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Demesa-Arevalo E, Narasimhan M, Simon R. Intercellular Communication in Shoot Meristems. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:319-344. [PMID: 38424066 DOI: 10.1146/annurev-arplant-070523-035342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The shoot meristem of land plants maintains the capacity for organ generation throughout its lifespan due to a group of undifferentiated stem cells. Most meristems are shaped like a dome with a precise spatial arrangement of functional domains, and, within and between these domains, cells interact through a network of interconnected signaling pathways. Intercellular communication in meristems is mediated by mobile transcription factors, small RNAs, hormones, and secreted peptides that are perceived by membrane-localized receptors. In recent years, we have gained deeper insight into the underlying molecular processes of the shoot meristem, and we discuss here how plants integrate internal and external inputs to control shoot meristem activities.
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Affiliation(s)
- Edgar Demesa-Arevalo
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany;
| | - Madhumitha Narasimhan
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany;
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany;
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2
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Seo MG, Lim Y, Hendelman A, Robitaille G, Beak HK, Hong WJ, Park SJ, Lippman ZB, Park YJ, Kwon CT. Evolutionary conservation of receptor compensation for stem cell homeostasis in Solanaceae plants. HORTICULTURE RESEARCH 2024; 11:uhae126. [PMID: 38919555 PMCID: PMC11197305 DOI: 10.1093/hr/uhae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/21/2024] [Indexed: 06/27/2024]
Abstract
Stem cell homeostasis is pivotal for continuous and programmed formation of organs in plants. The precise control of meristem proliferation is mediated by the evolutionarily conserved signaling that encompasses complex interactions among multiple peptide ligands and their receptor-like kinases. Here, we identified compensation mechanisms involving the CLAVATA1 (CLV1) receptor and its paralogs, BARELY ANY MERISTEMs (BAMs), for stem cell proliferation in two Solanaceae species, tomato and groundcherry. Genetic analyses of higher-order mutants deficient in multiple receptor genes, generated via CRISPR-Cas9 genome editing, reveal that tomato SlBAM1 and SlBAM2 compensate for slclv1 mutations. Unlike the compensatory responses between orthologous receptors observed in Arabidopsis, tomato slclv1 mutations do not trigger transcriptional upregulation of four SlBAM genes. The compensation mechanisms within receptors are also conserved in groundcherry, and critical amino acid residues of the receptors associated with the physical interaction with peptide ligands are highly conserved in Solanaceae plants. Our findings demonstrate that the evolutionary conservation of both compensation mechanisms and critical coding sequences between receptor-like kinases provides a strong buffering capacity during stem cell homeostasis in tomato and groundcherry.
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Affiliation(s)
- Myeong-Gyun Seo
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Yoonseo Lim
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Gina Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Hong Kwan Beak
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan, Jeonbuk 54538, Republic of Korea
| | - Woo-Jong Hong
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Soon Ju Park
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Young-Joon Park
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Choon-Tak Kwon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
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3
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Wen Y, Yang Y, Liu J, Han H. CLV3-CLV1 signaling governs flower primordia outgrowth across environmental temperatures. TRENDS IN PLANT SCIENCE 2024; 29:400-402. [PMID: 38102046 DOI: 10.1016/j.tplants.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
The initiation and outgrowth of floral primordia are critical for flower formation and reproductive success; however, the underlying mechanisms are still unclear. Two reports (Jones et al.; John et al.) shed light on how CLV3-CLV1 signaling promoted flower primordia formation and outgrowth by regulating auxin biosynthesis under distinct environmental temperatures.
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Affiliation(s)
- Yufang Wen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China
| | - Youxin Yang
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianping Liu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huibin Han
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi, Nanchang, 330045, China.
