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Liu S, Cheng H, Zhang Y, He M, Zuo D, Wang Q, Lv L, Lin Z, Song G. Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement. Genes (Basel) 2024; 15:378. [PMID: 38540437 PMCID: PMC10970022 DOI: 10.3390/genes15030378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 06/14/2024] Open
Abstract
Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort's fingerprint genomic sites. The FPFinder was developed based on the term frequency-inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these pedigree-featured sites had a role in cotton development. In addition, we applied FPFinder to evaluate the geographical bias of fiber-length-related genomic sites from a modern cotton cohort consisting of 410 accessions. Enriching elite sites in cultivars from the Yangtze River region resulted in the longer fiber length of Yangze River-sourced accessions. Apart from characterizing functional sites, we also identified 12,536 region-specific genomic sites. Combining the transcriptome data of multiple tissues and samples under various abiotic stresses, we found that several region-specific sites contributed to environmental adaptation. In this research, FPFinder revealed the role of the cotton pedigree fingerprint and region-specific sites in cotton development and environmental adaptation, respectively. The FPFinder can be applied broadly in other crops and contribute to genetic breeding in the future.
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Affiliation(s)
- Shang Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Hailiang Cheng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
- Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China
| | - Youping Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Man He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Dongyun Zuo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Qiaolian Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Limin Lv
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
| | - Zhongxv Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Guoli Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (S.L.); (Y.Z.); (M.H.); (D.Z.); (Q.W.); (L.L.)
- Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China
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Hong L, Rusnak B, Ko CS, Xu S, He X, Qiu D, Kang SE, Pruneda-Paz JL, Roeder AHK. Enhancer activation via TCP and HD-ZIP and repression by Dof transcription factors mediate giant cell-specific expression. THE PLANT CELL 2023; 35:2349-2368. [PMID: 36814410 PMCID: PMC10226562 DOI: 10.1093/plcell/koad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 05/30/2023]
Abstract
Proper cell-type identity relies on highly coordinated regulation of gene expression. Regulatory elements such as enhancers can produce cell type-specific expression patterns, but the mechanisms underlying specificity are not well understood. We previously identified an enhancer region capable of driving specific expression in giant cells, which are large, highly endoreduplicated cells in the Arabidopsis thaliana sepal epidermis. In this study, we use the giant cell enhancer as a model to understand the regulatory logic that promotes cell type-specific expression. Our dissection of the enhancer revealed that giant cell specificity is mediated primarily through the combination of two activators and one repressor. HD-ZIP and TCP transcription factors are involved in the activation of expression throughout the epidermis. High expression of HD-ZIP transcription factor genes in giant cells promoted higher expression driven by the enhancer in giant cells. Dof transcription factors repressed the activity of the enhancer such that only giant cells maintained enhancer activity. Thus, our data are consistent with a conceptual model whereby cell type-specific expression emerges from the combined activities of three transcription factor families activating and repressing expression in epidermal cells.
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Affiliation(s)
- Lilan Hong
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Byron Rusnak
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Clint S Ko
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Shouling Xu
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xi He
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dengying Qiu
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - S Earl Kang
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jose L Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
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Li B, Zeng Y, Jiang L. COPII vesicles in plant autophagy and endomembrane trafficking. FEBS Lett 2022; 596:2314-2323. [PMID: 35486434 DOI: 10.1002/1873-3468.14362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 11/06/2022]
Abstract
In eukaryotes, the endomembrane system allows for spatiotemporal compartmentation of complicated cellular processes. The plant endomembrane system consists of the endoplasmic reticulum (ER), the Golgi apparatus (GA), the trans-Golgi network (TGN), the multivesicular body (MVB), and the vacuole. Anterograde traffic from the ER to GA is mediated by coat protein complex II (COPII) vesicles. Autophagy, an evolutionarily conserved catabolic process that turns over cellular materials upon nutrient deprivation or in adverse environments, exploits double-membrane autophagosomes to recycle unwanted constituents in the lysosome/vacuole. Accumulating evidence reveals novel functions of plant COPII vesicles in autophagy and their regulation by abiotic stresses. Here, we summarize current knowledge about plant COPII vesicles in the endomembrane trafficking and then highlight recent findings showing their distinct roles in modulating the autophagic flux and stress responses.
