Structural and operational complexity of the Geobacter sulfurreducens genome

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Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 5'-end transcripts allowed for a most precise annotation. The structural annotation is comprised of numerous previously undetected genes, noncoding RNAs, prevalent leaderless mRNA transcripts, and antisense transcripts. When compared with other prokaryotes, we found that the number of antisense transcripts reversely correlated with genome size. The operational annotation consists of 1453 operons, 22% of which have multiple transcription start sites that use different RNA polymerase holoenzymes. Several operons with multiple transcription start sites encoded genes with essential functions, giving insight into the regulatory complexity of the genome. The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes.
Publisher
COLD SPRING HARBOR LAB PRESS
Issue Date
2010-09
Language
English
Article Type
Article
Keywords

ESCHERICHIA-COLI; GLOBAL ANALYSIS; ACCURATE MASS; SP-NOV; RNAS; TRANSCRIPTION; REDUCTION; BACTERIA; IDENTIFICATION; MICROORGANISM

Citation

GENOME RESEARCH, v.20, no.9, pp.1304 - 1311

ISSN
1088-9051
DOI
10.1101/gr.107540.110
URI
http://hdl.handle.net/10203/97438
Appears in Collection
BS-Journal Papers(저널논문)
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