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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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Roy S, Griffiths M, Torres-Jerez I, Sanchez B, Antonelli E, Jain D, Krom N, Zhang S, York LM, Scheible WR, Udvardi M. Application of Synthetic Peptide CEP1 Increases Nutrient Uptake Rates Along Plant Roots. FRONTIERS IN PLANT SCIENCE 2022; 12:793145. [PMID: 35046980 PMCID: PMC8763272 DOI: 10.3389/fpls.2021.793145] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/03/2021] [Indexed: 05/26/2023]
Abstract
The root system of a plant provides vital functions including resource uptake, storage, and anchorage in soil. The uptake of macro-nutrients like nitrogen (N), phosphorus (P), potassium (K), and sulphur (S) from the soil is critical for plant growth and development. Small signaling peptide (SSP) hormones are best known as potent regulators of plant growth and development with a few also known to have specialized roles in macronutrient utilization. Here we describe a high throughput phenotyping platform for testing SSP effects on root uptake of multiple nutrients. The SSP, CEP1 (C-TERMINALLY ENCODED PEPTIDE) enhanced nitrate uptake rate per unit root length in Medicago truncatula plants deprived of N in the high-affinity transport range. Single structural variants of M. truncatula and Arabidopsis thaliana specific CEP1 peptides, MtCEP1D1:hyp4,11 and AtCEP1:hyp4,11, enhanced uptake not only of nitrate, but also phosphate and sulfate in both model plant species. Transcriptome analysis of Medicago roots treated with different MtCEP1 encoded peptide domains revealed that hundreds of genes respond to these peptides, including several nitrate transporters and a sulfate transporter that may mediate the uptake of these macronutrients downstream of CEP1 signaling. Likewise, several putative signaling pathway genes including LEUCINE-RICH REPEAT RECPTOR-LIKE KINASES and Myb domain containing transcription factors, were induced in roots by CEP1 treatment. Thus, a scalable method has been developed for screening synthetic peptides of potential use in agriculture, with CEP1 shown to be one such peptide.
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Affiliation(s)
- Sonali Roy
- Noble Research Institute LLC, Ardmore, OK, United States
- College of Agriculture, Tennessee State University, Nashville, TN, United States
| | | | | | - Bailey Sanchez
- Noble Research Institute LLC, Ardmore, OK, United States
| | | | - Divya Jain
- College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Nicholas Krom
- Noble Research Institute LLC, Ardmore, OK, United States
| | - Shulan Zhang
- Noble Research Institute LLC, Ardmore, OK, United States
| | - Larry M. York
- Noble Research Institute LLC, Ardmore, OK, United States
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Lin H, Wang W, Chen X, Sun Z, Han X, Wang S, Li Y, Ye W, Yin Z. Molecular Traits and Functional Analysis of the CLAVATA3/Endosperm Surrounding Region-Related Small Signaling Peptides in Three Species of Gossypium Genus. FRONTIERS IN PLANT SCIENCE 2021; 12:671626. [PMID: 34149772 PMCID: PMC8213210 DOI: 10.3389/fpls.2021.671626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
The CLAVATA3/endosperm surrounding region-related (CLE) small peptides are a group of C-terminally encoded and post-translationally modified signal molecules involved in regulating the growth and development of various plants. However, the function and evolution of these peptides have so far remained elusive in cotton. In this study, 55, 56, and 86 CLE genes were identified in the Gossypium raimondii, Gossypium arboreum, and Gossypium hirsutum genomes, respectively, and all members were divided into seven groups. These groups were distinctly different in their protein characteristics, gene structures, conserved motifs, and multiple sequence alignment. Whole genome or segmental duplications played a significant role in the expansion of the CLE family in cotton, and experienced purifying selection during the long evolutionary process in cotton. Cis-acting regulatory elements and transcript profiling revealed that the CLE genes of cotton exist in different tissues, developmental stages, and respond to abiotic stresses. Protein properties, structure prediction, protein interaction network prediction of GhCLE2, GhCLE33.2, and GhCLE28.1 peptides were, respectively, analyzed. In addition, the overexpression of GhCLE2, GhCLE33.2, or GhCLE28.1 in Arabidopsis, respectively, resulted in a distinctive shrub-like dwarf plant, slightly purple leaves, large rosettes with large malformed leaves, and lack of reproductive growth. This study provides important insights into the evolution of cotton CLEs and delineates the functional conservatism and divergence of CLE genes in the growth and development of cotton.