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Affiliation(s)
- Baiying Li
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, New Territories, Hong Kong, China
| | - Yonglun Zeng
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, New Territories, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, New Territories, Hong Kong, China.,CUHK Shenzhen Research Institute, Shenzhen, China.,Institute of Plant Molecular Biology and Agricultural Biotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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A unique AtSar1D-AtRabD2a nexus modulates autophagosome biogenesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2021; 118:2021293118. [PMID: 33879613 DOI: 10.1073/pnas.2021293118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In eukaryotes, secretory proteins traffic from the endoplasmic reticulum (ER) to the Golgi apparatus via coat protein complex II (COPII) vesicles. Intriguingly, during nutrient starvation, the COPII machinery acts constructively as a membrane source for autophagosomes during autophagy to maintain cellular homeostasis by recycling intermediate metabolites. In higher plants, essential roles of autophagy have been implicated in plant development and stress responses. Nonetheless, the membrane sources of autophagosomes, especially the participation of the COPII machinery in the autophagic pathway and autophagosome biogenesis, remains elusive in plants. Here, we provided evidence in support of a novel role of a specific Sar1 homolog AtSar1d in plant autophagy in concert with a unique Rab1/Ypt1 homolog AtRabD2a. First, proteomic analysis of the plant ATG (autophagy-related gene) interactome uncovered the mechanistic connections between ATG machinery and specific COPII components including AtSar1d and Sec23s, while a dominant negative mutant of AtSar1d exhibited distinct inhibition on YFP-ATG8 vacuolar degradation upon autophagic induction. Second, a transfer DNA insertion mutant of AtSar1d displayed starvation-related phenotypes. Third, AtSar1d regulated autophagosome progression through specific recognition of ATG8e by a noncanonical motif. Fourth, we demonstrated that a plant-unique Rab1/Ypt1 homolog AtRabD2a coordinates with AtSar1d to function as the molecular switch in mediating the COPII functions in the autophagy pathway. AtRabD2a appears to be essential for bridging the specific AtSar1d-positive COPII vesicles to the autophagy initiation complex and therefore contributes to autophagosome formation in plants. Taken together, we identified a plant-specific nexus of AtSar1d-AtRabD2a in regulating autophagosome biogenesis.
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Roeder AHK. Arabidopsis sepals: A model system for the emergent process of morphogenesis. QUANTITATIVE PLANT BIOLOGY 2021; 2:e14. [PMID: 36798428 PMCID: PMC9931181 DOI: 10.1017/qpb.2021.12] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
During development, Arabidopsis thaliana sepal primordium cells grow, divide and interact with their neighbours, giving rise to a sepal with the correct size, shape and form. Arabidopsis sepals have proven to be a good system for elucidating the emergent processes driving morphogenesis due to their simplicity, their accessibility for imaging and manipulation, and their reproducible development. Sepals undergo a basipetal gradient of growth, with cessation of cell division, slow growth and maturation starting at the tip of the sepal and progressing to the base. In this review, I discuss five recent examples of processes during sepal morphogenesis that yield emergent properties: robust size, tapered tip shape, laminar shape, scattered giant cells and complex gene expression patterns. In each case, experiments examining the dynamics of sepal development led to the hypotheses of local rules. In each example, a computational model was used to demonstrate that these local rules are sufficient to give rise to the emergent properties of morphogenesis.
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Affiliation(s)
- Adrienne H. K. Roeder
- Section of Plant Biology, School of Integrative Plant Science and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
- Author for correspondence: Adrienne H. K. Roeder, E-mail:
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Yu X, Wang L, Ran L, Chen X, Sheng J, Yang Y, Wu Y, Chen G, Xiong F. New insights into the mechanism of storage protein biosynthesis in wheat caryopsis under different nitrogen levels. PROTOPLASMA 2020; 257:1289-1308. [PMID: 32405873 DOI: 10.1007/s00709-020-01489-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/12/2020] [Indexed: 06/11/2023]
Abstract
Effect of different nitrogen levels (0, 150, and 300 kg hm-2) at booting stage on storage protein biosynthesis and processing quality of wheat was investigated using microstructural and ultrastructural observation, RNA sequencing, and quality analysis in this study. The results showed that the storage protein genes encoding ω- and γ-gliadin and low molecular weight glutenin subunit were upregulated at N150, and the genes encoding α- or β-gliadin and avenin-like protein were upregulated at N300. Two nitrogen levels induced expression of some interesting regulating genes, such as USE1, STX1B_2_3, SEC23, SEC24, SEC61A, HSP A1_8, HSP20, and HSP90B/TRA1. These regulatory genes were enriched in the KEGG pathway protein export, SNARE interactions in vesicular transport, and protein processing in endoplasmic reticulum. The amount, morphology, and accumulation pattern of protein body in four different endosperm regions in developing caryopsis show different response to N150 and N300, of which N300 had greater influence than N150. N150 and N300 both enhanced the contents of protein components, endosperm fullness, grain hardness, and parameters of processing quality, with the latter showing a greater degree of influence. Contrary to the accumulation pattern of protein body, N300 reduced the ratio of the amount of starch granules to the area ratio of protein body to starch granule. Results suggested that the difference of different nitrogen levels affecting storage protein biosynthesis might be through affecting the expression of the encoding and regulating gene of storage protein.