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4
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Ciren D, Zebell S, Lippman ZB. Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. PLoS Genet 2024; 20:e1011174. [PMID: 38437180 PMCID: PMC10911594 DOI: 10.1371/journal.pgen.1011174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergent cis-regulatory sequences. It remains unclear how such drastic cis-regulatory evolution across species allows preservation of gene function, and to what extent these differences influence how cis-regulatory variation arising within species impacts phenotypic change. Here, we investigated these questions using a plant stem cell regulator conserved in expression pattern and function over ~125 million years. Using in-vivo genome editing in two distantly related models, Arabidopsis thaliana (Arabidopsis) and Solanum lycopersicum (tomato), we generated over 70 deletion alleles in the upstream and downstream regions of the stem cell repressor gene CLAVATA3 (CLV3) and compared their individual and combined effects on a shared phenotype, the number of carpels that make fruits. We found that sequences upstream of tomato CLV3 are highly sensitive to even small perturbations compared to its downstream region. In contrast, Arabidopsis CLV3 function is tolerant to severe disruptions both upstream and downstream of the coding sequence. Combining upstream and downstream deletions also revealed a different regulatory outcome. Whereas phenotypic enhancement from adding downstream mutations was predominantly weak and additive in tomato, mutating both regions of Arabidopsis CLV3 caused substantial and synergistic effects, demonstrating distinct distribution and redundancy of functional cis-regulatory sequences. Our results demonstrate remarkable malleability in cis-regulatory structural organization of a deeply conserved plant stem cell regulator and suggest that major reconfiguration of cis-regulatory sequence space is a common yet cryptic evolutionary force altering genotype-to-phenotype relationships from regulatory variation in conserved genes. Finally, our findings underscore the need for lineage-specific dissection of the spatial architecture of cis-regulation to effectively engineer trait variation from conserved productivity genes in crops.
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Affiliation(s)
- Danielle Ciren
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, New York, United States of America
| | - Sophia Zebell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, New York, United States of America
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
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5
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Bashyal S, Gautam CK, Müller LM. CLAVATA signaling in plant-environment interactions. PLANT PHYSIOLOGY 2024; 194:1336-1357. [PMID: 37930810 PMCID: PMC10904329 DOI: 10.1093/plphys/kiad591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Plants must rapidly and dynamically adapt to changes in their environment. Upon sensing environmental signals, plants convert them into cellular signals, which elicit physiological or developmental changes that allow them to respond to various abiotic and biotic cues. Because plants can be simultaneously exposed to multiple environmental cues, signal integration between plant cells, tissues, and organs is necessary to induce specific responses. Recently, CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides and their cognate CLAVATA-type receptors received increased attention for their roles in plant-environment interactions. CLE peptides are mobile signaling molecules, many of which are induced by a variety of biotic and abiotic stimuli. Secreted CLE peptides are perceived by receptor complexes on the surface of their target cells, which often include the leucine-rich repeat receptor-like kinase CLAVATA1. Receptor activation then results in cell-type and/or environment-specific responses. This review summarizes our current understanding of the diverse roles of environment-regulated CLE peptides in modulating plant responses to environmental cues. We highlight how CLE signals regulate plant physiology by fine-tuning plant-microbe interactions, nutrient homeostasis, and carbon allocation. Finally, we describe the role of CLAVATA receptors in the perception of environment-induced CLE signals and discuss how diverse CLE-CLAVATA signaling modules may integrate environmental signals with plant physiology and development.
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Affiliation(s)
- Sagar Bashyal
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | | | - Lena Maria Müller
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
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Wulf K, Sun J, Wang C, Ho-Plagaro T, Kwon CT, Velandia K, Correa-Lozano A, Tamayo-Navarrete MI, Reid JB, García Garrido JM, Foo E. The Role of CLE Peptides in the Suppression of Mycorrhizal Colonization of Tomato. PLANT & CELL PHYSIOLOGY 2024; 65:107-119. [PMID: 37874980 PMCID: PMC10799714 DOI: 10.1093/pcp/pcad124] [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: 02/21/2023] [Revised: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023]
Abstract
Symbioses with beneficial microbes are widespread in plants, but these relationships must balance the energy invested by the plants with the nutrients acquired. Symbiosis with arbuscular mycorrhizal (AM) fungi occurs throughout land plants, but our understanding of the genes and signals that regulate colonization levels is limited, especially in non-legumes. Here, we demonstrate that in tomato, two CLV3/EMBRYO-SURROUNDING REGION (CLE) peptides, SlCLE10 and SlCLE11, act to suppress AM colonization of roots. Mutant studies and overexpression via hairy transformation indicate that SlCLE11 acts locally in the root to limit AM colonization. Indeed, SlCLE11 expression is strongly induced in AM-colonized roots, but SlCLE11 is not required for phosphate suppression of AM colonization. SlCLE11 requires the FIN gene that encodes an enzyme required for CLE peptide arabinosylation to suppress mycorrhizal colonization. However, SlCLE11 suppression of AM does not require two CLE receptors with roles in regulating AM colonization, SlFAB (CLAVATA1 ortholog) or SlCLV2. Indeed, multiple parallel pathways appear to suppress mycorrhizal colonization in tomato, as double mutant studies indicate that SlCLV2 and FIN have an additive influence on mycorrhizal colonization. SlCLE10 appears to play a more minor or redundant role, as cle10 mutants did not influence intraradical AM colonization. However, the fact that cle10 mutants had an elevated number of hyphopodia and that ectopic overexpression of SlCLE10 did suppress mycorrhizal colonization suggests that SlCLE10 may also play a role in suppressing AM colonization. Our findings show that CLE peptides regulate AM colonization in tomato and at least SlCLE11 likely requires arabinosylation for activity.
