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Nigro F, Ippolito A. UV-C light to reduce decay and improve quality of stored fruit and vegetables: a short review. ACTA ACUST UNITED AC 2016. [DOI: 10.17660/actahortic.2016.1144.43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lin YM, Shih SL, Lin WC, Wu JW, Chen YT, Hsieh CY, Guan LC, Lin L, Cheng CP. Phytoalexin biosynthesis genes are regulated and involved in plant response to Ralstonia solanacearum infection. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 224:86-94. [PMID: 24908509 DOI: 10.1016/j.plantsci.2014.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 05/03/2023]
Abstract
Genes encoding phytoalexin biosynthesis enzymes are transcriptionally regulated and are required for defense against fungi and oomycetes. Here, we studied the regulation of tobacco 5-epi-aristolochene synthase 4 (EAS4) promoters on bacterial infection and investigated the roles of tomato and Arabidopsis phytoalexin biosynthesis genes in defense against pathogenic bacteria. Our results showed that the Nicotiana glutinosa EAS4 (NgEAS4) promoter was significantly induced by treatments with several bacteria in treated and systemic leaves of transgenic plants. This promoter was also partially induced by treatments with type-III secretion-deficient mutants and total lysate of R. solanacearum (Rs), revealing that both bacterial pathogen-associated molecular patterns (PAMPs) and effectors are involved in R. solanacearum-induced local and systemic activation of the NgEAS4 promoter. Furthermore, the absence of a cis-element GT-1 box in the NgEAS4 promoter abolished systemic activation in non-treated leaves, whereas disruption of the GT-1 box of the N. tabacum EAS4 (NtEAS4) promoter led to constitutive expression. Moreover, silencing of tomato sesquiterpene synthase genes and disruption of the key gene PAD3 for Arabidopsis camalexin biosynthesis resulted in decreased tolerance to R. solanacearum. These results together, reveal the varied function of GT-1 boxes in regulating tobacco EAS4 promoters and the involvement of phytoalexin-biosythesis genes in plant defense against R. solanacearum.
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Affiliation(s)
- Yu-Mei Lin
- Graduate Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Shu-Lein Shih
- Graduate Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Wan-Chi Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Jia-Wei Wu
- Graduate Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Ya-Ting Chen
- Graduate Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Chi-Ying Hsieh
- Graduate Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Li-Ching Guan
- Graduate Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Lu Lin
- Graduate Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Chiu-Ping Cheng
- Graduate Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan, ROC; Department of Life Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan, ROC.
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Shameer K, Shingate PN, Manjunath SCP, Karthika M, Pugalenthi G, Sowdhamini R. 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2011; 2011:bar042. [PMID: 21959866 PMCID: PMC3294423 DOI: 10.1093/database/bar042] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Three-dimensional domain swapping is a unique protein structural phenomenon where two or more protein chains in a protein oligomer share a common structural segment between individual chains. This phenomenon is observed in an array of protein structures in oligomeric conformation. Protein structures in swapped conformations perform diverse functional roles and are also associated with deposition diseases in humans. We have performed in-depth literature curation and structural bioinformatics analyses to develop an integrated knowledgebase of proteins involved in 3D domain swapping. The hallmark of 3D domain swapping is the presence of distinct structural segments such as the hinge and swapped regions. We have curated the literature to delineate the boundaries of these regions. In addition, we have defined several new concepts like ‘secondary major interface’ to represent the interface properties arising as a result of 3D domain swapping, and a new quantitative measure for the ‘extent of swapping’ in structures. The catalog of proteins reported in 3DSwap knowledgebase has been generated using an integrated structural bioinformatics workflow of database searches, literature curation, by structure visualization and sequence–structure–function analyses. The current version of the 3DSwap knowledgebase reports 293 protein structures, the analysis of such a compendium of protein structures will further the understanding molecular factors driving 3D domain swapping. Database URL:http://caps.ncbs.res.in/3dswap
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Affiliation(s)
- Khader Shameer
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
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Shameer K, Pugalenthi G, Kandaswamy KK, Suganthan PN, Archunan G, Sowdhamini R. Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach. Bioinform Biol Insights 2010; 4:33-42. [PMID: 20634983 PMCID: PMC2901629 DOI: 10.4137/bbi.s4464] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
3-dimensional domain swapping is a mechanism where two or more protein molecules form higher order oligomers by exchanging identical or similar subunits. Recently, this phenomenon has received much attention in the context of prions and neurodegenerative diseases, due to its role in the functional regulation, formation of higher oligomers, protein misfolding, aggregation etc. While 3-dimensional domain swap mechanism can be detected from three-dimensional structures, it remains a formidable challenge to derive common sequence or structural patterns from proteins involved in swapping. We have developed a SVM-based classifier to predict domain swapping events using a set of features derived from sequence and structural data. The SVM classifier was trained on features derived from 150 proteins reported to be involved in 3D domain swapping and 150 proteins not known to be involved in swapped conformation or related to proteins involved in swapping phenomenon. The testing was performed using 63 proteins from the positive dataset and 63 proteins from the negative dataset. We obtained 76.33% accuracy from training and 73.81% accuracy from testing. Due to high diversity in the sequence, structure and functions of proteins involved in domain swapping, availability of such an algorithm to predict swapping events from sequence and structure-derived features will be an initial step towards identification of more putative proteins that may be involved in swapping or proteins involved in deposition disease. Further, the top features emerging in our feature selection method may be analysed further to understand their roles in the mechanism of domain swapping.
