Dataset Information

Genome-wide survey and expression analysis of the putative non-specific lipid transfer proteins in Brassica rapa L.

ABSTRACT:

Background

Plant non-specific lipid transfer proteins (nsLtps) are small, basic proteins encoded by multigene families and have reported functions in many physiological processes such as mediating phospholipid transfer, defense reactions against phytopathogens, the adaptation of plants to various environmental conditions, and sexual reproduction. To date, no genome-wide overview of the Brassica rapa nsLtp (BrnsLtp) gene family has been performed. Therefore, as the first step and as a helpful strategy to elucidate the functions of BrnsLtps, a genome-wide study for this gene family is necessary.

Methodology/principal finding

In this study, a total of 63 putative BrnsLtp genes were identified through a comprehensive in silico analysis of the whole genome of B. rapa. Based on the sequence similarities, these BrnsLtps was grouped into nine types (I, II, III, IV, V, VI, VIII, IX, and XI). There is no type VII nsLtps in B. rapa, and a new type, XI nsLtps, was identified in B. rapa. Furthermore, nine type II AtLtps have no homologous genes in B. rapa. Gene duplication analysis demonstrated that the conserved collinear block of each BrnsLtp is highly identical to those in Arabidopsis and that both segmental duplications and tandem duplications seem to play equal roles in the diversification of this gene family. Expression analysis indicated that 29 out of the 63 BrnsLtps showed specific expression patterns. After careful comparison and analysis, we hypothesize that some of the type I BrnsLtps may function like Arabidopsis pathogenesis-related-14 (PR-14) proteins to protect the plant from phytopathogen attack. Eleven BrnsLtps with inflorescence-specific expression may play important roles in sexual reproduction. Additionally, BrnsLtpI.3 may have functions similar to Arabidopsis LTP1.

Conclusions/significance

The genome-wide identification, bioinformatic analysis and expression analysis of BrnsLtp genes should facilitate research of this gene family and polyploidy evolution and provide new insight towards elucidating their biological functions in plants.

SUBMITTER: Li J

PROVIDER: S-EPMC3908880 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-wide survey and expression analysis of the putative non-specific lipid transfer proteins in Brassica rapa L.

Li Jun J Gao Guizhen G Xu Kun K Chen Biyun B Yan Guixin G Li Feng F Qiao Jiangwei J Zhang Tianyao T Wu Xiaoming X

PloS one 20140131 1

<h4>Background</h4>Plant non-specific lipid transfer proteins (nsLtps) are small, basic proteins encoded by multigene families and have reported functions in many physiological processes such as mediating phospholipid transfer, defense reactions against phytopathogens, the adaptation of plants to various environmental conditions, and sexual reproduction. To date, no genome-wide overview of the Brassica rapa nsLtp (BrnsLtp) gene family has been performed. Therefore, as the first step and as a hel ...[more]

PMID: 24497919

Similar Datasets

Project description:BACKGROUND: In plant, non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that have been reported to be involved in numerous biological processes such as transfer of phospholipids, reproductive development, pathogen defence and abiotic stress response. To date, only a tiny fraction of plant nsLTPs have been functionally identified, and even fewer have been identified in maize [Zea mays (Zm)]. RESULTS: In this study, we carried out a genome-wide analysis of nsLTP gene family in maize and identified 63 nsLTP genes, which can be divided into five types (1, 2, C, D and G). Similar intron/exon structural patterns were observed in the same type, strongly supporting their close evolutionary relationship. Gene duplication analysis indicated that both tandem and segmental duplication contribute to the diversification of this gene family. Additionally, the three-dimensional structures of representative nsLTPs were studied with homology modeling to understand their molecular functions. Gene ontology analysis was performed to obtain clues about biological function of the maize nsLTPs (ZmLTPs). The analyses of putative upstream regulatory elements showed both shared and distinct transcriptional regulation motifs of ZmLTPs, further indicating that ZmLTPs may play roles in diverse biological processes. The dynamic expression patterns of ZmLTPs family across the different developmental stages showed that several of them exhibit tissue-specific expression, indicative of their important roles in maize life cycle. Furthermore, we focused on the roles of maize nsLTPs in biotic and abiotic stress responses. Our analyses demonstrated that some ZmLTPs exhibited a delayed expression pattern after the infection of Ustilago maydis and differentially expressed under drought, salt and cold stresses, and these may be a great help for further studies to improve the stress resistance and tolerance in maize breeding. CONCLUSIONS: Our results provide new insights into the phylogenetic relationships and characteristic functions of maize nsLTPs and will be useful in studies aimed at revealing the global regulatory network in maize development and stress responses, thereby contributing to the maize molecular breeding with enhanced quality traits.

Project description:BackgroundDiscovered and described 40 years ago, non-specific lipid transfer proteins (nsLTP) are present in many plant species and play an important role protecting plants from stressors such as heat or drought. In the last 20 years, sensitization to nsLTP and consequent reactions to plant foods has become an increasing concern.AimThe aim of this paper is to review the evidence for the structure and function of nsLTP allergens, and cross-reactivity, sensitization, and epidemiology of nsLTP allergy.Materials and methodsA Task Force, supported by the European Academy of Allergy & Clinical Immunology (EAACI), reviewed current evidence and provide a signpost for future research. The search terms for this paper were "Non-specific Lipid Transfer Proteins", "LTP syndrome", "Pru p 3", "plant food allergy", "pollen-food syndrome".ResultsMost nsLTP allergens have a highly conserved structure stabilised by 4-disulphide bridges. Studies on the peach nsLTP, Pru p 3, demonstrate that nsLTPs are very cross-reactive, with the four major IgE epitopes of Pru p 3 being shared by nsLTP from other botanically related fruits. These nsLTP allergens are to varying degrees resistant to heat and digestion, and sensitization may occur through the oral, inhaled or cutaneous routes. In some populations, Pru p 3 is the primary and sole sensitizing allergen, but many are poly-sensitised both to botanically un-related nsLTP in foods, and non-food sources of nsLTP such as Cannabis sativa, Platanus acerifolia, (plane tree), Ambrosia artemisiifolia (ragweed) and Artemisia vulgaris (mugwort). Initially, nsLTP sensitization appeared to be limited to Mediterranean countries, however more recent studies suggest clinically relevant sensitization occurs in North Atlantic regions and also countries in Northern Europe, with nsLTP sensitisation profiles being broadly similar.DiscussionThese robust allergens have the potential to sensitize and provoke symptoms to a large number of plant foods, including those which are raw, cooked or processed. It is unknown why some sensitized individuals develop clinical symptoms to foods whereas others do not, or indeed what other allergens besides Pru p 3 may be primary sensitising allergens. It is clear that these allergens are also relevant in non-Mediterranean populations and there needs to be more recognition of this.ConclusionNon-specific LTP allergens, present in a wide variety of plant foods and pollens, are structurally robust and so may be present in both raw and cooked foods. More studies are needed to understand routes of sensitization and the world-wide prevalence of clinical symptoms associated with sensitization to these complex allergens.

Dataset Information

Genome-wide survey and expression analysis of the putative non-specific lipid transfer proteins in Brassica rapa L.

Background

Methodology/principal finding

Conclusions/significance

Publications

Genome-wide survey and expression analysis of the putative non-specific lipid transfer proteins in Brassica rapa L.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets