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Sami A, Fu M, Yin H, Ali U, Tian L, Wang S, Zhang J, Chen X, Li H, Chen M, Yao W, Wu L. NCPbook: A comprehensive database of noncanonical peptides. PLANT PHYSIOLOGY 2024; 196:67-76. [PMID: 38808472 DOI: 10.1093/plphys/kiae311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/26/2024] [Accepted: 05/10/2024] [Indexed: 05/30/2024]
Abstract
Noncanonical peptides (NCPs) are a class of peptides generated from regions previously thought of as noncoding, such as introns, 5' UTRs, 3' UTRs, and intergenic regions. In recent years, the significance and diverse functions of NCPs have come to light, yet a systematic and comprehensive NCP database remains absent. Here, we developed NCPbook (https://ncp.wiki/ncpbook/), a database of evidence-supported NCPs, which aims to provide a resource for efficient exploration, analysis, and manipulation of NCPs. NCPbook incorporates data from diverse public databases and scientific literature. The current version of NCPbook includes 180,676 NCPs across 29 different species, evidenced by MS, ribosome profiling, or molecular experiments. These NCPs are distributed across kingdoms, comprising 123,408 from 14 plant species, 56,999 from 7 animal species, and 269 from 8 microbial species. Furthermore, NCPbook encompasses 9,166 functionally characterized NCPs playing important roles in immunity, stress resistance, growth, and development. Equipped with a user-friendly interface, NCPbook allows users to search, browse, visualize, and retrieve data, making it an indispensable platform for researching NCPs in various plant, animal, and microbial species.
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Affiliation(s)
- Abdul Sami
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Mengjia Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Haoqiang Yin
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Usman Ali
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Lei Tian
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Shunxi Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Xueyan Chen
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Hehuan Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Minghui Chen
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Liuji Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
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Yu X, Huang Z, Cheng Y, Hu K, Zhou Y, Yao H, Shen J, Huang Y, Zhuang X, Cai Y. Comparative Genomics Screens Identify a Novel Small Secretory Peptide, SlSolP12, which Activates Both Local and Systemic Immune Response in Tomatoes and Exhibits Broad-Spectrum Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18507-18519. [PMID: 39113497 DOI: 10.1021/acs.jafc.4c03633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Small secreted peptides (SSPs) are essential for defense mechanisms in plant-microbe interactions, acting as danger-associated molecular patterns (DAMPs). Despite the first discovery of SSPs over three decades ago, only a limited number of SSP families, particularly within Solanaceae plants, have been identified due to inefficient approaches. This study employed comparative genomics screens with Solanaceae proteomes (tomato, tobacco, and pepper) to discover a novel SSP family, SolP. Bioinformatics analysis suggests that SolP may serve as an endogenous signal initiating the plant PTI response. Interestingly, SolP family members from tomato, tobacco, and pepper share an identical sequence (VTSNALALVNRFAD), named SlSolP12 (also referred to as NtSolP15 or CaSolP1). Biochemical and phenotypic analyses revealed that synthetic SlSolP12 peptide triggers multiple defense responses: ROS burst, MAPK activation, callose deposition, stomatal closure, and expression of immune defense genes. Furthermore, SlSolP12 enhances systemic resistance against Botrytis cinerea infection in tomato plants and interferes with classical peptides, flg22 and Systemin, which modulate the immune response. Remarkably, SolP12 activates ROS in diverse plant species, such as Arabidopsis thaliana, soybean, and rice, showing a broad spectrum of biological activities. This study provides valuable approaches for identifying endogenous SSPs and highlights SlSolP12 as a novel DAMP that could serve as a useful target for crop protection.
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Affiliation(s)
- Xiaosong Yu
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Zhongchao Huang
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Yuanyuan Cheng
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Keyi Hu
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Yan Zhou
- Chengdu Lusyno Biotechnology Co., Ltd., Chengdu 610000, Sichuan, China
| | - Huipeng Yao
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 310000, Zhejiang, China
| | - Yan Huang
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Xiaohong Zhuang
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yi Cai
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
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3
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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.
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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
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4
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Li H, Liu Y, Gao W, Zhu J, Zhang H, Wang Z, Liu C, Li X. Genome-wide Characterization of Small Secreted Peptides in Nicotiana tabacum and Functional Assessment of NtLTP25 in Plant Immunity. PHYSIOLOGIA PLANTARUM 2024; 176:e14436. [PMID: 39019771 DOI: 10.1111/ppl.14436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/12/2024] [Accepted: 06/29/2024] [Indexed: 07/19/2024]
Abstract
Small secreted peptides (SSPs), serving as signaling molecules for intercellular communication, play significant regulatory roles in plant growth, development, pathogen immunity, and responses to abiotic stress. Despite several SSPs, such as PIP, PSK, and PSY having been identified to participate in plant immunity, the majority of SSPs remain understudied, necessitating the exploration and identification of SSPs regulating plant immunity from vast genomic resources. Here we systematically characterized 756 putative SSPs across the genome of Nicotiana tabacum. 173 SSPs were further annotated as established SSPs, such as nsLTP, CAPE, and CEP. Furthermore, we detected the expression of 484 putative SSP genes in five tissues, with 83 SSPs displaying tissue-specific expression. Transcriptomic analysis of tobacco roots under plant defense hormones revealed that 46 SSPs exhibited specific responsiveness to salicylic acid (SA), and such response was antagonistically regulated by methyl jasmonate. It's worth noting that among these 46 SSPs, 16 members belong to nsLTP family, and one of them, NtLTP25, was discovered to enhance tobacco's resistance against Phytophthora nicotianae. Overexpression of NtLTP25 in tobacco enhanced the expression of ICS1, subsequently stimulating the biosynthesis of SA and the expression of NPR1 and pathogenesis-related genes. Concurrently, NtLTP25 overexpression activated genes associated with ROS scavenging, consequently mitigating the accumulation of ROS during the subsequent phases of pathogenesis. These discoveries indicate that these 46 SSPs, especially the 16 nsLTPs, might have a vital role in governing plant immunity that relies on SA signaling. This offers a valuable source for pinpointing SSPs involved in regulating plant immunity.
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Affiliation(s)
- Han Li
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Yanxia Liu
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Weichang Gao
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Jingwei Zhu
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Heng Zhang
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
| | - Zhiyao Wang
- College of Tobacco Science, Guizhou University, Guiyang, P. R. China
| | - Changying Liu
- School of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
| | - Xiang Li
- Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, Guiyang, P. R. China
- Guizhou Branch Company of China Tobacco Corporation, Guiyang, P. R. China
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5
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Guéablé YKD, Jemo M, Soulaimani A, Hafidi M, El Gharous M, El Mejahed K. Sustainable strategy for rehabilitating phosphate mining sites and valorisation of phosphate industry by-products and sludge using pistachio tree (Pistacia atlantica), false pepper (Schinus molle), and eucalyptus (Eucalyptus globulus) trees. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 937:173485. [PMID: 38797404 DOI: 10.1016/j.scitotenv.2024.173485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
The development of anthroposols has been proposed as a new environmentally friendly approach to ensuring the successful revegetation of phosphate mining sites. The phosphate industry's by-products, including phosphogypsum (PG), phosphate sludge (PS), and sewage sludge (SS), can be valuable resources in restoring the ecological balance of mined soil areas. The aim of this study was to safely and sustainably restore the ecological integrity of the phosphate mining site through the evaluation of nutrients and heavy metals dynamics in soil and plant tissues of three tree species and treated by-products containing 65 % PG, 30 % PS, and 5 % SS. The tree species used were Pistacia atlantica, Schinus molle, and Eucalyptus globulus. The experimental layout was a randomised complete block design with six replicates and three treatments. Growth diameter, height, nutrient uptakes and heavy metal dynamic were evaluated from the rhizosphere soils and plant tissues over two years. Hierarchical head maps of correlations between the measured growth parameters, soil and nutrient uptakes of the tree species were analysed using a phylogenetic generalised linear mixed model. S. molle and E. globulus had higher average diameter and height than P. atlantica plants. P. atlantica and S. molle showed greater nitrogen, phosphorus, potassium, calcium, and magnesium concentrations than E. globulus trees. Tree growth parameters were closely linked to soil nutrient bioavailability. The heavy metal accumulation ratio was higher in the E. globulus and S. molle leaves than in stems. Using by-products could be valorised for rehabilitating mine sites together with E. globulus and S. molle species.
