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Shokri-Gharelo R, Derakhti-Dizaji M, Dadashi D, Chalekaei M, Rostami-Tobnag G. Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses. Biosystems 2024; 237:105165. [PMID: 38430956 DOI: 10.1016/j.biosystems.2024.105165] [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: 10/30/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Abiotic stresses are predominant and main causes of the losses in the crop yield. A complexity of systems biology and involvement of numerous genes in the response to abiotic factors have challenged efforts to create tolerant cultivars with sustainable production. The root is the main organ of the plant and determines a plant tolerance under stressful conditions. In this study, we carried out a meta-analysis of expression datasets from wheat root to identify differentially expressed genes, followed by the weighted gene co-expression network analysis (WGCNA) to construct the weighted gene co-expression network. The aim was to identify consensus differentially expressed genes with regulatory functions, gene networks, and biological pathways involved in response of wheat root to a set of abiotic stresses. The meta-analysis using Fisher method (FDR<0.05) identified consensus 526 DEGs from 55,367 probe sets. Although the annotated expression data are limited for wheat, the functional analysis based on the data from model plants could identify the up-regulated seven regulatory genes involved in chromosome organization and response to oxygen-containing compounds. WGCNA identified four gene modules that were mostly associated with the ribosome biogenesis and polypeptide synthesis. This study's findings enhance our understanding of key players and gene networks related to wheat root response to multiple abiotic stresses.
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Affiliation(s)
- Reza Shokri-Gharelo
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran; Researcher of Sugar Beet Seed Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Morteza Derakhti-Dizaji
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran
| | - Davod Dadashi
- Department of Plant Breeding and Biotechnology, College of Agriculture, University of Tabriz, Tabriz, Iran
| | - Maryam Chalekaei
- Department of Agronomy and Plant Breeding, Agricultural College, University of Tehran, Iran
| | - Ghader Rostami-Tobnag
- Department of Horticulture, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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2
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Xie S, Luo G, An G, Wang B, Kuang H, Wang X. Lskipk Lsatpase double mutants are necessary and sufficient for the compact plant architecture of butterhead lettuce. HORTICULTURE RESEARCH 2024; 11:uhad280. [PMID: 38371637 PMCID: PMC10873588 DOI: 10.1093/hr/uhad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/11/2023] [Indexed: 02/20/2024]
Abstract
Lettuce, an important leafy vegetable crop worldwide, has rich variations in plant architecture. Butterhead lettuce, a popular horticultural type, has a unique plant architecture with loose leafy heads. The genetic and molecular mechanisms for such a compact plant architecture remain unclear. In this study we constructed a segregating population through crossing a butterhead cultivar and a stem lettuce cultivar. Genetic analysis identified the LsKIPK gene, which encodes a kinase, as the candidate gene controlling butterhead plant architecture. The Lskipk gene in the butterhead parent had a nonsense mutation, leading to a partial predicted protein. CRISPR/Cas9 and complementation tests verified its functions in plant architecture. We showed that the loss of function of LsKIPK is necessary but not sufficient for the butterhead plant architecture. To identify additional genes required for butterhead lettuce, we crossed a butterhead cultivar and a crisphead cultivar, both with the mutated Lskipk gene. Genetic mapping identified a new gene encoding an ATPase contributing to butterhead plant architecture. Knockout and complementation tests showed that loss of function of LsATPase is also required for the development of butterhead plant architecture. The Lskipk Lsatpase double mutation could reduce leaf size and leaf angle, leading to butterhead plant architecture. Expression and cytology analysis indicated that the loss of function of LsKIPK and LsATPase contributed to butterhead plant architecture by regulating cell wall development, a regulatory mechanism different from that for crisphead. This study provides new gene resources and theory for the breeding of the crop ideotype.
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Affiliation(s)
- Sai Xie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Guangbao Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Guanghui An
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
- College of Horticulture, Henan Agricultural University, 450002 Zhengzhou, China
| | - Bincai Wang
- North Park, Wuhan Academy of Agricultural Sciences, Wuhu Eco-park, Huangpi District, Wuhan, China
| | - Hanhui Kuang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops; Hubei Hongshan Laboratory; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, China
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3
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Cheng SY, Chu PK, Chen YJ, Wu YH, Huang MD. Exploring the extensin gene family: an updated genome-wide survey in plants and algae. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:152-167. [PMID: 37769205 DOI: 10.1093/jxb/erad380] [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: 06/21/2023] [Accepted: 09/27/2023] [Indexed: 09/30/2023]
Abstract
Extensins (EXTs), a class of hydroxyproline-rich glycoprotein with multiple Ser-Pro3-5 motifs, are known to play roles in cell wall reinforcement and environmental responses. EXTs with repetitive Tyr-X-Tyr (YXY) motifs for crosslinking are referred as crosslinking EXTs. Our comprehensive study spanned 194 algal and plant species, categorizing EXTs into seven subfamilies: classical extensins (EXT I and II), arabinogalactan-protein extensins (AGP-EXTs), proline-rich extensin-like receptor kinases (PERKs), leucine-rich repeat extensins (LRX I and II), formin homology (FH) domain-containing extensins (FH-EXTs), proline-rich, arabinogalactan proteins, conserved cysteines (PAC) domain-containing extensins (PAC I and II), and eight-cysteine motif (8CM)-containing extensins (8CM-EXTs). In the examined dataset, EXTs were detected ubiquitously in plants but infrequently in algae, except for one Coccomyxa and four Chlamydomonadales species. No crosslinking EXTs were found in Poales or certain Zingiberales species. Notably, the previously uncharacterized EXT II, PAC II, and liverwort-specific 8CM-EXTs were found to be crosslinking EXTs. EXT II, featuring repetitive YY motifs instead of the conventional YXY motif, was exclusively identified in Solanaceae. Furthermore, tandem genes encoding distinctive 8CM-EXTs specifically expressed in the germinating spores of Marchantia polymorpha. This updated classification of EXT types allows us to propose a plausible evolutionary history of EXT genes during the course of plant evolution.
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Affiliation(s)
- Sou-Yu Cheng
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Ping-Kuan Chu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Yi-Jing Chen
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Yun-Hsuan Wu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Ming-Der Huang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
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4
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Gandhi A, Oelmüller R. Emerging Roles of Receptor-like Protein Kinases in Plant Response to Abiotic Stresses. Int J Mol Sci 2023; 24:14762. [PMID: 37834209 PMCID: PMC10573068 DOI: 10.3390/ijms241914762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
The productivity of plants is hindered by unfavorable conditions. To perceive stress signals and to transduce these signals to intracellular responses, plants rely on membrane-bound receptor-like kinases (RLKs). These play a pivotal role in signaling events governing growth, reproduction, hormone perception, and defense responses against biotic stresses; however, their involvement in abiotic stress responses is poorly documented. Plant RLKs harbor an N-terminal extracellular domain, a transmembrane domain, and a C-terminal intracellular kinase domain. The ectodomains of these RLKs are quite diverse, aiding their responses to various stimuli. We summarize here the sub-classes of RLKs based on their domain structure and discuss the available information on their specific role in abiotic stress adaptation. Furthermore, the current state of knowledge on RLKs and their significance in abiotic stress responses is highlighted in this review, shedding light on their role in influencing plant-environment interactions and opening up possibilities for novel approaches to engineer stress-tolerant crop varieties.
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Affiliation(s)
| | - Ralf Oelmüller
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, 07743 Jena, Germany;
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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.
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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.
