Document Type

Journal Article

Department/Unit

Department of Biology; Department of Computer Science

Language

English

Abstract

In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets. To facilitate study of the mobile signaling macromolecules, we compiled the PlaMoM (Plant Mobile Macromolecules) database, a resource that provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM contains detailed information such as nucleotide/amino acid sequences, ortholog partners, related experiments, gene functions and literature. For the model plant Arabidopsis thaliana, protein–protein interactions of mobile transcripts are presented as interactive molecular networks. Furthermore, PlaMoM provides a built-in tool to identify potential RNA mobility signals such as tRNA-like structures. The current version of PlaMoM compiles a total of 17 991 mobile macromolecules from 14 plant species/ecotypes from published data and literature.

Keywords

signal transduction, stress response, amino acid sequence, angiosperms, arabidopsis, bile fluid, genes, nucleotides, plants, rna, messenger, transfer rna, technology, rna, macromolecule, mobility

Publication Date

10-2016

Source Publication Title

Nucleic Acids Research

Volume

45

Issue

D1

Start Page

D1021

End Page

D1028

Publisher

Oxford University Press

Peer Reviewed

1

Copyright

© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Funder

Hong Kong Baptist University start-up fund [38-40-160 to S.Z., 38-40-159 to D.G.]; HKBU FRG grants [FRG1/14-15/055, FRG2/15-16/006 to S.Z., FRG1/14-15/070 to D.G.]; National Nature Science Foundation of China [31501080 to D.G.]; HKBU Strategic Development Fund [SDF 15-1012-P04 to Y.X.]. Funding for open access charge: Hong Kong Baptist University start-up fund [38-40-160].

DOI

10.1093/nar/gkw988

Link to Publisher's Edition

http://dx.doi.org/10.1093/nar/gkw988

ISSN (print)

03051048

ISSN (electronic)

13624962

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