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Affiliation(s)
- Kate Wulf
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Jiacan Sun
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Chenglei Wang
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
- Enza Zaden Australia, 218 Eumungerie Road, Narromine, NSW 2821, Australia
| | - Tania Ho-Plagaro
- Department of Soil Microbiology and Symbiotic Systems, Zaidín Experimental Station (EEZ), CSIC, C. Prof. Albareda, 1, Granada 18008, Spain
| | - Choon-Tak Kwon
- Department of Smart Farm Science, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do, Yongin 17104, Republic of Korea
- Graduate School of Green-Bio Science, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do, Yongin 17104, Republic of Korea
| | - Karen Velandia
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Alejandro Correa-Lozano
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - María Isabel Tamayo-Navarrete
- Department of Soil Microbiology and Symbiotic Systems, Zaidín Experimental Station (EEZ), CSIC, C. Prof. Albareda, 1, Granada 18008, Spain
| | - James B Reid
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Jose Manuel García Garrido
- Department of Soil Microbiology and Symbiotic Systems, Zaidín Experimental Station (EEZ), CSIC, C. Prof. Albareda, 1, Granada 18008, Spain
| | - Eloise Foo
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
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7
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Zhang Y, Shen C, Shi J, Shi J, Zhang D. Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:17-35. [PMID: 37935244 DOI: 10.1093/jxb/erad386] [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: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
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8
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Ciren D, Zebell S, Lippman ZB. Extreme restructuring of cis -regulatory regions controlling a deeply conserved plant stem cell regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572550. [PMID: 38187729 PMCID: PMC10769289 DOI: 10.1101/2023.12.20.572550] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergent cis -regulatory sequences. It remains unclear how such drastic cis -regulatory evolution across species allows preservation of gene function, and to what extent these differences influence how cis- regulatory variation arising within species impacts phenotypic change. Here, we investigated these questions using a plant stem cell regulator conserved in expression pattern and function over ∼125 million years. Using in-vivo genome editing in two distantly related models, Arabidopsis thaliana (Arabidopsis) and Solanum lycopersicum (tomato), we generated over 70 deletion alleles in the upstream and downstream regions of the stem cell repressor gene CLAVATA3 ( CLV3 ) and compared their individual and combined effects on a shared phenotype, the number of carpels that make fruits. We found that sequences upstream of tomato CLV3 are highly sensitive to even small perturbations compared to its downstream region. In contrast, Arabidopsis CLV3 function is tolerant to severe disruptions both upstream and downstream of the coding sequence. Combining upstream and downstream deletions also revealed a different regulatory outcome. Whereas phenotypic enhancement from adding downstream mutations was predominantly weak and additive in tomato, mutating both regions of Arabidopsis CLV3 caused substantial and synergistic effects, demonstrating distinct distribution and redundancy of functional cis -regulatory sequences. Our results demonstrate remarkable malleability in cis -regulatory structural organization of a deeply conserved plant stem cell regulator and suggest that major reconfiguration of cis -regulatory sequence space is a common yet cryptic evolutionary force altering genotype-to-phenotype relationships from regulatory variation in conserved genes. Finally, our findings underscore the need for lineage-specific dissection of the spatial architecture of cis -regulation to effectively engineer trait variation from conserved productivity genes in crops. Author summary We investigated the evolution of cis -regulatory elements (CREs) and their interactions in the regulation of a plant stem cell regulator gene, CLAVATA3 (CLV3) , in Arabidopsis and tomato. Despite diverging ∼125 million years ago, the function and expression of CLV3 is conserved in these species; however, cis -regulatory sequences upstream and downstream have drastically diverged, preventing identification of conserved non-coding sequences between them. We used CRISPR-Cas9 to engineer dozens of mutations within the cis -regulatory regions of Arabidopsis and tomato CLV3. In tomato, our results show that tomato CLV3 function primarily relies on interactions among CREs in the 5' non-coding region, unlike Arabidopsis CLV3 , which depends on a more balanced distribution of functional CREs between the 5' and 3' regions. Therefore, despite a high degree of functional conservation, our study demonstrates divergent regulatory strategies between two distantly related CLV3 orthologs, with substantial alterations in regulatory sequences, their spatial arrangement, and their relative effects on CLV3 regulation. These results suggest that regulatory regions are not only extremely robust to mutagenesis, but also that the sequences underlying this robustness can be lineage-specific for conserved genes, due to the complex and often redundant interactions among CREs that ensure proper gene function amidst large-scale sequence turnover.
