scholarly journals The Yersinia enterocolitica pYV Virulence Plasmid Contains Multiple Intrinsic DNA Bends Which Melt at 37°C

1999 ◽  
Vol 181 (14) ◽  
pp. 4198-4204 ◽  
Author(s):  
John R. Rohde ◽  
Xing-she Luan ◽  
Harold Rohde ◽  
James M. Fox ◽  
S. A. Minnich
Keyword(s):  
Gene Expression ◽  
Yersinia Enterocolitica ◽  
Conformational Transition ◽  
Dna Supercoiling ◽  
Dna Topology ◽  
Phenotypic Switching ◽  
Virulence Plasmid ◽  
Secretion Systems ◽  
Temperature Dependent ◽  
Virulence Gene Expression

ABSTRACT Temperature has a pleiotropic effect on Yersinia enterocolitica gene expression. Temperature-dependent phenotypes include the switching between two type III protein secretion systems, flagellum biosynthesis (≤30°C) and virulence plasmid-encoded Yop secretion (37°C). The mechanism by which temperature exerts this change in genetic programming is unclear; however, altered gene expression by temperature-dependent changes in DNA topology has been implicated. Here, we present evidence that the Y. enterocolitica virulence plasmid, pYV, undergoes a conformational transition between 30 and 37°C. Using a simplified two-dimensional, single-gel assay, we show that pYV contains multiple regions of intrinsic curvature, including virF, the positive activator of virulence genes. These bends are detectable at 30°C but melt at 37°C, the temperature at which the cells undergo phenotypic switching. We also show that pACYC184, a plasmid used as a reporter of temperature-induced changes in DNA supercoiling, has a single region of intrinsic bending detected by our assay. Topoisomers of pACYC184, with and without this bend, isolated from Y. enterocolitica were resolved by using chloroquine gels. The single bend has a dramatic influence on temperature-dependent DNA supercoiling. These data suggest that the Y. enterocolitica pYV plasmid may undergo a conformational change at the host temperature due to melting of DNA bends followed by compensatory adjustments in superhelical density. Hence, changes in DNA topology may be the temperature-sensing mechanism for virulence gene expression in Y. enterocolitica and other enteric pathogens.

scholarly journals Comparison of Yersinia enterocolitica DNA methylation at ambient and host temperatures

2019 ◽  
Author(s):  
Dustin J. Van Hofwegen ◽  
Carolyn J. Hovde ◽  
Scott A. Minnich
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Yersinia Enterocolitica ◽  
Type Iii Secretion ◽  
Pathogenic Bacteria ◽  
Type Iii Secretion System ◽  
Secretion System ◽  
Virulence Plasmid ◽  
Temperature Dependent ◽  
Promoter Regions

ABSTRACTPathogenic bacteria recognize environmental cues to vary gene expression for host adaptation. Moving from ambient to host temperature, Yersinia enterocolitica responds by immediately repressing flagella synthesis and inducing the virulence plasmid (pYV)-encoded type III secretion system. In contrast, shifting from host to ambient temperature requires 2.5 generations to restore motility suggesting a link to the cell cycle. We hypothesized that differential DNA methylation contributes to temperature-regulated gene expression. We tested this hypothesis by comparing single-molecule real-time (SMRT) sequencing of Y. enterocolitica DNA from cells growing exponentially at 22°C and 37°C. The inter-pulse duration ratio rather than the traditional QV scoring was the kinetic metric to compare DNA from cells grown at each temperature. All 565 YenI restriction sites were fully methylated at both temperatures. Among the 27,118 DNA adenine methylase (Dam) sites, 42 had differential methylation patterns while 17 remained unmethylated regardless of temperature. A subset of the differentially methylated Dam sites localized to promoter regions of predicted regulatory genes including LysR-type and PadR-like transcriptional regulators, and a cyclic-di-GMP phosphodiesterase. The unmethylated Dam sites localized with a bias to the replication terminus, suggesting they were protected from Dam methylase. No cytosine methylation was detected at Dcm sites.DATA SUMMARYAll methylation/base modification data are available at figshare at https://dx.doi.org/10.6084/m9.figshare.3493247 and https://dx.doi.org/10.6084/m9.figshare.3493310.IMPACT STATEMENTOrganisms sense and respond to their environment, in part, by epigenetic variation mediated by DNA methylation. Pathogenic bacteria vary gene expression to allow survival and activate virulence systems in response to host temperature. Yersinia enterocolitica, a facultative intracellular pathogen, respond by immediately repressing flagella synthesis and inducing the virulence plasmid-encoded type III secretion system. In this work, we examined the locations of DNA methylation throughout the Y. enterocolitica genome. While most methylation target sites were fully methylated, we identified sites with disparate temperature-dependent methylation. Several of these sites were within promoter regions of predicted regulatory genes. Differences in DNA methylation in promoter sequences are often responsible for variations in transcription. Identification of these differences in methylation provide likely candidates for regulators responsible for temperature-dependent phenotypes.

