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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 59-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:
; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1028591
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Genome Research
Additional Journal Information:
Journal Volume: 20
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; FUNCTIONALS; GENES; METABOLISM; RNA POLYMERASES; TRANSCRIPTION; Environmental Molecular Sciences Laboratory

Citation Formats

Qiu, Yu, Cho, Byung-Kwan, Park, Young S, Lovley, Derek R, Palsson, Bernhard O, and Zengler, Karsten. Structural and Operational Complexity of the Geobacter Sulfurreducens Genome. United States: N. p., 2010. Web. doi:10.1101/gr.107540.110.
Qiu, Yu, Cho, Byung-Kwan, Park, Young S, Lovley, Derek R, Palsson, Bernhard O, & Zengler, Karsten. Structural and Operational Complexity of the Geobacter Sulfurreducens Genome. United States. https://doi.org/10.1101/gr.107540.110
Qiu, Yu, Cho, Byung-Kwan, Park, Young S, Lovley, Derek R, Palsson, Bernhard O, and Zengler, Karsten. 2010. "Structural and Operational Complexity of the Geobacter Sulfurreducens Genome". United States. https://doi.org/10.1101/gr.107540.110.
@article{osti_1028591,
title = {Structural and Operational Complexity of the Geobacter Sulfurreducens Genome},
author = {Qiu, Yu and Cho, Byung-Kwan and Park, Young S and Lovley, Derek R and Palsson, Bernhard O and Zengler, Karsten},
abstractNote = {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 59-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.},
doi = {10.1101/gr.107540.110},
url = {https://www.osti.gov/biblio/1028591}, journal = {Genome Research},
number = ,
volume = 20,
place = {United States},
year = {Wed Jun 30 00:00:00 EDT 2010},
month = {Wed Jun 30 00:00:00 EDT 2010}
}