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Shi C, Zou W, Liu X, Zhang H, Li X, Fu G, Fei Q, Qian Q, Shang L. Programmable RNA N 6-methyladenosine editing with CRISPR/dCas13a in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1867-1880. [PMID: 38363049 PMCID: PMC11182597 DOI: 10.1111/pbi.14307] [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: 04/12/2023] [Revised: 10/07/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
N6-methyladenonsine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) and plays critical roles in mRNA processing and metabolism. However, perturbation of individual m6A modification to reveal its function and the phenotypic effects is still lacking in plants. Here, we describe the construction and characterization of programmable m6A editing tools by fusing the m6A writers, the core catalytic domain of the MTA and MTB complex, and the AlkB homologue 5 (ALKBH5) eraser, to catalytically dead Cas13a (dCas13a) to edit individual m6A sites on mRNAs. We demonstrated that our m6A editors could efficiently and specifically deposit and remove m6A modifications on specific RNA transcripts in both Nicotiana benthamiana and Arabidopsis thaliana. Moreover, we found that targeting SHORT-ROOT (SHR) transcripts with a methylation editor could significantly increase its m6A levels with limited off-target effects and promote its degradation. This leads to a boost in plant growth with enlarged leaves and roots, increased plant height, plant biomass, and total grain weight in Arabidopsis. Collectively, these findings suggest that our programmable m6A editing tools can be applied to study the functions of individual m6A modifications in plants, and may also have potential applications for future crop improvement.
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Affiliation(s)
- Chuanlin Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Wenli Zou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Xiangpei Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Hong Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Xiaofang Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- Zhengzhou Research Base, State Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhouChina
| | - Guiling Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- College of AgricultureShanxi Agricultural UniversityTaiyuanShanxiChina
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouZhejiangChina
- Yazhouwan National LaboratorySanya CityHainan ProvinceChina
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- Yazhouwan National LaboratorySanya CityHainan ProvinceChina
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2
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Rana D, Sharma P, Arpita K, Srivastava H, Sharma S, Gaikwad K. Genome-wide identification and characterization of GRAS gene family in pigeonpea ( Cajanus cajan (L.) Millspaugh). 3 Biotech 2023; 13:363. [PMID: 37840881 PMCID: PMC10570252 DOI: 10.1007/s13205-023-03782-x] [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: 06/02/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
The GRAS proteins are plant-specific transcription factors (TFs) that play a crucial role in various plant physiological processes, including tissue development and stress responses. To date, GRAS family has been comprehensively characterized in Arabidopsis, soybean, rice, chickpea and other plant species. To understand the structural and functional aspects of pigeonpea (C. cajan), we identified 60 putative GRAS (CcGRAS) genes from pigeonpea genome and further analysed their physicochemical properties, subcellular locations, evolutionary classification, exon-intron structures, conserved domains, gene duplication events and cis-promoter regions. Based on the sequence similarity, CcGRAS family was clustered into 9 subfamilies and the genes with a similar structure and motif distribution were clustered in the same group. The gene duplication studies revealed that these genes were derived from tandem and dispersed duplication events. The cis-promoter regulatory analysis of CcGRAS genes indicated the presence of three types of cis-acting elements including light-responsive, hormone-responsive and plant growth and development related. The expression profiling of CcGRAS genes revealed their tissue-specific functions and differential nature. Collectively, this study highlights relevant functional and regulatory elements of GRAS family in pigeonpea creating a significant resource for future functional studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03782-x.
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Affiliation(s)
- Divyansh Rana
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313 India
| | - Priya Sharma
- Department of Biotechnology, Jamia Hamdard, New Delhi, Delhi 110062 India
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kumari Arpita
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Harsha Srivastava
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Sandhya Sharma
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kishor Gaikwad
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
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Bahafid E, Bradtmöller I, Thies AM, Nguyen TTON, Gutierrez C, Desvoyes B, Stahl Y, Blilou I, Simon RGW. The Arabidopsis SHORTROOT network coordinates shoot apical meristem development with auxin-dependent lateral organ initiation. eLife 2023; 12:e83334. [PMID: 37862096 PMCID: PMC10642969 DOI: 10.7554/elife.83334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Plants produce new organs post-embryonically throughout their entire life cycle. This is due to stem cells present in the shoot and root apical meristems, the SAM and RAM, respectively. In the SAM, stem cells are located in the central zone where they divide slowly. Stem cell daughters are displaced laterally and enter the peripheral zone, where their mitotic activity increases and lateral organ primordia are formed. How the spatial arrangement of these different domains is initiated and controlled during SAM growth and development, and how sites of lateral organ primordia are determined in the peripheral zone is not yet completely understood. We found that the SHORTROOT (SHR) transcription factor together with its target transcription factors SCARECROW (SCR), SCARECROW-LIKE23 (SCL23) and JACKDAW (JKD), promotes formation of lateral organs and controls shoot meristem size. SHR, SCR, SCL23, and JKD are expressed in distinct, but partially overlapping patterns in the SAM. They can physically interact and activate expression of key cell cycle regulators such as CYCLIND6;1 (CYCD6;1) to promote the formation of new cell layers. In the peripheral zone, auxin accumulates at sites of lateral organ primordia initiation and activates SHR expression via the auxin response factor MONOPTEROS (MP) and auxin response elements in the SHR promoter. In the central zone, the SHR-target SCL23 physically interacts with the key stem cell regulator WUSCHEL (WUS) to promote stem cell fate. Both SCL23 and WUS expression are subject to negative feedback regulation from stem cells through the CLAVATA signaling pathway. Together, our findings illustrate how SHR-dependent transcription factor complexes act in different domains of the shoot meristem to mediate cell division and auxin dependent organ initiation in the peripheral zone, and coordinate this activity with stem cell maintenance in the central zone of the SAM.
