Bacterial-induced pH shifts link individual cell physiology to macroscale collective behavior

Bacteria have evolved a diverse array of signaling pathways that enable them to quickly respond to environmental changes. Understanding how these pathways reflect environmental conditions and produce an orchestrated response is an ongoing challenge. Herein, we present a role for collective modifications of environmental pH carried out by microbial colonies living on a surface. We show that by collectively adjusting the local pH value, Paenibacillus spp., specifically, regulate their swarming motility. Moreover, we show that such pH-dependent regulation can converge with the carbon repression pathway to down-regulate flagellin expression and inhibit swarming in the presence of glucose. Interestingly, our results demonstrate that the observed glucose-dependent swarming repression is not mediated by the glucose molecule per se, as commonly thought to occur in carbon repression pathways, but rather is governed by a decrease in pH due to glucose metabolism. In fact, modification of the environmental pH by neighboring bacterial species could override this glucose-dependent repression and induce swarming of Paenibacillus spp. away from a glucose-rich area. Our results suggest that bacteria can use local pH modulations to reflect nutrient availability and link individual bacterial physiology to macroscale collective behavior.

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Bacterial response to graphene oxide and reduced graphene oxide integrated in agar plates

Royal Society Open Science ◽

10.1098/rsos.181083 ◽

2018 ◽

Vol 5 (11) ◽

pp. 181083 ◽

Cited By ~ 6

Author(s):

V. R. S. S. Mokkapati ◽

Santosh Pandit ◽

Jinho Kim ◽

Anders Martensson ◽

Martin Lovmar ◽

...

Keyword(s):

Graphene Oxide ◽

Reduced Graphene Oxide ◽

Bacterial Growth ◽

Bacterial Species ◽

Bacterial Activity ◽

Bacterial Physiology ◽

Bacterial Response ◽

Solid Agar ◽

Reduced Graphene ◽

Set Up

There are contradictory reports in the literature regarding the anti-bacterial activity of graphene, graphene oxide (GO) and reduced graphene oxide (rGO). This controversy is mostly due to variations in key parameters of the reported experiments, like: type of substrate, form of graphene, number of layers, type of solvent and most importantly, type of bacteria. Here, we present experimental data related to bacterial response to GO and rGO integrated in solid agar-based nutrient plates—a standard set-up for bacterial growth that is widely used by microbiologists. Bacillus subtilis and Pseudomonas aeruginosa strains were used for testing bacterial growth. We observed that plate-integrated rGO showed strong anti-bacterial activity against both bacterial species. By contrast, plate-integrated GO was harmless to both bacteria. These results reinforce the notion that the response of bacteria depends critically on the type of graphene material used and can vary dramatically from one bacterial strain to another, depending on bacterial physiology.

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Spontaneous adaptation of ion selectivity in a bacterial flagellar motor

10.1101/2021.01.26.427765 ◽

2021 ◽

Author(s):

Pietro Ridone ◽

Tsubasa Ishida ◽

Yoshiyuki Sowa ◽

Matthew A. B. Baker

Keyword(s):

Genome Engineering ◽

Environmental Changes ◽

Ion Selectivity ◽

Bacterial Species ◽

Selective Advantage ◽

Flagellar Motor ◽

Novel Mutations ◽

Power Sources ◽

Motor Complex ◽

Bacterial Flagellar Motor

ABSTRACTMotility provides a selective advantage to many bacterial species and is often achieved by rotation of flagella that propel the cell towards more favourable conditions. In most species, the rotation of the flagellum, driven by the Bacterial Flagellar Motor (BFM), is powered by H+ or Na+ ion transit through the torque-generating stator subunits of the motor complex. The ionic requirements for motility appear to have adapted to environmental changes throughout history but the molecular basis of this adaptation, and the constraints which govern the evolution of the stator proteins are unknown. Here we use CRISPR-mediated genome engineering to replace the native H+-powered stator genes of Escherichia coli with a compatible sodium-powered stator set from Vibrio alginolyticus and subsequently direct the evolution of the stators to revert to H+-powered motility. Evidence from whole genome sequencing indicates both flagellar- and non-flagellar-associated genes that are involved in longer-term adaptation to new power sources. Overall, transplanted Na+-powered stator genes can spontaneously incorporate novel mutations that allow H+-motility when environmental Na+ is lacking.

