scholarly journals Genome rearrangements induce biofilm formation in Escherichia coli C – an old model organism with a new application in biofilm research

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jarosław E. Król ◽  
Donald C. Hall ◽  
Sergey Balashov ◽  
Steven Pastor ◽  
Justin Sibert ◽  
...  

Abstract Background Escherichia coli C forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Results Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43, waaSBOJYZUL for lipopolysaccharide (LPS) synthesis, and cpsB for curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the − 35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of the csgD gene. And finally, E. coli C encodes an additional sigma70 subunit driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions provided insights into understanding this regulatory pathway in E. coli. Conclusions Biofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains of E. coli grown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain of E. coli C produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence of this classic strain, which provides for a base level of characterization and makes it useful for many biofilm-based applications.

2019 ◽  
Author(s):  
Jarosław E. Król ◽  
Donald C. Hall ◽  
Sergey Balashov ◽  
Steven Pastor ◽  
Justin Siebert ◽  
...  

AbstractEscherichia coliC forms more robust biofilms than the other laboratory strains. Biofilm formation and cell aggregation under a high shear force depends on temperature and salt concentrations. It is the last of fiveE. colistrains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43,waaSBOJYZULfor LPS synthesis, andcpsBfor curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulatorcsrAgene. This insertion is located 86 bp upstream of thecsrAstart codon inside the −35 region of P4 promoter and blocks the transcription from the sigma32and sigma70promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of thecsgDgene, which may drive its overexpression in biofilm. And finally,E. coliC encodes an additional sigma70subunit overexpressed in biofilm and driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions and total expression profiles using RNA-seq analyses comparing planktonic and biofilm envirovars provided insights into understanding this regulatory pathway inE. coli.IMPORTANCEBiofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains ofE. coligrown for decadesin vitrohave evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain ofE. coliC produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence as well as gene expression profiles of both the biofilm and planktonic envirovars of this classic strain, which provide for a base level of characterization and make it useful for many biofilm-based applications.