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6
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Ahouvi Y, Haber Z, Zach YY, Rosental L, Toubiana D, Sharma D, Alseekh S, Tajima H, Fernie AR, Brotman Y, Blumwald E, Sade N. The Alteration of Tomato Chloroplast Vesiculation Positively Affects Whole-Plant Source-Sink Relations and Fruit Metabolism under Stress Conditions. PLANT & CELL PHYSIOLOGY 2023; 63:2008-2026. [PMID: 36161338 DOI: 10.1093/pcp/pcac133] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/14/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Changes in climate conditions can negatively affect the productivity of crop plants. They can induce chloroplast degradation (senescence), which leads to decreased source capacity, as well as decreased whole-plant carbon/nitrogen assimilation and allocation. The importance, contribution and mechanisms of action regulating source-tissue capacity under stress conditions in tomato (Solanum lycopersicum) are not well understood. We hypothesized that delaying chloroplast degradation by altering the activity of the tomato chloroplast vesiculation (CV) under stress would lead to more efficient use of carbon and nitrogen and to higher yields. Tomato CV is upregulated under stress conditions. Specific induction of CV in leaves at the fruit development stage resulted in stress-induced senescence and negatively affected fruit yield, without any positive effects on fruit quality. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/CAS9) knockout CV plants, generated using a near-isogenic tomato line with enhanced sink capacity, exhibited stress tolerance at both the vegetative and the reproductive stages, leading to enhanced fruit quantity, quality and harvest index. Detailed metabolic and transcriptomic network analysis of sink tissue revealed that the l-glutamine and l-arginine biosynthesis pathways are associated with stress-response conditions and also identified putative novel genes involved in tomato fruit quality under stress. Our results are the first to demonstrate the feasibility of delayed stress-induced senescence as a stress-tolerance trait in a fleshy fruit crop, to highlight the involvement of the CV pathway in the regulation of source strength under stress and to identify genes and metabolic pathways involved in increased tomato sink capacity under stress conditions.
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Affiliation(s)
- Yoav Ahouvi
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Yair Yehoshua Zach
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Leah Rosental
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, 1 David Ben Gurion Blvd., Beer-Sheva 8410501, Israel
| | - David Toubiana
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Davinder Sharma
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Saleh Alseekh
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany
- Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria
| | - Hiromi Tajima
- Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Alisdair R Fernie
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany
- Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, 1 David Ben Gurion Blvd., Beer-Sheva 8410501, Israel
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
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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.
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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
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8
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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.
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Guo R, Wu YN, Liu CC, Liu YN, Tian L, Cheng JF, Pan Z, Wang D, Wang B. OsADK1, a novel kinase regulating arbuscular mycorrhizal symbiosis in rice. THE NEW PHYTOLOGIST 2022; 234:256-268. [PMID: 35133010 DOI: 10.1111/nph.17979] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis relies on the formation of arbuscules for efficient nutrient exchange between plants and AM fungi. In this study, we identified a novel kinase gene in rice named OsADK1 (Arbuscule Development Kinase 1) that is required for arbuscule development. By obtaining OsADK1pro::GUS transgenic rice plants and also generating Osadk1 mutants via CRISPR/Cas9 technique, OsADK1 was revealed to be specifically induced in the arbusculated cortical cells and mutations in OsADK1 resulted in an extremely low colonisation rate (c. 3%) of rice roots by AM fungus Rhizophagus irregularis. In the mutant roots, the very few observed arbuscules nearly all arrested at an early 'trunk-forming' phase without forming any branches. Increasing the inoculum strength of AM fungus or cocultivation with a wild-type nurse plant did not result in the rescue of the arbuscule phenotype. Transcriptome sequencing of both nursed and un-nursed Osadk1 mutants then revealed that the mutation of OsADK1 could greatly affect the AM symbiotic programme, including many key transcription factors such as RAM1 and WRI5. OsADK1 therefore represents a new rice kinase that is required for arbuscule branching. Its identification opens a new window to explore the elaborate signal transduction pathway that determines arbuscule development during plant-fungus symbiosis.
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Affiliation(s)
- Rui Guo
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ya-Nan Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Cheng-Chen Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ying-Na Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Li Tian
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jian-Fei Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhiyong Pan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dong Wang
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Bin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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10
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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:plants11040496. [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] [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.
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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;
- Correspondence:
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11
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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.
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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
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12
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Behnami S, Bonetta D. With an Ear Up against the Wall: An Update on Mechanoperception in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2021; 10:1587. [PMID: 34451632 PMCID: PMC8398075 DOI: 10.3390/plants10081587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
Cells interpret mechanical signals and adjust their physiology or development appropriately. In plants, the interface with the outside world is the cell wall, a structure that forms a continuum with the plasma membrane and the cytoskeleton. Mechanical stress from cell wall damage or deformation is interpreted to elicit compensatory responses, hormone signalling, or immune responses. Our understanding of how this is achieved is still evolving; however, we can refer to examples from animals and yeast where more of the details have been worked out. Here, we provide an update on this changing story with a focus on candidate mechanosensitive channels and plasma membrane-localized receptors.
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Affiliation(s)
| | - Dario Bonetta
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada;
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13
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Oliver J, Fan M, McKinley B, Zemelis‐Durfee S, Brandizzi F, Wilkerson C, Mullet JE. The AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolor. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1053-1071. [PMID: 33211340 PMCID: PMC7983884 DOI: 10.1111/tpj.15086] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 05/31/2023]
Abstract
Stems of bioenergy sorghum (Sorghum bicolor L. Moench.), a drought-tolerant C4 grass, contain up to 50 nodes and internodes of varying length that span 4-5 m and account for approximately 84% of harvested biomass. Stem internode growth impacts plant height and biomass accumulation and is regulated by brassinosteroid signaling, auxin transport, and gibberellin biosynthesis. In addition, an AGCVIII kinase (Dw2) regulates sorghum stem internode growth, but the underlying mechanism and signaling network are unknown. Here we provide evidence that mutation of Dw2 reduces cell proliferation in internode intercalary meristems, inhibits endocytosis, and alters the distribution of heteroxylan and mixed linkage glucan in cell walls. Phosphoproteomic analysis showed that Dw2 signaling influences the phosphorylation of proteins involved in lipid signaling (PLDδ), endomembrane trafficking, hormone, light, and receptor signaling, and photosynthesis. Together, our results show that Dw2 modulates endomembrane function and cell division during sorghum internode growth, providing insight into the regulation of monocot stem development.
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Affiliation(s)
- Joel Oliver
- Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTexas77843USA
| | - Mingzhu Fan
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824USA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichigan48824USA
| | - Brian McKinley
- Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTexas77843USA
| | - Starla Zemelis‐Durfee
- MSU‐DOE Plant Research LabMichigan State UniversityEast LansingMichigan48824USA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichigan48824USA
| | - Federica Brandizzi
- MSU‐DOE Plant Research LabMichigan State UniversityEast LansingMichigan48824USA
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824USA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichigan48824USA
| | - Curtis Wilkerson
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824USA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichigan48824USA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichigan48824USA
| | - John E. Mullet
- Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTexas77843USA
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14
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Shi P, Gu M. Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress. BMC PLANT BIOLOGY 2020; 20:568. [PMID: 33380327 PMCID: PMC7774241 DOI: 10.1186/s12870-020-02753-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/24/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance. RESULTS The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. One hundred seventeen DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. CONCLUSIONS We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.
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Affiliation(s)
- Pibiao Shi
- Xinyang Agricultural Experiment Station of Yancheng City, Yancheng, 224049, Jiangsu, China
| | - Minfeng Gu
- Xinyang Agricultural Experiment Station of Yancheng City, Yancheng, 224049, Jiangsu, China.
