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Wybouw B, Zhang X, Mähönen AP. Vascular cambium stem cells: past, present and future. THE NEW PHYTOLOGIST 2024; 243:851-865. [PMID: 38890801 DOI: 10.1111/nph.19897] [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: 03/05/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
Secondary xylem and phloem originate from a lateral meristem called the vascular cambium that consists of one to several layers of meristematic cells. Recent lineage tracing studies have shown that only one of the cambial cells in each radial cell file functions as the stem cell, capable of producing both secondary xylem and phloem. Here, we first review how phytohormones and signalling peptides regulate vascular cambium formation and activity. We then propose how the stem cell concept, familiar from apical meristems, could be applied to cambium studies. Finally, we discuss how this concept could set the basis for future research.
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Affiliation(s)
- Brecht Wybouw
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Xixi Zhang
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Ari Pekka Mähönen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
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2
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Liu W, Yang Z, Cai G, Li B, Liu S, Willemsen V, Xu L. MpANT regulates meristem development in Marchantia polymorpha. Cell Rep 2024; 43:114466. [PMID: 38985681 DOI: 10.1016/j.celrep.2024.114466] [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: 05/19/2023] [Revised: 03/05/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024] Open
Abstract
Meristems are crucial for organ formation, but our knowledge of their molecular evolution is limited. Here, we show that AINTEGUMENTA (MpANT) in the euANT branch of the APETALA2-like transcription factor family is essential for meristem development in the nonvascular plant Marchantia polymorpha. MpANT is expressed in the thallus meristem. Mpant mutants show defects to maintain meristem identity and undergo meristem duplication, while MpANT overexpressers show ectopic thallus growth. MpANT directly upregulates MpGRAS9 in the SHORT-ROOT (SHR) branch of the GRAS family. In the vascular plant Arabidopsis thaliana, the euANT-branch genes PLETHORAs (AtPLTs) and AtANT are involved in the formation and maintenance of root/shoot apical meristems and lateral organ primordia, and AtPLTs directly target SHR-branch genes. In addition, euANTs bind through a similar DNA-binding motif to many conserved homologous genes in M. polymorpha and A. thaliana. Overall, the euANT pathway has an evolutionarily conserved role in meristem development.
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Affiliation(s)
- Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Zhengfei Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Bingyu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Shujing Liu
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Viola Willemsen
- Cluster of Plant Developmental Biology, Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China.
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3
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Liu Z, Sun P, Li X, Xiao W, Pi L, Liang YK. BIG coordinates auxin and SHORT ROOT to promote asymmetric stem cell divisions in Arabidopsis roots. PLANT CELL REPORTS 2024; 43:188. [PMID: 38960994 DOI: 10.1007/s00299-024-03274-z] [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: 04/24/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
KEY MESSAGE BIG regulates ground tissue formative divisions by bridging the auxin gradient with SHR abundance in Arabidopsis roots. The formative divisions of cortex/endodermis initials (CEIs) and CEI daughter cells (CEIDs) in Arabidopsis roots are coordinately controlled by the longitudinal auxin gradient and the radial SHORT ROOT (SHR) abundance. However, the mechanism underlying this coordination remains poorly understood. In this study, we demonstrate that BIG regulates ground tissue formative divisions by bridging the auxin gradient with SHR abundance. Mutations in BIG gene repressed cell cycle progression, delaying the formative divisions within the ground tissues and impairing the establishment of endodermal and cortical identities. In addition, we uncovered auxin's suppressive effect on BIG expression, triggering CYCLIND6;1 (CYCD6;1) activation in an SHR-dependent fashion. Moreover, the degradation of RETINOBLASTOMA-RELATED (RBR) is jointly regulated by BIG and CYCD6;1. The loss of BIG function led to RBR protein accumulation, detrimentally impacting the SHR/SCARECROW (SCR) protein complex and the CEI/CEID formative divisions. Collectively, these findings shed light on a fundamental mechanism wherein BIG intricately coordinates the interplay between SHR/SCR and auxin, steering ground tissue patterning within Arabidopsis root tissue.
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Affiliation(s)
- Zhongming Liu
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Pengyue Sun
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xuemei Li
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Wen Xiao
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Limin Pi
- State Key Laboratory of Hybrid Rice, The Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Yun-Kuan Liang
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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4
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Chen C, Hu Y, Ikeuchi M, Jiao Y, Prasad K, Su YH, Xiao J, Xu L, Yang W, Zhao Z, Zhou W, Zhou Y, Gao J, Wang JW. Plant regeneration in the new era: from molecular mechanisms to biotechnology applications. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1338-1367. [PMID: 38833085 DOI: 10.1007/s11427-024-2581-2] [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: 01/31/2024] [Accepted: 03/26/2024] [Indexed: 06/06/2024]
Abstract
Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.
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Affiliation(s)
- Chunli Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences (CAS), China National Botanical Garden, Beijing, 100093, China.
| | - Momoko Ikeuchi
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan.
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| | - Kalika Prasad
- Indian Institute of Science Education and Research, Pune, 411008, India.
- , Thiruvananthapuram, 695551, India.
| | - Ying Hua Su
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology (IGDB), CAS, Beijing, 100101, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), IGDB, CAS, Beijing, 100101, China.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- CEPAMS, SIPPE, CAS, Shanghai, 200032, China.
| | - Zhong Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale, CEMPS, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Wenkun Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Yun Zhou
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, 47907, USA.
| | - Jian Gao
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Key Laboratory of Plant Carbon Capture, CAS, Shanghai, 200032, China.
- New Cornerstone Science Laboratory, Shanghai, 200032, China.
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5
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Tang J, Huang X, Sun M, Liang W. DWARF TILLER1 regulates apical-basal pattern formation and proper orientation of rice embryos. PLANT PHYSIOLOGY 2024:kiae318. [PMID: 38905146 DOI: 10.1093/plphys/kiae318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/10/2024] [Indexed: 06/23/2024]
Abstract
Body axis establishment is one of the earliest patterning events in plant embryogenesis. Asymmetric zygote division is critical for apical-basal axis formation in Arabidopsis (Arabidopsis thaliana). However, how the orientation of the cell division plane is regulated and its relation to apical-basal axis establishment and proper position of embryos in grasses remain poorly understood. By characterizing mutants of 3 rice (Oryza sativa) WUSCHEL HOMEOBOX9 (WOX9) genes, whose paralogs in Arabidopsis play essential roles in zygotic asymmetric cell division and cell fate determination, we found 2 kinds of independent embryonic defects: topsy-turvy embryos, in which apical-basal axis twists from being parallel to the longitudinal axis of the seed to being perpendicular; and organ-less embryos. In contrast to their Arabidopsis orthologs, OsWOX9s displayed dynamic distribution during embryo development. Both DWT1/OsWOX9A and DWL2/WOX9C play major roles in the apical-basal axis formation and initiation of stem cells. In addition, DWT1 has a distinct function in regulating the first few embryonic cell divisions to ensure the correct orientation of the embryo in the ovary. In summary, DWT1 acts in 2 steps during rice embryo pattern formation: the initial zygotic division, and with DWL2 to establish the main body axes and stem cell fate 2 to 3 d after pollination.
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Affiliation(s)
- Jingyao Tang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaorong Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mengxiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572024, China
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6
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Kerstens M, Galinha C, Hofhuis H, Nodine M, Pardal R, Scheres B, Willemsen V. PLETHORA transcription factors promote early embryo development through induction of meristematic potential. Development 2024; 151:dev202527. [PMID: 38884589 PMCID: PMC11234262 DOI: 10.1242/dev.202527] [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: 11/10/2023] [Accepted: 05/10/2024] [Indexed: 06/18/2024]
Abstract
Plants are dependent on divisions of stem cells to establish cell lineages required for growth. During embryogenesis, early division products are considered to be stem cells, whereas during post-embryonic development, stem cells are present in meristems at the root and shoot apex. PLETHORA/AINTEGUMENTA-LIKE (PLT/AIL) transcription factors are regulators of post-embryonic meristem function and are required to maintain stem cell pools. Despite the parallels between embryonic and post-embryonic stem cells, the role of PLTs during early embryogenesis has not been thoroughly investigated. Here, we demonstrate that the PLT regulome in the zygote, and apical and basal cells is in strong congruence with that of post-embryonic meristematic cells. We reveal that out of all six PLTs, only PLT2 and PLT4/BABY BOOM (BBM) are expressed in the zygote, and that these two factors are essential for progression of embryogenesis beyond the zygote stage and first divisions. Finally, we show that other PLTs can rescue plt2 bbm defects when expressed from the PLT2 and BBM promoters, establishing upstream regulation as a key factor in early embryogenesis. Our data indicate that generic PLT factors facilitate early embryo development in Arabidopsis by induction of meristematic potential.
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Affiliation(s)
- Merijn Kerstens
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Carla Galinha
- Department of Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hugo Hofhuis
- Department of Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Michael Nodine
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Renan Pardal
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ben Scheres
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Viola Willemsen
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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7
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He L, Wu L, Li J. Sulfated peptides and their receptors: Key regulators of plant development and stress adaptation. PLANT COMMUNICATIONS 2024; 5:100918. [PMID: 38600699 PMCID: PMC11211552 DOI: 10.1016/j.xplc.2024.100918] [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: 12/29/2023] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Four distinct types of sulfated peptides have been identified in Arabidopsis thaliana. These peptides play crucial roles in regulating plant development and stress adaptation. Recent studies have revealed that Xanthomonas and Meloidogyne can secrete plant-like sulfated peptides, exploiting the plant sulfated peptide signaling pathway to suppress plant immunity. Over the past three decades, receptors for these four types of sulfated peptides have been identified, all of which belong to the leucine-rich repeat receptor-like protein kinase subfamily. A number of regulatory proteins have been demonstrated to play important roles in their corresponding signal transduction pathways. In this review, we comprehensively summarize the discoveries of sulfated peptides and their receptors, mainly in Arabidopsis thaliana. We also discuss their known biological functions in plant development and stress adaptation. Finally, we put forward a number of questions for reference in future studies.
