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Kaur A, Best NB, Hartwig T, Budka J, Khangura RS, McKenzie S, Aragón-Raygoza A, Strable J, Schulz B, Dilkes BP. A maize semi-dwarf mutant reveals a GRAS transcription factor involved in brassinosteroid signaling. PLANT PHYSIOLOGY 2024; 195:3072-3096. [PMID: 38709680 PMCID: PMC11288745 DOI: 10.1093/plphys/kiae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 05/08/2024]
Abstract
Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa). These maize mutants exhibited semi-dwarf stature, shorter and wider leaves, and more upright leaf angle. Transcriptome analysis revealed a role for GRAS42 as a determinant of BR signaling. Analysis of the expression consequences from loss of GRAS42 in the gras42-mu1021149 mutant indicated a weak loss of BR signaling in the mutant, consistent with its previously demonstrated role in BR signaling in rice. Loss of BR signaling was also evident by the enhancement of weak BR biosynthetic mutant alleles in double mutants of nana plant1-1 and gras42-mu1021149. The gras42-mu1021149 mutant had little effect on GA-regulated gene expression, suggesting that GRAS42 is not a regulator of core GA signaling genes in maize. Single-cell expression data identified gras42 expressed among cells in the G2/M phase of the cell cycle consistent with its previously demonstrated role in cell cycle gene expression in Arabidopsis (Arabidopsis thaliana). Cis-acting natural variation controlling GRAS42 transcript accumulation was identified by expression genome-wide association study (eGWAS) in maize. Our results demonstrate a conserved role for GRAS42/SCARECROW-LIKE 28 (SCL28)/DLT in BR signaling, clarify the role of this gene in GA signaling, and suggest mechanisms of tillering and leaf angle control by BR.
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Affiliation(s)
- Amanpreet Kaur
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907USA
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Norman B Best
- Plant Genetics Research Unit, USDA-ARS, Columbia, MO 65211, USA
| | - Thomas Hartwig
- Institute for Molecular Physiology, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Josh Budka
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907USA
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Rajdeep S Khangura
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907USA
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Steven McKenzie
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907USA
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Alejandro Aragón-Raygoza
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Josh Strable
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Burkhard Schulz
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907USA
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
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Wang C, Li J, Fang K, Yao H, Chai X, Du Y, Wang J, Hao N, Cao J, Li B, Wu T. CsHLS1-CsSCL28 module regulates compact plant architecture in cucumber. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1724-1739. [PMID: 38261466 PMCID: PMC11123426 DOI: 10.1111/pbi.14298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
Increased planting densities boost crop yields. A compact plant architecture facilitates dense planting. However, the mechanisms regulating compact plant architecture in cucurbits remain unclear. In this study, we identified a cucumber (Cucumis sativus) compact plant architecture (cpa1) mutant from an ethyl methane sulfonate (EMS)-mutagenized library that exhibited distinctive phenotypic traits, including reduced leaf petiole angle and leaf size. The candidate mutation causes a premature stop codon in CsaV3_1G036420, which shares similarity to Arabidopsis HOOKLESS 1 (HLS1) encoding putative histone N-acetyltransferase (HAT) protein and was named CsHLS1. Consistent with the mutant phenotype, CsHLS1 was predominantly expressed in leaf petiole bases and leaves. Constitutive overexpressing CsHLS1 in cpa1 restored the wild-type plant architecture. Knockout of CsHLS1 resulted in reduces leaf petiole angle and leaf size and as well as decreased acetylation levels. Furthermore, CsHLS1 directly interacted with CsSCL28 and negatively regulated compact plant architecture in cucumber. Importantly, CsHLS1 knockout increased the photosynthesis rate and leaf nitrogen in cucumbers, thereby maintaining cucumber yield at normal density. Overall, our research provides valuable genetic breeding resource and gene target for creating a compact plant architecture for dense cucumber planting.
