1
|
Jaiswal M, Kumar S. smAMPsTK: a toolkit to unravel the smORFome encoding AMPs of plant species. J Biomol Struct Dyn 2024; 42:6600-6612. [PMID: 37464885 DOI: 10.1080/07391102.2023.2235605] [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: 04/07/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
The pervasive repertoire of plant molecules with the potential to serve as a substitute for conventional antibiotics has led to obtaining better insights into plant-derived antimicrobial peptides (AMPs). The massive distribution of Small Open Reading Frames (smORFs) throughout eukaryotic genomes with proven extensive biological functions reflects their practicality as antimicrobials. Here, we have developed a pipeline named smAMPsTK to unveil the underlying hidden smORFs encoding AMPs for plant species. By applying this pipeline, we have elicited AMPs of various functional activity of lengths ranging from 5 to 100 aa by employing publicly available transcriptome data of five different angiosperms. Later, we studied the coding potential of AMPs-smORFs, the inclusion of diverse translation initiation start codons, and amino acid frequency. Codon usage study signifies no such codon usage biases for smORFs encoding AMPs. Majorly three start codons are prominent in generating AMPs. The evolutionary and conservational study proclaimed the widespread distribution of AMPs encoding genes throughout the plant kingdom. Domain analysis revealed that nearly all AMPs have chitin-binding ability, establishing their role as antifungal agents. The current study includes a developed methodology to characterize smORFs encoding AMPs, and their implications as antimicrobial, antibacterial, antifungal, or antiviral provided by SVM score and prediction status calculated by machine learning-based prediction models. The pipeline, complete package, and the results derived for five angiosperms are freely available at https://github.com/skbinfo/smAMPsTK.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mohini Jaiswal
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| |
Collapse
|
2
|
Zhiling L, Wenhua D, Fangyuan Z. Genome-wide identification and phylogenetic and expression pattern analyses of EPF/EPFL family genes in the Rye (Secale cereale L.). BMC Genomics 2024; 25:532. [PMID: 38816796 PMCID: PMC11137924 DOI: 10.1186/s12864-024-10425-9] [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: 01/25/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024] Open
Abstract
Rye (Secale cereale L.) is one of the major cereal crop species in the Triticeae family and is known to be most tolerant to diverse abiotic stresses, such as cold, heat, osmotic, and salt stress. The EPIDERMAL PATTERNING FACTOR (EPF) and EPF-LIKE (EPFL) families of small secreted peptides act to regulate many aspects of plant growth and development; however, their functions are not widely characterized in rye. In this study, we identified 12 ScEPF/EPFL genes, which can be divided into six groups and are evenly distributed on six rye chromosomes. Further examination of the gene structure and protein conservation motifs of EPF/EPFL family members demonstrated the high conservation of the ScEPF/EPFL sequence. Interactions between ScEPF/EPFL proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of ScEPF/EPFL expression is complex. Expression profiling analyses revealed that ScEPF/EPFL genes exhibited tissue-specific expression patterns. Notably, ScEPFL1,ScEPFL7, ScEPFL9, and ScEPFL10 displayed significantly higher expression levels in spikelets compared to other tissues. Moreover, fluorescence quantification experiments demonstrated that these genes exhibited distinct expression patterns in response to various stress conditions, suggesting that each gene plays a unique role in stress signaling pathways. Our research findings provide a solid basis for further investigation into the functions of ScEPF/EPFLs. Furthermore, these genes can serve as potential candidates for breeding stress-resistant rye varieties and improving production yields.
Collapse
Affiliation(s)
- Lin Zhiling
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Centers for Grazing Land Ecosystem Sustainability, Gansu Agricultural University, Lanzhou, China
| | - Du Wenhua
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Centers for Grazing Land Ecosystem Sustainability, Gansu Agricultural University, Lanzhou, China.
| | - Zhao Fangyuan
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Centers for Grazing Land Ecosystem Sustainability, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
3
|
Erokhina TN, Ryazantsev DY, Zavriev SK, Morozov SY. Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long "Non-Coding" RNAs. PLANTS (BASEL, SWITZERLAND) 2024; 13:1137. [PMID: 38674546 PMCID: PMC11055055 DOI: 10.3390/plants13081137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. Requirement for the additional studies in these directions is highlighted by alternative findings concerning positive regulation of pri-miRNA/miRNA expression by synthetic miPEPs in plants. Further extensive studies are also needed to understand the full set of their roles in eukaryotic organisms. This review mainly aims to consider the available data on the regulatory functions of the synthetic miPEPs. Studies of chemically synthesized miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed. Brief description of the studies to identify lncORFs (open reading frames of long non-coding RNAs) and the encoded protein products is also provided.
Collapse
Affiliation(s)
- T. N. Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - D. Y. Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. K. Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. Y. Morozov
- Biological Faculty, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Yadav A, Mathan J, Dubey AK, Singh A. The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling. Noncoding RNA 2024; 10:13. [PMID: 38392968 PMCID: PMC10893181 DOI: 10.3390/ncrna10010013] [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: 12/11/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.
Collapse
Affiliation(s)
- Amit Yadav
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Jyotirmaya Mathan
- Sashi Bhusan Rath Government Autonomous Women’s College, Brahmapur 760001, India;
| | - Arvind Kumar Dubey
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Anuradha Singh
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
6
|
Xie S, Luo G, An G, Wang B, Kuang H, Wang X. Lskipk Lsatpase double mutants are necessary and sufficient for the compact plant architecture of butterhead lettuce. HORTICULTURE RESEARCH 2024; 11:uhad280. [PMID: 38371637 PMCID: PMC10873588 DOI: 10.1093/hr/uhad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/11/2023] [Indexed: 02/20/2024]
Abstract
Lettuce, an important leafy vegetable crop worldwide, has rich variations in plant architecture. Butterhead lettuce, a popular horticultural type, has a unique plant architecture with loose leafy heads. The genetic and molecular mechanisms for such a compact plant architecture remain unclear. In this study we constructed a segregating population through crossing a butterhead cultivar and a stem lettuce cultivar. Genetic analysis identified the LsKIPK gene, which encodes a kinase, as the candidate gene controlling butterhead plant architecture. The Lskipk gene in the butterhead parent had a nonsense mutation, leading to a partial predicted protein. CRISPR/Cas9 and complementation tests verified its functions in plant architecture. We showed that the loss of function of LsKIPK is necessary but not sufficient for the butterhead plant architecture. To identify additional genes required for butterhead lettuce, we crossed a butterhead cultivar and a crisphead cultivar, both with the mutated Lskipk gene. Genetic mapping identified a new gene encoding an ATPase contributing to butterhead plant architecture. Knockout and complementation tests showed that loss of function of LsATPase is also required for the development of butterhead plant architecture. The Lskipk Lsatpase double mutation could reduce leaf size and leaf angle, leading to butterhead plant architecture. Expression and cytology analysis indicated that the loss of function of LsKIPK and LsATPase contributed to butterhead plant architecture by regulating cell wall development, a regulatory mechanism different from that for crisphead. This study provides new gene resources and theory for the breeding of the crop ideotype.
Collapse
Affiliation(s)
- Sai Xie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Guangbao Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Guanghui An
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
- College of Horticulture, Henan Agricultural University, 450002 Zhengzhou, China
| | - Bincai Wang
- North Park, Wuhan Academy of Agricultural Sciences, Wuhu Eco-park, Huangpi District, Wuhan, China
| | - Hanhui Kuang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| |
Collapse
|
7
|
Li W, Ye T, Ye W, Liang J, Wang W, Han D, Liu X, Huang L, Ouyang Y, Liao J, Chen T, Yang C, Lai J. S-acylation of a non-secreted peptide controls plant immunity via secreted-peptide signal activation. EMBO Rep 2024; 25:489-505. [PMID: 38177916 PMCID: PMC10897394 DOI: 10.1038/s44319-023-00029-x] [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: 06/12/2023] [Revised: 11/25/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Small peptides modulate multiple processes in plant cells, but their regulation by post-translational modification remains unclear. ROT4 (ROTUNDIFOLIA4) belongs to a family of Arabidopsis non-secreted small peptides, but knowledge on its molecular function and how it is regulated is limited. Here, we find that ROT4 is S-acylated in plant cells. S-acylation is an important form of protein lipidation, yet so far it has not been reported to regulate small peptides in plants. We show that this modification is essential for the plasma membrane association of ROT4. Overexpression of S-acylated ROT4 results in a dramatic increase in immune gene expression. S-acylation of ROT4 enhances its interaction with BSK5 (BRASSINOSTEROID-SIGNALING KINASE 5) to block the association between BSK5 and PEPR1 (PEP RECEPTOR1), a receptor kinase for secreted plant elicitor peptides (PEPs), thereby activating immune signaling. Phenotype analysis indicates that S-acylation is necessary for ROT4 functions in pathogen resistance, PEP response, and the regulation of development. Collectively, our work reveals an important role for S-acylation in the cross-talk of non-secreted and secreted peptide signaling in plant immunity.