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Affiliation(s)
- Elmehdi Bahafid
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Imke Bradtmöller
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Ann M Thies
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Thi TON Nguyen
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, CantoblancoMadridSpain
| | - Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, CantoblancoMadridSpain
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology, Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Rüdiger GW Simon
- Institute for Developmental Genetics, Heinrich Heine UniversityDüsseldorfGermany
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4
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Oh J, Choi JW, Jang S, Kim SW, Heo JO, Yoon EK, Kim SH, Lim J. Transcriptional control of hydrogen peroxide homeostasis regulates ground tissue patterning in the Arabidopsis root. FRONTIERS IN PLANT SCIENCE 2023; 14:1242211. [PMID: 37670865 PMCID: PMC10475948 DOI: 10.3389/fpls.2023.1242211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/01/2023] [Indexed: 09/07/2023]
Abstract
In multicellular organisms, including higher plants, asymmetric cell divisions (ACDs) play a crucial role in generating distinct cell types. The Arabidopsis root ground tissue initially has two layers: endodermis (inside) and cortex (outside). In the mature root, the endodermis undergoes additional ACDs to produce the endodermis itself and the middle cortex (MC), located between the endodermis and the pre-existing cortex. In the Arabidopsis root, gibberellic acid (GA) deficiency and hydrogen peroxide (H2O2) precociously induced more frequent ACDs in the endodermis for MC formation. Thus, these findings suggest that GA and H2O2 play roles in regulating the timing and extent of MC formation. However, details of the molecular interaction between GA signaling and H2O2 homeostasis remain elusive. In this study, we identified the PEROXIDASE 34 (PRX34) gene, which encodes a class III peroxidase, as a molecular link to elucidate the interconnected regulatory network involved in H2O2- and GA-mediated MC formation. Under normal conditions, prx34 showed a reduced frequency of MC formation, whereas the occurrence of MC in prx34 was restored to nearly WT levels in the presence of H2O2. Our results suggest that PRX34 plays a role in H2O2-mediated MC production. Furthermore, we provide evidence that SCARECROW-LIKE 3 (SCL3) regulates H2O2 homeostasis by controlling transcription of PRX34 during root ground tissue maturation. Taken together, our findings provide new insights into how H2O2 homeostasis is achieved by SCL3 to ensure correct radial tissue patterning in the Arabidopsis root.
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Affiliation(s)
- Jiyeong Oh
- Department of Systems Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Ji Won Choi
- Department of Systems Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Sejeong Jang
- Department of Systems Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Seung Woo Kim
- Department of Systems Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Jung-Ok Heo
- Department of Systems Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Eun Kyung Yoon
- Department of Systems Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Soo-Hwan Kim
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Jun Lim
- Department of Systems Biotechnology, Konkuk University, Seoul, Republic of Korea
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Yoon EK, Oh J, Lim J. (Don't) Look Up!: Is short-root just a short-root plant? FRONTIERS IN PLANT SCIENCE 2022; 13:1069996. [PMID: 36466291 PMCID: PMC9712719 DOI: 10.3389/fpls.2022.1069996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
SHORT-ROOT (SHR) is a mobile transcription factor that plays important roles in ground tissue patterning, stem cell niche specification and maintenance, and vascular development in Arabidopsis roots. Although mRNA and protein of SHR are also found in hypocotyls, inflorescence stems, and leaves, its role in the above-ground organs has been less explored. In most developmental cases, SHR, together with its partner SCARECROW (SCR), regulates the expression of downstream target genes in controlling formative and proliferative cell divisions. Accumulating evidence on the regulatory role of SHR in shoots suggests that SHR may also play key roles in the above-ground organs. Interestingly, recent work has provided new evidence that SHR is also required for cell elongation in the hypocotyl of the etiolated seedling. This suggests that the novel roles of SHR and SHR-mediated regulatory networks can be found in shoots. Furthermore, comparative research on SHR function in roots and shoots will broaden and deepen our understanding of plant growth and development.
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6
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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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7
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Dhar S, Kim J, Yoon EK, Jang S, Ko K, Lim J. SHORT-ROOT Controls Cell Elongation in the Etiolated Arabidopsis Hypocotyl. Mol Cells 2022; 45:243-256. [PMID: 35249891 PMCID: PMC9001151 DOI: 10.14348/molcells.2021.5008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 12/01/2021] [Indexed: 11/27/2022] Open
Abstract
Transcriptional regulation, a core component of gene regulatory networks, plays a key role in controlling individual organism's growth and development. To understand how plants modulate cellular processes for growth and development, the identification and characterization of gene regulatory networks are of importance. The SHORT-ROOT (SHR) transcription factor is known for its role in cell divisions in Arabidopsis (Arabidopsis thaliana). However, whether SHR is involved in hypocotyl cell elongation remains unknown. Here, we reveal that SHR controls hypocotyl cell elongation via the transcriptional regulation of XTH18, XTH22, and XTH24, which encode cell wall remodeling enzymes called xyloglucan endotransglucosylase/hydrolases (XTHs). Interestingly, SHR activates transcription of the XTH genes, independently of its partner SCARECROW (SCR), which is different from the known mode of action. In addition, overexpression of the XTH genes can promote cell elongation in the etiolated hypocotyl. Moreover, confinement of SHR protein in the stele still induces cell elongation, despite the aberrant organization in the hypocotyl ground tissue. Therefore, it is likely that SHR-mediated growth is uncoupled from SHR-mediated radial patterning in the etiolated hypocotyl. Our findings also suggest that intertissue communication between stele and endodermis plays a role in coordinating hypocotyl cell elongation of the Arabidopsis seedling. Taken together, our study identifies SHR as a new crucial regulator that is necessary for cell elongation in the etiolated hypocotyl.