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Affiliation(s)
- Chunhua Wang
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Jie Li
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Kai Fang
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Hongxin Yao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Xingwen Chai
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Yalin Du
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Junwei Wang
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Ning Hao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Jiajian Cao
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
| | - Baohai Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource ScienceZhejiang UniversityHangzhouChina
| | - Tao Wu
- College of Horticulture/Yuelushan Lab/Whampoa Innovation Research InstituteHunan Agricultural UniversityChangshaHunanChina
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops (Vegetables, Tea, etc.), Ministry of Agriculture and Rural Affairs of ChinaChangshaChina
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Zhang M, Jian H, Shang L, Wang K, Wen S, Li Z, Liu R, Jia L, Huang Z, Lyu D. Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato. PLANTS (BASEL, SWITZERLAND) 2024; 13:795. [PMID: 38592791 PMCID: PMC10975680 DOI: 10.3390/plants13060795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
The formation and development of tubers, the primary edible and economic organ of potatoes, directly affect their yield and quality. The regulatory network and mechanism of tuberization have been preliminarily revealed in recent years, but plenty of relevant genes remain to be discovered. A few candidate genes were provided due to the simplicity of sampling and result analysis of previous transcriptomes related to tuberization. We sequenced and thoroughly analyzed the transcriptomes of thirteen tissues from potato plants at the tuber proliferation phase to provide more reference information and gene resources. Among them, eight tissues were stolons and tubers at different developmental stages, which we focused on. Five critical periods of tuberization were selected to perform an analysis of differentially expressed genes (DEGs), according to the results of the tissue correlation. Compared with the unswollen stolons (Sto), 2751, 4897, 6635, and 9700 DEGs were detected in the slightly swollen stolons (Sto1), swollen stolons (Sto2), tubers of proliferation stage 1 (Tu1), and tubers of proliferation stage 4 (Tu4). A total of 854 transcription factors and 164 hormone pathway genes were identified in the DEGs. Furthermore, three co-expression networks associated with Sto-Sto1, Sto2-Tu1, and tubers of proliferation stages two to five (Tu2-Tu5) were built using the weighted gene co-expression network analysis (WGCNA). Thirty hub genes (HGs) and 30 hub transcription factors (HTFs) were screened and focalized in these networks. We found that five HGs were reported to regulate tuberization, and most of the remaining HGs and HTFs co-expressed with them. The orthologs of these HGs and HTFs were reported to regulate processes (e.g., flowering, cell division, hormone synthesis, metabolism and signal transduction, sucrose transport, and starch synthesis) that were also required for tuberization. Such results further support their potential to control tuberization. Our study provides insights and countless candidate genes of the regulatory network of tuberization, laying the foundation for further elucidating the genetic basis of tuber development.
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Affiliation(s)
- Meihua Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Hongju Jian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing 400715, China
| | - Lina Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ke Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Zihan Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Rongrong Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Lijun Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Zhenlin Huang
- Chongqing Agricultural Technical Extension Station, Chongqing 401121, China;
| | - Dianqiu Lyu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing 400715, China
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Kim JH, Kim MS, Seo YW. Overexpression of a TaATL1 encoding RING-type E3 ligase negatively regulates cell division and flowering time in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111966. [PMID: 38151074 DOI: 10.1016/j.plantsci.2023.111966] [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: 08/23/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 12/29/2023]
Abstract
The transition of food crops from the vegetative to reproductive stages is an important process that affects the final yield. Despite extensive characterization of E3 ligases in model plants, their roles in wheat development remain unknown. In this study, we elucidated the molecular function of wheat TaATL1 (Arabidopsis thaliana Toxicos EN Levadura), which acts as a negative regulator of flowering time and cell division. TaATL1 amino acid residues contain a RING domain and exist mainly in a beta-turn form. The expression level of TaATL1 was highly reduced during the transition from vegetative to reproductive stages. TaATL1 is localized in the nucleus and exhibits E3 ligase activity. Transgenic Arabidopsis plants, in which the TaATL1 gene is constitutively overexpressed under the control of the cauliflower mosaic virus 35 S promoter, exhibited regulation of cell numbers, thereby influencing both leaf and root growth. Moreover, TaATL1 overexpression plants showed a late-flowering phenotype compared to wild-type (WT) plants. Following transcriptome analysis, it was discovered that 1661 and 901 differentially expressed genes were down- or up- regulated, respectively, in seedling stages between WT and TaATL1 overexpression. TaATL1 transcripts are involved in cell division, flowering, and signaling. Overall, our findings demonstrated that the regulatory mechanism of wheat TaATL1 gene plays a significant role in cell division-mediated flowering in Arabidopsis.
