scholarly journals The impact of global transcriptional regulation on bacterial gene order

2018 ◽  
Author(s):  
Pablo Yubero ◽  
Juan F. Poyatos
Keyword(s):  
Large Scale ◽  
A Priori ◽  
Bacterial Genome ◽  
Origin Of Replication ◽  
Bacterial Gene ◽  
E Coli ◽  
Scale Method ◽  
Bacterial Gene Expression ◽  
The Impact ◽  
Specific Control

AbstractBacterial gene expression depends on the allocation of limited transcriptional resources provided a particular growth rate and growth condition. Early studies in a few genes suggested this global regulation to generate a unifying hyperbolic expression pattern. Here, we developed a large-scale method that generalizes these experiments to quantify the response to growth of over 700 genes thata priorido not exhibit any specific control. We distinguish a core subset following a promoter-specific hyperbolic response. Within this group, we sort genes with regard to their responsiveness to the global regulatory program to show that those with a particularly sensitive linear response are located near the origin of replication. We then find evidence that this genomic architecture is biologically significant by examining position conservation ofE. coligenes in 100 bacteria. The response to the transcriptional resources of the cell results consequently in an additional feature contributing to bacterial genome organization.

scholarly journals The Location of Substitutions and Bacterial Genome Arrangements

2020 ◽  
Author(s):  
Daniella F Lato ◽  
G Brian Golding
Keyword(s):  
Sinorhizobium Meliloti ◽  
Bacterial Genome ◽  
Evolutionary Analysis ◽  
Origin Of Replication ◽  
Ancestral Reconstruction ◽  
Molecular Change ◽  
E Coli ◽  
A Genome ◽  
The Impact ◽  
Molecular Evolutionary Analysis

Abstract Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, while substitution rates usually increases with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and distance from the origin of replication is often significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), while others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.

scholarly journals Small RNA profiling in Mycobacterium tuberculosis identifies MrsI as necessary for an anticipatory iron sparing response

2018 ◽  
Vol 115 (25) ◽  
pp. 6464-6469 ◽  
Author(s):  
Elias R. Gerrick ◽  
Thibault Barbier ◽  
Michael R. Chase ◽  
Raylin Xu ◽  
Josie François ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Large Scale ◽  
Direct Interaction ◽  
Human Macrophage ◽  
Binding Interaction ◽  
Bacterial Gene ◽  
Rna Profiling ◽  
Iron Deprivation ◽  
Bacterial Gene Expression ◽  
Small Regulatory Rnas

One key to the success of Mycobacterium tuberculosis as a pathogen is its ability to reside in the hostile environment of the human macrophage. Bacteria adapt to stress through a variety of mechanisms, including the use of small regulatory RNAs (sRNAs), which posttranscriptionally regulate bacterial gene expression. However, very little is currently known about mycobacterial sRNA-mediated riboregulation. To date, mycobacterial sRNA discovery has been performed primarily in log-phase growth, and no direct interaction between any mycobacterial sRNA and its targets has been validated. Here, we performed large-scale sRNA discovery and expression profiling in M. tuberculosis during exposure to five pathogenically relevant stresses. From these data, we identified a subset of sRNAs that are highly induced in multiple stress conditions. We focused on one of these sRNAs, ncRv11846, here renamed mycobacterial regulatory sRNA in iron (MrsI). We characterized the regulon of MrsI and showed in mycobacteria that it regulates one of its targets, bfrA, through a direct binding interaction. MrsI mediates an iron-sparing response that is required for optimal survival of M. tuberculosis under iron-limiting conditions. However, MrsI is induced by multiple host-like stressors, which appear to trigger MrsI as part of an anticipatory response to impending iron deprivation in the macrophage environment.

scholarly journals Evaluation of Live Bacterial Prophylactics to Decrease IncF Plasmid Transfer and Association With Intestinal Small RNAs

2021 ◽  
Vol 11 ◽  
Author(s):  
Graham A. J. Redweik ◽  
Mary Kate Horak ◽  
Ryley Hoven ◽  
Logan Ott ◽  
Melha Mellata
Keyword(s):  
Virulence Genes ◽  
Positive Association ◽  
Multidrug Resistant ◽  
Plasmid Transfer ◽  
Siderophore Production ◽  
Causal Mechanism ◽  
Bacterial Gene ◽  
E Coli ◽  
Bacterial Gene Expression

