1
|
Mani B, Maurya K, Kohli PS, Giri J. Chickpea (Cicer arietinum) PHO1 family members function redundantly in Pi transport and root nodulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108712. [PMID: 38733940 DOI: 10.1016/j.plaphy.2024.108712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Phosphorus (P), a macronutrient, plays key roles in plant growth, development, and yield. Phosphate (Pi) transporters (PHTs) and PHOSPHATE1 (PHO1) are central to Pi acquisition and distribution. Potentially, PHO1 is also involved in signal transduction under low P. The current study was designed to identify and functionally characterize the PHO1 gene family in chickpea (CaPHO1s). Five CaPHO1 genes were identified through a comprehensive genome-wide search. Phylogenetically, CaPHO1s formed two clades, and protein sequence analyses confirmed the presence of conserved domains. CaPHO1s are expressed in different plant organs including root nodules and are induced by Pi-limiting conditions. Functional complementation of atpho1 mutant with three CaPHO1 members, CaPHO1, CaPHO1;like, and CaPHO1;H1, independently demonstrated their role in root to shoot Pi transport, and their redundant functions. To further validate this, we raised independent RNA-interference (RNAi) lines of CaPHO1, CaPHO1;like, and CaPHO1;H1 along with triple mutant line in chickpea. While single gene RNAi lines behaved just like WT, triple knock-down RNAi lines (capho1/like/h1) showed reduced shoot growth and shoot Pi content. Lastly, we showed that CaPHO1s are involved in root nodule development and Pi content. Our findings suggest that CaPHO1 members function redundantly in root to shoot Pi export and root nodule development in chickpea.
Collapse
Affiliation(s)
- Balaji Mani
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanika Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Pawandeep Singh Kohli
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitender Giri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
2
|
Kumar A, Singh S, Mishra A. Genome-wide identification and analyses of the AHL gene family in rice ( Oryza sativa). 3 Biotech 2023; 13:248. [PMID: 37366497 PMCID: PMC10290627 DOI: 10.1007/s13205-023-03666-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/11/2023] [Indexed: 06/28/2023] Open
Abstract
AHL (AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED) family members play a critical role in stress resistance regulation by DNA-protein and protein-protein interactions in a number of plant biological processes. Using genomic data, an attempt was made to evaluate AHL genes in rice. Using a genome database, we performed in silico detection and characterization of AHL family genes in rice. The data of the gene were obtained from the Rice Genome Annotation Project (RGAP) database. The rice genome data were analyzed using bioinformatics software. The main objectives of the research are genome-wide recognition, expression, structural examination, phylogenetic analysis of AHL gene family, classification of AHL proteins into different classes based on motif and domain composition, analysis of promoter regions to identify stress and phytohormone-associated cis-elements, expression analysis of OsAHL genes in diverse tissues and stressful situations and understanding the roles of AHLs in controlling rice plant development. The genome-wide recognition, expression, and structural examination of the AHL gene family were undertaken in this research to evaluate the structural activities of AHLs in rice. From the Oryza sativa genome, 26 AHL genes have been identified. WoLF PSORT analysis predicted different subcellular localizations for these proteins, including nuclear, cytoplasmic, chloroplast, and endoplasmic reticulum. According to a phylogenetic study, rice AHLs resulted in two clades: Clade-A with no introns (excluding OsAHL15 and OsAHL21) and Clade-B with four introns. Depending on the AT-hook motif (s) (AHM) and PPC/DUF 296 domain composition, the AHL proteins are categorized into the following three classes: Type-I, Type-II, and Type-III, among Type-I AHLs constituting Clade-A, Type-II, and Type-III creating Clade-B. Type-I was the largest gene family, representing 57.69% of OsAHL genes. The exon-intron organization within clades of OsAHL genes was similar. Multiple sequence alignment identified 15 conserved motifs, including AT-hook motifs and the PPC domain, suggesting DNA-binding functionality. OsAHL genes were distributed across 12 chromosomes, with chromosome 2 and 8 harboring the highest number of genes. Gene duplication analysis revealed eight paralogous pairs, indicating evolutionary divergence between 13.32 and 35.59 million years ago. The emergence of OsAHL paralogous pairs was favored by purifying selection. Synteny analysis between rice and Arabidopsis demonstrated collinearity among AHL gene pairs, implying comparable structure and function in the two species. The role of stress- and phytohormone-associated cis-elements in the OsAHL genes was discovered by promoter analysis. OsAHL genes participated in various biological processes, with a prominent involvement in cellular and metabolic processes. They exhibited a significant enrichment in binding functions, including a substantial proportion of transcription regulators. OsAHL genes displayed diverse expression patterns in different tissues and under abiotic stress conditions. According to their expression patterns, the majority of OsAHLs of Clade-B were expressed mainly in the pistil indicating their roles in flower formation, while Clade-A OsAHLs had the minimal expression in pistil and highly expressed in embryos, indicating that the AHLs within each clade had the same expression patterns. Some OsAHL genes were also expressed in stressful situations, such as cold, salt, and drought. Protein interaction analysis revealed networks involving AHL proteins and other proteins, suggesting their participation in phytohormone responses, abiotic stress, and plant development. In this work, 26 OsAHL genes were found in the genome of rice. Rice OsAHLs were grouped into two phylogenetic groups. It is further divided into three types on the basis of the motif and domain composition. At various phases of development, the expression analysis of OsAHLs showed numerous variations in expression levels in diverse tissues and stress situations. Our findings shed light on the significant roles of AHLs in controlling rice plant development. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03666-0.
