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PMID: 21367939 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Discovery and annotation of small proteins using genomics, proteomics, and computational approaches.

Genome research ·Vol. 21 ·No. 4 ·2011-04-00 ·Pages 634-41

Yang X, Tschaplinski TJ, Hurst GB, Jawdy S, Abraham PE, Lankford PK, Adams RM, Shah MB, Hettich RL, Lindquist E, Kalluri UC, Gunter LE, Pennacchio C, Tuskan GA

Abstract

Small proteins (10-200 amino acids [aa] in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained ~2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10-200 aa in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: (1) coding-potential prediction, (2) evolutionary conservation between P. deltoides and other plant species, and (3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were supported by proteomics data. Of the 611 highest-confidence candidate sORF genes, 56 were new to the current Populus genome annotation. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.

MeSH Terms
Computational Biology Expressed Sequence Tags Genomics Molecular Sequence Annotation/methods Molecular Sequence Data Open Reading Frames Plant Leaves/genetics Plant Proteins/genetics Populus/genetics Proteomics RNA, Untranslated/genetics Research Design
Chemicals
Plant Proteins RNA, Untranslated
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Yang Xiaohan
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. [email protected]
Tschaplinski Timothy J
Hurst Gregory B
Jawdy Sara
Abraham Paul E
Lankford Patricia K
Adams Rachel M
Shah Manesh B
Hettich Robert L
Lindquist Erika
Kalluri Udaya C
Gunter Lee E
Pennacchio Christa
Tuskan Gerald A
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1549-5469
DOI
10.1101/gr.109280.110
Email
[email protected]
Published
2011-04-00
Epub
2011-00-02
Pages
634-41
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC3065711
Subset
IM
Databases
GENBANK
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External Links
PubMed source DOI: 10.1101/gr.109280.110 PMC Full Text View journal details
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