Global Protein−Protein Interaction Network in the Human Pathogen <i>Mycobacterium tuberculosis</i> H37Rv

Wang, Yi; Cui, Tao; Zhang, Cong; Yang, Min; Huang, Yuanxia; Li, Weihui; Zhang, Lei; Gao, Chunhui; Yang, He; Li, Yuqing; Huang, Feng; Zeng, Jumei; Huang, Cheng; Yang, Qiong; Tian, Yuxi; Zhao, Chun-Chao; Chen, Huanchun; Zhang, Hua; He, Zheng‐Guo

doi:10.1021/pr100808n

Cited by 93 publications

(99 citation statements)

References 53 publications

(159 reference statements)

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“…We obtained information for all unique, binary PPIs in the genomes of M. tuberculosis, Synechocystis sp., Helicobacter pylori, Campylobacter jejuni, Treponema pallidum, Mycoplasma pneumonia, and Escherichia coli (Rain et al 2001;Parrish et al 2007;Sato et al 2007;Titz et al 2008;Kuhner et al 2009;Peregrin-Alvarez et al 2009;Wang et al 2010).…”

Section: Methodsmentioning

confidence: 99%

Genome Reduction Promotes Increase in Protein Functional Complexity in Bacteria

Kelkar

Ochman

2013

Genetics

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Obligate pathogenic and endosymbiotic bacteria typically experience gene loss due to functional redundancy, asexuality, and genetic drift. We hypothesize that reduced genomes increase their functional complexity through protein multitasking, in which many genes adopt new roles to counteract gene loss. Comparisons of interaction networks among six bacteria that have varied genome sizes (Mycoplasma pneumoniae, Treponema pallidum, Helicobacter pylori, Campylobacter jejuni, Synechocystis sp., and Mycobacterium tuberculosis) reveal that proteins in small genomes interact with proteins from a wider range of functions than do their orthologs in larger genomes. This suggests that surviving proteins form increasingly complex functional relationships to compensate for genes that are lost.

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Section: Methodsmentioning

confidence: 99%

Genome Reduction Promotes Increase in Protein Functional Complexity in Bacteria

Kelkar

Ochman

2013

Genetics

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“…Bacterial meta-protein interaction data -We used 2,231 binary interactions between E. coli proteins that we have previously determined through yeast two-hybrid screens (7 (9). Utilizing all-versus-all BLASTP searches with the InParanoid script (38) in protein sets of two species, sequence pairs with mutually best scores were selected as central orthologous pairs.…”

Section: Protein-protein Interactions In Hmentioning

confidence: 99%

“…Only a few comprehensive bacterial interactome studies have been published to date, such as E. coli (7), C. jejuni (8) and M. tuberculosis (9). In particular, protein interactions of H. pylori were among the first to be determined in bacteria (10), an interactome that has been recently expanded (11), capturing roughly 70% of the proteome.…”

Section: Introductionmentioning

confidence: 99%

Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori

Wuchty¹,

Müller

Caufield

et al. 2018

Molecular & Cellular Proteomics

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Helicobacter pylori is a common pathogen that is estimated to infect half of the human population, causing several diseases such as duodenal ulcer. Despite one of the first pathogens to be sequenced, its proteome remains poorly characterised as about one third of its proteins have no functional annotation. Here, we integrate and analyze known protein interactions with proteomic and genomic data from different sources. We find that proteins with similar abundances tend to interact. Such an observation is accompanied by a trend of interactions to appear between proteins of similar functions, although some show marked cross-talk to others. Protein function prediction with protein interactions is significantly improved when interactions from other bacteria are included in our network, allowing us to obtain putative functions of more than 300 poorly or previously uncharacterized proteins. Proteins that are critical for the topological controllability of the underlying network are significantly enriched with genes that are up-regulated in the spiral compared to the coccoid form of H. pylori. Determining their evolutionary conservation, we present evidence for 80 protein complexes to be identical in composition with their counterparts in E. coli while 85 are partially conserved but 120 complexes are completely absent. Furthermore, we determine network clusters that coincide with related functions gene essentiality, genetic context, cellular localization, and gene expression in different cellular states.

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“…In sum, in the past few years novel genome-wide technologies (46) and comprehensive biochemical analyses (3) have been employed to characterize the Mtb Wbl proteins. However, the methodology and exact experimental conditions should be critically evaluated in order to yield accurate information on the biological functions of Wbl proteins.…”

Section: Protein Network and Wbl Functionmentioning

confidence: 99%

Mycobacterium tuberculosisWhiB3: A Novel Iron–Sulfur Cluster Protein That Regulates Redox Homeostasis and Virulence

Saini

Farhana²,

Steyn³

2012

Antioxidants & Redox Signaling

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Significance: Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), can persist in a latent state for decades without causing overt disease. Since latent Mtb is refractory to current antimycobacterial drugs, the discovery and characterization of the biological mechanisms controlling the entry, maintenance, and emergence from latent infection is critical to the development of novel clinical therapies. Recent Advances: Recently, Mtb WhiB3, a member of the family of intracellular iron-sulfur (Fe-S) cluster proteins has emerged as a redox sensor and effector molecule controlling several aspects of Mtb virulence. WhiB3 was shown to contain a 4Fe-4S cluster that specifically reacts with important host gases (O 2 and NO), and exogenous and endogenous metabolic signals to maintain redox balance. Notably, the concept of reductive stress emerged from studies on WhiB3. Critical Issues: The detailed mechanism of how WhiB3 functions as an intracellular redox sensor is unknown. Sustaining Mtb redox balance is particularly important since the bacilli encounter a large number of redox stressors during infection, and because several antimycobacterial prodrugs are effective only upon bioreductive activation in the mycobacterial cytoplasm. Future Directions: How Mtb WhiB3 monitors its internal and external surroundings and modulates endogenous oxido-reductive pathways which in turn alter Mtb signal transduction, nucleic acid and protein synthesis, and enzymatic activation, is mostly unexplored. Modern expression, metabolomic and proteomic technologies should provide fresh insights into these yet unanswered questions. Antioxid. Redox Signal. 16, 687-697.

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Global Protein−Protein Interaction Network in the Human Pathogen Mycobacterium tuberculosis H37Rv

Cited by 93 publications

References 53 publications

Genome Reduction Promotes Increase in Protein Functional Complexity in Bacteria

Genome Reduction Promotes Increase in Protein Functional Complexity in Bacteria

Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori

Mycobacterium tuberculosisWhiB3: A Novel Iron–Sulfur Cluster Protein That Regulates Redox Homeostasis and Virulence

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