Collapse
Affiliation(s)
- Arun Kumar
- Department of Agricultural Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, 250110 India
| | - Shilpy Singh
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Noida,
Gautam Budh Nagar, UP 203201 India
| | - Anurag Mishra
- Divison of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| |
Collapse
|
3
|
Li L, Ren X, Shao L, Huang X, Zhang C, Wang X, Yang J, Li C. Comprehensive Analysis of the NF-YB Gene Family and Expression under Abiotic Stress and Hormone Treatment in Larix kaempferi. Int J Mol Sci 2023; 24:ijms24108910. [PMID: 37240255 DOI: 10.3390/ijms24108910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/27/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
NF-YB, a subfamily of Nuclear Factor Y (NF-Y) transcription factor, play crucial role in many biological processes of plant growth and development and abiotic stress responses, and they can therefore be good candidate factors for breeding stress-resistant plants. However, the NF-YB proteins have not yet been explored in Larix kaempferi, a tree species with high economic and ecological values in northeast China and other regions, limiting the breeding of anti-stress L. kaempferi. In order to explore the roles of NF-YB transcription factors in L. kaempferi, we identified 20 LkNF-YB family genes from L. kaempferi full-length transcriptome data and carried out preliminary characterization of them through series of analyses on their phylogenetic relationships, conserved motif structure, subcellular localization prediction, GO annotation, promoter cis-acting elements as well as expression profiles under treatment of phytohormones (ABA, SA, MeJA) and abiotic stresses (salt and drought). The LkNF-YB genes were classified into three clades through phylogenetic analysis and belong to non-LEC1 type NF-YB transcription factors. They have 10 conserved motifs; all genes contain a common motif, and their promoters have various phytohormones and abiotic stress related cis-acting elements. Quantitative real time reverse transcription PCR (RT-qPCR) analysis showed that the sensitivity of the LkNF-YB genes to drought and salt stresses was higher in leaves than roots. The sensitivity of LKNF-YB genes to ABA, MeJA, SA stresses was much lower than that to abiotic stress. Among the LkNF-YBs, LkNF-YB3 showed the strongest responses to drought and ABA treatments. Further protein interaction prediction analysis for LkNF-YB3 revealed that LkNF-YB3 interacts with various factors associated with stress responses and epigenetic regulation as well as NF-YA/NF-YC factors. Taken together, these results unveiled novel L. kaempferi NF-YB family genes and their characteristics, providing the basic knowledge for further in-depth studies on their roles in abiotic stress responses of L. kaempferi.
Collapse
Affiliation(s)
- Lu Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Xi Ren
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Liying Shao
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Xun Huang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Chunyan Zhang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Xuhui Wang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Jingli Yang
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| |
Collapse
|
4
|
Hibbert L, Taylor G. Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale). HORTICULTURE RESEARCH 2022; 9:uhac011. [PMID: 35147194 PMCID: PMC8969064 DOI: 10.1093/hr/uhac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.
Collapse
Affiliation(s)
- Lauren Hibbert
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
| | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
| |
Collapse
|
5
|
Fang Y, Jiang J, Hou X, Guo J, Li X, Zhao D, Xie X. Plant protein-coding gene families: Their origin and evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:995746. [PMID: 36160967 PMCID: PMC9490259 DOI: 10.3389/fpls.2022.995746] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/15/2022] [Indexed: 05/13/2023]
Abstract
Steady advances in genome sequencing methods have provided valuable insights into the evolutionary processes of several gene families in plants. At the core of plant biodiversity is an extensive genetic diversity with functional divergence and expansion of genes across gene families, representing unique phenomena. The evolution of gene families underpins the evolutionary history and development of plants and is the subject of this review. We discuss the implications of the molecular evolution of gene families in plants, as well as the potential contributions, challenges, and strategies associated with investigating phenotypic alterations to explain the origin of plants and their tolerance to environmental stresses.