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Affiliation(s)
- Xurun Yu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Leilei Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Liping Ran
- Guangling College of Yangzhou University, Yangzhou, China
| | - Xinyu Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Jieyue Sheng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yunfei Wu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Gang Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Fei Xiong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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Perroud PF, Meyberg R, Demko V, Quatrano RS, Olsen OA, Rensing SA. DEK1 displays a strong subcellular polarity during Physcomitrella patens 3D growth. THE NEW PHYTOLOGIST 2020; 226:1029-1041. [PMID: 31913503 DOI: 10.1111/nph.16417] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/24/2019] [Indexed: 05/18/2023]
Abstract
Defective Kernel 1 (DEK1) is genetically at the nexus of the 3D morphogenesis of land plants. We aimed to localize DEK1 in the moss Physcomitrella patens to decipher its function during this process. To detect DEK1 in vivo, we inserted the tdTomato fluorophore into PpDEK1 gene locus. Confocal microscopy coupled with the use of time-gating allowed the precise DEK1 subcellular localization during 3D morphogenesis. DEK1 localization displays a strong polarized signal, as it is restricted to the plasma membrane domain between recently divided cells during the early steps of 3D growth development as well as during the subsequent vegetative growth. The signal furthermore displays a clear developmental pattern because it is only detectable in recently divided and elongating cells. Additionally, DEK1 localization appears to be independent of its calpain domain proteolytic activity. The DEK1 polar subcellular distribution in 3D tissue developing cells defines a functional cellular framework to explain its role in this developmental phase. Also, the observation of DEK1 during spermatogenesis suggests another biological function for this protein in plants. Finally the DEK1-tagged strain generated here provides a biological platform upon which further investigations into 3D developmental processes can be performed.
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Affiliation(s)
- Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, Marburg, 35043, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, Marburg, 35043, Germany
| | - Viktor Demko
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, Bratislava, 84215, Slovakia
| | - Ralph S Quatrano
- Department of Biology, Washington University in St Louis, One Brookings Dr., Campus, Box 1137, St Louis, MO, 63130, USA
| | - Odd-Arne Olsen
- Norwegian University of Life Sciences, PO Box 5003, Aas, NO-1432, Norway
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch Str. 8, Marburg, 35043, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, Freiburg im Breisgau, 79104, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Hans-Meerwein-Straße 6, Marburg, 35043, Germany
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Kesawat MS, Kim DK, Zeba N, Suh MC, Xia X, Hong CB. Ectopic RING zinc finger gene from hot pepper induces totally different genes in lettuce and tobacco. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:70. [PMID: 29780273 PMCID: PMC5956013 DOI: 10.1007/s11032-018-0812-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 03/27/2018] [Indexed: 05/28/2023]
Abstract
Advances in molecular biology have improved crops through transferring genes from one organism to new hosts, and these efforts have raised concerns about potential unexpected outcomes. Here, we provide evidence that a gene with a specific function in one organism can yield completely different effects in a new host. CaRZFP1 is a C3HC4-type RING zinc finger protein gene previously isolated from a cDNA library for heat-stressed hot pepper. In our previous work investigating in vivo CaRZFP1 function, we transferred CaRZFP1 into tobacco; transgenic tobacco exhibited enhanced growth and tolerance to abiotic stresses. As further analysis of CaRZFP1 ectopic expression in a heterologous host plant, here we mobilized and constitutively overexpressed CaRZFP1 in lettuce. In contrast to tobacco, transgenic lettuce exhibited poorer growth and delayed flowering compared with vector-only controls. To identify genes that might be involved in this phenotypic effect, transcriptome analyses on transgenic plants of both species were performed, uncovering dozens of genes that reflect the different outcomes between tobacco and lettuce. These included protein kinase, transcriptional factor, transporter protein, hormone and metabolism-related genes, and some unannotated genes. The opposite effects of CaRZFP1 ectopic expression in lettuce and tobacco address concerns of unexpectedly different outcomes in different host species.