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Gallagher JP, Man J, Chiaramida A, Rozza IK, Patterson EL, Powell MM, Schrager-Lavelle A, Multani DS, Meeley RB, Bartlett ME. GRASSY TILLERS1 ( GT1) and SIX-ROWED SPIKE1 ( VRS1) homologs share conserved roles in growth repression. Proc Natl Acad Sci U S A 2023; 120:e2311961120. [PMID: 38096411 PMCID: PMC10742383 DOI: 10.1073/pnas.2311961120] [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: 07/21/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Crop engineering and de novo domestication using gene editing are new frontiers in agriculture. However, outside of well-studied crops and model systems, prioritizing engineering targets remains challenging. Evolution can guide us, revealing genes with deeply conserved roles that have repeatedly been selected in the evolution of plant form. Homologs of the transcription factor genes GRASSY TILLERS1 (GT1) and SIX-ROWED SPIKE1 (VRS1) have repeatedly been targets of selection in domestication and evolution, where they repress growth in many developmental contexts. This suggests a conserved role for these genes in regulating growth repression. To test this, we determined the roles of GT1 and VRS1 homologs in maize (Zea mays) and the distantly related grass brachypodium (Brachypodium distachyon) using gene editing and mutant analysis. In maize, gt1; vrs1-like1 (vrl1) mutants have derepressed growth of floral organs. In addition, gt1; vrl1 mutants bore more ears and more branches, indicating broad roles in growth repression. In brachypodium, Bdgt1; Bdvrl1 mutants have more branches, spikelets, and flowers than wild-type plants, indicating conserved roles for GT1 and VRS1 homologs in growth suppression over ca. 59 My of grass evolution. Importantly, many of these traits influence crop productivity. Notably, maize GT1 can suppress growth in arabidopsis (Arabidopsis thaliana) floral organs, despite ca. 160 My of evolution separating the grasses and arabidopsis. Thus, GT1 and VRS1 maintain their potency as growth regulators across vast timescales and in distinct developmental contexts. This work highlights the power of evolution to inform gene editing in crop improvement.
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Affiliation(s)
- Joseph P. Gallagher
- Biology Department, University of Massachusetts, Amherst, MA01003
- Forage Seed and Cereal Research Unit, US Department of Agriculture, Agricultural Research Service, Corvallis, OR97331
| | - Jarrett Man
- Biology Department, University of Massachusetts, Amherst, MA01003
| | | | | | | | - Morgan M. Powell
- Biology Department, University of Massachusetts, Amherst, MA01003
| | | | - Dilbag S. Multani
- Corteva Agriscience, Johnston, IA50131
- Napigen, Inc., Wilmington, DE19803
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Lee ES, Heo J, Bang WY, Chougule KM, Waminal NE, Hong NT, Kim MJ, Beak HK, Kim YJ, Priatama RA, Jang JI, Cha KI, Son SH, Rajendran S, Choo Y, Bae JH, Kim CM, Lee YK, Bae S, Jones JDG, Sohn KH, Lee J, Kim HH, Hong JC, Ware D, Kim K, Park SJ. Engineering homoeologs provide a fine scale for quantitative traits in polyploid. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2458-2472. [PMID: 37530518 PMCID: PMC10651150 DOI: 10.1111/pbi.14141] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023]
Abstract
Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome engineering. The hexaploid black nightshade species Solanum nigrum has immense potential as a beneficial food supplement. We assembled its genome at the scaffold level. After functional annotations, we identified homoeologous gene sets, with similar sequence and expression profiles, based on comparative analyses of orthologous genes with close diploid relatives Solanum americanum and S. lycopersicum. Using CRISPR-Cas9-mediated mutagenesis, we generated various mutation combinations in homoeologous genes. Multiple mutants showed quantitative phenotypic changes based on the genotype, resulting in a broad-spectrum effect on the quantitative traits of hexaploid S. nigrum. Furthermore, we successfully improved the fruit productivity of Boranong, an orphan cultivar of S. nigrum suggesting that engineering homoeologous genes could be useful for agricultural improvement of polyploid crops.