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Affiliation(s)
- Liming He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Liangfan Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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Zhang X, Chen Y, Chen H, Guo C, Su X, Mu T, Feng B, Wang Y, Liu Z, Zhang B, Li Y, Zhang H, Yuan W, Li H. Genome-wide analysis of TOPLESS/TOPLESS-RELATED co-repressors and functional characterization of BnaA9.TPL regulating the embryogenesis and leaf morphology in rapeseed. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112149. [PMID: 38851591 DOI: 10.1016/j.plantsci.2024.112149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins belong to the Groucho (Gro)/Tup1 family co-repressors and act as broad co-repressors that modulate multiple phytohormone signalling pathways and various developmental processes in plant. However, TPL/TPR co-repressors so far are poorly understood in the rapeseed, one of the world-wide important oilseed crops. In this study, we comprehensively characterized eighteen TPL/TPR genes into five groups in the rapeseed genome. Members of TPL/TPR1/TPR4 and TPR2/TPR3 had close evolutionary relationship, respectively. All TPL/TPRs had similar expression patterns and encode conserved protein domain. In addition, we demonstrated that BnaA9.TPL interacted with all known plant repression domain (RD) sequences, which were distributed in non-redundant 24,238 (22.6 %) genes and significantly enriched in transcription factors in the rapeseed genome. These transcription factors were largely co-expressed with the TPL/TPR genes and involved in diverse pathway, including phytohormone signal transduction, protein kinases and circadian rhythm. Furthermore, BnaA9.TPL was revealed to regulate apical embryonic fate by interaction with Bna.IAA12 and suppression of PLETHORA1/2. BnaA9.TPL was also identified to regulate leaf morphology by interaction with Bna.AS1 (Asymmetric leaves 1) and suppression of KNOTTED-like homeobox genes and YABBY5. These data not only suggest the rapeseed TPL/TPRs play broad roles in different processes, but also provide useful information to uncover more TPL/TPR-mediated control of plant development in rapeseed.
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Affiliation(s)
- Xiaolong Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yingying Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Hongyu Chen
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Chaocheng Guo
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue Su
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Tingting Mu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Bin Feng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yu Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhixin Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Biaoming Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Haitao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wenya Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Haitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
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9
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Lian X, Zhong L, Bai Y, Guang X, Tang S, Guo X, Wei T, Yang F, Zhang Y, Huang G, Zhang J, Shao L, Lei G, Li Z, Sahu SK, Zhang S, Liu H, Hu F. Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1652-1668. [PMID: 38345936 PMCID: PMC11123419 DOI: 10.1111/pbi.14294] [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: 10/10/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double-haplotype genome of O. longistaminata, which displays a 48-fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding.
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Affiliation(s)
- Xiaoping Lian
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Liyuan Zhong
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Yixuan Bai
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Xuanmin Guang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Sijia Tang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Xing Guo
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Tong Wei
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Feng Yang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Yujiao Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Guangfu Huang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Jing Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Lin Shao
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Guijie Lei
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Zheng Li
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Shilai Zhang
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
| | - Huan Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenGuangdongChina
| | - Fengyi Hu
- New Cornerstone Science Laboratory, State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, Key Laboratory of Biology and Germplasm Innovation of Perennial rice (Co‐construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Center of Innovation for Perennial Rice Technology in Yunnan, School of AgricultureYunnan UniversityKunmingChina
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10
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Chu Y, Duan R, Song H, Zhang W, Zhou Y, Ma Y, Yin X, Tian L, Ausin I, Han Z. AtHD2D is involved in regulating lateral root development and participates in abiotic stress response in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2024; 297:154242. [PMID: 38614048 DOI: 10.1016/j.jplph.2024.154242] [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: 10/19/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/15/2024]
Abstract
Roots are essential to terrestrial plants, as their growth and morphology are crucial for plant development. The growth of the roots is affected and regulated by several internal and external environmental signals and metabolic pathways. Among them, chromatin modification plays an important regulatory role. In this study, we explore the potential roles of the histone deacetylase AtHD2D in root development and lay the foundation for further research on the biological processes and molecular mechanisms of AtHD2D in the future. Our study indicates that AtHD2D affects the root tip microenvironment homeostasis by affecting the gene transcription levels required to maintain the root tip microenvironment. In addition, we confirmed that AtHD2D is involved in regulating Arabidopsis lateral root development and further explained the possible role of AtHD2D in auxin-mediated lateral root development. AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. We believe that AtHD2D is involved in coping with abiotic stress by promoting the development of lateral roots. Overexpression of AtHD2D promotes the accumulation of reactive oxygen species (ROS) in roots, indicating that AtHD2D is also involved in developing lateral roots mediated by ROS. Previous studies have shown that the overexpression of AtHD2D can effectively enhance the resistance of Arabidopsis thaliana to abiotic stress. Based on our data, we believe that AtHD2D participates in the response to abiotic stress by promoting the development of lateral roots. AtHD2D-mediated lateral root development provides new ideas for studying the mechanism of HDAC protein in regulating root development.
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Affiliation(s)
- Yueyang Chu
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Ruochen Duan
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Haoran Song
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Wenshuo Zhang
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Yuxuan Zhou
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Yutong Ma
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Xiaotong Yin
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-food Canada, London, Ontario, N5V 4T3, Canada
| | - Israel Ausin
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China
| | - Zhaofen Han
- College of Life Science, Northwest A & F University, Yangling, Shanxi, 712100, China.
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11
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Yu Q, Li H, Zhang B, Song Y, Sun Y, Ding Z. ATP Hydrolases Superfamily Protein 1 (ASP1) Maintains Root Stem Cell Niche Identity through Regulating Reactive Oxygen Species Signaling in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1469. [PMID: 38891278 PMCID: PMC11174532 DOI: 10.3390/plants13111469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
The maintenance of the root stem cell niche identity in Arabidopsis relies on the delicate balance of reactive oxygen species (ROS) levels in root tips; however, the intricate molecular mechanisms governing ROS homeostasis within the root stem cell niche remain unclear. In this study, we unveil the role of ATP hydrolase superfamily protein 1 (ASP1) in orchestrating root stem cell niche maintenance through its interaction with the redox regulator cystathionine β-synthase domain-containing protein 3 (CBSX3). ASP1 is exclusively expressed in the quiescent center (QC) cells and governs the integrity of the root stem cell niche. Loss of ASP1 function leads to enhanced QC cell division and distal stem cell differentiation, attributable to reduced ROS levels and diminished expression of SCARECROW and SHORT ROOT in root tips. Our findings illuminate the pivotal role of ASP1 in regulating ROS signaling to maintain root stem cell niche homeostasis, achieved through direct interaction with CBSX3.
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Affiliation(s)
- Qianqian Yu
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Hongyu Li
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Bing Zhang
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Yun Song
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Yueying Sun
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China; (H.L.); (B.Z.); (Y.S.); (Y.S.)
| | - Zhaojun Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao 266237, China;
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12
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Sessa G, Carabelli M, Sassi M. The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development. Int J Mol Sci 2024; 25:5657. [PMID: 38891845 PMCID: PMC11171833 DOI: 10.3390/ijms25115657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.
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Affiliation(s)
| | | | - Massimiliano Sassi
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy; (G.S.); (M.C.)
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13
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Han E, Geng Z, Qin Y, Wang Y, Ma S. Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism. PLANT COMMUNICATIONS 2024:100978. [PMID: 38783601 DOI: 10.1016/j.xplc.2024.100978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/24/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The analysis identified 149 gene co-expression modules, which we considered to be gene expression programs (GEPs). By examining their spatiotemporal expression, we identified GEPs specifically expressed in major root cell types along their developmental trajectories. These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators. As examples, a GEP specific for the quiescent center (QC) contains 20 genes regulating QC and stem cell niche homeostasis, and four GEPs are expressed in sieve elements (SEs) from early to late developmental stages, with the early-stage GEP containing 17 known SE developmental regulators. We also identified GEPs for metabolic pathways with cell-type-specific expression, suggesting the existence of cell-type-specific metabolism in roots. Using the GEPs, we discovered and verified a columella-specific gene, NRL27, as a regulator of the auxin-related root gravitropism response. Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.
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Affiliation(s)
- Ershang Han
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Zhenxing Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Yue Qin
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Yuewei Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China
| | - Shisong Ma
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei 230027, China; School of Data Science, University of Science and Technology of China, Hefei 230027, China.
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14
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Hou L, Liu Z, Zhang D, Liu S, Chen Z, Wu Q, Shang Z, Wang J, Wang J. BR regulates wheat root salt tolerance by maintaining ROS homeostasis. PLANTA 2024; 260:5. [PMID: 38777878 DOI: 10.1007/s00425-024-04429-8] [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: 01/02/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
MAIN CONCLUSION Trace amounts of epibrassinolide (EpiBL) could partially rescue wheat root length inhibition in salt-stressed situation by scavenging ROS, and ectopic expression of TaDWF4 or TaBAK1 enhances root salt tolerance in Arabidopsis by balancing ROS level. Salt stress often leads to ion toxicity and oxidative stress, causing cell structure damage and root development inhibition in plants. While prior research indicated the involvement of exogenous brassinosteroid (BR) in plant responses to salt stress, the precise cytological role and the function of BR in wheat root development under salt stress remain elusive. Our study demonstrates that 100 mM NaCl solution inhibits wheat root development, but 5 nM EpiBL partially rescues root length inhibition by decreasing H2O2 content, oxygen free radical (OFR) content, along with increasing the peroxidase (POD) and catalase (CAT) activities in salt-stressed roots. The qRT-PCR experiment also shows that expression of the ROS-scavenging genes (GPX2 and CAT2) increased in roots after applying BR, especially during salt stress situation. Transcriptional analysis reveals decreased expression of BR synthesis and root meristem development genes under salt stress in wheat roots. Differential expression gene (DEG) enrichment analysis highlights the significant impact of salt stress on various biological processes, particularly "hydrogen peroxide catabolic process" and "response to oxidative stress". Additionally, the BR biosynthesis pathway is enriched under salt stress conditions. Therefore, we investigated the involvement of wheat BR synthesis gene TaDWF4 and BR signaling gene TaBAK1 in salt stress responses in roots. Our results demonstrate that ectopic expression of TaDWF4 or TaBAK1 enhances salt tolerance in Arabidopsis by balancing ROS (Reactive oxygen species) levels in roots.