Collapse
Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Jiyuan Guo
- Department of Resources and Environment, Moutai Institute, Zunyi, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Degang Zhao
- Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Ministry of Education, College of Life Sciences, Institute of Agricultural Bioengineering, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- *Correspondence: Degang Zhao,
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- Xin Xie,
| |
Collapse
|
6
|
Nezamivand-Chegini M, Ebrahimie E, Tahmasebi A, Moghadam A, Eshghi S, Mohammadi-Dehchesmeh M, Kopriva S, Niazi A. New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean. BMC Genomics 2021; 22:915. [PMID: 34969367 PMCID: PMC8717665 DOI: 10.1186/s12864-021-08242-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/09/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes. RESULTS We analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs. CONCLUSION This comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.
Collapse
Affiliation(s)
| | - Esmaeil Ebrahimie
- Institute of biotechnology, Shiraz university, Shiraz, Iran
- La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne, VIC, 3086, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, 5371, Australia
| | | | - Ali Moghadam
- Institute of biotechnology, Shiraz university, Shiraz, Iran
| | - Saeid Eshghi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Ali Niazi
- Institute of biotechnology, Shiraz university, Shiraz, Iran.
| |
Collapse
|
7
|
Wang H, Leng X, Yang J, Zhang M, Zeng M, Xu X, Wang F, Li C. Comprehensive analysis of AHL gene family and their expression under drought stress and ABA treatment in Populus trichocarpa. PeerJ 2021; 9:e10932. [PMID: 33643717 PMCID: PMC7896510 DOI: 10.7717/peerj.10932] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022] Open
Abstract
The AT-hook motif nuclear-localized (AHL) family is a plant transcription factor family, which plays an important role in growth and development and stress responses. We identified and analyzed 37 AHL genes in poplar (Populus trichocarpa). Phylogenetic analysis classified the PtrAHL members into three subfamilies based on their conserved domain. All PtrAHL paralogous pairs evolved under purifying selection. The promoter analysis revealed the presence of stress-related and phytohormone-related cis-elements of the PtrAHL genes. Our analysis of the tissue-specific expression pattern of PtrAHL genes indicated their significance in tissue and organ development. Network-based prediction suggested that PtrAHL genes may interact with histone deacetylases (HDAC) and participate in the development of organs, such as roots. Drought negatively impacts plant growth and development. ABA is produced under osmotic stress condition, and it takes an important part in the stress response and tolerance of plants. Real-time quantitative PCR (qRT-PCR) showed that PtrAHL genes were induced by drought stress and ABA treatment. These insights into the expression of PtrAHL genes under stress provide a basis for PtrAHL gene functional analysis. Our study will help develop new breeding strategies to improve drought tolerance in poplar.
Collapse
Affiliation(s)
- Hanzeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xue Leng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jia Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Mengqiu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Minzhen Zeng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xuemei Xu
- Library of Northeast Forestry University, Harbin, China
| | - Fude Wang
- Institute of Forestry Science, Harbin, China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| |
Collapse
|
8
|
Nguyen NNT, Clua J, Vetal PV, Vuarambon DJ, De Bellis D, Pervent M, Lepetit M, Udvardi M, Valentine AJ, Poirier Y. PHO1 family members transport phosphate from infected nodule cells to bacteroids in Medicago truncatula. PLANT PHYSIOLOGY 2021; 185:196-209. [PMID: 33631809 PMCID: PMC8133656 DOI: 10.1093/plphys/kiaa016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/14/2020] [Indexed: 05/20/2023]
Abstract
Legumes play an important role in the soil nitrogen availability via symbiotic nitrogen fixation (SNF). Phosphate (Pi) deficiency severely impacts SNF because of the high Pi requirement of symbiosis. Whereas PHT1 transporters are involved in Pi uptake into nodules, it is unknown how Pi is transferred from the plant infected cells to nitrogen-fixing bacteroids. We hypothesized that Medicago truncatula genes homologous to Arabidopsis PHO1, encoding a vascular apoplastic Pi exporter, are involved in Pi transfer to bacteroids. Among the seven MtPHO1 genes present in M. truncatula, we found that two genes, namely MtPHO1.1 and MtPHO1.2, were broadly expressed across the various nodule zones in addition to the root vascular system. Expressions of MtPHO1.1 and MtPHO1.2 in Nicotiana benthamiana mediated specific Pi export. Plants with nodule-specific downregulation of both MtPHO1.1 and MtPHO1.2 were generated by RNA interference (RNAi) to examine their roles in nodule Pi homeostasis. Nodules of RNAi plants had lower Pi content and a three-fold reduction in SNF, resulting in reduced shoot growth. Whereas the rate of 33Pi uptake into nodules of RNAi plants was similar to control, transfer of 33Pi from nodule cells into bacteroids was reduced and bacteroids activated their Pi-deficiency response. Our results implicate plant MtPHO1 genes in bacteroid Pi homeostasis and SNF via the transfer of Pi from nodule infected cells to bacteroids.