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Affiliation(s)
- Mahipal Singh Kesawat
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 151-742 South Korea
| | - Dong Kyun Kim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 151-742 South Korea
| | - Naheed Zeba
- Present Address: Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207 Bangladesh
| | - Mi Chung Suh
- Present Address: Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757 South Korea
| | - Xinli Xia
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Choo Bong Hong
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 151-742 South Korea
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Aboulela M, Nakagawa T, Oshima A, Nishimura K, Tanaka Y. The Arabidopsis COPII components, AtSEC23A and AtSEC23D, are essential for pollen wall development and exine patterning. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1615-1633. [PMID: 29390074 PMCID: PMC5889017 DOI: 10.1093/jxb/ery015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/16/2018] [Indexed: 05/04/2023]
Abstract
The specialized multilayered pollen wall plays multiple roles to ensure normal microspore development. The major components of the pollen wall (e.g. sporopollenin and lipidic precursors) are provided from the tapetum. Material export from the endoplasmic reticulum (ER) is mediated by coat protein complex II (COPII) vesicles. The Arabidopsis thaliana genome encodes seven homologs of SEC23, a COPII component. However, the functional importance of this diversity remains elusive. Here, we analyzed knockout and knockdown lines for AtSEC23A and AtSEC23D, two of the A. thaliana SEC23 homologs, respectively. Single atsec23a and atsec23d mutant plants, despite normal fertility, showed an impaired exine pattern. Double atsec23ad mutant plants were semi-sterile and exhibited developmental defects in pollen and tapetal cells. Pollen grains of atsec23ad had defective exine and intine, and showed signs of cell degeneration. Moreover, the development of tapetal cells was altered, with structural abnormalities in organelles. AtSEC23A and AtSEC23D exhibited the characteristic localization pattern of COPII proteins and were highly expressed in the tapetum. Our work suggests that AtSEC23A and AtSEC23D may organize pollen wall development and exine patterning by regulating ER export of lipids and proteins necessary for pollen wall formation. Also, our results shed light on the functional heterogeneity of SEC23 homologs.
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Affiliation(s)
- Mostafa Aboulela
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan
- Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, Egypt
| | - Tsuyoshi Nakagawa
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan
- Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - Akinobu Oshima
- Department of Biological Science, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Kohji Nishimura
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan
- Bioresources Science, The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - Yuji Tanaka
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Matsue, Japan
- Department of Applied Bioscience and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
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Brandizzi F. Transport from the endoplasmic reticulum to the Golgi in plants: Where are we now? Semin Cell Dev Biol 2017; 80:94-105. [PMID: 28688928 DOI: 10.1016/j.semcdb.2017.06.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/11/2017] [Accepted: 06/27/2017] [Indexed: 11/26/2022]
Abstract
The biogenesis of about one third of the cellular proteome is initiated in the endoplasmic reticulum (ER), which exports proteins to the Golgi apparatus for sorting to their final destination. Notwithstanding the close proximity of the ER with other secretory membranes (e.g., endosomes, plasma membrane), the ER is also important for the homeostasis of non-secretory organelles such as mitochondria, peroxisomes, and chloroplasts. While how the plant ER interacts with most of the non-secretory membranes is largely unknown, the knowledge on the mechanisms for ER-to-Golgi transport is relatively more advanced. Indeed, over the last fifteen years or so, a large number of exciting results have contributed to draw parallels with non-plant species but also to highlight the complexity of the plant ER-Golgi interface, which bears unique features. This review reports and discusses results on plant ER-to-Golgi traffic, focusing mainly on research on COPII-mediated transport in the model species Arabidopsis thaliana.
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Affiliation(s)
- Federica Brandizzi
- MSU-DOE Plant Research Lab and Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.