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Affiliation(s)
- Yao Kohou Donatien Guéablé
- Agricultural Innovation and Technology Transfer Center (AITTC), College of Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Martin Jemo
- Agrobiosciences Program, College of Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic (UM6P), 43150 Ben Guerir, Morocco
| | - Aziz Soulaimani
- Agricultural Innovation and Technology Transfer Center (AITTC), College of Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Mohamed Hafidi
- Labelled Research Unit N°4 CNRST, Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco; African Sustainable Agriculture Research Institute (ASARI), College of Sustainable Agriculture and Environmental Science, Mohammed VI Polytechnic University (UM6P), Laayoune, Morocco.
| | - Mohamed El Gharous
- Agricultural Innovation and Technology Transfer Center (AITTC), College of Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Khalil El Mejahed
- Agricultural Innovation and Technology Transfer Center (AITTC), College of Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco.
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6
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Roy S, Torres-Jerez I, Zhang S, Liu W, Schiessl K, Jain D, Boschiero C, Lee HK, Krom N, Zhao PX, Murray JD, Oldroyd GED, Scheible WR, Udvardi M. The peptide GOLVEN10 alters root development and noduletaxis in Medicago truncatula. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:607-625. [PMID: 38361340 DOI: 10.1111/tpj.16626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/27/2023] [Accepted: 12/27/2023] [Indexed: 02/17/2024]
Abstract
The conservation of GOLVEN (GLV)/ROOT MERISTEM GROWTH FACTOR (RGF) peptide encoding genes across plant genomes capable of forming roots or root-like structures underscores their potential significance in the terrestrial adaptation of plants. This study investigates the function and role of GOLVEN peptide-coding genes in Medicago truncatula. Five out of fifteen GLV/RGF genes were notably upregulated during nodule organogenesis and were differentially responsive to nitrogen deficiency and auxin treatment. Specifically, the expression of MtGLV9 and MtGLV10 at nodule initiation sites was contingent upon the NODULE INCEPTION transcription factor. Overexpression of these five nodule-induced GLV genes in hairy roots of M. truncatula and application of their synthetic peptide analogues led to a decrease in nodule count by 25-50%. Uniquely, the GOLVEN10 peptide altered the positioning of the first formed lateral root and nodule on the primary root axis, an observation we term 'noduletaxis'; this decreased the length of the lateral organ formation zone on roots. Histological section of roots treated with synthetic GOLVEN10 peptide revealed an increased cell number within the root cortical cell layers without a corresponding increase in cell length, leading to an elongation of the root likely introducing a spatiotemporal delay in organ formation. At the transcription level, the GOLVEN10 peptide suppressed expression of microtubule-related genes and exerted its effects by changing expression of a large subset of Auxin responsive genes. These findings advance our understanding of the molecular mechanisms by which GOLVEN peptides modulate root morphology, nodule ontogeny, and interactions with key transcriptional pathways.
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Affiliation(s)
- Sonali Roy
- College of Agriculture, Tennessee State University, Nashville, Tennessee, 37209, USA
- Noble Research Institute, LLC, Ardmore, Oklahoma, 73401, USA
| | - Ivone Torres-Jerez
- Noble Research Institute, LLC, Ardmore, Oklahoma, 73401, USA
- Institute of Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, 73401, USA
| | - Shulan Zhang
- Noble Research Institute, LLC, Ardmore, Oklahoma, 73401, USA
- Institute of Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, 73401, USA
| | - Wei Liu
- Noble Research Institute, LLC, Ardmore, Oklahoma, 73401, USA
| | | | - Divya Jain
- College of Agriculture, Tennessee State University, Nashville, Tennessee, 37209, USA
| | | | - Hee-Kyung Lee
- Institute of Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, 73401, USA
| | - Nicholas Krom
- Noble Research Institute, LLC, Ardmore, Oklahoma, 73401, USA
| | - Patrick X Zhao
- Noble Research Institute, LLC, Ardmore, Oklahoma, 73401, USA
| | - Jeremy D Murray
- Shanghai Institute of Plant Physiology and Ecology, Shanghai, 200032, China
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | | | - Michael Udvardi
- Noble Research Institute, LLC, Ardmore, Oklahoma, 73401, USA
- University of Queensland, Brisbane, Australia
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Xu C, Xiang L, Huang W, Zhang X, Mao C, Wu S, Li T, Wang S, Wang S. Unraveling a Small Secreted Peptide SUBPEP3 That Positively Regulates Salt-Stress Tolerance in Pyrus betulifolia. Int J Mol Sci 2024; 25:4612. [PMID: 38731831 PMCID: PMC11083645 DOI: 10.3390/ijms25094612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
Small secreted peptides (SSPs) play important roles in regulating plants' growth and development in response to external stimulus, but the genes and functions of SSPs in many species are still unknown. Therefore, it is particularly significant to characterize and annotate SSP genes in plant genomes. As a widely used stock of pears, Pyrus betulifolia has strong resistance to biotic and abiotic stresses. In this study, we analyzed the SSPs genes in the genome of P. betulifolia according to their characteristics and homology. A total of 1195 SSP genes were identified, and most of them are signaling molecules. Among these, we identified a new SSP, subtilase peptide 3 (SUBPEP3), which derived from the PA region of preSUBPEP3, increasing the expression level under salt stress. Both adding synthetic peptide SUBPEP3 to the culture medium of pears and the overexpression of SUBPEP3 in tobacco can improve the salt tolerance of plants. In summary, we annotated the SSP genes in the P. betulifolia genome and identified a small secreted peptide SUBPEP3 that regulates the salt tolerance of P. betulifolia, which provides an important theoretical basis for further revealing the function of SSPs.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shengnan Wang
- College of Horticulture, China Agricultural University, Beijing 100080, China
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8
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Wang R, Zhou Z, Wu X, Jiang X, Zhuo L, Liu M, Li H, Fu X, Yao X. An Effective Plant Small Secretory Peptide Recognition Model Based on Feature Correction Strategy. J Chem Inf Model 2024; 64:2798-2806. [PMID: 37643082 DOI: 10.1021/acs.jcim.3c00868] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Plant small secretory peptides (SSPs) play an important role in the regulation of biological processes in plants. Accurately predicting SSPs enables efficient exploration of their functions. Traditional experimental verification methods are very reliable and accurate, but they require expensive equipment and a lot of time. The method of machine learning speeds up the prediction process of SSPs, but the instability of feature extraction will also lead to further limitations of this type of method. Therefore, this paper proposes a new feature-correction-based model for SSP recognition in plants, abbreviated as SE-SSP. The model mainly includes the following three advantages: First, the use of transformer encoders can better reveal implicit features. Second, design a feature correction module suitable for sequences, named 2-D SENET, to adaptively adjust the features to obtain a more robust feature representation. Third, stack multiple linear modules to further dig out the deep information on the sample. At the same time, the training based on a contrastive learning strategy can alleviate the problem of sparse samples. We construct experiments on publicly available data sets, and the results verify that our model shows an excellent performance. The proposed model can be used as a convenient and effective SSP prediction tool in the future. Our data and code are publicly available at https://github.com/wrab12/SE-SSP/.