2021 ◽  
Author(s):  
◽  
Madeleine Huber

Operons wurden zuerst im Jahre 1961 beschrieben. Bis heute ist bekannt, dass die prokaryotischen Domänen Bacteria und Archaea Gene sowohl in monocistronischen als auch in bi- oder polycistronischen Transkripten exprimieren können. Häufig überlappen Gene sogar in ihren Sequenzen. Diese überlappenden Genpaare stehen nicht in Korrelation mit der Kompaktheit ihres Genoms. Das führt zu der Annahme, dass eine Art der Regulation vorliegt, welche weitere Proteine oder Gene nicht benötigt. Diese könnte eine gekoppelte Translation sein. Das bedeutet die Translation des stromabwärts-liegenden Gens ist abhängig von der Translation eines stromaufwärts-liegenden Gens. Diese Abhängigkeit kann zum Beispiel durch lang reichende Sekundärstrukturen entstehen, bei welchen Ribosomenbindestellen (RBS) des stromabwärts-liegenden Gens blockiert sind. Die de novo-Initiation am stromabwärts-liegenden Gen kann nur stattfinden, wenn das erste Gen translatiert wird und dabei die Sekundärstruktur an der RBS aufgeschmolzen wird. Für Genpaare in E. coli ist dieser Mechanismus gut untersucht. Ein anderes Beispiel für die Translationskopplung ist die Termination-Reinitiation, bei welcher ein Ribosom das erste Gen translatiert bis zum Stop-Codon, dort terminiert und direkt am stromabwärts-liegenden Start-Codon reinitiiert. Der Mechanismus via Termination-Reinitiation ist bis jetzt nur für eukaryontische Viren beschrieben worden. Im Gegensatz zu einer Kopplung über Sekundärstrukturen kommt es bei der Termination-Reinitiation am stromabwärts-liegenden Gen nicht zu einer de novo-Initiation sondern eine Reinitiation des Ribosoms findet statt. Diese Arbeit analysiert jene Art der Translationskopplung an Genen polycistronischer mRNAs in jeweils einem Modellorganismus als Vertreter der Archaea (Haloferax volcanii) und Bacteria (Escherichia coli). Hierfür wurden Reportergenvektoren erstellt, welche die überlappenden Genpaare an Reportergene fusionierten. Für diese Reportergene ist es möglich die Transkriptmenge zu quantifizieren sowie für die exprimierten Proteine Enzymassays durchgeführt werden können. Aus beiden Werten können Translationseffizienzen berechnet werden indem jeweils die Enzymaktivität pro Transkriptmenge ermittelt wird. Durch ein prämatures Stop-Codon in diesen Konstrukten ist es möglich zu unterscheiden ob es für die Translation des zweiten Gens essentiell ist, dass das Ribosom den Überlapp erreicht. Hiermit konnte für neun Genpaare in H. volcanii und vier Genpaare in E. coli gezeigt werden, dass eine Art der Kopplung stattfindet bei der es sich um eine Termination-Reinitiation handelt. Des Weiteren wurde analysiert, welche Auswirkungen intragene Shine-Dalgarno Sequenzen bei dem Event der Translationskopplung besitzen. Durch die Mutation solcher Motive und dem Vergleich der Translationseffizienzen der Konstrukte, mit und ohne einer SD Sequenz, wird für alle analysierten Genpaare beider Modellorganismen gezeigt, dass die SD Sequenz einen Einfluss auf diese Art der Kopplung hat. Zwischen den Genpaaren ist dieser Einfluss jedoch stark variabel. Weiterhin wurde der maximale Abstand zwischen zwei bicistronischen Genen untersucht, für welchen Translationskopplung via Termination-Reinitiation noch stattfinden kann. Hierfür wird durch site-directed mutagenesis jeweils ein prämatures Stop-Codon im stromaufwärts-liegenden Gen eingebracht, welches den intergenen Abstand zwischen den Genen in den jeweiligen Konstrukten vergrößert. Der Vergleich aller Konstrukte eines Genpaars zeigt in beiden Modellorganismen, dass die Termination-Reinitiation vom intergenen Abstand abhängig ist und die Translationseffizienz des stromabwärts-liegenden Reporters bereits ab 15 Nukleotiden Abstand abnimmt. Eine weitere Fragestellung dieser Arbeit war es, den genauen Mechanismus der Termination-Reinitiation zu analysieren. Für Ribosomen gibt es an der mRNA nach der Termination der Translation zwei Möglichkeiten: Entweder als 70S Ribosom bestehen zu bleiben und ein weiteres Start-Codon auf der mRNA zu suchen oder in seine beiden Untereinheiten zu dissoziieren, während die 50S Untereinheit die mRNA verlässt und die 30S Untereinheit über Wechselwirkungen an der mRNA verbleiben kann. Um diesen Mechanismus auf molekularer Ebene zu untersuchen, wird ein Versuchsablauf vorgestellt. Dieser ermöglicht das Event bei der Termination-Reinitiation in vitro zu analysieren. Eine Unterscheidung von 30S oder 70S Ribosomen bei der Reinitiation der Translation des stromabwärts-liegenden Gens wird ermöglicht. Die Idee dabei basiert auf einem ribosome display, bei welchem Translationskomplexe am Ende der Translation nicht in ihre Bestandteile zerfallen können, da die eingesetzte mRNA kein Stop-Codon enthält Der genaue Versuchsablauf, die benötigten Bestandteile sowie proof-of-principal Versuche sind in der Arbeit dargestellt und mögliche Optimierungen werden diskutiert.


2020 ◽  
Vol 83 (7) ◽  
pp. 1261-1267
Author(s):  
TING LIU ◽  
JINGFAN WANG ◽  
XIAOMAN GONG ◽  
XIAOXIA WU ◽  
LIU LIU ◽  
...  