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Affiliation(s)
- Huan Lin
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Xiugui Chen
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhenting Sun
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiulan Han
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Shuai Wang
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yan Li
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wuwei Ye
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zujun Yin
- Research Base, Zhengzhou University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
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Moreau C, Gautrat P, Frugier F. Nitrate-induced CLE35 signaling peptides inhibit nodulation through the SUNN receptor and miR2111 repression. PLANT PHYSIOLOGY 2021; 185:1216-1228. [PMID: 33793938 PMCID: PMC8133669 DOI: 10.1093/plphys/kiaa094] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/09/2020] [Indexed: 05/26/2023]
Abstract
Legume plants form nitrogen (N)-fixing symbiotic nodules when mineral N is limiting in soils. As N fixation is energetically costly compared to mineral N acquisition, these N sources, and in particular nitrate, inhibit nodule formation and N fixation. Here, in the model legume Medicago truncatula, we characterized a CLAVATA3-like (CLE) signaling peptide, MtCLE35, the expression of which is upregulated locally by high-N environments and relies on the Nodule Inception-Like Protein (NLP) MtNLP1. MtCLE35 inhibits nodule formation by affecting rhizobial infections, depending on the Super Numeric Nodules (MtSUNN) receptor. In addition, high N or the ectopic expression of MtCLE35 represses the expression and accumulation of the miR2111 shoot-to-root systemic effector, thus inhibiting its positive effect on nodulation. Conversely, ectopic expression of miR2111 or downregulation of MtCLE35 by RNA interference increased miR2111 accumulation independently of the N environment, and thus partially bypasses the nodulation inhibitory action of nitrate. Overall, these results demonstrate that the MtNLP1-dependent, N-induced MtCLE35 signaling peptide acts through the MtSUNN receptor and the miR2111 systemic effector to inhibit nodulation.
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Affiliation(s)
- Corentin Moreau
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. d’Evry, University of Paris, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Gautrat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. d’Evry, University of Paris, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. d’Evry, University of Paris, University of Paris-Saclay, Gif-sur-Yvette, France
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Zhang Z, Liu L, Kucukoglu M, Tian D, Larkin RM, Shi X, Zheng B. Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences. BMC Genomics 2020; 21:709. [PMID: 33045986 PMCID: PMC7552357 DOI: 10.1186/s12864-020-07114-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 09/29/2020] [Indexed: 11/21/2022] Open
Abstract
Background The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity. Results We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor. Conclusions Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Liu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Melis Kucukoglu
- Institute of Biotechnology, Helsinki Institute of Life Science (HILIFE), University of Helsinki, 00014, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, 00014, Helsinki, Finland
| | - Dongdong Tian
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueping Shi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China. .,College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
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Yoro E, Nishida H, Ogawa-Ohnishi M, Yoshida C, Suzaki T, Matsubayashi Y, Kawaguchi M. PLENTY, a hydroxyproline O-arabinosyltransferase, negatively regulates root nodule symbiosis in Lotus japonicus. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:507-517. [PMID: 30351431 PMCID: PMC6322572 DOI: 10.1093/jxb/ery364] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 10/12/2018] [Indexed: 05/21/2023]
Abstract
Legumes can survive in nitrogen-deficient environments by forming root-nodule symbioses with rhizobial bacteria; however, forming nodules consumes energy, and nodule numbers must thus be strictly controlled. Previous studies identified major negative regulators of nodulation in Lotus japonicus, including the small peptides CLAVATA3/ESR (CLE)-RELATED-ROOT SIGNAL1 (CLE-RS1), CLE-RS2, and CLE-RS3, and their putative major receptor HYPERNODULATION AND ABERRANT ROOT FORMATION1 (HAR1). CLE-RS2 is known to be expressed in rhizobia-inoculated roots, and is predicted to be post-translationally arabinosylated, a modification essential for its activity. Moreover, all three CLE-RSs suppress nodulation in a HAR1-dependent manner. Here, we identified PLENTY as a gene responsible for the previously isolated hypernodulation mutant plenty. PLENTY encoded a hydroxyproline O-arabinosyltransferase orthologous to ROOT DETERMINED NODULATION1 in Medicago truncatula. PLENTY was localized to the Golgi, and an in vitro analysis of the recombinant protein demonstrated its arabinosylation activity, indicating that CLE-RS1/2/3 may be substrates for PLENTY. The constitutive expression experiments showed that CLE-RS3 was the major candidate substrate for PLENTY, suggesting the substrate preference of PLENTY for individual CLE-RS peptides. Furthermore, a genetic analysis of the plenty har1 double mutant indicated the existence of another PLENTY-dependent and HAR1-independent pathway negatively regulating nodulation.
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Affiliation(s)
- Emiko Yoro
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
| | - Hanna Nishida
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Mari Ogawa-Ohnishi
- Division of Biological Science, Graduate School of Science, Nagoya University Chikusa, Nagoya, Japan
| | - Chie Yoshida
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takuya Suzaki
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshikatsu Matsubayashi
- Division of Biological Science, Graduate School of Science, Nagoya University Chikusa, Nagoya, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
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