Characterization and expression analysis of dirigent family genes related to stresses in Brassica

Arasan, Senthil Kumar Thamil; Park, Jong-In; Ahmed, Nasar Uddin; Jung, Hee-Jeong; Hur, Yoonkang; Kang, Kwon-Kyoo; Lim, Yong-Pyo; Nou, Ill–Sup

doi:10.1016/j.plaphy.2013.02.030

Cited by 52 publications

(62 citation statements)

References 32 publications

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“…This is in accordance with Arasan’s finding in B. rapa DIRs [19]. It is well known that DIR genes are participate in lignin biosynthesis.…”

Section: Discussionsupporting

confidence: 93%

“…The best hit homology genes of these 19 sequences were summarized in Additional file 2. The number and subfamily designation of the IiDIR genes were based on the topology of the 19 IiDIRs with other 178 DIRs according to Ralph [17] and Arasan [19]. Typical dirigent domains were found in these 19 IiDIR protein sequences though simple modular architecture research tool (SMART, http://smart.embl-heidelberg.de/) [20] (Additional file 3).…”

Section: Resultsmentioning

confidence: 99%

“…These gene sequences were as follows: 29 genes from Brassica rapa , 25 genes from Arabidopsis thaliana , 54 genes from Oryza sativa , 35 genes from spruce, 9 genes from Thuja plicata , and an additional 27 DIRs identified from a variety of species, including pea, cotton, corn, sesame, etc. [17, 19]. In this tree, different subfamilies according to Ralph [17] were colored in different colors.…”

Section: Resultsmentioning

confidence: 99%

“…There are 25 DIRs in A. thaliana , 29 DIRs in B . rapa and 54 DIRs in rice [17, 19]. In this study, 19 DIRs are discovered from I indigotica by bioinformatics methods for the first time.…”

Section: Discussionmentioning

confidence: 99%

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The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance

Chen

Xiao

et al. 2014

BMC Genomics

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BackgroundIsatis indigotica Fort. is one of the most commonly used traditional Chinese medicines. Its antiviral compound is a kind of lignan, which is formed with the action of dirigent proteins (DIR). DIR proteins are members of a large family of proteins which impart stereoselectivity on the phenoxy radical-coupling reaction, yielding optically active lignans from two molecules of E-coniferyl alcohol. They exist in almost every vascular plant. However, the DIR and DIR-like protein gene family in I. indigotica has not been analyzed in detail yet. This study focuses on discovery and analysis of this protein gene family in I. indigotica for the first time.ResultsAnalysis of transcription profiling database from I. indigotica revealed a family of 19 full-length unique DIR and DIR-like proteins. Sequence analysis found that I. indigotica DIR and DIR-like proteins (IiDIR) were all-beta strand proteins, with a signal peptide at the N-terminus. Phylogenetic analysis of the 19 proteins indicated that the IiDIR genes cluster into three distinct subfamilies, DIR-a, DIR-b/d, and DIR-e, of a larger plant DIR and DIR-like gene family. Gene-specific primers were designed for 19 unique IiDIRs and were used to evaluate patterns of constitutive expression in different organs. It showed that most IiDIR genes were expressed comparatively higher in roots and flowers than stems and leaves.ConclusionsNew DIR and DIR-like proteins were discovered from the transcription profiling database of I. indigotica through bioinformatics methods for the first time. Sequence characteristics and transcript abundance of these new genes were analyzed. This study will provide basic data necessary for further studies.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-388) contains supplementary material, which is available to authorized users.

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“…This is in accordance with Arasan’s finding in B. rapa DIRs [19]. It is well known that DIR genes are participate in lignin biosynthesis.…”

Section: Discussionsupporting

confidence: 93%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…There are 25 DIRs in A. thaliana , 29 DIRs in B . rapa and 54 DIRs in rice [17, 19]. In this study, 19 DIRs are discovered from I indigotica by bioinformatics methods for the first time.…”

Section: Discussionmentioning

confidence: 99%

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The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance

Chen

Xiao

et al. 2014

BMC Genomics

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“…Chitin-binding proteins (CBP), encoded by chitin-gene family, are PR proteins, which enhance resistance to different stresses in several crop plants [10,11,12,13,14]. These CBP proteins consist of one or several chitin-binding domains with high affinity and have a range of numerous complex glycoconjugates covering GlcNAc or N -acetyl- d -neuraminic acid (NeuNAc) as building blocks.…”

Section: Introductionmentioning

confidence: 99%

Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (Capsicum annuum L.) and Transcriptional Regulation to Phytophthora capsici, Abiotic Stresses and Hormonal Applications

Ali

Luo

Khan

et al. 2018

IJMS

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Chitin-binding proteins are pathogenesis-related gene family, which play a key role in the defense response of plants. However, thus far, little is known about the chitin-binding family genes in pepper (Capsicum annuum L.). In current study, 16 putative chitin genes (CaChi) were retrieved from the latest pepper genome database, and were classified into four distinct classes (I, III, IV and VI) based on their sequence structure and domain architectures. Furthermore, the structure of gene, genome location, gene duplication and phylogenetic relationship were examined to clarify a comprehensive background of the CaChi genes in pepper. The tissue-specific expression analysis of the CaChi showed the highest transcript levels in seed followed by stem, flower, leaf and root, whereas the lowest transcript levels were noted in red-fruit. Phytophthora capsici post inoculation, most of the CaChi (CaChiI3, CaChiIII1, CaChiIII2, CaChiIII4, CaChiIII6, CaChiIII7, CaChiIV1, CaChiVI1 and CaChiVI2) were induced by both strains (PC and HX-9). Under abiotic and exogenous hormonal treatments, the CaChiIII2, CaChiIII7, CaChiVI1 and CaChiVI2 were upregulated by abiotic stress, while CaChiI1, CaChiIII7, CaChiIV1 and CaChiIV2 responded to hormonal treatments. Furthermore, CaChiIV1-silenced plants display weakened defense by reducing (60%) root activity and increase susceptibility to NaCl stress. Gene ontology (GO) enrichment analysis revealed that CaChi genes primarily contribute in response to biotic, abiotic stresses and metabolic/catabolic process within the biological process category. These results exposed that CaChi genes are involved in defense response and signal transduction, suggesting their vital roles in growth regulation as well as response to stresses in pepper plant. In conclusion, these finding provide basic insights for functional validation of the CaChi genes in different biotic and abiotic stresses.

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Lignins and Abiotic Stress: An Overview

Bhardwaj

Handa

Sharma

et al. 2013

Physiological Mechanisms and Adaptation Strategies in Plants Under Changing Environment

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Characterization and expression analysis of dirigent family genes related to stresses in Brassica

Cited by 52 publications

References 32 publications

The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance

The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance

Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (Capsicum annuum L.) and Transcriptional Regulation to Phytophthora capsici, Abiotic Stresses and Hormonal Applications

Lignins and Abiotic Stress: An Overview

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