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Affiliation(s)
- Lijiang Hou
- Key Laboratory of Anyang Wheat Breeding Engineering Research Center, Anyang Institute of Technology, Anyang, 455000, Henan, China
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zihui Liu
- Department of Biochemistry, Baoding University, Baoding, 071000, Hebei, China
| | - Dongzhi Zhang
- College of Life Sciences and Engineering, Hexi University, Zhangye, Gansu, 734000, China
| | - Shuhan Liu
- College of Agronomy, Xinyang Agriculture and Forestry University, Xinyang, 464000, Henan, China
| | - Zhenzhen Chen
- Xinyang Academy of Agricultural Sciences, Xinyang, 464000, Henan, China
| | - Qiufang Wu
- Key Laboratory of Anyang Wheat Breeding Engineering Research Center, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Zengzhen Shang
- Key Laboratory of Anyang Wheat Breeding Engineering Research Center, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Jingshun Wang
- Key Laboratory of Anyang Wheat Breeding Engineering Research Center, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Junwei Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
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15
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Yin R, Chen R, Xia K, Xu X. A single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis. PLANT COMMUNICATIONS 2024:100941. [PMID: 38720464 DOI: 10.1016/j.xplc.2024.100941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 06/16/2024]
Abstract
The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement. This developmental process incorporates a series of cell fate transitions and reprogramming. However, our understanding of cell heterogeneity and mechanisms of cell fate transition during callus induction remains quite limited. Here, we report a time-series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0, 1, and 4 days, and the construction of a detailed single-cell transcriptional atlas of the callus induction process. We identify the cell types responsible for initiating the early callus: lateral root primordium-initiating (LRPI)-like cells and quiescent center (QC)-like cells. LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia. We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells. QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration. We also identify the transcription factors that regulate QC-like cells and the gene expression signatures that are related to cell fate decisions. Overall, our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transitions during callus formation, significantly improving our understanding of callus formation.
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Affiliation(s)
- Ruilian Yin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 10049, China; BGI Research, Beijing 102601, China
| | - Ruiying Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 10049, China; BGI Research, Beijing 102601, China
| | - Keke Xia
- BGI Research, Beijing 102601, China.
| | - Xun Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 10049, China; BGI Research, Beijing 102601, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, Guangdong, China.
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16
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Bellino C, Herrera FE, Rodrigues D, Garay AS, Huck SV, Reinheimer R. Molecular Evolution of RAMOSA1 (RA1) in Land Plants. Biomolecules 2024; 14:550. [PMID: 38785957 PMCID: PMC11117814 DOI: 10.3390/biom14050550] [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: 03/16/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controls plant meristem fate and identity and has played an important role in maize domestication. Despite its importance, the origin of RA1 is unknown, and the evolution in plants is only partially understood. In this paper, we present a well-resolved phylogeny based on 73 amino acid sequences from 48 embryophyte species. The recovered tree topology indicates that, during grass evolution, RA1 arose from two consecutive SUPERMAN duplications, resulting in three distinct grass sequence lineages: RA1-like A, RA1-like B, and RA1; however, most of these copies have unknown functions. Our findings indicate that RA1 and RA1-like play roles in the nucleus despite lacking a traditional nuclear localization signal. Here, we report that copies diversified their coding region and, with it, their protein structure, suggesting different patterns of DNA binding and protein-protein interaction. In addition, each of the retained copies diversified regulatory elements along their promoter regions, indicating differences in their upstream regulation. Taken together, the evidence indicates that the RA1 and RA1-like gene families in grasses underwent subfunctionalization and neofunctionalization enabled by gene duplication.
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Affiliation(s)
- Carolina Bellino
- Fellow of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe S3000, Argentina;
| | - Fernando E. Herrera
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, Santa Fe S3000, Argentina; (F.E.H.); (D.R.)
| | - Daniel Rodrigues
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, Santa Fe S3000, Argentina; (F.E.H.); (D.R.)
| | - A. Sergio Garay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, Paraje El Pozo, Santa Fe S3000, Argentina;
| | - Sofía V. Huck
- Fellow of Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe S3000, Argentina;
| | - Renata Reinheimer
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, FCA, CONICET, CCT-Santa Fe, Ruta Nacional N° 168 Km 0, s/n, Paraje el Pozo, Santa Fe S3000, Argentina
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17
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Liu H, Mu Y, Xuan Y, Wu X, Wang W, Zhang H. Hydrogen Peroxide Signaling in the Maintenance of Plant Root Apical Meristem Activity. Antioxidants (Basel) 2024; 13:554. [PMID: 38790659 PMCID: PMC11118955 DOI: 10.3390/antiox13050554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Hydrogen peroxide (H2O2) is a prevalent reactive oxygen species (ROS) found in cells and takes a central role in plant development and stress adaptation. The root apical meristem (RAM) has evolved strong plasticity to adapt to complex and changing environmental conditions. Recent advances have made great progress in explaining the mechanism of key factors, such as auxin, WUSCHEL-RELATED HOMEOBOX 5 (WOX5), PLETHORA (PLT), SHORTROOT (SHR), and SCARECROW (SCR), in the regulation of RAM activity maintenance. H2O2 functions as an emerging signaling molecule to control the quiescent center (QC) specification and stem cell niche (SCN) activity. Auxin is a key signal for the regulation of RAM maintenance, which largely depends on the formation of auxin regional gradients. H2O2 regulates the auxin gradients by the modulation of intercellular transport. H2O2 also modulates the expression of WOX5, PLTs, SHR, and SCR to maintain RAM activity. The present review is dedicated to summarizing the key factors in the regulation of RAM activity and discussing the signaling transduction of H2O2 in the maintenance of RAM activity. H2O2 is a significant signal for plant development and environmental adaptation.
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Affiliation(s)
| | | | | | | | - Wei Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China; (H.L.); (Y.M.); (Y.X.); (X.W.)
| | - Hui Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China; (H.L.); (Y.M.); (Y.X.); (X.W.)
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18
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Henry AR, Miller ND, Spalding EP. QTL for the Kinematic Traits That Define the Arabidopsis Root Elongation Zone and Their Relationship to Gravitropism. PLANTS (BASEL, SWITZERLAND) 2024; 13:1189. [PMID: 38732404 PMCID: PMC11085590 DOI: 10.3390/plants13091189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Cell expansion in a discrete region called the elongation zone drives root elongation. Analyzing time lapse images can quantify the expansion in kinematic terms as if it were fluid flow. We used horizontal microscopes to collect images from which custom software extracted the length of the elongation zone, the peak relative elemental growth rate (REGR) within it, the axial position of the REGR peak, and the root elongation rate. Automation enabled these kinematic traits to be measured in 1575 Arabidopsis seedlings representing 162 recombinant inbred lines (RILs) derived from a cross of Cvi and Ler ecotypes. We mapped ten quantitative trait loci (QTL), affecting the four kinematic traits. Three QTL affected two or more traits in these vertically oriented seedlings. We compared this genetic architecture with that previously determined for gravitropism using the same RIL population. The major QTL peaks for the kinematic traits did not overlap with the gravitropism QTL. Furthermore, no single kinematic trait correlated with quantitative descriptors of the gravitropism response curve across this population. In addition to mapping QTL for growth zone traits, this study showed that the size and shape of the elongation zone may vary widely without affecting the differential growth induced by gravity.
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Affiliation(s)
| | | | - Edgar P. Spalding
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA; (A.R.H.); (N.D.M.)
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19
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Lee S, Park YS, Rhee JH, Chu H, Frost JM, Choi Y. Insights into plant regeneration: cellular pathways and DNA methylation dynamics. PLANT CELL REPORTS 2024; 43:120. [PMID: 38634973 PMCID: PMC11026228 DOI: 10.1007/s00299-024-03216-9] [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: 02/26/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Plants, known for their immobility, employ various mechanisms against stress and damage. A prominent feature is the formation of callus tissue-a cellular growth phenomenon that remains insufficiently explored, despite its distinctive cellular plasticity compared to vertebrates. Callus formation involves dedifferentiated cells, with a subset attaining pluripotency. Calluses exhibit an extraordinary capacity to reinitiate cellular division and undergo structural transformations, generating de novo shoots and roots, thereby developing into regenerated plants-a testament to the heightened developmental plasticity inherent in plants. In this way, plant regeneration through clonal propagation is a widely employed technique for vegetative reproduction. Thus, exploration of the biological components involved in regaining pluripotency contributes to the foundation upon which methods of somatic plant propagation can be advanced. This review provides an overview of the cellular pathway involved in callus and subsequent de novo shoot formation from already differentiated plant tissue, highlighting key genes critical to this process. In addition, it explores the intricate realm of epigenetic regulatory processes, emphasizing the nuanced dynamics of DNA methylation that contribute to plant regeneration. Finally, we briefly discuss somaclonal variation, examining its relation to DNA methylation, and investigating the heritability of epigenomic changes in crops.
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Affiliation(s)
- Seunga Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
| | - Young Seo Park
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Ji Hoon Rhee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
| | - Hyojeong Chu
- Department of Biological Sciences, Seoul National University, Seoul, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
- The Research Institute of Basic Sciences, Seoul National University, Seoul, Korea
| | - Jennifer M Frost
- Genomics and Child Health, The Blizard Institute, Queen Mary University of London, London, UK
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul, Korea.
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea.
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20
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Yang L, Hu X, Ren M, Ma F, Fu J, Cui H. Stem-cell-expressed DEVIL-like small peptides maintain root growth under abiotic stress via abscisic acid signaling. PLANT PHYSIOLOGY 2024; 194:2372-2386. [PMID: 38096479 DOI: 10.1093/plphys/kiad659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 04/02/2024]
Abstract
Stem cells are essential to plant growth and development. Through data mining, we identified five DEVIL-like (DVL) small peptide genes that are preferentially expressed in the quiescent center of Arabidopsis (Arabidopsis thaliana) root but whose functions are unknown. When overexpressed, these genes caused a dramatic decrease in root length and pleiotropic phenotypes in the shoot. No root-growth defect was observed in the single-gene mutants, but the quintuple mutant exhibited slightly longer roots than the wild type (WT). Through transcriptome analysis with DVL20-overexpressing plants, we found that many genes involved in abscisic acid (ABA) signaling were regulated by these peptides. Consistent with this finding, we demonstrated that, relative to the WT, DVL20-overexpressing plants were more tolerant whereas the quintuple mutant was more sensitive to ABA. Using RT-qPCR, we showed that ABA signaling-associated genes were affected in an opposite manner when the plants were grown in normal or ABA-containing medium. Strikingly, ectopic expression of ABA signaling genes such as PYRABACTIN RESISTANCE 1-LIKE (PYL) 4, 5, or 6 or suppression of HIGHLY ABA-INDUCED 2 (HAI2) and MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 18 (MAPKKK18) not only largely rescued the root growth defects in DVL20-overexpressing plants in normal growth condition but also conferred tolerance to ABA. Based on these results, we propose that DVL1, 2, 5, 8 and 20 function redundantly in root stem-cell maintenance under abiotic stress, and this role is achieved via ABA signaling.