Collapse
Affiliation(s)
- Wenliang Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Tushu Ye
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Weixian Ye
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Jieyi Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Wen Wang
- Key Laboratory of Laser Life Science, MOE Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Xiaoshi Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Liting Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Youwei Ouyang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Jianwei Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Tongsheng Chen
- Key Laboratory of Laser Life Science, MOE Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
| |
Collapse
|
8
|
Sahgal A, Uversky V, Davé V. Microproteins transitioning into a new Phase: Defining the undefined. Methods 2023; 220:38-54. [PMID: 37890707 DOI: 10.1016/j.ymeth.2023.10.009] [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: 09/01/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Recent advancements in omics technologies have unveiled a hitherto unknown group of short polypeptides called microproteins (miPs). Despite their size, accumulating evidence has demonstrated that miPs exert varied and potent biological functions. They act in paracrine, juxtracrine, and endocrine fashion, maintaining cellular physiology and driving diseases. The present study focuses on biochemical and biophysical analysis and characterization of twenty-four human miPs using distinct computational methods, including RIDAO, AlphaFold2, D2P2, FuzDrop, STRING, and Emboss Pep wheel. miPs often lack well-defined tertiary structures and may harbor intrinsically disordered regions (IDRs) that play pivotal roles in cellular functions. Our analyses define the physicochemical properties of an essential subset of miPs, elucidating their structural characteristics and demonstrating their propensity for driving or participating in liquid-liquid phase separation (LLPS) and intracellular condensate formation. Notably, miPs such as NoBody and pTUNAR revealed a high propensity for LLPS, implicating their potential involvement in forming membrane-less organelles (MLOs) during intracellular LLPS and condensate formation. The results of our study indicate that miPs have functionally profound implications in cellular compartmentalization and signaling processes essential for regulating normal cellular functions. Taken together, our methodological approach explains and highlights the biological importance of these miPs, providing a deeper understanding of the unusual structural landscape and functionality of these newly defined small proteins. Understanding their functions and biological behavior will aid in developing targeted therapies for diseases that involve miPs.
Collapse
Affiliation(s)
- Aayushi Sahgal
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Vrushank Davé
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Biotechnology Graduate Program, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Pathology and Cell Biology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States; Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States.
| |
Collapse
|
9
|
Fan KT, Hsu CW, Chen YR. Mass spectrometry in the discovery of peptides involved in intercellular communication: From targeted to untargeted peptidomics approaches. MASS SPECTROMETRY REVIEWS 2023; 42:2404-2425. [PMID: 35765846 DOI: 10.1002/mas.21789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Endogenous peptide hormones represent an essential class of biomolecules, which regulate cell-cell communications in diverse physiological processes of organisms. Mass spectrometry (MS) has been developed to be a powerful technology for identifying and quantifying peptides in a highly efficient manner. However, it is difficult to directly identify these peptide hormones due to their diverse characteristics, dynamic regulations, low abundance, and existence in a complicated biological matrix. Here, we summarize and discuss the roles of targeted and untargeted MS in discovering peptide hormones using bioassay-guided purification, bioinformatics screening, or the peptidomics-based approach. Although the peptidomics approach is expected to discover novel peptide hormones unbiasedly, only a limited number of successful cases have been reported. The critical challenges and corresponding measures for peptidomics from the steps of sample preparation, peptide extraction, and separation to the MS data acquisition and analysis are also discussed. We also identify emerging technologies and methods that can be integrated into the discovery platform toward the comprehensive study of endogenous peptide hormones.
Collapse
Affiliation(s)
- Kai-Ting Fan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Wei Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
10
|
Huang S, Ma Y, Xu Y, Lu P, Yang J, Xie Y, Gan J, Li L. Shade-induced RTFL/DVL peptides negatively regulate the shade response by directly interacting with BSKs in Arabidopsis. Nat Commun 2023; 14:6898. [PMID: 37898648 PMCID: PMC10613268 DOI: 10.1038/s41467-023-42618-3] [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: 01/24/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023] Open
Abstract
For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. Here, we report that non-secreted ROT FOUR LIKE (RTFL)/DEVIL (DVL) peptides negatively regulate SAS by interacting with BRASSINOSTEROID SIGNALING KINASEs (BSKs) and reducing the protein level of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) in Arabidopsis. The transcription of at least five RTFLs (RTFL13/16/17/18/21) is induced by low R:FR light. The RTFL18 (DVL1) protein is stabilized under low R:FR conditions and localized to the plasma membrane. A phenotype analysis reveals that RTFL18 negatively regulates low R:FR-promoted petiole elongation. BSK3 and BSK6 are identified as partners of RTFL18 through binding assays and structural modeling. The overexpression of RTFL18 or knockdown of BSK3/6 reduces BRASSINOSTEROID signaling and reduces low R:FR-stabilized PIF4 levels. Genetically, the overexpression of BSK3/6 and PIF4 restores the petiole phenotype acquired by RTFL18-overexpressing lines. Collectively, our work characterizes a signaling cascade (the RTFLs-BSK3/6-PIF4 pathway) that prevents the excessive activation of the shade avoidance response in Arabidopsis.
Collapse
Affiliation(s)
- Sha Huang
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu Ma
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yitian Xu
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Pengfei Lu
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu Xie
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lin Li
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| |
Collapse
|
11
|
Feng YZ, Zhu QF, Xue J, Chen P, Yu Y. Shining in the dark: the big world of small peptides in plants. ABIOTECH 2023; 4:238-256. [PMID: 37970469 PMCID: PMC10638237 DOI: 10.1007/s42994-023-00100-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/24/2023] [Indexed: 11/17/2023]
Abstract
Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding. We review the biological functions and molecular mechanisms of small peptides in plants, discuss current problems in small peptide research and highlight future research directions in this field. Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.
Collapse
Affiliation(s)
- Yan-Zhao Feng
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Qing-Feng Zhu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jiao Xue
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Pei Chen
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yang Yu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Hirayama T, Mochida K. Plant Hormonomics: A Key Tool for Deep Physiological Phenotyping to Improve Crop Productivity. PLANT & CELL PHYSIOLOGY 2023; 63:1826-1839. [PMID: 35583356 PMCID: PMC9885943 DOI: 10.1093/pcp/pcac067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/07/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Agriculture is particularly vulnerable to climate change. To cope with the risks posed by climate-related stressors to agricultural production, global population growth, and changes in food preferences, it is imperative to develop new climate-smart crop varieties with increased yield and environmental resilience. Molecular genetics and genomic analyses have revealed that allelic variations in genes involved in phytohormone-mediated growth regulation have greatly improved productivity in major crops. Plant science has remarkably advanced our understanding of the molecular basis of various phytohormone-mediated events in plant life. These findings provide essential information for improving the productivity of crops growing in changing climates. In this review, we highlight the recent advances in plant hormonomics (multiple phytohormone profiling) and discuss its application to crop improvement. We present plant hormonomics as a key tool for deep physiological phenotyping, focusing on representative plant growth regulators associated with the improvement of crop productivity. Specifically, we review advanced methodologies in plant hormonomics, highlighting mass spectrometry- and nanosensor-based plant hormone profiling techniques. We also discuss the applications of plant hormonomics in crop improvement through breeding and agricultural management practices.
Collapse
Affiliation(s)
- Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046 Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumiku, Yokohama, Kanagawa, 230-0045 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maiokacho, Totsukaku, Yokohama, Kanagawa, 244-0813 Japan
- School of Information and Data Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521 Japan
- RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehirocho, Tsurumiku, Yokohama, Kanagawa 230-0045 Japan
| |
Collapse
|
14
|
Chen Z, Meng J, Zhao S, Yin C, Luan Y. sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs. Interdiscip Sci 2023; 15:189-201. [PMID: 36705893 DOI: 10.1007/s12539-023-00552-4] [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: 07/22/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/28/2023]
Abstract
Long non-coding RNAs (lncRNAs) are important regulators of biological processes. It has recently been shown that some lncRNAs include small open reading frames (sORFs) that can encode small peptides of no more than 100 amino acids. However, existing methods are commonly applied to human and animal datasets and still suffer from low feature representation capability. Thus, accurate and credible prediction of sORFs with coding ability in plant lncRNAs is imperative. This paper proposes a new method termed sORFPred, in which we design a model named MCSEN by combining multi-scale convolution and Squeeze-and-Excitation Networks to fully mine distinct information embedded in sORFs, integrate and optimize multiple sequence-based and physicochemical feature descriptors, and built a two-layer prediction classifier based on Bayesian optimization algorithm and Extra Trees. sORFPred has been evaluated on sORFs datasets of three species and experimentally validated sORFs dataset. Results indicate that sORFPred outperforms existing methods and achieves 97.28% accuracy, 97.06% precision, 97.52% recall, and 97.29% F1-score on Arabidopsis thaliana, which shows a significant improvement in prediction performance compared to various conventional shallow machine learning and deep learning models.
