Molecular Characterization, Evolution, and Expression Profiling of the Dirigent (DIR) Family Genes in Chinese White Pear (Pyrus bretschneideri)

Cheng, Xi; Su, Xueqiang; Abdullah, Muhammad; Li, Manli; Zhang, Jinyun; Sun, Yanming; Li, Guohui; Jin, Qing; Cai, Yongping; Lin, Yi

doi:10.3389/fgene.2018.00136

Cited by 45 publications

(34 citation statements)

References 55 publications

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“…The plant lignification process is a complex process of cell differentiation and development, which is driven by the co-expression of many transcription regulators and functional genes [63][64][65][66][67]. Studies have shown that KNAT7 interacts with the TALE homeodomain protein BLH6, and the KNAT7-BLH6 complex operates as a repression module in secondary cell wall formation [68].…”

Section: Lignin Synthesis Regulated By a Networkmentioning

confidence: 99%

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

Lou

Yang

et al. 2019

Biomolecules

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Homeobox (HB) genes play critical roles in regulating various aspects of plant growth and development. However, little is known about HB genes in bamboo. In this study, a total of 115 HB genes (PeHB001–PeHB115) were identified from moso bamboo (Phyllostachys edulis) and grouped into 13 distinct classes (BEL, DDT, HD-ZIP I–IV, KNOX, NDX, PHD, PINTOX, PLINC, SAWADEE, and WOX) based on the conserved domains and phylogenetic analysis. The number of members in the different classes ranged from 2 to 24, and they usually varied in terms of exon–intron distribution pattern and length. There were 20 conserved motifs found in 115 PeHBs, with motif 1 being the most common. Gene ontology (GO) analysis showed that PeHBs had diverse molecular functions, with 19 PeHBs being annotated as having xylem development, xylem, and phloem pattern formation functions. Co-expression network analysis showed that 10 of the 19 PeHBs had co-expression correlations, and three members of the KNOX class were hub proteins that interacted with other transcription factors (TFs) such as MYB, bHLH, and OVATE, which were associated with lignin synthesis. Yeast two-hybridization results further proved that PeHB037 (BEL class) interacted with PeHB057 (KNOX class). Transcriptome expression profiling indicated that all PeHBs except PeHB017 were expressed in at least one of the seven tissues of moso bamboo, and 90 PeHBs were expressed in all the tissues. The qRT-PCR results of the 19 PeHBs showed that most of them were upregulated in shoots as the height increased. Moreover, a KNOX binding site was found in the promoters of the key genes involved in lignin synthesis such as Pe4CL, PeC3H, PeCCR, and PeCOMT, which had positive expression correlations with five KNOX genes. Similar results were found in winter bamboo shoots with prolonged storage time, which was consistent with the degree of lignification. These results provide basic data on PeHBs in moso bamboo, which will be helpful for future functional research on PeHBs with positive regulatory roles in the process of lignification.

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Section: Lignin Synthesis Regulated By a Networkmentioning

confidence: 99%

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

Lou

Yang

et al. 2019

Biomolecules

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“…Stone cells are one of the key factors that determine the quality of pear fruits (Choi et al, 2007; Cai et al, 2010; Yan et al, 2014). The contents and sizes of stone cell clusters are significantly negatively correlated with the texture and sucrose content of pear fruit, and excessive stone cell clusters have resulted in a rough texture and poor flavor (Cheng et al, 2018; Xue et al, 2018). Therefore, the contents and sizes of stone cell clusters must be reduced to improve the quality of the “Dangshan Su” pear.…”

Section: Introductionmentioning

confidence: 99%

In Silico Genome-Wide Analysis of the Pear (Pyrus bretschneideri) KNOX Family and the Functional Characterization of PbKNOX1, an Arabidopsis BREVIPEDICELLUS Orthologue Gene, Involved in Cell Wall and Lignin Biosynthesis

Cheng

Abdullah

et al. 2019

Front. Genet.

