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Tian J, Zhang J, Francis F. Large-Scale Identification and Characterization Analysis of VQ Family Genes in Plants, Especially Gymnosperms. Int J Mol Sci 2023; 24:14968. [PMID: 37834416 PMCID: PMC10573558 DOI: 10.3390/ijms241914968] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/24/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
VQ motif-containing (VQ) proteins are a class of transcription regulatory cofactors widely present in plants, playing crucial roles in growth and development, stress response, and defense. Although there have been some reports on the member identification and functional research of VQ genes in some plants, there is still a lack of large-scale identification and clear graphical presentation of their basic characterization information to help us to better understand this family. Especially in gymnosperms, the VQ family genes and their evolutionary relationships have not yet been reported. In this study, we systematically identified 2469 VQ genes from 56 plant species, including bryophytes, gymnosperms, and angiosperms, and analyzed their molecular and evolutionary features. We found that amino acids are only highly conserved in the VQ domain, while other positions are relatively variable; most VQ genes encode relatively small proteins and do not have introns. The GC content in Poaceae plants is the highest (up to 70%); these VQ proteins can be divided into nine subgroups. In particular, we analyzed the molecular characteristics, chromosome distribution, duplication events, and expression levels of VQ genes in three gymnosperms: Ginkgo biloba, Taxus chinensis, and Pinus tabuliformis. In gymnosperms, VQ genes are classified into 11 groups, with highly similar motifs in each group; most VQ proteins have less than 300 amino acids and are predicted to be located in nucleus. Tandem duplication is an important driving force for the expansion of the VQ gene family, and the evolutionary processes of most VQ genes and duplication events are relatively independent; some candidate VQ genes are preliminarily screened, and they are likely to be involved in plant growth and stress and defense responses. These results provide detailed information and powerful references for further understanding and utilizing the VQ family genes in various plants.
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Affiliation(s)
- Jinfu Tian
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (J.T.)
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Jiahui Zhang
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (J.T.)
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Frédéric Francis
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (J.T.)
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2
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Powell AE, Heyl A. The origin and early evolution of cytokinin signaling. FRONTIERS IN PLANT SCIENCE 2023; 14:1142748. [PMID: 37457338 PMCID: PMC10338860 DOI: 10.3389/fpls.2023.1142748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/23/2023] [Indexed: 07/18/2023]
Abstract
Angiosperms, especially Arabidopsis and rice, have long been at the center of plant research. However, technological advances in sequencing have led to a dramatic increase in genome and transcriptome data availability across land plants and, more recently, among green algae. These data allowed for an in-depth study of the evolution of different protein families - including those involved in the metabolism and signaling of phytohormones. While most early studies on phytohormone evolution were phylogenetic, those studies have started to be complemented by genetic and biochemical studies in recent years. Examples of such functional analyses focused on ethylene, jasmonic acid, abscisic acid, and auxin. These data have been summarized recently. In this review, we will focus on the progress in our understanding of cytokinin biology. We will use these data to synthesize key points about the evolution of cytokinin metabolism and signaling, which might apply to the evolution of other phytohormones as well.
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Liu Y, Jiang Y, Liu X, Cheng H, Han Y, Zhang D, Wu J, Liu L, Yan M, Que Y, Zhou D. Identification and Expression Analysis of Hexokinases Family in Saccharum spontaneum L. under Drought and Cold Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:1215. [PMID: 36986904 PMCID: PMC10056587 DOI: 10.3390/plants12061215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/28/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
In plants, the multi-gene family of dual-function hexokinases (HXKs) plays an important role in sugar metabolism and sensing, that affects growth and stress adaptation. Sugarcane is an important sucrose crop and biofuel crop. However, little is known about the HXK gene family in sugarcane. A comprehensive survey of sugarcane HXKs, including physicochemical properties, chromosomal distribution, conserved motifs, and gene structure was conducted, identifying 20 members of the SsHXK gene family that were located on seven of the 32 Saccharum spontaneum L. chromosomes. Phylogenetic analysis showed that the SsHXK family could be divided into three subfamilies (group I, II and III). Motifs and gene structure were related to the classification of SsHXKs. Most SsHXKs contained 8-11 introns which was consistent with other monocots. Duplication event analysis indicated that HXKs in S. spontaneum L. primarily originated from segmental duplication. We also identified putative cis-elements in the SsHXK promoter regions which were involved in phytohormone, light and abiotic stress responses (drought, cold et al.). During normal growth and development, 17 SsHXKs were constitutively expressed in all ten tissues. Among them, SsHXK2, SsHXK12 and SsHXK14 had similar expression patterns and were more highly expressed than other genes at all times. The RNA-seq analysis showed that 14/20 SsHXKs had the highest expression level after cold stress for 6 h, especially SsHXK15, SsHXK16 and SsHXK18. As for drought treatment, 7/20 SsHXKs had the highest expression level after drought stress for 10 days, 3/20 (SsHKX1, SsHKX10 and SsHKX11) had the highest expression level after 10 days of recovery. Overall, our results revealed the potential biological function of SsHXKs, which may provide information for in-depth functional verification.