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Affiliation(s)
- Souvik Dhar
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
- Present address: School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Korea
| | - Jinkwon Kim
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Eun Kyung Yoon
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
- Present address: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Sejeong Jang
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Kangseok Ko
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Jun Lim
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
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8
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Lu L, Diao Z, Yang D, Wang X, Zheng X, Xiang X, Xiao Y, Chen Z, Wang W, Wu Y, Tang D, Li S. The 14-3-3 protein GF14c positively regulates immunity by modulating the protein homoeostasis of the GRAS protein OsSCL7 in rice. PLANT, CELL & ENVIRONMENT 2022; 45:1065-1081. [PMID: 35129212 DOI: 10.1111/pce.14278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/07/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Various types of transcription factors have been reported to be involved in plant-pathogen interactions by regulating defence-related genes. GRAS proteins, plant- specific transcription factors, have been shown to play essential roles in plant growth, development and stress responses. By performing a transcriptome study on rice early defence responses to Magnaporthe oryzae, we identified a GRAS protein, OsSCL7, which was induced by M. oryzae infection. We characterized the function of OsSCL7 in rice disease resistance. OsSCL7 was upregulated upon exposure to M. oryzae and pathogen-associated molecular pattern treatments, and knocking out OsSCL7 resulted in decreased disease resistance of rice to M. oryzae. In contrast, overexpression of OsSCL7 could improve rice disease resistance to M. oryzae. OsSCL7 was mainly localized in the nucleus and showed transcriptional activity. OsSCL7 can interact with GF14c, a 14-3-3 protein, and loss-of-function GF14c leads to enhanced susceptibility to M. oryzae. Additionally, OsSCL7 protein levels were reduced in the gf14c mutant and knocking out OsSCL7 affected the expression of a series of defence-related genes. Taken together, these findings uncover the important roles of OsSCL7 and GF14c in plant immunity and a potential mechanism by which plants fine-tune immunity by regulating the protein stability of a GRAS protein via a 14-3-3 protein.
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Affiliation(s)
- Ling Lu
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhijuan Diao
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dewei Yang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xun Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingxing Zheng
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinquan Xiang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yueping Xiao
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiwei Chen
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunkun Wu
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengping Li
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
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9
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Roszak P, Heo JO, Blob B, Toyokura K, Sugiyama Y, de Luis Balaguer MA, Lau WWY, Hamey F, Cirrone J, Madej E, Bouatta AM, Wang X, Guichard M, Ursache R, Tavares H, Verstaen K, Wendrich J, Melnyk CW, Oda Y, Shasha D, Ahnert SE, Saeys Y, De Rybel B, Heidstra R, Scheres B, Grossmann G, Mähönen AP, Denninger P, Göttgens B, Sozzani R, Birnbaum KD, Helariutta Y. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. Science 2021; 374:eaba5531. [PMID: 34941412 PMCID: PMC8730638 DOI: 10.1126/science.aba5531] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In the plant meristem, tissue-wide maturation gradients are coordinated with specialized cell networks to establish various developmental phases required for indeterminate growth. Here, we used single-cell transcriptomics to reconstruct the protophloem developmental trajectory from the birth of cell progenitors to terminal differentiation in the Arabidopsis thaliana root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development, broad maturation gradients interface with cell-type-specific transcriptional regulators to stage cellular differentiation.
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Affiliation(s)
- Pawel Roszak
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Jung-Ok Heo
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Bernhard Blob
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Koichi Toyokura
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
- Faculty of Science and Engineering, Konan University, Kobe, Japan
- GRA&GREEN Inc., Incubation Facility, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Yuki Sugiyama
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | | | - Winnie W Y Lau
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Fiona Hamey
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jacopo Cirrone
- Computer Science Department, Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Ewelina Madej
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Alida M Bouatta
- Plant Systems Biology, Technical University of Munich, Freising, Germany
| | - Xin Wang
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Marjorie Guichard
- Institute of Cell and Interaction Biology, CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Robertas Ursache
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Hugo Tavares
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Bioinformatics Training Facility, Department of Genetics, University of Cambridge, Cambridge, UK
| | - Kevin Verstaen
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Jos Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Charles W Melnyk
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yoshihisa Oda
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, the Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
| | - Dennis Shasha
- Computer Science Department, Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Sebastian E Ahnert
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, British Library, London, UK
| | - Yvan Saeys
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Renze Heidstra
- Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Ben Scheres
- Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
- Rijk Zwaan R&D, 4793 Fijnaart, Netherlands
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Philipp Denninger
- Plant Systems Biology, Technical University of Munich, Freising, Germany
| | - Berthold Göttgens
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Yrjö Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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10
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Onyenedum JG, Pace MR. The role of ontogeny in wood diversity and evolution. AMERICAN JOURNAL OF BOTANY 2021; 108:2331-2355. [PMID: 34761812 DOI: 10.1002/ajb2.1801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Evolutionary developmental biology (evo-devo) explores the link between developmental patterning and phenotypic change through evolutionary time. In this review, we highlight the scientific advancements in understanding xylem evolution afforded by the evo-devo approach, opportunities for further engagement, and future research directions for the field. We review evidence that (1) heterochrony-the change in rate and timing of developmental events, (2) homeosis-the ontogenetic replacement of features, (3) heterometry-the change in quantity of a feature, (4) exaptation-the co-opting and repurposing of an ancestral feature, (5) the interplay between developmental and capacity constraints, and (6) novelty-the emergence of a novel feature, have all contributed to generating the diversity of woods. We present opportunities for future research engagement, which combine wood ontogeny within the context of robust phylogenetic hypotheses, and molecular biology.
