1
|
Laghouaouta H, Laplana M, Ros-Freixedes R, Fraile LJ, Pena RN. Sequence variants associated with resilient responses in growing pigs. J Anim Breed Genet 2024. [PMID: 38967062 DOI: 10.1111/jbg.12886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024]
Abstract
The current work aimed to identify genomic regions and candidate genes associated with resilience in pigs. In previous work, we proposed the body weight deviation from the expected growth curve (ΔBW) and the increase of the positive acute-phase protein haptoglobin (ΔHP) after a vaccine challenge as resilience indicators which may be improved through selective breeding in pigs. Individuals with steady growth rate and minor activation of haptoglobin (high ΔBW and low ΔHP values) were considered resilient. In contrast, pigs with perturbed growth rate and high activation of haptoglobin (low ΔBW and high ΔHP values) were considered susceptible. Both ∆BW and ∆HP were simultaneously considered to select the most resilient (N = 40) and susceptible (N = 40) pigs. A genome-wide association study was carried out for the pigs' response classification to the challenge test using whole-genome sequence data (7,760,720 variants). Eleven associated genomic regions were identified, harbouring relevant candidate genes related to the immune response (such as pro- and anti-inflammatory responses) and growth pathways. These associated genomic regions harboured 41 potential functional mutations (frameshift, splice donor, splice acceptor, start loss and stop loss/gain) in candidate genes. Overall, this study advances our knowledge about the genetic determinism of resilience, highlighting its polygenic nature and strong relationship with immunity and growth.
Collapse
Affiliation(s)
- Houda Laghouaouta
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Marina Laplana
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Lorenzo J Fraile
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| |
Collapse
|
2
|
Liu M, Sui Y, Yu C, Wang X, Zhang W, Wang B, Yan J, Duan L. Coronatine-Induced Maize Defense against Gibberella Stalk Rot by Activating Antioxidants and Phytohormone Signaling. J Fungi (Basel) 2023; 9:1155. [PMID: 38132756 PMCID: PMC10744721 DOI: 10.3390/jof9121155] [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: 10/16/2023] [Revised: 11/25/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023] Open
Abstract
One of the most destructive diseases, Gibberella stalk rot (GSR), caused by Fusarium graminearum, reduces maize yields significantly. An induced resistance response is a potent and cost-effective plant defense against pathogen attack. The functional counterpart of JAs, coronatine (COR), has attracted a lot of interest recently due to its ability to control plant growth and stimulate secondary metabolism. Although several studies have focused on COR as a plant immune elicitor to improve plant resistance to pathogens, the effectiveness and underlying mechanisms of the suppressive ability against COR to F. graminearum in maize have been limited. We investigated the potential physiological and molecular mechanisms of COR in modulating maize resistance to F. graminearum. COR treatment strongly enhanced disease resistance and promoted stomatal closure with H2O2 accumulation, and 10 μg/mL was confirmed as the best concentration. COR treatment increased defense-related enzyme activity and decreased the malondialdehyde content with enhanced antioxidant enzyme activity. To identify candidate resistance genes and gain insight into the molecular mechanism of GSR resistance associated with COR, we integrated transcriptomic and metabolomic data to systemically explore the defense mechanisms of COR, and multiple hub genes were pinpointed using weighted gene correlation network analysis (WGCNA). We discovered 6 significant modules containing 10 candidate genes: WRKY transcription factor (LOC100279570), calcium-binding protein (LOC100382070), NBR1-like protein (LOC100275089), amino acid permease (LOC100382244), glutathione S-transferase (LOC541830), HXXXD-type acyl-transferase (LOC100191608), prolin-rich extensin-like receptor protein kinase (LOC100501564), AP2-like ethylene-responsive transcription factor (LOC100384380), basic leucine zipper (LOC100275351), and glycosyltransferase (LOC606486), which are highly correlated with the jasmonic acid-ethylene signaling pathway and antioxidants. In addition, a core set of metabolites, including alpha-linolenic acid metabolism and flavonoids biosynthesis linked to the hub genes, were identified. Taken together, our research revealed differentially expressed key genes and metabolites, as well as co-expression networks, associated with COR treatment of maize stems after F. graminearum infection. In addition, COR-treated maize had higher JA (JA-Ile and Me-JA) levels. We postulated that COR plays a positive role in maize resistance to F. graminearum by regulating antioxidant levels and the JA signaling pathway, and the flavonoid biosynthesis pathway is also involved in the resistance response against GSR.