Collapse
Affiliation(s)
- Ziwei Chen
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China. .,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China.
| | - Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Chao Yin
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Yushi Luan
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.,School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
| |
Collapse
|
15
|
Sruthi KB, Menon A, P A, Vasudevan Soniya E. Pervasive translation of small open reading frames in plant long non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2022; 13:975938. [PMID: 36352887 PMCID: PMC9638090 DOI: 10.3389/fpls.2022.975938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) are primarily recognized as non-coding transcripts longer than 200 nucleotides with low coding potential and are present in both eukaryotes and prokaryotes. Recent findings reveal that lncRNAs can code for micropeptides in various species. Micropeptides are generated from small open reading frames (smORFs) and have been discovered frequently in short mRNAs and non-coding RNAs, such as lncRNAs, circular RNAs, and pri-miRNAs. The most accepted definition of a smORF is an ORF containing fewer than 100 codons, and ribosome profiling and mass spectrometry are the most prevalent experimental techniques used to identify them. Although the majority of micropeptides perform critical roles throughout plant developmental processes and stress conditions, only a handful of their functions have been verified to date. Even though more research is being directed toward identifying micropeptides, there is still a dearth of information regarding these peptides in plants. This review outlines the lncRNA-encoded peptides, the evolutionary roles of such peptides in plants, and the techniques used to identify them. It also describes the functions of the pri-miRNA and circRNA-encoded peptides that have been identified in plants.
Collapse
|
16
|
Zhao S, Meng J, Kang Q, Luan Y. Identifying LncRNA-Encoded Short Peptides Using Optimized Hybrid Features and Ensemble Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2873-2881. [PMID: 34383651 DOI: 10.1109/tcbb.2021.3104288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Long non-coding RNA (lncRNA) contains short open reading frames (sORFs), and sORFs-encoded short peptides (SEPs) have become the focus of scientific studies due to their crucial role in life activities. The identification of SEPs is vital to further understanding their regulatory function. Bioinformatics methods can quickly identify SEPs to provide credible candidate sequences for verifying SEPs by biological experimenrts. However, there is a lack of methods for identifying SEPs directly. In this study, a machine learning method to identify SEPs of plant lncRNA (ISPL) is proposed. Hybrid features including sequence features and physicochemical features are extracted manually or adaptively to construct different modal features. In order to keep the stability of feature selection, the non-linear correction applied in Max-Relevance-Max-Distance (nocRD) feature selection method is proposed, which integrates multiple feature ranking results and uses the iterative random forest for different modal features dimensionality reduction. Classification models with different modal features are constructed, and their outputs are combined for ensemble classification. The experimental results show that the accuracy of ISPL is 89.86% percent on the independent test set, which will have important implications for further studies of functional genomic.
Collapse
|
17
|
Xiong L, Huang Y, Liu Z, Li C, Yu H, Shahid MQ, Lin Y, Qiao X, Xiao J, Gray JE, Jin J. Small EPIDERMAL PATTERNING FACTOR-LIKE2 peptides regulate awn development in rice. PLANT PHYSIOLOGY 2022; 190:516-531. [PMID: 35689635 PMCID: PMC9434303 DOI: 10.1093/plphys/kiac278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/16/2022] [Indexed: 05/06/2023]
Abstract
The EPIDERMAL PATTERNING FACTOR (EPF) and EPF-LIKE (EPFL) family of small secreted peptides act to regulate many aspects of plant growth and development; however, their functions are not widely characterized in rice (Oryza sativa). Here, we used clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) technology to individually knockout each of 11 EPF/EPFL genes in the rice cultivar Kasalath. Loss of function of most OsEPF/EPFL genes generated no obvious phenotype alteration, while disruption of OsEPFL2 in Kasalath caused a short or no awn phenotype and reduced grain size. OsEPFL2 is strongly expressed in the young panicle, consistent with a role in regulating awn and grain development. Haplotype analysis indicated that OsEPFL2 can be classified into six major haplotypes. Nucleotide diversity and genetic differentiation analyses suggested that OsEPFL2 was positively selected during the domestication of rice. Our work to systematically investigate the function of EPF/EPFL peptides demonstrates that different members of the same gene family have been independently selected for their ability to regulate a similar biological function and provides perspective on rice domestication.
Collapse
Affiliation(s)
| | | | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Muhammad Qasim Shahid
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yanhui Lin
- Institute of Food Crops, Hainan Academy of Agricultural Sciences, Hainan Key Laboratory of Crop Genetics and Breeding, Hainan Scientific Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture, Haikou 571100, China
| | - Xiaoyi Qiao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Junyi Xiao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Julie E Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | | |
Collapse
|
18
|
Zhao J, Shi X, Chen L, Chen Q, Tian X, Ai L, Zhao H, Yang C, Yan L, Zhang M. Genetic and transcriptome analyses reveal the candidate genes and pathways involved in the inactive shade-avoidance response enabling high-density planting of soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:973643. [PMID: 35991396 PMCID: PMC9382032 DOI: 10.3389/fpls.2022.973643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
High-density planting is a major way to improve crop yields. However, shade-avoidance syndrome (SAS) is a major factor limiting increased planting density. First Green Revolution addressed grass lodging problem by using dwarf/semi-dwarf genes. However, it is not suitable for soybean, which bear seeds on stalk and whose seed yield depends on plant height. Hence, mining shade-tolerant germplasms and elucidating the underlying mechanism could provide meaningful resources and information for high-yield breeding. Here, we report a high-plant density-tolerant soybean cultivar, JiDou 17, which exhibited an inactive SAS (iSAS) phenotype under high-plant density or low-light conditions at the seedling stage. A quantitative trait locus (QTL) mapping analysis using a recombinant inbred line (RIL) population showed that this iSAS phenotype is related to a major QTL, named shade-avoidance response 1 (qSAR1), which was detected. The mapping region was narrowed by a haplotype analysis into a 554 kb interval harboring 44 genes, including 4 known to be key regulators of the SAS network and 4 with a variance response to low-light conditions between near isogenic line (NIL) stems. Via RNA-seq, we identified iSAS-specific genes based on one pair of near isogenic lines (NILs) and their parents. The iSAS-specific genes expressed in the stems were significantly enriched in the "proteasomal protein catabolic" process and the proteasome pathway, which were recently suggested to promote the shade-avoidance response by enhancing PIF7 stability. Most iSAS-specific proteasome-related genes were downregulated under low-light conditions. The expression of genes related to ABA, CK, and GA significantly varied between the low- and normal-light conditions. This finding is meaningful for the cloning of genes that harbor beneficial variation(s) conferring the iSAS phenotype fixed in domestication and breeding practice.
Collapse
Affiliation(s)
- Jing Zhao
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- School of Life Sciences, Yantai University, Yantai, China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Lei Chen
- School of Life Sciences, Yantai University, Yantai, China
| | - Qiang Chen
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xuan Tian
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Lijuan Ai
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Hongtao Zhao
- Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Long Yan
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| |
Collapse
|
19
|
Zeng Y, Tang Y, Shen S, Zhang M, Chen L, Ye D, Zhang X. Plant-specific small peptide AtZSP1 interacts with ROCK1 to regulate organ size in Arabidopsis. THE NEW PHYTOLOGIST 2022; 234:1696-1713. [PMID: 35285523 DOI: 10.1111/nph.18093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Organ size is an important agronomic trait. Small peptides function in various stages of plant growth, but their regulatory mechanisms in organ growth remain poorly understood. Here, we characterize a novel small peptide, AtZSP1, which positively regulates organ size in Arabidopsis. Loss-of-function mutant atzsp1-1 exhibited small organs, whereas AtZSP1 overexpression plants (p35S:AtZSP1#1) produced larger organs. Differentially expressed genes in the shoots of atzsp1-1 and p35S:AtZSP1#1 were enriched in the cytokinin pathway. Further analysis on shoots of atzsp1-1 showed that endogenous cytokinin levels were significantly reduced, consistent with reduced expression of the cytokinin response genes ARR5/6/7 and a decrease in pARR5:GUS activity. By contrast, cytokinin levels were elevated in p35S:AtZSP1#1. These results indicate that AtZSP1 affects shoot size via changes in cytokinin levels. AtZSP1 is ubiquitously expressed and encodes a 57-amino acid endomembrane-associated protein that is highly conserved among plant species. AtZSP1 interacts with ROCK1 at the endomembrane. Genetic analysis confirmed that the small organs and low cytokinin levels in atzsp1-1 shoots are partially suppressed by the rock1-4 mutation, suggesting that AtZSP1 may function in a common pathway with ROCK1 to antagonistically regulate organ growth. Our study identified an unknown small peptide, AtZSP1, and defined its function in regulating organ size in Arabidopsis.