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Affiliation(s)
- Ying Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yaolan Jiang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xiaolan Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Hefen Cheng
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yuekun Han
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Dawei Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Jinfeng Wu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Lili Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410000, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dinggang Zhou
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
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Swinka C, Hellmann E, Zwack P, Banda R, Rashotte AM, Heyl A. Cytokinin Response Factor 9 Represses Cytokinin Responses in Flower Development. Int J Mol Sci 2023; 24:4380. [PMID: 36901811 PMCID: PMC10002603 DOI: 10.3390/ijms24054380] [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: 12/28/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
A multi-step phosphorelay system is the main conduit of cytokinin signal transduction. However, several groups of additional factors that also play a role in this signaling pathway have been found-among them the Cytokinin Response Factors (CRFs). In a genetic screen, CRF9 was identified as a regulator of the transcriptional cytokinin response. It is mainly expressed in flowers. Mutational analysis indicates that CRF9 plays a role in the transition from vegetative to reproductive growth and silique development. The CRF9 protein is localized in the nucleus and functions as a transcriptional repressor of Arabidopsis Response Regulator 6 (ARR6)-a primary response gene for cytokinin signaling. The experimental data suggest that CRF9 functions as a repressor of cytokinin during reproductive development.
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Affiliation(s)
- Christine Swinka
- Institut für Angewandte Genetik, Freie Universität Berlin, Albrecht Thaer Weg 6, 14195 Berlin, Germany
| | - Eva Hellmann
- Institut für Angewandte Genetik, Freie Universität Berlin, Albrecht Thaer Weg 6, 14195 Berlin, Germany
| | - Paul Zwack
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences, Auburn, AL 36849, USA
| | - Ramya Banda
- Department of Biology, Adelphi University, 1 South Ave, Garden City, NY 11530, USA
| | - Aaron M. Rashotte
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences, Auburn, AL 36849, USA
| | - Alexander Heyl
- Department of Biology, Adelphi University, 1 South Ave, Garden City, NY 11530, USA
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Du Y, Zhang Z, Gu Y, Li W, Wang W, Yuan X, Zhang Y, Yuan M, Du J, Zhao Q. Genome-wide identification of the soybean cytokinin oxidase/dehydrogenase gene family and its diverse roles in response to multiple abiotic stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1163219. [PMID: 37139113 PMCID: PMC10149856 DOI: 10.3389/fpls.2023.1163219] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Cytokinin oxidase/dehydrogenase (CKX) irreversibly degrades cytokinin, regulates growth and development, and helps plants to respond to environmental stress. Although the CKX gene has been well characterized in various plants, its role in soybean remains elusive. Therefore, in this study, the evolutionary relationship, chromosomal location, gene structure, motifs, cis-regulatory elements, collinearity, and gene expression patterns of GmCKXs were analyzed using RNA-seq, quantitative real-time PCR (qRT-PCR), and bioinformatics. We identified 18 GmCKX genes from the soybean genome and grouped them into five clades, each comprising members with similar gene structures and motifs. Cis-acting elements involved in hormones, resistance, and physiological metabolism were detected in the promoter regions of GmCKXs. Synteny analysis indicated that segmental duplication events contributed to the expansion of the soybean CKX family. The expression profiling of the GmCKXs genes using qRT-PCR showed tissue-specific expression patterns. The RNA-seq analysis also indicated that GmCKXs play an important role in response to salt and drought stresses at the seedling stage. The responses of the genes to salt, drought, synthetic cytokinin 6-benzyl aminopurine (6-BA), and the auxin indole-3-acetic acid (IAA) at the germination stage were further evaluated by qRT-PCR. Specifically, the GmCKX14 gene was downregulated in the roots and the radicles at the germination stage. The hormones 6-BA and IAA repressed the expression levels of GmCKX1, GmCKX6, and GmCKX9 genes but upregulated the expression levels of GmCKX10 and GmCKX18 genes. The three abiotic stresses also decreased the zeatin content in soybean radicle but enhanced the activity of the CKX enzymes. Conversely, the 6-BA and IAA treatments enhanced the CKX enzymes' activity but reduced the zeatin content in the radicles. This study, therefore, provides a reference for the functional analysis of GmCKXs in soybean in response to abiotic stresses.
