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Mattingly HH, Kamino K, Ong J, Kottou R, Emonet T, Machta BB. E. coli do not count single molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602750. [PMID: 39026702 PMCID: PMC11257612 DOI: 10.1101/2024.07.09.602750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Organisms must perform sensory-motor behaviors to survive. What bounds or constraints limit behavioral performance? Previously, we found that the gradient-climbing speed of a chemotaxing Escherichia coli is near a bound set by the limited information they acquire from their chemical environments (1). Here we ask what limits their sensory accuracy. Past theoretical analyses have shown that the stochasticity of single molecule arrivals sets a fundamental limit on the precision of chemical sensing (2). Although it has been argued that bacteria approach this limit, direct evidence is lacking. Here, using information theory and quantitative experiments, we find that E. coli's chemosensing is not limited by the physics of particle counting. First, we derive the physical limit on the behaviorally-relevant information that any sensor can get about a changing chemical concentration, assuming that every molecule arriving at the sensor is recorded. Then, we derive and measure how much information E. coli's signaling pathway encodes during chemotaxis. We find that E. coli encode two orders of magnitude less information than an ideal sensor limited only by shot noise in particle arrivals. These results strongly suggest that constraints other than particle arrival noise limit E. coli's sensory fidelity.
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Affiliation(s)
| | | | - Jude Ong
- Molecular, Cellular, and Developmental Biology, Yale University
| | - Rafaela Kottou
- Molecular, Cellular, and Developmental Biology, Yale University
| | - Thierry Emonet
- Molecular, Cellular, and Developmental Biology, Yale University
- Physics, Yale University
- QBio Institute, Yale University
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2
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Schumacher K, Braun D, Kleigrewe K, Jung K. Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli. Microbiol Spectr 2024; 12:e0054424. [PMID: 38651876 PMCID: PMC11237407 DOI: 10.1128/spectrum.00544-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g., in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e., they are induced under mild acid stress but not under severe acid stress. However, it was not known to what extent fine-tuned expression of motility genes is related to fitness and the ability to survive periods of acid shock. In this study, we demonstrate that the expression of FlhDC, the master regulator of flagellation, is inversely correlated with the acid shock survival of E. coli. We encountered this phenomenon when analyzing mutants from the Keio collection, in which the expression of flhDC was altered by an insertion sequence element. These results suggest a fitness trade-off between acid tolerance and motility.IMPORTANCEEscherichia coli is extremely acid-resistant, which is crucial for survival in the gastrointestinal tract of vertebrates. Recently, we systematically studied the response of E. coli to mild and severe acidic conditions using Ribo-Seq and RNA-Seq. We found that motility genes are induced at pH 5.8 but not at pH 4.4, indicating stress-dependent synthesis of flagellar components. In this study, we demonstrate that motility-activating mutations upstream of flhDC, encoding the master regulator of flagella genes, reduce the ability of E. coli to survive periods of acid shock. Furthermore, we show an inverse correlation between motility and acid survival using a chromosomal isopropyl β-D-thio-galactopyranoside (IPTG)-inducible flhDC promoter and by sampling differentially motile subpopulations from swim agar plates. These results reveal a previously undiscovered trade-off between motility and acid tolerance and suggest a differentiation of E. coli into motile and acid-tolerant subpopulations, driven by the integration of insertion sequence elements.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Djanna Braun
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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Kopkowski PW, Zhang Z, Saier MH. The effect of DNA-binding proteins on insertion sequence element transposition upstream of the bgl operon in Escherichia coli. Front Microbiol 2024; 15:1388522. [PMID: 38666260 PMCID: PMC11043490 DOI: 10.3389/fmicb.2024.1388522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The bglGFB operon in Escherichia coli K-12 strain BW25113, encoding the proteins necessary for the uptake and metabolism of β-glucosides, is normally not expressed. Insertion of either IS1 or IS5 upstream of the bgl promoter activates expression of the operon only when the cell is starving in the presence of a β-glucoside, drastically increasing transcription and allowing the cell to survive and grow using this carbon source. Details surrounding the exact mechanism and regulation of the IS insertional event remain unclear. In this work, the role of several DNA-binding proteins in how they affect the rate of insertion upstream of bgl are examined via mutation assays and protocols measuring transcription. Both Crp and IHF exert a positive effect on insertional Bgl+ mutations when present, active, and functional in the cell. Our results characterize IHF's effect in conjunction with other mutations, show that IHF's effect on IS insertion into bgl also affects other operons, and indicate that it may exert its effect by binding to and altering the DNA conformation of IS1 and IS5 in their native locations, rather than by directly influencing transposase gene expression. In contrast, the cAMP-CRP complex acts directly upon the bgl operon by binding upstream of the promoter, presumably altering local DNA into a conformation that enhances IS insertion.