Collapse
Affiliation(s)
- Mei Liu
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yiping Sui
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy, China Agricultural University, Beijing 100193, China
| | - Chunxin Yu
- Beijing Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wei Zhang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Baomin Wang
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy, China Agricultural University, Beijing 100193, China
| | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Liusheng Duan
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy, China Agricultural University, Beijing 100193, China
| |
Collapse
|
3
|
Kesawat MS, Kherawat BS, Katara JL, Parameswaran C, Misra N, Kumar M, Chung SM, Alamri S, Siddiqui MH. Genome-Wide Analysis of Proline-Rich Extensin-Like Receptor Kinases (PERKs) Gene Family Reveals Their Roles in Plant Development and Stress Conditions in Oryza sativa L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023:111749. [PMID: 37244501 DOI: 10.1016/j.plantsci.2023.111749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Proline-rich extensin-like receptor kinases (PERKs) play a crucial role in a wide range of biological processes in plants. In model plants like Arabidopsis, the PERK gene family has been well investigated. Conversely, no information available on the PERK gene family and their biological functions largely remained unknown in rice. This study analyzed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, Gene ontology (GO) annotation and protein-protein interaction of OsPERK gene family members using various bioinformatics tools based on the whole-genome data of O. sativa. Thus, in this work, 8 PERK genes in rice were identified, and their roles in plant development, growth, and response to various stresses were studied. A phylogenetic study revealed that OsPERKs are grouped into seven classes. Chromosomal mapping also displayed that 8 PERK genes were unevenly distributed on 12 chromosomes. Further, the prediction of subcellular localization indicated that OsPERKs were mainly located at the endomembrane system. Gene structure analysis of OsPERKs has shown a distinctive evolutionary path. In addition, synteny analysis exhibited the 40 orthologous gene pairs in Arabidopsis thaliana, Triticum aestivum, Hordeum vulgare and Medicago truncatula. Furthermore, Ka to Ks proportion shows that most OsPERK genes experienced resilient purifying selection during evolutionary processes. The OsPERK promoters contained several cis-acting regulatory, which are crucial for plant development processes, phytohormone signaling, stress, and defense response. Moreover, the expression pattern of OsPERK family members showed differential expression patterns in different tissues and various stress conditions. Taken together, these results provide clear messages for a better understanding the roles of OsPERK genes in various development stages, tissues, and multifactorial stress as well as enriched the related research of OsPERK family members in rice.
Collapse
Affiliation(s)
- Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India.
| | - Bhagwat Singh Kherawat
- Krishi Vigyan Kendra, Bikaner II, Swami Keshwanand Rajasthan Agricultural University, Bikaner 334603, Rajasthan, India.
| | - Jawahar Lal Katara
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack 753 006 Odisha, India.
| | | | - Namrata Misra
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology 13 (KIIT), Deemed to be University, Bhubaneswar-751024, Odisha, India.
| | - Manu Kumar
- Department of Life Science, Dongguk University Dong-gu-10326, Ilsan, Republic of South Korea.
| | - Sang-Min Chung
- Department of Life Science, Dongguk University Dong-gu-10326, Ilsan, Republic of South Korea.