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15
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Chen G, Wang J, Wang H, Wang C, Tang X, Li J, Zhang L, Song J, Hou J, Yuan L. Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development. BMC Genomics 2020; 21:401. [PMID: 32539701 PMCID: PMC7296749 DOI: 10.1186/s12864-020-06802-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development. RESULTS Our study identified 25 putative PERK genes from the whole Brassica rapa genome (AA). Phylogenetic analysis of PERK protein sequences from 16 Brassicaceae species divided them into four subfamilies. The biophysical properties of the BrPERKs were investigated. Gene duplication and synteny analyses and the calculation of Ka/Ks values suggested that all 80 orthologous/paralogous gene pairs between B. rapa and A. thaliana, B. nigra and B. oleracea have experienced strong purifying selection. RNA-Seq data and qRT-PCR analyses showed that several BrPERK genes were expressed in different tissues, while some BrPERKs exhibited high expression levels only in buds. Furthermore, comparative transcriptome analyses from six male-sterile lines of B. rapa indicated that 7 BrPERK genes were downregulated in all six male-sterile lines. Meanwhile, the interaction networks of the BrPERK genes were constructed and 13 PERK coexpressed genes were identified, most of which were downregulated in the male sterile buds. CONCLUSION Combined with interaction networks, coexpression and qRT-PCR analyses, these results demonstrated that two BrPERK genes, Bra001723.1 and Bra037558.1 (the orthologs of AtPERK6 (AT3G18810)), were downregulated beginning in the meiosis II period of male sterile lines and involved in anther development. Overall, this comprehensive analysis of some BrPERK genes elucidated their roles in male sterility.
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Affiliation(s)
- Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China. .,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China. .,Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200, China.
| | - Jian Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China.,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China
| | - Hao Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China. .,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China. .,Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200, China.
| | - Xiaoyan Tang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China.,Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei, 230036, China
| | - Jie Li
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Lei Zhang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Jianghua Song
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University, Hefei, 230036, China
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16
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Uemura T, Hachisu M, Desaki Y, Ito A, Hoshino R, Sano Y, Nozawa A, Mujiono K, Galis I, Yoshida A, Nemoto K, Miura S, Nishiyama M, Nishiyama C, Horito S, Sawasaki T, Arimura GI. Soy and Arabidopsis receptor-like kinases respond to polysaccharide signals from Spodoptera species and mediate herbivore resistance. Commun Biol 2020; 3:224. [PMID: 32385340 PMCID: PMC7210110 DOI: 10.1038/s42003-020-0959-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/21/2020] [Indexed: 12/22/2022] Open
Abstract
Plants respond to herbivory by perceiving herbivore danger signal(s) (HDS(s)), including "elicitors", that are present in herbivores' oral secretions (OS) and act to induce defense responses. However, little is known about HDS-specific molecules and intracellular signaling. Here we explored soybean receptor-like kinases (RLKs) as candidates that might mediate HDS-associated RLKs' (HAKs') actions in leaves in response to OS extracted from larvae of a generalist herbivore, Spodoptera litura. Fractionation of OS yielded Frα, which consisted of polysaccharides. The GmHAKs composed of their respective homomultimers scarcely interacted with Frα. Moreover, Arabidopsis HAK1 homomultimers interacted with cytoplasmic signaling molecule PBL27, resulting in herbivory resistance, in an ethylene-dependent manner. Altogether, our findings suggest that HAKs are herbivore-specific RLKs mediating HDS-transmitting, intracellular signaling through interaction with PBL27 and the subsequent ethylene signaling for plant defense responses in host plants.
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Affiliation(s)
- Takuya Uemura
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Masakazu Hachisu
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Yoshitake Desaki
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Ayaka Ito
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Ryosuke Hoshino
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Yuka Sano
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Akira Nozawa
- Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Kadis Mujiono
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
- Faculty of Agriculture, Mulawarman University, Samarinda, Indonesia
| | - Ivan Galis
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Ayako Yoshida
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | | | - Shigetoshi Miura
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Chiharu Nishiyama
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Shigeomi Horito
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan
| | | | - Gen-Ichiro Arimura
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Tokyo, Japan.
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17
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Sari E, Cabral AL, Polley B, Tan Y, Hsueh E, Konkin DJ, Knox RE, Ruan Y, Fobert PR. Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat. BMC Genomics 2019; 20:925. [PMID: 31795948 PMCID: PMC6891979 DOI: 10.1186/s12864-019-6161-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/09/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Fusarium head blight (FHB) resistance in the durum wheat breeding gene pool is rarely reported. Triticum turgidum ssp. carthlicum line Blackbird is a tetraploid relative of durum wheat that offers partial FHB resistance. Resistance QTL were identified for the durum wheat cv. Strongfield × Blackbird population on chromosomes 1A, 2A, 2B, 3A, 6A, 6B and 7B in a previous study. The objective of this study was to identify the defense mechanisms underlying the resistance of Blackbird and report candidate regulator defense genes and single nucleotide polymorphism (SNP) markers within these genes for high-resolution mapping of resistance QTL reported for the durum wheat cv. Strongfield/Blackbird population. RESULTS Gene network analysis identified five networks significantly (P < 0.05) associated with the resistance to FHB spread (Type II FHB resistance) one of which showed significant correlation with both plant height and relative maturity traits. Two gene networks showed subtle differences between Fusarium graminearum-inoculated and mock-inoculated plants, supporting their involvement in constitutive defense. The candidate regulator genes have been implicated in various layers of plant defense including pathogen recognition (mainly Nucleotide-binding Leucine-rich Repeat proteins), signaling pathways including the abscisic acid and mitogen activated protein (MAP) kinase, and downstream defense genes activation including transcription factors (mostly with dual roles in defense and development), and cell death regulator and cell wall reinforcement genes. The expression of five candidate genes measured by quantitative real-time PCR was correlated with that of RNA-seq, corroborating the technical and analytical accuracy of RNA-sequencing. CONCLUSIONS Gene network analysis allowed identification of candidate regulator genes and genes associated with constitutive resistance, those that will not be detected using traditional differential expression analysis. This study also shed light on the association of developmental traits with FHB resistance and partially explained the co-localization of FHB resistance with plant height and maturity QTL reported in several previous studies. It also allowed the identification of candidate hub genes within the interval of three previously reported FHB resistance QTL for the Strongfield/Blackbird population and associated SNPs for future high resolution mapping studies.
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Affiliation(s)
- Ehsan Sari
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada.
| | - Adrian L Cabral
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Brittany Polley
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Yifang Tan
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Emma Hsueh
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - David J Konkin
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Pierre R Fobert
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
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18
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Nitrogen Starvation Differentially Influences Transcriptional and Uptake Rate Profiles in Roots of Two Maize Inbred Lines with Different NUE. Int J Mol Sci 2019; 20:ijms20194856. [PMID: 31574923 PMCID: PMC6801476 DOI: 10.3390/ijms20194856] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Nitrogen use efficiency (NUE) of crops is estimated to be less than 50%, with a strong impact on environment and economy. Genotype-dependent ability to cope with N shortage has been only partially explored in maize and, in this context, the comparison of molecular responses of lines with different NUE is of particular interest in order to dissect the key elements underlying NUE. Changes in root transcriptome and NH4+/NO3- uptake rates during growth (after 1 and 4 days) without N were studied in high (Lo5) and low (T250) NUE maize inbred lines. Results suggests that only a small set of transcripts were commonly modulated in both lines in response to N starvation. However, in both lines, transcripts linked to anthocyanin biosynthesis and lateral root formation were positively affected. On the contrary, those involved in root elongation were downregulated. The main differences between the two lines reside in the ability to modulate the transcripts involved in the transport, distribution and assimilation of mineral nutrients. With regard to N mineral forms, only the Lo5 line responded to N starvation by increasing the NH4+ fluxes as supported by the upregulation of a transcript putatively involved in its transport.
