Prediction of operons in microbial genomes

Ermolaeva, Maria D.

doi:10.1093/nar/29.5.1216

Cited by 261 publications

(225 citation statements)

References 23 publications

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“…S1 in the supplement shows the alignment of the consensus protein abundance ratio results with the directons predicted computationally by TIGR and the University of Maryland [26], see also www.cbcb.umd.edu/cgi-bin/operons/paris.cgi?taxon_id=20119. The authors of this study defined a directon as the maximal number of conserved adjacent genes located on the same DNA strand.…”

Section: Comparison Of Protein Abundance Ratios With Theoretical Genementioning

confidence: 99%

“…Others have yet to be validated by orthogonal approaches such as functional studies, real time RT-PCR or Northern blot analysis. Because P. gingivalis operon and regulon structures are still largely unknown, we have also compared the directionality of protein abundance change observed experimentally with the bioinformatic gene pair predictions of Ermolaeva et al [26], who examined spatially and genetically conserved gene pairs over 34 sequenced prokaryotic genomes, including P. gingivalis.…”

Section: Introductionmentioning

confidence: 99%

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Quantitative proteomics of intracellular Porphyromonas gingivalis

Xia¹,

Wang²,

Taub³

et al. 2007

Proteomics

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Whole-cell quantitative proteomic analyses were conducted to investigate the change from an extracellular to intracellular lifestyle for Porphyromonas gingivalis, a Gram-negative intracellular pathogen associated with periodontal disease. Global protein abundance data for P. gingivalis strain ATCC 33277 internalized for 18 hours within human gingival epithelial cells and controls exposed to gingival cell culture medium were obtained at sufficient coverage to provide strong evidence that these changes are profound. A total of 385 proteins were over-expressed in internalized P. gingivalis relative to controls; 240 proteins were shown to be under-expressed. This represented in total about 28% of the protein encoding ORFs annotated for this organism, and slightly less than half of the proteins that were observed experimentally. Production of several proteases, including the classical virulence factors RgpA, RgpB, and Kgp, was decreased. A separate validation study was carried out in which a 16-fold dilution of the P. gingivalis proteome was compared to the undiluted sample in order to assess the quantitative false negative rate (all ratios truly alternative). Truly null (no change) abundance ratios from technical replicates were used to assess the rate of quantitative false positives over the entire proteome. A global comparison between the direction of abundance change observed and previously published bioinformatic gene pair predictions for P. gingivalis will assist with future studies of P. gingivalis gene regulation and operon prediction.

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Section: Comparison Of Protein Abundance Ratios With Theoretical Genementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Quantitative proteomics of intracellular Porphyromonas gingivalis

Xia¹,

Wang²,

Taub³

et al. 2007

Proteomics

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“…One other issue we were interested in testing was the effect of BLASTP stringency on the algorithm. The original comparative data were compiled with the requirement that potential orthologs were required to have a BLASTP expect value of less than 10 Ϫ4 ; this value is relatively permissive and is similar to the cutoff values used in earlier studies (9). We therefore tested whether making this cutoff value more stringent might affect the predictive value of the comparative data.…”

Section: Figmentioning

confidence: 99%

“…This method has previously been used as a means of assessing functional relatedness among proteins (17), and several studies have shown that operons in a given bacterial genome could be identified with a very high degree of specificity using this approach (98%, as reported by Ermolaeva et al [9]). The drawback, however, is that its accuracy is derived from genes being conserved in a relatively large number of species, and the method tends to miss operons containing genes that are unique or less conserved.…”

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confidence: 93%

Operon Prediction for Sequenced Bacterial Genomes without Experimental Information

Bergman

Passalacqua

Hanna

et al. 2007

Appl Environ Microbiol

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Various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes. In this study, we explored the possibility of using phylogenetic information to aid in operon prediction, and we constructed a Bayesian hidden Markov model that incorporates comparative genomic data with traditional predictors, such as intergenic distances. The prediction algorithm performs as well as the best previously reported method, with several significant advantages. It uses fewer data sources and so it is easier to implement, and the method is more broadly applicable than previous methods-it can be applied to essentially every gene in any sequenced bacterial genome. Furthermore, we show that near-optimal performance is easily reached with a generic set of comparative genomes and does not depend on a specific relationship between the subject genome and the comparative set. We applied the algorithm to the Bacillus anthracis genome and found that it successfully predicted all previously verified B. anthracis operons. To further test its performance, we chose a predicted operon (BA1489-92) containing several genes with little apparent functional relatedness and tested their cotranscriptional nature. Experimental evidence shows that these genes are cotranscribed, and the data have interesting implications for B. anthracis biology. Overall, our findings show that this algorithm is capable of highly sensitive and accurate operon prediction in a wide range of bacterial genomes and that these predictions can lead to the rapid discovery of new functional relationships among genes.