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Affiliation(s)
- Rui Wang
- Wenzhou University of Technology, 325000 Wenzhou, China
| | - Zhecheng Zhou
- Wenzhou University of Technology, 325000 Wenzhou, China
| | - Xiaonan Wu
- Wenzhou University of Technology, 325000 Wenzhou, China
| | - Xin Jiang
- Wenzhou University of Technology, 325000 Wenzhou, China
| | - Linlin Zhuo
- Wenzhou University of Technology, 325000 Wenzhou, China
| | - Mingzhe Liu
- Wenzhou University of Technology, 325000 Wenzhou, China
| | - Hao Li
- Central South University, 410083 Changsha, China
| | - Xiangzheng Fu
- Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
| | - Xiaojun Yao
- Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
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9
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Gasser M, Keller J, Fournier P, Pujic P, Normand P, Boubakri H. Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24. Sci Rep 2023; 13:16020. [PMID: 37749152 PMCID: PMC10520049 DOI: 10.1038/s41598-023-41117-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023] Open
Abstract
Non-specific lipid transfer proteins (nsLTPs) are antimicrobial peptides, involved in several plant biological processes including root nodule nitrogen fixation (RNF). Nodulating plants belonging to the RNF clade establish symbiosis with the nitrogen-fixing bacteria rhizobia (legumes symbiosis model) and Frankia (actinorhizal symbiosis model) leading to root nodule formation. nsLTPs are involved in processes active in early step of symbiosis and functional nodule in both models. In legumes, nsLTPs have been shown to regulate symbiont entry, promote root cortex infection, membrane biosynthesis, and improve symbiosis efficiency. More recently, a nsLTP, AgLTP24 has been described in the context of actinorhizal symbiosis between Alnus glutinosa and Frankia alni ACN14a. AgLTP24 is secreted at an early step of symbiosis on the deformed root hairs and targets the symbiont in the nitrogen-fixing vesicles in functional nodules. nsLTPs are involved in RNF, but their functions and evolutionary history are still largely unknown. Numerous putative nsLTPs were found up-regulated in functional nodules compared to non-infected roots in different lineages within the RNF clade. Here, results highlight that nodulating plants that are co-evolving with their nitrogen-fixing symbionts appear to have independently specialized nsLTPs for this interaction, suggesting a possible convergence of function, which opens perspectives to investigate nsLTPs functions in RNF.
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Affiliation(s)
- Mélanie Gasser
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Jean Keller
- LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Pascale Fournier
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Petar Pujic
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Philippe Normand
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Hasna Boubakri
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France.
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10
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Xu K, Tian D, Wang T, Zhang A, Elsadek MAY, Liu W, Chen L, Guo Y. Small secreted peptides (SSPs) in tomato and their potential roles in drought stress response. MOLECULAR HORTICULTURE 2023; 3:17. [PMID: 37789434 PMCID: PMC10515272 DOI: 10.1186/s43897-023-00063-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/28/2023] [Indexed: 10/05/2023]
Abstract
Tomato (Solanum lycopersicum) is one of the most important vegetable crops in the world and abiotic stresses often cause serious problems in tomato production. It is thus important to identify new regulators in stress response and to devise new approaches to promote stress tolerance in tomato. Previous studies have shown that small secreted peptides (SSPs) are important signal molecules regulating plant growth and stress response by mediating intercellular communication. However, little is known about tomato SSPs, especially their roles in responding to abiotic stresses. Here we report the identification of 1,050 putative SSPs in the tomato genome, 557 of which were classified into 38 known SSP families based on their conserved domains. GO and transcriptome analyses revealed that a large proportion of SlSSPs might be involved in abiotic stress response. Further analysis indicated that stress response related cis-elements were present on the SlCEP promotors and a number of SlCEPs were significantly upregulated by drought treatments. Among the drought-inducible SlCEPs, SlCEP10 and SlCEP11b were selected for further analysis via exogenous application of synthetic peptides. The results showed that treatments with both SlCEP10 and SlCEP11b peptides enhanced tomato drought stress tolerance, indicating the potential roles of SlSSPs in abiotic stress response.
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Affiliation(s)
- Kexin Xu
- Department of HorticultureCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Dongdong Tian
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - TingJin Wang
- Department of HorticultureCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Aijun Zhang
- Department of HorticultureCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | | | - Weihong Liu
- Department of HorticultureCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Liping Chen
- Department of HorticultureCollege of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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11
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Ruperao P, Rangan P, Shah T, Thakur V, Kalia S, Mayes S, Rathore A. The Progression in Developing Genomic Resources for Crop Improvement. Life (Basel) 2023; 13:1668. [PMID: 37629524 PMCID: PMC10455509 DOI: 10.3390/life13081668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Sequencing technologies have rapidly evolved over the past two decades, and new technologies are being continually developed and commercialized. The emerging sequencing technologies target generating more data with fewer inputs and at lower costs. This has also translated to an increase in the number and type of corresponding applications in genomics besides enhanced computational capacities (both hardware and software). Alongside the evolving DNA sequencing landscape, bioinformatics research teams have also evolved to accommodate the increasingly demanding techniques used to combine and interpret data, leading to many researchers moving from the lab to the computer. The rich history of DNA sequencing has paved the way for new insights and the development of new analysis methods. Understanding and learning from past technologies can help with the progress of future applications. This review focuses on the evolution of sequencing technologies, their significant enabling role in generating plant genome assemblies and downstream applications, and the parallel development of bioinformatics tools and skills, filling the gap in data analysis techniques.
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Affiliation(s)
- Pradeep Ruperao
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi 110012, India;
| | - Trushar Shah
- International Institute of Tropical Agriculture (IITA), Nairobi 30709-00100, Kenya;
| | - Vivek Thakur
- Department of Systems & Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India;
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi 110003, India;
| | - Sean Mayes
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Abhishek Rathore
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad 502324, India
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12
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Lagunas B, Richards L, Sergaki C, Burgess J, Pardal AJ, Hussain RMF, Richmond BL, Baxter L, Roy P, Pakidi A, Stovold G, Vázquez S, Ott S, Schäfer P, Gifford ML. Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth. MICROBIOME 2023; 11:146. [PMID: 37394496 DOI: 10.1186/s40168-023-01592-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Despite the knowledge that the soil-plant-microbiome nexus is shaped by interactions amongst its members, very little is known about how individual symbioses regulate this shaping. Even less is known about how the agriculturally important symbiosis of nitrogen-fixing rhizobia with legumes is impacted according to soil type, yet this knowledge is crucial if we are to harness or improve it. We asked how the plant, soil and microbiome are modulated by symbiosis between the model legume Medicago truncatula and different strains of Sinorhizobium meliloti or Sinorhizobium medicae whose nitrogen-fixing efficiency varies, in three distinct soil types that differ in nutrient fertility, to examine the role of the soil environment upon the plant-microbe interaction during nodulation. RESULTS The outcome of symbiosis results in installment of a potentially beneficial microbiome that leads to increased nutrient uptake that is not simply proportional to soil nutrient abundance. A number of soil edaphic factors including Zn and Mo, and not just the classical N/P/K nutrients, group with microbial community changes, and alterations in the microbiome can be seen across different soil fertility types. Root endosphere emerged as the plant microhabitat more affected by this rhizobial efficiency-driven community reshaping, manifested by the accumulation of members of the phylum Actinobacteria. The plant in turn plays an active role in regulating its root community, including sanctioning low nitrogen efficiency rhizobial strains, leading to nodule senescence in particular plant-soil-rhizobia strain combinations. CONCLUSIONS The microbiome-soil-rhizobial dynamic strongly influences plant nutrient uptake and growth, with the endosphere and rhizosphere shaped differentially according to plant-rhizobial interactions with strains that vary in nitrogen-fixing efficiency levels. These results open up the possibility to select inoculation partners best suited for plant, soil type and microbial community. Video Abstract.