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
| |
Collapse
|
4
|
Wang L, Wu S, Liu X, Liu N. The carbon and nitrogen metabolisms of Ardisia quinquegona were altered in different degrees by canopy and understory nitrogen addition in a subtropical forest. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:57653-57666. [PMID: 36971945 DOI: 10.1007/s11356-023-26478-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/12/2023] [Indexed: 05/10/2023]
Abstract
Although effects of atmospheric nitrogen (N) deposition on forest plants have been widely investigated, N interception and absorption effects by forest canopy should not be neglected. Moreover, how N deposition change the molecular biological process of understory dominant plants, which was easily influenced by canopy interception so as to further change physiological performance, remains poorly understood. To assess the effects of N deposition on forest plants, we investigated the effects of understory (UAN) and canopy N addition (CAN) on the transcriptome and physiological properties of Ardisia quinquegona, a dominant subtropical understory plant species in an evergreen broad-leaved forest in China. We identified a total of 7394 differentially expressed genes (DEGs). Three of these genes were found to be co-upregulated in CAN as compared to control (CK) after 3 and 6 h of N addition treatment, while 133 and 3 genes were respectively found to be co-upregulated and co-downregulated in UAN as compared to CK. In addition, highly expressed genes including GP1 (a gene involved in cell wall biosynthesis) and STP9 (sugar transport protein 9) were detected in CAN, which led to elevated photosynthetic capacity and accumulation of protein and amino acid as well as decrease in glucose, sucrose, and starch contents. On the other hand, genes associated with transport, carbon and N metabolism, redox response, protein phosphorylation, cell integrity, and epigenetic regulation mechanism were affected by UAN, resulting in enhanced photosynthetic capacity and carbohydrates and accumulation of protein and amino acid. In conclusion, our results showed that the CAN compared to UAN treatment had less effects on gene regulation and carbon and N metabolism. Canopy interception of N should be considered through CAN treatment to simulate N deposition in nature.
Collapse
Affiliation(s)
- Liyuan Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shuhua Wu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuncheng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| | - Nan Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| |
Collapse
|
5
|
Dong Y, Feng ZQ, Ye F, Li T, Li GL, Li ZS, Hao YC, Zhang XH, Liu WX, Xue JQ, Xu ST. Genome-wide association analysis for grain moisture content and dehydration rate on maize hybrids. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:5. [PMID: 37312866 PMCID: PMC10248682 DOI: 10.1007/s11032-022-01349-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/13/2022] [Indexed: 06/15/2023]
Abstract
For mechanized maize production, a low grain water content (GWC) at harvest is necessary. However, as a complex quantitative trait, understand the genetic mechanism of GWC remains a large gap, especially in hybrids. In this study, a hybrid population through two environments including 442 F1 was used for genome-wide association analysis of GWC and the grain dehydration rate (GDR), using the area under the dry down curve (AUDDC) as the index. Then, we identified 19 and 17 associated SNPs for GWC and AUDDC, including 10 co-localized SNPs, along with 64 and 77 pairs of epistatic SNPs for GWC and AUDDC, respectively. These loci could explain 11.39-68.2% of the total phenotypic variation for GWC and 41.07-67.02% for AUDDC at different stages, whose major effect was the additive and epistatic effect. By exploring the candidate genes around the significant sites, a total of 398 and 457 possible protein-coding genes were screened, including autophagy pathway and auxin regulation-related genes, and five inbred lines with the potential to reduce GWC in the combined F1 hybrid were identified. Our research not only provides a certain reference for the genetic mechanism analysis of GWC in hybrids but also provides an added reference for breeding low-GWC materials. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01349-x.