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The functional ClpXP protease of Chlamydia trachomatis requires distinct clpP genes from separate genetic loci

Scientific Reports ◽

10.1038/s41598-019-50505-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 9

Author(s):

Stefan Pan ◽

Imran T. Malik ◽

Dhana Thomy ◽

Beate Henrichfreise ◽

Peter Sass

Keyword(s):

Chlamydia Trachomatis ◽

Bacterial Species ◽

Human Pathogens ◽

Bacterial Physiology ◽

Sexually Transmitted ◽

Clp Proteases ◽

Obligate Intracellular Pathogen ◽

Antibacterial Target ◽

Insight Into

Abstract Clp proteases play a central role in bacterial physiology and, for some bacterial species, are even essential for survival. Also due to their conservation among bacteria including important human pathogens, Clp proteases have recently attracted considerable attention as antibiotic targets. Here, we functionally reconstituted and characterized the ClpXP protease of Chlamydia trachomatis (ctClpXP), an obligate intracellular pathogen and the causative agent of widespread sexually transmitted diseases in humans. Our in vitro data show that ctClpXP is formed by a hetero-tetradecameric proteolytic core, composed of two distinct homologs of ClpP (ctClpP1 and ctClpP2), that associates with the unfoldase ctClpX via ctClpP2 for regulated protein degradation. Antibiotics of the ADEP class interfere with protease functions by both preventing the interaction of ctClpX with ctClpP1P2 and activating the otherwise dormant proteolytic core for unregulated proteolysis. Thus, our results reveal molecular insight into ctClpXP function, validating this protease as an antibacterial target.

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Regulation of OmpA Translation and Shigella dysenteriae Virulence by an RNA Thermometer

Infection and Immunity ◽

10.1128/iai.00871-19 ◽

2019 ◽

Vol 88 (3) ◽

Cited By ~ 1

Author(s):

Erin R. Murphy ◽

Johanna Roßmanith ◽

Jacob Sieg ◽

Megan E. Fris ◽

Hebaallaha Hussein ◽

...

Keyword(s):

In Silico ◽

Bacterial Species ◽

Regulation Of Gene Expression ◽

Structure And Function ◽

Shigella Dysenteriae ◽

Content Type ◽

Bacterial Physiology ◽

Wide Range ◽

Rna Thermometer ◽

And Function

ABSTRACT RNA thermometers are cis-acting riboregulators that mediate the posttranscriptional regulation of gene expression in response to environmental temperature. Such regulation is conferred by temperature-responsive structural changes within the RNA thermometer that directly result in differential ribosomal binding to the regulated transcript. The significance of RNA thermometers in controlling bacterial physiology and pathogenesis is becoming increasingly clear. This study combines in silico, molecular genetics, and biochemical analyses to characterize both the structure and function of a newly identified RNA thermometer within the ompA transcript of Shigella dysenteriae. First identified by in silico structural predictions, genetic analyses have demonstrated that the ompA RNA thermometer is a functional riboregulator sufficient to confer posttranscriptional temperature-dependent regulation, with optimal expression observed at the host-associated temperature of 37°C. Structural studies and ribosomal binding analyses have revealed both increased exposure of the ribosomal binding site and increased ribosomal binding to the ompA transcript at permissive temperatures. The introduction of site-specific mutations predicted to alter the temperature responsiveness of the ompA RNA thermometer has predictable consequences for both the structure and function of the regulatory element. Finally, in vitro tissue culture-based analyses implicate the ompA RNA thermometer as a bona fide S. dysenteriae virulence factor in this bacterial pathogen. Given that ompA is highly conserved among Gram-negative pathogens, these studies not only provide insight into the significance of riboregulation in controlling Shigella virulence, but they also have the potential to facilitate further understanding of the physiology and/or pathogenesis of a wide range of bacterial species.