Collapse
Affiliation(s)
- Yuejuan Zeng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Tang
- University of California, Berkeley, 371 Koshland Hall, Berkeley, CA, 94720, USA
| | - Simin Shen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Man Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Liqun Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - De Ye
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueqin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
20
|
Pei MS, Liu HN, Wei TL, Yu YH, Guo DL. Large-scale discovery of non-conventional peptides in grape ( Vitis vinifera L.) through peptidogenomics. HORTICULTURE RESEARCH 2022; 9:uhac023. [PMID: 35531313 PMCID: PMC9070638 DOI: 10.1093/hr/uhac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Non-conventional peptides (NCPs), which are peptides derived from previously unannotated coding sequences, play important biological roles in plants. In this study, we used peptidogenomic methods that integrated mass spectrometry (MS) peptidomics and a six-frame translation database to extensively identify NCPs in grape. In total, 188 and 2021 non-redundant peptides from the Arabidopsis thaliana and Vitis vinifera L. protein database at Ensembl/URGI and an individualized peptidogenomic database were identified. Unlike conventional peptides, these NCPs derived mainly from intergenic, intronic, upstream ORF, 5'UTR, 3'UTR, and downstream ORF regions. These results show that unannotated regions are translated more broadly than we thought. We also found that most NCPs were derived from regions related to phenotypic variations, LTR retrotransposons, and domestication selection, indicating that the NCPs have an important function in complex biological processes. We also found that the NCPs were developmentally specific and had transient and specific functions in grape berry development. In summary, our study is the first to extensively identify NCPs in grape. It demonstrated that there was a large amount of translation in the genome. These results lay a foundation for studying the functions of NCPs and also provide a reference for the discovery of new functional genes in grape.
Collapse
Affiliation(s)
- Mao-Song Pei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Hai-Nan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Tong-Lu Wei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang 471023, China
| | | |
Collapse
|
21
|
Small open reading frames in plant research: from prediction to functional characterization. 3 Biotech 2022; 12:76. [PMID: 35251879 PMCID: PMC8873315 DOI: 10.1007/s13205-022-03147-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 02/11/2022] [Indexed: 11/01/2022] Open
Abstract
Gene prediction is a laborious and time-consuming task. The advancement of sequencing technologies and bioinformatics tools, coupled with accelerated rate of ribosome profiling and mass spectrometry development, have made identification of small open reading frames (sORFs) (< 100 codons) in various plant genomes possible. The past 50 years have seen sORFs being isolated from many organisms. However, to date, a comprehensive sORF annotation pipeline is as yet unavailable, hence, addressed in our review. Here, we also provide current information on classification and functions of plant sORFs and their potential applications in crop improvement programs.
Collapse
|
22
|
Lyapina I, Ivanov V, Fesenko I. Peptidome: Chaos or Inevitability. Int J Mol Sci 2021; 22:13128. [PMID: 34884929 PMCID: PMC8658490 DOI: 10.3390/ijms222313128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the mechanisms of generation and properties of peptidomes across different organisms. Based on their origin, we propose three large peptide groups-functional protein "degradome", small open reading frame (smORF)-encoded peptides (smORFome) and specific precursor-derived peptides. The composition of peptide pools identified by mass-spectrometry analysis in human cells, plants, yeast and bacteria is compared and discussed. The functions of different peptide groups, for example the role of the "degradome" in promoting defense signaling, are also considered.
Collapse
Affiliation(s)
| | | | - Igor Fesenko
- Department of Functional Genomics and Proteomics of Plants, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, 117997 Moscow, Russia; (I.L.); (V.I.)
| |
Collapse
|
23
|
Yang W, Yao D, Wu H, Zhao W, Chen Y, Tong C. Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree. PLoS One 2021; 16:e0259278. [PMID: 34710178 PMCID: PMC8553126 DOI: 10.1371/journal.pone.0259278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/16/2021] [Indexed: 11/19/2022] Open
Abstract
Leaf morphology exhibits tremendous diversity between and within species, and is likely related to adaptation to environmental factors. Most poplar species are of great economic and ecological values and their leaf morphology can be a good predictor for wood productivity and environment adaptation. It is important to understand the genetic mechanism behind variation in leaf shape. Although some initial efforts have been made to identify quantitative trait loci (QTLs) for poplar leaf traits, more effort needs to be expended to unravel the polygenic architecture of the complex traits of leaf shape. Here, we performed a genome-wide association analysis (GWAS) of poplar leaf shape traits in a randomized complete block design with clones from F1 hybrids of Populus deltoides and Populus simonii. A total of 35 SNPs were identified as significantly associated with the multiple traits of a moderate number of regular polar radii between the leaf centroid and its edge points, which could represent the leaf shape, based on a multivariate linear mixed model. In contrast, the univariate linear mixed model was applied as single leaf traits for GWAS, leading to genomic inflation; thus, no significant SNPs were detected for leaf length, measures of leaf width, leaf area, or the ratio of leaf length to leaf width under genomic control. Investigation of the candidate genes showed that most flanking regions of the significant leaf shape-associated SNPs harbored genes that were related to leaf growth and development and to the regulation of leaf morphology. The combined use of the traditional experimental design and the multivariate linear mixed model could greatly improve the power in GWAS because the multiple trait data from a large number of individuals with replicates of clones were incorporated into the statistical model. The results of this study will enhance the understanding of the genetic mechanism of leaf shape variation in Populus. In addition, a moderate number of regular leaf polar radii can largely represent the leaf shape and can be used for GWAS of such a complicated trait in Populus, instead of the higher-dimensional regular radius data that were previously considered to well represent leaf shape.
Collapse
Affiliation(s)
- Wenguo Yang
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Dan Yao
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Hainan Wu
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Wei Zhao
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Yuhua Chen
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Chunfa Tong
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
- * E-mail:
| |
Collapse
|
24
|
Wang H, Kong F, Zhou C. From genes to networks: The genetic control of leaf development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1181-1196. [PMID: 33615731 DOI: 10.1111/jipb.13084] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/16/2021] [Indexed: 05/15/2023]
Abstract
Substantial diversity exists for both the size and shape of the leaf, the main photosynthetic organ of flowering plants. The two major forms of leaf are simple leaves, in which the leaf blade is undivided, and compound leaves, which comprise several leaflets. Leaves form at the shoot apical meristem from a group of undifferentiated cells, which first establish polarity, then grow and differentiate. Each of these processes is controlled by a combination of transcriptional regulators, microRNAs and phytohormones. The present review documents recent advances in our understanding of how these various factors modulate the development of both simple leaves (focusing mainly on the model plant Arabidopsis thaliana) and compound leaves (focusing mainly on the model legume species Medicago truncatula).
Collapse
Affiliation(s)
- Hongfeng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266101, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266101, China
| |
Collapse
|
25
|
Hussain S, Wang W, Ahmed S, Wang X, Adnan, Cheng Y, Wang C, Wang Y, Zhang N, Tian H, Chen S, Hu X, Wang T, Wang S. PIP2, An Auxin Induced Plant Peptide Hormone Regulates Root and Hypocotyl Elongation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:646736. [PMID: 34054893 PMCID: PMC8161498 DOI: 10.3389/fpls.2021.646736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/29/2021] [Indexed: 02/01/2024]
Abstract
Auxin is one of the traditional plant hormones, whereas peptide hormones are peptides with hormone activities. Both auxin and plant peptide hormones regulate multiple aspects of plant growth and development, and there are cross-talks between auxin and plant peptide hormones. PAMP-INDUCED SECRETED PEPTIDES (PIPs) and PIP-LIKEs (PIPLs) are a new family of plant peptide hormone, and PIPL3/TARGET OF LBD SIXTEEN 2 (TOLS2) has been shown to regulate lateral root formation in Arabidopsis. We report here the identification of PIP2 as an auxin response gene, and we found it plays a role in regulating root and hypocotyl development in Arabidopsis. By using quantitative RT-PCR, we found that the expression of PIP2 but not PIP1 and PIP3 was induced by auxin, and auxin induced expression of PIP2 was reduced in nph4-1 and arf19-4, the lost-of-function mutants of Auxin Response Factor 7 (ARF7) and ARF19, respectively. By generating and characterizing overexpressing transgenic lines and gene edited mutants for PIP2, we found that root length in the PIP2 overexpression plant seedlings was slightly shorter when compared with that in the Col wild type plants, but root length of the pip2 mutant seedlings remained largely unchanged. For comparison, we also generated overexpressing transgenic lines and gene edited mutants for PIP3, as well as pip2 pip3 double mutants. Surprisingly, we found that root length in the PIP3 overexpression plant seedlings is shorter than that of the PIP2 overexpression plant seedlings, and the pip3 mutant seedlings also produced short roots. However, root length in the pip2 pip3 double mutant seedlings is largely similar to that in the pip3 single mutant seedlings. On the other hand, hypocotyl elongation assays indicate that only the 35S:PIP2 transgenic plant seedlings produced longer hypocotyls when compared with the Col wild type seedlings. Further analysis indicates that PIP2 promotes cell division as well as cell elongation in hypocotyls. Taken together, our results suggest that PIP2 is an auxin response gene, and PIP2 plays a role in regulating root and hypocotyl elongation in Arabidopsis likely via regulating cell division and cell elongation.