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19
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Liu M, He X, Feng T, Zhuo R, Qiu W, Han X, Qiao G, Zhang D. cDNA Library for Mining Functional Genes in Sedum alfredii Hance Related to Cadmium Tolerance and Characterization of the Roles of a Novel SaCTP2 Gene in Enhancing Cadmium Hyperaccumulation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:10926-10940. [PMID: 31449747 DOI: 10.1021/acs.est.9b03237] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Heavy metal contamination presents serious threats to living organisms. Functional genes related to cadmium (Cd) hypertolerance or hyperaccumulation must be explored to enhance phytoremediation. Sedum alfredii Hance is a Zn/Cd cohyperaccumulator exhibiting abundant genes associated with Cd hypertolerance. Here, we developed a method for screening genes related to Cd tolerance by expressing a cDNA-library for S. alfredii Hance. Yeast functional complementation validated 42 of 48 full-length genes involved in Cd tolerance, and the majority of them were strongly induced in roots and exhibited diverse expression profiles across tissues. Coexpression network analysis suggested that 15 hub genes were connected with genes involved in metabolic processes, response to stimuli, and metal transporter and antioxidant activity. The functions of a novel SaCTP2 gene were validated by heterologous expression in Arabidopsis, responsible for retarding chlorophyll content decrease, maintaining membrane integrity, promoting reactive oxygen species (ROS) scavenger activities, and reducing ROS levels. Our findings suggest a highly complex network of genes related to Cd hypertolerance in S. alfredii Hance, accomplished via the antioxidant system, defense genes induction, and the calcium signaling pathway. The proposed cDNA-library method is an effective approach for mining candidate genes associated with Cd hypertolerance to develop genetically engineered plants for use in phytoremediation.
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Affiliation(s)
- Mingying Liu
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
- School of Basic Medical Sciences , Zhejiang Chinese Medical University , Hangzhou 310053 , People's Republic of China
| | - Xuelian He
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Tongyu Feng
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Wenmin Qiu
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Guirong Qiao
- State Key Laboratory of Tree Genetics and Breeding , Xiangshan Road , Beijing 100091 , People's Republic of China
- Key Laboratory of Tree Breeding of Zhejiang Province , Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400 , People's Republic of China
| | - Dayi Zhang
- School of Environment , Tsinghua University , Beijing 100084 , People's Republic of China
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20
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Fawke S, Torode TA, Gogleva A, Fich EA, Sørensen I, Yunusov T, Rose JKC, Schornack S. Glycerol-3-phosphate acyltransferase 6 controls filamentous pathogen interactions and cell wall properties of the tomato and Nicotiana benthamiana leaf epidermis. THE NEW PHYTOLOGIST 2019; 223:1547-1559. [PMID: 30980530 PMCID: PMC6767537 DOI: 10.1111/nph.15846] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 03/29/2019] [Indexed: 05/30/2023]
Abstract
The leaf outer epidermal cell wall acts as a barrier against pathogen attack and desiccation, and as such is covered by a cuticle, composed of waxes and the polymer cutin. Cutin monomers are formed by the transfer of fatty acids to glycerol by glycerol-3-phosphate acyltransferases, which facilitate their transport to the surface. The extent to which cutin monomers affect leaf cell wall architecture and barrier properties is not known. We report a dual functionality of pathogen-inducible GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE 6 (GPAT6) in controlling pathogen entry and cell wall properties affecting dehydration in leaves. Silencing of Nicotiana benthamiana NbGPAT6a increased leaf susceptibility to infection by the oomycetes Phytophthora infestans and Phytophthora palmivora, whereas overexpression of NbGPAT6a-GFP rendered leaves more resistant. A loss-of-function mutation in tomato SlGPAT6 similarly resulted in increased susceptibility of leaves to Phytophthora infection, concomitant with changes in haustoria morphology. Modulation of GPAT6 expression altered the outer wall diameter of leaf epidermal cells. Moreover, we observed that tomato gpat6-a mutants had an impaired cell wall-cuticle continuum and fewer stomata, but showed increased water loss. This study highlights a hitherto unknown role for GPAT6-generated cutin monomers in influencing epidermal cell properties that are integral to leaf-microbe interactions and in limiting dehydration.
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Affiliation(s)
- Stuart Fawke
- Sainsbury Laboratory (SLCU)University of CambridgeCambridgeUK
| | | | - Anna Gogleva
- Sainsbury Laboratory (SLCU)University of CambridgeCambridgeUK
| | - Eric A. Fich
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Iben Sørensen
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Temur Yunusov
- Sainsbury Laboratory (SLCU)University of CambridgeCambridgeUK
| | - Jocelyn K. C. Rose
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
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21
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Cao J. Molecular Evolution of the Vacuolar Iron Transporter ( VIT) Family Genes in 14 Plant Species. Genes (Basel) 2019; 10:E144. [PMID: 30769903 PMCID: PMC6409731 DOI: 10.3390/genes10020144] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/14/2022] Open
Abstract
The vacuolar iron transporter (VIT) proteins are involved in the storage and transport of iron. However, the evolution of this gene family in plants is unknown. In this study, I first identified 114 VIT genes in 14 plant species and classified these genes into seven groups by phylogenetic analysis. Conserved gene organization and motif distribution implied conserved function in each group. I also found that tandem duplication, segmental duplication and transposition contributed to the expansion of this gene family. Additionally, several positive selection sites were identified. Divergent expression patterns of soybean VIT genes were further investigated in different development stages and under iron stress. Functional network analysis exhibited 211 physical or functional interactions. The results will provide the basis for further functional studies of the VIT genes in plants.
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Affiliation(s)
- Jun Cao
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
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22
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Kölling M, Kumari P, Bürstenbinder K. Calcium- and calmodulin-regulated microtubule-associated proteins as signal-integration hubs at the plasma membrane-cytoskeleton nexus. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:387-396. [PMID: 30590729 DOI: 10.1093/jxb/ery397] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/06/2018] [Indexed: 05/09/2023]
Abstract
Plant growth and development are a genetically predetermined series of events but can change dramatically in response to environmental stimuli, involving perpetual pattern formation and reprogramming of development. The rate of growth is determined by cell division and subsequent cell expansion, which are restricted and controlled by the cell wall-plasma membrane-cytoskeleton continuum, and are coordinated by intricate networks that facilitate intra- and intercellular communication. An essential role in cellular signaling is played by calcium ions, which act as universal second messengers that transduce, integrate, and multiply incoming signals during numerous plant growth processes, in part by regulation of the microtubule cytoskeleton. In this review, we highlight recent advances in the understanding of calcium-mediated regulation of microtubule-associated proteins, their function at the microtubule cytoskeleton, and their potential role as hubs in crosstalk with other signaling pathways.
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Affiliation(s)
- Malte Kölling
- Leibniz Institute of Plant Biochemistry, Weinberg, Halle/Saale, Germany
| | - Pratibha Kumari
- Leibniz Institute of Plant Biochemistry, Weinberg, Halle/Saale, Germany
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23
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Vavrdová T, ˇSamaj J, Komis G. Phosphorylation of Plant Microtubule-Associated Proteins During Cell Division. FRONTIERS IN PLANT SCIENCE 2019; 10:238. [PMID: 30915087 PMCID: PMC6421500 DOI: 10.3389/fpls.2019.00238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 05/20/2023]
Abstract
Progression of mitosis and cytokinesis depends on the reorganization of cytoskeleton, with microtubules driving the segregation of chromosomes and their partitioning to two daughter cells. In dividing plant cells, microtubules undergo global reorganization throughout mitosis and cytokinesis, and with the aid of various microtubule-associated proteins (MAPs), they form unique systems such as the preprophase band (PPB), the acentrosomal mitotic spindle, and the phragmoplast. Such proteins include nucleators of de novo microtubule formation, plus end binding proteins involved in the regulation of microtubule dynamics, crosslinking proteins underlying microtubule bundle formation and members of the kinesin superfamily with microtubule-dependent motor activities. The coordinated function of such proteins not only drives the continuous remodeling of microtubules during mitosis and cytokinesis but also assists the positioning of the PPB, the mitotic spindle, and the phragmoplast, affecting tissue patterning by controlling cell division plane (CDP) orientation. The affinity and the function of such proteins is variably regulated by reversible phosphorylation of serine and threonine residues within the microtubule binding domain through a number of protein kinases and phosphatases which are differentially involved throughout cell division. The purpose of the present review is to provide an overview of the function of protein kinases and protein phosphatases involved in cell division regulation and to identify cytoskeletal substrates relevant to the progression of mitosis and cytokinesis and the regulation of CDP orientation.