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Affiliation(s)
- Yanli Du
- Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- National Cereals Technology Engineering Research Center, Daqing, Heilongjiang, China
| | - Zhaoning Zhang
- Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Yanhua Gu
- Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Weijia Li
- Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Weiyu Wang
- Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Xiankai Yuan
- Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Yuxian Zhang
- National Cereals Technology Engineering Research Center, Daqing, Heilongjiang, China
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, Heilongjiang, China
| | - Ming Yuan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, Heilongjiang, China
| | - Jidao Du
- Agricultural College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
- National Cereals Technology Engineering Research Center, Daqing, Heilongjiang, China
- Research Center of Saline and Alkali Land Improvement Engineering Technology in Heilongjiang Province, Daqing, Heilongjiang, China
- *Correspondence: Jidao Du, ; Qiang Zhao,
| | - Qiang Zhao
- Heilongjiang Bayi Agricultural University, Key Laboratory of Ministry of Agriculture and Rural Affairs of Soybean Mechanized Production, Daqing, Heilongjiang, China
- Research Center of Saline and Alkali Land Improvement Engineering Technology in Heilongjiang Province, Daqing, Heilongjiang, China
- *Correspondence: Jidao Du, ; Qiang Zhao,
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Barten R, van Workum DJM, de Bakker E, Risse J, Kleisman M, Navalho S, Smit S, Wijffels RH, Nijveen H, Barbosa MJ. Genetic mechanisms underlying increased microalgal thermotolerance, maximal growth rate, and yield on light following adaptive laboratory evolution. BMC Biol 2022; 20:242. [PMID: 36303154 PMCID: PMC9615354 DOI: 10.1186/s12915-022-01431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adaptive laboratory evolution (ALE) is a powerful method for strain optimization towards abiotic stress factors and for identifying adaptation mechanisms. In this study, the green microalga Picochlorum sp. BPE23 was cultured under supra-optimal temperature to force genetic adaptation. The robustness and adaptive capacity of Picochlorum strains turned them into an emerging model for evolutionary studies on abiotic stressors such as temperature, salinity, and light. RESULTS Mutant strains showed an expanded maximal growth temperature of 44.6 °C, whereas the maximal growth temperature of the wild-type strain was 42 °C. Moreover, at the optimal growth temperature of 38 °C, the biomass yield on light was 22.3% higher, and the maximal growth rate was 70.5% higher than the wild type. Genome sequencing and transcriptome analysis were performed to elucidate the mechanisms behind the improved phenotype. A de novo assembled phased reference genome allowed the identification of 21 genic mutations involved in various processes. Moreover, approximately half of the genome contigs were found to be duplicated or even triplicated in all mutants, suggesting a causal role in adaptation. CONCLUSIONS The developed tools and mutant strains provide a strong framework from whereupon Picochlorum sp. BPE23 can be further developed. Moreover, the extensive strain characterization provides evidence of how microalgae evolve to supra-optimal temperature and to photobioreactor growth conditions. With this study, microalgal evolutionary mechanisms were identified by combining ALE with genome sequencing.