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Affiliation(s)
- Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Luke Richards
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jamie Burgess
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Rana M F Hussain
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Laura Baxter
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Proyash Roy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Anastasia Pakidi
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Gina Stovold
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Saúl Vázquez
- University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Sascha Ott
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Present Address: Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, 35392, Germany.
| | - Miriam L Gifford
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV47AL, UK.
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13
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Huertas R, Torres-Jerez I, Curtin SJ, Scheible W, Udvardi M. Medicago truncatula PHO2 genes have distinct roles in phosphorus homeostasis and symbiotic nitrogen fixation. FRONTIERS IN PLANT SCIENCE 2023; 14:1211107. [PMID: 37409286 PMCID: PMC10319397 DOI: 10.3389/fpls.2023.1211107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
Three PHO2-like genes encoding putative ubiquitin-conjugating E2 enzymes of Medicago truncatula were characterized for potential roles in phosphorous (P) homeostasis and symbiotic nitrogen fixation (SNF). All three genes, MtPHO2A, B and C, contain miR399-binding sites characteristic of PHO2 genes in other plant species. Distinct spatiotemporal expression patterns and responsiveness of gene expression to P- and N-deprivation in roots and shoots indicated potential roles, especially for MtPHO2B, in P and N homeostasis. Phenotypic analysis of pho2 mutants revealed that MtPHO2B is integral to Pi homeostasis, affecting Pi allocation during plant growth under nutrient-replete conditions, while MtPHO2C had a limited role in controlling Pi homeostasis. Genetic analysis also revealed a connection between Pi allocation, plant growth and SNF performance. Under N-limited, SNF conditions, Pi allocation to different organs was dependent on MtPHO2B and, to a lesser extent, MtPHO2C and MtPHO2A. MtPHO2A also affected Pi homeostasis associated with nodule formation. Thus, MtPHO2 genes play roles in systemic and localized, i.e., nodule, P homeostasis affecting SNF.
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Affiliation(s)
- Raul Huertas
- Noble Research Institute LLC, Ardmore, OK, United States
| | | | - Shaun J. Curtin
- United States Department of Agriculture, Plant Science Research Unit, St. Paul, MN, United States
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
| | - Wolf Scheible
- Noble Research Institute LLC, Ardmore, OK, United States
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14
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Schnabel EL, Chavan SA, Gao Y, Poehlman WL, Feltus FA, Frugoli JA. A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2. Curr Issues Mol Biol 2023; 45:4612-4631. [PMID: 37367042 DOI: 10.3390/cimb45060293] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Nodule number regulation in legumes is controlled by a feedback loop that integrates nutrient and rhizobia symbiont status signals to regulate nodule development. Signals from the roots are perceived by shoot receptors, including a CLV1-like receptor-like kinase known as SUNN in Medicago truncatula. In the absence of functional SUNN, the autoregulation feedback loop is disrupted, resulting in hypernodulation. To elucidate early autoregulation mechanisms disrupted in SUNN mutants, we searched for genes with altered expression in the loss-of-function sunn-4 mutant and included the rdn1-2 autoregulation mutant for comparison. We identified constitutively altered expression of small groups of genes in sunn-4 roots and in sunn-4 shoots. All genes with verified roles in nodulation that were induced in wild-type roots during the establishment of nodules were also induced in sunn-4, including autoregulation genes TML2 and TML1. Only an isoflavone-7-O-methyltransferase gene was induced in response to rhizobia in wild-type roots but not induced in sunn-4. In shoot tissues of wild-type, eight rhizobia-responsive genes were identified, including a MYB family transcription factor gene that remained at a baseline level in sunn-4; three genes were induced by rhizobia in shoots of sunn-4 but not wild-type. We cataloged the temporal induction profiles of many small secreted peptide (MtSSP) genes in nodulating root tissues, encompassing members of twenty-four peptide families, including the CLE and IRON MAN families. The discovery that expression of TML2 in roots, a key factor in inhibiting nodulation in response to autoregulation signals, is also triggered in sunn-4 in the section of roots analyzed, suggests that the mechanism of TML regulation of nodulation in M. truncatula may be more complex than published models.
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Affiliation(s)
- Elise L Schnabel
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | - Yueyao Gao
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | - Frank Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, USA
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29636, USA
| | - Julia A Frugoli
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
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15
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Ivanovici A, Laffont C, Larrainzar E, Patel N, Winning CS, Lee HC, Imin N, Frugier F, Djordjevic MA. The Medicago SymCEP7 hormone increases nodule number via shoots without compromising lateral root number. PLANT PHYSIOLOGY 2023; 191:2012-2026. [PMID: 36653329 PMCID: PMC10022606 DOI: 10.1093/plphys/kiad012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Legumes acquire soil nutrients through nitrogen-fixing root nodules and lateral roots. To balance the costs and benefits of nodulation, legumes negatively control root nodule number by autoregulatory and hormonal pathways. How legumes simultaneously coordinate root nodule and lateral root development to procure nutrients remains poorly understood. In Medicago (Medicago truncatula), a subset of mature C-TERMINALLY ENCODED PEPTIDE (CEP) hormones can systemically promote nodule number, but all CEP hormones tested to date negatively regulate lateral root number. Here we showed that Medicago CEP7 produces a mature peptide, SymCEP7, that promotes nodulation from the shoot without compromising lateral root number. Rhizobial inoculation induced CEP7 in the susceptible root nodulation zone in a Nod factor-dependent manner, and, in contrast to other CEP genes, its transcription level was elevated in the ethylene signaling mutant sickle. Using mass spectrometry, fluorescence microscopy and expression analysis, we demonstrated that SymCEP7 activity requires the COMPACT ROOT ARCHITECTURE 2 receptor and activates the shoot-to-root systemic effector, miR2111. Shoot-applied SymCEP7 rapidly promoted nodule number in the pM to nM range at concentrations up to five orders of magnitude lower than effects mediated by root-applied SymCEP7. Shoot-applied SymCEP7 also promoted nodule number in White Clover (Trifolium repens) and Lotus (Lotus japonicus), which suggests that this biological function may be evolutionarily conserved. We propose that SymCEP7 acts in the Medicago shoot to counter balance the autoregulation pathways induced rapidly by rhizobia to enable nodulation without compromising lateral root growth, thus promoting the acquisition of nutrients other than nitrogen to support their growth.
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Affiliation(s)
- Ariel Ivanovici
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Carole Laffont
- University of Paris-Saclay, CNRS, INRAE, University Paris-Cité, Univ. d’Evry, Gif-sur-Yvette, France
| | - Estíbaliz Larrainzar
- Sciences Department, Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Pamplona 31006, Spain
| | - Neha Patel
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Courtney S Winning
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Han-Chung Lee
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Nijat Imin
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
- School of Science, Western Sydney University, Penrith, New South Wales 2751, Australia
- School of Biological Sciences, Faculty of Science, The University of Auckland, Auckland, New Zealand
| | - Florian Frugier
- University of Paris-Saclay, CNRS, INRAE, University Paris-Cité, Univ. d’Evry, Gif-sur-Yvette, France
| | - Michael A Djordjevic
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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16
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Nandety RS, Wen J, Mysore KS. Medicago truncatula resources to study legume biology and symbiotic nitrogen fixation. FUNDAMENTAL RESEARCH 2023; 3:219-224. [PMID: 38932916 PMCID: PMC11197554 DOI: 10.1016/j.fmre.2022.06.018] [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: 03/28/2022] [Revised: 06/01/2022] [Accepted: 06/19/2022] [Indexed: 10/17/2022] Open
Abstract
Medicago truncatula is a chosen model for legumes towards deciphering fundamental legume biology, especially symbiotic nitrogen fixation. Current genomic resources for M. truncatula include a completed whole genome sequence information for R108 and Jemalong A17 accessions along with the sparse draft genome sequences for other 226 M. truncatula accessions. These genomic resources are complemented by the availability of mutant resources such as retrotransposon (Tnt1) insertion mutants in R108 and fast neutron bombardment (FNB) mutants in A17. In addition, several M. truncatula databases such as small secreted peptides (SSPs) database, transporter protein database, gene expression atlas, proteomic atlas, and metabolite atlas are available to the research community. This review describes these resources and provide information regarding how to access these resources.