Collapse
Affiliation(s)
- Nga N T Nguyen
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Joaquin Clua
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Pallavi V Vetal
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Dominique Jacques Vuarambon
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Damien De Bellis
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
- Electron Microscopy Facility, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
| | - Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditerranéennes UMR 1342 INRAE-IRD-CIRAD-UM-Montpellier SupAgro, Montpellier, France
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes UMR 1342 INRAE-IRD-CIRAD-UM-Montpellier SupAgro, Montpellier, France
| | - Michael Udvardi
- The Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, USA
| | - Alexander J Valentine
- Botany & Zoology Department, University of Stellenbosch, Matieland 7602, South Africa
| | - Yves Poirier
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne 1015, Switzerland
- Author for communication:
| |
Collapse
|
9
|
Gallinari RH, Coletta RD, Araújo P, Menossi M, Nery MF. Bringing to light the molecular evolution of GUX genes in plants. Genet Mol Biol 2020; 43:e20180208. [PMID: 32232316 PMCID: PMC7198009 DOI: 10.1590/1678-4685-gmb-2018-0208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 05/06/2019] [Indexed: 11/30/2022] Open
Abstract
Hemicellulose and cellulose are essential polysaccharides for plant development and major components of cell wall. They are also an important energy source for the production of ethanol from plant biomass, but their conversion to fermentable sugars is hindered by the complex structure of cell walls. The glucuronic acid substitution of xylan (GUX) enzymes attach glucuronic acid to xylan, a major component of hemicellulose, decreasing the efficiency of enzymes used for ethanol production. Since loss-of-function gux mutants of Arabidopsis thaliana enhance enzyme accessibility and cell wall digestion without adverse phenotypes, GUX genes are potential targets for genetically improving energy crops. However, comprehensive identification of GUX in important species and their evolutionary history are largely lacking. Here, we identified putative GUX proteins using hidden Markov model searches with the GT8 domain and a GUX-specific motif, and inferred the phylogenetic relationship of 18 species with Maximum likelihood and Bayesian approaches. Each species presented a variable number of GUX, and their evolution can be explained by a mixture of divergent, concerted and birth-and-death evolutionary models. This is the first broad insight into the evolution of GUX gene family in plants and will potentially guide genetic and functional studies in species used for biofuel production.
Collapse
Affiliation(s)
- Rafael Henrique Gallinari
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Rafael Della Coletta
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Pedro Araújo
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Marcelo Menossi
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Mariana Freitas Nery
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| |
Collapse
|
10
|
Wang Y, Gao H, He L, Zhu W, Yan L, Chen Q, He C. The PHOSPHATE1 genes participate in salt and Pi signaling pathways and play adaptive roles during soybean evolution. BMC PLANT BIOLOGY 2019; 19:353. [PMID: 31412775 PMCID: PMC6694516 DOI: 10.1186/s12870-019-1959-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 07/31/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND The PHOSPHATE1 (PHO1) gene family plays diverse roles in inorganic phosphate (Pi) transfer and signal transduction, and plant development. However, the functions and diversification of soybean PHO1 family are poorly understood. RESULTS Cultivated soybean (Glycine max) was domesticated from wild soybean (Glycine soja). To illuminate their roles in this evolutionary process, we comparatively investigated the G. max PHO1 genes (GmPHO1) in Suinong 14 (SN14) and G. soja PHO1 genes (GsPHO1) in ZYD00006 (ZYD6). The sequences of the orthologous Gm-GsPHO1 pairs were grouped into two Classes. The expression of Class I in both SN14 and ZYD6 was widely but relatively high in developing fruits, whereas Class II was predominantly expressed in the roots. The whole family displayed diverse response patterns to salt stresses and Pi-starvation in roots. Between SN14 and ZYD6, most PHO1 genes responded similarly to salinity stresses, and half had sharp contrasts in response to Pi-starvation, which corroborated the differential response capacities to salinity and low-Pi stress between SN14 and ZYD6. Furthermore, in transgenic Arabidopsis plants, most Class II members and GmPHO1;H9 from Class I could enhance salt tolerance, while only two Class II genes (GmPHO1;H4 and GmPHO1;H8) differently altered sensitivity to Pi-starvation. The expression of critical genes was accordingly altered in either salt or Pi signaling pathways in transgenic Arabidopsis plants. CONCLUSIONS Our work identifies some PHO1 genes as promising genetic materials for soybean improvement, and suggests that expression variation is decisive to functional divergence of the orthologous Gm-GsPHO1 pairs, which plays an adaptive role during soybean evolution.