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Affiliation(s)
- Joyce G Onyenedum
- School of Integrative Plant Sciences and L. H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Marcelo R Pace
- Department of Botany, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n de Ciudad Universitaria, Mexico City, 04510, Mexico
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11
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Fan Y, Wei X, Lai D, Yang H, Feng L, Li L, Niu K, Chen L, Xiang D, Ruan J, Yan J, Cheng J. Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.). BMC PLANT BIOLOGY 2021; 21:508. [PMID: 34732123 PMCID: PMC8565077 DOI: 10.1186/s12870-021-03277-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/18/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted. RESULTS In this study, 57 GRAS genes of foxtail millet (SiGRASs) were identified and renamed according to the chromosomal distribution of the SiGRAS genes. Based on the number of conserved domains and gene structure, the SiGRAS genes were divided into 13 subfamilies via phylogenetic tree analysis. The GRAS genes were unevenly distributed on nine chromosomes, and members of the same subfamily had similar gene structures and motif compositions. Genetic structure analysis showed that most SiGRAS genes lacked introns. Some SiGRAS genes were derived from gene duplication events, and segmental duplications may have contributed more to GRAS gene family expansion than tandem duplications. Quantitative polymerase chain reaction showed significant differences in the expression of SiGRAS genes in different tissues and stages of fruits development, which indicated the complexity of the physiological functions of SiGRAS. In addition, exogenous paclobutrazol treatment significantly altered the transcription levels of DELLA subfamily members, downregulated the gibberellin content, and decreased the plant height of foxtail millet, while it increased the fruit weight. In addition, SiGRAS13 and SiGRAS25 may have the potential for genetic improvement and functional gene research in foxtail millet. CONCLUSIONS Collectively, this study will be helpful for further analysing the biological function of SiGRAS. Our results may contribute to improving the genetic breeding of foxtail millet.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Xiaobao Wei
- Guizhou provincial Center For Disease Control And Prevention, Guiyang, 550025, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610030, People's Republic of China
| | - Long Li
- Henan university of technology, Zhengzhou, 450001, People's Republic of China
| | - Kexin Niu
- Henan university of technology, Zhengzhou, 450001, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, Mianzhu, 618200, People's Republic of China
| | - Dabing Xiang
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China.
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12
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Zhang W, Lin J, Li J, Zheng S, Zhang X, Chen S, Ma X, Dong F, Jia H, Xu X, Yang Z, Ma P, Deng F, Deng B, Huang Y, Li Z, Lv X, Ma Y, Liao Z, Lin Z, Lin J, Zhang S, Matsumoto T, Xia R, Zhang J, Ming R. Rambutan genome revealed gene networks for spine formation and aril development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1037-1052. [PMID: 34519122 DOI: 10.1111/tpj.15491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/28/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Rambutan is a popular tropical fruit known for its exotic appearance, has long flexible spines on shells, extraordinary aril growth, desirable nutrition, and a favorable taste. The genome of an elite rambutan cultivar Baoyan 7 was assembled into 328 Mb in 16 pseudo-chromosomes. Comparative genomics analysis between rambutan and lychee revealed that rambutan chromosomes 8 and 12 are collinear with lychee chromosome 1, which resulted in a chromosome fission event in rambutan (n = 16) or a fusion event in lychee (n = 15) after their divergence from a common ancestor 15.7 million years ago. Root development genes played a crucial role in spine development, such as endoplasmic reticulum pathway genes, jasmonic acid response genes, vascular bundle development genes, and K+ transport genes. Aril development was regulated by D-class genes (STK and SHP1), plant hormone and phenylpropanoid biosynthesis genes, and sugar metabolism genes. The lower rate of male sterility of hermaphroditic flowers appears to be regulated by MYB24. Population genomic analyses revealed genes in selective sweeps during domestication that are related to fruit morphology and environment stress response. These findings enhance our understanding of spine and aril development and provide genomic resources for rambutan improvement.
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Affiliation(s)
- Wenping Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jishan Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jianguo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Litchi Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Shaoquan Zheng
- Fujian Fruit Breeding Engineering Technology Research Center for Longan and Loquat, Fuzhou, Fujian, 350013, China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Shuai Chen
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Fei Dong
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Haifeng Jia
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiuming Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Ziqin Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570100, China
| | - Panpan Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Fang Deng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Ban Deng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yongji Huang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhanjie Li
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaozhou Lv
- Tropical Crops Institute, Baoting, Hainan, 572311, China
| | - Yaying Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhenyang Liao
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhicong Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jing Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Shengcheng Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Tracie Matsumoto
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - Rui Xia
- Tropical Crops Institute, Baoting, Hainan, 572311, China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 6180, USA
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13
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Wu W, Li J, Wang Q, Lv K, Du K, Zhang W, Li Q, Kang X, Wei H. Growth-regulating factor 5 (GRF5)-mediated gene regulatory network promotes leaf growth and expansion in poplar. THE NEW PHYTOLOGIST 2021; 230:612-628. [PMID: 33423287 PMCID: PMC8048564 DOI: 10.1111/nph.17179] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/28/2020] [Indexed: 05/07/2023]
Abstract
Although polyploid plants have larger leaves than their diploid counterparts, the molecular mechanisms underlying this difference (or trait) remain elusive. Differentially expressed genes (DEGs) between triploid and full-sib diploid poplar trees were identified from two transcriptomic data sets followed by a gene association study among DEGs to identify key leaf growth regulators. Yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay were employed to substantiate that PpnGRF5-1 directly regulated PpnCKX1. The interactions between PpnGRF5-1 and growth-regulating factor (GRF)-interacting factors (GIFs) were experimentally validated and a multilayered hierarchical regulatory network (ML-hGRN)-mediated by PpnGRF5-1 was constructed with top-down graphic Gaussian model (GGM) algorithm by combining RNA-sequencing data from its overexpression lines and DAP-sequencing data. PpnGRF5-1 is a negative regulator of PpnCKX1. Overexpression of PpnGRF5-1 in diploid transgenic lines resulted in larger leaves resembling those of triploids, and significantly increased zeatin and isopentenyladenine in the apical buds and third leaves. PpnGRF5-1 also interacted with GIFs to increase its regulatory diversity and capacity. An ML-hGRN-mediated by PpnGRF5-1 was obtained and could largely elucidate larger leaves. PpnGRF5-1 and the ML-hGRN-mediated by PpnGRF5-1 were underlying the leaf growth and development.
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Affiliation(s)
- Wenqi Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijing100083China
| | - Jiang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijing100083China
| | - Qiao Wang
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijing100091China
| | - Kaiwen Lv
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinHeilongjiang150040China
| | - Kang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijing100083China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingJiangsu210095China
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijing100091China
| | - Xiangyang Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijing100083China
| | - Hairong Wei
- College of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonMI49931USA
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14
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Geng Y, Cai C, McAdam SAM, Banks JA, Wisecaver JH, Zhou Y. A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants. Genome Biol Evol 2021; 13:6157829. [PMID: 33681974 PMCID: PMC7975763 DOI: 10.1093/gbe/evab042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2021] [Indexed: 01/26/2023] Open
Abstract
As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, we uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.