DNA supercoiling and environmental regulation of virulence gene expression in Shigella flexneri

Nature ◽  
1990 ◽  
Vol 344 (6268) ◽  
pp. 789-792 ◽  
Author(s):  
Charles J. Dorman ◽  
Niamh Ni Bhriain ◽  
Christopher F. Higgins
Keyword(s):  
Gene Expression ◽  
Environmental Regulation ◽  
Shigella Flexneri ◽  
Virulence Gene ◽  
Dna Supercoiling ◽  
Virulence Gene Expression

scholarly journals Murine Neonates Infected with Yersinia enterocolitica Develop Rapid and Robust Proinflammatory Responses in Intestinal Lymphoid Tissues

2013 ◽  
Vol 82 (2) ◽  
pp. 762-772 ◽  
Author(s):  
David T. Siefker ◽  
Andrea Echeverry ◽  
Roberta Brambilla ◽  
Masayuki Fukata ◽  
Kurt Schesser ◽  
...  
Keyword(s):  
Gene Expression ◽  
Yersinia Enterocolitica ◽  
Lymphoid Tissues ◽  
Virulence Plasmid ◽  
Wild Type ◽  
Mesenteric Lymph Nodes ◽  
Content Type ◽  
Proinflammatory Responses ◽  
Proinflammatory Gene ◽  
Proinflammatory Gene Expression

ABSTRACTNeonatal animals are generally very susceptible to infection with bacterial pathogens. However, we recently reported that neonatal mice are highly resistant to orogastric infection withYersinia enterocolitica. Here, we show that proinflammatory responses greatly exceeding those in adults arise very rapidly in the mesenteric lymph nodes (MLN) of neonates. High-level induction of proinflammatory gene expression occurred in the neonatal MLN as early as 18 h postinfection. Marked innate phagocyte recruitment was subsequently detected at 24 h postinfection. Enzyme-linked immunosorbent spot assay (ELISPOT) analyses indicated that enhanced inflammation in neonatal MLN is contributed to, in part, by an increased frequency of proinflammatory cytokine-secreting cells. Moreover, both CD11b+and CD11b−cell populations appeared to play a role in proinflammatory gene expression. The level of inflammation in neonatal MLN was also dependent on key bacterial components.Y. enterocoliticalacking the virulence plasmid failed to induce innate phagocyte recruitment. In contrast, tumor necrosis factor alpha (TNF-α) protein expression and neutrophil recruitment were strikingly higher in neonatal MLN after infection with ayopP-deficient strain than with wild-typeY. enterocolitica, whereas only modest increases occurred in adults. This hyperinflammatory response was associated with greater colonization of the spleen and higher mortality in neonates, while there was no difference in mortality among adults. This model highlights the dynamic levels of inflammation in the intestinal lymphoid tissues and reveals the protective (wild-type strain) versus harmful (yopP-deficient strain) consequences of inflammation in neonates. Moreover, these results reveal that the neonatal intestinal lymphoid tissues have great potential to rapidly mobilize innate components in response to infection with bacterial enteropathogens.

scholarly journals Structural Coupling between RNA Polymerase Composition and DNA Supercoiling in Coordinating Transcription: a Global Role for the Omega Subunit?

mBio ◽  
2011 ◽  
Vol 2 (4) ◽  
Author(s):  
Marcel Geertz ◽  
Andrew Travers ◽  
Sanja Mehandziska ◽  
Patrick Sobetzko ◽  
Sarath Chandra Janga ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Dna Supercoiling ◽  
Dna Topology ◽  
Chromosomal Dna ◽  
Tight Coupling ◽  
Structural Coupling ◽  
Bacterial Physiology ◽  
Transcription Machinery ◽  
The Impact