Chicken intestinal Escherichia coli are a reservoir for virulence and antimicrobial resistance (AMR) genes that are often carried on incompatibility group F (IncF) plasmids. The rapid transfer of these plasmids between bacteria in the gut contributes to the emergence of new multidrug-resistant and virulent bacteria that threaten animal agriculture and human health. Thus, the aim of the present study was to determine whether live bacterial prophylactics could affect the distribution of large virulence plasmids and AMR in the intestinal tract and the potential role of smRNA in this process. In this study, we tested ∼100 randomly selected E. coli from pullet feces (n = 3 per group) given no treatment (CON), probiotics (PRO), a live Salmonella vaccine (VAX), or both (P + V). E. coli isolates were evaluated via plasmid profiles and several phenotypic (siderophore production and AMR), and genotypic (PCR for virulence genes and plasmid typing) screens. P + V isolates exhibited markedly attenuated siderophore production, lack of AMR and virulence genes, which are all related to the loss of IncF and ColV plasmids (P < 0.0001). To identify a causal mechanism, we evaluated smRNA levels in the ceca mucus and found a positive association between smRNA concentrations and plasmid content, with both being significantly reduced in P + V birds compared to other groups (P < 0.01). To test this positive association between IncF plasmid transfer and host smRNA concentration, we evenly pooled smRNA per group and treated E. coli mating pairs with serial concentrations of smRNA in vitro. Higher smRNA concentrations resulted in greater rates of IncF plasmid transfer between E. coli donors (APEC O2 or VAX isolate IA-EC-001) and recipient (HS-4) (all groups; P < 0.05). Finally, RNAHybrid predictive analyses detected several chicken miRNAs that hybridize with pilus assembly and plasmid transfer genes on the IncF plasmid pAPEC-O2-R. Overall, we demonstrated P + V treatment reduced smRNA levels in the chicken ceca, which was associated with a reduction in potentially virulent E. coli. Furthermore, we propose a novel mechanism in which intestinal smRNAs signal plasmid exchange between E. coli. Investigations to understand the changes in bacterial gene expression as well as smRNAs responsible for this phenomenon are currently underway.

scholarly journals Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli

2019 ◽  
Vol 8 (1) ◽  
pp. 28 ◽  
Author(s):  
Virali J. Parekh ◽  
Brittany A. Niccum ◽  
Rachna Shah ◽  
Marisa A. Rivera ◽  
Mark J. Novak ◽  
...  
Keyword(s):  
Genomic Instability ◽  
Dna Repeats ◽  
Loop Formation ◽  
Bacterial Gene ◽  
Quadruplex Dna ◽  
E Coli ◽  
Alternative Structures ◽  
Bacterial Gene Expression ◽  
G Quadruplex

Certain G-rich DNA repeats can form quadruplex in bacterial chromatin that can present blocks to DNA replication and, if not properly resolved, may lead to mutations. To understand the participation of quadruplex DNA in genomic instability in Escherichia coli (E. coli), mutation rates were measured for quadruplex-forming DNA repeats, including (G3T)4, (G3T)8, and a RET oncogene sequence, cloned as the template or nontemplate strand. We evidence that these alternative structures strongly influence mutagenesis rates. Precisely, our results suggest that G-quadruplexes form in E. coli cells, especially during transcription when the G-rich strand can be displaced by R-loop formation. Structure formation may then facilitate replication misalignment, presumably associated with replication fork blockage, promoting genomic instability. Furthermore, our results also evidence that the nucleoid-associated protein Hfq is involved in the genetic instability associated with these sequences. Hfq binds and stabilizes G-quadruplex structure in vitro and likely in cells. Collectively, our results thus implicate quadruplexes structures and Hfq nucleoid protein in the potential for genetic change that may drive evolution or alterations of bacterial gene expression.

scholarly journals 1508. Carbapenem vs. Non-carbapenem as Empiric Regimens for Bacteremia Caused by ESBL Producing Escherichia coli and Klebsiella pneumoniae in Children: Preliminary Study