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“…Operon prediction (36) was obtained from The Institute for Genomic Research website at http://www.tigr.org/tdb/. PFAM searches and protein domain assignments (37) were performed using the Washington University mirror site http://pfam.wustl.edu.…”

Section: Other Analysesmentioning

confidence: 99%

Identification of Rv3230c as the NADPH Oxidoreductase of a Two-Protein DesA3 Acyl-CoA Desaturase inMycobacterium tuberculosisH37Rv

Chen

Fox

2006

Biochemistry

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DesA3 is a membrane-bound stearoyl-CoA Δ9 desaturase that produces oleic acid, a precursor of mycobacterial membrane phospholipids and triglycerides. DesA3 has sequence homology with other membrane desaturases including the presence of the eight His motif proposed to bind the diiron center active site. This family of desaturases function as multi-component complexes, and thus require electron transfer proteins for efficient catalytic turnover. Here we present evidence that Rv3230c from Mycobacterium tuberculosis H37Rv is a biologically relevant electron transfer partner for DesA3 from the same pathogen. For these studies, Rv3230c was expressed as a partially soluble protein in Escherichia coli; recombinant DesA3 was expressed in Mycobacterium smegmatis as a catalytically active membrane protein. The addition of E. coli lysates containing Rv3230c to lysates of M. smegmatis expressing DesA3 gave strong conversion of [1-14 C]-18:0-CoA to [1-14 C]-cis-Δ 9 -18:1-CoA and of [1-14 C]-16:0-CoA to [1-14 C]-cis-Δ 9 -16:1-CoA. Both M. tuberculosis proteins were required to reconstitute activity, as various combinations of control lysates lacking either Rv3230c or DesA3 gave minimal or no activity. Furthermore, the specificity of interaction between Rv3230c and DesA3 was implied by the inability of other related redox systems to substitute for Rv3230c. The reconstituted activity was dependent upon the presence of NADPH, could be saturated by increasing the amount of Rv3230c added and was also sensitive to the salt concentration in the buffer. The results are consistent with the formation of a protein-protein complex, possibly with electrostatic character. This work defines a multi-protein, acyl-CoA desaturase complex from M. tuberculosis H37Rv to minimally consist of a soluble Rv3230c reductase and integral membrane DesA3 desaturase. Further implications of this finding relative to the properties of other multi-protein iron enzyme complexes are discussed.Mycobacterium tuberculosis is a human pathogen that causes one of the world's deadliest diseases, tuberculosis (TB 1 ). Current estimates are that up to one-third of the world's population may be infected with M. tuberculosis and that over two million people die from TB-related diseases each year (1-4). TB has resurged, in part due to the appearance of multipledrug-resistant strains. Consequently, the development of new drugs and the reexamination of drugs formerly deemed effective have become major focuses of world-wide TB research (3)(4)(5). This intense effort has included genome sequencing (6), proteome functional analysis by micro-array approaches (7-11), the TB Protein Structure Initiative [(12), * To whom correspondence should be addressed: Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706. Telephone: (608) . E-mail: bgfox@biochem.wisc.edu. † This work was supported by the National Institutes of Health Grant R01 GM-50853 to B.G.F.1 Abbreviations: AlkB, alkane ω-hydroxylase; DesA3, product of Mycobacterium tuberculosis H37Rv gene rv3229c, a...

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Prediction of operons in microbial genomes

Cited by 261 publications

References 23 publications

Quantitative proteomics of intracellular Porphyromonas gingivalis

Quantitative proteomics of intracellular Porphyromonas gingivalis

Operon Prediction for Sequenced Bacterial Genomes without Experimental Information

Identification of Rv3230c as the NADPH Oxidoreductase of a Two-Protein DesA3 Acyl-CoA Desaturase inMycobacterium tuberculosisH37Rv

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