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24
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Marzol E, Borassi C, Bringas M, Sede A, Rodríguez Garcia DR, Capece L, Estevez JM. Filling the Gaps to Solve the Extensin Puzzle. MOLECULAR PLANT 2018; 11:645-658. [PMID: 29530817 DOI: 10.1016/j.molp.2018.03.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/28/2018] [Accepted: 03/04/2018] [Indexed: 05/20/2023]
Abstract
Extensins (EXTs) are highly repetitive plant O-glycoproteins that require several post-translational modifications (PTMs) to become functional in plant cell walls. First, they are hydroxylated on contiguous proline residues; then they are O-glycosylated on hydroxyproline and serine. After secretion into the apoplast, O-glycosylated EXTs form a tridimensional network organized by inter- and intra-Tyr linkages. Recent studies have made significant progress in the identification of the enzymatic machinery required to process EXTs, which includes prolyl 4-hydroxylases, glycosyltransferases, papain-type cysteine endopeptidases, and peroxidases. EXTs are abundant in plant tissues and are particularly important in rapidly expanding root hairs and pollen tubes, which grow in a polar manner. Small changes in EXT PTMs affect fast-growing cells, although the molecular mechanisms underlying this regulation are unknown. In this review, we highlight recent advances in our understanding of EXT modifications throughout the secretory pathway, EXT assembly in cell walls, and possible sensing mechanisms involving the Catharanthus roseus cell surface sensor receptor-like kinases located at the interface between the apoplast and the cytoplasmic side of the plasma membrane.
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Affiliation(s)
- Eliana Marzol
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina
| | - Cecilia Borassi
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina
| | - Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (INQUIMAE-CONICET), Buenos Aires, CP C1428EGA, Argentina
| | - Ana Sede
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina; Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Dr. Héctor Torres (INGEBI-CONICET), Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina
| | - Diana Rosa Rodríguez Garcia
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (INQUIMAE-CONICET), Buenos Aires, CP C1428EGA, Argentina
| | - Jose M Estevez
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Avenida Patricias Argentinas 435, Buenos Aires, CP C1405BWE, Argentina.
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25
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Tandonnet JP, Marguerit E, Cookson SJ, Ollat N. Genetic architecture of aerial and root traits in field-grown grafted grapevines is largely independent. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:903-915. [PMID: 29305700 DOI: 10.1007/s00122-017-3046-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/21/2017] [Indexed: 05/21/2023]
Abstract
QTLs were identified for traits assessed on field-grown grafted grapevines. Root number and section had the largest phenotypic variance explained. Genetic control of root and aerial traits was independent. Breeding new rootstocks for perennial crops remains challenging, mainly because of the number of desirable traits which have to be combined, these traits include good rooting ability and root development. Consequently, the present study analyzes the genetic architecture of root traits in grapevine. A segregating progeny of 138 F1 genotypes issued from an inter-specific cross between Vitis vinifera cv. Cabernet-Sauvignon × V. riparia cv. Gloire de Montpellier, used as rootstock, was phenotyped in grafted plants grown for 2 years in the field. Seven traits, related to aerial and root development, were quantified. Heritability ranged between 0.44 for aerial biomass to 0.7 for root number. Total root number was related to the number of fine roots, while root biomass was related to the number of coarse roots. Significant quantitative trait loci (QTLs) were identified for all the traits studied with some of them explaining approximately 20% of phenotypic variance. Only a single QTL co-localized for root and aerial biomass. Identified QTLs for aerial-to-root biomass ratio suggest that aerial and root traits are controlled independently. Genes known to be involved in auxin signaling pathways and phosphorus nutrition, whose orthologues were previously shown to regulate root development in Arabidopsis, were located in the confidence intervals of several QTLs. This study opens new perspectives for breeding rootstocks with improved root development capacities.
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Affiliation(s)
- Jean-Pascal Tandonnet
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Elisa Marguerit
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Sarah J Cookson
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France.
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26
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Zhang M, Zhou C, Song Z, Weng Q, Li M, Ji H, Mo X, Huang H, Lu W, Luo J, Li F, Gan S. The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér. (Myrtaceae). Sci Rep 2018; 8:2319. [PMID: 29396525 DOI: 10.1038/s41598-41018-20780-41599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 01/24/2018] [Indexed: 05/28/2023] Open
Abstract
Genomic loci related with resistance to gall-inducing insects have not been identified in any plants. Here, association mapping was used to identify molecular markers for resistance to the gall wasp Leptocybe invasa in two Eucalyptus species. A total of 86 simple sequence repeats (SSR) markers were screened out from 839 SSRs and used for association mapping in E. grandis. By applying the mixed linear model, seven markers were identified to be associated significantly (P ≤ 0.05) with the gall wasp resistance in E. grandis, including two validated with a correction of permutation test (P ≤ 0.008). The proportion of the variance in resistance explained by a significant marker ranged from 3.3% to 37.8%. Four out of the seven significant associations in E. grandis were verified and also validated (P ≤ 0.073 in a permutation test) in E. tereticornis, with the variation explained ranging from 24.3% to 48.5%. Favourable alleles with positive effect were also mined from the significant markers in both species. These results provide insight into the genetic control of gall wasp resistance in plants and have great potential for marker-assisted selection for resistance to L. invasa in the important tree genus Eucalyptus.
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Affiliation(s)
- Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou, 510642, China
| | - Changpin Zhou
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Zhijiao Song
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- Baoshan University, Yuanzheng Road, Baoshan, 678000, China
| | - Qijie Weng
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Mei Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Hongxia Ji
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Xiaoyong Mo
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou, 510642, China
| | - Huanhua Huang
- Guangdong Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Wanhong Lu
- China Eucalypt Research Centre, Zhanjiang, 524022, China
| | - Jianzhong Luo
- China Eucalypt Research Centre, Zhanjiang, 524022, China
| | - Fagen Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
| | - Siming Gan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
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27
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Zhang M, Zhou C, Song Z, Weng Q, Li M, Ji H, Mo X, Huang H, Lu W, Luo J, Li F, Gan S. The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér. (Myrtaceae). Sci Rep 2018; 8:2319. [PMID: 29396525 PMCID: PMC5797152 DOI: 10.1038/s41598-018-20780-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 01/24/2018] [Indexed: 01/30/2023] Open
Abstract
Genomic loci related with resistance to gall-inducing insects have not been identified in any plants. Here, association mapping was used to identify molecular markers for resistance to the gall wasp Leptocybe invasa in two Eucalyptus species. A total of 86 simple sequence repeats (SSR) markers were screened out from 839 SSRs and used for association mapping in E. grandis. By applying the mixed linear model, seven markers were identified to be associated significantly (P ≤ 0.05) with the gall wasp resistance in E. grandis, including two validated with a correction of permutation test (P ≤ 0.008). The proportion of the variance in resistance explained by a significant marker ranged from 3.3% to 37.8%. Four out of the seven significant associations in E. grandis were verified and also validated (P ≤ 0.073 in a permutation test) in E. tereticornis, with the variation explained ranging from 24.3% to 48.5%. Favourable alleles with positive effect were also mined from the significant markers in both species. These results provide insight into the genetic control of gall wasp resistance in plants and have great potential for marker-assisted selection for resistance to L. invasa in the important tree genus Eucalyptus.
