Large-scale identification of protein–protein interaction of <i>Escherichia coli</i> K-12

Arifuzzaman, Mohammad; Maeda, Maki; Itoh, Aya; Nishikata, Kensaku; Takita, Chiharu; Saito, Rintaro; Ara, Takeshi; Nakahigashi, Kenji; Huang, Hsuan‐Cheng; Hirai, Atsuko; Tsuzuki, Kohei; Nakamura, Seira; Altaf-Ul-Amin, Mohammad; Oshima, Taku; Baba, Tomoya; Yamamoto, Nobuto; Kawamura, Tomoyo; Ioka-Nakamichi, Tomoko; Kitagawa, Masanari; Tomita, Masaru; Kanaya, Shigehiko; Wada, Chieko; Mori, Hirotada

doi:10.1101/gr.4527806

Cited by 377 publications

(447 citation statements)

References 41 publications

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“…As expected, proteins with a higher degree had a higher RIP. We repeated the analysis with three large PPI datasets (13)(14)(15) that used different stringency cutoffs, and found no significant difference in this trend in any of these datasets.…”

Section: Resultsmentioning

confidence: 99%

Lateral acquisition of genes is affected by the friendliness of their products

Gophna

Ofran

2010

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

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A major factor in the evolution of microbial genomes is the lateral acquisition of genes that evolved under the functional constraints of other species. Integration of foreign genes into a genome that has different components and circuits poses an evolutionary challenge. Moreover, genes belonging to complex modules in the pretransfer species are unlikely to maintain their functionality when transferred alone to new species. Thus, it is widely accepted that lateral gene transfer favors proteins with only a few proteinprotein interactions. The propensity of proteins to participate in protein-protein interactions can be assessed using computational methods that identify putative interaction sites on the protein.Here we report that laterally acquired proteins contain significantly more putative interaction sites than native proteins. Thus, genes encoding proteins with multiple protein-protein interactions may in fact be more prone to transfer than genes with fewer interactions. We suggest that these proteins have a greater chance of forming new interactions in new species, thus integrating into existing modules. These results reveal basic principles for the incorporation of novel genes into existing systems. network evolution | genomics | horizontal gene transfer | systems biology T he horizontal transfer of DNA, known as lateral gene transfer (LGT), is considered a major mechanism for the acquisition of novel biological functions in bacteria (1). Transfer of a single gene introduces an evolutionary puzzle; biological processes are typically carried out by the interaction of several proteins, not by a single gene product. Genes that belong to complex modules might not be functional when transferred alone to a new species. Thus, it is widely accepted that genes with fewer interactions are more likely to be transferred to, and retained in, a new species. This postulate is known as the complexity hypothesis (2). Subsequent studies that elaborated on the importance of proteinprotein interactions (PPIs) in this context provide some support for the principles laid out in the complexity hypothesis (3-5); for example, it has been shown that proteins encoded by genes that have been more frequently transferred in evolution tend to have fewer interactions than other proteins (5). However, supporting evidence for the complexity hypothesis comes from analysis of the PPIs of transferred genes within their contemporary, posttransfer species, not from the number of PPIs in their pretransfer host. Indeed, fewer contemporary PPIs might imply a small number of PPIs in the pretransfer host as well, thus corroborating the assumption that highly interacting proteins are less likely to be transferred and retained. Alternatively, fewer contemporary PPIs might merely imply that horizontally acquired genes had less time to develop interactions with proteins in their new host compared with vertically acquired genes. Thus, such a posttransfer analysis does not provide conclusive evidence regarding the relationship between PPI and LGT. Unfortun...

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Section: Resultsmentioning

confidence: 99%

Lateral acquisition of genes is affected by the friendliness of their products

Gophna

Ofran

2010

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

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“…Interacts with FdhD-To ascertain the interaction of IscS with FdhD reported by large-scale studies (7,8), bacterial two-hybrid experiments were conducted (Fig. 1A).…”

Section: Iscs Specificallymentioning

confidence: 99%

“…TusA participates in a pathway that modifies tRNA, and IscU is a so-called [Fe-S] scaffold protein. In addition to TusA and IscU, large-scale interactome studies identified FdhD as a binding partner of IscS (7,8). FdhD has been shown to be required for the activity of formate dehydrogenases (FDHs) 2 in E. coli through an unknown mechanism (9,10).…”

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confidence: 99%

A Sulfurtransferase Is Essential for Activity of Formate Dehydrogenases in Escherichia coli

Thomé

Gust

Toci

et al. 2012

Journal of Biological Chemistry

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“…This complex may constitute a sulfate assimilation metabolon (Shibagaki 2007), deletion or mutation of which increases resistance to selenate toxicity (El Kassis et al 2007). Interestingly, E. coli CysA also can bind to OASTLa/CysK (Arifuzzaman et al 2006). STAS domains in plant SulP and mammalian SLC26 transporters are essential for plasma membrane targeting and for transport function.…”

Section: Role Of the Stas Domain In Rv1739c Functionmentioning

confidence: 99%

Increased sulfate uptake by E. coli overexpressing the SLC26-related SulP protein Rv1739c from Mycobacterium tuberculosis

Zolotarev

Unnikrishnan

Shmukler

et al. 2008

Comparative Biochemistry and Physiology Part A: Molecular &

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Growth and virulence of mycobacteria requires sulfur uptake. The Mycobacterium tuberculosis genome contains, in addition to the ABC sulfate permease cysTWA, three SLC26-related SulP genes of unknown function. We report that induction of Rv1739c expression in E. coli increased bacterial uptake of sulfate, but not Cl − , formate, or oxalate. Uptake was time-dependent, maximal at pH 6.0, and exhibited a K 1/2 for sulfate of 4.0 μM. Na + -independent sulfate uptake was not reduced by bicarbonate, nitrate, or phosphate, but was inhibited by sulfite, selenate, thiosulfate, Nethylmaleimide and carbonyl cyanide 3-chloro-phenylhydrazone. Sulfate uptake was also increased by overexpression of the Rv1739c transmembrane domain, but not of the cytoplasmic C-terminal STAS domain. Mutation to serine of the three cysteine residues of Rv1739c did not affect magnitude, pH-dependence, or pharmacology of sulfate uptake. Expression of Rv1739c in a M. bovis BCG strain lacking the ABC sulfate permease subunit CysA could not complement sulfate auxotrophy. Moreover, inducible expression of Rv1739c in an E. coli strain lacking CysA did not increase sulfate uptake by intact cells. Our data show that facilitation of bacterial sulfate uptake by Rv1739c requires CysA and its associated sulfate permease activity, and suggest that Rv1739c may be a CysTWAdependent sulfate transporter.

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Large-scale identification of protein–protein interaction of Escherichia coli K-12

Cited by 377 publications

References 41 publications

Lateral acquisition of genes is affected by the friendliness of their products

Lateral acquisition of genes is affected by the friendliness of their products

A Sulfurtransferase Is Essential for Activity of Formate Dehydrogenases in Escherichia coli

Increased sulfate uptake by E. coli overexpressing the SLC26-related SulP protein Rv1739c from Mycobacterium tuberculosis

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