scholarly journals Genomic signatures of UV resistance evolution in Escherichia coli depend on the growth phase during exposure

2021 ◽  
Author(s):  
S Selveshwari ◽  
Kasturi Lele ◽  
Sutirth Dey
Keyword(s):  
Escherichia Coli ◽  
Growth Phase ◽  
Uv Resistance ◽  
Resistance Evolution ◽  
Genomic Signatures

scholarly journals Genomic signatures of UV resistance evolution in Escherichia coli depend on the growth phase during exposure

2021 ◽  
Author(s):  
S Selveshwari ◽  
Kasturi Lele ◽  
Sutirth Dey
Keyword(s):  
Escherichia Coli ◽  
Growth Phase ◽  
Physiological State ◽  
Lag Phase ◽  
Cellular Transport ◽  
Uv Resistance ◽  
Phenotypic Differences ◽  
E Coli ◽  
Resistance Evolution ◽  
Genomic Signatures

AbstractPhysiological states can determine the ability of organisms to handle stress. Does this mean that the same selection pressure will lead to different evolutionary outcomes, depending on the organisms’ physiological state? If yes, what will be the genomic signatures of such adaptation(s)? We used experimental evolution in Escherichia coli followed by whole-genome whole-population sequencing to investigate these questions. The sensitivity of Escherichia coli to ultraviolet (UV) radiation depends on the growth phase during which it experiences the radiation. We evolved replicate E. coli populations under two different conditions of UV exposures, namely exposure during the lag and the exponential growth phases. Initially, the UV sensitivity of the ancestor was greater during the exponential phase than the lag phase. However, at the end of 100 cycles of exposure, UV resistance evolved to similar extents in both treatments. Genome analysis showed that mutations in genes involved in DNA repair, cell membrane structure and RNA polymerase were common in both treatments. However, different functional groups were found mutated in populations experiencing lag and exponential UV treatment. In the former, genes involved in transcriptional and translational regulations and cellular transport were mutated, whereas the latter treatment showed mutations in genes involved in signal transduction and cell adhesion. Interestingly, the treatments showed no phenotypic differences in a number of novel environments. Taken together, these results suggest that selection pressures at different physiological stages can lead to differences in the genomic signatures of adaptation, which need not necessarily translate into observable phenotypic differences.

scholarly journals Mutations in the Escherichia coli UvrB ATPase motif compromise excision repair capacity

1989 ◽  
Vol 86 (17) ◽  
pp. 6577-6581 ◽  
Author(s):  
T W Seeley ◽  
L Grossman
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Excision Repair ◽  
Site Directed Mutagenesis ◽  
Sequence Motif ◽  
Amino Acid Side Chain ◽  
Uv Resistance ◽  
Wild Type ◽  
General Applicability ◽  
Repair Capacity

The Escherichia coli UvrB protein possesses an amino acid sequence motif common to many ATPases. The role of this motif in UvrB has been investigated by site-directed mutagenesis. Three UvrB mutants, with amino acid replacements at lysine-45, failed to confer UV resistance when tested in the UV-sensitive strain N364 (delta uvrB), while five other mutants constructed near this region of UvrB confer wild-type levels of UV resistance. Because even the conservative substitution of arginine for lysine-45 in UvrB results in failure to confer UV resistance, we believe we have identified an amino acid side chain in UvrB essential to nucleotide excision repair in E. coli. The properties of two purified mutant UvrB proteins, lysine-45 to alanine (K45A) and asparagine-51 to alanine (N51A), were analyzed in vitro. While the K45A mutant is fully defective in incision of UV-irradiated DNA, K45A is capable of interaction with UvrA in forming an ATP-dependent nucleoprotein complex. The K45A mutant, however, fails to activate the characteristic increase in ATPase activity observed with the wild-type UvrB in the presence of UvrA and DNA. From these results we conclude that there is a second nucleotide-dependent step in incision following initial complex formation, which is defective in the K45A mutant. This experimental approach may prove of general applicability in the study of function and mechanism of other ATPase motif proteins.

scholarly journals Functional Analysis of Genes Comprising the Locus of Heat Resistance in Escherichia coli

2017 ◽  
Vol 83 (20) ◽  
Author(s):  
Ryan Mercer ◽  
Oanh Nguyen ◽  
Qixing Ou ◽  
Lynn McMullen ◽  
Michael G. Gänzle
Keyword(s):  
Escherichia Coli ◽  
Heat Shock ◽  
Heat Shock Proteins ◽  
Heat Resistance ◽  
Growth Phase ◽  
Genomic Island ◽  
Enteric Bacteria ◽  
Content Type ◽  
E Coli ◽  
Shock Proteins