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Mechanisms by Which Small RNAs Affect Bacterial Activity

Journal of Dental Research ◽

10.1177/0022034519876898 ◽

2019 ◽

Vol 98 (12) ◽

pp. 1315-1323

Author(s):

L. Lei ◽

Y. Yang ◽

S. Wu ◽

X. Ma ◽

...

Keyword(s):

Stress Responses ◽

Small Rnas ◽

Environmental Changes ◽

Expression Profiles ◽

Bacterial Flora ◽

Oral Disease ◽

Bacterial Gene ◽

Bacterial Physiology ◽

Cellular Processes ◽

Regulatory Rnas

The oral cavity contains a distinct habitat that supports diverse bacterial flora. Recent observations have provided additional evidence that sRNAs are key regulators of bacterial physiology and pathogenesis. These sRNAs have been divided into 5 functional groups: cis-encoded RNAs, trans-encoded RNAs, RNA regulators of protein activity, bacterial CRISPR (clustered regularly interspaced short palindromic repeat) RNAs, and a novel category of miRNA-size small RNAs (msRNAs). In this review, we discuss a critical group of key commensal and opportunistic oral pathogens. In general, supragingival bacterial sRNAs function synergistically to fine-tune the regulation of cellular processes and stress responses in adaptation to environmental changes. Particularly in the cariogenic bacteria Streptococcus mutans, both the antisense vicR RNA and msRNA1657 can impede the metabolism of bacterial exopolysaccharides, prevent biofilm formation, and suppress its cariogenicity. In Enterococcus faecalis, selected sRNAs control the expression of proteins involved in diverse cellular processes and stress responses. In subgingival plaques, sRNAs from periodontal pathogens can function as novel bacterial signaling molecules that mediate bacterial-human interactions in periodontal homeostasis. In Porphyromonas gingivalis, the expression profiles of putative sRNA101 and sRNA42 were found to respond to hemin availability after hemin starvation. Regarding Aggregatibacter actinomycetemcomitans (previously Actinobacillus actinomycetemcomitans), a major periodontal pathogen associated with aggressive periodontitis, the predicted sRNAs interact with several virulence genes, including those encoding leukotoxin and cytolethal distending toxin. Furthermore, in clinical isolates, these associated RNAs could be explored not only as potential biomarkers for oral disease monitoring but also as alternative types of regulators for drug design. Thus, this emerging subspecialty of bacterial regulatory RNAs could reshape our understanding of bacterial gene regulation from their key roles of endogenous regulatory RNAs to their activities in pathologic processes.

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The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins

Open Biology ◽

10.1098/rsob.190223 ◽

2019 ◽

Vol 9 (12) ◽

pp. 190223 ◽

Cited By ~ 6

Author(s):

L. Qin ◽

A. M. Erkelens ◽

F. Ben Bdira ◽

R. T. Dame

Keyword(s):

Environmental Changes ◽

Bacterial Species ◽

Dna Duplexes ◽

New Members ◽

Bacterial Dna ◽

Architectural Proteins ◽

Bacterial Chromosomes ◽

Associated Proteins ◽

Chromatin Proteins ◽

Dna Binding Properties

Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns − phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.