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Affiliation(s)
- Liyun Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaochen Hu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengfei Ren
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Ma
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Fu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongchang Cui
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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21
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Kevei Z, Larriba E, Romero-Bosquet MD, Nicolás-Albujer M, Kurowski TJ, Mohareb F, Rickett D, Pérez-Pérez JM, Thompson AJ. Genes involved in auxin biosynthesis, transport and signalling underlie the extreme adventitious root phenotype of the tomato aer mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:76. [PMID: 38459215 PMCID: PMC10923741 DOI: 10.1007/s00122-024-04570-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 03/10/2024]
Abstract
The use of tomato rootstocks has helped to alleviate the soaring abiotic stresses provoked by the adverse effects of climate change. Lateral and adventitious roots can improve topsoil exploration and nutrient uptake, shoot biomass and resulting overall yield. It is essential to understand the genetic basis of root structure development and how lateral and adventitious roots are produced. Existing mutant lines with specific root phenotypes are an excellent resource to analyse and comprehend the molecular basis of root developmental traits. The tomato aerial roots (aer) mutant exhibits an extreme adventitious rooting phenotype on the primary stem. It is known that this phenotype is associated with restricted polar auxin transport from the juvenile to the more mature stem, but prior to this study, the genetic loci responsible for the aer phenotype were unknown. We used genomic approaches to define the polygenic nature of the aer phenotype and provide evidence that increased expression of specific auxin biosynthesis, transport and signalling genes in different loci causes the initiation of adventitious root primordia in tomato stems. Our results allow the selection of different levels of adventitious rooting using molecular markers, potentially contributing to rootstock breeding strategies in grafted vegetable crops, especially in tomato. In crops vegetatively propagated as cuttings, such as fruit trees and cane fruits, orthologous genes may be useful for the selection of cultivars more amenable to propagation.
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Affiliation(s)
- Zoltan Kevei
- Centre for Soil, AgriFood and Biosciences, Cranfield University, College Road, Bedfordshire, MK43 0AL, UK.
| | - Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202, Elche, Spain
| | | | | | - Tomasz J Kurowski
- Centre for Soil, AgriFood and Biosciences, Cranfield University, College Road, Bedfordshire, MK43 0AL, UK
| | - Fady Mohareb
- Centre for Soil, AgriFood and Biosciences, Cranfield University, College Road, Bedfordshire, MK43 0AL, UK
| | - Daniel Rickett
- Syngenta Crop Protection, Jealott's Hill International Research Centre, Bracknell Berkshire, RG42 6EY, UK
| | | | - Andrew J Thompson
- Centre for Soil, AgriFood and Biosciences, Cranfield University, College Road, Bedfordshire, MK43 0AL, UK
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22
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Ercoli MF, Shigenaga AM, de Araujo AT, Jain R, Ronald PC. Tyrosine-sulfated peptide hormone induces flavonol biosynthesis to control elongation and differentiation in Arabidopsis primary root. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578681. [PMID: 38352507 PMCID: PMC10862922 DOI: 10.1101/2024.02.02.578681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
In Arabidopsis roots, growth initiation and cessation are organized into distinct zones. How regulatory mechanisms are integrated to coordinate these processes and maintain proper growth progression over time is not well understood. Here, we demonstrate that the peptide hormone PLANT PEPTIDE CONTAINING SULFATED TYROSINE 1 (PSY1) promotes root growth by controlling cell elongation. Higher levels of PSY1 lead to longer differentiated cells with a shootward displacement of characteristics common to mature cells. PSY1 activates genes involved in the biosynthesis of flavonols, a group of plant-specific secondary metabolites. Using genetic and chemical approaches, we show that flavonols are required for PSY1 function. Flavonol accumulation downstream of PSY1 occurs in the differentiation zone, where PSY1 also reduces auxin and reactive oxygen species (ROS) activity. These findings support a model where PSY1 signals the developmental-specific accumulation of secondary metabolites to regulate the extent of cell elongation and the overall progression to maturation.
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Affiliation(s)
- Maria Florencia Ercoli
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Innovative Genomics Institute, University of California, Berkeley 94720
| | - Alexandra M Shigenaga
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Artur Teixeira de Araujo
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Joint Bioenergy Institute, Emeryville, California
| | - Rashmi Jain
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, CA 95616
- The Genome Center, University of California, Davis, CA 95616
- The Innovative Genomics Institute, University of California, Berkeley 94720
- The Joint Bioenergy Institute, Emeryville, California
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23
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Daniel K, Hartman S. How plant roots respond to waterlogging. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:511-525. [PMID: 37610936 DOI: 10.1093/jxb/erad332] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Plant submergence is a major abiotic stress that impairs plant performance. Under water, reduced gas diffusion exposes submerged plant cells to an environment that is enriched in gaseous ethylene and is limited in oxygen (O2) availability (hypoxia). The capacity for plant roots to avoid and/or sustain critical hypoxia damage is essential for plants to survive waterlogging. Plants use spatiotemporal ethylene and O2 dynamics as instrumental flooding signals to modulate potential adaptive root growth and hypoxia stress acclimation responses. However, how non-adapted plant species modulate root growth behaviour during actual waterlogged conditions to overcome flooding stress has hardly been investigated. Here we discuss how changes in the root growth rate, lateral root formation, density, and growth angle of non-flood adapted plant species (mainly Arabidopsis) could contribute to avoiding and enduring critical hypoxic conditions. In addition, we discuss current molecular understanding of how ethylene and hypoxia signalling control these adaptive root growth responses. We propose that future research would benefit from less artificial experimental designs to better understand how plant roots respond to and survive waterlogging. This acquired knowledge would be instrumental to guide targeted breeding of flood-tolerant crops with more resilient root systems.
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Affiliation(s)
- Kevin Daniel
- Plant Environmental Signalling and Development, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Sjon Hartman
- Plant Environmental Signalling and Development, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
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24
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Jain D, Schmidt W. Protein Phosphorylation Orchestrates Acclimations of Arabidopsis Plants to Environmental pH. Mol Cell Proteomics 2024; 23:100685. [PMID: 38000714 PMCID: PMC10837763 DOI: 10.1016/j.mcpro.2023.100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 10/18/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Environment pH (pHe) is a key parameter dictating a surfeit of conditions critical to plant survival and fitness. To elucidate the mechanisms that recalibrate cytoplasmic and apoplastic pH homeostasis, we conducted a comprehensive proteomic/phosphoproteomic inventory of plants subjected to transient exposure to acidic or alkaline pH, an approach that covered the majority of protein-coding genes of the reference plant Arabidopsis thaliana. Our survey revealed a large set-of so far undocumented pHe-dependent phospho-sites, indicative of extensive post-translational regulation of proteins involved in the acclimation to pHe. Changes in pHe altered both electrogenic H+ pumping via P-type ATPases and H+/anion co-transport processes, putatively leading to altered net trans-plasma membrane translocation of H+ ions. In pH 7.5 plants, the transport (but not the assimilation) of nitrogen via NRT2-type nitrate and AMT1-type ammonium transporters was induced, conceivably to increase the cytosolic H+ concentration. Exposure to both acidic and alkaline pH resulted in a marked repression of primary root elongation. No such cessation was observed in nrt2.1 mutants. Alkaline pH decreased the number of root hairs in the wild type but not in nrt2.1 plants, supporting a role of NRT2.1 in developmental signaling. Sequestration of iron into the vacuole via alterations in protein abundance of the vacuolar iron transporter VTL5 was inversely regulated in response to high and low pHe, presumptively in anticipation of associated changes in iron availability. A pH-dependent phospho-switch was also observed for the ABC transporter PDR7, suggesting changes in activity and, possibly, substrate specificity. Unexpectedly, the effect of pHe was not restricted to roots and provoked pronounced changes in the shoot proteome. In both roots and shoots, the plant-specific TPLATE complex components AtEH1 and AtEH2-essential for clathrin-mediated endocytosis-were differentially phosphorylated at multiple sites in response to pHe, indicating that the endocytic cargo protein trafficking is orchestrated by pHe.
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Affiliation(s)
- Dharmesh Jain
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan; Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wolfgang Schmidt
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan; Biotechnology Center, National Chung-Hsing University, Taichun, Taiwan; Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan.
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25
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Xu C, Chang P, Guo S, Yang X, Liu X, Sui B, Yu D, Xin W, Hu Y. Transcriptional activation by WRKY23 and derepression by removal of bHLH041 coordinately establish callus pluripotency in Arabidopsis regeneration. THE PLANT CELL 2023; 36:158-173. [PMID: 37804093 PMCID: PMC10734573 DOI: 10.1093/plcell/koad255] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/22/2023] [Accepted: 09/13/2023] [Indexed: 10/08/2023]
Abstract
Induction of the pluripotent cell mass termed callus from detached organs or tissues is an initial step in typical in vitro plant regeneration, during which auxin-induced ectopic activation of root stem cell factors is required for subsequent de novo shoot regeneration. While Arabidopsis (Arabidopsis thaliana) AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 and their downstream transcription factors LATERAL ORGAN BOUNDARIES DOMAIN (LBD) are known to play key roles in directing callus formation, the molecules responsible for activation of root stem cell factors and thus establishment of callus pluripotency are unclear. Here, we identified Arabidopsis WRKY23 and BASIC HELIX-LOOP-HELIX 041 (bHLH041) as a transcriptional activator and repressor, respectively, of root stem cell factors during establishment of auxin-induced callus pluripotency. We show that auxin-induced WRKY23 downstream of ARF7 and ARF19 directly activates the transcription of PLETHORA 3 (PLT3) and PLT7 and thus that of the downstream genes PLT1, PLT2, and WUSCHEL-RELATED HOMEOBOX 5 (WOX5), while LBD-induced removal of bHLH041 derepresses the transcription of PLT1, PLT2, and WOX5. We provide evidence that transcriptional activation by WRKY23 and loss of bHLH041-imposed repression act synergistically in conferring shoot-regenerating capability on callus cells. Our findings thus disclose a transcriptional mechanism underlying auxin-induced cellular reprogramming, which, together with previous studies, outlines the molecular framework of auxin-induced pluripotent callus formation for in vitro plant regeneration programs.