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Affiliation(s)
- Jae Ho Kim
- Department of Plant Biotechnology, Korea University, Seoul, Republic of Korea; Institute of Animal Molecular Biotechnology, Korea University, Seoul, Republic of Korea
| | - Moon Seok Kim
- Department of Plant Biotechnology, Korea University, Seoul, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul, Republic of Korea; Ojeong Plant Breeding Research Center, Korea University, Seoul, Republic of Korea.
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Acheampong A, Wang R, Elsherbiny SM, Bondzie-Quaye P, Huang Q. Exogenous arginine promotes the coproduction of biomass and astaxanthin under high-light conditions in Haematococcus pluvialis. BIORESOURCE TECHNOLOGY 2024; 393:130001. [PMID: 37956949 DOI: 10.1016/j.biortech.2023.130001] [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: 09/25/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
The economical way of Haematococcus pluvialis farming is to simultaneously achieve biomass, astaxanthin and lipid using less expensive chemicals. This paper explores the role of exogenous arginine in promoting growth and astaxanthin accumulation under stressful conditions. The application of arginine exerts a synergic effect on biomass, astaxanthin and lipid by improving carbon utilization, activating the arginine pathway and regulating carotenoid and lipid-related genes. Genes related to arginine catabolism, such as ADC, OCT, ASS1, NOS, and OAT, were up-regulated at both the cultivation and astaxanthin induction stages, signifying their importance in both growth and astaxanthin synthesis. Furthermore, transcriptome analysis revealed that arginine up-regulated transcription levels of genes involved carbon fixing, lipid biosynthesis, pyruvate metabolism, carotenoid, tricarboxylic acid cycle, and arginine and proline metabolism. The results provide a significant mechanism and applicability of using exogenous arginine and high light to stimulate bioproducts from Haematococcus pluvialis.
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Affiliation(s)
- Adolf Acheampong
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Rong Wang
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China; School of Environment and Energy Engineering, Anhui Jianzhu University, Heifei 230601, China
| | - Shereen M Elsherbiny
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China; Department of Physics, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Precious Bondzie-Quaye
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Qing Huang
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China; School of Environment and Energy Engineering, Anhui Jianzhu University, Heifei 230601, China.
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Mineta K, Hirota J, Yamada K, Itoh T, Chen P, Iwakawa H, Takatsuka H, Nomoto Y, Ito M. MYB3R-mediated and cell cycle-dependent transcriptional regulation of a tobacco ortholog of SCARECROW-LIKE28 in synchronized cultures of BY-2 cells. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:353-359. [PMID: 38434109 PMCID: PMC10905365 DOI: 10.5511/plantbiotechnology.23.0515a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/15/2023] [Indexed: 03/05/2024]
Abstract
Although it is well known that hierarchical transcriptional networks are essential for various aspects of plant development and environmental response, little has been investigated about whether and how they also regulate the plant cell cycle. Recent studies on cell cycle regulation in Arabidopsis thaliana identified SCARECROW-LIKE28 (SCL28), a GRAS-type transcription factor, that constitutes a hierarchical transcriptional pathway comprised of MYB3R, SCL28 and SIAMESE-RELATED (SMR). In this pathway, MYB3R family proteins regulate the G2/M-specific transcription of the SCL28 gene, of which products, in turn, positively regulate the transcription of SMR genes encoding a group of plant-specific inhibitor proteins of cyclin-dependent kinases. However, this pathway with a role in cell cycle inhibition is solely demonstrated in A. thaliana, thus leaving open the question of whether and to what extent this pathway is evolutionarily conserved in plants. In this study, we conducted differential display RT-PCR on synchronized Nicotiana tabacum (tobacco) BY-2 cells and identified several M-phase-specific cDNA clones, one of which turned out to be a tobacco ortholog of SCL28 and was designated NtSCL28. We showed that NtSCL28 is expressed specifically during G2/M and early G1 in the synchronized cultures of BY-2 cells. NtSCL28 contains MYB3R-binding promoter elements, so-called mitosis-specific activator elements, and is upregulated by a hyperactive form of NtmybA2, one of the MYB3R proteins from tobacco. Our study indicated that a part of the hierarchical pathway identified in A. thaliana is equally operating in tobacco cells, suggesting the conservation of this pathway across different families in evolution of angiosperm.