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Affiliation(s)
- Robin Barten
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands.
| | - Dirk-Jan M van Workum
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Emma de Bakker
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands
| | - Judith Risse
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Michelle Kleisman
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Sofia Navalho
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Rene H Wijffels
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands.,Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Maria J Barbosa
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands
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A Comprehensive Identification and Expression Analysis of VQ Motif-Containing Proteins in Sugarcane (Saccharum spontaneum L.) under Phytohormone Treatment and Cold Stress. Int J Mol Sci 2022; 23:ijms23116334. [PMID: 35683012 PMCID: PMC9181594 DOI: 10.3390/ijms23116334] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 11/18/2022] Open
Abstract
The VQ motif-containing proteins play a vital role in various processes such as growth, resistance to biotic and abiotic stresses and development. However, there is currently no report on the VQ genes in sugarcane (Saccharum spp.). Herein, 78 VQ genes in Saccharum spontaneum were identified and classified into nine subgroups (I-IX) by comparative genomic analyses. Each subgroup had a similar structural and conservative motif. These VQ genes expanded mainly through whole-genome segmental duplication. The cis-regulatory elements (CREs) of the VQ genes were widely involved in stress responses, phytohormone responses and physiological regulation. The RNA-seq data showed that SsVQ gene expression patterns in 10 different samples, including different developmental stages, revealed distinct temporal and spatial patterns. A total of 23 SsVQ genes were expressed in all tissues, whereas 13 SsVQ genes were not expressed in any tissues. Sequence Read Archive (SRA) data showed that the majority of SsVQs responded to cold and drought stress. In addition, quantitative real-time PCR analysis showed that the SsVQs were variously expressed under salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and cold treatment. This study conducted a full-scale analysis of the VQ gene family in sugarcane, which could be beneficial for the functional characterization of sugarcane VQ genes and provide candidate genes for molecular resistance breeding in cultivated sugarcane in the future.
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Cytokinin Perception in Ancient Plants beyond Angiospermae. Int J Mol Sci 2021; 22:ijms222313077. [PMID: 34884882 PMCID: PMC8657898 DOI: 10.3390/ijms222313077] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
Cytokinins (CKs) control many plant developmental processes and responses to environmental cues. Although the CK signaling is well understood, we are only beginning to decipher its evolution. Here, we investigated the CK perception apparatus in early-divergent plant species such as bryophyte Physcomitrium patens, lycophyte Selaginella moellendorffii, and gymnosperm Picea abies. Of the eight CHASE-domain containing histidine kinases (CHKs) examined, two CHKs, PpCHK3 and PpCHK4, did not bind CKs. All other CHK receptors showed high-affinity CK binding (KD of nM range), with a strong preference for isopentenyladenine over other CK nucleobases in the moss and for trans-zeatin over cis-zeatin in the gymnosperm. The pH dependences of CK binding for these six CHKs showed a wide range, which may indicate different subcellular localization of these receptors at either the plasma- or endoplasmic reticulum membrane. Thus, the properties of the whole CK perception apparatuses in early-divergent lineages were demonstrated. Data show that during land plant evolution there was a diversification of the ligand specificity of various CHKs, in particular, the rise in preference for trans-zeatin over cis-zeatin, which indicates a steadily increasing specialization of receptors to various CKs. Finally, this distinct preference of individual receptors to different CK versions culminated in vascular plants, especially angiosperms.
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Liao X, Hu K, Salhi A, Zou Y, Wang J, Gao X. msRepDB: a comprehensive repetitive sequence database of over 80 000 species. Nucleic Acids Res 2021; 50:D236-D245. [PMID: 34850956 PMCID: PMC8728181 DOI: 10.1093/nar/gkab1089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).