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Affiliation(s)
- Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou, 510642, China
| | - Changpin Zhou
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Zhijiao Song
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- Baoshan University, Yuanzheng Road, Baoshan, 678000, China
| | - Qijie Weng
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Mei Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Hongxia Ji
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Xiaoyong Mo
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou, 510642, China
| | - Huanhua Huang
- Guangdong Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Wanhong Lu
- China Eucalypt Research Centre, Zhanjiang, 524022, China
| | - Jianzhong Luo
- China Eucalypt Research Centre, Zhanjiang, 524022, China
| | - Fagen Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
| | - Siming Gan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
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28
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Hilley JL, Weers BD, Truong SK, McCormick RF, Mattison AJ, McKinley BA, Morishige DT, Mullet JE. Sorghum Dw2 Encodes a Protein Kinase Regulator of Stem Internode Length. Sci Rep 2017; 7:4616. [PMID: 28676627 PMCID: PMC5496852 DOI: 10.1038/s41598-017-04609-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/10/2017] [Indexed: 12/30/2022] Open
Abstract
Sorghum is an important C4 grass crop grown for grain, forage, sugar, and bioenergy production. While tall, late flowering landraces are commonly grown in Africa, short early flowering varieties were selected in US grain sorghum breeding programs to reduce lodging and to facilitate machine harvesting. Four loci have been identified that affect stem length (Dw1-Dw4). Subsequent research showed that Dw3 encodes an ABCB1 auxin transporter and Dw1 encodes a highly conserved protein involved in the regulation of cell proliferation. In this study, Dw2 was identified by fine-mapping and further confirmed by sequencing the Dw2 alleles in Dwarf Yellow Milo and Double Dwarf Yellow Milo, the progenitor genotypes where the recessive allele of dw2 originated. The Dw2 locus was determined to correspond to Sobic.006G067700, a gene that encodes a protein kinase that is homologous to KIPK, a member of the AGCVIII subgroup of the AGC protein kinase family in Arabidopsis.
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Affiliation(s)
- Josie L Hilley
- Interdisciplinary Program in Genetics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, USA
| | - Brock D Weers
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, USA
| | - Sandra K Truong
- Interdisciplinary Program in Genetics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, USA
| | - Ryan F McCormick
- Interdisciplinary Program in Genetics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, USA
| | - Ashley J Mattison
- Interdisciplinary Program in Genetics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, USA
| | - Brian A McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, USA
| | - Daryl T Morishige
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, USA
| | - John E Mullet
- Interdisciplinary Program in Genetics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, USA. .,Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, USA.
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29
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Bürstenbinder K, Möller B, Plötner R, Stamm G, Hause G, Mitra D, Abel S. The IQD Family of Calmodulin-Binding Proteins Links Calcium Signaling to Microtubules, Membrane Subdomains, and the Nucleus. PLANT PHYSIOLOGY 2017; 173:1692-1708. [PMID: 28115582 PMCID: PMC5338658 DOI: 10.1104/pp.16.01743] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/20/2017] [Indexed: 05/20/2023]
Abstract
Calcium (Ca2+) signaling and dynamic reorganization of the cytoskeleton are essential processes for the coordination and control of plant cell shape and cell growth. Calmodulin (CaM) and closely related calmodulin-like (CML) polypeptides are principal sensors of Ca2+ signals. CaM/CMLs decode and relay information encrypted by the second messenger via differential interactions with a wide spectrum of targets to modulate their diverse biochemical activities. The plant-specific IQ67 DOMAIN (IQD) family emerged as possibly the largest class of CaM-interacting proteins with undefined molecular functions and biological roles. Here, we show that the 33 members of the IQD family in Arabidopsis (Arabidopsis thaliana) differentially localize, using green fluorescent protein (GFP)-tagged proteins, to multiple and distinct subcellular sites, including microtubule (MT) arrays, plasma membrane subdomains, and nuclear compartments. Intriguingly, the various IQD-specific localization patterns coincide with the subcellular patterns of IQD-dependent recruitment of CaM, suggesting that the diverse IQD members sequester Ca2+-CaM signaling modules to specific subcellular sites for precise regulation of Ca2+-dependent processes. Because MT localization is a hallmark of most IQD family members, we quantitatively analyzed GFP-labeled MT arrays in Nicotiana benthamiana cells transiently expressing GFP-IQD fusions and observed IQD-specific MT patterns, which point to a role of IQDs in MT organization and dynamics. Indeed, stable overexpression of select IQD proteins in Arabidopsis altered cellular MT orientation, cell shape, and organ morphology. Because IQDs share biochemical properties with scaffold proteins, we propose that IQD families provide an assortment of platform proteins for integrating CaM-dependent Ca2+ signaling at multiple cellular sites to regulate cell function, shape, and growth.
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Affiliation(s)
- Katharina Bürstenbinder
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (K.B., R.P., G.S., D.M., S.A.);
- Institute of Computer Science (B.M.), Biocenter (G.H.), and Institute of Biochemistry and Biotechnology (S.A.), Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; and
- Department of Plant Sciences, University of California, Davis, California 95616 (S.A.)
| | - Birgit Möller
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (K.B., R.P., G.S., D.M., S.A.)
- Institute of Computer Science (B.M.), Biocenter (G.H.), and Institute of Biochemistry and Biotechnology (S.A.), Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; and
- Department of Plant Sciences, University of California, Davis, California 95616 (S.A.)
| | - Romina Plötner
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (K.B., R.P., G.S., D.M., S.A.)
- Institute of Computer Science (B.M.), Biocenter (G.H.), and Institute of Biochemistry and Biotechnology (S.A.), Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; and
- Department of Plant Sciences, University of California, Davis, California 95616 (S.A.)
| | - Gina Stamm
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (K.B., R.P., G.S., D.M., S.A.)
- Institute of Computer Science (B.M.), Biocenter (G.H.), and Institute of Biochemistry and Biotechnology (S.A.), Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; and
- Department of Plant Sciences, University of California, Davis, California 95616 (S.A.)
| | - Gerd Hause
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (K.B., R.P., G.S., D.M., S.A.)
- Institute of Computer Science (B.M.), Biocenter (G.H.), and Institute of Biochemistry and Biotechnology (S.A.), Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; and
- Department of Plant Sciences, University of California, Davis, California 95616 (S.A.)
| | - Dipannita Mitra
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (K.B., R.P., G.S., D.M., S.A.)
- Institute of Computer Science (B.M.), Biocenter (G.H.), and Institute of Biochemistry and Biotechnology (S.A.), Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; and
- Department of Plant Sciences, University of California, Davis, California 95616 (S.A.)
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (K.B., R.P., G.S., D.M., S.A.)
- Institute of Computer Science (B.M.), Biocenter (G.H.), and Institute of Biochemistry and Biotechnology (S.A.), Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; and
- Department of Plant Sciences, University of California, Davis, California 95616 (S.A.)
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Ihsan MZ, Ahmad SJN, Shah ZH, Rehman HM, Aslam Z, Ahuja I, Bones AM, Ahmad JN. Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:233. [PMID: 28289422 PMCID: PMC5326801 DOI: 10.3389/fpls.2017.00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/07/2017] [Indexed: 05/29/2023]
Abstract
The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.