Collapse
Affiliation(s)
- Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093 China
| | - Huihui Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049 China
| | - Lingli He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049 China
| | - Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049 China
| | - Lixin Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049 China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093 China
- University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing, 100049 China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| |
Collapse
|
11
|
Nawaz Z, Kakar KU, Ullah R, Yu S, Zhang J, Shu QY, Ren XL. Genome-wide identification, evolution and expression analysis of cyclic nucleotide-gated channels in tobacco (Nicotiana tabacum L.). Genomics 2019; 111:142-158. [PMID: 29476784 DOI: 10.1016/j.ygeno.2018.01.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/31/2017] [Accepted: 01/17/2018] [Indexed: 12/30/2022]
Abstract
Tobacco (Nicotiana tabacum) serve as the top leading commercial, non-food, and model crop worldwide. Cyclic nucleotide-gated channels (CNGCs) are ligand-gated, calcium-permeable, divalent, cation-selective channels, involved in important biological functions. Here, we systematically characterized thirty-five CNGC genes in the genome of Nicotiana tabacum, and classified into four phylogenetic groups. Evolutionary analysis showed that NtabCNGC family of N. tabacum originated from the parental genome of N. sylvestris and N. tomentosiformis, and further expanded via tandem and segmental duplication events. Tissue-specific expression analysis showed that twenty-three NtabCNGC genes are involved in the development of various tobacco tissues. Subsequent RT-qPCR analyses indicated that these genes are sensitive towards external abiotic and biotic stresses. Notable performances were exhibited by group-I and IV CNGC genes against black shank, Cucumber mosaic virus, Potato virus Y, cold, drought, and cadmium stresses. Our analyses also suggested that NtabCNGCs can be regulated by phosphorylation and miRNAs, and multiple light, temperature, and pathogen-responsive cis-acting regulatory elements present in promotors. These results will be useful for elaborating the biological roles of NtabCNGCs in tobacco growth and development.
Collapse
Affiliation(s)
- Zarqa Nawaz
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China.
| | - Kaleem U Kakar
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310058, China.
| | - Raqeeb Ullah
- Department of Environmental Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shizou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jie Zhang
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Qing-Yao Shu
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou 310058, China.
| | - Xue-Liang Ren
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China.
| |
Collapse
|
12
|
Zeng H, Zhang X, Zhang X, Pi E, Xiao L, Zhu Y. Early Transcriptomic Response to Phosphate Deprivation in Soybean Leaves as Revealed by RNA-Sequencing. Int J Mol Sci 2018; 19:E2145. [PMID: 30041471 PMCID: PMC6073939 DOI: 10.3390/ijms19072145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/17/2018] [Accepted: 07/17/2018] [Indexed: 01/15/2023] Open
Abstract
Low phosphate (Pi) availability is an important limiting factor affecting soybean production. However, the underlying molecular mechanisms responsible for low Pi stress response and tolerance remain largely unknown, especially for the early signaling events under low Pi stress. Here, a genome-wide transcriptomic analysis in soybean leaves treated with a short-term Pi-deprivation (24 h) was performed through high-throughput RNA sequencing (RNA-seq) technology. A total of 533 loci were found to be differentially expressed in response to Pi deprivation, including 36 mis-annotated loci and 32 novel loci. Among the differentially expressed genes (DEGs), 303 were induced and 230 were repressed by Pi deprivation. To validate the reliability of the RNA-seq data, 18 DEGs were randomly selected and analyzed by quantitative RT-PCR (reverse transcription polymerase chain reaction), which exhibited similar fold changes with RNA-seq. Enrichment analyses showed that 29 GO (Gene Ontology) terms and 8 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were significantly enriched in the up-regulated DEGs and 25 GO terms and 16 KEGG pathways were significantly enriched in the down-regulated DEGs. Some DEGs potentially involved in Pi sensing and signaling were up-regulated by short-term Pi deprivation, including five SPX-containing genes. Some DEGs possibly associated with water and nutrient uptake, hormonal and calcium signaling, protein phosphorylation and dephosphorylation and cell wall modification were affected at the early stage of Pi deprivation. The cis-elements of PHO (phosphatase) element, PHO-like element and P responsive element were present more frequently in promoter regions of up-regulated DEGs compared to that of randomly-selected genes in the soybean genome. Our transcriptomic data showed an intricate network containing transporters, transcription factors, kinases and phosphatases, hormone and calcium signaling components is involved in plant responses to early Pi deprivation.