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Affiliation(s)
| | - Zhongge Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Milton H. Saier
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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Pradhan P, Taviti AC, Beuria TK. The bacterial division protein MinDE has an independent function in flagellation. J Biol Chem 2024; 300:107117. [PMID: 38403244 PMCID: PMC10963238 DOI: 10.1016/j.jbc.2024.107117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024] Open
Abstract
Before preparing for division, bacteria stop their motility. During the exponential growth phase in Escherichia coli, when the rate of bacterial division is highest, the expression of flagellar genes is repressed and bacterial adhesion is enhanced. Hence, it is evident that cell division and motility in bacteria are linked; however, the specific molecular mechanism by which these two processes are linked is not known. While observing E. coli, we found that compared to the WT, the E. coli (Δmin) cells show higher motility and flagellation. We demonstrated that the higher motility was due to the absence of the Min system and can be restored to normal in the presence of Min proteins, where Min system negatively regulates flagella formation. The Min system in E. coli is widely studied for its role in the inhibition of polar Z-ring formation through its pole-to-pole oscillation. However, its role in bacterial motility is not explored. MinD homologs, FlhG and FleN, are known to control flagellar expression through their interaction with FlrA and FleQ, respectively. AtoC, a part of the two-component system AtoSC complex, is homologous to FlrA/FleQ, and the complex is involved in E. coli flagellation via its interaction with the fliA promoter. We have shown that MinD interacts directly with the AtoS of AtoSC complex and controls the fliA expression. Our findings suggest that the Min system acts as a link between cell division and motility in E. coli.
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Affiliation(s)
- Pinkilata Pradhan
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India; Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Ashoka Chary Taviti
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Tushar Kant Beuria
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India.
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Buchmann D, Schwabe M, Weiss R, Kuss AW, Schaufler K, Schlüter R, Rödiger S, Guenther S, Schultze N. Natural phenolic compounds as biofilm inhibitors of multidrug-resistant Escherichia coli - the role of similar biological processes despite structural diversity. Front Microbiol 2023; 14:1232039. [PMID: 37731930 PMCID: PMC10507321 DOI: 10.3389/fmicb.2023.1232039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 09/22/2023] Open
Abstract
Multidrug-resistant gram-negative pathogens such as Escherichia coli have become increasingly difficult to treat and therefore alternative treatment options are needed. Targeting virulence factors like biofilm formation could be one such option. Inhibition of biofilm-related structures like curli and cellulose formation in E. coli has been shown for different phenolic natural compounds like epigallocatechin gallate. This study demonstrates this effect for other structurally unrelated phenolics, namely octyl gallate, scutellarein and wedelolactone. To verify whether these structurally different compounds influence identical pathways of biofilm formation in E. coli a broad comparative RNA-sequencing approach was chosen with additional RT-qPCR to gain initial insights into the pathways affected at the transcriptomic level. Bioinformatical analysis of the RNA-Seq data was performed using DESeq2, BioCyc and KEGG Mapper. The comparative bioinformatics analysis on the pathways revealed that, irrespective of their structure, all compounds mainly influenced similar biological processes. These pathways included bacterial motility, chemotaxis, biofilm formation as well as metabolic processes like arginine biosynthesis and tricarboxylic acid cycle. Overall, this work provides the first insights into the potential mechanisms of action of novel phenolic biofilm inhibitors and highlights the complex regulatory processes of biofilm formation in E. coli.