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S549-S549
Author(s):  
Saera Park ◽  
Jina Lee
Keyword(s):  
Large Scale ◽  
Pediatric Patients ◽  
Medical Center ◽  
Empirical Therapy ◽  
Antibiotics Resistance ◽  
Cure Rate ◽  
E Coli ◽  
Empiric Antibiotics ◽  
The Impact ◽  
Microbiological Cure

Abstract Background The clinical efficacy of non-carbapenem for the treatment of extended-spectrum β-lactamase (ESBL) bacteremia in children with underlying comorbidities is controversial. We aimed to compare clinical and microbiological outcomes between pediatric patients received carbapenem and non-carbapenem as empiric regimens for bacteremia caused by ESBL producing E. coli and K. pneumoniae. Methods Pediatric patients aged <19 years who hospitalized between January 2014 to Jun. 2018 at Asan medical center with monomicrobial ESBL producing E. coli and K. pneumoniae bacteremia were included. Patients were excluded if they did not receive a carbapenem after ESBL production was identified. We compared outcomes between patients who had empirical therapy with a carbapenem to those who had empirical therapy with a non-carbapenem. Results Among total 161 E. coli and K. pneumoniae bacteremia, 46 (28.6%) fulfilled the criteria, of which 25 (54.3%) were caused by E. coli and 21 (45.7%) by K. pneumoniae. The most common underlying diseases were hemato-oncologic diseases (47.8%) and prematurity (23.9%). The main sources of bacteremia were vascular catheter (37.0%) and necrotizing enterocolitis (10.9%). 25 cases were treated with empiric carbapenem, and the remaining 21 cases with non-carbapenem agents. The all-cause 30-day fatality in the carbapenem group was 32% (8/25) and 5% (1/21) in the non-carbapenem group (P = 0.023). Microbiological cure rate at 3 days after the first culture positive day was 75.3% in the carbapenem group and 89.6% in the non-carbapenem group (P = 0.046). However, adjusting initial presentation with septic shock, the choice of initial empiric antibiotic was not a risk factor for the 30-day fatality and microbiological cure rate at 3 days (aHR 4.82, 95% CI 0.592–39.231; aHR 0.648, 95% CI 0.333- 1.259, respectively). Conclusion For the medically fragile pediatric patients with bacteremia caused by ESBL producing E. coli and K. pneumoniae, the impact of empiric antibiotics on clinical and microbiological outcomes was not significant if early transition to definitive carbapenem regimen is possible when susceptibility is proven. A large-scale multicenter study will be needed to select the most appropriate empiric antibiotics and minimize the spread of antibiotics resistance. Disclosures All authors: No reported disclosures.

scholarly journals In situ reprogramming of gut bacteria by oral delivery

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Bryan B. Hsu ◽  
Isaac N. Plant ◽  
Lorena Lyon ◽  
Frances M. Anastassacos ◽  
Jeffrey C. Way ◽  
...  
Keyword(s):  
Oral Delivery ◽  
Multidisciplinary Approach ◽  
Gut Bacteria ◽  
Release Mechanism ◽  
Bacterial Gene ◽  
E Coli ◽  
Bacterial Gene Expression ◽  
Bacterial Function

Abstract Abundant links between the gut microbiota and human health indicate that modification of bacterial function could be a powerful therapeutic strategy. The inaccessibility of the gut and inter-connections between gut bacteria and the host make it difficult to precisely target bacterial functions without disrupting the microbiota and/or host physiology. Herein we describe a multidisciplinary approach to modulate the expression of a specific bacterial gene within the gut by oral administration. We demonstrate that an engineered temperate phage λ expressing a programmable dCas9 represses a targeted E. coli gene in the mammalian gut. To facilitate phage administration while minimizing disruption to host processes, we develop an aqueous-based encapsulation formulation with a microbiota-based release mechanism and show that it facilitates oral delivery of phage in vivo. Finally we combine these technologies and show that bacterial gene expression in the mammalian gut can be precisely modified in situ with a single oral dose.

scholarly journals A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli

mSystems ◽  
2016 ◽  
Vol 1 (1) ◽  
Author(s):  
Divya Balasubramanian ◽  
Preethi T. Ragunathan ◽  
Jingyi Fei ◽  
Carin K. Vanderpool
Keyword(s):  
Gene Expression ◽  
Cell Division ◽  
Posttranscriptional Control ◽  
Bacterial Gene ◽  
Content Type ◽  
E Coli ◽  
Bacterial Gene Expression ◽  
Metabolic Gene Expression ◽  
Defective Prophage ◽  
Ectopic Production