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Affiliation(s)
- Keito Mineta
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Junya Hirota
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Kesuke Yamada
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takashi Itoh
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Poyu Chen
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hidekazu Iwakawa
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuji Nomoto
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaki Ito
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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Ding Y, Gao W, Qin Y, Li X, Zhang Z, Lai W, Yang Y, Guo K, Li P, Zhou S, Hu H. Single-cell RNA landscape of the special fiber initiation process in Bombax ceiba. PLANT COMMUNICATIONS 2023; 4:100554. [PMID: 36772797 PMCID: PMC10518721 DOI: 10.1016/j.xplc.2023.100554] [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: 08/07/2022] [Revised: 12/19/2022] [Accepted: 01/20/2023] [Indexed: 06/03/2023]
Abstract
As a new source of natural fibers, the Bombax ceiba tree can provide thin, light, extremely soft and warm fiber material for the textile industry. Natural fibers are an ideal model system for studying cell growth and differentiation, but the molecular mechanisms that regulate fiber initiation are not fully understood. In B. ceiba, we found that fiber cells differentiate from the epidermis of the inner ovary wall. Each initiated cell then divides into a cluster of fiber cells that eventually develop into mature fibers, a process very different from the classical fiber initiation process of cotton. We used high-throughput single-cell RNA sequencing (scRNA-seq) to examine the special characteristics of fiber initiation in B. ceiba. A total of 15 567 high-quality cells were identified from the inner wall of the B. ceiba ovary, and 347 potential marker genes for fiber initiation cell types were identified. Two major cell types, initiated fiber cells and epidermal cells, were identified and verified by RNA in situ hybridization. A developmental trajectory analysis was used to reconstruct the process of fiber cell differentiation in B. ceiba. Comparative analysis of scRNA-seq data from B. ceiba and cotton (Gossypium hirsutum) confirmed that the additional cell division process in B. ceiba is a novel species-specific mechanism for fiber cell development. Candidate genes and key regulators that may contribute to fiber cell differentiation and division in B. ceiba were identified. This work reveals gene expression signatures during B. ceiba fiber initiation at a single-cell resolution, providing a new strategy and viewpoint for investigation of natural fiber cell differentiation and development.
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Affiliation(s)
- Yuanhao Ding
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572000, China
| | - Wei Gao
- State Key Laboratory of Cotton Biology, School of Life Science, Henan University, Kaifeng, Henan, P.R. China
| | - Yuan Qin
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Xinping Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Zhennan Zhang
- State Key Laboratory of Cotton Biology, School of Life Science, Henan University, Kaifeng, Henan, P.R. China
| | - Wenjie Lai
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yong Yang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Kai Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Ping Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Shihan Zhou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Haiyan Hu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572000, China.
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8
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Lu L, Yang H, Xu Y, Zhang L, Wu J, Yi H. Laser capture microdissection-based spatiotemporal transcriptomes uncover regulatory networks during seed abortion in seedless Ponkan (Citrus reticulata). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:642-661. [PMID: 37077034 DOI: 10.1111/tpj.16251] [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: 11/09/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Seed abortion is an important process in the formation of seedless characteristics in citrus fruits. However, the molecular regulatory mechanism underlying citrus seed abortion is poorly understood. Laser capture microdissection-based RNA-seq combined with Pacbio-seq was used to profile seed development in the Ponkan cultivars 'Huagan No. 4' (seedless Ponkan) (Citrus reticulata) and 'E'gan No. 1' (seeded Ponkan) (C. reticulata) in two types of seed tissue across three developmental stages. Through comparative transcriptome and dynamic phytohormone analyses, plant hormone signal, cell division and nutrient metabolism-related processes were revealed to play critical roles in the seed abortion of 'Huagan No. 4'. Moreover, several genes may play indispensable roles in seed abortion of 'Huagan No. 4', such as CrWRKY74, CrWRKY48 and CrMYB3R4. Overexpression of CrWRKY74 in Arabidopsis resulted in severe seed abortion. By analyzing the downstream regulatory network, we further determined that CrWRKY74 participated in seed abortion regulation by inducing abnormal programmed cell death. Of particular importance is that a preliminary model was proposed to depict the regulatory networks underlying seed abortion in citrus. The results of this study provide novel insights into the molecular mechanism across citrus seed development, and reveal the master role of CrWRKY74 in seed abortion of 'Huagan No. 4'.