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Affiliation(s)
- Eun Song Lee
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Jung Heo
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
| | - Woo Young Bang
- Biological and Genetic Resources Assessment DivisionNational Institute of Biological ResourcesIncheonKorea
| | | | - Nomar Espinosa Waminal
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
- BioScience Institute, Department of Chemistry & Life ScienceSahmyook UniversitySeoulKorea
| | - Nguyen Thi Hong
- BioScience Institute, Department of Chemistry & Life ScienceSahmyook UniversitySeoulKorea
| | - Min Ji Kim
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Hong Kwan Beak
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Yong Jun Kim
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Ryza A. Priatama
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Institute of Plasma TechnologyKorea Institute of Fusion EnergyGunsan‐siKorea
| | - Ji In Jang
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
| | - Kang Il Cha
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Seung Han Son
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | | | - Young‐Kug Choo
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Jong Hyang Bae
- Division of Horticulture IndustryWonkwang UniversityIksanKorea
| | - Chul Min Kim
- Division of Horticulture IndustryWonkwang UniversityIksanKorea
| | - Young Koung Lee
- Institute of Plasma TechnologyKorea Institute of Fusion EnergyGunsan‐siKorea
| | - Sangsu Bae
- Department of Biomedical SciencesSeoul National University College of MedicineSeoulSouth Korea
| | - Jonathan D. G. Jones
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Kee Hoon Sohn
- Department of Agricultural Biotechnology, Plant Immunity Research Center, Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource CenterKorea Research Institute of Bioscience and BiotechnologyJeongeupKorea
| | - Hyun Hee Kim
- BioScience Institute, Department of Chemistry & Life ScienceSahmyook UniversitySeoulKorea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
| | - Doreen Ware
- Cold Spring Harbor LaboratoryCold Spring HarborNYUSA
- U.S. Department of Agriculture‐Agricultural Research ServiceNEA Robert W. Holley Center for Agriculture and HealthIthacaNYUSA
| | - Keunhwa Kim
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
| | - Soon Ju Park
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
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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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12
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Aguirre L, Hendelman A, Hutton SF, McCandlish DM, Lippman ZB. Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science 2023; 382:315-320. [PMID: 37856609 PMCID: PMC10602613 DOI: 10.1126/science.adi5222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/06/2023] [Indexed: 10/21/2023]
Abstract
Epistasis between genes is traditionally studied with mutations that eliminate protein activity, but most natural genetic variation is in cis-regulatory DNA and influences gene expression and function quantitatively. In this study, we used natural and engineered cis-regulatory alleles in a plant stem-cell circuit to systematically evaluate epistatic relationships controlling tomato fruit size. Combining a promoter allelic series with two other loci, we collected over 30,000 phenotypic data points from 46 genotypes to quantify how allele strength transforms epistasis. We revealed a saturating dose-dependent relationship but also allele-specific idiosyncratic interactions, including between alleles driving a step change in fruit size during domestication. Our approach and findings expose an underexplored dimension of epistasis, in which cis-regulatory allelic diversity within gene regulatory networks elicits nonlinear, unpredictable interactions that shape phenotypes.
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Affiliation(s)
- Lyndsey Aguirre
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, NY, USA
| | - Anat Hendelman
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
| | - Samuel F. Hutton
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, USA
| | | | - Zachary B. Lippman
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, NY, USA
- Cold Spring Harbor Laboratory; Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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13
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Selby R, Jones DS. Complex peptide hormone signaling in plant stem cells. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102442. [PMID: 37672866 DOI: 10.1016/j.pbi.2023.102442] [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: 06/09/2023] [Revised: 07/26/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023]
Abstract
Peptide hormones influence diverse aspects of plant development through highly coordinated cell-cell signaling pathways. Many peptide hormone families play key roles in stem cell maintenance across land plants. In this review, we focus on recent work in two conserved peptide hormone families, CLAVATA3/EMBRYO-SURROUNDING REGION (CLEs) and ROOT MERISTEM GROWTH FACTOR (RGFs), and their roles in regulating plant stem cells. We discuss recent work establishing downstream crosstalk between peptide hormones and other conserved signaling mechanisms in meristem maintenance as well as highlight advances in peptide hormone gene identification that provide important context for CLE/RGF family evolution across diverse plant lineages. CLE and RGF gene families have greatly expanded in angiosperms, contributing to the complex genetic regulation of stem cell homeostasis observed in model systems over the last 30 years. Peptide hormone duplications have resulted in genetic compensation mechanisms that ensure robust development through the function of paralogous genes. Broad conservation of genetic compensation across angiosperms highlights the importance of these mechanisms in developmental signaling and understanding their regulation could inform broader understanding of morphological diversity and evolutionary innovation.