ABSTRACT The locus of heat resistance (LHR) is a 15- to 19-kb genomic island conferring exceptional heat resistance to organisms in the family Enterobacteriaceae, including pathogenic strains of Salmonella enterica and Escherichia coli. The complement of LHR-comprising genes that is necessary for heat resistance and the stress-induced or growth-phase-induced expression of LHR-comprising genes are unknown. This study determined the contribution of the seven LHR-comprising genes yfdX1 GI, yfdX2, hdeD GI, orf11, trx GI, kefB, and psiE GI by comparing the heat resistances of E. coli strains harboring plasmid-encoded derivatives of the different LHRs in these genes. (Genes carry a subscript “GI” [genomic island] if an ortholog of the same gene is present in genomes of E. coli.) LHR-encoded heat shock proteins sHSP20, ClpKGI, and sHSPGI are not sufficient for the heat resistance phenotype; YfdX1, YfdX2, and HdeD are necessary to complement the LHR heat shock proteins and to impart a high level of resistance. Deletion of trx GI, kefB, and psiE GI from plasmid-encoded copies of the LHR did not significantly affect heat resistance. The effect of the growth phase and the NaCl concentration on expression from the putative LHR promoter p2 was determined by quantitative reverse transcription-PCR and by a plasmid-encoded p2:GFP promoter fusion. The expression levels of exponential- and stationary-phase E. coli cells were not significantly different, but the addition of 1% NaCl significantly increased LHR expression. Remarkably, LHR expression in E. coli was dependent on a chromosomal copy of evgA. In conclusion, this study improved our understanding of the genes required for exceptional heat resistance in E. coli and factors that increase their expression in food. IMPORTANCE The locus of heat resistance (LHR) is a genomic island conferring exceptional heat resistance to several foodborne pathogens. The exceptional level of heat resistance provided by the LHR questions the control of pathogens by current food processing and preparation techniques. The function of LHR-comprising genes and their regulation, however, remain largely unknown. This study defines a core complement of LHR-encoded proteins that are necessary for heat resistance and demonstrates that regulation of the LHR in E. coli requires a chromosomal copy of the gene encoding EvgA. This study provides insight into the function of a transmissible genomic island that allows otherwise heat-sensitive enteric bacteria, including pathogens, to lead a thermoduric lifestyle and thus contributes to the detection and control of heat-resistant enteric bacteria in food.

scholarly journals Growth Phase-Dependent Regulation and Stringent Control of fis Are Conserved Processes in Enteric Bacteria and Involve a Single Promoter (fis P) in Escherichia coli

2004 ◽  
Vol 186 (1) ◽  
pp. 122-135 ◽  
Author(s):  
Prabhat Mallik ◽  
Timothy S. Pratt ◽  
Michael B. Beach ◽  
Meranda D. Bradley ◽  
Jayanthi Undamatla ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Phase ◽  
Primer Extension ◽  
E Coli ◽  
Stringent Control ◽  
Regulatory Processes ◽  
Nutritional Environment ◽  
Nuclease Mapping ◽  
Single Promoter

ABSTRACT The intracellular concentration of the Escherichia coli factor for inversion stimulation (Fis), a global regulator of transcription and a facilitator of certain site-specific DNA recombination events, varies substantially in response to changes in the nutritional environment and growth phase. Under conditions of nutritional upshift, fis is transiently expressed at very high levels, whereas under induced starvation conditions, fis is repressed by stringent control. We show that both of these regulatory processes operate on the chromosomal fis genes of the enterobacteria Klebsiella pneumoniae, Serratia marcescens, Erwinia carotovora, and Proteus vulgaris, strongly suggesting that the physiological role of Fis is closely tied to its transcriptional regulation in response to the nutritional environment. These transcriptional regulatory processes were previously shown to involve a single promoter (fis P) preceding the fis operon in E. coli. Recent work challenged this notion by presenting evidence from primer extension assays which appeared to indicate that there are multiple promoters upstream of fis P that contribute significantly to the expression and regulation of fis in E. coli. Thus, a rigorous analysis of the fis promoter region was conducted to assess the contribution of such additional promoters. However, our data from primer extension analysis, S1 nuclease mapping, β-galactosidase assays, and in vitro transcription analysis all indicate that fis P is the sole E. coli fis promoter in vivo and in vitro. We further show how certain conditions used in the primer extension reactions can generate artifacts resulting from secondary annealing events that are the likely source of incorrect assignment of additional fis promoters.

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