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Stone cells are a characteristic trait of pear fruit, but the contents and sizes of stone cells negatively correlate with fruit texture and flavor. Secondary cell wall thickening and lignification have been established as key steps of stone cell development. KNOTTED-LIKE HOMEOBOX (KNOX) proteins play important roles in plant cell growth and development, including cell wall formation and lignification. Although the characteristics and biological functions of KNOX proteins have been investigated in other plants, this gene family has not been functionally characterized in pear. Eighteen PbKNOX genes were identified in the present study, and all of the identified family members contained the KNOX I and/or KNOX II domains. Based on the phylogenetic tree and chromosomal localization, the 18 PbKNOX genes were divided into five subfamilies [ SHOOT MERISTEMLESS ( STM )-like, BREVIPEDICELLUS ( BP )-like, KNOTTED ARABIDOPSIS THALIANA 2/6 ( KNAT2/6 )-like, KNAT7 -like, and KNAT3-5 -like] and were distributed among 10 chromosomes. In addition, we identified 9, 11, and 11 KNOX genes in the genomes of grape, mei, and strawberry, respectively, and the greatest number of collinear KNOX gene pairs formed between pears and peaches. Analyses of the spatiotemporal expression patterns showed that the tissue specificity of PbKNOX gene expression was not very significant and that the level of the PbKNOX1 transcript showed an opposite trend to the levels of stone cells and lignin accumulation. Furthermore, PbKNOX1 has high sequence identity and similarity with Arabidopsis BP. Compared with wild-type Arabidopsis , plants overexpressing PbKNOX1 not only showed an approximately 19% decrease in the secondary cell wall thickness of vessel cells but also exhibited an approximately 13% reduction in the lignin content of inflorescence stems. Moreover, the expression of several genes involved in lignin biosynthesis was downregulated in transgenic lines. Based on our results, PbKNOX1 / BP participates in cell wall-thickening and lignin biosynthesis and represses the transcription of key structural genes involved in lignin synthesis, providing genetic evidence for the roles of KNOX in cell wall thickening and lignin biosynthesis in pear.

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“…In pepper ( Capsicum annuum L.), Pfam ID “PF03018” was used as keyword for the identification of dirigent gene family [ 42 ]. DIR proteins were also reported in numerous plant species, including lichens, ferns, gymnosperms, and angiosperms [ [1] , [2] , [3] ]. The phylogenetic classification along with the identified motifs, as shown in Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Dirigent proteins are extracellular glycoproteins with high β-strand content and have been found in all vascular plants, including lichens, ferns, gymnosperms and angiosperms [ [2] , [3] , [4] ]. DIRs involved in secondary metabolism, lignan and lignin biosynthesis [ 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

In silico identification and validation of miRNA and their DIR specific targets in Oryza sativa Indica under abiotic stress

Singh

Mehra

Chatterjee

et al. 2020

Non-coding RNA Research

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Several biotic (bacterial and viral pathogenesis) and abiotic stress factors like salt, drought, cold, and extreme temperatures significantly reduce crop productivity and grain quality throughout the world. MicroRNAs (miRNAs) are small (~22 nucleotides) non-coding endogenous RNA molecules which negatively regulate gene expression at the post-transcriptional level either by degrading the target protein-coding mRNA genes or suppressing translation in plants. Dirigent (DIR) gene protein plays a crucial role as they are involved to dictate the stereochemistry of a compound synthesized by other enzymes as well as in lignifications against biotic and abiotic stress. In plants, several miRNAs, as well as their targets, are known to regulate stress response but systematic identification of the same is limited. The present work has been designed for in silico identification of miRNAs against a total of sixty-one DIR genes in Oryza sativa Indica followed by target prediction of identified miRNAs through the computational approach and thereafter validation of potential miRNAs in rice genotypes. We systematically identified 3 miRNA and their respective DIR specific target gene in Oryza sativa Indica. The expression of these three miRNAs and their respective DIR specific targets were validated in rice seedlings subjected to five different abiotic stress conditions (heavy metal, high temperature, low temperature, salinity and drought) by quantitative Real-Time PCR (qRT-PCR). Expression analysis indicated that miRNA under stress conditions regulates the gene expression of the DIR gene in rice. To the best of our knowledge this is this is the first report in any organism showing the expression of ath-miRf10317-akr, and osamiRf10761-akr miRNAs in response to various abiotic stresses.

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Molecular Characterization, Evolution, and Expression Profiling of the Dirigent (DIR) Family Genes in Chinese White Pear (Pyrus bretschneideri)

Cited by 45 publications

References 55 publications

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

In Silico Genome-Wide Analysis of the Pear (Pyrus bretschneideri) KNOX Family and the Functional Characterization of PbKNOX1, an Arabidopsis BREVIPEDICELLUS Orthologue Gene, Involved in Cell Wall and Lignin Biosynthesis

In silico identification and validation of miRNA and their DIR specific targets in Oryza sativa Indica under abiotic stress

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