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Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Chao Cai
- Purdue University Libraries and School of Information Studies, Purdue University, West Lafayette, Indiana, USA
| | - Scott A M McAdam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jennifer H Wisecaver
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA.,Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
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15
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BAM1/2 receptor kinase signaling drives CLE peptide-mediated formative cell divisions in Arabidopsis roots. Proc Natl Acad Sci U S A 2020; 117:32750-32756. [PMID: 33288706 PMCID: PMC7768756 DOI: 10.1073/pnas.2018565117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proper elaboration of the plant body plan requires that cell division patterns are coordinated during development in complex tissues. Activation of cell cycle machinery is critical for this process, but it is not clear how or if this links to cell-to-cell communication networks that are important during development. Here we show that key cell divisions that generate the plant root are controlled by cell-to-cell signaling peptides which act through plant-specific receptor kinases to control expression of a specific cyclinD cell cycle regulatory gene. We show that cyclinD gene expression depends on both receptor signaling and the SHORT-ROOT transcription factor to ensure timely and robust cell division patterns. Cell division is often regulated by extracellular signaling networks to ensure correct patterning during development. In Arabidopsis, the SHORT-ROOT (SHR)/SCARECROW (SCR) transcription factor dimer activates CYCLIND6;1 (CYCD6;1) to drive formative divisions during root ground tissue development. Here, we show plasma-membrane-localized BARELY ANY MERISTEM1/2 (BAM1/2) family receptor kinases are required for SHR-dependent formative divisions and CYCD6;1 expression, but not SHR-dependent ground tissue specification. Root-enriched CLE ligands bind the BAM1 extracellular domain and are necessary and sufficient to activate SHR-mediated divisions and CYCD6;1 expression. Correspondingly, BAM-CLE signaling contributes to the restriction of formative divisions to the distal root region. Additionally, genetic analysis reveals that BAM-CLE and SHR converge to regulate additional cell divisions outside of the ground tissues. Our work identifies an extracellular signaling pathway regulating formative root divisions and provides a framework to explore this pathway in patterning and evolution.
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16
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Genome-Wide Analysis of the GRAS Gene Family in Barley ( Hordeum vulgare L.). Genes (Basel) 2020; 11:genes11050553. [PMID: 32423019 PMCID: PMC7290968 DOI: 10.3390/genes11050553] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 11/16/2022] Open
Abstract
The GRAS (named after first three identified proteins within this family, GAI, RGA, and SCR) family contains plant-specific genes encoding transcriptional regulators that play a key role in gibberellin (GA) signaling, which regulates plant growth and development. Even though GRAS genes have been characterized in some plant species, little research is known about the GRAS genes in barley (Hordeum vulgare L.). In this study, we observed 62 GRAS members from barley genome, which were grouped into 12 subgroups by using phylogenomic analysis together with the GRAS genes from Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). Chromosome localization and gene structure analysis suggested that duplication events and abundant presence of intronless genes might account for the massive expansion of GRAS gene family in barley. The analysis of RNA-seq data indicates the expression pattern of GRAS genes in various tissues at different stages in barley. Noteworthy, our qRT-PCR analysis showed the expression of 18 candidate GRAS genes abundantly in the developing inflorescence, indicating their potential roles in the barley inflorescence development and reproduction. Collectively, our evolutionary and expression analysis of GRAS family are useful for future functional characterization of GA signaling in barley and agricultural improvement.
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17
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Guo P, Wen J, Yang J, Ke Y, Wang M, Liu M, Ran F, Wu Y, Li P, Li J, Du H. Genome-wide survey and expression analyses of the GRAS gene family in Brassica napus reveals their roles in root development and stress response. PLANTA 2019; 250:1051-1072. [PMID: 31161396 DOI: 10.1007/s00425-019-03199-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
Genome-wide identification, classification, expression analyses, and functional characterization of GRAS genes in oil crop, Brassica napus, indicate their importance in root development and stress response. GRAS proteins are a plant-specific transcription factor gene family involved in tissues development and stress response. We classified 87 putative GRAS genes in the Brassica napus genome (BnGRASs) into 13 subfamilies by phylogenetic analysis. The C-terminal GRAS domains of Brassica napus (B. napus) proteins were less conserved among subfamilies, but were conserved within each subfamily. A series of analyses revealed that 89.7% of the BnGRASs did not have intron insertions, and 24 specific-motifs were found at the N-terminal. A highly conserved microRNA 171 (miRNA171) target was observed specifically in the HAM subfamily across land plants. A total of 868 pairs of interaction proteins were predicted, the primary of which were transcription factors involved in transcriptional regulation and signal transduction. Integrated comparative analysis of GRAS genes across 26 species of algae, mosses, ferns, gymnosperms, and angiosperms revealed that this gene family originated in early mosses and was classified into 19 subfamilies, 14 of which may have originated prior to bryophyte evolution. RNA-Seq analysis demonstrated that most BnGRASs were widely expressed in different tissues/organs at different stages in B. napus, and 24 BnGRASs were highly/specifically expressed in roots. Results from a qRT-PCR analysis suggested that two BnGRASs belonging to SCR and LISCL subfamilies potentially have important roles in the stress response of roots.