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Affiliation(s)
- Chongyi Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China
| | - Pengjie Chang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiqi Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaona Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinchun Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baofeng Sui
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongxue Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China
- National Center for Plant Gene Research, Beijing 100093, China
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26
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Zhang H, Mu Y, Zhang H, Yu C. Maintenance of stem cell activity in plant development and stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1302046. [PMID: 38155857 PMCID: PMC10754534 DOI: 10.3389/fpls.2023.1302046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
Stem cells residing in plant apical meristems play an important role during postembryonic development. These stem cells are the wellspring from which tissues and organs of the plant emerge. The shoot apical meristem (SAM) governs the aboveground portions of a plant, while the root apical meristem (RAM) orchestrates the subterranean root system. In their sessile existence, plants are inextricably bound to their environment and must adapt to various abiotic stresses, including osmotic stress, drought, temperature fluctuations, salinity, ultraviolet radiation, and exposure to heavy metal ions. These environmental challenges exert profound effects on stem cells, potentially causing severe DNA damage and disrupting the equilibrium of reactive oxygen species (ROS) and Ca2+ signaling in these vital cells, jeopardizing their integrity and survival. In response to these challenges, plants have evolved mechanisms to ensure the preservation, restoration, and adaptation of the meristematic stem cell niche. This enduring response allows plants to thrive in their habitats over extended periods. Here, we presented a comprehensive overview of the cellular and molecular intricacies surrounding the initiation and maintenance of the meristematic stem cell niche. We also delved into the mechanisms employed by stem cells to withstand and respond to abiotic stressors.
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Affiliation(s)
- Huankai Zhang
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Yangwei Mu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hui Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Caiyu Yu
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
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27
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Wójcikowska B, Belaidi S, Robert HS. Game of thrones among AUXIN RESPONSE FACTORs-over 30 years of MONOPTEROS research. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6904-6921. [PMID: 37450945 PMCID: PMC10690734 DOI: 10.1093/jxb/erad272] [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: 02/28/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
For many years, research has been carried out with the aim of understanding the mechanism of auxin action, its biosynthesis, catabolism, perception, and transport. One central interest is the auxin-dependent gene expression regulation mechanism involving AUXIN RESPONSE FACTOR (ARF) transcription factors and their repressors, the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins. Numerous studies have been focused on MONOPTEROS (MP)/ARF5, an activator of auxin-dependent gene expression with a crucial impact on plant development. This review summarizes over 30 years of research on MP/ARF5. We indicate the available analytical tools to study MP/ARF5 and point out the known mechanism of MP/ARF5-dependent regulation of gene expression during various developmental processes, namely embryogenesis, leaf formation, vascularization, and shoot and root meristem formation. However, many questions remain about the auxin dose-dependent regulation of gene transcription by MP/ARF5 and its isoforms in plant cells, the composition of the MP/ARF5 protein complex, and, finally, all the genes under its direct control. In addition, information on post-translational modifications of MP/ARF5 protein is marginal, and knowledge about their consequences on MP/ARF5 function is limited. Moreover, the epigenetic factors and other regulators that act upstream of MP/ARF5 are poorly understood. Their identification will be a challenge in the coming years.
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Affiliation(s)
- Barbara Wójcikowska
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Samia Belaidi
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hélène S Robert
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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28
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Yin R, Xia K, Xu X. Spatial transcriptomics drives a new era in plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1571-1581. [PMID: 37651723 DOI: 10.1111/tpj.16437] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/25/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
SUMMARYThe plant community lags far behind the animal and human fields concerning the application of single‐cell methodologies. This is primarily due to the challenges associated with plant tissue dissection and the limitations of the available technologies. However, recent advances in spatial transcriptomics enable the study of single‐cells derived from plant tissues from a spatial perspective. This technology is already successfully used to identify cell types, reconstruct cell‐fate lineages, and reveal cell‐to‐cell interactions. Future technological advancements will overcome the challenges in sample processing, data analysis, and the integration of multiple‐omics technologies. Thanks to spatial transcriptomics, we anticipate several plant research projects to significantly advance our understanding of critical aspects of plant biology.
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Affiliation(s)
- Ruilian Yin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- BGI Research, Shenzhen, 518083, China
| | - Keke Xia
- BGI Research, Shenzhen, 518083, China
| | - Xun Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518120, China
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29
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Okazaki K, Ito S, Nakamura H, Asami T, Shimomura K, Umehara M. Increase in ENHANCER OF SHOOT REGENERATION2 expression by treatment with strigolactone-related inhibitors and kinetin during adventitious shoot formation in ipecac. PLANT CELL REPORTS 2023; 42:1927-1936. [PMID: 37803214 DOI: 10.1007/s00299-023-03073-y] [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: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
KEY MESSAGE Increase of ENHANCER OF SHOOT REGENERATION 2 expression was consistent to treatment with kinetin, TIS108, and KK094 in adventitious shoot formation of ipecac. Unlike many plant species, ipecac (Carapichea ipecacuanha (Brot.) L. Andersson) can form adventitious shoots in tissue culture without cytokinin (CK) treatment. Strigolactone (SL) biosynthesis and signaling inhibitors stimulate adventitious shoot formation in ipecac, suggesting their potential use as novel growth regulators in plant tissue culture, but the molecular mechanism of their action is unclear. In this study, we compared the effects of SL-related inhibitors (TIS108 and KK094) and CKs (2iP, tZ, and kinetin) on adventitious shoot formation in ipecac. Exogenously applied SL-related inhibitors and CKs stimulated adventitious shoot formation. Combinations of SL-related inhibitors and kinetin also promoted adventitious shoot formation, but without additive effects. We also analyzed the expression of CK biosynthesis genes in ipecac. TIS108 increased the expression of the ipecac homolog of ISOPENTENYL TRANSFERASE 3 (CiIPT3) but decreased that of LONELY GUY 7 homolog (CiLOG7), presumably resulting in no change in 2iP-type CK levels. KK094 and kinetin increased CiLOG7 expression, elevating 2iP-type CK levels. Among pluripotency- and meristem-related genes, TIS108, KK094, and kinetin consistently increased the expression of ENHANCER OF SHOOT REGENERATION 2 homolog (CiESR2), which has a key role in shoot regeneration, in the internodal segment region that formed adventitious shoots. We propose that CiESR2 might be a key stimulator of adventitious shoot formation in ipecac.
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Affiliation(s)
- Karin Okazaki
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-Machi, Ora-Gun, Gunma, 374-0193, Japan
| | - Shinsaku Ito
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Hidemitsu Nakamura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Tadao Asami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Koichiro Shimomura
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-Machi, Ora-Gun, Gunma, 374-0193, Japan
| | - Mikihisa Umehara
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-Machi, Ora-Gun, Gunma, 374-0193, Japan.
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30
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Luo Z, Liu H, Xie F. Cellular and molecular basis of symbiotic nodule development. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102478. [PMID: 37857037 DOI: 10.1016/j.pbi.2023.102478] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023]
Abstract
Root nodule development plays a vital role in establishing the mutualistic relationship between legumes and nitrogen-fixing rhizobia. Two primary processes are involved in nodule development: formative cell divisions in the root cortex and the subsequent differentiation of nodule cells. The first process involves the mitotic reactivation of differentiated root cortex cells to form nodule primordium after perceiving symbiotic signals. The second process enables the nascent nodule primordium cells to develop into various cell types, leading to the creation of a functional nodule capable of supporting nitrogen fixation. Thus, both division and differentiation of nodule cells are crucial for root nodule development. This review provides an overview of the most recent advancements in comprehending the cellular and molecular mechanisms underlying symbiotic nodule development in legumes.
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Affiliation(s)
- Zhenpeng Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Haiyue Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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31
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Song X, Yu Y, Zhu J, Li C. BRIP1 and BRIP2 maintain root meristem by affecting auxin-mediated regulation. PLANTA 2023; 259:8. [PMID: 38019301 DOI: 10.1007/s00425-023-04283-0] [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: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023]
Abstract
MAIN CONCLUSION This study reveals that mutations in BRIP1/2 subunits of the BAS complex disrupt root meristem development by decreasing PIN genes expression, affecting auxin transport, and downregulating essential root genes PLT. Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes play vital roles in plant development. BRAHMA-interacting proteins1 (BRIP1) and BRIP2 are subunits of BRAHMA (BRM)-associated SWI/SNF complex (BAS) in plants; however, their role and underlying regulatory mechanism in root development are still unknown. Here, we show that brip1 brip2 double mutants have a significantly shortened root meristem and an irregular arrangement in a portion of the root stem cell niche. The mutations in BRIP1 and BRIP2 cause decreased expression of the PIN-FORMED (PIN) genes, which in turn reduces the transport of auxin at the root tip, leading to the disruption of the accurate establishment of normal auxin concentration gradients in the stem cells. Chromatin immunoprecipitation (ChIP) experiments indicated that BRIP1 and BRIP2 directly bind to the PINs. Furthermore, we found a significant down-regulation in the expression of key root development genes, PLETHORA (PLT), in brip1 brip2. The brip1 brip2 plt1 plt2 quadruple mutations do not show further exacerbation in the short-root phenotype compared to plt1 plt2 double mutants. Using a dexamethasone (DEX)-inducible PLT2 transgenic line, we showed that acute overexpression of PLT2 partially rescues root meristem defects of brip1 brip2, suggesting that BRIP1 and BRIP2 act in part through the PLT1/2 pathway. Taken together, our results identify the critical role and the underlying mechanism of BRIP1/2 in maintaining the development of root meristem through the regulation of auxin output and expression of PLTs.