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11
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Variable Cell Growth Yields Reproducible OrganDevelopment through Spatiotemporal Averaging. Dev Cell 2017; 38:15-32. [PMID: 27404356 DOI: 10.1016/j.devcel.2016.06.016] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 05/04/2016] [Accepted: 06/09/2016] [Indexed: 11/22/2022]
Abstract
Organ sizes and shapes are strikingly reproducible, despite the variable growth and division of individual cells within them. To reveal which mechanisms enable this precision, we designed a screen for disrupted sepal size and shape uniformity in Arabidopsis and identified mutations in the mitochondrial i-AAA protease FtsH4. Counterintuitively, through live imaging we observed that variability of neighboring cell growth was reduced in ftsh4 sepals. We found that regular organ shape results from spatiotemporal averaging of the cellular variability in wild-type sepals, which is disrupted in the less-variable cells of ftsh4 mutants. We also found that abnormal, increased accumulation of reactive oxygen species (ROS) in ftsh4 mutants disrupts organ size consistency. In wild-type sepals, ROS accumulate in maturing cells and limit organ growth, suggesting that ROS are endogenous signals promoting termination of growth. Our results demonstrate that spatiotemporal averaging of cellular variability is required for precision in organ size.
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12
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Hong L, Brown J, Segerson NA, Rose JKC, Roeder AHK. CUTIN SYNTHASE 2 Maintains Progressively Developing Cuticular Ridges in Arabidopsis Sepals. MOLECULAR PLANT 2017; 10:560-574. [PMID: 28110092 DOI: 10.1016/j.molp.2017.01.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 12/19/2016] [Accepted: 01/04/2017] [Indexed: 05/27/2023]
Abstract
The cuticle is a crucial barrier on the aerial surfaces of land plants. In many plants, including Arabidopsis, the sepals and petals form distinctive nanoridges in their cuticles. However, little is known about how the formation and maintenance of these nanostructures is coordinated with the growth and development of the underlying cells. Here we report the characterization of the Arabidopsis cutin synthase 2 (cus2) mutant, which causes a great reduction in cuticular ridges on the mature sepal epidermis, but only a moderate effect on petal cone cell ridges. Using scanning electron microscopy and confocal live imaging combined with quantification of cellular growth, we find that cuticular ridge formation progresses down the sepal from tip to base as the sepal grows. pCUS2::GFP-GUS reporter expression coincides with cuticular ridge formation, descending the sepal from tip to base. Ridge formation also coincides with the reduction in growth rate and termination of cell division of the underlying epidermal cells. Surprisingly, cuticular ridges at first form normally in the cus2 mutant, but are lost progressively at later stages of sepal development, indicating that CUS2 is crucial for the maintenance of cuticular ridges after they are formed. Our results reveal the dynamics of both ridge formation and maintenance as the sepal grows.
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Affiliation(s)
- Lilan Hong
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Joel Brown
- Field of Genetics Genomics and Development, Cornell University, Ithaca, NY 14853, USA
| | - Nicholas A Segerson
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; Field of Genetics Genomics and Development, Cornell University, Ithaca, NY 14853, USA.
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13
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Balduzzi M, Binder BM, Bucksch A, Chang C, Hong L, Iyer-Pascuzzi AS, Pradal C, Sparks EE. Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology. FRONTIERS IN PLANT SCIENCE 2017; 8:117. [PMID: 28217137 PMCID: PMC5289971 DOI: 10.3389/fpls.2017.00117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/19/2017] [Indexed: 05/04/2023]
Abstract
An emerging challenge in plant biology is to develop qualitative and quantitative measures to describe the appearance of plants through the integration of mathematics and biology. A major hurdle in developing these metrics is finding common terminology across fields. In this review, we define approaches for analyzing plant geometry, topology, and shape, and provide examples for how these terms have been and can be applied to plants. In leaf morphological quantifications both geometry and shape have been used to gain insight into leaf function and evolution. For the analysis of cell growth and expansion, we highlight the utility of geometric descriptors for understanding sepal and hypocotyl development. For branched structures, we describe how topology has been applied to quantify root system architecture to lend insight into root function. Lastly, we discuss the importance of using morphological descriptors in ecology to assess how communities interact, function, and respond within different environments. This review aims to provide a basic description of the mathematical principles underlying morphological quantifications.