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Affiliation(s)
- Raja Sekhar Nandety
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401, United States
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, United States
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401, United States
| | - Kirankumar S. Mysore
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401, United States
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States
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17
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Li Z, Jin J, Wang Y, Long W, Ding Y, Hu H, Wei L. ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides. BIOINFORMATICS (OXFORD, ENGLAND) 2023; 39:7075544. [PMID: 36897030 PMCID: PMC10027287 DOI: 10.1093/bioinformatics/btad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 03/11/2023]
Abstract
MOTIVATION Plant Small Secreted Peptides (SSPs) play an important role in plant growth, development, and plant-microbe interactions. Therefore, the identification of SSPs is essential for revealing the functional mechanisms. Over the last few decades, machine learning-based methods have been developed, accelerating the discovery of SSPs to some extent. However, existing methods highly depend on handcrafted feature engineering, which easily ignores the latent feature representations and impacts the predictive performance. RESULTS Here, we propose ExamPle, a novel deep learning model using Siamese network and multi-view representation for the explainable prediction of the plant SSPs. Benchmarking comparison results show that our ExamPle performs significantly better than existing methods in the prediction of plant SSPs. Also, our model shows excellent feature extraction ability. Importantly, by utilizing in silicomutagenesis experiment, ExamPle can discover sequential characteristics and identify the contribution of each amino acid for the predictions. The key novel principle learned by our model is that the head region of the peptide and some specific sequential patterns are strongly associated with the SSPs' functions. Thus, ExamPle is expected to be a useful tool for predicting plant SSPs and designing effective plant SSPs. AVAILABILITY AND IMPLEMENTATION Our codes and datasets are available at https://github.com/Johnsunnn/ExamPle.
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Affiliation(s)
- Zhongshen Li
- School of Software, Shandong University, Jinan 250101, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250101, China
| | - Junru Jin
- School of Software, Shandong University, Jinan 250101, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250101, China
| | - Yu Wang
- School of Software, Shandong University, Jinan 250101, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250101, China
| | - Wentao Long
- School of Software, Shandong University, Jinan 250101, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250101, China
| | - Yuanhao Ding
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Haiyan Hu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Leyi Wei
- School of Software, Shandong University, Jinan 250101, China
- Joint SDU-NTU Centre for Artificial Intelligence Research (C-FAIR), Shandong University, Jinan 250101, China
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18
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Reynoso MA, Blanco FA, Zanetti ME. Nuclear and cytoplasmic lncRNAs in root tips of the model legume Medicago truncatula under control and submergence. IUBMB Life 2023. [PMID: 36852968 DOI: 10.1002/iub.2712] [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: 10/10/2022] [Accepted: 01/21/2023] [Indexed: 03/01/2023]
Abstract
In this study, we aimed to identify long noncoding RNAs (lncRNAs) in root tips of the model legume Medicago truncatula using previously generated nuclear, total polyA, ribosome-associated polyA, and Riboseq RNA datasets, which might shed light on their localization and potential regulatory roles. RNA-seq data were mapped to the version 5 of the M. truncatula A17 genome and analyzed to identify genome annotated lncRNAs and putative new root tip (NRT) lncRNAs. lncRNAs were classified according to their genomic location relative to chromatin accessible regions, protein-coding genes and transposable elements (TE), finding differences between annotated lncRNAs and NRT lncRNAs, both in their genomic position as well as in the type of TEs in their vicinity. We investigated their response to submergence and found a set of regulated lncRNAs that were preferentially upregulated in the nucleus, some of which were located nearby genes of the conserved submergence upregulated gene families, and chromatin accessible regions suggesting a potential regulatory role. Finally, the accumulation of lncRNAs under submergence was validated by reverse transcription quantitative polymerase chain reaction on nuclear RNA, providing additional evidence of their localization, which could ultimately be required for their function.
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Affiliation(s)
- Mauricio A Reynoso
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina.,Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, USA
| | - Flavio Antonio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
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19
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Álvarez-Urdiola R, Borràs E, Valverde F, Matus JT, Sabidó E, Riechmann JL. Peptidomics Methods Applied to the Study of Flower Development. Methods Mol Biol 2023; 2686:509-536. [PMID: 37540375 DOI: 10.1007/978-1-0716-3299-4_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Understanding the global and dynamic nature of plant developmental processes requires not only the study of the transcriptome, but also of the proteome, including its largely uncharacterized peptidome fraction. Recent advances in proteomics and high-throughput analyses of translating RNAs (ribosome profiling) have begun to address this issue, evidencing the existence of novel, uncharacterized, and possibly functional peptides. To validate the accumulation in tissues of sORF-encoded polypeptides (SEPs), the basic setup of proteomic analyses (i.e., LC-MS/MS) can be followed. However, the detection of peptides that are small (up to ~100 aa, 6-7 kDa) and novel (i.e., not annotated in reference databases) presents specific challenges that need to be addressed both experimentally and with computational biology resources. Several methods have been developed in recent years to isolate and identify peptides from plant tissues. In this chapter, we outline two different peptide extraction protocols and the subsequent peptide identification by mass spectrometry using the database search or the de novo identification methods.
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Affiliation(s)
- Raquel Álvarez-Urdiola
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Federico Valverde
- Institute for Plant Biochemistry and Photosynthesis CSIC - University of Seville, Seville, Spain
| | - José Tomás Matus
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - José Luis Riechmann
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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20
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Lebedeva MA, Gancheva MS, Kulaeva OA, Zorin EA, Dobychkina DA, Romanyuk DA, Sulima AS, Zhukov VA, Lutova LA. Identification and Expression Analysis of the C-TERMINALLY ENCODED PEPTIDE Family in Pisum sativum L. Int J Mol Sci 2022; 23:14875. [PMID: 36499210 PMCID: PMC9739355 DOI: 10.3390/ijms232314875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The C-TERMINALLY ENCODED PEPTIDE(CEP) peptides play crucial roles in plant growth and response to environmental factors. These peptides were characterized as positive regulators of symbiotic nodule development in legume plants. However, little is known about the CEP peptide family in pea. Here, we discovered in pea genome 21 CEP genes (PsCEPs), among which three genes contained additional conserved motifs corresponding to the PIP (PAMP-induced secreted peptides) consensus sequences. We characterized the expression patterns of pea PsCEP genes based on transcriptomic data, and for six PsCEP genes with high expression levels in the root and symbiotic nodules the detailed expression analysis at different stages of symbiosis and in response to nitrate treatment was performed. We suggest that at least three PsCEP genes, PsCEP1, PsCEP7 and PsCEP2, could play a role in symbiotic nodule development, whereas the PsCEP1 and PsCEP13 genes, downregulated by nitrate addition, could be involved in regulation of nitrate-dependent processes in pea. Further functional studies are required to elucidate the functions of these PsCEP genes.