Collapse
Affiliation(s)
- Yuan Dong
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Zhi-qian Feng
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Fan Ye
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Ting Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Guo-liang Li
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193 China
| | - Zhou-Shuai Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Yin-chuan Hao
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Xing-hua Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Wen-xin Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193 China
| | - Ji-quan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| | - Shu-tu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100 Shaanxi China
| |
Collapse
|
6
|
Qiu Z, Zhuang K, Liu Y, Ge X, Chen C, Hu S, Han H. Functional characterization of C-TERMINALLY ENCODED PEPTIDE (CEP) family in Brassica rapa L. PLANT SIGNALING & BEHAVIOR 2022; 17:2021365. [PMID: 34968412 PMCID: PMC8920145 DOI: 10.1080/15592324.2021.2021365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The small regulatory C-TERMINALLY ENCODED PEPTIDE (CEP) peptide family plays crucial roles in plant growth and stress response. However, little is known about this peptide family in Brassica species. Here, we performed a systematic analysis to identify the putative Brassica rapa L. CEP (BrCEP) gene family. In total, 27 BrCEP genes were identified and they were classified into four subgroups based on the CEP motifs similarity. BrCEP genes displayed distinct expression patterns in response to both developmental and several environmental signals, suggesting their broad roles during Brassica rapa development. Furthuremore, the synthetic BrCEP3 peptide accelerated Brassica rapa primary root growth in a hydrogen peroxide (H2O2) and Ca2+ dependent manner. In summary, our work will provide fundamental insights into the physiological function of CEP peptides during Brassica rapa development.
Collapse
Affiliation(s)
- Ziwen Qiu
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Keqing Zhuang
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Yiting Liu
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaomin Ge
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an City, Shaanxi Province, China
| | - Chen Chen
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi’an City, Shaanxi Province, China
| | - Songping Hu
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Huibin Han
- Research Center for Plant Functional Genes and Tissue Culture Technology; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| |
Collapse
|
7
|
Invernizzi M, Hanemian M, Keller J, Libourel C, Roby D. PERKing up our understanding of the proline-rich extensin-like receptor kinases, a forgotten plant receptor kinase family. THE NEW PHYTOLOGIST 2022; 235:875-884. [PMID: 35451507 DOI: 10.1111/nph.18166] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Proline-rich extensin-like receptor kinases (PERKs) are an important class of receptor-like kinases (RLKs) containing an extracellular proline-rich domain. While they are thought to be putative sensors of the cell wall integrity, there are very few reports on their biological functions in the plant, as compared with other RLKs. Several studies support a role for PERKs in plant growth and development, but their effect on the cell wall composition to regulate cell expansion is still lacking. Gene expression data suggest that they may intervene in response to environmental changes, in agreement with their subcellular localization. And there is growing evidence for PERKs as novel sensors of environmental stresses such as insects and viruses. However, little is known about their precise role in plant immunity and in the extracellular network of RLKs, as no PERK-interacting RLK or any coreceptor has been identified as yet. Similarly, their signaling activities and downstream signaling components are just beginning to be deciphered, including Ca2+ fluxes, reactive oxygen species accumulation and phosphorylation events. Here we outline emerging roles for PERKs as novel sensors of environmental stresses, and we discuss how to better understand this overlooked class of receptor kinases via several avenues of research.
Collapse
Affiliation(s)
- Marie Invernizzi
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Mathieu Hanemian
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), CNRS, UPS, INP Toulouse, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), CNRS, UPS, INP Toulouse, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Dominique Roby
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
| |
Collapse
|
8
|
Insight into the Roles of Proline-Rich Extensin-like Receptor Protein Kinases of Bread Wheat ( Triticum aestivum L.). LIFE (BASEL, SWITZERLAND) 2022; 12:life12070941. [PMID: 35888032 PMCID: PMC9323123 DOI: 10.3390/life12070941] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 12/26/2022]
Abstract
Proline-rich extensin-like receptor protein kinases (PERKs) are known for their roles in the developmental processes and stress responses of many plants. We have identified 30 TaPERK genes in the genome of T. aestivum, exploring their evolutionary and syntenic relationship and analyzing their gene and protein structures, various cis-regulatory elements, expression profiling, and interacting miRNAs. The TaPERK genes formed 12 homeologous groups and clustered into four phylogenetic clades. All the proteins exhibited a typical domain organization of PERK and consisted of conserved proline residue repeats and serine-proline and proline-serine repeats. Further, the tyrosine-x-tyrosine (YXY) motif was also found conserved in thirteen TaPERKs. The cis-regulatory elements and expression profiling under tissue developmental stages suggested their role in plant growth processes. Further, the differential expression of certain TaPERK genes under biotic and abiotic stress conditions suggested their involvement in defense responses as well. The interaction of TaPERK genes with different miRNAs further strengthened evidence for their diverse biological roles. In this study, a comprehensive analysis of obtained TaPERK genes was performed, enriching our knowledge of TaPERK genes and providing a foundation for further possible functional analyses in future studies.