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Affiliation(s)
- Reid Selby
- Department of Biological Sciences, Auburn University, 36849, Auburn, AL, USA
| | - Daniel S Jones
- Department of Biological Sciences, Auburn University, 36849, Auburn, AL, USA.
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14
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Zu Q, Deng X, Qu Y, Chen X, Cai Y, Wang C, Li Y, Chen Q, Zheng K, Liu X, Chen Q. Genetic Channelization Mechanism of Four Chalcone Isomerase Homologous Genes for Synergistic Resistance to Fusarium wilt in Gossypium barbadense L. Int J Mol Sci 2023; 24:14775. [PMID: 37834230 PMCID: PMC10572676 DOI: 10.3390/ijms241914775] [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: 08/15/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Duplication events occur very frequently during plant evolution. The genes in the duplicated pathway or network can evolve new functions through neofunctionalization and subfunctionalization. Flavonoids are secondary metabolites involved in plant development and defense. Our previous transcriptomic analysis of F6 recombinant inbred lines (RILs) and the parent lines after Fusarium oxysporum f. sp. vasinfectum (Fov) infection showed that CHI genes have important functions in cotton. However, there are few reports on the possible neofunctionalization differences of CHI family paralogous genes involved in Fusarium wilt resistance in cotton. In this study, the resistance to Fusarium wilt, expression of metabolic pathway-related genes, metabolite content, endogenous hormone content, reactive oxygen species (ROS) content and subcellular localization of four paralogous CHI family genes in cotton were investigated. The results show that the four paralogous CHI family genes may play a synergistic role in Fusarium wilt resistance. These results revealed a genetic channelization mechanism that can regulate the metabolic flux homeostasis of flavonoids under the mediation of endogenous salicylic acid (SA) and methyl jasmonate (MeJA) via the four paralogous CHI genes, thereby achieving disease resistance. Our study provides a theoretical basis for studying the evolutionary patterns of homologous plant genes and using homologous genes for molecular breeding.
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Affiliation(s)
- Qianli Zu
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Xiaojuan Deng
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Xunji Chen
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), No. 403, Nanchang Road, Urumqi 830052, China;
| | - Yongsheng Cai
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Caoyue Wang
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Ying Li
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Qin Chen
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Xiaodong Liu
- College of Life Science, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China;
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
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15
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Bird KA, Pires JC, VanBuren R, Xiong Z, Edger PP. Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus. Genetics 2023; 225:iyad114. [PMID: 37338008 PMCID: PMC10471226 DOI: 10.1093/genetics/iyad114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/10/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023] Open
Abstract
The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions of networks, pathways, and protein complexes to maintain balanced stoichiometry of interacting proteins, because perturbations to stoichiometric balance can result in reduced fitness. This selection has been called dosage balance selection. Dosage balance selection is also hypothesized to constrain expression responses to dosage changes, making dosage-sensitive genes (those encoding members of interacting proteins) experience more similar expression changes. In allopolyploids, where whole-genome duplication involves hybridization of diverged lineages, organisms often experience homoeologous exchanges that recombine, duplicate, and delete homoeologous regions of the genome and alter the expression of homoeologous gene pairs. Although the gene balance hypothesis makes predictions about the expression response to homoeologous exchanges, they have not been empirically tested. We used genomic and transcriptomic data from 6 resynthesized, isogenic Brassica napus lines over 10 generations to identify homoeologous exchanges, analyzed expression responses, and tested for patterns of genomic imbalance. Groups of dosage-sensitive genes had less variable expression responses to homoeologous exchanges than dosage-insensitive genes, a sign that their relative dosage is constrained. This difference was absent for homoeologous pairs whose expression was biased toward the B. napus A subgenome. Finally, the expression response to homoeologous exchanges was more variable than the response to whole-genome duplication, suggesting homoeologous exchanges create genomic imbalance. These findings expand our knowledge of the impact of dosage balance selection on genome evolution and potentially connect patterns in polyploid genomes over time, from homoeolog expression bias to duplicate gene retention.