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Affiliation(s)
- Xin Song
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jiameng Zhu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Smet W, Blilou I. A blast from the past: Understanding stem cell specification in plant roots using laser ablation. QUANTITATIVE PLANT BIOLOGY 2023; 4:e14. [PMID: 38034417 PMCID: PMC10685261 DOI: 10.1017/qpb.2023.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 12/02/2023]
Abstract
In the Arabidopsis root, growth is sustained by the meristem. Signalling from organiser cells, also termed the quiescent centre (QC), is essential for the maintenance and replenishment of the stem cells. Here, we highlight three publications from the founder of the concept of the stem cell niche in Arabidopsis and a pioneer in unravelling regulatory modules governing stem cell specification and maintenance, as well as tissue patterning in the root meristem: Ben Scheres. His research has tremendously impacted the plant field. We have selected three publications from the Scheres legacy, which can be considered a breakthrough in the field of plant developmental biology. van den Berg et al. (1995) and van den Berg et al. (1997) uncovered that positional information-directed patterning. Sabatini et al. (1999), discovered that auxin maxima determine tissue patterning and polarity. We describe how simple but elegant experimental designs have provided the foundation of our current understanding of the functioning of the root meristem.
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Affiliation(s)
- Wouter Smet
- Biological and Environmental Science and Engineering (BESE) Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ikram Blilou
- Biological and Environmental Science and Engineering (BESE) Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
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Perez-Garcia P, Pucciariello O, Sanchez-Corrionero A, Cabrera J, Del Barrio C, Del Pozo JC, Perales M, Wabnik K, Moreno-Risueno MA. The cold-induced factor CBF3 mediates root stem cell activity, regeneration, and developmental responses to cold. PLANT COMMUNICATIONS 2023; 4:100737. [PMID: 37865820 PMCID: PMC10721530 DOI: 10.1016/j.xplc.2023.100737] [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: 01/13/2023] [Revised: 09/01/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Plant growth and development involve the specification and regeneration of stem cell niches (SCNs). Although plants are exposed to disparate environmental conditions, how environmental cues affect developmental programs and stem cells is not well understood. Root stem cells are accommodated in meristems in SCNs around the quiescent center (QC), which maintains their activity. Using a combination of genetics and confocal microscopy to trace morphological defects and correlate them with changes in gene expression and protein levels, we show that the cold-induced transcription factor (TF) C-REPEAT BINDING FACTOR 3 (CBF3), which has previously been associated with cold acclimation, regulates root development, stem cell activity, and regeneration. CBF3 is integrated into the SHORT-ROOT (SHR) regulatory network, forming a feedback loop that maintains SHR expression. CBF3 is primarily expressed in the root endodermis, whereas the CBF3 protein is localized to other meristematic tissues, including root SCNs. Complementation of cbf3-1 using a wild-type CBF3 gene and a CBF3 fusion with reduced mobility show that CBF3 movement capacity is required for SCN patterning and regulates root growth. Notably, cold induces CBF3, affecting QC activity. Furthermore, exposure to moderate cold around 10°C-12°C promotes root regeneration and QC respecification in a CBF3-dependent manner during the recuperation period. By contrast, CBF3 does not appear to regulate stem cell survival, which has been associated with recuperation from more acute cold (∼4°C). We propose a role for CBF3 in mediating the molecular interrelationships among the cold response, stem cell activity, and development.
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Affiliation(s)
- Pablo Perez-Garcia
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain.
| | - Ornella Pucciariello
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Alvaro Sanchez-Corrionero
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Cristina Del Barrio
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Juan Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - CSIC (INIA-CSIC)), Madrid, Spain.
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Iohannes SD, Jackson D. Tackling redundancy: genetic mechanisms underlying paralog compensation in plants. THE NEW PHYTOLOGIST 2023; 240:1381-1389. [PMID: 37724752 DOI: 10.1111/nph.19267] [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: 05/17/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023]
Abstract
Gene duplication is a powerful source of biological innovation giving rise to paralogous genes that undergo diverse fates. Redundancy between paralogous genes is an intriguing outcome of duplicate gene evolution, and its maintenance over evolutionary time has long been considered a paradox. Redundancy can also be dubbed 'a geneticist's nightmare': It hinders the predictability of genome editing outcomes and limits our ability to link genotypes to phenotypes. Genetic studies in yeast and plants have suggested that the ability of ancient redundant duplicates to compensate for dosage perturbations resulting from a loss of function depends on the reprogramming of gene expression, a phenomenon known as active compensation. Starting from considerations on the stoichiometric constraints that drive the evolutionary stability of redundancy, this review aims to provide insights into the mechanisms of active compensation between duplicates that could be targeted for breaking paralog dependencies - the next frontier in plant functional studies.
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Affiliation(s)
- Sessen Daniel Iohannes
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
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35
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Kuznetsova K, Efremova E, Dodueva I, Lebedeva M, Lutova L. Functional Modules in the Meristems: "Tinkering" in Action. PLANTS (BASEL, SWITZERLAND) 2023; 12:3661. [PMID: 37896124 PMCID: PMC10610496 DOI: 10.3390/plants12203661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). CONCLUSIONS The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.
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Affiliation(s)
| | | | - Irina Dodueva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia; (K.K.); (E.E.); (M.L.); (L.L.)
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36
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Li M, Wu S. Root evolution: Evidence for convergent evolution of root meristem. Curr Biol 2023; 33:R1009-R1010. [PMID: 37816319 DOI: 10.1016/j.cub.2023.08.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
The root system is thought to have evolved independently during the process of plant terrestrialization. It is unclear how the molecular regulation of the root meristem has been modified during these independent root evolutions. Two new reports provide important evidence in support of the putative convergent evolution of lycophyte roots.
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Affiliation(s)
- Meng Li
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuang Wu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
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37
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Liu W, Cai G, Zhai N, Wang H, Tang T, Zhang Y, Zhang Z, Sun L, Zhang Y, Beeckman T, Xu L. Genome and transcriptome of Selaginella kraussiana reveal evolution of root apical meristems in vascular plants. Curr Biol 2023; 33:4085-4097.e5. [PMID: 37716350 DOI: 10.1016/j.cub.2023.08.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/30/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The evolution of roots allowed vascular plants to adapt to land environments. Fossil evidence indicates that roots evolved independently in euphyllophytes (ferns and seed plants) and lycophytes, the two lineages of extant vascular plants. Based on a high-quality genome assembly, mRNA sequencing (mRNA-seq) data, and single-cell RNA-seq data for the lycophyte Selaginella kraussiana, we show that the two root origin events in lycophytes and euphyllophytes adopted partially similar molecular modules in the regulation of root apical meristem (RAM) development. In S. kraussiana, the RAM initiates from the rhizophore primordium guided by auxin and duplicates itself by dichotomous branching. The auxin signaling pathway directly upregulates euAINTEGUMENTAb (SkeuANTb), and then SkeuANTb directly promotes the expression of SkeuANTa and the WUSCHEL-RELATED HOMEOBOX13b (SkWOX13b) for RAM maintenance, partially similar to the molecular pathway involving the euANT-branch PLETHORA (AtPLT) genes and AtWOX5 in root initiation in the seed plant Arabidopsis thaliana. Other molecular modules, e.g., SHORT-ROOT and SCARECROW, also have partially similar expression patterns in the RAMs of S. kraussiana and A. thaliana. Overall, our study not only provides genome and transcriptome tools of S. kraussiana but also indicates the employment of some common molecular modules in RAMs during root origins in lycophytes and euphyllophytes.
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Affiliation(s)
- Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Tengfei Tang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhiyao Zhang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Lijun Sun
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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38
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Hill RD, Igamberdiev AU, Stasolla C. Preserving root stem cell functionality under low oxygen stress: the role of nitric oxide and phytoglobins. PLANTA 2023; 258:89. [PMID: 37759033 DOI: 10.1007/s00425-023-04246-5] [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: 06/17/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
MAIN CONCLUSION The preservation of quiescent center stem cell integrity in hypoxic roots by phytoglobins is exercised through their ability to scavenge nitric oxide and attenuate its effects on auxin transport and cell degradation. Under low oxygen stress, the retention or induction of phytoglobin expression maintains cell viability while loss or lack of induction of phytoglobin leads to cell degradation. Plants have evolved unique attributes to ensure survival in the environment in which they must exist. Common among the attributes is the ability to maintain stem cells in a quiescent (or low proliferation) state in unfriendly environments. From the seed embryo to meristematic regions of the plant, quiescent stem cells exist to regenerate the organism when environmental conditions are suitable to allow plant survival. Frequently, plants dispose of mature cells or organs in the process of acclimating to the stresses to ensure survival of meristems, the stem cells of which are capable of regenerating cells and organs that have been sacrificed, a feature not generally available to mammals. Most of the research on plant stress responses has dealt with how mature cells respond because of the difficulty of specifically examining plant meristem responses to stress. This raises the question as to whether quiescent stem cells behave in a similar fashion to mature cells in their response to stress and what factors within these critical cells determine whether they survive or degrade when exposed to environmental stress. This review attempts to examine this question with respect to the quiescent center (QC) stem cells of the root apical meristem. Emphasis is put on how varying levels of nitric oxide, influenced by the expression of phytoglobins, affect QC response to hypoxic stress.
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Affiliation(s)
- Robert D Hill
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
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Hao R, Zhou W, Li J, Luo M, Scheres B, Guo Y. On salt stress, PLETHORA signaling maintains root meristems. Dev Cell 2023; 58:1657-1669.e5. [PMID: 37480843 DOI: 10.1016/j.devcel.2023.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 04/02/2023] [Accepted: 06/30/2023] [Indexed: 07/24/2023]
Abstract
Salt stress is one of the unfavorable environmental factors to affect plants. Salinity represses root growth, resulting in reduced biomass of agricultural plants. Little is known about how plants maintain root growth to counteract salt stress. The AP2-domain transcription factors PLETHORA1/2 (PLT1/2) act as master regulators in root meristem maintenance in Arabidopsis. In this study, we report that the salt overly sensitive (SOS) pathway component SOS2 regulates PLT1/2 at the post-transcriptional level. Salt-activated SOS2 interacts and phosphorylates PLT1/2 through their conserved C-terminal motifs to stabilize PLT1/2, critical for root apical meristem maintenance under salt stress. The phospho-mimetic version of PLT1/2 restored meristem and primary root length reduction of sos2-2 and plt1-4 plt2-2 mutants on salt treatment. Moreover, SOS2-mediated PLT1/2 phosphorylation improves root growth recovery after salt stress alleviation. We identify a SOS2-PLT1/2 core protein module that is required for protecting primary root growth and meristem maintenance from salt stress.