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Affiliation(s)
| | - Brad M. Binder
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee-KnoxvilleKnoxville, TN, USA
| | - Alexander Bucksch
- Department of Plant Biology, University of GeorgiaAthens, GA, USA
- Warnell School of Forestry and Environmental Resources, University of GeorgiaAthens, GA, USA
- Institute of Bioinformatics, University of GeorgiaAthens, GA, USA
| | - Cynthia Chang
- Division of Biological Sciences, University of Washington-BothellBothell, WA, USA
| | - Lilan Hong
- Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell UniversityIthaca, NY, USA
| | | | - Christophe Pradal
- INRIA, Virtual PlantsMontpellier, France
- CIRAD, UMR AGAPMontpellier, France
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14
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Meyer HM, Teles J, Formosa-Jordan P, Refahi Y, San-Bento R, Ingram G, Jönsson H, Locke JCW, Roeder AHK. Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. eLife 2017; 6:e19131. [PMID: 28145865 PMCID: PMC5333958 DOI: 10.7554/elife.19131] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 01/31/2017] [Indexed: 12/22/2022] Open
Abstract
Multicellular development produces patterns of specialized cell types. Yet, it is often unclear how individual cells within a field of identical cells initiate the patterning process. Using live imaging, quantitative image analyses and modeling, we show that during Arabidopsis thaliana sepal development, fluctuations in the concentration of the transcription factor ATML1 pattern a field of identical epidermal cells to differentiate into giant cells interspersed between smaller cells. We find that ATML1 is expressed in all epidermal cells. However, its level fluctuates in each of these cells. If ATML1 levels surpass a threshold during the G2 phase of the cell cycle, the cell will likely enter a state of endoreduplication and become giant. Otherwise, the cell divides. Our results demonstrate a fluctuation-driven patterning mechanism for how cell fate decisions can be initiated through a random yet tightly regulated process.
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Affiliation(s)
- Heather M Meyer
- Weill Institute for Cell and Molecular Biology, Cornell University, United States
- The graduate field of Genetics, Genomics, and Development, Cornell University, Ithaca, United States
| | - José Teles
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Pau Formosa-Jordan
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Yassin Refahi
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Rita San-Bento
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Henrik Jönsson
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Computational Biology and Biological Physics, Lund University, Lund, Sweden
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Microsoft Research, Cambridge, United Kingdom
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, United States
- The graduate field of Genetics, Genomics, and Development, Cornell University, Ithaca, United States
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, United States
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15
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Zhao B, Shi H, Wang W, Liu X, Gao H, Wang X, Zhang Y, Yang M, Li R, Guo Y. Secretory COPII Protein SEC31B Is Required for Pollen Wall Development. PLANT PHYSIOLOGY 2016; 172:1625-1642. [PMID: 27634427 PMCID: PMC5100771 DOI: 10.1104/pp.16.00967] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/13/2016] [Indexed: 05/03/2023]
Abstract
The pollen wall protects pollen grains from abiotic and biotic stresses. During pollen wall development, tapetal cells play a vital role by secreting proteins, signals, and pollen wall material to ensure microspore development. But the regulatory mechanism underlying the secretory pathway of the tapetum is largely unknown. Here, we characterize the essential role of the Arabidopsis (Arabidopsis thaliana) COPII protein SECRETORY31B (SEC31B) in pollen wall development and the secretory activity of tapetal cells. The sporophyte-controlled atsec31b mutant exhibits severe pollen and seed abortion. Transmission electron microscopy observation indicates that pollen exine formation in the atsec31b mutant is disrupted significantly. AtSEC31B is a functional COPII protein revealed by endoplasmic reticulum (ER) exit site localization, interaction with AtSEC13A, and retarded ER-Golgi protein trafficking in the atsec31b mutant. A genetic tapetum-specific rescue assay indicates that AtSEC31B functions primarily in the tapetum. Moreover, deletion of AtSEC31B interrupted the formation of the ER-derived tapetosome and altered the location of the ATP-BINDING CASSETTE TRANSPORTER9 protein in the tapetum. Therefore, this work demonstrates that AtSEC31B plays a vital role in pollen wall development by regulating the secretory pathway of the tapetal cells.
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Affiliation(s)
- Bingchun Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
| | - Haidan Shi
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
| | - Wanlei Wang
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
| | - Xiaoyu Liu
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
| | - Hui Gao
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
| | - Xiaoxiao Wang
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
| | - Yinghui Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
| | - Meidi Yang
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
| | - Rui Li
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
| | - Yi Guo
- Hebei Key Laboratory of Molecular and Cellular Biology and Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Science, Hebei Normal University, Shijia Zhuang 050024, People's Republic of China; and
- Hebei Collaboration Innovation Center for Cell Signaling, Shijia Zhuang 050024, People's Republic of China
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16
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Chung KP, Zeng Y, Jiang L. COPII Paralogs in Plants: Functional Redundancy or Diversity? TRENDS IN PLANT SCIENCE 2016; 21:758-769. [PMID: 27317568 DOI: 10.1016/j.tplants.2016.05.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/27/2016] [Accepted: 05/27/2016] [Indexed: 05/04/2023]
Abstract
In eukaryotes, the best-described mechanism of endoplasmic reticulum (ER) export is mediated by coat protein complex II (COPII) vesicles, which comprise five conserved cytosolic components [secretion-associated, Ras-related protein 1 (Sar1), Sec23-24, and Sec13-31]. In higher organisms, multiple paralogs of COPII components are created due to gene duplication. However, the functional diversity of plant COPII subunit isoforms remains largely elusive. Here we summarize and discuss the latest findings derived from studies of various arabidopsis COPII subunit isoforms and their functional diversity. We also put forward testable hypotheses on distinct populations of COPII vesicles performing unique functions in ER export in developmental and stress-related pathways in plants.