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Improved performance of botia fish Chromobotia macracanthus with the utilization of blood clam shell in the recirculation system

Jurnal Akuakultur Indonesia ◽

10.19027/jai.19.2.160-170 ◽

2020 ◽

Vol 19 (2) ◽

pp. 160-170

Author(s):

Rani Ria Rizki ◽

Iis Diatin ◽

Tatag Budiardi ◽

Irzal Effendi

Keyword(s):

Water Quality ◽

Environmental Changes ◽

Ph Value ◽

Stocking Density ◽

Production Performance ◽

Randomized Design ◽

Fish Samples ◽

Recirculation System ◽

Blood Clam ◽

Improved Performance

ABSTRACT Intermediate and holding rearing of botia face several problems such as the limited land, water quality, and decreased growth. The application of a recirculation culture system using the blood clam filter is increased to water quality and expected to solve the problems. This study aimed to analyze the production performance of botia fish on intermediate and holding rearing in the recirculation system by utilizing blood clams as the filter. This study used a factorial completely randomized design with two factors; clam particle sizes (1 mm, 2 mm, and 3 mm) and dosages (1.4 g/L, 1.8 g/L, and 2.2 g/L). Every experiment was conducted in three replication. The aquarium used in this study was 40×40×60 cm3. The size of fish samples was 3.5 ± 0.5 cm with the stocking density (3 fish/L, each test aquarium). The recirculation system was applied seven days before the fish were stocked. Every 15 days, weight and length of fish were measured (for 60 days). The results of physical (temperature) and chemical (pH, dissolved oxygen, ammonia dan nitrite) water quality in the recirculation system using the blood clam filter showed good conditions for botia fish. The stress response of botia blood glucose and TKO fluctuates with environmental changes. Mineral water and fish produced by calcium, magnesium, and phosphorus increase until the end of maintenance. There is an interaction at TKH between particle size and the dose of blood shells, whereas, LMPW, LMPL, and RKP significantly different only the use of dose 2.2 g/L. Keywords: Clamshells, botia fish, pH value, minerals, recirculation. ABSTRAK Permasalahan pada proses penampungan ikan botia yaitu keterbatasan lahan, kualitas air yang buruk dan pertumbuhan ikan botia yang lambat. Penerapan sistem resirkulasi menggunakan cangkang darah dapat meningkatkan kualitas air dan kinerja produksi. Penelitian ini bertujuan menganalisis kinerja produksi budidaya ikan botia pada sistem resirkulasi dengan pemanfataan cangkang kerang darah sebagai bahan filter. Penelitian ini menggunakan rancangan acak lengkap faktorial dua faktor, yaitu ukuran partikel cangkang kerang darah (1 mm, 2 mm, dan 3 mm) dan dosis cangkang kerang darah (1.4g/L, 1.8g/L dan 2.2g/L). Setiap perlakuan dilakukan dengan tiga kali ulangan. Akuarium yang digunakan dalam penelitian berukuran 40×40×60 cm3. Ikan yang digunakan berukuran 3.5 ± 0.5 cm dengan padat tebar 3 ekor/L. Sistem resirkulasi dioperasikan selama tujuh hari sebelum ikan ditebar. Bobot dan panjang ikan diukur setiap 15 hari selama 60 hari pemeliharaan. Penelitian dalam sistem resirkulasi menggunakan cangkang kerang darah pada media filter menghasilkan kondisi kualitas air suhu, pH, oksigen terlarut, amonia dan nitrit air. Respons stres ikan berupa glukosa darah dan tingkat konsumsi oksigen (TKO) berfluktuasi seiring dengan perubahan lingkungan. Mineral air dan ikan yang dihasilkan meliputi kalsium, magnesium dan fosfos meningkat hingga akhir pemeliharaan. Parameter tingkat kelangsungan hidup (TKH) memiliki interaksi antara ukuran partikel dan dosis cangkang kerang darah, sedangkan untuk laju pertumbuhan bobot mutlak (LPMB), laju pertumbuhan panjang mutlak (LPMP) dan rasio konversi pakan (RKP) berbeda nyata dengan penggunaan dosis 2.2 g/L. Kata kunci: Cangkang kerang darah, ikan botia, pH, mineral, resirkulasi.