Collapse
Affiliation(s)
- Saddam Hussain
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Wei Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Sajjad Ahmed
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Adnan
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Yuxin Cheng
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Chen Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Yating Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Na Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Hainan Tian
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Siyu Chen
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Xiaojun Hu
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| | - Shucai Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi, China
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, China
| |
Collapse
|
26
|
Hu DG, Wang N, Wang DH, Cheng L, Wang YX, Zhao YW, Ding JY, Gu KD, Xiao X, Hao YJ. A basic/helix-loop-helix transcription factor controls leaf shape by regulating auxin signaling in apple. THE NEW PHYTOLOGIST 2020; 228:1897-1913. [PMID: 32712992 DOI: 10.1111/nph.16828] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Climate-driven phenological change across local spatial gradients leads to leaf shape variation. At higher elevations, leaves of broadleaf species tend to become narrower, but the underlying molecular mechanism is largely unknown. In this study, a series of morphometric analyses and biochemical assays, combined with functional identification in apple, were performed. We show that the decrease in apple leaf width with increasing altitude is controlled by a basic/helix-loop-helix transcription factor (bHLH TF), MdbHLH3. The MdbHLH3-overexpressing lines have a lower transcript abundance of MdPIN1 encoding an auxin efflux carrier but a higher transcript abundance of MdGH3-2 encoding a putative auxin amido conjugate synthase, resulting in a lower free auxin concentration; feeding the transgenic leaves with exogenous auxin partially restores leaf width. MdbHLH3 transcriptionally suppresses and activates MdPIN1 and MdGH3-2, respectively, by specifically binding to their promoters. This alters auxin homeostasis and transport, consequently leading to changes in leaf shape. These findings suggest that the bHLH TF MdbHLH3 directly modulates auxin signaling in controlling leaf shape in response to local spatial gradients in apple.
Collapse
Affiliation(s)
- Da-Gang Hu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Nian Wang
- State Key Laboratory of Crop Biology, State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Dong-Hui Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Lailiang Cheng
- Department of Horticulture, Cornell University, 134A Plant Science, Ithaca, NY, 14853, USA
| | - Yan-Xiu Wang
- College of Agricultural Sciences, Gansu Agricultural University, Lanzhou, 730000, China
| | - Yu-Wen Zhao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jun-Yi Ding
- State Key Laboratory of Crop Biology, State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Kai-Di Gu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xu Xiao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| |
Collapse
|
27
|
Li J, Zhang X, Liu C. The computational approaches of lncRNA identification based on coding potential: Status quo and challenges. Comput Struct Biotechnol J 2020; 18:3666-3677. [PMID: 33304463 PMCID: PMC7710504 DOI: 10.1016/j.csbj.2020.11.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) make up a large proportion of transcriptome in eukaryotes, and have been revealed with many regulatory functions in various biological processes. When studying lncRNAs, the first step is to accurately and specifically distinguish them from the colossal transcriptome data with complicated composition, which contains mRNAs, lncRNAs, small RNAs and their primary transcripts. In the face of such a huge and progressively expanding transcriptome data, the in-silico approaches provide a practicable scheme for effectively and rapidly filtering out lncRNA targets, using machine learning and probability statistics. In this review, we mainly discussed the characteristics of algorithms and features on currently developed approaches. We also outlined the traits of some state-of-the-art tools for ease of operation. Finally, we pointed out the underlying challenges in lncRNA identification with the advent of new experimental data.
Collapse
Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| |
Collapse
|
28
|
Wang S, Tian L, Liu H, Li X, Zhang J, Chen X, Jia X, Zheng X, Wu S, Chen Y, Yan J, Wu L. Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline. MOLECULAR PLANT 2020; 13:1078-1093. [PMID: 32445888 DOI: 10.1016/j.molp.2020.05.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/04/2020] [Accepted: 05/18/2020] [Indexed: 05/10/2023]
Abstract
Non-conventional peptides (NCPs), which include small open reading frame-encoded peptides, play critical roles in fundamental biological processes. In this study, we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants.A total of 1993 and 1860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. These NCPs showed distinct characteristics compared with conventional peptides and were derived from introns, 3' UTRs, 5' UTRs, junctions, and intergenic regions. Furthermore, our results showed that translation events in unannotated transcripts occur more broadly than previously thought. In addition, we found that dozens of maize NCPs are enriched within regions associated with phenotypic variations and domestication selection, indicating that they potentially are involved in genetic regulation of complex traits and domestication in maize. Taken together, our study developed an integrated peptidogenomic pipeline for large-scale identification of NCPs in plants, which would facilitate global characterization of NCPs from other plants. The identification of large-scale NCPs in both monocot (maize) and dicot (Arabidopsis) plants indicates that a large portion of plant genome can be translated into biologically functional molecules, which has important implications for functional genomic studies.
Collapse
Affiliation(s)
- Shunxi Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Lei Tian
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xueyan Chen
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xingmeng Jia
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xu Zheng
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Shubiao Wu
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Yanhui Chen
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Liuji Wu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| |
Collapse
|
29
|
Luo W, Xiao Y, Liang Q, Su Y, Xiao L. Identification of Potential Auxin-Responsive Small Signaling Peptides through a Peptidomics Approach in Arabidopsis thaliana. Molecules 2019; 24:E3146. [PMID: 31470600 PMCID: PMC6749465 DOI: 10.3390/molecules24173146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/14/2019] [Accepted: 08/28/2019] [Indexed: 12/20/2022] Open
Abstract
Small signaling peptides (SSPs) are a class of short peptides playing critical roles in plant growth and development. SSPs are also involved in the phytohormone signaling pathway. However, identification of mature SSPs is still a technical challenge because of their extremely low concentrations in plant tissue and complicated interference by many other metabolites. Here, we report an optimized protocol to extract SSPs based on protoplast extraction and to analyze SSPs based on tandem mass spectrometry peptidomics. Using plant protoplasts as the material, soluble peptides were directly extracted into phosphate buffer. The interference of non-signaling peptides was significantly decreased. Moreover, we applied the protocol to identify potential SSPs in auxin treated wild type and auxin biosynthesis defective mutant yuc2yuc6. Over 100 potential SSPs showed a response to auxin in Arabidopsis thaliana.
Collapse
Affiliation(s)
- Weigui Luo
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Yuan Xiao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiwen Liang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Yi Su
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China.
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China.
| |
Collapse
|
30
|
Fesenko I, Kirov I, Kniazev A, Khazigaleeva R, Lazarev V, Kharlampieva D, Grafskaia E, Zgoda V, Butenko I, Arapidi G, Mamaeva A, Ivanov V, Govorun V. Distinct types of short open reading frames are translated in plant cells. Genome Res 2019; 29:1464-1477. [PMID: 31387879 PMCID: PMC6724668 DOI: 10.1101/gr.253302.119] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.
Collapse
Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Ilya Kirov
- Laboratory of marker-assisted and genomic selection of plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russian Federation
| | - Andrey Kniazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Regina Khazigaleeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vassili Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Daria Kharlampieva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Ekaterina Grafskaia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Viktor Zgoda
- Laboratory of System Biology, Institute of Biomedical Chemistry, 119121 Moscow, Russian Federation
| | - Ivan Butenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Georgy Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation.,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Ivanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| |
Collapse
|
31
|
Zhou Y, Sarker U, Neumann G, Ludewig U. The LaCEP1 peptide modulates cluster root morphology in Lupinus albus. PHYSIOLOGIA PLANTARUM 2019; 166:525-537. [PMID: 29984412 DOI: 10.1111/ppl.12799] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 05/26/2023]
Abstract
White lupin cluster roots are specialized brush-like root structures that are formed in some species under phosphorus (P)-deficient conditions. They intensely secrete protons and organic acid anions for solubilization and acquisition of sparingly soluble phosphates. Phytohormones and sucrose modulate cluster root number, but the molecular mechanisms of cluster root formation have been elusive. Here, a novel peptide phytohormone was identified that affects cluster root development. It belongs to the C-TERMINALLY-ENCODED PEPTIDE (CEP) family. Members of that family arrest root growth and modulate branching in model species. LaCEP1 was highly expressed in the pre-emergence zone of clusters. Over-expression of the gene encoding the LaCEP1 propeptide resulted in moderate inhibition of cluster root formation. The primary and lateral root lengths of lupin were little affected by the overexpression, but LaCEP1 reduced cluster rootlet and root hair elongation. Addition of a 15-mer core peptide derived from LaCEP1 similarly altered root morphology and modified cluster activity, suggesting that a core sequence of the propeptide is functionally sufficient. Stable overexpression in Arabidopsis confirmed the LaCEP1 function in root growth inhibition across species. Taken together, the root inhibitory effects of the LaCEP1 phytohormone suggest a role as of a regulatory module involved in cluster root development in white lupin.