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Affiliation(s)
- David Buchmann
- Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Michael Schwabe
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Romano Weiss
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Andreas W. Kuss
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Sebastian Guenther
- Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Nadin Schultze
- Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
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Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes. Appl Environ Microbiol 2023; 89:e0172722. [PMID: 36695629 PMCID: PMC9972950 DOI: 10.1128/aem.01727-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This study investigates migration phenotypes of 265 Escherichia coli soil isolates from the Buffalo River basin in Minnesota, USA. Migration rates on semisolid tryptone swim plates ranged from nonmotile to 190% of the migration rate of a highly motile E. coli K-12 strain. The nonmotile isolate, LGE0550, had mutations in flagellar and chemotaxis genes, including two IS3 elements in the flagellin-encoding gene fliC. A genome-wide association study (GWAS), associating the migration rates with genetic variants in specific genes, yielded two metabolic variants (rygD-serA and metR-metE) with previous implications in chemotaxis. As a novel way of confirming GWAS results, we used minimal medium swim plates to confirm the associations. Other variants in metabolic genes and genes that are associated with biofilm were positively or negatively associated with migration rates. A determination of growth phenotypes on Biolog EcoPlates yielded differential growth for the 10 tested isolates on d-malic acid, putrescine, and d-xylose, all of which are important in the soil environment. IMPORTANCE E. coli is a Gram-negative, facultative anaerobic bacterium whose life cycle includes extra host environments in addition to human, animal, and plant hosts. The bacterium has the genomic capability of being motile. In this context, the significance of this study is severalfold: (i) the great diversity of migration phenotypes that we observed within our isolate collection supports previous (G. NandaKafle, A. A. Christie, S. Vilain, and V. S. Brözel, Front Microbiol 9:762, 2018, https://doi.org/10.3389/fmicb.2018.00762; Y. Somorin, F. Abram, F. Brennan, and C. O'Byrne, Appl Environ Microbiol 82:4628-4640, 2016, https://doi.org/10.1128/AEM.01175-16) ideas of soil promoting phenotypic heterogeneity, (ii) such heterogeneity may facilitate bacterial growth in the many different soil niches, and (iii) such heterogeneity may enable the bacteria to interact with human, animal, and plant hosts.
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Browning DF, Hobman JL, Busby SJW. Laboratory strains of Escherichia coli K-12: things are seldom what they seem. Microb Genom 2023; 9:mgen000922. [PMID: 36745549 PMCID: PMC9997739 DOI: 10.1099/mgen.0.000922] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli K-12 was originally isolated 100 years ago and since then it has become an invaluable model organism and a cornerstone of molecular biology research. However, despite its pedigree, since its initial isolation E. coli K-12 has been repeatedly cultured, passaged and mutagenized, resulting in an organism that carries many genetic changes. To understand more about this important model organism, we have sequenced the genomes of two ancestral K-12 strains, WG1 and EMG2, considered to be the progenitors of many key laboratory strains. Our analysis confirms that these strains still carry genetic elements such as bacteriophage lambda (λ) and the F plasmid, but also indicates that they have undergone extensive laboratory-based evolution. Thus, scrutinizing the genomes of ancestral E. coli K-12 strains leads us to examine whether E. coli K-12 is a sufficiently robust model organism for 21st century microbiology.