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Affiliation(s)
- Khader Shameer
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, 560065, India
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Degenhardt J, Köllner TG, Gershenzon J. Monoterpene and sesquiterpene synthases and the origin of terpene skeletal diversity in plants. PHYTOCHEMISTRY 2009; 70:1621-37. [PMID: 19793600 DOI: 10.1016/j.phytochem.2009.07.030] [Citation(s) in RCA: 611] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 07/23/2009] [Accepted: 07/24/2009] [Indexed: 05/20/2023]
Abstract
The multitude of terpene carbon skeletons in plants is formed by enzymes known as terpene synthases. This review covers the monoterpene and sesquiterpene synthases presenting an up-to-date list of enzymes reported and evidence for their ability to form multiple products. The reaction mechanisms of these enzyme classes are described, and information on how terpene synthase proteins mediate catalysis is summarized. Correlations between specific amino acid motifs and terpene synthase function are described, including an analysis of the relationships between active site sequence and cyclization type and a discussion of whether specific protein features might facilitate multiple product formation.
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Affiliation(s)
- Jörg Degenhardt
- Martin Luther University Halle-Wittenberg, Institute for Pharmacy, Halle/Saale, Germany.
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Withers ST, Keasling JD. Biosynthesis and engineering of isoprenoid small molecules. Appl Microbiol Biotechnol 2006; 73:980-90. [PMID: 17115212 DOI: 10.1007/s00253-006-0593-1] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Revised: 07/25/2006] [Accepted: 08/07/2006] [Indexed: 12/22/2022]
Abstract
Isoprenoid secondary metabolites are a rich source of commercial products that have not been fully explored. At present, there are isoprenoid products used in cancer therapy, the treatment of infectious diseases, and crop protection. All isoprenoids share universal prenyl diphosphate precursors synthesized via two distinct pathways. From these universal precursors, the biosynthetic pathways to specific isoprenoids diverge resulting in a staggering array of products. Taking advantage of this diversity has been the focus of much effort in metabolic engineering heterologous hosts. In addition, the engineering of the mevalonate pathway has increased levels of the universal precursors available for heterologous production. Finally, we will describe the efforts to produce to commercial terpenoids, paclitaxel and artemisinin.
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Affiliation(s)
- Sydnor T Withers
- Department of Chemical Engineering, University of California, Berkeley, CA, USA
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Back K, Jang SM, Lee BC, Schmidt A, Strack D, Kim KM. Cloning and characterization of a hydroxycinnamoyl-CoA:tyramine N-(hydroxycinnamoyl)transferase induced in response to UV-C and wounding from Capsicum annuum. PLANT & CELL PHYSIOLOGY 2001; 42:475-81. [PMID: 11382813 DOI: 10.1093/pcp/pce060] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Hydroxycinnamoyl-CoA : tyramine N-(hydroxycinnamoyl) transferase (THT) is a pivotal enzyme in the synthesis of N-(hydroxycinnamoyl)-amines, which are associated with cell wall fortification in plants. The cDNA encoding THT was cloned from the leaves of UV-C treated Capsicum annuum (hot pepper) using a differential screening strategy. The predicted protein encoded by the THT cDNA is 250 amino acids in length and has a relative molecular mass of 28,221. The protein sequence derived from the cDNA shares 76% and 67% identity with the potato and tobacco THT protein sequences, respectively. The recombinant pepper THT enzyme was purified using a bacterial overexpression system. The purified enzyme has a broad substrate specificity including acyl donors such as cinnamoyl-, sinapoyl-, feruloyl-, caffeoyl-, and 4-coumaroyl-CoA and acceptors such as tyramine and octopamine. In UV-C treated plants, the THT mRNA was strongly induced in leaves, and the elevated level of expression was stable for up to 36 h. THT mRNA also increased in leaves that were detached from the plant but not treated with UV-C. THT expression was measured in different plant tissues, and was constitutive at a similar level in leaf, root, stem, flower and fruit. Induction of THT mRNA was correlated with an increase in THT protein.
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Affiliation(s)
- K Back
- Department of Genetic Engineering, Biotechnology Research Institute, Chonnam National University, Kwangju, 500-757 South Korea.
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