ABSTRACT sRNAs are ubiquitous and versatile regulators of bacterial gene expression. A number of well-characterized examples in E. coli are highly conserved and present in the E. coli core genome. In contrast, the sRNA DicF (identified over 20 years ago but remaining poorly characterized) is encoded by a gene carried on a defective prophage element in many E. coli genomes. Here, we characterize DicF in order to better understand how horizontally acquired sRNA regulators impact bacterial gene expression and physiology. Our data confirm the long-hypothesized DicF-mediated regulation of ftsZ, encoding the bacterial tubulin homolog required for cell division. We further uncover DicF-mediated posttranscriptional control of metabolic gene expression. Ectopic production of DicF is highly toxic to E. coli cells, but the toxicity is not attributable to DicF regulation of ftsZ. Further work is needed to reveal the biological roles of and benefits for the host conferred by DicF and other products encoded by defective prophages. Hundreds of small RNAs (sRNAs) have been identified in diverse bacterial species, and while the functions of most remain unknown, some regulate key processes, particularly stress responses. The sRNA DicF was identified over 25 years ago as an inhibitor of cell division but since then has remained uncharacterized. DicF consists of 53 nucleotides and is encoded by a gene carried on a prophage (Qin) in the genomes of many Escherichia coli strains. We demonstrated that DicF inhibits cell division via direct base pairing with ftsZ mRNA to repress translation and prevent new synthesis of the bacterial tubulin homolog FtsZ. Systems analysis using computational and experimental methods identified additional mRNA targets of DicF: xylR and pykA mRNAs, encoding the xylose uptake and catabolism regulator and pyruvate kinase, respectively. Genetic analyses showed that DicF directly base pairs with and represses translation of these targets. Phenotypes of cells expressing DicF variants demonstrated that DicF-associated growth inhibition is not solely due to repression of ftsZ, indicating that the physiological consequences of DicF-mediated regulation extend beyond effects on cell division caused by reduced FtsZ synthesis. IMPORTANCE sRNAs are ubiquitous and versatile regulators of bacterial gene expression. A number of well-characterized examples in E. coli are highly conserved and present in the E. coli core genome. In contrast, the sRNA DicF (identified over 20 years ago but remaining poorly characterized) is encoded by a gene carried on a defective prophage element in many E. coli genomes. Here, we characterize DicF in order to better understand how horizontally acquired sRNA regulators impact bacterial gene expression and physiology. Our data confirm the long-hypothesized DicF-mediated regulation of ftsZ, encoding the bacterial tubulin homolog required for cell division. We further uncover DicF-mediated posttranscriptional control of metabolic gene expression. Ectopic production of DicF is highly toxic to E. coli cells, but the toxicity is not attributable to DicF regulation of ftsZ. Further work is needed to reveal the biological roles of and benefits for the host conferred by DicF and other products encoded by defective prophages.

scholarly journals Ecological Perturbations Impact Species-Specific Gene Expression of the Oral Microbiota

2020 ◽  
Author(s):  
Daniel Belstrøm ◽  
Florentin Constancias ◽  
Daniela I Drautz-Moses ◽  
Stephan C Schuster ◽  
Mark Veleba ◽  
...  
Keyword(s):  
Gene Expression ◽  
Carbohydrate Metabolism ◽  
Taxonomic Composition ◽  
Bacterial Activity ◽  
Oral Microbiota ◽  
Bacterial Gene ◽  
Bacterial Gene Expression ◽  
Oral Site ◽  
Species Specific ◽  
The Impact