Collapse
Affiliation(s)
- Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Xiajun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Xin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China.
| | - Liang Xiao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yiyong Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
13
|
Kakar KU, Nawaz Z, Cui Z, Cao P, Jin J, Shu Q, Ren X. Evolutionary and expression analysis of CAMTA gene family in Nicotiana tabacum yielded insights into their origin, expansion and stress responses. Sci Rep 2018; 8:10322. [PMID: 29985386 PMCID: PMC6037683 DOI: 10.1038/s41598-018-28148-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 06/18/2018] [Indexed: 02/06/2023] Open
Abstract
Calmodulin-binding transcription activators (CAMTAs) represent the novel gene family of transcriptional regulators, which play important biological functions. Though, the first ever plant CAMTA gene was evidenced in Nicotiana tabacum in 2002. But, the systematic identification, origin and function of this gene family has not been performed due to the lack of reference genome information until now. Here, we identified 29 CAMTA genes in four Nicotiana species, including thirteen NtabCAMTAs, six NsylCAMTAs, and five NtomCAMTAs and NbenCAMTAs. These CAMTA families were classified into five phylogenetic groups (I-V), among which, the group-IV CAMTAs probably emerged the earliest. The NtabCAMTA family genes have diverse structures, and are randomly localized on five chromosomes and scaffolds. N. tabacum acquired 11 copies of homolog CAMATA genes from the parental genomes of N. tomentosiformis and N. sylvestris, followed by expansion through polyploidization and duplication. The NtabCAMTA genes were differentially expressed in different plant parts, and showed sensitivity towards different abiotic and biotic stresses. Co-expression network analysis revealed that some NtabCAMTA subunits interact with each other, and co-expressed. The current study is the first report presenting a comprehensive overview of Nicotiana CAMTA families, and opens a new avenue for the improvement of the cultivated tobacco.
Collapse
Affiliation(s)
- Kaleem U Kakar
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou, 310058, China
- Department of Microbiology, Faculty of Life Sciences & Informatics, Balochistan University of Information Technology, Engineering, and Management Sciences, Quetta, 87300, Pakistan
| | - Zarqa Nawaz
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Zhouqi Cui
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experimental Station, New haven, CT, 06511, USA
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Qingyao Shu
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Xueliang Ren
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China.
| |
Collapse
|
14
|
Gruenstaeudl M. WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps.1500120. [PMID: 26949580 PMCID: PMC4760752 DOI: 10.3732/apps.1500120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 12/20/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. METHODS AND RESULTS A set of command line-based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results. CONCLUSIONS WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion.
Collapse
Affiliation(s)
- Michael Gruenstaeudl
- Institut für Biologie-Botanik, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Altensteinstraße 6, 14195 Berlin, Germany
| |
Collapse
|
15
|
Wege S, Khan GA, Jung JY, Vogiatzaki E, Pradervand S, Aller I, Meyer AJ, Poirier Y. The EXS Domain of PHO1 Participates in the Response of Shoots to Phosphate Deficiency via a Root-to-Shoot Signal. PLANT PHYSIOLOGY 2016; 170:385-400. [PMID: 26546667 PMCID: PMC4704572 DOI: 10.1104/pp.15.00975] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/04/2015] [Indexed: 05/17/2023]
Abstract
The response of shoots to phosphate (Pi) deficiency implicates long-distance communication between roots and shoots, but the participating components are poorly understood. We have studied the topology of the Arabidopsis (Arabidopsis thaliana) PHOSPHATE1 (PHO1) Pi exporter and defined the functions of its different domains in Pi homeostasis and signaling. The results indicate that the amino and carboxyl termini of PHO1 are both oriented toward the cytosol and that the protein spans the membrane twice in the EXS domain, resulting in a total of six transmembrane α-helices. Using transient expression in Nicotiana benthamiana leaf, we demonstrated that the EXS domain of PHO1 is essential for Pi export activity and proper localization to the Golgi and trans-Golgi network, although the EXS domain by itself cannot mediate Pi export. In contrast, removal of the amino-terminal hydrophilic SPX domain does not affect the Pi export capacity of the truncated PHO1 in N. benthamiana. While the Arabidopsis pho1 mutant has low shoot Pi and shows all the hallmarks associated with Pi deficiency, including poor shoot growth and overexpression of numerous Pi deficiency-responsive genes, expression of only the EXS domain of PHO1 in the roots of the pho1 mutant results in a remarkable improvement of shoot growth despite low shoot Pi. Transcriptomic analysis of pho1 expressing the EXS domain indicates an attenuation of the Pi signaling cascade and the up-regulation of genes involved in cell wall synthesis and the synthesis or response to several phytohormones in leaves as well as an altered expression of genes responsive to abscisic acid in roots.
