the Arabidopsis SAM epidermis. These results suggest a plausible dynamic feedback principle by which the SAM stem cell niche is patterned.
Collapse
|
49
|
Perales M, Reddy GV. Stem cell maintenance in shoot apical meristems. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:10-6. [PMID: 22079787 DOI: 10.1016/j.pbi.2011.10.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/06/2011] [Accepted: 10/19/2011] [Indexed: 05/18/2023]
Abstract
Stem cell homeostasis in shoot apical meristems of higher plants is regulated through a dynamic balance between spatial regulation of gene expression, cell growth patterns and patterns of differentiation. Cell-cell communication mediated by both the local factors and long-range signals have been implicated in stem cell homeostasis. Here we have reviewed recent developments on spatio-temporal regulation of cell-cell communication processes with an emphasis on how ubiquitously utilized signals such as plant hormones function with local factors in mediating stem cell homeostasis. We also provide a brief overview of how the activity of ubiquitously utilized epigenetic regulators are modulated locally to orchestrate gene expression.
Collapse
Affiliation(s)
- Mariano Perales
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, United States
| | | |
Collapse
|
50
|
Abstract
Multicellular organisms possess pluripotent stem cells to form new organs, replenish the daily loss of cells, or regenerate organs after injury. Stem cells are maintained in specific environments, the stem cell niches, that provide signals to block differentiation. In plants, stem cell niches are situated in the shoot, root, and vascular meristems-self-perpetuating units of organ formation. Plants' lifelong activity-which, as in the case of trees, can extend over more than a thousand years-requires that a robust regulatory network keep the balance between pluripotent stem cells and differentiating descendants. In this review, we focus on current models in plant stem cell research elaborated during the past two decades, mainly in the model plant Arabidopsis thaliana. We address the roles of mobile signals on transcriptional modules involved in balancing cell fates. In addition, we discuss shared features of and differences between the distinct stem cell niches of Arabidopsis.
Collapse
Affiliation(s)
- Ernst Aichinger
- BIOSS Centre for Biological Signalling Studies, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | | | | |
Collapse
|