High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans

Cao, Xing-Jun; Dai, Jie; Xu, Hao; Nie, Song; Chang, Xiao; Hu, Bao-Yu; Sheng, Quanhu; Wang, Lian-Shui; Ning, Zhibin; Li, Yixue; Guo, Xin; Zhao, Guoping; Zeng, Rong

doi:10.1038/cr.2009.127

Cited by 62 publications

(61 citation statements)

References 52 publications

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“…Three other trans-regulators were affected with nonsynonymous SNV in coding regions. As revealed by the previous work of Yin-yang MDLC-MS/MS, the anti-sigma factor antagonist (LA_3096) can be phosphorylated in vivo [17], indicating an essential role in transcription regulation. These signal transduction pathways regulate a wide variety of intracellular processes in bacteria and sometimes are essential for coordinating responses to environmental changes.…”

Section: Discussionmentioning

confidence: 99%

“…Transfer RNA genes were identified with tRNAscan-SE [75]. Considering that the original sequence of 56601 was revised in this work, we reannotated this genome in parallel with IPAV (reannotation for strain 56601 has been done before [6,17], both of which were based on the old version of genome sequence). Comparison of the chromosome sequences was performed using ACT [76].…”

Section: Sequence Annotation and Analysismentioning

confidence: 99%

“…These "hypothetical proteins" shared no homology with known proteins/domains and are not expressed in the cell, as we discovered through proteomic profiling. In this reannotation, the length of coding sequences was reevaluated according to our new proteomic knowledge [17]. With the length of 60 codons as the cutoff value, only 3 653 CDSs were predicted for strain 56601.…”

Section: Wwwcell-researchcom | Cell Researchmentioning

confidence: 99%

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Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601

et al. 2011

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The virulence-attenuated Leptospira interrogans serovar Lai strain IPAV was derived by prolonged laboratory passage from a highly virulent ancestral strain isolated in China. We studied the genetic variations of IPAV that render it avirulent via comparative analysis against the pathogenic L. interrogans serovar Lai strain 56601. The complete genome sequence of the IPAV strain was determined and used to compare with, and then rectify and reannotate the genome sequence of strain 56601. Aside from their highly similar genomic structure and gene order, a total of 33 insertions, 53 deletions and 301 single-nucleotide variations (SNVs) were detected throughout the genome of IPAV directly affecting 101 genes, either in their 5′ upstream region or within their coding region. Among them, the majority of the 44 functional genes are involved in signal transduction, stress response, transmembrane transport and nitrogen metabolism. Comparative proteomic analysis based on quantitative liquid chromatography (LC)-MS/MS data revealed that among 1 627 selected pairs of orthologs, 174 genes in the IPAV strain were upregulated, with enrichment mainly in classes of energy production and lipid metabolism. In contrast, 228 genes in strain 56601 were upregulated, with the majority enriched in the categories of protein translation and DNA replication/repair. The combination of genomic and proteomic approaches illustrated that altered expression or mutations in critical genes, such as those encoding a Ser/Thr kinase, carbon-starvation protein CstA, glutamine synthetase, GTP-binding protein BipA, ribonucleotidediphosphate reductase and phosphate transporter, and alterations in the translational profile of lipoproteins or outer membrane proteins are likely to account for the virulence attenuation in strain IPAV.

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Section: Discussionmentioning

confidence: 99%

Section: Sequence Annotation and Analysismentioning

confidence: 99%

Section: Wwwcell-researchcom | Cell Researchmentioning

confidence: 99%

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Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601

et al. 2011

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“…Global PTM Discovery in H. pylori-The proteogenomic study can not only be employed to reannotated genomes but also be used to obtain PTM events (79,80). Recently, we reported a proteogenomic analysis and global profiling of PTMs in model cyanobacterium Synechococcus sp.…”

Section: Resultsmentioning

confidence: 99%

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes

Zhang

Yang

Zeng

et al. 2016

Molecular & Cellular Proteomics

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Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/ projects/gappproteogenomic/. Molecular & Cellular

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“…Moreover, the same experimental proteomic datasets are also useful in identifying PTMs on a proteome wide level [100,101]. Our group developed a proteogenomic approach to carry out genome annotation and whole-proteome analysis of PTMs in prokaryotes by employing high resolution and high accuracy MS data, and we used this approach to study the global PTMs in the model cyanobacterium Synechococcus 7002 [27].…”

Section: Global Discovery Of Ptmsmentioning

confidence: 99%

Proteomic analysis of post translational modifications in cyanobacteria

Xiong

Chen

2016

Journal of Proteomics

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High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans

Abstract: Leptospirosis is a widespread zoonotic disease caused by pathogenic spirochetes of the genus

Cited by 62 publications

References 52 publications

Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601

Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes

Proteomic analysis of post translational modifications in cyanobacteria

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