Collapse
Affiliation(s)
- Stefanie Wege
- Department for Plant Molecular Biology (S.W., G.A.K., J.-Y.J., E.V., Y.P.) and Genomic Technologies Facility, Center for Integrative Genomics (S.P.), University of Lausanne, 1015 Lausanne, Switzerland;Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland (S.P.); andInstitute for Crop Science and Natural Resources, Chemical Signaling, University of Bonn, 53113 Bonn, Germany (I.A., A.J.M.)
| | - Ghazanfar Abbas Khan
- Department for Plant Molecular Biology (S.W., G.A.K., J.-Y.J., E.V., Y.P.) and Genomic Technologies Facility, Center for Integrative Genomics (S.P.), University of Lausanne, 1015 Lausanne, Switzerland;Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland (S.P.); andInstitute for Crop Science and Natural Resources, Chemical Signaling, University of Bonn, 53113 Bonn, Germany (I.A., A.J.M.)
| | - Ji-Yul Jung
- Department for Plant Molecular Biology (S.W., G.A.K., J.-Y.J., E.V., Y.P.) and Genomic Technologies Facility, Center for Integrative Genomics (S.P.), University of Lausanne, 1015 Lausanne, Switzerland;Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland (S.P.); andInstitute for Crop Science and Natural Resources, Chemical Signaling, University of Bonn, 53113 Bonn, Germany (I.A., A.J.M.)
| | - Evangelia Vogiatzaki
- Department for Plant Molecular Biology (S.W., G.A.K., J.-Y.J., E.V., Y.P.) and Genomic Technologies Facility, Center for Integrative Genomics (S.P.), University of Lausanne, 1015 Lausanne, Switzerland;Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland (S.P.); andInstitute for Crop Science and Natural Resources, Chemical Signaling, University of Bonn, 53113 Bonn, Germany (I.A., A.J.M.)
| | - Sylvain Pradervand
- Department for Plant Molecular Biology (S.W., G.A.K., J.-Y.J., E.V., Y.P.) and Genomic Technologies Facility, Center for Integrative Genomics (S.P.), University of Lausanne, 1015 Lausanne, Switzerland;Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland (S.P.); andInstitute for Crop Science and Natural Resources, Chemical Signaling, University of Bonn, 53113 Bonn, Germany (I.A., A.J.M.)
| | - Isabel Aller
- Department for Plant Molecular Biology (S.W., G.A.K., J.-Y.J., E.V., Y.P.) and Genomic Technologies Facility, Center for Integrative Genomics (S.P.), University of Lausanne, 1015 Lausanne, Switzerland;Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland (S.P.); andInstitute for Crop Science and Natural Resources, Chemical Signaling, University of Bonn, 53113 Bonn, Germany (I.A., A.J.M.)
| | - Andreas J Meyer
- Department for Plant Molecular Biology (S.W., G.A.K., J.-Y.J., E.V., Y.P.) and Genomic Technologies Facility, Center for Integrative Genomics (S.P.), University of Lausanne, 1015 Lausanne, Switzerland;Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland (S.P.); andInstitute for Crop Science and Natural Resources, Chemical Signaling, University of Bonn, 53113 Bonn, Germany (I.A., A.J.M.)
| | - Yves Poirier
- Department for Plant Molecular Biology (S.W., G.A.K., J.-Y.J., E.V., Y.P.) and Genomic Technologies Facility, Center for Integrative Genomics (S.P.), University of Lausanne, 1015 Lausanne, Switzerland;Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland (S.P.); andInstitute for Crop Science and Natural Resources, Chemical Signaling, University of Bonn, 53113 Bonn, Germany (I.A., A.J.M.)