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Affiliation(s)
- Kevin A Bird
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Inner Mongolia University, Hohhot, Inner Mongolia 010070, China
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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16
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Zheng H, Huang W, Li X, Huang H, Yuan Q, Liu R, Di H, Liang S, Wang M, Li M, Huang Z, Tang Y, Zheng Y, Miao H, Ma J, Li H, Wang Q, Sun B, Zhang F. CRISPR/Cas9-mediated BoaAOP2s editing alters aliphatic glucosinolate side-chain metabolic flux and increases the glucoraphanin content in Chinese kale. Food Res Int 2023; 170:112995. [PMID: 37316021 DOI: 10.1016/j.foodres.2023.112995] [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: 01/16/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/16/2023]
Abstract
Glucoraphanin (GRA) is an aliphatic glucosinolate (GSL), and its hydrolysis product has powerful anticancer activity. ALKENYL HYDROXALKYL PRODUCING 2 (AOP2) gene, encodes a 2-oxoglutarate-dependent dioxygenase, which can catalyze GRA to form gluconapin (GNA). However, GRA only present in trace amounts in Chinese kale. To increase the content of GRA in Chinese kale, three copies of BoaAOP2 were isolated and edited using CRISPR/Cas9 system. The content of GRA was 11.71- to 41.29-fold (0.082-0.289 μmol g-1 FW) higher in T1 generation of boaaop2 mutants than in wild-type plants, and this was accompanied by an increase in the GRA/GNA ratio and reductions in the content of GNA and total aliphatic GSLs. BoaAOP2.1 is an effective gene for the alkenylation of aliphatic GSLs in Chinese kale. Overall, targeted editing of CRISPR/Cas9-mediated BoaAOP2s altered aliphatic GSL side-chain metabolic flux and enhanced the GRA content in Chinese kale, suggesting that metabolic engineering of BoaAOP2s has huge potential in improving nutritional quality of Chinese kale.
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Affiliation(s)
- Hao Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenli Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiangxiang Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanhuan Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiao Yuan
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Ruobin Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongmei Di
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Sha Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Mengyu Wang
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Huiying Miao
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Jie Ma
- Bijie Institute of Agricultural Science, Bijie 551700, China
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.
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17
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Wang Z, Cui Q, Su C, Zhao S, Wang R, Wang Z, Meng J, Luan Y. Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress. Int J Biol Macromol 2023:124952. [PMID: 37257526 DOI: 10.1016/j.ijbiomac.2023.124952] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
Non-coding RNAs (ncRNAs) are not conventionally involved in protein encoding. However, recent findings indicate that ncRNAs possess the capacity to code for proteins or peptides. These ncRNA-encoded peptides (ncPEPs) are vital for diverse plant life processes and exhibit significant potential value. Despite their importance, research on plant ncPEPs is limited, with only a few studies conducted and less information on the underlying mechanisms, and the field remains in its nascent stage. This manuscript provides a comprehensive overview of ncPEPs mining methods in plants, focusing on prediction, identification, and functional analysis. We discuss the strengths and weaknesses of various techniques, identify future research directions in the ncPEPs domain, and elucidate the biological functions and agricultural application prospects of plant ncPEPs. By highlighting the immense potential and research value of ncPEPs, we aim to lay a solid foundation for more in-depth studies in plant science.
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Affiliation(s)
- Zhengjie Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Qi Cui
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ruiming Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China.
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18
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Martignago D, da Silveira Falavigna V, Lombardi A, Gao H, Korwin Kurkowski P, Galbiati M, Tonelli C, Coupland G, Conti L. The bZIP transcription factor AREB3 mediates FT signalling and floral transition at the Arabidopsis shoot apical meristem. PLoS Genet 2023; 19:e1010766. [PMID: 37186640 PMCID: PMC10212096 DOI: 10.1371/journal.pgen.1010766] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/25/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
The floral transition occurs at the shoot apical meristem (SAM) in response to favourable external and internal signals. Among these signals, variations in daylength (photoperiod) act as robust seasonal cues to activate flowering. In Arabidopsis, long-day photoperiods stimulate production in the leaf vasculature of a systemic florigenic signal that is translocated to the SAM. According to the current model, FLOWERING LOCUS T (FT), the main Arabidopsis florigen, causes transcriptional reprogramming at the SAM, so that lateral primordia eventually acquire floral identity. FT functions as a transcriptional coregulator with the bZIP transcription factor FD, which binds DNA at specific promoters. FD can also interact with TERMINAL FLOWER 1 (TFL1), a protein related to FT that acts as a floral repressor. Thus, the balance between FT-TFL1 at the SAM influences the expression levels of floral genes targeted by FD. Here, we show that the FD-related bZIP transcription factor AREB3, which was previously studied in the context of phytohormone abscisic acid signalling, is expressed at the SAM in a spatio-temporal pattern that strongly overlaps with FD and contributes to FT signalling. Mutant analyses demonstrate that AREB3 relays FT signals redundantly with FD, and the presence of a conserved carboxy-terminal SAP motif is required for downstream signalling. AREB3 shows unique and common patterns of expression with FD, and AREB3 expression levels are negatively regulated by FD thus forming a compensatory feedback loop. Mutations in another bZIP, FDP, further aggravate the late flowering phenotypes of fd areb3 mutants. Therefore, multiple florigen-interacting bZIP transcription factors have redundant functions in flowering at the SAM.