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Affiliation(s)
- Muhammad Z. Ihsan
- Cholistan Institute of Desert Studies, The Islamia University BahawalpurBahawalpur, Pakistan
| | - Samina J. N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, Faculty of Meteorology, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Hafiz M. Rehman
- Department of Electronic and Biomedical Engineering, Chonnam National UniversityGwangju, South Korea
| | - Zubair Aslam
- Department of Agronomy, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Ishita Ahuja
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Atle M. Bones
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Jam N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
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Ma Y, Yan C, Li H, Wu W, Liu Y, Wang Y, Chen Q, Ma H. Bioinformatics Prediction and Evolution Analysis of Arabinogalactan Proteins in the Plant Kingdom. FRONTIERS IN PLANT SCIENCE 2017; 8:66. [PMID: 28184232 PMCID: PMC5266747 DOI: 10.3389/fpls.2017.00066] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/12/2017] [Indexed: 05/21/2023]
Abstract
Arabinogalactan proteins (AGPs) are a family of extracellular glycoproteins implicated in plant growth and development. With a rapid growth in the number of genomes sequenced in many plant species, the family members of AGPs can now be predicted to facilitate functional investigation. Building upon previous advances in identifying Arabidopsis AGPs, an integrated strategy of systematical AGP screening for "classical" and "chimeric" family members is proposed in this study. A Python script named Finding-AGP is compiled to find AGP-like sequences and filter AGP candidates under the given thresholds. The primary screening of classical AGPs, Lys-rich classical AGPs, AGP-extensin hybrids, and non-classical AGPs was performed using the existence of signal peptides as a necessary requirement, and BLAST searches were conducted mainly for fasciclin-like, phytocyanin-like and xylogen-like AGPs. Then glycomodule index and partial PAST (Pro, Ala, Ser, and Thr) percentage are adopted to identify AGP candidates. The integrated strategy successfully discovered AGP gene families in 47 plant species and the main results are summarized as follows: (i) AGPs are abundant in angiosperms and many "ancient" AGPs with Ser-Pro repeats are found in Chlamydomonas reinhardtii; (ii) Classical AGPs, AG-peptides, and Lys-rich classical AGPs first emerged in Physcomitrella patens, Selaginella moellendorffii, and Picea abies, respectively; (iii) Nine subfamilies of chimeric AGPs are introduced as newly identified chimeric subfamilies similar to fasciclin-like, phytocyanin-like, and xylogen-like AGPs; (iv) The length and amino acid composition of Lys-rich domains are largely variable, indicating an insertion/deletion model during evolution. Our findings provide not only a powerful means to identify AGP gene families but also probable explanations of AGPs in maintaining the plant cell wall and transducing extracellular signals into the cytoplasm.
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Affiliation(s)
- Yuling Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- National Base for the Talents on Life-Science and Technology, Innovation Experimental College, Northwest A&F UniversityYangling, China
| | - Chenchao Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Huimin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- National Base for the Talents on Life-Science and Technology, Innovation Experimental College, Northwest A&F UniversityYangling, China
| | - Wentao Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- National Base for the Talents on Life-Science and Technology, Innovation Experimental College, Northwest A&F UniversityYangling, China
| | - Yaxue Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- National Base for the Talents on Life-Science and Technology, Innovation Experimental College, Northwest A&F UniversityYangling, China
| | - Yuqian Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- National Base for the Talents on Life-Science and Technology, Innovation Experimental College, Northwest A&F UniversityYangling, China
| | - Qin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Haoli Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
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Baldoni E, Bagnaresi P, Locatelli F, Mattana M, Genga A. Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress. RICE (NEW YORK, N.Y.) 2016; 9:25. [PMID: 27216147 PMCID: PMC4877341 DOI: 10.1186/s12284-016-0098-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/14/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions and is characterized by a low water-use efficiency and a high sensitivity to a water deficit, with yield reductions occurring at lower stress levels compared to most other crops. To identify genes and pathways involved in the tolerant response to dehydration, a powerful approach consists in the genome-wide analysis of stress-induced expression changes by comparing drought-tolerant and drought-sensitive genotypes. RESULTS The physiological response to osmotic stress of 17 japonica rice genotypes was evaluated. A clear differentiation of the most tolerant and the most sensitive phenotypes was evident, especially after 24 and 48 h of treatment. Two genotypes, which were characterized by a contrasting response (tolerance/sensitivity) to the imposed stress, were selected. A parallel transcriptomic analysis was performed on roots and leaves of these two genotypes at 3 and 24 h of stress treatment. RNA-Sequencing data showed that the tolerant genotype Eurosis and the sensitive genotype Loto mainly differed in the early response to osmotic stress in roots. In particular, the tolerant genotype was characterized by a prompt regulation of genes related to chromatin, cytoskeleton and transmembrane transporters. Moreover, a differential expression of transcription factor-encoding genes, genes involved in hormone-mediate signalling and genes involved in the biosynthesis of lignin was observed between the two genotypes. CONCLUSIONS Our results provide a transcriptomic characterization of the osmotic stress response in rice and identify several genes that may be important players in the tolerant response.
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Affiliation(s)
- Elena Baldoni
- Institute of Agricultural Biology and Biotechnology - National Research Council, via Bassini 15, 20133, Milan, Italy.
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy.
| | - Paolo Bagnaresi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, Italy
| | - Franca Locatelli
- Institute of Agricultural Biology and Biotechnology - National Research Council, via Bassini 15, 20133, Milan, Italy
| | - Monica Mattana
- Institute of Agricultural Biology and Biotechnology - National Research Council, via Bassini 15, 20133, Milan, Italy
| | - Annamaria Genga
- Institute of Agricultural Biology and Biotechnology - National Research Council, via Bassini 15, 20133, Milan, Italy.
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Cho HT. Arabinogalactan protein motif-containing receptor-like kinases are likely to play the negative feedback factor to maintain proper root hair length. PLANT SIGNALING & BEHAVIOR 2016; 11:e1226454. [PMID: 27562432 PMCID: PMC5155492 DOI: 10.1080/15592324.2016.1226454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 08/11/2016] [Indexed: 05/21/2023]
Abstract
Coordination of the events between cytoplasm and cell wall is necessary for the proper cellular activity of plants. Cell wall-associated receptor kinases are likely to play the interface for the extra-to-internal signaling process. Arabidopsis ROOT HAIR SPECIFIC 10 (RHS10), belonging to the proline-rich extensin-like receptor kinase (PERK) family, is a Ser/Thr protein kinase with arabinogalactan protein (AGP) motifs in its extracellular domain (ECD). RHS10 and other angiosperm PERK homologs are inhibitory in root hair tip growth. The ECD deletion analysis of RHS10 indicates that proline residues, including AGP motifs, in the ECD are required for the root hair inhibition. The kinase domain of RHS10 physically interacts with an RNase (RNS2), and both RHS10 and RNS2 show the consistent genetic interaction in terms of root hair phenotype and root RNA levels. The root hair-inhibitory function of the cell wall-associated receptor kinase RHS10 may provide a negative feedback tool between cell wall and cytoplasm for the determination of proper length of the root hair.
