Molecular, functional, and evolutionary analysis of sequences specific to Salmonella.

Groisman, Eduardo A.; Sturmoski, Mark; Solomon, Felix; Lin, Robert C.; Ochman, Howard

doi:10.1073/pnas.90.3.1033

Cited by 72 publications

(66 citation statements)

References 41 publications

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“…The 0.9-kb BamHI fragment of plasmid pKRP10 harboring the cat gene was cloned into the single BglII site of plasmid pEG7245, which carries a mutant derivative of the pmrA gene. Then, the mutant copy of the pmrA gene in plasmid pEG7246 was used to replace the wild-type copy of the pmrA gene in the chromosome as described previously (17). The structure of the pmrA chromosomal region in the pmrA mutant was verified by Southern hybridization using both pmrA-and cat-specific probes (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The resulting plasmid, pEG7245, was used to disrupt the pmrA gene by introducing the cat-containing, 0.9-kb BamHI fragment from pKRP10 into the single BglII site to form pEG7246. The pmrA::cat mutation in pEG7246 was transferred to the chromosome as described previously (17). The structure of the pmrA gene in the mutant strains was verified by Southern hybridization using both pmrA-and cat-specific probes (Fig.…”

Section: Methodsmentioning

confidence: 99%

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Two-component regulatory systems can interact to process multiple environmental signals

1996

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The PhoP/PhoQ two-component system of Salmonella typhimurium governs transcription of some 25 loci in response to the extracellular concentration of Mg 2؉. We have now identified one of these loci as pmrCAB, which codes for a two-component system that mediates resistance to the antibiotic polymyxin B. Transcription of seven of 25 PhoP-activated loci was dependent on a functional PmrA protein, the response regulator of the PmrA/PmrB system. Expression of the PmrA-dependent loci was induced by either Mg 2؉ limitation or mild acidification, whereas transcription of a PmrA-independent gene was activated by Mg 2؉ limitation but not acid pH. Induction of PmrA-activated genes by Mg 2؉ limitation required the PhoP and PhoQ proteins. In contrast, the acid-mediated activation of PmrA-regulated genes occurred in strains that were missing either one of these proteins. Transcriptional regulation by a cascade of two-component systems allows pathogenic bacteria to express their virulence determinants in response to a broader spectrum of environmental cues.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Two-component regulatory systems can interact to process multiple environmental signals

1996

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“…tRNA availability during the evolution of an organism may play a significant role in determining its characteristic preferred codon usage. However, genes obtained by horizontal transmission from a phylogenetically divergent organism with GC content and codon usage different from those of the recipient bacterium approach the values characteristic of their newly acquired host only after hundreds of millions of years [5]. This fact suggests, first, that differences in codon usage must have arisen relatively early during prokaryotic evolution, and, second, that the pressure for a newly acquired gene to assume the codon usage of the host organism is minimal.…”

Section: Codon Usage and Gene Expressionmentioning

confidence: 99%

Differential codon usage: a safeguard against inappropriate expression of specialized genes?

Saier

1995

FEBS Letters

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Recent work has suggested that rare codons are sometimes used for the regulation of specialized gene expression in bacteria. Moreover, the cellular levels of certain tRNAs may fluctuate with growth conditions. Evidence implicating such mechanisms in the control of photosynthesis in Rhodobacter, solventogenesis in Clostridium, sporulation in Streptomyces, and fimbrial phase variation in E. coli is summarized. It is suggested that such mechanisms will prove applicable to the control of numerous additional specialized functions, and that the empirical tools for testing this possibility are currently available.

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“…Thus, we have concentrated on the major known differences between the maps of S. typhimurium and E. coli that may be partly responsible for their different lifestyles and pathogenicities. Some genes have been ascribed to five of the loops that are unique to Salmonella spp., and some Salmonella-specific clones have been obtained from these loops for functional and evolutionary analysis (4). For example, the region between 91 min and 96 min presented here has a loop at 92 min which is unique to S. typhimurium compared with E. coli, and an S. typhimurium-specific gene, inlA, that is responsible for utilization of inositol has been mapped to 92 min (10).…”

Section: Discussionmentioning

confidence: 99%

High-resolution restriction map for a 240-kilobase region spanning 91 to 96 minutes on the Salmonella typhimurium LT2 chromosome

Wong

Rudd

et al. 1994

J Bacteriol

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A hierarchical approach allows the completion of contiguous sets of overlapping clones for small regions of a genome, one at a time rather than tackling the whole genome at once. On the basis of the BlnI restriction map for Salmonella typhimurium LT2, we dissected the chromosome into 21 different fragments by using a TnS transposon carrying a BlnI site. Dissected chromosomal fragments were purified by pulsed-field gel electrophoresis and used as probes for sorting a lambda DASHII genomic library of 2,304 primary clones. A total of 129 clones identified as spanning the region from 91 min to 98 min were partly ordered on the basis of the intensity of hybridization with mitomycin-induced Mud-P22 phage DNAs from insertions with pac sites in opposite orientations at 93 min used as probes. Decreased signal intensity with the Mud-P22 probes corresponded to the increased distance of the clone from the site of Mud-P22 insertion and allowed the clones to be placed in two groups from 91 min to 93 min and from 93 min to 98 min and into four intensity categories within the two groups. A member of each category was used to generate a riboprobe from the T3 promoter flanking the insert. This probe identified overlapping clones among the 129 clones. This subchromosomal library was then screened again with riboprobes from nonoverlapping clones. After four cycles of this strategy, a minimal contiguous sequence of 19 partly overlapping clones was selected for restriction mapping. A detailed map of 378 sites for eight restriction enzymes is presented for a region of about 240 kb. Working clockwise, the following genes were placed on this physical map on the basis of their restriction maps: malFEK, lamB, malM, lexA, qor, dnaB, air, uvrA, proP, pmrB, pmrA, melA, meiB, phoN, amiB, mutL, and miaA.In 1987, a restriction map of the Escherichia coli genome was produced by using partial restriction digests of 3,400 bacteriophage lambda clones generated with the eight restriction enzymes BamHI, HindIII, EcoRI, EcoRV, BglI, KpnI, PstI, and PvuII (7). The genomic sequence of E. coli is going to be completed soon (2 enzymes used for E. coli was employed here. However, we took a different approach which allows the completion of contiguous sequences (contigs) for manageable regions of the genome, one at a time rather than tackling the whole genome at once, and which requires restriction mapping of only a small number of the lambda clones. MATERIALS AND METHODSPhage and bacterial strains. All bacterial strains were LT2 derivatives. Strains were constructed via P22 HT12/4 int-3 transductions (6) as described previously (16). TnlO insertions (13), Tn5(pfm) insertions (15), and Mud-P22 strains (1) have been described previously.Construction of pulsed-field gel electrophoresis strains. A set of random Tn5(pfm) insertions were generated and mapped as described previously (14

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Molecular, functional, and evolutionary analysis of sequences specific to Salmonella.

Cited by 72 publications

References 41 publications

Two-component regulatory systems can interact to process multiple environmental signals

Two-component regulatory systems can interact to process multiple environmental signals

Differential codon usage: a safeguard against inappropriate expression of specialized genes?

High-resolution restriction map for a 240-kilobase region spanning 91 to 96 minutes on the Salmonella typhimurium LT2 chromosome

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