Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea

Liu, Chenyang; Yuan, Dongliang; Liu, Tong; Xing, Mengge; Xu, Wenying; Zhang, Huiying; Jin, Hanqi; Cai, Chunmei; Li, Shuai

doi:10.1155/2020/2568640

Cited by 3 publications

(2 citation statements)

References 52 publications

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“…Here we also predicted that the proteins encoded by these genes have almost similar motifs hence they are associated with the specific functions of symbiotic relationships. For instance L. japonicus and M. truncatula has Nucleoporin [41,42], RWP-RK in Arachis duranensis and Arachis ipaensis [43], EF-hand domain in soybean [44], LRR in L. japonicus [45] were found to be involved in nodulation.…”

Section: Plos Onementioning

confidence: 99%

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Genome wide identification and characterization of nodulation related genes in Arachis hypogaea

Khurshid

Akram²,

Ali³

et al. 2022

PLoS ONE

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Nitrogen is an important plant nutrient that has a significant role in crop yield. Hence, to fulfill the needs of sustainable agriculture, it is necessary to improve biological nitrogen fixation in leguminous crops. Nod inducing gene families plays a crucial role in the interaction between rhizobia and legumes, leading to biological nitrogen fixation. However, nod inducing genes identification and characterization has not yet been performed in Arachis hypogaea. In this study, identification and genome-wide analysis of nod inducing genes are performed so that to explore their potential functions in the Arachis hypogaea for the first time. Nod genes were comprehensively analyzed by phylogenetic clustering analysis, gene structure determination, detection of conserved motifs, subcellular localization, conserved motifs, cis-acting elements and promoter region analysis. This study identified 42 Nod inducing genes in Arachis hypogaea, their sequences were submitted to NCBI and accession numbers were obtained. Potential involvement of these genes in biological nitrogen fixation has been unraveled, such as, phylogenetic analysis revealed that nod inducing genes evolved independently in Arachis hypogaea, the amino acid structures exhibited 20 highly conserved motifs, the proteins are present at different locations in cells and the gene structures revealed that all the genes are full-length genes with upstream intronic regions. Further, the promoter analysis determined a large number of cis-regulatory elements involved in nodulation. Moreover, this study not only provides identification and characterization of genes underlying developmental and functional stages of nodulation and biological nitrogen fixation but also lays the foundation for further revelation of nod inducing gene family. Besides, identification and structural analysis of these genes in Arachis hypogaea may provide a theoretical basis for the study of evolutionary relationships in future analysis.

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Section: Plos Onementioning

confidence: 99%

“…In addition, few elements might play role in cellular development. Furthermore, different numbers of such cis-acting elements were also discovered in wild species (A. duranensis and A. ipaensis), representing, distinct functions of these genes, vital for plant growth and development [43].…”

Section: Plos Onementioning

confidence: 99%

Genome wide identification and characterization of nodulation related genes in Arachis hypogaea

Khurshid

Akram²,

Ali³

et al. 2022

PLoS ONE

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Evolution of antimicrobial cysteine-rich peptides in plants

Cao

Jia

et al. 2023

Plant Cell Rep

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To defend against diverse groups of pathogens, plants produce cysteine-rich peptides (CRPs) with longlasting broad-spectrum antimicrobial activity. We analyzed 240 plant genomes ranging from algae to eudicots and our comparative genomics results revealed that CRPs are widely distributed in plants.Further, we found that CRP genes have been ampli ed through both whole genome and local tandem duplication. Their copy number varied signi cantly across lineages and was associated with the plant ecotype, which may be the result of resistance to changing pathogenic environments. The conserved and lineage-speci c CRP families contribute to diverse antimicrobial activities. Moreover, we investigated the unique bi-domain CRPs that result from unequal crossover events. Our ndings provide a unique evolutionary perspective on CRPs and provide insights into their antimicrobial and symbiosis characteristics. Key MessageWe analyzed the evolutionary pattern of cysteine-rich peptides (CRPs) to infer the relationship between CRP copy number and plant ecotype, and the origin of bi-domains CRPs.

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Identification and Molecular Characterization of RWP-RK Transcription Factors in Soybean

Amin

Ahmad

Khalifa

et al. 2023

Genes

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The RWP-RK is a small family of plant-specific transcription factors that are mainly involved in nitrate starvation responses, gametogenesis, and root nodulation. To date, the molecular mechanisms underpinning nitrate-regulated gene expression in many plant species have been extensively studied. However, the regulation of nodulation-specific NIN proteins during nodulation and rhizobial infection under nitrogen starvation in soybean still remain unclear. Here, we investigated the genome-wide identification of RWP-RK transcription factors and their essential role in nitrate-inducible and stress-responsive gene expression in soybean. In total, 28 RWP-RK genes were identified from the soybean genome, which were unevenly distributed on 20 chromosomes from 5 distinct groups during phylogeny classification. The conserved topology of RWP-RK protein motifs, cis-acting elements, and functional annotation has led to their potential as key regulators during plant growth, development, and diverse stress responses. The RNA-seq data revealed that the up-regulation of GmRWP-RK genes in the nodules indicated that these genes might play crucial roles during root nodulation in soybean. Furthermore, qRT-PCR analysis revealed that most GmRWP-RK genes under Phytophthora sojae infection and diverse environmental conditions (such as heat, nitrogen, and salt) were significantly induced, thus opening a new window of possibilities into their regulatory roles in adaptation mechanisms that allow soybean to tolerate biotic and abiotic stress. In addition, the dual luciferase assay indicated that GmRWP-RK1 and GmRWP-RK2 efficiently bind to the promoters of GmYUC2, GmSPL9, and GmNIN, highlighting their possible involvement in nodule formation. Together, our findings provide novel insights into the functional role of the RWP-RK family during defense responses and root nodulation in soybean.

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Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea

Cited by 3 publications

References 52 publications

Genome wide identification and characterization of nodulation related genes in Arachis hypogaea

Genome wide identification and characterization of nodulation related genes in Arachis hypogaea

Evolution of antimicrobial cysteine-rich peptides in plants

Identification and Molecular Characterization of RWP-RK Transcription Factors in Soybean

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