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Affiliation(s)
- Xingyu Liao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Kang Hu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Adil Salhi
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - You Zou
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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Dabravolski SA, Isayenkov SV. Evolution of the Cytokinin Dehydrogenase (CKX) Domain. J Mol Evol 2021; 89:665-677. [PMID: 34757471 DOI: 10.1007/s00239-021-10035-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/30/2021] [Indexed: 01/05/2023]
Abstract
Plant hormone cytokinins are important regulators of plant development, response to environmental stresses and interplay with other plant hormones. Cytokinin dehydrogenases (CKXs) are proteins responsible for the irreversible break-down of cytokinins to the adenine and aldehyde. Even though plant CKXs have been extensively studied, homologous proteins from other taxa remain mainly uncharacterised. Here we present our study on the molecular evolution and divergence of the CKX from bacteria, fungi, amoeba and viridiplantae. Although CKXs are present in eukaryotes and prokaryotes, they are missing in algae and metazoan taxa. The prevalent domain architecture consists of the FAD-binding and cytokinin binding domains, whereas some bacteria appear to have only cytokinin binding domain proteins. The CKXs play important role in the various aspects of plant life including control of plant development, response to biotic and abiotic stress, influence nutrition. Results of our study suggested that CKX originates from the FAD-linked C-terminal oxidase and has a defence-oriented function. The obtained results significantly extend the current understanding of the cytokinin dehydrogenases structure-function from the relationship to homologues from other taxa and provide a starting point baseline for their future functional characterization.
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Affiliation(s)
- Siarhei A Dabravolski
- Department of Clinical Diagnostics, Vitebsk State Academy of Veterinary Medicine [UO VGAVM], Dovatora str. 7/11, 21002, Vitebsk, Belarus
| | - Stanislav V Isayenkov
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China.
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics, NAS of Ukraine, Osipovskogo str., 2a, Kyiv-123, Kyiv, 04123, Ukraine.
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11
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Liao X, Li M, Hu K, Wu FX, Gao X, Wang J. A sensitive repeat identification framework based on short and long reads. Nucleic Acids Res 2021; 49:e100. [PMID: 34214175 PMCID: PMC8464074 DOI: 10.1093/nar/gkab563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous studies have shown that repetitive regions in genomes play indispensable roles in the evolution, inheritance and variation of living organisms. However, most existing methods cannot achieve satisfactory performance on identifying repeats in terms of both accuracy and size, since NGS reads are too short to identify long repeats whereas SMS (Single Molecule Sequencing) long reads are with high error rates. In this study, we present a novel identification framework, LongRepMarker, based on the global de novo assembly and k-mer based multiple sequence alignment for precisely marking long repeats in genomes. The major characteristics of LongRepMarker are as follows: (i) by introducing barcode linked reads and SMS long reads to assist the assembly of all short paired-end reads, it can identify the repeats to a greater extent; (ii) by finding the overlap sequences between assemblies or chomosomes, it locates the repeats faster and more accurately; (iii) by using the multi-alignment unique k-mers rather than the high frequency k-mers to identify repeats in overlap sequences, it can obtain the repeats more comprehensively and stably; (iv) by applying the parallel alignment model based on the multi-alignment unique k-mers, the efficiency of data processing can be greatly optimized and (v) by taking the corresponding identification strategies, structural variations that occur between repeats can be identified. Comprehensive experimental results show that LongRepMarker can achieve more satisfactory results than the existing de novo detection methods (https://github.com/BioinformaticsCSU/LongRepMarker).
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Affiliation(s)
- Xingyu Liao
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Kang Hu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
| | - Fang-Xiang Wu
- Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N5A9, Canada
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China
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12
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Zhang H, Xie J, Wang W, Wang J. Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations. PLANT MOLECULAR BIOLOGY 2021; 106:193-206. [PMID: 33742369 DOI: 10.1007/s11103-021-01137-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
We provided a study on homeologous gene evolution of homeologous genes by comparing Brassica genomes. Polyploidy has played fundamental roles during the evolution of plants. Following polyploidization, many duplicated genes are diversified or lost in a process termed diploidization. Understanding the retention and diversification of homeologs after polyploidization will help elucidate the process of diploidization. Here, we investigated the evolution of homeologous genes in Brassica genomes and observed similarly asymmetrical gene retention among different functional groups and consistent retention after recurrent polyploidizations. In the comparative analysis of Brassica diploid genomes, we found that preferentially retained genes show different patterns on sequence and expression divergence: genes with the function of 'biosynthetic process' and 'transport' were under much stronger purifying selection, while transcriptional regulatory genes diverged much faster than other genes. Duplicate pairs of the former two functional groups show conserved high expression patterns, while most of transcriptional regulatory genes are simultaneously lowly expressed. Furthermore, homeologs in diploids and allotetraploids showed similar loss and retention patterns: duplicates in progenitor genomes were more likely to be retained and accumulated fewer substitutions. However, transcriptional regulation is also enriched in the genes that do not have any non-synonymous mutations in the Brassica allotetraploids, indicating that some of these genes were under strong purifying selection. Overall, our study provided insight into the evolution of homeologs genes during diploidization process.
