title: Structural and operational complexity of the Geobacter sulfurreducens genome.
abstract: 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.
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Qiu
authors.forename: Byung-Kwan
authors.initials: BK
authors.lastname: Cho
authors.forename: Young Seoub
authors.initials: YS
authors.lastname: Park
authors.forename: Derek
authors.initials: D
authors.lastname: Lovley
authors.forename: Bernhard Ø
authors.initials: BØ
authors.lastname: Palsson
authors.forename: Karsten
authors.initials: K
authors.lastname: Zengler
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D045302:Geobacter / Q000235:genetics*; D009876:Operon; D012333:RNA, Messenger / Q000378:metabolism; D024363:Transcription Initiation Site
chemical_list: D012333:RNA, Messenger; D012321:DNA-Directed RNA Polymerases