Collapse
|
9
|
Kesawat MS, Kherawat BS, Singh A, Dey P, Routray S, Mohapatra C, Saha D, Ram C, Siddique KHM, Kumar A, Gupta R, Chung SM, Kumar M. Genome-Wide Analysis and Characterization of the Proline-Rich Extensin-like Receptor Kinases (PERKs) Gene Family Reveals Their Role in Different Developmental Stages and Stress Conditions in Wheat ( Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:496. [PMID: 35214830 PMCID: PMC8880425 DOI: 10.3390/plants11040496] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 05/19/2023]
Abstract
Proline-rich extensin-like receptor kinases (PERKs) are a class of receptor kinases implicated in multiple cellular processes in plants. However, there is a lack of information on the PERK gene family in wheat. Therefore, we identified 37 PERK genes in wheat to understand their role in various developmental processes and stress conditions. Phylogenetic analysis of PERK genes from Arabidopsis thaliana, Oryza sativa, Glycine max, and T. aestivum grouped them into eight well-defined classes. Furthermore, synteny analysis revealed 275 orthologous gene pairs in B. distachyon, Ae. tauschii, T. dicoccoides, O. sativa and A. thaliana. Ka/Ks values showed that most TaPERK genes, except TaPERK1, TaPERK2, TaPERK17, and TaPERK26, underwent strong purifying selection during evolutionary processes. Several cis-acting regulatory elements, essential for plant growth and development and the response to light, phytohormones, and diverse biotic and abiotic stresses, were predicted in the promoter regions of TaPERK genes. In addition, the expression profile of the TaPERK gene family revealed differential expression of TaPERK genes in various tissues and developmental stages. Furthermore, TaPERK gene expression was induced by various biotic and abiotic stresses. The RT-qPCR analysis also revealed similar results with slight variation. Therefore, this study's outcome provides valuable information for elucidating the precise functions of TaPERK in developmental processes and diverse stress conditions in wheat.
Collapse
Affiliation(s)
- Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Bhagwat Singh Kherawat
- Krishi Vigyan Kendra, Bikaner II, Swami Keshwanand Rajasthan Agricultural University, Bikaner 334603, Rajasthan, India;
| | - Anupama Singh
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
| | - Prajjal Dey
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
| | - Snehasish Routray
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (S.R.); (C.M.)
| | - Chinmayee Mohapatra
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (S.R.); (C.M.)