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Affiliation(s)
- Hyung-Taeg Cho
- Department of Biological Sciences, Seoul National
University, Seoul, Korea
- CONTACT Hyung-Taeg Cho
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Wang X, Gao B, Liu X, Dong X, Zhang Z, Fan H, Zhang L, Wang J, Shi S, Tu P. Salinity stress induces the production of 2-(2-phenylethyl)chromones and regulates novel classes of responsive genes involved in signal transduction in Aquilaria sinensis calli. BMC PLANT BIOLOGY 2016; 16:119. [PMID: 27230436 PMCID: PMC4881210 DOI: 10.1186/s12870-016-0803-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/13/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND Agarwood, is a resinous portion derived from Aquilaria sinensis, has been widely used in traditional medicine and incense. 2-(2-phenylethyl)chromones are principal components responsible for the quality of agarwood. However, the molecular basis of 2-(2-phenylethyl)chromones biosynthesis and regulation remains almost unknown. Our research indicated that salt stress induced production of several of 2-(2-phenylethyl)chromones in A. sinensis calli. Transcriptome analysis of A. sinensis calli treated with NaCl is required to further facilitate the multiple signal pathways in response to salt stress and to understand the mechanism of 2-(2-phenylethyl)chromones biosynthesis. RESULTS Forty one 2-(2-phenylethyl)chromones were identified from NaCl-treated A. sinensis calli. 93 041 unigenes with an average length of 1562 nt were generated from the control and salt-treated calli by Illmunina sequencing after assembly, and the unigenes were annotated by comparing with the public databases including NR, Swiss-Prot, KEGG, COG, and GO database. In total, 18 069 differentially expressed transcripts were identified by the transcriptome comparisons on the control calli and calli induced by 24 h or 120 h salinity stress. Numerous genes involved in signal transduction pathways including the genes responsible for hormone signal transduction, receptor-like kinases, MAPK cascades, Ca(2+) signal transduction, and transcription factors showed clear differences between the control calli and NaCl-treated calli. Furthermore, our data suggested that the genes annotated as chalcone synthases and O-methyltransferases may contribute to the biosynthesis of 2-(2-phenylethyl)chromones. CONCLUSIONS Salinity stress could induce the production of 41 2-(2-phenylethyl)chromones in A. sinensis calli. We conducted the first deep-sequencing transcriptome profiling of A. sinensis under salt stress and observed a large number of differentially expressed genes in response to salinity stress. Moreover, salt stress induced dynamic changes in transcript abundance for novel classes of responsive genes involved in signal transduction, including the genes responsible for hormone signal transduction, receptor-like kinases, MAPK cascades, Ca(2+) signal transduction, and transcription factors. This study will aid in selecting the target genes to genetically regulate A. sinensis salt-stress signal transduction and elucidating the biosynthesis of 2-(2-phenylethyl)chromones under salinity stress.
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Affiliation(s)
- Xiaohui Wang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Bowen Gao
- Baotou Medical College, Baotou, 014060, China
| | - Xiao Liu
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xianjuan Dong
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhongxiu Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Huiyan Fan
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Le Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Juan Wang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Shepo Shi
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Pengfei Tu
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Hwang Y, Lee H, Lee YS, Cho HT. Cell wall-associated ROOT HAIR SPECIFIC 10, a proline-rich receptor-like kinase, is a negative modulator of Arabidopsis root hair growth. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2007-22. [PMID: 26884603 PMCID: PMC4783376 DOI: 10.1093/jxb/erw031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Plant cell growth is restricted by the cell wall, and cell wall dynamics act as signals for the cytoplasmic and nuclear events of cell growth. Among various receptor kinases, ROOT HAIR SPECIFIC 10 (RHS10) belongs to a poorly known receptor kinase subfamily with a proline-rich extracellular domain. Here, we report that RHS10 defines the root hair length of Arabidopsis thaliana by negatively regulating hair growth. RHS10 modulates the duration of root hair growth rather than the growth rate. As poplar and rice RHS10 orthologs also showed a root hair-inhibitory function, this receptor kinase-mediated function appears to be conserved in angiosperms. RHS10 showed a strong association with the cell wall, most probably through its extracellular proline-rich domain (ECD). Deletion analysis of the ECD demonstrated that a minimal extracellular part, which includes a few proline residues, is required for RHS10-mediated root hair inhibition. RHS10 suppressed the accumulation of reactive oxygen species (ROS) in the root, which are necessary for root hair growth. A yeast two-hybrid screening identified an RNase (RNS2) as a putative downstream target of RHS10. Accordingly, RHS10 overexpression decreased and RHS10 loss increased RNA levels in the hair-growing root region. Our results suggest that RHS10 mediates cell wall-associated signals to maintain proper root hair length, at least in part by regulating RNA catabolism and ROS accumulation.
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Affiliation(s)
- Youra Hwang
- Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Hyodong Lee
- Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Young-Sook Lee
- Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Hyung-Taeg Cho
- Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea
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Borassi C, Sede AR, Mecchia MA, Salgado Salter JD, Marzol E, Muschietti JP, Estevez JM. An update on cell surface proteins containing extensin-motifs. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:477-87. [PMID: 26475923 DOI: 10.1093/jxb/erv455] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In recent years it has become clear that there are several molecular links that interconnect the plant cell surface continuum, which is highly important in many biological processes such as plant growth, development, and interaction with the environment. The plant cell surface continuum can be defined as the space that contains and interlinks the cell wall, plasma membrane and cytoskeleton compartments. In this review, we provide an updated view of cell surface proteins that include modular domains with an extensin (EXT)-motif followed by a cytoplasmic kinase-like domain, known as PERKs (for proline-rich extensin-like receptor kinases); with an EXT-motif and an actin binding domain, known as formins; and with extracellular hybrid-EXTs. We focus our attention on the EXT-motifs with the short sequence Ser-Pro(3-5), which is found in several different protein contexts within the same extracellular space, highlighting a putative conserved structural and functional role. A closer understanding of the dynamic regulation of plant cell surface continuum and its relationship with the downstream signalling cascade is a crucial forthcoming challenge.
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Affiliation(s)
- Cecilia Borassi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires, C1405BWE, Argentina
| | - Ana R Sede
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Dr. Héctor Torres (INGEBI-CONICET), Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina
| | - Martin A Mecchia
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Dr. Héctor Torres (INGEBI-CONICET), Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina
| | - Juan D Salgado Salter
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires, C1405BWE, Argentina
| | - Eliana Marzol
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires, C1405BWE, Argentina
| | - Jorge P Muschietti
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Dr. Héctor Torres (INGEBI-CONICET), Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina. Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Pabellón II, C1428EGA Buenos Aires, Argentina.
| | - Jose M Estevez
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires, C1405BWE, Argentina.
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Tian J, Han L, Feng Z, Wang G, Liu W, Ma Y, Yu Y, Kong Z. Orchestration of microtubules and the actin cytoskeleton in trichome cell shape determination by a plant-unique kinesin. eLife 2015; 4. [PMID: 26287478 PMCID: PMC4574192 DOI: 10.7554/elife.09351] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/18/2015] [Indexed: 11/13/2022] Open
Abstract
Microtubules (MTs) and actin filaments (F-actin) function cooperatively to regulate plant cell morphogenesis. However, the mechanisms underlying the crosstalk between these two cytoskeletal systems, particularly in cell shape control, remain largely unknown. In this study, we show that introduction of the MyTH4-FERM tandem into KCBP (kinesin-like calmodulin-binding protein) during evolution conferred novel functions. The MyTH4 domain and the FERM domain in the N-terminal tail of KCBP physically bind to MTs and F-actin, respectively. During trichome morphogenesis, KCBP distributes in a specific cortical gradient and concentrates at the branching sites and the apexes of elongating branches, which lack MTs but have cortical F-actin. Further, live-cell imaging and genetic analyses revealed that KCBP acts as a hub integrating MTs and actin filaments to assemble the required cytoskeletal configuration for the unique, polarized diffuse growth pattern during trichome cell morphogenesis. Our findings provide significant insights into the mechanisms underlying cytoskeletal regulation of cell shape determination.
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Affiliation(s)
- Juan Tian
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Libo Han
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhidi Feng
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guangda Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Weiwei Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yinping Ma
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanjun Yu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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