Collapse
Affiliation(s)
- Yaping Zhou
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, D-70593, Germany
| | - Upama Sarker
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, D-70593, Germany
| | - Günter Neumann
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, D-70593, Germany
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, D-70593, Germany
| |
Collapse
|
32
|
Li J, Liu C. Coding or Noncoding, the Converging Concepts of RNAs. Front Genet 2019; 10:496. [PMID: 31178900 PMCID: PMC6538810 DOI: 10.3389/fgene.2019.00496] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Technological advances over the past decade have unraveled the remarkable complexity of RNA. The identification of small peptides encoded by long non-coding RNAs (lncRNAs) as well as regulatory functions mediated by non-coding regions of mRNAs have further complicated our understanding of the multifaceted functions of RNA. In this review, we summarize current evidence pointing to dual roles of RNA molecules defined by their coding and non-coding potentials. We also discuss how the emerging roles of RNA transform our understanding of gene expression and evolution.
Collapse
Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
33
|
Nitrate Reductase-Mediated Nitric Oxide Regulates the Leaf Shape in Arabidopsis by Mediating the Homeostasis of Reactive Oxygen Species. Int J Mol Sci 2019; 20:ijms20092235. [PMID: 31067654 PMCID: PMC6539879 DOI: 10.3390/ijms20092235] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 12/30/2022] Open
Abstract
As a gaseous biological signaling molecule, nitric oxide (NO) regulates many physiological processes in plants. Over the last decades, this low molecular weight compound has been identified as a key signaling molecule to regulate plant stress responses, and also plays an important role in plant development. However, elucidation of the molecular mechanisms for NO in leaf development has so far been limited due to a lack of mutant resources. Here, we employed the NO-deficient mutant nia1nia2 to examine the role of NO in leaf development. We have found that nia1nia2 mutant plants displayed very different leaf phenotypes as compared to wild type Col-0. Further studies have shown that reactive oxygen species (ROS) levels are higher in nia1nia2 mutant plants. Interestingly, ROS-related enzymes ascorbate peroxidase (APX), catalases (CAT), and peroxidases (POD) have shown decreases in their activities. Our transcriptome data have revealed that the ROS synthesis gene RBOHD was enhanced in nia1nia2 mutants and the photosynthesis-related pathway was impaired, which suggests that NO is required for chloroplast development and leaf development. Together, these results imply that NO plays a significant role in plant leaf development by regulating ROS homeostasis.
Collapse
|
34
|
Ren T, Weraduwage SM, Sharkey TD. Prospects for enhancing leaf photosynthetic capacity by manipulating mesophyll cell morphology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1153-1165. [PMID: 30590670 DOI: 10.1093/jxb/ery448] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
Leaves are beautifully specialized organs designed to maximize the use of light and CO2 for photosynthesis. Engineering leaf anatomy therefore holds great potential to enhance photosynthetic capacity. Here we review the effect of the dominant leaf anatomical traits on leaf photosynthesis and confirm that a high chloroplast surface area exposed to intercellular airspace per unit leaf area (Sc) is critical for efficient photosynthesis. The possibility of improving Sc through appropriately increasing mesophyll cell density is further analyzed. The potential influences of modifying mesophyll cell morphology on CO2 diffusion, light distribution within the leaf, and other physiological processes are also discussed. Some potential target genes regulating leaf mesophyll cell proliferation and expansion are explored. Indeed, more comprehensive research is needed to understand how manipulating mesophyll cell morphology through editing the potential target genes impacts leaf photosynthetic capacity and related physiological processes. This will pinpoint the targets for engineering leaf anatomy to maximize photosynthetic capacity.
Collapse
Affiliation(s)
- Tao Ren
- College of Resources and Environment, Huazhong Agricultural University, China
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
| | - Sarathi M Weraduwage
- Department of Energy Plant Research Laboratory and Plant Resiience Institute, Michigan State University, East Lansing, USA
| | - Thomas D Sharkey
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
- Department of Energy Plant Research Laboratory and Plant Resiience Institute, Michigan State University, East Lansing, USA
| |
Collapse
|
35
|
Fu X, Xu J, Zhou M, Chen M, Shen L, Li T, Zhu Y, Wang J, Hu J, Zhu L, Gao Z, Dong G, Guo L, Ren D, Chen G, Lin J, Qian Q, Zhang G. Enhanced Expression of QTL qLL9/DEP1 Facilitates the Improvement of Leaf Morphology and Grain Yield in Rice. Int J Mol Sci 2019; 20:E866. [PMID: 30781568 PMCID: PMC6412340 DOI: 10.3390/ijms20040866] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 01/22/2023] Open
Abstract
In molecular breeding of super rice, it is essential to isolate the best quantitative trait loci (QTLs) and genes of leaf shape and explore yield potential using large germplasm collections and genetic populations. In this study, a recombinant inbred line (RIL) population was used, which was derived from a cross between the following parental lines: hybrid rice Chunyou84, that is, japonica maintainer line Chunjiang16B (CJ16); and indica restorer line Chunhui 84 (C84) with remarkable leaf morphological differences. QTLs mapping of leaf shape traits was analyzed at the heading stage under different environmental conditions in Hainan (HN) and Hangzhou (HZ). A major QTL qLL9 for leaf length was detected and its function was studied using a population derived from a single residual heterozygote (RH), which was identified in the original population. qLL9 was delimitated to a 16.17 kb region flanked by molecular markers C-1640 and C-1642, which contained three open reading frames (ORFs). We found that the candidate gene for qLL9 is allelic to DEP1 using quantitative real-time polymerase chain reaction (qRT-PCR), sequence comparison, and the clustered regularly interspaced short palindromic repeat-associated Cas9 nuclease (CRISPR/Cas9) genome editing techniques. To identify the effect of qLL9 on yield, leaf shape and grain traits were measured in near isogenic lines (NILs) NIL-qLL9CJ16 and NIL-qLL9C84, as well as a chromosome segment substitution line (CSSL) CSSL-qLL9KASA with a Kasalath introgressed segment covering qLL9 in the Wuyunjing (WYJ) 7 backgrounds. Our results showed that the flag leaf lengths of NIL-qLL9C84 and CSSL-qLL9KASA were significantly different from those of NIL-qLL9CJ16 and WYJ 7, respectively. Compared with NIL-qLL9CJ16, the spike length, grain size, and thousand-grain weight of NIL-qLL9C84 were significantly higher, resulting in a significant increase in yield of 15.08%. Exploring and pyramiding beneficial genes resembling qLL9C84 for super rice breeding could increase both the source (e.g., leaf length and leaf area) and the sink (e.g., yield traits). This study provides a foundation for future investigation of the molecular mechanisms underlying the source⁻sink balance and high-yield potential of rice, benefiting high-yield molecular design breeding for global food security.
Collapse
Affiliation(s)
- Xue Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jing Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Mengyu Zhou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Minmin Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Ting Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Yuchen Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jiajia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Guang Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jianrong Lin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| |
Collapse
|
36
|
Affiliation(s)
- Maria E. Sousa
- Ophthalmology, Jacobs School of Medicine and Biomedical Science, University of New York at Buffalo, Buffalo, NY, United States of America
- Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, United States of America
| | - Michael H. Farkas
- Ophthalmology, Jacobs School of Medicine and Biomedical Science, University of New York at Buffalo, Buffalo, NY, United States of America
- Research Service, Veterans Administration Western New York Healthcare System, Buffalo, NY, United States of America
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Science, State University of New York at Buffalo, Buffalo, NY, United States of America
| |
Collapse
|
37
|
Brito MS, DePaoli HC, Cossalter V, Avanci NC, Ferreira PB, Azevedo MS, Strini EJ, Quiapim AC, Goldman GH, Peres LEP, Goldman MHS. A novel cysteine-rich peptide regulates cell expansion in the tobacco pistil and influences its final size. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:55-67. [PMID: 30466601 DOI: 10.1016/j.plantsci.2018.09.002] [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: 07/14/2018] [Revised: 09/01/2018] [Accepted: 09/04/2018] [Indexed: 06/09/2023]
Abstract
Plant morphogenesis is dependent on cell proliferation and cell expansion, which are responsible for establishing final organ size and shape during development. Several genes have been described as encoding components of the plant cell development machinery, among which are the plant peptides. Here we describe a novel cysteine-rich plant peptide (68 amino acids), encoded by a small open reading frame gene (sORF). It is specifically expressed in the reproductive organs of Nicotiana tabacum and is developmentally regulated. N- and C-terminal translational fusions with GFP in protoplasts have demonstrated that the peptide is not secreted. Knockdown transgenic plants produced by RNAi exhibited enlarged pistils due to cell expansion and the gene was named Small Peptide Inhibitor of Cell Expansion (SPICE). Estimation of nuclear DNA content using flow cytometry has shown that cell expansion in pistils was not correlated with endoreduplication. Decreased SPICE expression also affected anther growth and pollen formation, resulting in male sterility in at least one transgenic plant. Our results revealed that SPICE is a novel reproductive organ specific gene that controls cell expansion, probably as a component of a signal transduction pathway.