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Loss of O-linked protein glycosylation in Burkholderia cenocepacia impairs biofilm formation and siderophore production via alteration of quorum sensing regulation

10.1101/757575 ◽

2019 ◽

Author(s):

Cameron C. Oppy ◽

Leila Jebeli ◽

Miku Kuba ◽

Clare V. Oates ◽

Richard Strugnell ◽

...

Keyword(s):

Quorum Sensing ◽

Biofilm Formation ◽

Bacterial Species ◽

Protein Glycosylation ◽

Siderophore Production ◽

Burkholderia Cenocepacia ◽

Luciferase Reporter ◽

Direct Result ◽

Bacterial Physiology ◽

Virulence Attenuation

AbstractO-linked protein glycosylation is a conserved feature of the Burkholderia genus. For Burkholderia cenocepacia, the addition of the trisaccharide β-Gal-(1,3)-α-GalNAc-(1,3)-β-GalNAc to membrane exported proteins is required for virulence and resistance to environmental stress. However, the underlying causes of the defects observed in the absence of glycosylation are unclear. This study demonstrates that the global B. cenocepacia proteome undergoes dramatic changes consistent with alterations in global transcriptional regulation in the absence of glycosylation. Using luciferase reporter assays and DNA cross-linking analysis, we confirm the repression of the master quorum sensing regulon CepR/I in response to the loss of glycosylation, which leads to the abolition of biofilm formation, defects in siderophore production, and reduced virulence. The abundance of most of the known glycosylated proteins did not significantly change in the glycosylation-defective mutants except for BCAL1086 and BCAL2974, which were found in reduced amount, suggesting they could be degraded. However, the loss of these two proteins was not responsible for driving the proteomic alterations, as well as for reduced virulence and siderophore production. Together, our results show that loss of glycosylation in B. cenocepacia results in a global cell reprogramming via alteration of the CepR/I regulon, which cannot be explained by the abundance changes in known B. cenocepacia glycoproteins.IMPORTANCEProtein glycosylation is increasingly recognised as a common protein modification in bacterial species. Despite this commonality our understanding of the role of most glycosylation systems in bacterial physiology and pathogenesis is incomplete. In this work, we investigated the effect of the disruption of O-linked glycosylation in the opportunistic pathogen Burkholderia cenocepacia using a combination of proteomic, molecular and phenotypic assays. We find that in contrast to recent findings on the N-linked glycosylation systems of Campylobacter jejuni, O-linked glycosylation does not appear to play a role in proteome stabilization of most glycoproteins. Our results reveal that virulence attenuation observed within glycosylation-null B. cenocepacia strains are consistent with alteration of the master virulence regulator CepR. The repression of CepR transcription and its associated phenotypes support a model in which the virulence defects observed in glycosylation-null strains are at least in part due to transcriptional alteration and not the direct result of the loss of glycosylation per-se. This research unravels the pleotropic effects of O-linked glycosylation in B. cenocepacia, demonstrating that its loss does not simply affect the stability of the glycoproteome, but also interferes with transcription and the broader proteome.

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Retarded swarming motility in Bacillus subtilis NRS-762 and Pseudomonas aeruginosa PRD-10

10.7287/peerj.preprints.26914 ◽

2018 ◽

Author(s):

Wenfa Ng

Keyword(s):