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Affiliation(s)
- Kin Pan Chung
- Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Yonglun Zeng
- Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Liwen Jiang
- Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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17
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Demko V, Ako E, Perroud PF, Quatrano R, Olsen OA. The phenotype of the CRINKLY4 deletion mutant of Physcomitrella patens suggests a broad role in developmental regulation in early land plants. PLANTA 2016; 244:275-84. [PMID: 27100110 DOI: 10.1007/s00425-016-2526-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/08/2016] [Indexed: 05/05/2023]
Abstract
Deletion of the ancestral gene of the land plant multigene family of receptor like kinase CR4 in Physcomitrella patens demonstrates involvement in developmental control of gametophytic and sporophytic organs. The CRINKLY4 (CR4) family of receptor kinases in angiosperms consists of three clades, one including CR4, the CR4-related CCR1 and CCR2, a second including CCR3 and CCR4 family members, and a third and more distant clade. In addition to crinkly leaves in maize, which gave rise to the mutant gene name, CR4 is implicated in ovule, embryo, flower and root development in Arabidopsis thaliana. In root tips of the same species the module including a CLAVATA3/ESR-related protein, an Arabidopsis CR4, a CLAVATA1 and a WUSCHEL-related homeobox 5 (CLE40-ACR4-CLV1-WOX5) is implicated in meristem cell regulation. In embryos and shoots, CR4 acts together with A. thaliana MERISTEM LAYER 1 and PROTODERMAL FACTOR 2 to promote A. thaliana epidermis differentiation. Phylogenetic analysis has demonstrated that early land plants, e.g. mosses carry a single ancestral CR4 gene, together with genes encoding the other members of the CLE40-ACR4-CLV1-WOX5 signaling module. Here we show that CR4 serves as a broad regulator of morphogenesis both in gametophyte phyllids, archegonia and in sporophyte epidermis of the moss Physcomitrella patens. The phenotype of the CR4 deletion mutant in moss provides insight into the role of the ancestral CR4 gene as a regulator of development in early land plants.
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Affiliation(s)
- Viktor Demko
- Norwegian University of Life Sciences, P.O.Box 5003, 1432, Ås, Norway
- Department of Plant Physiology, Faculty of Natural Sciences, Mlynska Dolina, 84215, Bratislava, Slovakia
| | - Eugene Ako
- Department of Natural Science and Technology, Hedmark University of Applied Sciences, 2318, Hamar, Norway
| | - Pierre-François Perroud
- Department of Biology, Washington University in St Louis, Campus Box 1137, St. Louis, MO, 63130, USA
- Plant Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Ralph Quatrano
- Department of Biology, Washington University in St Louis, Campus Box 1137, St. Louis, MO, 63130, USA
| | - Odd-Arne Olsen
- Norwegian University of Life Sciences, P.O.Box 5003, 1432, Ås, Norway.
- Department of Natural Science and Technology, Hedmark University of Applied Sciences, 2318, Hamar, Norway.
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18
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Tauriello G, Meyer HM, Smith RS, Koumoutsakos P, Roeder AHK. Variability and Constancy in Cellular Growth of Arabidopsis Sepals. PLANT PHYSIOLOGY 2015; 169:2342-58. [PMID: 26432876 PMCID: PMC4677887 DOI: 10.1104/pp.15.00839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/01/2015] [Indexed: 05/18/2023]
Abstract
Growth of tissues is highly reproducible; yet, growth of individual cells in a tissue is highly variable, and neighboring cells can grow at different rates. We analyzed the growth of epidermal cell lineages in the Arabidopsis (Arabidopsis thaliana) sepal to determine how the growth curves of individual cell lineages relate to one another in a developing tissue. To identify underlying growth trends, we developed a continuous displacement field to predict spatially averaged growth rates. We showed that this displacement field accurately describes the growth of sepal cell lineages and reveals underlying trends within the variability of in vivo cellular growth. We found that the tissue, individual cell lineages, and cell walls all exhibit growth rates that are initially low, accelerate to a maximum, and decrease again. Accordingly, these growth curves can be represented by sigmoid functions. We examined the relationships among the cell lineage growth curves and surprisingly found that all lineages reach the same maximum growth rate relative to their size. However, the cell lineages are not synchronized; each cell lineage reaches this same maximum relative growth rate but at different times. The heterogeneity in observed growth results from shifting the same underlying sigmoid curve in time and scaling by size. Thus, despite the variability in growth observed in our study and others, individual cell lineages in the developing sepal follow similarly shaped growth curves.