Collapse
Affiliation(s)
- Michael S Brito
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil; PPG - Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Brazil.
| | - Henrique C DePaoli
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil; PPG - Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Brazil
| | - Viviani Cossalter
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil; PPG - Biologia Comparada, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil
| | - Nilton C Avanci
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil; PPG - Biologia Comparada, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil
| | - Pedro B Ferreira
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil; PPG - Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Brazil
| | | | - Edward J Strini
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil; PPG - Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Brazil
| | - Andréa C Quiapim
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil
| | - Gustavo H Goldman
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903, Brazil
| | - Lázaro E P Peres
- Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz Universidade de São Paulo, 13418-900, Brazil
| | - Maria Helena S Goldman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Brazil.
| |
Collapse
|
38
|
Lee YK, Kim IJ. Functional conservation of Arabidopsis LNG1 in tobacco relating to leaf shape change by increasing longitudinal cell elongation by overexpression. Genes Genomics 2018; 40:1053-1062. [PMID: 29949075 DOI: 10.1007/s13258-018-0712-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
The LONGIFOLIA1 (LNG1) gene of Arabidopsis regulates leaf shape by polar cell elongation independent of ROTUNDAFOLIA3 (ROT3). To expand our knowledge on the function of this gens in plant systems, Arabidopsis LNG1 (AtLNG1) was introduced both sense and antisense orientation under the control of 35S CaMV promoter into tobacco plants that lack AtLNG1 homolog. Resulting transgenic tobacco plants were analyzed by their phenotype, anatomy and transcript levels. AtLNG1-overexpressing tobacco lines showed increase in the leaf petiole and leaf blade compared with wild type tobacco line. The overexpressors also showed elongated palisade cells as well as epidermal cells in the leaf length direction, but no increase in cell number. Ectopic expression of AtLNG1 in tobacco plants also increased the expression of cell wall modification-related genes, such as NT_XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE9 (NT_XTH9), NT_XTH15 and NT_XTH33, indicating that these genes appear to be target of AtLNG1. As results of molecular and cellular examination, AtLNG1 seemed to have a conserved functional role in shaping leaf morphology in both Arabidopsis and tobacco.
Collapse
Affiliation(s)
- Young Koung Lee
- Cold Spring Harbor Laboratory, 1 Bungtown Road,, Cold Spring Harbor, NY, 11724, USA
- Division of Biological Sciences and Institute for Basic Science/Division of Biological Sciences and Research Institute for Glycoscience, Wonkwang University, Iksan, 54538, South Korea
| | - In-Jung Kim
- Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju, 690-756, South Korea.
- Research Institute for Subtropical Agriculture and Biotechnology, SARI, Jeju National University, Jeju, 63243, South Korea.
| |
Collapse
|
39
|
Kereszt A, Mergaert P, Montiel J, Endre G, Kondorosi É. Impact of Plant Peptides on Symbiotic Nodule Development and Functioning. FRONTIERS IN PLANT SCIENCE 2018; 9:1026. [PMID: 30065740 PMCID: PMC6056668 DOI: 10.3389/fpls.2018.01026] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/25/2018] [Indexed: 05/20/2023]
Abstract
Ribosomally synthesized peptides have wide ranges of functions in plants being, for example, signal molecules, transporters, alkaloids, or antimicrobial agents. Legumes are an unprecedented rich source of peptides, which are used to control the symbiosis of these plants with the nitrogen-fixing Rhizobium bacteria. Here, we discuss the function and the evolution of these peptides playing an important role in the formation or functioning of the symbiotic organs, the root nodules. We distinguish peptides that can be either cell-autonomous or secreted short-range or long-range signals, carrying messages in or between plant cells or that can act as effectors interacting with the symbiotic bacteria. Peptides are further classified according to the stage of the symbiotic process where they act. Several peptide classes, including RALF, DLV, ENOD40, and others, control Rhizobium infection and the initiation of cell divisions and the formation of nodule primordia. CLE and CEP peptides are implicated in systemic and local control of nodule initiation during autoregulation of nodulation and in response to the nutritional demands of the plant. Still other peptides act at later stages of the symbiosis. The PSK peptide is thought to be involved in the suppression of immunity in nodules and the nodule-specific cysteine-rich, GRP, and SNARP (LEED..PEED) peptide families are essential in the functioning of the nitrogen fixing root nodules. The NCRs and possibly also the GRP and SNARPs are targeted to the endosymbionts and play essential roles in the terminal differentiation of these bacteria.
Collapse
Affiliation(s)
- Attila Kereszt
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Peter Mergaert
- Institute of Integrative Biology of the Cell, UMR 9198, CNRS – CEA – Université Paris-Sud, Gif-sur-Yvette, France
| | - Jesús Montiel
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gabriella Endre
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Éva Kondorosi
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| |
Collapse
|
40
|
Budamgunta H, Olexiouk V, Luyten W, Schildermans K, Maes E, Boonen K, Menschaert G, Baggerman G. Comprehensive Peptide Analysis of Mouse Brain Striatum Identifies Novel sORF-Encoded Polypeptides. Proteomics 2018; 18:e1700218. [DOI: 10.1002/pmic.201700218] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/30/2018] [Indexed: 11/10/2022]
Affiliation(s)
| | - Volodimir Olexiouk
- BioBix; Lab for Bioinformatics and Computational Genomics; Department of Mathematical Modelling; Statistics and Bio-informatics; Ghent University; Ghent Belgium
| | - Walter Luyten
- Animal Physiology and Neurobiology; KULeuven; Leuven Belgium
| | | | - Evelyne Maes
- Centre for Proteomics; UAntwerp; Antwerp Belgium
- Proteins and Biomaterials; AgResearch; Christchurch New Zealand
| | - Kurt Boonen
- Centre for Proteomics; UAntwerp; Antwerp Belgium
- Unit Environmental Risk and Health; VITO; Mol Belgium
| | - Gerben Menschaert
- BioBix; Lab for Bioinformatics and Computational Genomics; Department of Mathematical Modelling; Statistics and Bio-informatics; Ghent University; Ghent Belgium
| | - Geert Baggerman
- Centre for Proteomics; UAntwerp; Antwerp Belgium
- Unit Environmental Risk and Health; VITO; Mol Belgium
| |
Collapse
|
41
|
Lee YK, Rhee JY, Lee SH, Chung GC, Park SJ, Segami S, Maeshima M, Choi G. Functionally redundant LNG3 and LNG4 genes regulate turgor-driven polar cell elongation through activation of XTH17 and XTH24. PLANT MOLECULAR BIOLOGY 2018; 97:23-36. [PMID: 29616436 DOI: 10.1007/s11103-018-0722-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/25/2018] [Indexed: 05/03/2023]
Abstract
In this work, we genetically characterized the function of Arabidopsis thaliana, LONGIFOLIA (LNG1), LNG2, LNG3, LNG4, their contribution to regulate vegetative architecture in plant. We used molecular and biophysical approaches to elucidate a gene function that regulates vegetative architecture, as revealed by the leaf phenotype and later effects on flowering patterns in Arabidopsis loss-of-function mutants. As a result, LNG genes play an important role in polar cell elongation by turgor pressure controlling the activation of XTH17 and XTH24. Plant vegetative architecture is related to important traits that later influence the floral architecture involved in seed production. Leaf morphology is the primary key trait to compose plant vegetative architecture. However, molecular mechanism on leaf shape determination is not fully understood even in the model plant A. thaliana. We previously showed that LONGIFOLIA (LNG1) and LONGIFOLIA2 (LNG2) genes regulate leaf morphology by promoting longitudinal cell elongation in Arabidopsis. In this study, we further characterized two homologs of LNG1, LNG3, and LNG4, using genetic, biophysical, and molecular approaches. Single loss-of-function mutants, lng3 and lng4, do not show any phenotypic difference, but mutants of lng quadruple (lngq), and lng1/2/3 and lng1/2/4 triples, display reduced leaf length, compared to wild type. Using the paradermal analysis, we conclude that the reduced leaf size of lngq is due to decreased cell elongation in the direction of longitudinal leaf growth, and not decreased cell proliferation. This data indicate that LNG1/2/3/4 are functionally redundant, and are involved in polar cell elongation in Arabidopsis leaf. Using a biophysical approach, we show that the LNGs contribute to maintain high turgor pressure, thus regulating turgor pressure-dependent polar cell elongation. In addition, gene expression analysis showed that LNGs positively regulate the expression of the cell wall modifying enzyme encoded by a multi-gene family, xyloglucan endotransglucosylase/hydrolase (XTH). Taking all of these together, we propose that LNG related genes play an important role in polar cell elongation by changing turgor pressure and controlling the activation of XTH17 and XTH24.