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Affiliation(s)
- Liqing Lu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Haijian Yang
- Fruit Tree Research Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, P.R. China
| | - Yanhui Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Li Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Juxun Wu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Hualin Yi
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
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9
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Ke W, Xing J, Chen Z, Zhao Y, Xu W, Tian L, Guo J, Xie X, Du D, Wang Z, Li Y, Xu J, Xin M, Guo W, Hu Z, Su Z, Liu J, Peng H, Yao Y, Sun Q, Ni Z. The TaTCP4/10-B1 cascade regulates awn elongation in wheat (Triticum aestivum L.). PLANT COMMUNICATIONS 2023:100590. [PMID: 36919240 PMCID: PMC10363512 DOI: 10.1016/j.xplc.2023.100590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Awns are important morphological markers for wheat and exert a strong physiological effect on wheat yield. The awn elongation suppressor B1 has recently been cloned through association and linkage analysis in wheat. However, the mechanism of awn inhibition centered around B1 remains to be clarified. Here, we identified an allelic variant in the coding region of B1 through analysis of re-sequencing data; this variant causes an amino acid substitution and premature termination, resulting in a long-awn phenotype. Transcriptome analysis indicated that B1 inhibited awn elongation by impeding cytokinin- and auxin-promoted cell division. Moreover, B1 directly repressed the expression of TaRAE2 and TaLks2, whose orthologs have been reported to promote awn development in rice or barley. More importantly, we found that TaTCP4 and TaTCP10 synergistically inhibited the expression of B1, and a G-to-A mutation in the B1 promoter attenuated its inhibition by TaTCP4/10. Taken together, our results reveal novel mechanisms of awn development and provide genetic resources for trait improvement in wheat.
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Affiliation(s)
- Wensheng Ke
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jiewen Xing
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaoyan Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yidi Zhao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weiya Xu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lulu Tian
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jinquan Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaoming Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Dejie Du
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yufeng Li
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jin Xu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhenqi Su
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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10
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Domingo G, Vannini C, Bracale M, Bonfante P. Proteomics as a tool to decipher plant responses in arbuscular mycorrhizal interactions: a meta-analysis. Proteomics 2023; 23:e2200108. [PMID: 36571480 DOI: 10.1002/pmic.202200108] [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: 09/20/2022] [Revised: 11/09/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
The beneficial symbiosis between plants and arbuscular mycorrhizal (AM) fungi leads to a deep reprogramming of plant metabolism, involving the regulation of several molecular mechanisms, many of which are poorly characterized. In this regard, proteomics is a powerful tool to explore changes related to plant-microbe interactions. This study provides a comprehensive proteomic meta-analysis conducted on AM-modulated proteins at local (roots) and systemic (shoots/leaves) level. The analysis was implemented by an in-depth study of root membrane-associated proteins and by a comparison with a transcriptome meta-analysis. A total of 4262 differentially abundant proteins were retrieved and, to identify the most relevant AM-regulated processes, a range of bioinformatic studies were conducted, including functional enrichment and protein-protein interaction network analysis. In addition to several protein transporters which are present in higher amounts in AM plants, and which are expected due to the well-known enhancement of AM-induced mineral uptake, our analysis revealed some novel traits. We detected a massive systemic reprogramming of translation with a central role played by the ribosomal translational apparatus. On one hand, these new protein-synthesis efforts well support the root cellular re-organization required by the fungal penetration, and on the other they have a systemic impact on primary metabolism.
