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The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli

View Article: PubMed Central - PubMed

ABSTRACT

Conventional efforts to describe essential genes in bacteria have typically emphasized nutrient-rich growth conditions. Of note, however, are the set of genes that become essential when bacteria are grown under nutrient stress. For example, more than 100 genes become indispensable when the model bacterium Escherichia coli is grown on nutrient-limited media, and many of these nutrient stress genes have also been shown to be important for the growth of various bacterial pathogens in vivo. To better understand the genetic network that underpins nutrient stress in E. coli, we performed a genome-scale cross of strains harboring deletions in some 82 nutrient stress genes with the entire E. coli gene deletion collection (Keio) to create 315,400 double deletion mutants. An analysis of the growth of the resulting strains on rich microbiological media revealed an average of 23 synthetic sick or lethal genetic interactions for each nutrient stress gene, suggesting that the network defining nutrient stress is surprisingly complex. A vast majority of these interactions involved genes of unknown function or genes of unrelated pathways. The most profound synthetic lethal interactions were between nutrient acquisition and biosynthesis. Further, the interaction map reveals remarkable metabolic robustness in E. coli through pathway redundancies. In all, the genetic interaction network provides a powerful tool to mine and identify missing links in nutrient synthesis and to further characterize genes of unknown function in E. coli. Moreover, understanding of bacterial growth under nutrient stress could aid in the development of novel antibiotic discovery platforms.

No MeSH data available.


Related in: MedlinePlus

yigM encodes the biotin transporter BioP. (A) Index plot showing the synthetic interaction value of every double deletion mutant resulting from the mating of the bioA strain with the Keio collection. The region between the ilvC and metE genes is highlighted (right panel). (B) The genetic locus between the ilvC and metE genes. The genes that are involved in synthetic sick/lethal interactions with bioA within that locus are shown in red. (C) Effect of the BioA inhibitor MAC13772 on the growth of E. coli strain BW25113 (red) or the kanamycin-resistant yigM mutant (blue) in LB. The growth was normalized to that of LB with no drugs.
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fig5: yigM encodes the biotin transporter BioP. (A) Index plot showing the synthetic interaction value of every double deletion mutant resulting from the mating of the bioA strain with the Keio collection. The region between the ilvC and metE genes is highlighted (right panel). (B) The genetic locus between the ilvC and metE genes. The genes that are involved in synthetic sick/lethal interactions with bioA within that locus are shown in red. (C) Effect of the BioA inhibitor MAC13772 on the growth of E. coli strain BW25113 (red) or the kanamycin-resistant yigM mutant (blue) in LB. The growth was normalized to that of LB with no drugs.

Mentions: In our synthetic genetic array, bioA formed synthetic sick or lethal interactions with three genes present between the ilvC and metE genes: wecB, yigM, and metR (Fig. 5A and B). Of these three genes, only yigM was a gene of unknown function. Furthermore, only yigM is predicted to be an inner membrane protein and could potentially be a transporter. Interestingly, the yigM gene overlaps substantially with the metR gene (Fig. 5B). It is, therefore, likely that the synthetic lethal phenotype of the metR-bioA pair is due to the concomitant disruption of the yigM gene by the metR deletion mutant. In agreement with this hypothesis, a metR deletion mutant formed a synthetic lethal interaction with bioA (see Table S2 in the supplemental material). The wecB gene, involved in the biosynthesis of the enterobacterial common antigen, is involved in synthetic interactions across ~25% of the synthetic genetic array. Thus, yigM was the most likely candidate for the biotin transporter.


The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli
yigM encodes the biotin transporter BioP. (A) Index plot showing the synthetic interaction value of every double deletion mutant resulting from the mating of the bioA strain with the Keio collection. The region between the ilvC and metE genes is highlighted (right panel). (B) The genetic locus between the ilvC and metE genes. The genes that are involved in synthetic sick/lethal interactions with bioA within that locus are shown in red. (C) Effect of the BioA inhibitor MAC13772 on the growth of E. coli strain BW25113 (red) or the kanamycin-resistant yigM mutant (blue) in LB. The growth was normalized to that of LB with no drugs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120140&req=5

fig5: yigM encodes the biotin transporter BioP. (A) Index plot showing the synthetic interaction value of every double deletion mutant resulting from the mating of the bioA strain with the Keio collection. The region between the ilvC and metE genes is highlighted (right panel). (B) The genetic locus between the ilvC and metE genes. The genes that are involved in synthetic sick/lethal interactions with bioA within that locus are shown in red. (C) Effect of the BioA inhibitor MAC13772 on the growth of E. coli strain BW25113 (red) or the kanamycin-resistant yigM mutant (blue) in LB. The growth was normalized to that of LB with no drugs.
Mentions: In our synthetic genetic array, bioA formed synthetic sick or lethal interactions with three genes present between the ilvC and metE genes: wecB, yigM, and metR (Fig. 5A and B). Of these three genes, only yigM was a gene of unknown function. Furthermore, only yigM is predicted to be an inner membrane protein and could potentially be a transporter. Interestingly, the yigM gene overlaps substantially with the metR gene (Fig. 5B). It is, therefore, likely that the synthetic lethal phenotype of the metR-bioA pair is due to the concomitant disruption of the yigM gene by the metR deletion mutant. In agreement with this hypothesis, a metR deletion mutant formed a synthetic lethal interaction with bioA (see Table S2 in the supplemental material). The wecB gene, involved in the biosynthesis of the enterobacterial common antigen, is involved in synthetic interactions across ~25% of the synthetic genetic array. Thus, yigM was the most likely candidate for the biotin transporter.

View Article: PubMed Central - PubMed

ABSTRACT

Conventional efforts to describe essential genes in bacteria have typically emphasized nutrient-rich growth conditions. Of note, however, are the set of genes that become essential when bacteria are grown under nutrient stress. For example, more than 100 genes become indispensable when the model bacterium Escherichia coli is grown on nutrient-limited media, and many of these nutrient stress genes have also been shown to be important for the growth of various bacterial pathogens in vivo. To better understand the genetic network that underpins nutrient stress in E. coli, we performed a genome-scale cross of strains harboring deletions in some 82 nutrient stress genes with the entire E. coli gene deletion collection (Keio) to create 315,400 double deletion mutants. An analysis of the growth of the resulting strains on rich microbiological media revealed an average of 23 synthetic sick or lethal genetic interactions for each nutrient stress gene, suggesting that the network defining nutrient stress is surprisingly complex. A vast majority of these interactions involved genes of unknown function or genes of unrelated pathways. The most profound synthetic lethal interactions were between nutrient acquisition and biosynthesis. Further, the interaction map reveals remarkable metabolic robustness in E. coli through pathway redundancies. In all, the genetic interaction network provides a powerful tool to mine and identify missing links in nutrient synthesis and to further characterize genes of unknown function in E. coli. Moreover, understanding of bacterial growth under nutrient stress could aid in the development of novel antibiotic discovery platforms.

No MeSH data available.


Related in: MedlinePlus