ABSTRACT The purpose of the present study was to determine the bioactive compounds in rosemary essential oil (REO) and tea tree essential oil (TEO) and to investigate their antibacterial and antibiofilm activities against Staphylococcus aureus and Escherichia coli in vitro. The MIC and MBC assays were performed to assess the antibacterial activity of these two EOs against S. aureus and E. coli with the broth microdilution method. A crystal violet assay was used to ascertain the effects of EOs on the biofilm formation of the test strains, and a tetrazolium bromide (MTT) assay was used to measure the level of inactivation of mature biofilms by EOs. Gas chromatography–mass spectrometry revealed 15 compounds in REO and 27 compounds in TEO, representing 97.78 and 98.13% of the total EO, respectively. Eucalyptol and α-pinene were found in high concentrations in REO, and the two major compounds in TEO were 4-terpineol and terpinolene. The MICs of REO for the two S. aureus and E. coli test strains were both 0.5 mg/mL, and the MICs of TEO for the two strains were both 0.25 mg/mL. Therefore, these EOs can significantly inhibit the formation of biofilms and induced morphological biofilm changes, as verified by scanning electron microscopy. Both EOs had destructive effects on the mature biofilm of the two test strains. TEO was more inhibitory than REO for biofilm formation by the two test strains. HIGHLIGHTS


2006 ◽  
Vol 189 (5) ◽  
pp. 1627-1632 ◽  
Author(s):  
Maria D. Bodero ◽  
M. Carolina Pilonieta ◽  
George P. Munson

ABSTRACT The expression of the inner membrane protein NlpA is repressed by the enterotoxigenic Escherichia coli (ETEC) virulence regulator Rns, a member of the AraC/XylS family. The Rns homologs CfaD from ETEC and AggR from enteroaggregative E. coli also repress expression of nlpA. In vitro DNase I and potassium permanganate footprinting revealed that Rns binds to a site overlapping the start codon of nlpA, preventing RNA polymerase from forming an open complex at nlpAp. A second Rns binding site between positions −152 and −195 relative to the nlpA transcription start site is not required for repression. NlpA is not essential for growth of E. coli under laboratory conditions, but it does contribute to the biogenesis of outer membrane vesicles. As outer membrane vesicles have been shown to contain ETEC heat-labile toxin, the repression of nlpA may be an indirect mechanism through which the virulence regulators Rns and CfaD limit the release of toxin.


2009 ◽  
Vol 75 (6) ◽  
pp. 1723-1733 ◽  
Author(s):  
Claire Perrin ◽  
Romain Briandet ◽  
Gregory Jubelin ◽  
Philippe Lejeune ◽  
Marie-Andrée Mandrand-Berthelot ◽  
...  

ABSTRACT The survival of bacteria exposed to toxic compounds is a multifactorial phenomenon, involving well-known molecular mechanisms of resistance but also less-well-understood mechanisms of tolerance that need to be clarified. In particular, the contribution of biofilm formation to survival in the presence of toxic compounds, such as nickel, was investigated in this study. We found that a subinhibitory concentration of nickel leads Escherichia coli bacteria to change their lifestyle, developing biofilm structures rather than growing as free-floating cells. Interestingly, whereas nickel and magnesium both alter the global cell surface charge, only nickel promotes biofilm formation in our system. Genetic evidence indicates that biofilm formation induced by nickel is mediated by the transcriptional induction of the adhesive curli-encoding genes. Biofilm formation induced by nickel does not rely on efflux mechanisms using the RcnA pump, as these require a higher concentration of nickel to be activated. Our results demonstrate that the nickel-induced biofilm formation in E. coli is an adaptational process, occurring through a transcriptional effect on genes coding for adherence structures. The biofilm lifestyle is obviously a selective advantage in the presence of nickel, but the means by which it improves bacterial survival needs to be investigated.


