Genome-wide identification and expression analysis of dirigent-jacalin genes from plant chimeric lectins in Moso bamboo (Phyllostachys edulis)

Ma, Ruifang; Huang, Bin; Chen, Jialu; Huang, Zhinuo; Yu, Peng; Ruan, Shiyu; Zhang, Zhijun

doi:10.1371/journal.pone.0248318

Cited by 9 publications

(6 citation statements)

References 87 publications

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“…Many members of the DIR-c subfamily have a distinctive amino acid extension at their C-terminus that is highly comparable to the jacalin-like domain found in lectin proteins. This extension may help members defend against biotic and abiotic stressors [ 21 , 61 ]. None of the identified genes from P. leptostachya were clustered in this category.…”

Section: Discussionmentioning

confidence: 99%

Identification and functional characterization of the dirigent gene family in Phryma leptostachya and the contribution of PlDIR1 in lignan biosynthesis

Pei

Cao

et al. 2023

BMC Plant Biol

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Background Furofuran lignans, the main insecticidal ingredient in Phryma leptostachya, exhibit excellent controlling efficacy against a variety of pests. During the biosynthesis of furofuran lignans, Dirigent proteins (DIRs) are thought to be dominant in the stereoselective coupling of coniferyl alcohol to form ( ±)-pinoresinol. There are DIR family members in almost every vascular plant, but members of DIRs in P. leptostachya are unknown. To identify the PlDIR genes and elucidate their functions in lignan biosynthesis, this study performed transcriptome-wide analysis and characterized the catalytic activity of the PlDIR1 protein. Results Fifteen full-length unique PlDIR genes were identified in P. leptostachya. A phylogenetic analysis of the PlDIRs classified them into four subfamilies (DIR-a, DIR-b/d, DIR-e, and DIR-g), and 12 conserved motifs were found among them. In tissue-specific expression analysis, except for PlDIR7, which displayed the highest transcript abundance in seeds, the other PlDIRs showed preferential expression in roots, leaves, and stems. Furthermore, the treatments with signaling molecules demonstrated that PlDIRs could be significantly induced by methyl jasmonate (MeJA), salicylic acid (SA), and ethylene (ETH), both in the roots and leaves of P. leptostachya. In examining the tertiary structure of the protein and the critical amino acids, it was found that PlDIR1, one of the DIR-a subfamily members, might be involved in the region- and stereo-selectivity of the phenoxy radical. Accordingly, LC–MS/MS analysis demonstrated the catalytic activity of recombinant PlDIR1 protein from Escherichia coli to direct coniferyl alcohol coupling into ( +)-pinoresinol. The active sites and hydrogen bonds of the interaction between PlDIR1 and bis-quinone methide (bisQM), the intermediate in ( +)-pinoresinol formation, were analyzed by molecular docking. As a result, 18 active sites and 4 hydrogen bonds (Asp-42, Ala-113, Leu-138, Arg-143) were discovered in the PlDIR1-bisQM complex. Moreover, correlation analysis indicated that the expression profile of PlDIR1 was closely connected with lignan accumulations after SA treatment. Conclusions The results of this study will provide useful clues for uncovering P. leptostachya's lignan biosynthesis pathway as well as facilitate further studies on the DIR family.

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Section: Discussionmentioning

confidence: 99%

Identification and functional characterization of the dirigent gene family in Phryma leptostachya and the contribution of PlDIR1 in lignan biosynthesis

Pei

Cao

et al. 2023

BMC Plant Biol

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“…Access to the moso bamboo genome [210,211] provides a chance to many researchers for genome-wide classifications of TFs such as aquaporin, AAAP, UBP, IQD, HD-Zip, Hexokinase, Aux/IAA and ARF, NAC, PeUGE, HSF, and CONSTANS-like in moso bamboo [188,[214][215][216][217][218][219][220][221][222][223]. Genome-wide classifications of TFs' families in moso bamboo have been carried out and have demonstrated a limited molecular characterization in model plants by exogenous gene transfer in rice and Arabidopsis and the expression profile against stresses [224][225][226]. The expression of PeLAC was high in stem and its promoter sequence contains ABRE cisregulatory element that responds to ABA and GA treatments by upregulating and downregulating the transcript of PeLAC, respectively [227].…”

Section: Understanding the Bamboos' Tolerance Using Ngs And Metabolomementioning

confidence: 99%

“…Genome-wide classifications of TFs’ families in moso bamboo have been carried out and have demonstrated a limited molecular characterization in model plants by exogenous gene transfer in rice and Arabidopsis and the expression profile against stresses [ 224 , 225 , 226 ]. The expression of PeLAC was high in stem and its promoter sequence contains ABRE cisregulatory element that responds to ABA and GA treatments by upregulating and downregulating the transcript of PeLAC , respectively [ 227 ].…”

Section: Understanding the Bamboos’ Tolerance Using Ngs And Metabolomementioning

confidence: 99%

Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance

Hou

Hussain

Imran

et al. 2022

IJMS

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Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists’ emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants’ genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.

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“…In addition, several grass species (including wheat (Triticum aestivum L.), rice, maize (Zea mays L.) and bamboo (Phyllostachys edulis (Carrière) J.Houz.) express chimeric lectins composed of an N-terminal 'dirigent' domain fused to a C-terminal jacalin domain [107][108][109][110][111][112]. Chimeric lectins containing a Kelch motif, an F-box motif, a tyrosine protein kinase domain or an NB-ARC domain have also been documented.…”

Section: Stress-inducible Jacalin-related Lectinsmentioning

confidence: 99%

Review: The multiple roles of plant lectins

Coninck

Damme

2021

Plant Science

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Genome-wide identification and expression analysis of dirigent-jacalin genes from plant chimeric lectins in Moso bamboo (Phyllostachys edulis)

Cited by 9 publications

References 87 publications

Identification and functional characterization of the dirigent gene family in Phryma leptostachya and the contribution of PlDIR1 in lignan biosynthesis

Identification and functional characterization of the dirigent gene family in Phryma leptostachya and the contribution of PlDIR1 in lignan biosynthesis

Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance

Review: The multiple roles of plant lectins

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