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Affiliation(s)
- Maria A. Lebedeva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
| | - Maria S. Gancheva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
| | - Olga A. Kulaeva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Evgeny A. Zorin
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Daria A. Dobychkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
| | - Daria A. Romanyuk
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Anton S. Sulima
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Vladimir A. Zhukov
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Lyudmila A. Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
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21
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Carbonnel S, Falquet L, Hazak O. Deeper genomic insights into tomato CLE genes repertoire identify new active peptides. BMC Genomics 2022; 23:756. [PMID: 36396987 PMCID: PMC9670457 DOI: 10.1186/s12864-022-08980-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
In eukaryotes, cell-to-cell communication relies on the activity of small signaling peptides. In plant genomes, many hundreds of genes encode for such short peptide signals. However, only few of them are functionally characterized and due to the small gene size and high sequence variability, the comprehensive identification of such peptide-encoded genes is challenging. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) gene family encodes for short peptides that have a role in plant meristem maintenance, vascular patterning and responses to environment. The full repertoire of CLE genes and the role of CLE signaling in tomato (Solanum lycopersicum)- one of the most important crop plants- has not yet been fully studied.
Results
By using a combined approach, we performed a genome-wide identification of CLE genes using the current tomato genome version SL 4.0. We identified 52 SlCLE genes, including 37 new non annotated before. By analyzing publicly available RNAseq datasets we could confirm the expression of 28 new SlCLE genes. We found that SlCLEs are often expressed in a tissue-, organ- or condition-specific manner. Our analysis shows an interesting gene diversification within the SlCLE family that seems to be a result of gene duplication events. Finally, we could show a biological activity of selected SlCLE peptides in the root growth arrest that was SlCLV2-dependent.
Conclusions
Our improved combined approach revealed 37 new SlCLE genes. These findings are crucial for better understanding of the CLE signaling in tomato. Our phylogenetic analysis pinpoints the closest homologs of Arabidopsis CLE genes in tomato genome and can give a hint about the function of newly identified SlCLEs. The strategy described here can be used to identify more precisely additional short genes in plant genomes. Finally, our work suggests that the mechanism of root-active CLE peptide perception is conserved between Arabidopsis and tomato. In conclusion, our work paves the way to further research on the CLE-dependent circuits modulating tomato development and physiological responses.
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22
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Tian D, Xie Q, Deng Z, Xue J, Li W, Zhang Z, Dai Y, Zheng B, Lu T, De Smet I, Guo Y. Small secreted peptides encoded on the wheat ( triticum aestivum L.) genome and their potential roles in stress responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1000297. [PMID: 36212358 PMCID: PMC9532867 DOI: 10.3389/fpls.2022.1000297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Small secreted peptides (SSPs) are important signals for cell-to-cell communication in plant, involved in a variety of growth and developmental processes, as well as responses to stresses. While a large number of SSPs have been identified and characterized in various plant species, little is known about SSPs in wheat, one of the most important cereal crops. In this study, 4,981 putative SSPs were identified on the wheat genome, among which 1,790 TaSSPs were grouped into 38 known SSP families. The result also suggested that a large number of the putaitive wheat SSPs, Cys-rich peptides in particular, remained to be characterized. Several TaSSP genes were found to encode multiple SSP domains, including CLE, HEVEIN and HAIRPININ domains, and two potentially novel TaSSP family DYY and CRP8CI were identified manually among unpredicted TaSSPs. Analysis on the transcriptomic data showed that a great proportion of TaSSPs were expressed in response to abiotic stresses. Exogenous application of the TaCEPID peptide encoded by TraesCS1D02G130700 enhanced the tolerance of wheat plants to drought and salinity, suggesting porential roles of SSPs in regulating stress responses in wheat.
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Affiliation(s)
- Dongdong Tian
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qi Xie
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Zhichao Deng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jin Xue
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wei Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yifei Dai
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
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23
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Roy S, Müller LM. A rulebook for peptide control of legume-microbe endosymbioses. TRENDS IN PLANT SCIENCE 2022; 27:870-889. [PMID: 35246381 DOI: 10.1016/j.tplants.2022.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/25/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Plants engage in mutually beneficial relationships with microbes, such as arbuscular mycorrhizal fungi or nitrogen-fixing rhizobia, for optimized nutrient acquisition. In return, the microbial symbionts receive photosynthetic carbon from the plant. Both symbioses are regulated by the plant nutrient status, indicating the existence of signaling pathways that allow the host to fine-tune its interactions with the beneficial microbes depending on its nutrient requirements. Peptide hormones coordinate a plethora of developmental and physiological processes and, recently, various peptide families have gained special attention as systemic and local regulators of plant-microbe interactions and nutrient homeostasis. In this review, we identify five 'rules' or guiding principles that govern peptide function during symbiotic plant-microbe interactions, and highlight possible points of integration with nutrient acquisition pathways.
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Affiliation(s)
- Sonali Roy
- College of Agriculture, Tennessee State University, Nashville, TN 37209, USA.
| | - Lena Maria Müller
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA.
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24
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Rhodes J, Roman AO, Bjornson M, Brandt B, Derbyshire P, Wyler M, Schmid MW, Menke FLH, Santiago J, Zipfel C. Perception of a conserved family of plant signalling peptides by the receptor kinase HSL3. eLife 2022; 11:74687. [PMID: 35617122 PMCID: PMC9191895 DOI: 10.7554/elife.74687] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Plant genomes encode hundreds of secreted peptides; however, relatively few have been characterised. We report here an uncharacterised, stress-induced family of plant signalling peptides, which we call CTNIPs. Based on the role of the common co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) in CTNIP-induced responses, we identified in Arabidopsis thaliana the orphan receptor kinase HAESA-LIKE 3 (HSL3) as the CTNIP receptor via a proteomics approach. CTNIP binding, ligand-triggered complex formation with BAK1, and induced downstream responses all involve HSL3. Notably, the HSL3-CTNIP signalling module is evolutionarily conserved amongst most extant angiosperms. The identification of this novel signalling module will further shed light on the diverse functions played by plant signalling peptides and will provide insights into receptor-ligand co-evolution.
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Affiliation(s)
- Jack Rhodes
- The Sainsbury Laboratory, Norwich, United Kingdom
| | - Andra-Octavia Roman
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Marta Bjornson
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Benjamin Brandt
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | | | | | | | | | - Julia Santiago
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Cyril Zipfel
- Department of Plant Molecular Biology, University of Zurich, Zurich, Switzerland
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25
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Liu C, Xiang D, Wu Q, Ye X, Yan H, Zhao G, Zou L. Dynamic transcriptome and co-expression analysis suggest the potential roles of small secreted peptides from Tartary buckwheat (Fagopyrum tataricum) in low nitrogen stress response. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111091. [PMID: 34763875 DOI: 10.1016/j.plantsci.2021.111091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 10/03/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
Small secreted peptides (SSPs) regulate nitrogen (N) response and signaling in plants. Although much progress has been made in understanding the functions of SSPs in N response, very little information is available regarding non-model plants. Tartary buckwheat (Fagopyrum tataricum), a dicotyledonous crop, has a good adaptability to low N (LN) stress; however, little is known regarding the associated mechanisms underlying this adaptation. In this study, 932 putative SSPs were genome-wide characterized in TB genome. Of these SSPs, 233 SSPs were annotated as established SSPs, such as CLE, RALF, PSK, and CEP peptides. The gene expression of 675 putative SSPs was detected in five tissues and 258 SSPs were tissue-specific expressed genes. To analyze the responses of TB SSPs to LN, the dynamic expression analysis of TB roots under LN stress was conducted by RNA-seq. The expression of 378 putative TB SSP genes was detected with diverse expression patterns under LN stress, and some important LN-responsive SSPs were identified. Co-expression analysis suggested SSPs may regulate the adaptability of TB under LN conditions by modulating the expression of the genes involved in N transport and assimilation and IAA signaling. Furthermore, 53 LN stress-responsive RLKs encoding genes were identified and they were predicted as potential SSP receptors. This study expands the repertoire of SSPs in plants and provides useful information for further investigation of the functions of Tartary buckwheat SSPs in LN stress responses.