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Affiliation(s)
- Rong Hao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenkun Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Jingrui Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Manqing Luo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ben Scheres
- Laboratory of Plant Developmental Biology, Wageningen University and Research, 6708 PB Wageningen, the Netherlands; Rijk Zwaan R&D, 4793 RS Fijnaart, the Netherlands
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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40
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Nakamura A, Hirota Y, Shigihara M, Watanabe M, Sato A, Tsuji H, Shimada Y. Molecular and cellular insights into auxin-regulated primary root growth: a comparative study of Arabidopsis and rice. Biosci Biotechnol Biochem 2023; 87:1145-1154. [PMID: 37385821 DOI: 10.1093/bbb/zbad089] [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: 03/29/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023]
Abstract
Auxin regulation of primary root growth in Arabidopsis and rice was compared by analyzing root growth in response to changes in auxin levels. A bell-shaped root-growth curve was identified in both Arabidopsis and rice in response to change in auxin levels. In Arabidopsis, cell division was the main regulator of root growth in response to auxin; in rice, auxin promoted root growth by regulating cell division and cell length. The expression levels of PLETHORA (PLT) genes in response to change in auxin level followed a bell-shaped curve and closely correlated with cell division in Arabidopsis but not in rice, implying that PLT gene expression plays key role to control root growth in Arabidopsis. The level of auxin in Arabidopsis was optimal for primary root elongation, while in rice it was higher than optimal. These differences may explain the species-dependent development of root systems.
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Affiliation(s)
- Ayako Nakamura
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka, Yokohama, Kanagawa, Japan
| | - Yuna Hirota
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka, Yokohama, Kanagawa, Japan
| | - Masaru Shigihara
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka, Yokohama, Kanagawa, Japan
| | - Mayu Watanabe
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka, Yokohama, Kanagawa, Japan
| | - Akiko Sato
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka, Yokohama, Kanagawa, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka, Yokohama, Kanagawa, Japan
| | - Yukihisa Shimada
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka, Yokohama, Kanagawa, Japan
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41
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Qi F, Wang F, Xiaoyang C, Wang Z, Lin Y, Peng Z, Zhang J, Wang N, Zhang J. Gene Expression Analysis of Different Organs and Identification of AP2 Transcription Factors in Flax ( Linum usitatissimum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3260. [PMID: 37765422 PMCID: PMC10535939 DOI: 10.3390/plants12183260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023]
Abstract
Flax (Linum usitatissimum L.) is an important oilseed crop widely cultivated for its oil and fiber. This study conducted transcriptome analysis to analyze the gene expression profiles of roots, leaves, stamens, pistils, and fruits in the flax cultivar Longya10. A total of 43,471 genes were detected in the RNA-seq data, with 34,497 genes showing differential expression levels between different organs. Gene expression patterns varied across different organs, with differences observed in expression-regulating genes within specific organs. However, 23,448 genes were found to be commonly expressed across all organs. Further analysis revealed organ-specific gene expressions, with 236, 690, 544, 909, and 1212 genes identified in pistils, fruits, leaves, roots, and stamens, respectively. Gene Ontology (GO) enrichment analysis was performed on these organ-specific genes, and significant enrichment was observed in various biological processes, cellular components, and molecular functions, providing new insights for the specific growth patterns of flax organs. Furthermore, we investigated the expression differences of AP2 transcription factors in various tissues and organs of Longya10. We identified 96 AP2 genes that were differentially expressed in different organs and annotated them into various biological pathways. Our results suggest that AP2 transcription factors may play important roles in regulating the growth and development of flax organs including stress response. In summary, our study provides a comprehensive analysis of gene expression patterns in different organs and tissues of flax plant and identifies potential critical regulators of flax organ growth and development. These findings contribute to a better understanding of the molecular mechanisms underlying flax organ development and may have important implications for the genetic improvement of flax crops.
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Affiliation(s)
- Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Fu Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Chunxiao Xiaoyang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Yujie Lin
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun 130000, China;
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC V1V 1V7, Canada
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42
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Yan T, Hou Q, Wei X, Qi Y, Pu A, Wu S, An X, Wan X. Promoting genotype-independent plant transformation by manipulating developmental regulatory genes and/or using nanoparticles. PLANT CELL REPORTS 2023; 42:1395-1417. [PMID: 37311877 PMCID: PMC10447291 DOI: 10.1007/s00299-023-03037-2] [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: 02/01/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE This review summarizes the molecular basis and emerging applications of developmental regulatory genes and nanoparticles in plant transformation and discusses strategies to overcome the obstacles of genotype dependency in plant transformation. Plant transformation is an important tool for plant research and biotechnology-based crop breeding. However, Plant transformation and regeneration are highly dependent on species and genotype. Plant regeneration is a process of generating a complete individual plant from a single somatic cell, which involves somatic embryogenesis, root and shoot organogeneses. Over the past 40 years, significant advances have been made in understanding molecular mechanisms of embryogenesis and organogenesis, revealing many developmental regulatory genes critical for plant regeneration. Recent studies showed that manipulating some developmental regulatory genes promotes the genotype-independent transformation of several plant species. Besides, nanoparticles penetrate plant cell wall without external forces and protect cargoes from degradation, making them promising materials for exogenous biomolecule delivery. In addition, manipulation of developmental regulatory genes or application of nanoparticles could also bypass the tissue culture process, paving the way for efficient plant transformation. Applications of developmental regulatory genes and nanoparticles are emerging in the genetic transformation of different plant species. In this article, we review the molecular basis and applications of developmental regulatory genes and nanoparticles in plant transformation and discuss how to further promote genotype-independent plant transformation.
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Affiliation(s)
- Tingwei Yan
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Quancan Hou
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
| | - Yuchen Qi
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Suowei Wu
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Xueli An
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Zhongzhi International Institute of Agricultural Biosciences, Beijing, 100083, China.
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing, 100192, China.
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Fehér A. A Common Molecular Signature Indicates the Pre-Meristematic State of Plant Calli. Int J Mol Sci 2023; 24:13122. [PMID: 37685925 PMCID: PMC10488067 DOI: 10.3390/ijms241713122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
In response to different degrees of mechanical injury, certain plant cells re-enter the division cycle to provide cells for tissue replenishment, tissue rejoining, de novo organ formation, and/or wound healing. The intermediate tissue formed by the dividing cells is called a callus. Callus formation can also be induced artificially in vitro by wounding and/or hormone (auxin and cytokinin) treatments. The callus tissue can be maintained in culture, providing starting material for de novo organ or embryo regeneration and thus serving as the basis for many plant biotechnology applications. Due to the biotechnological importance of callus cultures and the scientific interest in the developmental flexibility of somatic plant cells, the initial molecular steps of callus formation have been studied in detail. It was revealed that callus initiation can follow various ways, depending on the organ from which it develops and the inducer, but they converge on a seemingly identical tissue. It is not known, however, if callus is indeed a special tissue with a defined gene expression signature, whether it is a malformed meristem, or a mass of so-called "undifferentiated" cells, as is mostly believed. In this paper, I review the various mechanisms of plant regeneration that may converge on callus initiation. I discuss the role of plant hormones in the detour of callus formation from normal development. Finally, I compare various Arabidopsis gene expression datasets obtained a few days, two weeks, or several years after callus induction and identify 21 genes, including genes of key transcription factors controlling cell division and differentiation in meristematic regions, which were upregulated in all investigated callus samples. I summarize the information available on all 21 genes that point to the pre-meristematic nature of callus tissues underlying their wide regeneration potential.
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Affiliation(s)
- Attila Fehér
- Institute of Plant Biology, Biological Research Centre, 62 Temesvári Körút, 6726 Szeged, Hungary; or
- Department of Plant Biology, University of Szeged, 52 Közép Fasor, 6726 Szeged, Hungary
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44
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Bailey M, Hsieh EJ, Tsai HH, Ravindran A, Schmidt W. Alkalinity modulates a unique suite of genes to recalibrate growth and pH homeostasis. FRONTIERS IN PLANT SCIENCE 2023; 14:1100701. [PMID: 37457359 PMCID: PMC10348880 DOI: 10.3389/fpls.2023.1100701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Alkaline soils pose a conglomerate of constraints to plants, restricting the growth and fitness of non-adapted species in habitats with low active proton concentrations. To thrive under such conditions, plants have to compensate for a potential increase in cytosolic pH and restricted softening of the cell wall to invigorate cell elongation in a proton-depleted environment. To discern mechanisms that aid in the adaptation to external pH, we grew plants on media with pH values ranging from 5.5 to 8.5. Growth was severely restricted above pH 6.5 and associated with decreasing chlorophyll levels at alkaline pH. Bicarbonate treatment worsened plant performance, suggesting effects that differ from those exerted by pH as such. Transcriptional profiling of roots subjected to short-term transfer from optimal (pH 5.5) to alkaline (pH 7.5) media unveiled a large set of differentially expressed genes that were partially congruent with genes affected by low pH, bicarbonate, and nitrate, but showed only a very small overlap with genes responsive to the availability of iron. Further analysis of selected genes disclosed pronounced responsiveness of their expression over a wide range of external pH values. Alkalinity altered the expression of various proton/anion co-transporters, possibly to recalibrate cellular proton homeostasis. Co-expression analysis of pH-responsive genes identified a module of genes encoding proteins with putative functions in the regulation of root growth, which appears to be conserved in plants subjected to low pH or bicarbonate. Our analysis provides an inventory of pH-sensitive genes and allows comprehensive insights into processes that are orchestrated by external pH.