| |
Collapse
|
16
|
Nawaz Z, Kakar KU, Saand MA, Shu QY. Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses. BMC Genomics 2014; 15:853. [PMID: 25280591 PMCID: PMC4197254 DOI: 10.1186/1471-2164-15-853] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 09/24/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Cyclic nucleotide-gated channels (CNGCs) are Ca2+-permeable cation transport channels, which are present in both animal and plant systems. They have been implicated in the uptake of both essential and toxic cations, Ca2+ signaling, pathogen defense, and thermotolerance in plants. To date there has not been a genome-wide overview of the CNGC gene family in any economically important crop, including rice (Oryza sativa L.). There is an urgent need for a thorough genome-wide analysis and experimental verification of this gene family in rice. RESULTS In this study, a total of 16 full length rice CNGC genes distributed on chromosomes 1-6, 9 and 12, were identified by employing comprehensive bioinformatics analyses. Based on phylogeny, the family of OsCNGCs was classified into four major groups (I-IV) and two sub-groups (IV-A and IV- B). Likewise, the CNGCs from all plant lineages clustered into four groups (I-IV), where group II was conserved in all land plants. Gene duplication analysis revealed that both chromosomal segmentation (OsCNGC1 and 2, 10 and 11, 15 and 16) and tandem duplications (OsCNGC1 and 2) significantly contributed to the expansion of this gene family. Motif composition and protein sequence analysis revealed that the CNGC specific domain "cyclic nucleotide-binding domain (CNBD)" comprises a "phosphate binding cassette" (PBC) and a "hinge" region that is highly conserved among the OsCNGCs. In addition, OsCNGC proteins also contain various other functional motifs and post-translational modification sites. We successively built a stringent motif: (LI-X(2)-[GS]-X-[FV]-X-G-[1]-ELL-X-W-X(12,22)-SA-X(2)-T-X(7)-[EQ]-AF-X-L) that recognizes the rice CNGCs specifically. Prediction of cis-acting regulatory elements in 5' upstream sequences and expression analyses through quantitative qPCR demonstrated that OsCNGC genes were highly responsive to multiple stimuli including hormonal (abscisic acid, indoleacetic acid, kinetin and ethylene), biotic (Pseudomonas fuscovaginae and Xanthomonas oryzae pv. oryzae) and abiotic (cold) stress. CONCLUSIONS There are 16 CNGC genes in rice, which were probably expanded through chromosomal segmentation and tandem duplications and comprise a PBC and a "hinge" region in the CNBD domain, featured by a stringent motif. The various cis-acting regulatory elements in the upstream sequences may be responsible for responding to multiple stimuli, including hormonal, biotic and abiotic stresses.
Collapse
Affiliation(s)
- Zarqa Nawaz
- />State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 China
- />Institute of Biotechnology, Zhejiang University, Hangzhou, China
- />Institute of Crop Sciences, Zhejiang University, Hangzhou, 310029 China
| | | | - Mumtaz A Saand
- />Department of Botany, Shah Abdul Latif University, Khairpur mir’s, Sindh Pakistan
| | - Qing-Yao Shu
- />State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 China
- />Institute of Crop Sciences, Zhejiang University, Hangzhou, 310029 China
| |
Collapse
|
17
|
López-Arredondo DL, Leyva-González MA, González-Morales SI, López-Bucio J, Herrera-Estrella L. Phosphate nutrition: improving low-phosphate tolerance in crops. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:95-123. [PMID: 24579991 DOI: 10.1146/annurev-arplant-050213-035949] [Citation(s) in RCA: 382] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Phosphorus is an essential nutrient that is required for all major developmental processes and reproduction in plants. It is also a major constituent of the fertilizers required to sustain high-yield agriculture. Levels of phosphate--the only form of phosphorus that can be assimilated by plants--are suboptimal in most natural and agricultural ecosystems, and when phosphate is applied as fertilizer in soils, it is rapidly immobilized owing to fixation and microbial activity. Thus, cultivated plants use only approximately 20-30% of the applied phosphate, and the rest is lost, eventually causing water eutrophication. Recent advances in the understanding of mechanisms by which wild and cultivated species adapt to low-phosphate stress and the implementation of alternative bacterial pathways for phosphorus metabolism have started to allow the design of more effective breeding and genetic engineering strategies to produce highly phosphate-efficient crops, optimize fertilizer use, and reach agricultural sustainability with a lower environmental cost. In this review, we outline the current advances in research on the complex network of plant responses to low-phosphorus stress and discuss some strategies used to manipulate genes involved in phosphate uptake, remobilization, and metabolism to develop low-phosphate-tolerant crops, which could help in designing more efficient crops.
Collapse
|