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Affiliation(s)
- Guido Domingo
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | - Candida Vannini
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | - Marcella Bracale
- Biotechnology and Life Science Department, University of Insubria, Varese, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
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11
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Goldy C, Barrera V, Taylor I, Buchensky C, Vena R, Benfey PN, De Veylder L, Rodriguez RE. SCARECROW-LIKE28 modulates organ growth in Arabidopsis by controlling mitotic cell cycle exit, endoreplication, and cell expansion dynamics. THE NEW PHYTOLOGIST 2023; 237:1652-1666. [PMID: 36451535 DOI: 10.1111/nph.18650] [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: 10/09/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
The processes that contribute to plant organ morphogenesis are spatial-temporally organized. Within the meristem, mitosis produces new cells that subsequently engage in cell expansion and differentiation programs. The latter is frequently accompanied by endoreplication, being an alternative cell cycle that replicates the DNA without nuclear division, causing a stepwise increase in somatic ploidy. Here, we show that the Arabidopsis SCL28 transcription factor promotes organ growth by modulating cell expansion dynamics in both root and leaf cells. Gene expression studies indicated that SCL28 regulates members of the SIAMESE/SIAMESE-RELATED (SIM/SMR) family, encoding cyclin-dependent kinase inhibitors with a role in promoting mitotic cell cycle (MCC) exit and endoreplication, both in response to developmental and environmental cues. Consistent with this role, mutants in SCL28 displayed reduced endoreplication, both in roots and leaves. We also found evidence indicating that SCL28 co-expresses with and regulates genes related to the biogenesis, assembly, and remodeling of the cytoskeleton and cell wall. Our results suggest that SCL28 controls, not only cell proliferation as reported previously but also cell expansion and differentiation by promoting MCC exit and endoreplication and by modulating aspects of the biogenesis, assembly, and remodeling of the cytoskeleton and cell wall.
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Affiliation(s)
- Camila Goldy
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Virginia Barrera
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Isaiah Taylor
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA
| | - Celeste Buchensky
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Rodrigo Vena
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Philip N Benfey
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Ramiro E Rodriguez
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, 2000, Argentina
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12
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Revalska M, Radkova M, Iantcheva A. Functional characterization of Medicago truncatula GRAS7, a member of the GRAS family transcription factors, in response to abiotic stress. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2074893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Miglena Revalska
- Department of Functional Genetics, Abiotic and Biotic Stress, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Mariana Radkova
- Department of Functional Genetics, Abiotic and Biotic Stress, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Anelia Iantcheva
- Department of Functional Genetics, Abiotic and Biotic Stress, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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13
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León-Ruiz JA, Cruz Ramírez A. Predicted landscape of RETINOBLASTOMA-RELATED LxCxE-mediated interactions across the Chloroplastida. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1507-1524. [PMID: 36305297 DOI: 10.1111/tpj.16012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/20/2022] [Accepted: 10/14/2022] [Indexed: 05/16/2023]
Abstract
The colonization of land by a single streptophyte algae lineage some 450 million years ago has been linked to multiple key innovations such as three-dimensional growth, alternation of generations, the presence of stomata, as well as innovations inherent to the birth of major plant lineages, such as the origins of vascular tissues, roots, seeds and flowers. Multicellularity, which evolved multiple times in the Chloroplastida coupled with precise spatiotemporal control of proliferation and differentiation were instrumental for the evolution of these traits. RETINOBLASTOMA-RELATED (RBR), the plant homolog of the metazoan Retinoblastoma protein (pRB), is a highly conserved and multifunctional core cell cycle regulator that has been implicated in the evolution of multicellularity in the green lineage as well as in plant multicellularity-related processes such as proliferation, differentiation, stem cell regulation and asymmetric cell division. RBR fulfills these roles through context-specific protein-protein interactions with proteins containing the Leu-x-Cys-x-Glu (LxCxE) short-linear motif (SLiM); however, how RBR-LxCxE interactions have changed throughout major innovations in the Viridiplantae kingdom is a question that remains unexplored. Here, we employ an in silico evo-devo approach to predict and analyze potential RBR-LxCxE interactions in different representative species of key Chloroplastida lineages, providing a valuable resource for deciphering RBR-LxCxE multiple functions. Furthermore, our analyses suggest that RBR-LxCxE interactions are an important component of RBR functions and that interactions with chromatin modifiers/remodelers, DNA replication and repair machinery are highly conserved throughout the Viridiplantae, while LxCxE interactions with transcriptional regulators likely diversified throughout the water-to-land transition.