| | - Debanjana Saha
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneshwar 752050, Odisha, India;
| | - Chet Ram
- ICAR-Central Institute for Arid Horticulture, Bikaner 334006, Rajasthan, India;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia;
| | - Ajay Kumar
- Agriculture Research Organization, Volcani Center, Department of Postharvest Science, Rishon Lezzion 50250, Israel;
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Korea;
| | - Sang-Min Chung
- Department of Life Science, Dongguk University, Dong-gu, Ilsan, Seoul 10326, Korea;
| | - Manu Kumar
- Department of Life Science, Dongguk University, Dong-gu, Ilsan, Seoul 10326, Korea;
| |
Collapse
|
10
|
Borassi C, Sede AR, Mecchia MA, Mangano S, Marzol E, Denita-Juarez SP, Salgado Salter JD, Velasquez SM, Muschietti JP, Estevez JM. Proline-rich extensin-like receptor kinases PERK5 and PERK12 are involved in pollen tube growth. FEBS Lett 2021; 595:2593-2607. [PMID: 34427925 DOI: 10.1002/1873-3468.14185] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/17/2021] [Accepted: 08/18/2021] [Indexed: 11/06/2022]
Abstract
Proline-rich extensin-like receptor kinases (PERKs) belong to the hydroxyproline-rich glycoprotein (HRGP) superfamily known to be involved in many plant developmental processes. Here, we characterized two pollen-expressed PERKs from Arabidopsis thaliana, PERK5 and PERK12. Pollen tube growth was impaired in single and double perk5-1 perk12-1 loss of function mutants, with an impact on seed production. When the segregation was analysed, a male gametophytic defect was found, indicating that perk5-1 and perk12-1 mutants carry deficient pollen transmission. Furthermore, perk5-1 perk12-1 displayed an excessive accumulation of pectins and cellulose at the cell wall of the pollen tubes. Our results indicate that PERK5 and PERK12 are necessary for proper pollen tube growth, highlighting their role in cell wall assembly and reactive oxygen species homeostasis.
Collapse
Affiliation(s)
- Cecilia Borassi
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE-UBA CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Ana R Sede
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina.,Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, "Dr. Héctor Torres" (INGEBI-CONICET), Buenos Aires, Argentina
| | - Martín A Mecchia
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Silvina Mangano
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE-UBA CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Eliana Marzol
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Silvina P Denita-Juarez
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE-UBA CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Juan D Salgado Salter
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE-UBA CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | | | - Jorge P Muschietti
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, "Dr. Héctor Torres" (INGEBI-CONICET), Buenos Aires, Argentina.,Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires, Argentina
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE-UBA CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina.,Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello and ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| |
Collapse
|
11
|
Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
Collapse
Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| |
Collapse
|
12
|
Petersen BL, MacAlister CA, Ulvskov P. Plant Protein O-Arabinosylation. FRONTIERS IN PLANT SCIENCE 2021; 12:645219. [PMID: 33815452 PMCID: PMC8012813 DOI: 10.3389/fpls.2021.645219] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/22/2021] [Indexed: 05/26/2023]
Abstract
A wide range of proteins with diverse functions in development, defense, and stress responses are O-arabinosylated at hydroxyprolines (Hyps) within distinct amino acid motifs of continuous stretches of Hyps, as found in the structural cell wall extensins, or at non-continuous Hyps as, for example, found in small peptide hormones and a variety of plasma membrane proteins involved in signaling. Plant O-glycosylation relies on hydroxylation of Prolines to Hyps in the protein backbone, mediated by prolyl-4-hydroxylase (P4H) which is followed by O-glycosylation of the Hyp C4-OH group by either galactosyltransferases (GalTs) or arabinofuranosyltranferases (ArafTs) yielding either Hyp-galactosylation or Hyp-arabinosylation. A subset of the P4H enzymes with putative preference to hydroxylation of continuous prolines and presumably all ArafT enzymes needed for synthesis of the substituted arabinose chains of one to four arabinose units, have been identified and functionally characterized. Truncated root-hair phenotype is one common denominator of mutants of Hyp formation and Hyp-arabinosylation glycogenes, which act on diverse groups of O-glycosylated proteins, e.g., the small peptide hormones and cell wall extensins. Dissection of different substrate derived effects may not be regularly feasible and thus complicate translation from genotype to phenotype. Recently, lack of proper arabinosylation on arabinosylated proteins has been shown to influence their transport/fate in the secretory pathway, hinting to an additional layer of functionality of O-arabinosylation. Here, we provide an update on the prevalence and types of O-arabinosylated proteins and the enzymatic machinery responsible for their modifications.
Collapse
Affiliation(s)
- Bent Larsen Petersen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Cora A. MacAlister
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|