2021 ◽  
Vol 4 (2) ◽  
pp. 166
Author(s):  
Ndaindila Haindongo ◽  
Amara Anyogu ◽  
Osmond Ekwebelem ◽  
Christian Anumudu ◽  
Helen Onyeaka

Biofilms are a significant concern in the food industry because of their potential to enhance bacterial survival and cause foodborne outbreaks. Escherichia coli (E. coli) is among the leading pathogens responsible for foodborne outbreaks and this can be attributed to its ability to form biofilms in food containers and food preparatory surfaces. The purpose of this study was to investigate the antibacterial and antibiofilm properties of garlic, ginger and mint and their potential to inhibit E.coli and biofilm formation. Disc diffusion assays and 96-well plate crystal violet-based methods were used to achieve these objectives. The plant extracts were diluted from 1 mg/ml to 0.1 mg/ml and incubated 25°C and 37°C to investigate the antimicrobial and antibiofilm effects on E. coli. The findings of this study showed that low temperatures induced the formation of E. coli biofilms and all tested extracts contain a broad spectrum of antibacterial and antibiofilm properties. This study provided new insights on the combined antimicrobial and antibiofilm properties of garlic, ginger and mint against planktonic cells and biofilms of E. coli MG 1655 and highlight the potential use of these extracts in the food industry to prevent biofilm formation by E. coli. 


2005 ◽  
Vol 71 (12) ◽  
pp. 8008-8015 ◽  
Author(s):  
Alfredo G. Torres ◽  
Cecelia Jeter ◽  
William Langley ◽  
Ann G. Matthysse

ABSTRACT Escherichia coli O157:H7 carried on plant surfaces, including alfalfa sprouts, has been implicated in food poisoning and outbreaks of disease in the United States. Adhesion to cell surfaces is a key component for bacterial establishment and colonization on many types of surfaces. Several E. coli O157:H7 surface proteins are thought to be important for adhesion and/or biofilm formation. Therefore, we examined whether mutations in several genes encoding potential adhesins and regulators of adherence have an effect on bacterial binding to plants and also examined the role of these genes during adhesion to Caco-2 cells and during biofilm formation on plastic in vitro. The genes tested included those encoding adhesins (cah, aidA1, and ompA) and mediators of hyperadherence (tdcA, yidE, waaI, and cadA) and those associated with fimbria formation (csgA, csgD, and lpfD2). The introduction of some of these genes (cah, aidA1, and csg loci) into an E. coli K-12 strain markedly increased its ability to bind to alfalfa sprouts and seed coats. The addition of more than one of these genes did not show an additive effect. In contrast, deletion of one or more of these genes in a strain of E. coli O157:H7 did not affect its ability to bind to alfalfa. Only the absence of the ompA gene had a significant effect on binding, and the plant-bacterium interaction was markedly reduced in a tdcA ompA double mutant. In contrast, the E. coli O157:H7 ompA and tdcA ompA mutant strains were only slightly affected in adhesion to Caco-2 cells and during biofilm formation. These findings suggest that some adhesins alone are sufficient to promote binding to alfalfa and that they may exist in E. coli O157:H7 as redundant systems, allowing it to compensate for the loss of one or more of these systems. Binding to the three types of surfaces appeared to be mediated by overlapping but distinct sets of genes. The only gene which appeared to be irreplaceable for binding to plant surfaces was ompA.


2020 ◽  
Vol 14 (4) ◽  
pp. 2577-2584
Author(s):  
Tariq Ahmad Shah ◽  
P. Preethishree ◽  
Ashwini ◽  
Vidya Pai

Urinary tract infection (UTI) is one of the most common complaints in the outpatient clinic and a major health problem owing to the emergence of antibiotic resistance and biofilm formation. The objective of this study was to isolate and identify the causative bacterial agent of UTI and detect in vitro biofilm formation by Escherichia coli and investigate its correlation with antibiotic resistance. Urine samples from 519 patients with suspected UTIs were collected and processed by conventional microbiological procedures. Antimicrobial susceptibility testing for E. coli isolates was performed on Mueller Hinton agar (MHA) plates using the Kirby-Bauer disk diffusion method. Biofilm production was evaluated using the tissue culture plate method. Of 519 urine samples, 115 (22.1%) showed significant bacteriuria. The most common isolate was E. coli (n=57, 49.6%), followed by Klebsiella spp. (n=23, 20%). All E. coli isolates were evaluated for their ability to form biofilms in vitro. Of 57 isolates, 50 (87.7%) were biofilm producers and 7 (12.3%) were non-biofilm producers. Antibiogram of E. coli isolates revealed the highest resistance to ampicillin (96.5%) and nitrofurantoin (91.2%), followed by amoxyclav (82.5%), ceftazidime (73.7%), cefepime (71.9%), and tetracycline (71.9%). A significant association (p<0.05) was observed between biofilm formation and resistance to amoxyclav, ceftazidime, cefepime, imipenem, and nitrofurantoin. A significant correlation was noted between biofilm production and antibiotic resistance. Hence, screening of all isolates of uropathogenic E. coli for biofilm production and studying their antibiogram would allow appropriate choice of antibiotic therapy.