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Affiliation(s)
- Pengcheng Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yunzhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mangmang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mingming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Feng Ran
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yunwen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Pengfeng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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18
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Liu M, Huang L, Ma Z, Sun W, Wu Q, Tang Z, Bu T, Li C, Chen H. Genome-wide identification, expression analysis and functional study of the GRAS gene family in Tartary buckwheat (Fagopyrum tataricum). BMC PLANT BIOLOGY 2019; 19:342. [PMID: 31387526 PMCID: PMC6683366 DOI: 10.1186/s12870-019-1951-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 07/29/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND GRAS are plant-specific transcription factors that play important roles in plant growth and development. Although the GRAS gene family has been studied in many plants, there has been little research on the GRAS genes of Tartary buckwheat (Fagopyrum tataricum), which is an important crop rich in rutin. The recently published whole genome sequence of Tartary buckwheat allows us to study the characteristics and expression patterns of the GRAS gene family in Tartary buckwheat at the genome-wide level. RESULTS In this study, 47 GRAS genes of Tartary buckwheat were identified and divided into 10 subfamilies: LISCL, HAM, DELLA, SCR, PAT1, SCL4/7, LAS, SHR, SCL3, and DLT. FtGRAS genes were unevenly distributed on 8 chromosomes, and members of the same subfamily contained similar gene structures and motif compositions. Some FtGRAS genes may have been produced by gene duplications; tandem duplication contributed more to the expansion of the GRAS gene family in Tartary buckwheat. Real-time PCR showed that the transcription levels of FtGRAS were significantly different in different tissues and fruit development stages, implying that FtGRAS might have different functions. Furthermore, an increase in fruit weight was induced by exogenous paclobutrazol, and the transcription level of the DELLA subfamily member FtGRAS22 was significantly upregulated during the whole fruit development stage. Therefore, FtGRAS22 may be a potential target for molecular breeding or genetic editing. CONCLUSIONS Collectively, this systematic analysis lays a foundation for further study of the functional characteristics of GRAS genes and for the improvement of Tartary buckwheat crops.
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Affiliation(s)
- Moyang Liu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Huang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Zhaotang Ma
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Wenjun Sun
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Zizhong Tang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Tongliang Bu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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Kumar M, Le DT, Hwang S, Seo PJ, Kim HU. Role of the INDETERMINATE DOMAIN Genes in Plants. Int J Mol Sci 2019; 20:ijms20092286. [PMID: 31075826 PMCID: PMC6539433 DOI: 10.3390/ijms20092286] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
The INDETERMINATE DOMAIN (IDD) genes comprise a conserved transcription factor family that regulates a variety of developmental and physiological processes in plants. Many recent studies have focused on the genetic characterization of IDD family members and revealed various biological functions, including modulation of sugar metabolism and floral transition, cold stress response, seed development, plant architecture, regulation of hormone signaling, and ammonium metabolism. In this review, we summarize the functions and working mechanisms of the IDD gene family in the regulatory network of metabolism and developmental processes.
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Affiliation(s)
- Manu Kumar
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Dung Thi Le
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
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20
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Li M, Sun B, Xie F, Gong R, Luo Y, Zhang F, Yan Z, Tang H. Identification of the GRAS gene family in the Brassica juncea genome provides insight into its role in stem swelling in stem mustard. PeerJ 2019; 7:e6682. [PMID: 30972257 PMCID: PMC6448559 DOI: 10.7717/peerj.6682] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/12/2019] [Indexed: 12/18/2022] Open
Abstract
GRAS transcription factors are known to play important roles in plant signal transduction and development. A comprehensive study was conducted to explore the GRAS family in the Brassica juncea genome. A total of 88 GRAS genes were identified which were categorized into nine groups according to the phylogenetic analysis. Gene structure analysis showed a high group-specificity, which corroborated the gene grouping results. The chromosome distribution and sequence analysis suggested that gene duplication events are vital for the expansion of GRAS genes in the B. juncea genome. The changes in evolution rates and amino acid properties among groups might be responsible for their functional divergence. Interaction networks and cis-regulatory elements were analyzed including DELLA and eight interaction proteins (including four GID1, two SLY1, and two PIF3 proteins) that are primarily involved in light and hormone signaling. To understand their regulatory role in growth and development, the expression profiles of BjuGRASs and interaction genes were examined based on transcriptome data and qRT-PCR, and selected genes (BjuGRAS3, 5, 7, 8, 10, BjuB006276, BjuB037910, and BjuA021658) had distinct temporal expression patterns during stem swelling, indicating that they possessed diverse regulatory functions during the developmental process. These results contribute to our understanding on the GRAS gene family and provide the basis for further investigations on the evolution and functional characterization of GRAS genes.
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Affiliation(s)
- Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Fangjie Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ronggao Gong
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zesheng Yan
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
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21
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Kim G, Jang S, Yoon EK, Lee SA, Dhar S, Kim J, Lee MM, Lim J. Involvement of Pyridoxine/Pyridoxamine 5'-Phosphate Oxidase (PDX3) in Ethylene-Induced Auxin Biosynthesis in the Arabidopsis Root. Mol Cells 2018; 41:1033-1044. [PMID: 30453730 PMCID: PMC6315319 DOI: 10.14348/molcells.2018.0363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/10/2018] [Indexed: 12/23/2022] Open
Abstract
As sessile organisms, plants have evolved to adjust their growth and development to environmental changes. It has been well documented that the crosstalk between different plant hormones plays important roles in the coordination of growth and development of the plant. Here, we describe a novel recessive mutant, mildly insensitive to ethylene (mine), which displayed insensitivity to the ethylene precursor, ACC (1-aminocyclopropane-1-carboxylic acid), in the root under the dark-grown conditions. By contrast, mine roots exhibited a normal growth response to exogenous IAA (indole-3-acetic acid). Thus, it appears that the growth responses of mine to ACC and IAA resemble those of weak ethylene insensitive (wei) mutants. To understand the molecular events underlying the crosstalk between ethylene and auxin in the root, we identified the MINE locus and found that the MINE gene encodes the pyridoxine 5'-phosphate (PNP)/pyridoxamine 5'-phosphate (PMP) oxidase, PDX3. Our results revealed that MINE/PDX3 likely plays a role in the conversion of the auxin precursor tryptophan to indole-3-pyruvic acid in the auxin biosynthesis pathway, in which TAA1 (TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1) and its related genes (TRYPTOPHAN AMINOTRANSFERASE RELATED 1 and 2; TAR1 and TAR2) are involved. Considering that TAA1 and TARs belong to a subgroup of PLP (pyridoxal-5'-phosphate)-dependent enzymes, we propose that PLP produced by MINE/PDX3 acts as a cofactor in TAA1/TAR-dependent auxin biosynthesis induced by ethylene, which in turn influences the crosstalk between ethylene and auxin in the Arabidopsis root.