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Affiliation(s)
- Mitylene Bailey
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - En-Jung Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Huei-Hsuan Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Arya Ravindran
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan
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Zhao Z, Wu S, Gao H, Tang W, Wu X, Zhang B. The BR signaling pathway regulates primary root development and drought stress response by suppressing the expression of PLT1 and PLT2 in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1187605. [PMID: 37441172 PMCID: PMC10333506 DOI: 10.3389/fpls.2023.1187605] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/02/2023] [Indexed: 07/15/2023]
Abstract
Introduction With the warming global climate, drought stress has become an important abiotic stress factor limiting plant growth and crop yield. As the most rapidly drought-sensing organs of plants, roots undergo a series of changes to enhance their ability to absorb water, but the molecular mechanism is unclear. Results and methods In this study, we found that PLT1 and PLT2, two important transcription factors of root development in Arabidopsis thaliana, are involved in the plant response to drought and are inhibited by BR signaling. PLT1- and PLT2-overexpressing plants showed greater drought tolerance than wild-type plants. Furthermore, we found that BZR1 could bind to the promoter of PLT1 and inhibit its transcriptional activity in vitro and in vivo. PLT1 and PLT2 were regulated by BR signaling in root development and PLT2 could partially rescue the drought sensitivity of bes1-D. In addition, RNA-seq data analysis showed that BR-regulated root genes and PLT1/2 target genes were also regulated by drought; for example, CIPK3, RCI2A, PCaP1, PIP1;5, ERF61 were downregulated by drought and PLT1/2 but upregulated by BR treatment; AAP4, WRKY60, and AT5G19970 were downregulated by PLT1/2 but upregulated by drought and BR treatment; and RGL2 was upregulated by drought and PLT1/2 but downregulated by BR treatment. Discussion Our findings not only reveal the mechanism by which BR signaling coordinates root growth and drought tolerance by suppressing the expression of PLT1 and PLT2 but also elucidates the relationship between drought and root development. The current study thus provides an important theoretical basis for the improvement of crop yield under drought conditions.
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Affiliation(s)
- Zhiying Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuting Wu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Han Gao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Wenqiang Tang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xuedan Wu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Baowen Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology; Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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46
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Li M, Niu X, Li S, Fu S, Li Q, Xu M, Wang C, Wu S. CRISPR/Cas9 Based Cell-Type Specific Gene Knock-Out in Arabidopsis Roots. PLANTS (BASEL, SWITZERLAND) 2023; 12:2365. [PMID: 37375990 DOI: 10.3390/plants12122365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
CRISPR/Cas9 (hereafter Cas9)-mediated gene knockout is one of the most important tools for studying gene function. However, many genes in plants play distinct roles in different cell types. Engineering the currently used Cas9 system to achieve cell-type-specific knockout of functional genes is useful for addressing the cell-specific functions of genes. Here we employed the cell-specific promoters of the WUSCHEL RELATED HOMEOBOX 5 (WOX5), CYCLIND6;1 (CYCD6;1), and ENDODERMIS7 (EN7) genes to drive the Cas9 element, allowing tissue-specific targeting of the genes of interest. We designed the reporters to verify the tissue-specific gene knockout in vivo. Our observation of the developmental phenotypes provides strong evidence for the involvement of SCARECROW (SCR) and GIBBERELLIC ACID INSENSITIVE (GAI) in the development of quiescent center (QC) and endodermal cells. This system overcomes the limitations of traditional plant mutagenesis techniques, which often result in embryonic lethality or pleiotropic phenotypes. By allowing cell-type-specific manipulation, this system has great potential to help us better understand the spatiotemporal functions of genes during plant development.
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Affiliation(s)
- Meng Li
- College of Life Sciences and Horticultural Plant Biology Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xufang Niu
- College of Life Sciences and Horticultural Plant Biology Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuang Li
- College of Life Sciences and Horticultural Plant Biology Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shasha Fu
- College of Life Sciences and Horticultural Plant Biology Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qianfang Li
- College of Life Sciences and Horticultural Plant Biology Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meizhi Xu
- College of Life Sciences and Horticultural Plant Biology Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunhua Wang
- College of Life Sciences and Horticultural Plant Biology Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuang Wu
- College of Life Sciences and Horticultural Plant Biology Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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47
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Considine MJ, Foyer CH. Metabolic regulation of quiescence in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1132-1148. [PMID: 36994639 PMCID: PMC10952390 DOI: 10.1111/tpj.16216] [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: 12/22/2022] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 05/31/2023]
Abstract
Quiescence is a crucial survival attribute in which cell division is repressed in a reversible manner. Although quiescence has long been viewed as an inactive state, recent studies have shown that it is an actively monitored process that is influenced by environmental stimuli. Here, we provide a perspective of the quiescent state and discuss how this process is tuned by energy, nutrient and oxygen status, and the pathways that sense and transmit these signals. We not only highlight the governance of canonical regulators and signalling mechanisms that respond to changes in nutrient and energy status, but also consider the central significance of mitochondrial functions and cues as key regulators of nuclear gene expression. Furthermore, we discuss how reactive oxygen species and the associated redox processes, which are intrinsically linked to energy carbohydrate metabolism, also play a key role in the orchestration of quiescence.
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Affiliation(s)
- Michael J. Considine
- The UWA Institute of Agriculture and the School of Molecular SciencesThe University of Western AustraliaPerthWestern Australia6009Australia
- The Department of Primary Industries and Regional DevelopmentPerthWestern Australia6000Australia
| | - Christine H. Foyer
- School of Biosciences, College of Life and Environmental SciencesUniversity of BirminghamEdgbastonB15 2TTUK
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48
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Wang B, Shi X, Gao J, Liao R, Fu J, Bai J, Cui H. SCARECROW maintains the stem cell niche in Arabidopsis roots by ensuring telomere integrity. PLANT PHYSIOLOGY 2023; 192:1115-1131. [PMID: 36943300 PMCID: PMC10231454 DOI: 10.1093/plphys/kiad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 06/01/2023]
Abstract
Stem cells are the ultimate source of cells for various tissues and organs and thus are essential for postembryonic plant growth and development. SCARECROW (SCR) is a plant-specific transcription regulator well known for its role in stem cell renewal in plant roots, but the mechanism by which SCR exerts this function remains unclear. To address this question, we carried out a genetic screen for mutants that no longer express SCR in the stem cell niche of Arabidopsis (Arabidopsis thaliana) roots and characterized 1 of these mutants. Molecular genetics methods allowed us to pinpoint the causal mutation in this mutant in TELOMERIC PATHWAYS IN ASSOCIATION WITH STN 1 (TEN1), encoding a factor that protects telomere ends. Interestingly, TEN1 expression was dramatically reduced in the scr mutant. Telomerase and STN1 and CONSERVED TELOMERE MAINTENANCE COMPONENT 1 (CTC1), components of the same protein complex as TEN1, were also dramatically downregulated in scr. Loss of STN1, CTC1, and telomerase caused defects in root stem cells. These results together suggest that SCR maintains root stem cells by promoting expression of genes that ensure genome integrity. Supporting this conclusion, we demonstrated that the scr mutant accumulates more DNA damage than wild-type Arabidopsis and that this problem is aggravated after exposure to zeocin, a DNA damage reagent. Finally, we identified 2 previously uncharacterized motifs in TEN1 and provide evidence that a conserved amino acid residue in 1 of the motifs is indispensable for TEN1 function. SCR thus provides a connection between genome integrity and stem cell maintenance in Arabidopsis roots.
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Affiliation(s)
- Bingxin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaowen Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jingbo Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rui Liao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Juan Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongchang Cui
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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49
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Hardtke CS. Phloem development. THE NEW PHYTOLOGIST 2023. [PMID: 37243530 DOI: 10.1111/nph.19003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/13/2023] [Indexed: 05/29/2023]
Abstract
The evolution of the plant vascular system is a key process in Earth history because it enabled plants to conquer land and transform the terrestrial surface. Among the vascular tissues, the phloem is particularly intriguing because of its complex functionality. In angiosperms, its principal components are the sieve elements, which transport phloem sap, and their neighboring companion cells. Together, they form a functional unit that sustains sap loading, transport, and unloading. The developmental trajectory of sieve elements is unique among plant cell types because it entails selective organelle degradation including enucleation. Meticulous analyses of primary, so-called protophloem in the Arabidopsis thaliana root meristem have revealed key steps in protophloem sieve element formation at single-cell resolution. A transcription factor cascade connects specification with differentiation and also orchestrates phloem pole patterning via noncell-autonomous action of sieve element-derived effectors. Reminiscent of vascular tissue patterning in secondary growth, these involve receptor kinase pathways, whose antagonists guide the progression of sieve element differentiation. Receptor kinase pathways may also safeguard phloem formation by maintaining the developmental plasticity of neighboring cell files. Our current understanding of protophloem development in the A. thaliana root has reached sufficient detail to instruct molecular-level investigation of phloem formation in other organs.
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Affiliation(s)
- Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, CH-1015, Lausanne, Switzerland
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50
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Kumar N, Caldwell C, Iyer-Pascuzzi AS. The NIN-LIKE PROTEIN 7 transcription factor modulates auxin pathways to regulate root cap development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3047-3059. [PMID: 36787214 DOI: 10.1093/jxb/erad058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/10/2023] [Indexed: 05/21/2023]
Abstract
The root cap is a small tissue located at the tip of the root with critical functions for root growth. Present in nearly all vascular plants, the root cap protects the root meristem, influences soil penetration, and perceives and transmits environmental signals that are critical for root branching patterns. To perform these functions, the root cap must remain relatively stable in size and must integrate endogenous developmental pathways with environmental signals, yet the mechanism is not clear. We previously showed that low pH conditions altered root cap development, and these changes are mediated by the NIN LIKE PROTEIN 7 (NLP7) transcription factor, a master regulator of nitrate signaling. Here we show that in Arabidopsis NLP7 integrates nitrate signaling with auxin pathways to regulate root cap development. We found that low nitrate conditions promote aberrant release of root cap cells. Nitrate deficiency impacts auxin pathways in the last layer of the root cap, and this is mediated in part by NLP7. Mutations in NLP7 abolish the auxin minimum in the last layer of the root cap and alter root cap expression of the auxin carriers PIN-LIKES 3 (PILS3) and PIN-FORMED 7 (PIN7) as well as transcription factors that regulate PIN expression. Together, our data reveal NLP7 as a link between endogenous auxin pathways and nitrate signaling in the root cap.
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Affiliation(s)
- Narender Kumar
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Chloe Caldwell
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
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