Abstract Background: The purpose of the present investigation was to use the oral cavity as an in-vivo model to study the impact of internal and external perturbations on bacterial biofilm communities. We tested the hypotheses that bacterial gene expression of the healthy microbiota reflects habituation to site-specific ecological perturbations, and that the perturbation effect of chronic inflammation, i.e. periodontitis, impacts bacterial gene expression not only locally, but also at other sites of the oral cavity. Oral microbial samples were collected from three oral sites – plaque, tongue and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterization of taxonomic composition and to determine species specific bacterial activity as expressed by the ratio of messenger RNA to the corresponding genomic DNA.Results: Here we show the impact of two perturbations – oral site and periodontitis - on bacterial gene expression of the oral microbiota. The oral site was the main determinant of taxonomic composition as well as bacterial gene expression. However, bacterial activity at the three oral sites (plaque, tongue, and saliva) was significantly impacted by periodontitis, with a reduction of the carbohydrate metabolism.Conclusions: Data from the present study characterize the impact of two perturbations – oral site and periodontitis - on bacterial gene expression of the oral microbiota. The oral site was the main determinant of taxonomic composition as well as bacterial gene expression. However, presence of periodontitis had impact on bacterial activity of both plaque but also on tongue and the salivary microbiota. Collectively, data suggest that periodontitis associates with impaired carbohydrate metabolism of the oral microbiota. Future longitudinal and interventional studies are warranted to evaluate the potential pathogenic role of impaired bacterial carbohydrate metabolism not only in periodontitis, but also in other diseases with low grade inflammation, such as type 2 diabetes mellitus.

scholarly journals In situ reprogramming of gut bacteria by oral delivery

2020 ◽  
Author(s):  
Bryan B. Hsu ◽  
Isaac N. Plant ◽  
Lorena Lyon ◽  
Frances M. Anastassacos ◽  
Jeffrey C. Way ◽  
...  
Keyword(s):  
Oral Delivery ◽  
Multidisciplinary Approach ◽  
Gut Bacteria ◽  
Release Mechanism ◽  
Bacterial Gene ◽  
E Coli ◽  
Bacterial Gene Expression ◽  
Bacterial Function

AbstractAbundant links between the gut microbiota and human health indicate that the modification of bacterial function could be a powerful therapeutic strategy. The inaccessibility of the gut and inter-connections between gut bacteria and the host make it difficult to precisely target bacterial functions without disrupting the microbiota and/or host physiology. Herein we describe a multidisciplinary approach to modulate the expression of a specific bacterial gene within the gut by oral administration. We first demonstrate that an engineered temperate phage λ expressing a programmable dCas9 represses a targeted E. coli gene in the mammalian gut. To facilitate phage administration while minimizing disruption to host processes, we develop an aqueous-based encapsulation formulation with a microbiota-based release mechanism and show that it facilitates the oral delivery of phage in vivo. Finally we combine these technologies and show that bacterial gene expression in the mammalian gut can be precisely modified in situ with a single oral dose.

scholarly journals Evaluating a Geriatric Educational Program: Exploring Opportunities for Increasing Impact and Scale

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. 758-758
Author(s):  
Shera Hosseini ◽  
Michelle Howard ◽  
Allison Ward
Keyword(s):  
Large Scale ◽  
Healthcare Professionals ◽  
Program Effectiveness ◽  
Qualitative Interviews ◽  
A Priori ◽  
The United States ◽  
Dissemination And Implementation ◽  
Geriatric Population ◽  
Learning Competencies ◽  
The Impact

Abstract The geriatric population is rapidly growing, and this growth is beyond the pace of increase in the number of healthcare professionals who are qualified to care for and tend to the various needs of this significant subgroup of the population. The current university curricula have not been sufficient in terms of quantity as well as their ability to address the ageism inherent in the perspectives of students from across the educational spectrum. In recognition of the absence of standardized geriatric guidelines, medical associations across Canada and the United States have established geriatric learning competencies for medical programs. Nevertheless, there are exiting gaps regarding the development and evaluation of geriatric-focused didactic programs that adequately train and build competency among the students interested in pursuing careers with geriatric-specific elements. A university-wide program was developed to enhance aging education and build competency through sparking interest, providing better education related to aging, and building better relationships between future healthcare professionals and older adults. To evaluate the impact of this program, a logical framework was developed a-priori and revised through constant iterations and following discussion with the program’s multidisciplinary stakeholder group. Quantitative measures are being augmented with in-depth qualitative interviews to explore elements influencing students’ experiences with the program and the effect on their interests in and attitudes towards geriatrics. The results will inform our conclusions regarding program effectiveness in enhancing interest in geriatric-focused education among the students and trainees and assist with recommending future directions regarding impact and large-scale dissemination and implementation.

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