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Affiliation(s)
- Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, PR China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, PR China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, PR China
| | - Xueling Ye
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, PR China
| | - Huiling Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, PR China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, PR China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, PR China.
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26
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Küster H. The Medicago truncatula Transcriptome Database MtExpress: Genome-Wide Expression Profiles at Your Fingertips. PLANT & CELL PHYSIOLOGY 2021; 62:1359-1361. [PMID: 34545409 DOI: 10.1093/pcp/pcab144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Helge Küster
- Unit IV-Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, Hannover 30419, Germany
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27
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Ray P, Guo Y, Chi MH, Krom N, Boschiero C, Watson B, Huhman D, Zhao P, Singan VR, Lindquist EA, Yan J, Adam C, Craven KD. Serendipita Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic Relationship. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1128-1142. [PMID: 34260261 DOI: 10.1094/mpmi-04-21-0084-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid, and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant responses to Serendipita spp. colonization by characterizing the switchgrass root transcriptome during different stages of symbiosis in vitro. For this, we included a native switchgrass strain, Serendipita bescii, and a related strain, S. vermifera, isolated from Australian orchids. Serendipita colonization progresses from thin hyphae that grow between root cells to, finally, the production of large, bulbous hyphae that fill root cells during the later stages of colonization. We report that switchgrass seems to perceive both fungi prior to physical contact, leading to the activation of chemical and structural defense responses and putative host disease resistance genes. Subsequently, the host defense system appears to be quenched and carbohydrate metabolism adjusted, potentially to accommodate the fungal symbiont. In addition, prior to contact, switchgrass exhibited significant increases in root hair density and root surface area. Furthermore, genes involved in phytohormone metabolism such as gibberellin, jasmonic acid, and salicylic acid were activated during different stages of colonization. Both fungal strains induced plant gene expression in a similar manner, indicating a conserved plant response to members of this fungal order. Understanding plant responsiveness to Serendipita spp. will inform our efforts to integrate them into forages and row crops for optimal plant-microbe functioning, thus facilitating low-input, sustainable agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Yingqing Guo
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Bonnie Watson
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - David Huhman
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Patrick Zhao
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Vasanth R Singan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Erika A Lindquist
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Juying Yan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Catherine Adam
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
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28
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Cobos-Porras L, Rubia MI, Huertas R, Kum D, Dalton DA, Udvardi MK, Arrese-Igor C, Larrainzar E. Increased Ascorbate Biosynthesis Does Not Improve Nitrogen Fixation Nor Alleviate the Effect of Drought Stress in Nodulated Medicago truncatula Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:686075. [PMID: 34262586 PMCID: PMC8273863 DOI: 10.3389/fpls.2021.686075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
Legume plants are able to establish nitrogen-fixing symbiotic relations with Rhizobium bacteria. This symbiosis is, however, affected by a number of abiotic constraints, particularly drought. One of the consequences of drought stress is the overproduction of reactive oxygen (ROS) and nitrogen species (RNS), leading to cellular damage and, ultimately, cell death. Ascorbic acid (AsA), also known as vitamin C, is one of the antioxidant compounds that plants synthesize to counteract this oxidative damage. One promising strategy for the improvement of plant growth and symbiotic performance under drought stress is the overproduction of AsA via the overexpression of enzymes in the Smirnoff-Wheeler biosynthesis pathway. In the current work, we generated Medicago truncatula plants with increased AsA biosynthesis by overexpressing MtVTC2, a gene coding for GDP-L-galactose phosphorylase. We characterized the growth and physiological responses of symbiotic plants both under well-watered conditions and during a progressive water deficit. Results show that increased AsA availability did not provide an advantage in terms of plant growth or symbiotic performance either under well-watered conditions or in response to drought.
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Affiliation(s)
- Libertad Cobos-Porras
- Institute for Multidisciplinary Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - María Isabel Rubia
- Institute for Multidisciplinary Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Raúl Huertas
- Plant Biology Division, Noble Research Institute LLC, Ardmore, OK, United States
| | - David Kum
- Biology Department, Reed College, Portland, OR, United States
| | - David A. Dalton
- Biology Department, Reed College, Portland, OR, United States
| | - Michael K. Udvardi
- Plant Biology Division, Noble Research Institute LLC, Ardmore, OK, United States
| | - Cesar Arrese-Igor
- Institute for Multidisciplinary Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Estíbaliz Larrainzar
- Institute for Multidisciplinary Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Pamplona, Spain
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29
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Hu XL, Lu H, Hassan MM, Zhang J, Yuan G, Abraham PE, Shrestha HK, Villalobos Solis MI, Chen JG, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Cheng ZMM, Yang X. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. HORTICULTURE RESEARCH 2021; 8:130. [PMID: 34059650 PMCID: PMC8167165 DOI: 10.1038/s41438-021-00570-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/26/2021] [Indexed: 05/02/2023]
Abstract
Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant-microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.
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Affiliation(s)
- Xiao-Li Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zong-Ming Max Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Xiaohan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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30
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Lyapina I, Filippova A, Kovalchuk S, Ziganshin R, Mamaeva A, Lazarev V, Latsis I, Mikhalchik E, Panasenko O, Ivanov O, Ivanov V, Fesenko I. Possible role of small secreted peptides (SSPs) in immune signaling in bryophytes. PLANT MOLECULAR BIOLOGY 2021; 106:123-143. [PMID: 33713297 DOI: 10.1007/s11103-021-01133-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Plants utilize a plethora of peptide signals to regulate their immune response. Peptide ligands and their cognate receptors involved in immune signaling share common motifs among many species of vascular plants. However, the origin and evolution of immune peptides is still poorly understood. Here, we searched for genes encoding small secreted peptides in the genomes of three bryophyte lineages-mosses, liverworts and hornworts-that occupy a critical position in the study of land plant evolution. We found that bryophytes shared common predicted small secreted peptides (SSPs) with vascular plants. The number of SSPs is higher in the genomes of mosses than in both the liverwort Marchantia polymorpha and the hornwort Anthoceros sp. The synthetic peptide elicitors-AtPEP and StPEP-specific for vascular plants, triggered ROS production in the protonema of the moss Physcomitrella patens, suggesting the possibility of recognizing peptide ligands from angiosperms by moss receptors. Mass spectrometry analysis of the moss Physcomitrella patens, both the wild type and the Δcerk mutant secretomes, revealed peptides that specifically responded to chitosan treatment, suggesting their role in immune signaling.
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Affiliation(s)
- Irina Lyapina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna Filippova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Kovalchuk
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Rustam Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vassili Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Ivan Latsis
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Elena Mikhalchik
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Oleg Panasenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Oleg Ivanov
- V.F. Kuprevich Institute of Experimental Botany of the National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Vadim Ivanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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31
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Yoshida T, Fernie AR, Shinozaki K, Takahashi F. Long-distance stress and developmental signals associated with abscisic acid signaling in environmental responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:477-488. [PMID: 33249671 DOI: 10.1111/tpj.15101] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 05/03/2023]
Abstract
Flowering plants consist of highly differentiated organs, including roots, leaves, shoots and flowers, which have specific roles: root system for water and nutrient uptake, leaves for photosynthesis and gas exchange and reproductive organs for seed production. The communication between organs through the vascular system, by which water, nutrient and signaling molecules are transported, is essential for coordinated growth and development of the whole plant, particularly under adverse conditions. Here, we highlight recent progress in understanding how signaling pathways of plant hormones are associated with long-distance stress and developmental signals, with particular focus on environmental stress responses. In addition to the root-to-shoot peptide signal that induces abscisic acid accumulation in leaves under drought stress conditions, we summarize the diverse stress-responsive peptide signals reported to date to play a role in environmental responses.