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Affiliation(s)
- Haorui Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiandan Xie
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Wenliang Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Jianbo Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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13
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Nguyen HN, Kambhampati S, Kisiala A, Seegobin M, Emery RJN. The soybean ( Glycine max L.) cytokinin oxidase/dehydrogenase multigene family; Identification of natural variations for altered cytokinin content and seed yield. PLANT DIRECT 2021; 5:e00308. [PMID: 33644633 PMCID: PMC7887454 DOI: 10.1002/pld3.308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 05/11/2023]
Abstract
Cytokinins (CKs) play a fundamental role in regulating dynamics of organ source/sink relationships during plant development, including flowering and seed formation stages. As a result, CKs are key drivers of seed yield. The cytokinin oxidase/dehydrogenase (CKX) is one of the critical enzymes responsible for regulating plant CK levels by causing their irreversible degradation. Variation of CKX activity is significantly correlated with seed yield in many crop species while in soybean (Glycine max L.), the possible associations between CKX gene family members (GFMs) and yield parameters have not yet been assessed. In this study, 17 GmCKX GFMs were identified, and natural variations among GmCKX genes were probed among soybean cultivars with varying yield characteristics. The key CKX genes responsible for regulating CK content during seed filling stages of reproductive development were highlighted using comparative phylogenetics, gene expression analysis and CK metabolite profiling. Five of the seventeen identified GmCKX GFMs, showed natural variations in the form of single nucleotide polymorphisms (SNPs). The gene GmCKX7-1, with high expression during critical seed filling stages, was found to have a non-synonymous mutation (H105Q), on one of the active site residues, Histidine 105, previously reported to be essential for co-factor binding to maintain structural integrity of the enzyme. Soybean lines with this mutation had higher CK content and desired yield characteristics. The potential for marker-assisted selection based on the identified natural variation within GmCKX7-1, is discussed in the context of hormonal control that can result in higher soybean yield.
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Affiliation(s)
| | - Shrikaar Kambhampati
- Department of BiologyTrent UniversityPeterboroughONCanada
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Anna Kisiala
- Department of BiologyTrent UniversityPeterboroughONCanada
| | - Mark Seegobin
- Department of BiologyTrent UniversityPeterboroughONCanada
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14
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Rashotte AM. The evolution of cytokinin signaling and its role in development before Angiosperms. Semin Cell Dev Biol 2021; 109:31-38. [DOI: 10.1016/j.semcdb.2020.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/12/2020] [Accepted: 06/13/2020] [Indexed: 02/02/2023]
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15
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Liu P, Wang S, Wang X, Yang X, Li Q, Wang C, Chen C, Shi Q, Ren Z, Wang L. Genome-wide characterization of two-component system (TCS) genes in melon (Cucumis melo L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:197-213. [PMID: 32229405 DOI: 10.1016/j.plaphy.2020.03.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 06/10/2023]
Abstract
To better understand cytokinin signaling in melon (Cucumis melo L.), one of the most important fruit crops in the Cucurbitaceae family, we identified and characterized melon two-component system (TCS) genes in this study. The results showed that there were 51 genes encoding putative TCS proteins in melon, and these TCS genes were classified into 3 subgroups, with 17 HK(L)s (histidine kinase/histidine-kinase like; 9 HKs and 8 HKLs), 9 HPs (histidine phosphotransfer proteins; 6 authentic and 3 pseudo), and 25 RRs (response regulators; 8 Type-A, 11 Type-B and 6 pseudo). The identity values of these cytokinin signaling proteins were revealed by analyzing their conserved motifs, domains and amino acid sequences. By analyzing TCS genes in different plant species, we found that melon HK(L)s, HPs and RRs had closer phylogenetic relationships with cucumber genes than with the genes of other plants, and the expansion of melon cytokinin signaling genes might be attributed to segmental duplication events. Analysis of the putative promoter regions (2-kb upstream regions of the start codon) revealed the enrichment of stress- and hormone-response cis-elements. The involvement of these putative TCS genes in melon cytokinin signaling was further supported by qRT-PCR data.