Pseudomonas Aeruginosa ◽

Bacillus Subtilis ◽

Bacterial Species ◽

Nutritional Stress ◽

Cellular Level ◽

Bacterial Cells ◽

Loss Of Function ◽

Swarming Motility ◽

Bacteria Growth ◽

Solid Media

Coping with nutritional stress is essential for cell survival, of which many strategies at the cellular level lend support for ensuring the survival of the population at a particular habitat. One postulated mechanism is swarming motility in bacterial cells, where, upon depletion of nutrients at a locale, cells would coordinate their movement, synthesize more flagella, and secrete lubricants for moving rapidly across surfaces in search for food. Known to engage in swarming motility, Bacillus subtilis and Pseudomonas aeruginosa are two common bacterial species with versatile metabolism that use the motility mode to colonize new habitats with more favourable environmental and nutritional conditions. However, experimental observations of bacteria growth on a variety of agar media revealed that B. subtilis NRS-762 (ATCC 8473) and P. aeruginosa PRD-10 (ATCC 15442) exhibited retarded swarming motility upon entry into stationary phase on solid media. Specifically, B. subtilis NRS-762 colonies exhibited round, wrinkled morphologies compared to complex filamented swarming patterns common in strains able to engage in swarming motility. On the other hand, P. aeruginosa PRD-10 colonies were round, mucoid, and expanded outwards from the colony centre without extending filaments from the centre; thereby, indicating retarded swarming motility. Thus, impaired cellular machinery for swarming motility or mutated and deleted genes likely account for observed retarded swarming motility in B. subtilis NRS-762 and P. aeruginosa PRD-10. More importantly, observations of small filaments extending radially from an expanded colony of P. aeruginosa PRD-10 grown on minimal salts medium supplemented with yeast extract highlighted possible loss of function of effector molecules that transmit cellular decision at swarming motility into movement, while sensory mechanisms feeding into the motility mechanism remained intact. More broadly, observations of impaired swarming motility in B. subtilis NRS-762 and P. aeruginosa PRD-10 in two species otherwise endowed with the motility mode highlighted that additional triggers for swarming motility are likely present, and the motility mode may have been evolutionary selected for other functions in addition to foraging for food in times of nutritional stress.

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Mitigating Milk-Associated Bacteria through Inducing Zinc Ions Antibiofilm Activity

Foods ◽

10.3390/foods9081094 ◽

2020 ◽

Vol 9 (8) ◽

pp. 1094

Author(s):

Carmel Hutchings ◽

Satish Kumar Rajasekharan ◽

Ram Reifen ◽

Moshe Shemesh

Keyword(s):

Heat Treatment ◽

Bacterial Species ◽

Dairy Industry ◽

Antimicrobial Effect ◽

Pcr Analysis ◽

Antibiofilm Activity ◽

Bacterial Cells ◽

Production Environment ◽

Bacterial Physiology ◽

Microscopic Evaluation

Dairy products are a sector heavily impacted by food loss, often due to bacterial contaminations. A major source of contamination is associated with the formation of biofilms by bacterial species adopted to proliferate in milk production environment and onto the surfaces of milk processing equipment. Bacterial cells within the biofilm are characterized by increased resistance to unfavorable environmental conditions and antimicrobial agents. Members of the Bacillus genus are the most commonly found spoilage microorganisms in the dairy environment. It appears that physiological behavior of these species is somehow depended on the availability of bivalent cations in the environment. One of the important cations that may affect the bacterial physiology as well as survivability are Zn2+ ions. Thus, the aim of this study was to examine the antimicrobial effect of Zn2+ ions, intending to elucidate the potential of a zinc-based antibacterial treatment suitable for the dairy industry. The antimicrobial effect of different doses of ZnCl2 was assessed microscopically. In addition, expression of biofilm related genes was evaluated using RT-PCR. Analysis of survival rates following heat treatment was conducted in order to exemplify a possible applicative use of Zn2+ ions. Addition of zinc efficiently inhibited biofilm formation by B. subtilis and further disrupted the biofilm bundles. Expression of matrix related genes was found to be notably downregulated. Microscopic evaluation showed that cell elongation was withheld when cells were grown in the presence of zinc. Finally, B. cereus and B. subtilis cells were more susceptible to heat treatment after being exposed to Zn2+ ions. It is believed that an anti-biofilm activity, expressed in downregulation of genes involved in construction of the extracellular matrix, would account for the higher sensitivity of bacteria during heat pasteurization. Consequently, we suggest that Zn2+ ions can be of used as an effective antimicrobial treatment in various applications in the dairy industry, targeting both biofilms and vegetative bacterial cells.

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