ABSTRACT In growing bacterial cells, the global reorganization of transcription is associated with alterations of RNA polymerase composition and the superhelical density of the DNA. However, the existence of any regulatory device coordinating these changes remains elusive. Here we show that in an exponentially growing Escherichia coli rpoZ mutant lacking the polymerase ω subunit, the impact of the Eσ38 holoenzyme on transcription is enhanced in parallel with overall DNA relaxation. Conversely, overproduction of σ70 in an rpoZ mutant increases both overall DNA supercoiling and the transcription of genes utilizing high negative superhelicity. We further show that transcription driven by the Eσ38 and Eσ70 holoenzymes from cognate promoters induces distinct superhelical densities of plasmid DNA in vivo. We thus demonstrate a tight coupling between polymerase holoenzyme composition and the supercoiling regimen of genomic transcription. Accordingly, we identify functional clusters of genes with distinct σ factor and supercoiling preferences arranging alternative transcription programs sustaining bacterial exponential growth. We propose that structural coupling between DNA topology and holoenzyme composition provides a basic regulatory device for coordinating genome-wide transcription during bacterial growth and adaptation. IMPORTANCE Understanding the mechanisms of coordinated gene expression is pivotal for developing knowledge-based approaches to manipulating bacterial physiology, which is a problem of central importance for applications of biotechnology and medicine. This study explores the relationships between variations in the composition of the transcription machinery and chromosomal DNA topology and suggests a tight interdependence of these two variables as the major coordinating principle of gene regulation. The proposed structural coupling between the transcription machinery and DNA topology has evolutionary implications and suggests a new methodology for studying concerted alterations of gene expression during normal and pathogenic growth both in bacteria and in higher organisms.

scholarly journals New Insights into Structural and Functional Roles of Indole-3-acetic acid (IAA): Changes in DNA Topology and Gene Expression in Bacteria

Biomolecules ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 522 ◽  
Author(s):  
Defez ◽  
Valenti ◽  
Andreozzi ◽  
Romano ◽  
Ciaramella ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acetic Acid ◽  
Conformational Changes ◽  
Regulation Of Gene Expression ◽  
Dna Supercoiling ◽  
Dna Topology ◽  
In Vitro Assays ◽  
Bacterial Cells ◽  
Indole 3 Acetic Acid

: Indole-3-acetic acid (IAA) is a major plant hormone that affects many cellular processes in plants, bacteria, yeast, and human cells through still unknown mechanisms. In this study, we demonstrated that the IAA-treatment of two unrelated bacteria, the Ensifer meliloti 1021 and Escherichia coli, harboring two different host range plasmids, influences the supercoiled state of the two plasmid DNAs in vivo. Results obtained from in vitro assays show that IAA interacts with DNA, leading to DNA conformational changes commonly induced by intercalating agents. We provide evidence that IAA inhibits the activity of the type IA topoisomerase, which regulates the DNA topological state in bacteria, through the relaxation of the negative supercoiled DNA. In addition, we demonstrate that the treatment of E. meliloti cells with IAA induces the expression of some genes, including the ones related to nitrogen fixation. In contrast, these genes were significantly repressed by the treatment with novobiocin, which reduces the DNA supercoiling in bacterial cells. Taking into account the overall results reported, we hypothesize that the IAA action and the DNA structure/function might be correlated and involved in the regulation of gene expression. This work points out that checking whether IAA influences the DNA topology under physiological conditions could be a useful strategy to clarify the mechanism of action of this hormone, not only in plants but also in other unrelated organisms.

Differences in Heat Resistance among Pathogenic Yersinia enterocolitica Depended on Growth Temperature and Serotype

2005 ◽  
Vol 68 (5) ◽  
pp. 1081-1082 ◽  
Author(s):  
H. HAYASHIDANI ◽  
Y. HARA-KUDO ◽  
S. KINOSHITA ◽  
K. SAEKI ◽  
A. T. OKATANI ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Heat Resistance ◽  
Outer Membrane ◽  
Yersinia Enterocolitica ◽  
Outer Membrane Protein ◽  
Growth Temperature ◽  
Virulence Plasmid ◽  
Temperature Dependent ◽  
Virulence Plasmids ◽  
Pathogenic Yersinia

To gain a better understanding about the effect of growth temperature on heat resistance of Yersinia enterocolitica, we determined decimal reduction times at 60°C (D60-values) for O:3; O:5,27; O:8; and O:9 strains harboring virulence plasmid coding for Yersinia outer membrane protein and experimentally virulence plasmid–deleted strains after they were grown to stationary phase at 7, 25, or 37°C. Bacteria were inoculated into Trypticase soy broth and were incubated at several temperatures. D60-values of O:3; O:5,27; and O:8 strains were larger when they were grown at 37°C than at 7 or 25°C, despite the presence or absence of virulence plasmids. However, similar D60-values were observed in O:9 strains, despite growth at 7, 25, or 37°C. The results indicate two types of Y. enterocolitica strains, growth temperature–dependent and –independent, and a Yersinia outer membrane protein that is not directly involved in growth temperature–dependent heat resistance.

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