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Affiliation(s)
- Damiano Martignago
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | | | | | - He Gao
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Massimo Galbiati
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Chiara Tonelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Lucio Conti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
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19
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Mylo MD, Speck O. Longevity of System Functions in Biology and Biomimetics: A Matter of Robustness and Resilience. Biomimetics (Basel) 2023; 8:biomimetics8020173. [PMID: 37092425 PMCID: PMC10123643 DOI: 10.3390/biomimetics8020173] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/04/2023] [Accepted: 04/19/2023] [Indexed: 04/25/2023] Open
Abstract
Within the framework of a circular economy, we aim to efficiently use raw materials and reduce waste generation. In this context, the longevity of biomimetic material systems can significantly contribute by providing robustness and resilience of system functionality inspired by biological models. The aim of this review is to outline various principles that can lead to an increase in robustness (e.g., safety factor, gradients, reactions to environmental changes) and resilience (e.g., redundancy, self-repair) and to illustrate the principles with meaningful examples. The study focuses on plant material systems with a high potential for transfer to biomimetic applications and on existing biomimetic material systems. Our fundamental concept is based on the functionality of the entire system as a function of time. We use functionality as a dimensionless measure of robustness and resilience to quantify the system function, allowing comparison within biological material systems and biomimetic material systems, but also between them. Together with the enclosed glossary of key terms, the review provides a comprehensive toolbox for interdisciplinary teams. Thus, allowing teams to communicate unambiguously and to draw inspiration from plant models when developing biomimetic material systems with great longevity potential.
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Affiliation(s)
- Max D Mylo
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany
- Plant Biomechanics Group @ Botanic Garden Freiburg, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Olga Speck
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Plant Biomechanics Group @ Botanic Garden Freiburg, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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20
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Nakayama H, Ichihashi Y, Kimura S. Diversity of tomato leaf form provides novel insights into breeding. BREEDING SCIENCE 2023; 73:76-85. [PMID: 37168814 PMCID: PMC10165341 DOI: 10.1270/jsbbs.22061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/29/2022] [Indexed: 05/13/2023]
Abstract
Tomato (Solanum lycopersicum L.) is cultivated widely globally. The crop exhibits tremendous morphological variations because of its long breeding history. Apart from the commercial tomato varieties, wild species and heirlooms are grown in certain regions of the world. Since the fruit constitutes the edible part, much of the agronomical research is focused on it. However, recent studies have indicated that leaf morphology influences fruit quality. As leaves are specialized photosynthetic organs and the vascular systems transport the photosynthetic products to sink organs, the architectural characteristics of the leaves have a strong influence on the final fruit quality. Therefore, comprehensive research focusing on both the fruit and leaf morphology is required for further tomato breeding. This review summarizes an overview of knowledge of the basic tomato leaf development, morphological diversification, and molecular mechanisms behind them and emphasizes its importance in breeding. Finally, we discuss how these findings and knowledge can be applied to future tomato breeding.
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Affiliation(s)
- Hokuto Nakayama
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Science Build. #2, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA 95616, U.S.A.
- Corresponding author (e-mail: )
| | | | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-Ku, Kyoto 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-Ku, Kyoto 603-8555, Japan
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21
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He J, Alonge M, Ramakrishnan S, Benoit M, Soyk S, Reem NT, Hendelman A, Van Eck J, Schatz MC, Lippman ZB. Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. THE PLANT CELL 2023; 35:351-368. [PMID: 36268892 PMCID: PMC9806562 DOI: 10.1093/plcell/koac305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative Physalis pruinosa and use these resources to study natural and engineered variations in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9-targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system and establish a paradigm in the search for factors driving ICS.
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Affiliation(s)
- Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | | | | | | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Preston JC. Buffering growth at the shoot tip. NATURE PLANTS 2022; 8:322-323. [PMID: 35332260 DOI: 10.1038/s41477-022-01128-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Jill C Preston
- Department of Plant Biology, University of Vermont, Burlington, VT, USA.
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