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Affiliation(s)
- Jesús A León-Ruiz
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato, 36821, Guanajuato, Mexico
| | - Alfredo Cruz Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato, 36821, Guanajuato, Mexico
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14
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Ge Y, Gao Y, Jiao Y, Wang Y. A conserved module in the formation of moss midribs and seed plant axillary meristems. SCIENCE ADVANCES 2022; 8:eadd7275. [PMID: 36399581 PMCID: PMC9674282 DOI: 10.1126/sciadv.add7275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Different evolutionary lineages have evolved distinct characteristic body plans and anatomical structures, but their origins are largely elusive. For example, seed plants evolve axillary meristems to enable lateral branching. In moss, the phyllid (leaf) midrib containing specialized cells is responsible for water conduction and support. Midribs function like vascular tissues in flowering plants but may have risen from a different evolutionary path. Here, we demonstrate that midrib formation in the model moss Physcomitrium patens is regulated by orthologs of Arabidopsis LATERAL SUPPRESSOR (LAS), a key regulator of axillary meristem initiation. Midribs are missing in loss-of-function mutants, and ectopic formation of midrib-like structures is induced in overexpression lines. Furthermore, the PpLAS/AtLAS genes have conserved functions in the promotion of cell division in both lineages, which alleviates phenotypes in both Physcomitrium and Arabidopsis las mutants. Our results show that a conserved regulatory module is reused in divergent developmental programs, water-conducting and supporting tissues in moss, and axillary meristem initiation in seed plants.
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Affiliation(s)
- Yanhua Ge
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Conde D, Triozzi PM, Pereira WJ, Schmidt HW, Balmant KM, Knaack SA, Redondo-López A, Roy S, Dervinis C, Kirst M. Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus. Development 2022; 149:dev200632. [PMID: 36178121 PMCID: PMC9720752 DOI: 10.1242/dev.200632] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/20/2022] [Indexed: 07/25/2023]
Abstract
Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. Presently, we lack a lineage map of the shoot apex cells in woody perennials - a crucial gap considering their role in determining primary and secondary growth. Here, we used single-nuclei RNA-sequencing to determine cell type-specific transcriptomes of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of the epidermis, leaf mesophyll and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we applied a pipeline for interspecific single-cell gene expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the principles underlying cell division and differentiation conserved between herbaceous and perennial species while also allowing us to examine species-specific differences at single-cell resolution.
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Affiliation(s)
- Daniel Conde
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid 28223, Spain
| | - Paolo M. Triozzi
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Wendell J. Pereira
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Henry W. Schmidt
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Kelly M. Balmant
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Sara A. Knaack
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Arturo Redondo-López
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid 28223, Spain
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
- Department of Computer Sciences, University of Wisconsin, Madison, WI 53792, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53792, USA
| | - Christopher Dervinis
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Matias Kirst
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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16
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Mills AM, Rasmussen CG. Defects in division plane positioning in the root meristematic zone affect cell organization in the differentiation zone. J Cell Sci 2022; 135:276936. [PMID: 36074053 DOI: 10.1242/jcs.260127] [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: 04/19/2022] [Accepted: 09/01/2022] [Indexed: 11/20/2022] Open
Abstract
Cell division plane orientation is critical for plant and animal development and growth. TANGLED1 (TAN1) and AUXIN-INDUCED-IN-ROOT-CULTURES9 (AIR9) are division-site localized microtubule-binding proteins required for division plane positioning. tan1 and air9 Arabidopsis thaliana single mutants have minor or no noticeable phenotypes but the tan1 air9 double mutant has synthetic phenotypes including stunted growth, misoriented divisions, and aberrant cell-file rotation in the root differentiation zone. These data suggest that TAN1 plays a role in nondividing cells. To determine whether TAN1 is required in elongating and differentiating cells in the tan1 air9 double mutant, we limited its expression to actively dividing cells using the G2/M-specific promoter of the syntaxin KNOLLE (pKN:TAN1-YFP). Unexpectedly, in addition to rescuing division plane defects, pKN:TAN1-YFP rescued root growth and the root differentiation zone cell file rotation defects in the tan1 air9 double mutant. This suggests that defects that occur in the meristematic zone later affect the organization of elongating and differentiating cells.
