A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF.
BACKGROUND
New strategies for high-throughput sequencing are constantly appearing, leading to a great increase in the number of completely sequenced genomes. Unfortunately, computational genome annotation is out of step with this progress. Thus, the accurate annotation of these genomes has become a bottleneck of knowledge acquisition.


RESULTS
We exploited a proteogenomic approach to improve conventional genome annotation by integrating proteomic data with genomic information. Using Shigella flexneri 2a as a model, we identified total 823 proteins, including 187 hypothetical proteins. Among them, three annotated ORFs were extended upstream through comprehensive analysis against an in-house N-terminal extension database. Two genes, which could not be translated to their full length because of stop codon 'mutations' induced by genome sequencing errors, were revised and annotated as fully functional genes. Above all, seven new ORFs were discovered, which were not predicted in S. flexneri 2a str.301 by any other annotation approaches. The transcripts of four novel ORFs were confirmed by RT-PCR assay. Additionally, most of these novel ORFs were overlapping genes, some even nested within the coding region of other known genes.


CONCLUSIONS
Our findings demonstrate that current Shigella genome annotation methods are not perfect and need to be improved. Apart from the validation of predicted genes at the protein level, the additional features of proteogenomic tools include revision of annotation errors and discovery of novel ORFs. The complementary dataset could provide more targets for those interested in Shigella to perform functional studies.
State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
Lina
L
Zhao
Liguo
L
Liu
Wenchuan
W
Leng
Candong
C
Wei
Qi
Q
Jin
D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D030561:Databases, Nucleic Acid; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D040901:Proteomics / Q000379:methods*; D017422:Sequence Analysis, DNA; D012763:Shigella flexneri / Q000235:genetics*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
D004269:DNA, Bacterial