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Affiliation(s)
- Takuya Yoshida
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan
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Echeverria A, Larrainzar E, Li W, Watanabe Y, Sato M, Tran CD, Moler JA, Hirai MY, Sawada Y, Tran LSP, Gonzalez EM. Medicago sativa and Medicago truncatula Show Contrasting Root Metabolic Responses to Drought. FRONTIERS IN PLANT SCIENCE 2021; 12:652143. [PMID: 33968107 PMCID: PMC8097159 DOI: 10.3389/fpls.2021.652143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/19/2021] [Indexed: 05/16/2023]
Abstract
Drought is an environmental stressor that affects crop yield worldwide. Understanding plant physiological responses to stress conditions is needed to secure food in future climate conditions. In this study, we applied a combination of plant physiology and metabolomic techniques to understand plant responses to progressive water deficit focusing on the root system. We chose two legume plants with contrasting tolerance to drought, the widely cultivated alfalfa Medicago sativa (Ms) and the model legume Medicago truncatula (Mt) for comparative analysis. Ms taproot (tapR) and Mt fibrous root (fibR) biomass increased during drought, while a progressive decline in water content was observed in both species. Metabolomic analysis allowed the identification of key metabolites in the different tissues tested. Under drought, carbohydrates, abscisic acid, and proline predominantly accumulated in leaves and tapRs, whereas flavonoids increased in fibRs in both species. Raffinose-family related metabolites accumulated during drought. Along with an accumulation of root sucrose in plants subjected to drought, both species showed a decrease in sucrose synthase (SUS) activity related to a reduction in the transcript level of SUS1, the main SUS gene. This study highlights the relevance of root carbon metabolism during drought conditions and provides evidence on the specific accumulation of metabolites throughout the root system.
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Affiliation(s)
- Andres Echeverria
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra, Pamplona, Spain
| | - Estíbaliz Larrainzar
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra, Pamplona, Spain
| | - Weiqiang Li
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, China
- Henan Joint International Laboratory for Crop Multi-Omics Research, Henan University, Kaifeng, China
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yasuko Watanabe
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Muneo Sato
- Metabolic System Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Cuong Duy Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Jose A. Moler
- Department of Statistics, Computing and Mathematics, Public University of Navarra, Pamplona, Spain
| | - Masami Yokota Hirai
- Metabolic System Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yuji Sawada
- Metabolic System Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Lam-Son Phan Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
- Lam-Son Phan Tran,
| | - Esther M. Gonzalez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra, Pamplona, Spain
- *Correspondence: Esther M. Gonzalez,
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Nitrate-Induced CLE Peptide Systemically Inhibits Nodulation in Medicago truncatula. PLANTS 2020; 9:plants9111456. [PMID: 33126720 PMCID: PMC7692534 DOI: 10.3390/plants9111456] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 01/03/2023]
Abstract
Legume plants form nitrogen-fixing nodules in symbiosis with soil bacteria rhizobia. The number of symbiotic nodules is controlled at the whole-plant level with autoregulation of nodulation (AON), which includes a shoot-acting CLV1-like receptor kinase and mobile CLE (CLAVATA3/ENDOSPERM SURROUNDING REGION-related) peptides that are produced in the root in response to rhizobia inoculation. In addition to rhizobia-induced CLE peptides, nitrate-induced CLE genes have been identified in Lotus japonicus and Glycine max, which inhibited nodulation when overexpressed. However, nitrate-induced CLE genes that systemically suppress nodulation in AON-dependent manner have not been identified in Medicago truncatula. Here, we found that MtCLE35 expression is activated by both rhizobia inoculation and nitrate treatment in M. truncatula, similarly to L. japonicus CLE genes. Moreover, we found that MtCLE35 systemically suppresses nodulation in AON-dependent manner, suggesting that MtCLE35 may mediate nitrate-induced inhibition of nodulation in M. truncatula.
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Larrainzar E, Villar I, Rubio MC, Pérez-Rontomé C, Huertas R, Sato S, Mun JH, Becana M. Hemoglobins in the legume-Rhizobium symbiosis. THE NEW PHYTOLOGIST 2020; 228:472-484. [PMID: 32442331 DOI: 10.1111/nph.16673] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/13/2020] [Indexed: 05/23/2023]
Abstract
Legume nodules have two types of hemoglobins: symbiotic or leghemoglobins (Lbs) and nonsymbiotic or phytoglobins (Glbs). The latter are categorized into three phylogenetic classes differing in heme coordination and O2 affinity. This review is focused on the roles of Lbs and Glbs in the symbiosis of rhizobia with crop legumes and the model legumes for indeterminate (Medicago truncatula) and determinate (Lotus japonicus) nodulation. Only two hemoglobin functions are well established in nodules: Lbs deliver O2 to the bacteroids and act as O2 buffers, preventing nitrogenase inactivation; and Glb1-1 modulates nitric oxide concentration during symbiosis, from the early stage, avoiding the plant's defense response, to nodule senescence. Here, we critically examine early and recent results, update and correct the information on Lbs and Glbs with the latest genome versions, provide novel expression data and identify targets for future research. Crucial unresolved questions include the expression of multiple Lbs in nodules, their presence in the nuclei and in uninfected nodule cells, and, intriguingly, their expression in nonsymbiotic tissues. RNA-sequencing data analysis shows that Lbs are expressed as early as a few hours after inoculation and that their mRNAs are also detectable in roots and pods, which clearly suggests that these heme proteins play additional roles unrelated to nitrogen fixation. Likewise, issues awaiting investigation are the functions of other Glbs in nodules, the spatiotemporal expression profiles of Lbs and Glbs at the mRNA and protein levels, and the molecular mechanisms underlying their regulation during nodule development and in response to stress and hormones.
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Affiliation(s)
- Estíbaliz Larrainzar
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Campus de Arrosadía, 31006, Pamplona, Spain
| | - Irene Villar
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Maria Carmen Rubio
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Carmen Pérez-Rontomé
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Raul Huertas
- Noble Research Institute LLC, 2510 Sam Noble Pkwy, Ardmore, OK, 73401, USA
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Jeong-Hwan Mun
- Department of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Korea
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
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Abstract
For the last century we have relied on model organisms to help understand fundamental biological processes. Now, with advancements in genome sequencing, assembly, and annotation, non-model organisms may be studied with the same advanced bioanalytical toolkit as model organisms. Proteomics is one such technique, which classically relies on predicted protein sequences to catalog and measure complex proteomes across tissues and biofluids. Applying proteomics to non-model organisms can advance and accelerate biomimicry studies, biomedical advancements, veterinary medicine, agricultural research, behavioral ecology, and food safety. In this postmodel organism era, we can study almost any species, meaning that many non-model organisms are, in fact, important emerging model organisms. Herein we specifically focus on eukaryotic organisms and discuss the steps to generate sequence databases, analyze proteomic data with or without a database, and interpret results as well as future research opportunities. Proteomics is more accessible than ever before and will continue to rapidly advance in the coming years, enabling critical research and discoveries in non-model organisms that were hitherto impossible.
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Affiliation(s)
- Michelle Heck
- Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, NY, USA
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Benjamin A. Neely
- Chemical Sciences Division, National Institute of Standards and Technology, Charleston, SC, USA
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Hellmann E. MtSSPdb: A New Database for the Small Secreted Peptide Research Community. PLANT PHYSIOLOGY 2020; 183:31-32. [PMID: 32385183 PMCID: PMC7210643 DOI: 10.1104/pp.20.00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Eva Hellmann
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
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