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Affiliation(s)
- Gyuree Kim
- Department of Systems Biotechnology, Konkuk University, Seoul,
Korea
| | - Sejeong Jang
- Department of Systems Biotechnology, Konkuk University, Seoul,
Korea
| | - Eun Kyung Yoon
- Department of Systems Biotechnology, Konkuk University, Seoul,
Korea
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore,
Singapore
| | - Shin Ae Lee
- Department of Systems Biotechnology, Konkuk University, Seoul,
Korea
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Wanju,
Korea
| | - Souvik Dhar
- Department of Systems Biotechnology, Konkuk University, Seoul,
Korea
| | - Jinkwon Kim
- Department of Systems Biotechnology, Konkuk University, Seoul,
Korea
| | - Myeong Min Lee
- Department of Systems Biology, Yonsei University, Seoul,
Korea
| | - Jun Lim
- Department of Systems Biotechnology, Konkuk University, Seoul,
Korea
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22
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Ratke C, Terebieniec BK, Winestrand S, Derba-Maceluch M, Grahn T, Schiffthaler B, Ulvcrona T, Özparpucu M, Rüggeberg M, Lundqvist SO, Street NR, Jönsson LJ, Mellerowicz EJ. Downregulating aspen xylan biosynthetic GT43 genes in developing wood stimulates growth via reprograming of the transcriptome. THE NEW PHYTOLOGIST 2018; 219:230-245. [PMID: 29708593 DOI: 10.1111/nph.15160] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/02/2018] [Indexed: 05/23/2023]
Abstract
Xylan is one of the main compounds determining wood properties in hardwood species. The xylan backbone is thought to be synthesized by a synthase complex comprising two members of the GT43 family. We downregulated all GT43 genes in hybrid aspen (Populus tremula × tremuloides) to understand their involvement in xylan biosynthesis. All three clades of the GT43 family were targeted for downregulation using RNA interference individually or in different combinations, either constitutively or specifically in developing wood. Simultaneous downregulation in developing wood of the B (IRX9) and C (IRX14) clades resulted in reduced xylan Xyl content relative to reducing end sequence, supporting their role in xylan backbone biosynthesis. This was accompanied by a higher lignocellulose saccharification efficiency. Unexpectedly, GT43 suppression in developing wood led to an overall growth stimulation, xylem cell wall thinning and a shift in cellulose orientation. Transcriptome profiling of these transgenic lines indicated that cell cycling was stimulated and secondary wall biosynthesis was repressed. We suggest that the reduced xylan elongation is sensed by the cell wall integrity surveying mechanism in developing wood. Our results show that wood-specific suppression of xylan-biosynthetic GT43 genes activates signaling responses, leading to increased growth and improved lignocellulose saccharification.
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Affiliation(s)
- Christine Ratke
- Department of Forest Genetics and Plant Physiology, SLU, Umeå Plant Science Centre (UPSC), S-901-83, Umeå, Sweden
| | - Barbara K Terebieniec
- Department of Forest Genetics and Plant Physiology, SLU, Umeå Plant Science Centre (UPSC), S-901-83, Umeå, Sweden
| | | | - Marta Derba-Maceluch
- Department of Forest Genetics and Plant Physiology, SLU, Umeå Plant Science Centre (UPSC), S-901-83, Umeå, Sweden
| | - Thomas Grahn
- Material Processes, RISE Innventia AB, SE-114-86, Stockholm, Sweden
| | | | - Thomas Ulvcrona
- Department of Forest Resource Management, SLU, S-901-83, Umeå, Sweden
| | - Merve Özparpucu
- Institute for Building Materials, Swiss Federal Institute of Technology (ETH Zürich), CH-8093, Zürich, Switzerland
| | - Markus Rüggeberg
- Institute for Building Materials, Swiss Federal Institute of Technology (ETH Zürich), CH-8093, Zürich, Switzerland
| | | | | | - Leif J Jönsson
- Department of Chemistry, Umeå University, S-901-87, Umeå, Sweden
| | - Ewa J Mellerowicz
- Department of Forest Genetics and Plant Physiology, SLU, Umeå Plant Science Centre (UPSC), S-901-83, Umeå, Sweden
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23
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Zhou S, Hu Z, Li F, Yu X, Naeem M, Zhang Y, Chen G. Manipulation of plant architecture and flowering time by down-regulation of the GRAS transcription factor SlGRAS26 in Solanum lycopersicum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:81-93. [PMID: 29650160 DOI: 10.1016/j.plantsci.2018.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 05/03/2023]
Abstract
Previous studies suggest that GRAS transcription factors act as essential regulators, not only in plant growth and development but also in response to biotic and abiotic stresses. Recently, 53 GRAS proteins have been identified, but only a few of them have been functionally studied in tomato. Here, we isolated a novel GRAS transcription factor SlGRAS26, its down-regulation generated pleiotropic phenotypes, including reduced plant height with more lateral shoots, internode length, leaf size, even leaflets, accelerated flowering transition and decreased trichome number. Transcription analysis showed that down-regulation of SlGRAS26 altered vegetative growth by suppressing gibberellin (GA) biosynthesis genes and activating the GA inactivating genes, thereby reducing endogenous GA content in transgenic plants. SlGRAS26 may regulate the initiation of lateral buds by regulating the expression of Blind (BL) and BRC1b. The earlier initiation of flower buds in transgenic lines may be controlled by significant up-regulation of SFT, CO1, SBP3, SBP13, and SBP15 genes, related to flowering time. These results demonstrate that SlGRAS26 may play a vital role in the initiation of lateral and inflorescence meristems in tomato.
