Reannotation of <i>Shewanella oneidensis</i> Genome

Daraselia, Nikolai; Dernovoy, Dmitry; Tian, Yuan; Borodovsky, Mark; Tatusov, Roman L.; Tatusova, Tatiana

doi:10.1089/153623103322246566

Cited by 50 publications

(38 citation statements)

References 7 publications

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“…8) (16), with an rms distance of 4.4 Å for 206 equivalent C␣ atoms, suggesting that SO4414 may also be a dioxygenase. Moreover, the structure contains an extra domain that is formed by residues at the N terminus, similar to the small domain in human IDO (SI Fig.…”

Section: Resultsmentioning

confidence: 99%

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase

Forouhar

Anderson

Mowat

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

169

284

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Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. Here, we report extensive structural and biochemical studies of the Xanthomonas campestris TDO and a related protein SO4414 from Shewanella oneidensis, including the structure at 1.6-Å resolution of the catalytically active, ferrous form of TDO in a binary complex with the substrate L-Trp. The carboxylate and ammonium moieties of tryptophan are recognized by electrostatic and hydrogen-bonding interactions with the enzyme and a propionate group of the heme, thus defining the L-stereospecificity. A second, possibly allosteric, L-Trp-binding site is present at the tetramer interface. The sixth coordination site of the heme-iron is vacant, providing a dioxygenbinding site that would also involve interactions with the ammonium moiety of L-Trp and the amide nitrogen of a glycine residue. The indole ring is positioned correctly for oxygenation at the C2 and C3 atoms. The active site is fully formed only in the binary complex, and biochemical experiments confirm this induced-fit behavior of the enzyme. The active site is completely devoid of water during catalysis, which is supported by our electrochemical studies showing significant stabilization of the enzyme upon substrate binding.cancer ͉ heme enzymes ͉ immunomodulation ͉ indoleamine 2,3-dioxygenase T ryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) catalyze the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring, the first and rate-limiting step in L-Trp catabolism through the kynurenine pathway (1-3). In addition, IDO has been implicated in a diverse range of physiological and pathological conditions, including suppression of T cell proliferation, maternal tolerance to allogenic fetus, and immune escape of cancers (4-8), and is an attractive target for drug discovery against cancer and autoimmune and other diseases (2, 9-12).Despite catalyzing identical biochemical reactions (Fig. 1a), the sequence similarity between TDO and IDO is extremely low. An alignment of their sequences is only possible based on their structures, which suggests a sequence identity of 10% between them (Fig. 1b). In comparison, Xanthomonas campestris TDO shares 34% sequence identity with human TDO (Fig. 1b), demonstrating the remarkable evolutionary conservation of this enzyme. TDO is a homotetrameric enzyme and is highly specific for L-Trp and related derivatives such as 6-fluoro-Trp as the substrate. In comparison, IDO is monomeric, and shows activity toward a larger collection of substrates, including L-Trp, Dtryptophan (D-Trp), serotonin, and tryptamine (3), although the K m for D-Trp is Ϸ100-fold higher than that for L-Trp (13). The structure of human IDO in the catalytically inactive, ferric [Fe(III)]-heme state in complex with the 4-phenylimidazole inhibitor has recently been reported (14). Although this structure gave information about important active site residues, the inhibitor is coordinat...

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Section: Resultsmentioning

confidence: 99%

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase

Forouhar

Anderson

Mowat

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

169

284

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“…Shewanella oneidensis MR-1 is among the most carefully annotated bacterial genomes: Gene predictions in this genome were studied in two papers (Nealson et al 2002;Daraselia et al 2003) and are being continuously improved by the Shewanella Federation (http://www.shewanella.org/). Significant manual effort (that took into account comparative genomics evidence) also went into the annotation of Shewanella frigidimarina and Shewanella putrefaciens CN-32.…”

Section: Discussionmentioning

confidence: 99%

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

Gupta¹,

Benhamida²,

Bhargava³

et al. 2008

Genome Res.

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Recent proliferation of low-cost DNA sequencing techniques will soon lead to an explosive growth in the number of sequenced genomes and will turn manual annotations into a luxury. Mass spectrometry recently emerged as a valuable technique for proteogenomic annotations that improves on the state-of-the-art in predicting genes and other features. However, previous proteogenomic approaches were limited to a single genome and did not take advantage of analyzing mass spectrometry data from multiple genomes at once. We show that such a comparative proteogenomics approach (like comparative genomics) allows one to address the problems that remained beyond the reach of the traditional "single proteome" approach in mass spectrometry. In particular, we show how comparative proteogenomics addresses the notoriously difficult problem of "one-hit-wonders" in proteomics, improves on the existing gene prediction tools in genomics, and allows identification of rare post-translational modifications. We therefore argue that complementing DNA sequencing projects by comparative proteogenomics projects can be a viable approach to improve both genomic and proteomic annotations.

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“…By analyzing the location of these segments, we identified eight new genes and extended the 5Ј boundaries for 30 genes (see Supplemental Table S2A,B). Of the eight new genes, all but two had been previously suggested in a second version of the annotation of the MR-1 genome (Daraselia et al 2003). The remaining two, which we have designated SO_4799 and SO_A0180, were similar to proteins found in other bacteria.…”

Section: Improving Genome Annotationmentioning

confidence: 99%

“…The organism has been extensively studied by the Shewanella Federation (http:// shewanella.org/). The difficulties in gene prediction are illustrated by the fact that just a year after S. oneidensis was first annotated, it was reannotated by Daraselia et al (2003). Some recent studies have attempted to use LC-MS/MS and LC-MS to further improve the annotations of S. oneidensis (Romine et al 2004;Elias et al 2005Elias et al , 2006.…”

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confidence: 99%

Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation

Gupta¹,

Tanner²,

Jaitly³

et al. 2007

Genome Res.

181

225

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While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavages of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs, and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.

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Reannotation of Shewanella oneidensis Genome

Cited by 50 publications

References 7 publications

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation

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