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Affiliation(s)
- Panjing Liu
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Shuoshuo Wang
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiangfei Wang
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiaoyu Yang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Qiang Li
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Chao Wang
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Chunhua Chen
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Qinghua Shi
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Zhonghai Ren
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.
| | - Lina Wang
- State Key Laboratory of Crop Biology, Tai'an, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Tai'an, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.
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16
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Ling L, Qu Y, Zhu J, Wang D, Guo C. Genome-wide identification and expression analysis of the VQ gene family in Cicer arietinum and Medicago truncatula. PeerJ 2020; 8:e8471. [PMID: 32117614 PMCID: PMC7006518 DOI: 10.7717/peerj.8471] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022] Open
Abstract
Valine-glutamine (VQ) proteins are plant-specific proteins that play crucial roles in plant development as well as biotic and abiotic stress responses. VQ genes have been identified in various plants; however, there are no systematic reports in Cicer arietinum or Medicago truncatula. Herein, we identified 19 and 32 VQ genes in C. arietinum and M. truncatula, respectively. A total of these VQ genes were divided into eight groups (I-VIII) based on phylogenetic analysis. Gene structure analyses and motif patterns revealed that these VQ genes might have originated from a common ancestor. In silico analyses demonstrated that these VQ genes were expressed in different tissues. qRT-PCR analysis indicated that the VQ genes were differentially regulated during multiple abiotic stresses. This report presents the first systematic analysis of VQ genes from C. arietinum and M. truncatula and provides a solid foundation for further research of the specific functions of VQ proteins.
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Affiliation(s)
- Lei Ling
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Yue Qu
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Jintao Zhu
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Dan Wang
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Changhong Guo
- College of Life Science and Technology, Harbin Normal University, Harbin, China
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17
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Abstract
Signal transduction systems configured around a core phosphotransfer step between a histidine kinase and a cognate response regulator protein occur in organisms from all domains of life. These systems, termed two-component systems, constitute the majority of multi-component signaling pathways in Bacteria but are less prevalent in Archaea and Eukarya. The core signaling domains are modular, allowing versatility in configuration of components into single-step phosphotransfer and multi-step phosphorelay pathways, the former being predominant in bacteria and the latter in eukaryotes. Two-component systems regulate key cellular regulatory processes that provide adaptive responses to environmental stimuli and are of interest for the development of antimicrobial therapeutics, biotechnology applications, and biosensor engineering. In bacteria, two-component systems have been found to mediate responses to an extremely broad array of extracellular and intracellular chemical and physical stimuli, whereas in archaea and eukaryotes, the use of two-component systems is more limited. This review summarizes recent advances in exploring the repertoire of sensor histidine kinases in the Archaea and Eukarya domains of life.