Toxins ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 48 ◽  
Author(s):  
Bruballa ◽  
Shiromizu ◽  
Bernal ◽  
Pineda ◽  
Sabbione ◽  
...  

Enterohemorrhagic Escherichia coli (EHEC) strains are food-borne pathogens that can cause different clinical conditions. Shiga toxin 2a and/or 2c (Stx2)-producing E. coli O157:H7 is the serotype most frequently associated with severe human disease. In this work we analyzed the hypothesis that host cells participate in Stx2 production, cell damage, and inflammation during EHEC infection. With this aim, macrophage-differentiated THP-1 cells and the intestinal epithelial cell line HCT-8 were incubated with E. coli O157:H7. A time course analysis of cellular and bacterial survival, Stx2 production, stx2 transcription, and cytokine secretion were analyzed in both human cell lines. We demonstrated that macrophages are able to internalize and kill EHEC. Simultaneously, Stx2 produced by internalized bacteria played a major role in macrophage death. In contrast, HCT-8 cells were completely resistant to EHEC infection. Besides, macrophages and HCT-8 infected cells produce IL-1β and IL-8 inflammatory cytokines, respectively. At the same time, bacterial stx2-specific transcripts were detected only in macrophages after EHEC infection. The interplay between bacteria and host cells led to Stx production, triggering of inflammatory response and cell damage, all of which could contribute to a severe outcome after EHEC infections.


2015 ◽  
Vol 65 (2) ◽  
pp. 202-216 ◽  
Author(s):  
Dubravka Milanov ◽  
Bojana Prunić ◽  
Maja Velhner ◽  
Dalibor Todorović ◽  
Vladimir Polaček

Abstract Escherichia coli is an opportunistic pathogen affecting bovine mammary gland causing mainly transient infections; however, some recent reports indicated that some strains are able to adhere to and internalize into the epithelial cells, which can result in the persistence of the pathogen in the tissue and development of recurrent mastitis. The mechanism of adaptation of E. coli to the mammary gland relies on structures that are distinctive components of its extracellular matrix - curli fimbriae (proteinaceous component) and cellulose (polysaccharide). Expression of these components varies among the isolates. In this study, we investigated the capacity of expression of curli fimbriae and cellulose (via colony morphotype on Congo Red agar) and ability of biofilm formation (microtiter plate test) in 25 strains of E. coli isolated from milk of cows with clinical mastitis. Phylogenetic grouping of the isolates was performed using PCR method based on detection of chuA, yjaA and TspE4-C2 amplicons. Antimicrobial susceptibility was examined using standard disk diffusion test. Production of both extracellular matrix components was established in 56%, and expression of curli fimbriae in 64% E. coli isolates. All isolates that produced curli fimbriae, demonstrated this ability at a temperature of 37°C, indicating the potential role of these adhesive structures in the pathogenesis of mastitis. The results of phylogenetic typing confirmed that E. coli strains isolated from milk of cows with mastitis are typical commensals mainly belonging to phylogenetic groups A and B1. All curli and curli/cellulose producing isolates formed biofilm under in vitro conditions. The biofilm potentially plays an important role in the development of persistent infections as well as recurrent clinical symptoms after antibiotic therapy in spite of quite good in vitro antimicrobial susceptibility of the agent.


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