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Affiliation(s)
- Alison M Mills
- Graduate Group in Biochemistry and Molecular Biology, USA
| | - Carolyn G Rasmussen
- Graduate Group in Biochemistry and Molecular Biology, USA.,Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California, Riverside, USA
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17
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Aragón-Raygoza A, Herrera-Estrella L, Cruz-Ramírez A. Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem. FRONTIERS IN PLANT SCIENCE 2022; 13:924660. [PMID: 36035690 PMCID: PMC9413220 DOI: 10.3389/fpls.2022.924660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Gene expression in roots has been assessed in different plant species in studies ranging from complete organs to specific cell layers, and more recently at the single cell level. While certain genes or functional categories are expressed in the root of all or most plant species, lineage-specific genes have also been discovered. An increasing amount of transcriptomic data is available for angiosperms, while a limited amount of data is available for ferns, and few studies have focused on fern roots. Here, we present a de novo transcriptome assembly from three different parts of the Ceratopteris richardii young sporophyte. Differential gene expression analysis of the root tip transcriptional program showed an enrichment of functional categories related to histogenesis and cell division, indicating an active apical meristem. Analysis of a diverse set of orthologous genes revealed conserved expression in the root meristem, suggesting a preserved role for different developmental roles in this tissue, including stem cell maintenance. The reconstruction of evolutionary trajectories for ground tissue specification genes suggests a high degree of conservation in vascular plants, but not for genes involved in root cap development, showing that certain genes are absent in Ceratopteris or have intricate evolutionary paths difficult to track. Overall, our results suggest different processes of conservation and divergence of genes involved in root development.
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Affiliation(s)
- Alejandro Aragón-Raygoza
- Molecular and Developmental Complexity Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
- Metabolic Engineering Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Metabolic Engineering Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, United States
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad De Genómica Avanzada, Laboratorio Nacional De Genómica Para la Biodiversidad, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
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18
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Jaiswal V, Kakkar M, Kumari P, Zinta G, Gahlaut V, Kumar S. Multifaceted Roles of GRAS Transcription Factors in Growth and Stress Responses in Plants. iScience 2022; 25:105026. [PMID: 36117995 PMCID: PMC9474926 DOI: 10.1016/j.isci.2022.105026] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Vandana Jaiswal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mrinalini Kakkar
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Priya Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Corresponding author
| | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
- Corresponding author
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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Nomoto Y, Takatsuka H, Yamada K, Suzuki T, Suzuki T, Huang Y, Latrasse D, An J, Gombos M, Breuer C, Ishida T, Maeo K, Imamura M, Yamashino T, Sugimoto K, Magyar Z, Bögre L, Raynaud C, Benhamed M, Ito M. A hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis. Nat Commun 2022; 13:1660. [PMID: 35351906 PMCID: PMC8964727 DOI: 10.1038/s41467-022-29316-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/07/2022] [Indexed: 12/13/2022] Open
Abstract
AbstractHow cell size and number are determined during organ development remains a fundamental question in cell biology. Here, we identified a GRAS family transcription factor, called SCARECROW-LIKE28 (SCL28), with a critical role in determining cell size in Arabidopsis. SCL28 is part of a transcriptional regulatory network downstream of the central MYB3Rs that regulate G2 to M phase cell cycle transition. We show that SCL28 forms a dimer with the AP2-type transcription factor, AtSMOS1, which defines the specificity for promoter binding and directly activates transcription of a specific set of SIAMESE-RELATED (SMR) family genes, encoding plant-specific inhibitors of cyclin-dependent kinases and thus inhibiting cell cycle progression at G2 and promoting the onset of endoreplication. Through this dose-dependent regulation of SMR transcription, SCL28 quantitatively sets the balance between cell size and number without dramatically changing final organ size. We propose that this hierarchical transcriptional network constitutes a cell cycle regulatory mechanism that allows to adjust cell size and number to attain robust organ growth.
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20
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Echevarría C, Gutierrez C, Desvoyes B. Tools for Assessing Cell-Cycle Progression in Plants. PLANT & CELL PHYSIOLOGY 2021; 62:1231-1238. [PMID: 34021583 PMCID: PMC8579159 DOI: 10.1093/pcp/pcab066] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/27/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Estimation of cell-cycle parameters is crucial for understanding the developmental programs established during the formation of an organism. A number of complementary approaches have been developed and adapted to plants to assess the cell-cycle status in different proliferative tissues. The most classical methods relying on metabolic labeling are still very much employed and give valuable information on cell-cycle progression in fixed tissues. However, the growing knowledge of plant cell-cycle regulators with defined expression pattern together with the development of fluorescent proteins technology enabled the generation of fusion proteins that function individually or in conjunction as cell-cycle reporters. Together with the improvement of imaging techniques, in vivo live imaging to monitor plant cell-cycle progression in normal growth conditions or in response to different stimuli has been possible. Here, we review these tools and their specific outputs for plant cell-cycle analysis.
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Affiliation(s)
- Clara Echevarría
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Crisanto Gutierrez
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, Madrid 28049, Spain
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