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Affiliation(s)
- Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), SFR ICAT 4208, UNIV Angers, UNIV Brest, Angers, France
| | - Ann M Stock
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
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18
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Tan S, Debellé F, Gamas P, Frugier F, Brault M. Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes. BMC Genomics 2019; 20:373. [PMID: 31088345 PMCID: PMC6518804 DOI: 10.1186/s12864-019-5724-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/22/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering root cortical cell divisions at the onset of nodule initiation. Cytokinin signaling is based on a Two-Component System (TCS) phosphorelay cascade, involving successively Cytokinin-binding Histidine Kinase receptors, phosphorelay proteins shuttling between the cytoplasm and the nucleus, and Type-B Response Regulator (RRB) transcription factors activating the expression of cytokinin primary response genes. Among those, Type-A Response Regulators (RRA) exert a negative feedback on the TCS signaling. To determine whether the legume plant nodulation capacity is linked to specific features of TCS proteins, a genome-wide identification was performed in six legume genomes (Cajanus cajan, pigeonpea; Cicer arietinum, chickpea; Glycine max, soybean; Phaseolus vulgaris, common bean; Lotus japonicus; Medicago truncatula). The diversity of legume TCS proteins was compared to the one found in two non-nodulating species, Arabidopsis thaliana and Vitis vinifera, which are references for functional analyses of TCS components and phylogenetic analyses, respectively. RESULTS A striking expansion of non-canonical RRBs was identified, notably leading to the emergence of proteins where the conserved phosphor-accepting aspartate residue is replaced by a glutamate or an asparagine. M. truncatula genome-wide expression datasets additionally revealed that only a limited subset of cytokinin-related TCS genes is highly expressed in different organs, namely MtCHK1/MtCRE1, MtHPT1, and MtRRB3, suggesting that this "core" module potentially acts in most plant organs including nodules. CONCLUSIONS Further functional analyses are required to determine the relevance of these numerous non-canonical TCS RRBs in symbiotic nodulation, as well as of canonical MtHPT1 and MtRRB3 core signaling elements.
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Affiliation(s)
- Sovanna Tan
- IPS2 (Institute of Plant Sciences Paris-Saclay), CNRS, Université Paris-Sud, Université Paris-Diderot, INRA, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
| | - Frédéric Debellé
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Pascal Gamas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Florian Frugier
- IPS2 (Institute of Plant Sciences Paris-Saclay), CNRS, Université Paris-Sud, Université Paris-Diderot, INRA, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
| | - Mathias Brault
- IPS2 (Institute of Plant Sciences Paris-Saclay), CNRS, Université Paris-Sud, Université Paris-Diderot, INRA, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
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Li P, Lei K, Li Y, He X, Wang S, Liu R, Ji L, Hou B. Identification and characterization of the first cytokinin glycosyltransferase from rice. RICE (NEW YORK, N.Y.) 2019; 12:19. [PMID: 30923923 PMCID: PMC6439077 DOI: 10.1186/s12284-019-0279-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/21/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cytokinins are one of the five major hormones families in plants and are important for their normal growth and environmental adaptability. In plants, cytokinins are mostly present as glycosides in plants, and their glycosylation modifications are catalyzed by family 1 glycosyltransferases. Current research on cytokinin glycosylation has focused on the biochemical identification of enzymes and the analysis of metabolites in Arabidopsis. There are few studies that examine how cytokinin glycosylation affects its synthesis and accumulation in plants. It is particularly important to understand these processes in food crops such as rice (Oryza sativa); however, to date, cytokinin glycosyltransferase genes in rice have not been reported. RESULTS In this study, we identified eight rice genes that were functionally homologous to an Arabidopsis cytokinin glycosyltransferase gene. These genes were cloned and expressed in a prokaryotic system to obtain their purified proteins. Through enzymatic analysis and liquid chromatography-mass spectrometry, a single rice glycosyltransferase, Os6, was identified that glycosylated cytokinin in vitro. Os6 was overexpressed in Arabidopsis, and the extraction of cytokinin glycosides showed that Os6 is functionally active in planta. CONCLUSIONS The identification and characterization of the first cytokinin glycosyltransferase from rice is important for future studies on the cytokinin metabolic pathway in rice. An improved understanding of rice cytokinin glycosyltransferases may facilitate genetic improvements in rice quality.
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Affiliation(s)
- Pan Li
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
- College of Life Science, Shandong University, Qingdao, 250000, Shandong, China
| | - Kang Lei
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Yanjie Li
- College of Life Science, Shandong University, Qingdao, 250000, Shandong, China
| | - Xingrui He
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Shuo Wang
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Renmin Liu
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China
| | - Lusha Ji
- College of Pharmacy, Liaocheng University, Liaocheng, 252000, Shandong, China.
| | - Bingkai Hou
- College of Life Science, Shandong University, Qingdao, 250000, Shandong, China.
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