Genome Scanning for Conditionally Essential Genes in Salmonella enterica Serotype Typhimurium

Khatiwara, Anita; Jiang, Tieshan; Sung, Samsun; Dawoud, Turki M.; Kim, Jeong Nam; Bhattacharya, Dhruva; Kim, Heebal; Ricke, Steven C.; Kwon, Young Min

doi:10.1128/aem.06865-11

Cited by 66 publications

(59 citation statements)

References 44 publications

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“…Should a similar pathway exist in Salmonella, the addition of taurocholate to the C-24 position would prevent such a reaction (19,52,53). Yet, if such genes exist in Salmonella and are necessary to process bile acids as a prerequisite for SPI-1 inactivation, they were not identified by our screen, suggesting that they are either essential (and perhaps conditionally essential for growth on bile-containing selective media) or functionally redundant (54,55). Similarly, our random and directed mutagenesis approaches failed to identify entry mechanisms for bile acids.…”

Section: Discussionmentioning

confidence: 65%

Bile Acids Function Synergistically To Repress Invasion Gene Expression in Salmonella by Destabilizing the Invasion Regulator HilD

et al. 2016

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bSalmonella spp. are carried by and can acutely infect agricultural animals and humans. After ingestion, salmonellae traverse the upper digestive tract and initiate tissue invasion of the distal ileum, a virulence process carried out by the type III secretion system encoded within Salmonella pathogenicity island 1 (SPI-1). Salmonellae coordinate SPI-1 expression with anatomical location via environmental cues, one of which is bile, a complex digestive fluid that causes potent repression of SPI-1 genes. The individual components of bile responsible for SPI-1 repression have not been previously characterized, nor have the bacterial signaling processes that modulate their effects been determined. Here, we characterize the mechanism by which bile represses SPI-1 expression. Individual bile acids exhibit repressive activity on SPI-1-regulated genes that requires neither passive diffusion nor OmpF-mediated entry. By using genetic methods, the effects of bile and bile acids were shown to require the invasion gene transcriptional activator hilD and to function independently of known upstream signaling pathways. Protein analysis techniques showed that SPI-1 repression by bile acids is mediated by posttranslational destabilization of HilD. Finally, we found that bile acids function synergistically to achieve the overall repressive activity of bile. These studies demonstrate a common mechanism by which diverse environmental cues (e.g., certain short-chain fatty acids and bile acids) inhibit SPI-1 expression. These data provide information relevant to Salmonella pathogenesis during acute infection in the intestine and during chronic infection of the gallbladder and inform the basis for development of therapeutics to inhibit invasion as a means of repressing Salmonella pathogenicity.

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Section: Discussionmentioning

confidence: 65%

Bile Acids Function Synergistically To Repress Invasion Gene Expression in Salmonella by Destabilizing the Invasion Regulator HilD

et al. 2016

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“…The Tn index of these genes is shown in Panels C and D of Figure 4. We further recorded the genes that Barquist and colleagues had originally selected (301 genes from S. Typhi and 299 for S. Typhimurium) which contained a reanalysis of the data from Langridge [9], as well as all genes previously identiied as 'essential' by Knuth [7], Khatiwari [10], Canals [11] and Thiele [13], regardless of whether such genes were successfully inactivated by others. This produced an 'all inclusive' list of 847 genes putatively essential for growth and survival, or under strong selection, in LB medium.…”

Section: Current Topics In Salmonella and Salmonellosismentioning

confidence: 99%

“…Some research groups selected for conditions more closely resembling natural conditions of infection, for instance growth at 42°C instead of 37°C, to resemble the body temperature of mice that S. Typhimurium would typically encounter, or in the presence of bile acid ( [10], work conducted with strain ATCC 14028). Exposure to low pH has also been tested [8].…”

Section: Essential Genes Based On Published Gene Inactivation Studiesmentioning

confidence: 99%

“…The conditional switch used here was growth temperature, while tetracycline-dependent expression was used by others [8], although they only reported indings for four essential genes. A few years later, transposon (Tn) mutagenesis combined with high-throughput sequencing became available and this was applied to S. enterica strains [9][10][11][12]. Typically, in this approach mutants are screened for growth in LB broth.…”

Section: Essential Genes Based On Published Gene Inactivation Studiesmentioning

confidence: 99%

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Insights from Comparative Genomics of the Genus Salmonella

Wassenaar¹,

Jun²,

Wanchai³

et al. 2017

Current Topics in Salmonella and Salmonellosis

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Comparative genomics have become a standard approach to gain insights into the interrelationships of microorganisms. Here, we have applied variable bioinformatic techniques to compare over 200 Salmonella genomes. First, we present a tree of all sequenced diferent members of the Enterobacteriaceae family, based on comparison of average amino acid identities. This technique was also applied to zoom in on the genomes of the genus Salmonella. The pan and core genomes of this genus were established and compared to experimental data available on the literature that identiied essential genes. Diiculties and shortcomings of both approaches are discussed. Metabolic pathways unique for Salmonella were identiied. Finally, we present an analysis of genes coding for small RNAs, an important part of the genetic repertoire of bacteria that is often ignored. The indings reported here are discussed and compared with available literature.

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“…For this, we used Tn-seq, a genome-wide screening method previously used for Streptococcus pneumoniae, Pseudomonas aeruginosa, Salmonella enterica serotype Typhimurium, and H. influenzae (7)(8)(9)(10)(11). We identified the H. influenzae carbonic anhydrase (HICA) gene to be absolutely essential for survival and growth of NTHi under ambient CO 2 conditions in vitro.…”

mentioning

confidence: 99%

Nontypeable Haemophilus influenzae Carbonic Anhydrase Is Important for Environmental and Intracellular Survival

et al. 2013

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c Nontypeable Haemophilus influenzae (NTHi) is one of the leading causes of noninvasive mucosal infections, such as otitis media, sinusitis, and conjunctivitis. During its life cycle, NTHi is exposed to different CO 2 levels, which vary from ϳ0.04% in ambient air during transmission to a new host to over 5% in the respiratory tract and tissues of the human host during colonization and disease. We used the next-generation sequencing Tn-seq technology to identify genes essential for NTHi adaptation to changes in environmental CO 2 levels. It appeared that H. influenzae carbonic anhydrase (HICA), which catalyzes the reversible hydration of CO 2 to bicarbonate, is a molecular factor that is conditionally essential for NTHi survival in ambient air. Growth of NTHi ⌬can strains was restored under 5% CO 2 -enriched conditions, by supplementation of the growth medium with sodium bicarbonate, or by genetic complementation with the can gene. Finally, we showed that HICA not only is essential for environmental survival but also appeared to be important for intracellular survival in host cells. Hence, HICA is important for NTHi niche adaptation.

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Genome Scanning for Conditionally Essential Genes in Salmonella enterica Serotype Typhimurium

Cited by 66 publications

References 44 publications

Bile Acids Function Synergistically To Repress Invasion Gene Expression in Salmonella by Destabilizing the Invasion Regulator HilD

Bile Acids Function Synergistically To Repress Invasion Gene Expression in Salmonella by Destabilizing the Invasion Regulator HilD

Insights from Comparative Genomics of the Genus Salmonella

Nontypeable Haemophilus influenzae Carbonic Anhydrase Is Important for Environmental and Intracellular Survival

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