Collapse
Affiliation(s)
- Young Koung Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea.
- Division of Biological Sciences and Institute for Basic Science/Division of Biological Sciences and Research Institute for Glycoscience, Wonkwang University, Iksan, 54538, South Korea.
| | - Ji Ye Rhee
- Department of Plant Biotechnology, Agricultural Plant Stress Research Center, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Seong Hee Lee
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
| | - Gap Chae Chung
- Department of Plant Biotechnology, Agricultural Plant Stress Research Center, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Soon Ju Park
- Division of Biological Sciences and Institute for Basic Science/Division of Biological Sciences and Research Institute for Glycoscience, Wonkwang University, Iksan, 54538, South Korea
| | - Shoji Segami
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Masayohi Maeshima
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea
| |
Collapse
|
42
|
Yeasmin F, Yada T, Akimitsu N. Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics. Front Genet 2018; 9:144. [PMID: 29922328 PMCID: PMC5996887 DOI: 10.3389/fgene.2018.00144] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Abstract
Integrative analysis using omics-based technologies results in the identification of a large number of putative short open reading frames (sORFs) with protein-coding capacity within transcripts previously identified as long noncoding RNAs (lncRNAs) or transcripts of unknown function (TUFs). sORFs were previously overlooked because of their diminutive size and the difficulty of identification by bioinformatics analyses. There is now growing evidence of the existence of potentially functional micropeptides produced from sORFs within cells of diverse species. Recent characterization of a few of these revealed their significant divergent roles in many fundamental biological processes, where some also show important relationships with pathogenesis. Recent works therefore provide new insights for exploring the wealth of information that may lie within sORF-encoded short proteins. Here, we summarize the current progress and view of micropeptides encoded in sORFs of protein-coding genes.
Collapse
Affiliation(s)
- Fouzia Yeasmin
- Isotope Science Centre, The University of Tokyo, Tokyo, Japan
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
| | | |
Collapse
|
43
|
Khazigaleeva RA, Fesenko IA. Biologically active peptides encoded by small open reading frames. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s106816201706005x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
44
|
Tsukaya H. A Consideration of Leaf Shape Evolution in the Context of the Primary Function of the Leaf as a Photosynthetic Organ. THE LEAF: A PLATFORM FOR PERFORMING PHOTOSYNTHESIS 2018. [DOI: 10.1007/978-3-319-93594-2_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
45
|
Kawade K, Tanimoto H, Horiguchi G, Tsukaya H. Spatially Different Tissue-Scale Diffusivity Shapes ANGUSTIFOLIA3 Gradient in Growing Leaves. Biophys J 2017; 113:1109-1120. [PMID: 28877493 DOI: 10.1016/j.bpj.2017.06.072] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 12/01/2022] Open
Abstract
The spatial gradient of signaling molecules is pivotal for establishing developmental patterns of multicellular organisms. It has long been proposed that these gradients could arise from the pure diffusion process of signaling molecules between cells, but whether this simplest mechanism establishes the formation of the tissue-scale gradient remains unclear. Plasmodesmata are unique channel structures in plants that connect neighboring cells for molecular transport. In this study, we measured cellular- and tissue-scale kinetics of molecular transport through plasmodesmata in Arabidopsis thaliana developing leaf primordia by fluorescence recovery assays. These trans-scale measurements revealed biophysical properties of diffusive molecular transport through plasmodesmata and revealed that the tissue-scale diffusivity, but not the cellular-scale diffusivity, is spatially different along the leaf proximal-to-distal axis. We found that the gradient in cell size along the developmental axis underlies this spatially different tissue-scale diffusivity. We then asked how this diffusion-based framework functions in establishing a signaling gradient of endogenous molecules. ANGUSTIFOLIA3 (AN3) is a transcriptional co-activator, and as we have shown here, it forms a long-range signaling gradient along the leaf proximal-to-distal axis to determine a cell-proliferation domain. By genetically engineering AN3 mobility, we assessed each contribution of cell-to-cell movement and tissue growth to the distribution of the AN3 gradient. We constructed a diffusion-based theoretical model using these quantitative data to analyze the AN3 gradient formation and demonstrated that it could be achieved solely by the diffusive molecular transport in a growing tissue. Our results indicate that the spatially different tissue-scale diffusivity is a core mechanism for AN3 gradient formation. This provides evidence that the pure diffusion process establishes the formation of the long-range signaling gradient in leaf development.
Collapse
Affiliation(s)
- Kensuke Kawade
- Okazaki Institute for Integrative Bioscience, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan; National Institute for Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan; Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan.
| | | | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan; Research Center for Life Science, Rikkyo University, Tokyo, Japan
| | - Hirokazu Tsukaya
- Okazaki Institute for Integrative Bioscience, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| |
Collapse
|
46
|
Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics 2017; 18:e1700038. [PMID: 28759167 DOI: 10.1002/pmic.201700038] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Indexed: 12/18/2022]
Abstract
Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.
Collapse
Affiliation(s)
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| |
Collapse
|
47
|
Overexpressed BRH1, a RING finger gene, alters rosette leaf shape in Arabidopsis thaliana. SCIENCE CHINA-LIFE SCIENCES 2017; 61:79-87. [DOI: 10.1007/s11427-017-9133-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 06/26/2017] [Indexed: 12/28/2022]
|
48
|
Wu Y, Gong W, Yang W. Shade Inhibits Leaf Size by Controlling Cell Proliferation and Enlargement in Soybean. Sci Rep 2017; 7:9259. [PMID: 28835715 PMCID: PMC5569092 DOI: 10.1038/s41598-017-10026-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/02/2017] [Indexed: 11/23/2022] Open
Abstract
To gain more insight into the physiological function of shade and how shade affects leaf size, we investigated the growth, leaf anatomical structure, hormones and genes expressions in soybean. Soybean seeds were sown in plastic pots and were allowed to germinate and grow for 30 days under shade or full sunlight conditions. Shade treated plants showed significantly increase on stem length and petiole length, and decrease on stem diameters, shoot biomass and its partition to leaf also were significantly lower than that in full sunlight. Smaller and thinner on shade treated leaves than corresponding leaves on full sunlight plants. The decreased leaf size caused by shade was largely attributable to cell proliferation in young leaves and both cell proliferation and enlargement in old leaves. Shade induced the expression of a set of genes related to cell proliferation and/or enlargement, but depended on the developmental stage of leaf. Shade significantly increased the auxin and gibberellin content, and significantly decreased the cytokinin content in young, middle and old leaves. Taken together, these results indicated that shade inhibited leaf size by controlling cell proliferation and enlargement, auxin, gibberellin and cytokinin may play important roles in this process.
Collapse
Affiliation(s)
- Yushan Wu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, P.R. China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, 611130, P.R. China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130, PR China
| | - Wanzhuo Gong
- Characteristic Crops Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, 402160, P.R. China
| | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, P.R. China.
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, 611130, P.R. China.
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130, PR China.
| |
Collapse
|
49
|
Abstract
A large body of evidence indicates that genome annotation pipelines have biased our view of coding sequences because they generally undersample small proteins and peptides. The recent development of genome-wide translation profiling reveals the prevalence of small/short open reading frames (smORFs or sORFs), which are scattered over all classes of transcripts, including both mRNAs and presumptive long noncoding RNAs. Proteomic approaches further confirm an unexpected variety of smORF-encoded peptides (SEPs), representing an overlooked reservoir of bioactive molecules. Indeed, functional studies in a broad range of species from yeast to humans demonstrate that SEPs can harbor key activities for the control of development, differentiation, and physiology. Here we summarize recent advances in the discovery and functional characterization of smORF/SEPs and discuss why these small players can no longer be ignored with regard to genome function.
Collapse
Affiliation(s)
- Serge Plaza
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse, Université Paul Sabatier, 31326 Castanet Tolosan, France; .,CNRS, UMR5546, Laboratoire de Recherches en Sciences Végétales, 31326 Castanet Tolosan, France
| | - Gerben Menschaert
- Department of Mathematical Modeling, Statistics and Bioinformatics, University of Ghent, 9000 Gent, Belgium
| | - François Payre
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier, 31062 Toulouse, France;
| |
Collapse
|
50
|
Abstract
Plants must adapt to multiple biotic and abiotic stresses ; thus, sensing and responding to environmental signals is imperative for their survival. Moreover, understanding these responses is imperative for efforts to improve plant yield and consistency. Regulation of transcript levels is a key aspect of the plant response to environmental signals. Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years with the advance of high-throughput sequencing technologies. As important biological regulators, lncRNAs have been implicated in a wide range of developmental processes and diseases in animals. However, knowledge of the role that lncRNAs play in plant stress tolerance remains limited. Here, we review recent studies on the identification, characteristics, classification, and biological functions of lncRNAs in response to various stresses, including bacterial pathogens, excess light, drought, salinity, hypoxia, extreme temperatures, and nitrogen/phosphate deficiency. We also discuss possible directions for future research.
Collapse
|