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Affiliation(s)
- Gerardo Tauriello
- Computational Science and Engineering Laboratory, ETH Zürich, 8092 Zurich, Switzerland (G.T., P.K.);Weill Institute for Cell and Molecular Biology (H.M.M., A.H.K.R.), Genetics, Genomics, and Development Program (H.M.M., A.H.K.R), and School of Integrative Plant Sciences, Section of Plant Biology (A.H.K.R), Cornell University, Ithaca, New York 14853; andDepartment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (R.S.S.)
| | - Heather M Meyer
- Computational Science and Engineering Laboratory, ETH Zürich, 8092 Zurich, Switzerland (G.T., P.K.);Weill Institute for Cell and Molecular Biology (H.M.M., A.H.K.R.), Genetics, Genomics, and Development Program (H.M.M., A.H.K.R), and School of Integrative Plant Sciences, Section of Plant Biology (A.H.K.R), Cornell University, Ithaca, New York 14853; andDepartment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (R.S.S.)
| | - Richard S Smith
- Computational Science and Engineering Laboratory, ETH Zürich, 8092 Zurich, Switzerland (G.T., P.K.);Weill Institute for Cell and Molecular Biology (H.M.M., A.H.K.R.), Genetics, Genomics, and Development Program (H.M.M., A.H.K.R), and School of Integrative Plant Sciences, Section of Plant Biology (A.H.K.R), Cornell University, Ithaca, New York 14853; andDepartment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (R.S.S.)
| | - Petros Koumoutsakos
- Computational Science and Engineering Laboratory, ETH Zürich, 8092 Zurich, Switzerland (G.T., P.K.);Weill Institute for Cell and Molecular Biology (H.M.M., A.H.K.R.), Genetics, Genomics, and Development Program (H.M.M., A.H.K.R), and School of Integrative Plant Sciences, Section of Plant Biology (A.H.K.R), Cornell University, Ithaca, New York 14853; andDepartment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (R.S.S.)
| | - Adrienne H K Roeder
- Computational Science and Engineering Laboratory, ETH Zürich, 8092 Zurich, Switzerland (G.T., P.K.);Weill Institute for Cell and Molecular Biology (H.M.M., A.H.K.R.), Genetics, Genomics, and Development Program (H.M.M., A.H.K.R), and School of Integrative Plant Sciences, Section of Plant Biology (A.H.K.R), Cornell University, Ithaca, New York 14853; andDepartment of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (R.S.S.)
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19
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Robinson DO, Roeder AHK. Themes and variations in cell type patterning in the plant epidermis. Curr Opin Genet Dev 2015; 32:55-65. [PMID: 25727387 DOI: 10.1016/j.gde.2015.01.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/26/2015] [Accepted: 01/27/2015] [Indexed: 01/16/2023]
Abstract
It has recently become evident that plant development, like animal development, has molecular patterning modules that are reused again and again to create different cell type patterns. Here we focus on three of these plant modules: (1) the MYB-bHLH-WD40 protein complex, (2) the transmembrane calpain protease DEFECTIVE KERNEL1 (DEK1), and (3) homeodomain leucine zipper (HD-ZIP) class IV transcription factors acting in concert with SIAMESE-related cyclin-dependent kinase inhibitors. These three modules initiate the patterning of multiple cell types in the plant epidermis: the regular spacing of trichomes (leaf hairs), the stripes of root hairs, diverse pigmentation patterns in petals, the scattering of giant cells, and the files of bulliform cells. Varied combinations of players and additional regulatory inputs partially account for the diversity of patterns that are generated by reusing the same molecular mechanisms.
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Affiliation(s)
- Dana Olivia Robinson
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY 14853, USA.
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