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Affiliation(s)
- Shengen Zhou
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Fenfen Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Xiaohui Yu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Muhammad Naeem
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Yanjie Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, People's Republic of China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
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24
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Augstein F, Carlsbecker A. Getting to the Roots: A Developmental Genetic View of Root Anatomy and Function From Arabidopsis to Lycophytes. FRONTIERS IN PLANT SCIENCE 2018; 9:1410. [PMID: 30319672 PMCID: PMC6167918 DOI: 10.3389/fpls.2018.01410] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/05/2018] [Indexed: 05/11/2023]
Abstract
Roots attach plants to the ground and ensure efficient and selective uptake of water and nutrients. These functions are facilitated by the morphological and anatomical structures of the root, formed by the activity of the root apical meristem (RAM) and consecutive patterning and differentiation of specific tissues with distinct functions. Despite the importance of this plant organ, its evolutionary history is not clear, but fossils suggest that roots evolved at least twice, in the lycophyte (clubmosses and their allies) and in the euphyllophyte (ferns and seed plants) lineages. Both lycophyte and euphyllophyte roots grow indeterminately by the action of an apical meristem, which is protected by a root cap. They produce root hairs, and in most species the vascular stele is guarded by a specialized endodermal cell layer. Hence, most of these traits must have evolved independently in these lineages. This raises the question if the development of these apparently analogous tissues is regulated by distinct or homologous genes, independently recruited from a common ancestor of lycophytes and euphyllophytes. Currently, there are few studies of the genetic and molecular regulation of lycophyte and fern roots. Therefore, in this review, we focus on key regulatory networks that operate in root development in the model angiosperm Arabidopsis. We describe current knowledge of the mechanisms governing RAM maintenance as well as patterning and differentiation of tissues, such as the endodermis and the vasculature, and compare with other species. We discuss the importance of comparative analyses of anatomy and morphology of extant and extinct species, along with analyses of gene regulatory networks and, ultimately, gene function in plants holding key phylogenetic positions to test hypotheses of root evolution.
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25
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Magnani E, Jiménez-Gómez JM, Soubigou-Taconnat L, Lepiniec L, Fiume E. Profiling the onset of somatic embryogenesis in Arabidopsis. BMC Genomics 2017; 18:998. [PMID: 29284399 PMCID: PMC5747089 DOI: 10.1186/s12864-017-4391-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Totipotency is the ability of a cell to regenerate a whole organism. Plant somatic embryogenesis (SE) is a remarkable example of totipotency because somatic cells reverse differentiation, respond to an appropriate stimulus and initiate embryo development. Although SE is an ideal system to investigate de-differentiation and differentiation, we still lack a deep molecular understanding of the phenomenon due to experimental restraints. RESULTS We applied the INTACT method to specifically isolate the nuclei of those cells undergoing SE among the majority of non-embryogenic cells that make up a callus. We compared the transcriptome of embryogenic cells to the one of proliferating callus cells. Our analyses revealed that embryogenic cells are transcriptionally rather than metabolically active. Embryogenic cells shut off biochemical pathways involved in carbohydrate and lipid metabolism and activate the transcriptional machinery. Furthermore, we show how early in SE, ground tissue and leaf primordia specification are switched on before the specification of a shoot apical meristem. CONCLUSIONS This is the first attempt to specifically profile embryogenic cells among the different cell types that constitute plant in vitro tissue cultures. Our comparative analyses provide insights in the gene networks regulating SE and open new research avenues in the field of plant regeneration.
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Affiliation(s)
- E Magnani
- Insitut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA, Route de St-Cyr (RD10), 78026, Versailles Cedex, France
| | - J M Jiménez-Gómez
- Insitut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA, Route de St-Cyr (RD10), 78026, Versailles Cedex, France
| | - L Soubigou-Taconnat
- POPS, Plateforme TranscriptOmique, Institute of Plant Sciences, Université Paris-Saclay, rue de Noetzlin, Plateau du Moulon, 91190, Gif-sur-Yvette, France
| | - L Lepiniec
- Insitut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA, Route de St-Cyr (RD10), 78026, Versailles Cedex, France
| | - E Fiume
- Insitut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA, Route de St-Cyr (RD10), 78026, Versailles Cedex, France.
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26
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Wang Z, Yin Y, Hua J, Fan W, Yu C, Xuan L, Yu F. Cloning and Characterization of ThSHRs and ThSCR Transcription Factors in Taxodium Hybrid 'Zhongshanshan 406'. Genes (Basel) 2017; 8:genes8070185. [PMID: 28726763 PMCID: PMC5541318 DOI: 10.3390/genes8070185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/03/2017] [Accepted: 07/17/2017] [Indexed: 01/25/2023] Open
Abstract
Among the GRAS family of transcription factors, SHORT ROOT (SHR) and SCARECROW (SCR) are key regulators of the formation of root tissues. In this study, we isolated and characterized two genes encoding SHR proteins and one gene encoding an SCR protein: ThSHR1 (Accession Number MF045148), ThSHR2 (Accession Number MF045149) and ThSCR (Accession Number MF045152) in the adventitious roots of Taxodium hybrid ‘Zhongshanshan’. Gene structure analysis indicated that ThSHR1, ThSHR2 and ThSCR are all intron free. Multiple protein sequence alignments showed that each of the corresponding proteins, ThSHR1, ThSHR2 and ThSCR, contained five well-conserved domains: leucine heptad repeat I (LHRI), the VHIID motif, leucine heptad repeat II (LHR II), the PFYRE motif, and the SAW motif. The phylogenetic analysis indicated that ThSCR was positioned in the SCR clade with the SCR proteins from eight other species, while ThSHR1 and ThSHR2 were positioned in the SHR clade with the SHR proteins from six other species. Temporal expression patterns of these genes were profiled during the process of adventitious root development on stem cuttings. Whereas expression of both ThSHR2 and ThSCR increased up to primary root formation before declining, that of ThSHR1 increased steadily throughout adventitious root formation. Subcellular localization studies in transgenic poplar protoplasts revealed that ThSHR1, ThSHR2 and ThSCR were localized in the nucleus. Collectively, these results suggest that the three genes encode Taxodium GRAS family transcription factors, and the findings contribute to improving our understanding of the expression and function of SHR and SCR during adventitious root production, which may then be manipulated to achieve high rates of asexual propagation of valuable tree species.
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Affiliation(s)
- Zhiquan Wang
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China.
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Yunlong Yin
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China.
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Jianfeng Hua
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Wencai Fan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Lei Xuan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Fangyuan Yu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forest Sciences, Nanjing Forestry University, Nanjing 210037, China.
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