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Affiliation(s)
- Douglas F Browning
- School of Biosciences, College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
| | - Stephen J W Busby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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Krutyakov YA, Khina AG. Bacterial Resistance to Nanosilver: Molecular Mechanisms and Possible Ways to Overcome them. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822050106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Honda T, Cremer J, Mancini L, Zhang Z, Pilizota T, Hwa T. Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions. Proc Natl Acad Sci U S A 2022; 119:e2110342119. [PMID: 36067284 PMCID: PMC9478672 DOI: 10.1073/pnas.2110342119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
To swim and navigate, motile bacteria synthesize a complex motility machinery involving flagella, motors, and a sensory system. A myriad of studies has elucidated the molecular processes involved, but less is known about the coordination of motility expression with cellular physiology: In Escherichia coli, motility genes are strongly up-regulated in nutrient-poor conditions compared to nutrient-replete conditions; yet a quantitative link to cellular motility has not been developed. Here, we systematically investigated gene expression, swimming behavior, cell growth, and available proteomics data across a broad spectrum of exponential growth conditions. Our results suggest that cells up-regulate the expression of motility genes at slow growth to compensate for reduction in cell size, such that the number of flagella per cell is maintained across conditions. The observed four or five flagella per cell is the minimum number needed to keep the majority of cells motile. This simple regulatory objective allows E. coli cells to remain motile across a broad range of growth conditions, while keeping the biosynthetic and energetic demands to establish and drive the motility machinery at the minimum needed. Given the strong reduction in flagella synthesis resulting from cell size increases at fast growth, our findings also provide a different physiological perspective on bacterial cell size control: A larger cell size at fast growth is an efficient strategy to increase the allocation of cellular resources to the synthesis of those proteins required for biomass synthesis and growth, while maintaining processes such as motility that are only needed on a per-cell basis.
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Affiliation(s)
- Tomoya Honda
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
- US Department of Energy, Joint Genome Institute, Berkeley, CA 94720
| | - Jonas Cremer
- Department of Physics, University of California at San Diego, La Jolla, CA 92093
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Leonardo Mancini
- School of Biological Sciences, Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, United Kingdom
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Zhongge Zhang
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
| | - Teuta Pilizota
- School of Biological Sciences, Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, United Kingdom
| | - Terence Hwa
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093
- Department of Physics, University of California at San Diego, La Jolla, CA 92093
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10
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Rosłoń IE, Japaridze A, Steeneken PG, Dekker C, Alijani F. Probing nanomotion of single bacteria with graphene drums. NATURE NANOTECHNOLOGY 2022; 17:637-642. [PMID: 35437320 DOI: 10.1038/s41565-022-01111-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Motion is a key characteristic of every form of life1. Even at the microscale, it has been reported that colonies of bacteria can generate nanomotion on mechanical cantilevers2, but the origin of these nanoscale vibrations has remained unresolved3,4. Here, we present a new technique using drums made of ultrathin bilayer graphene, where the nanomotion of single bacteria can be measured in its aqueous growth environment. A single Escherichia coli cell is found to generate random oscillations with amplitudes of up to 60 nm, exerting forces of up to 6 nN to its environment. Using mutant strains that differ by single gene deletions that affect motility, we are able to pinpoint the bacterial flagella as the main source of nanomotion. By real-time tracing of changes in nanomotion on administering antibiotics, we demonstrate that graphene drums can perform antibiotic susceptibility testing with single-cell sensitivity. These findings deepen our understanding of processes underlying cellular dynamics, and pave the way towards high-throughput and parallelized rapid screening of the effectiveness of antibiotics in bacterial infections with graphene devices.
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Affiliation(s)
- Irek E Rosłoń
- Delft University of Technology, Delft, the Netherlands
| | | | | | - Cees Dekker
- Delft University of Technology, Delft, the Netherlands
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Abstract
Ecotypic diversification and its associated cooperative behaviors are frequently observed in natural microbial populations whose access to resources is often sporadic. However, the extent to which fluctuations in resource availability influence the emergence of cooperative ecotypes is not fully understood. To determine how exposure to repeated resource limitation affects the establishment and long-term maintenance of ecotypes in a structured environment, we followed 32 populations of Escherichia coli evolving to either 1-day or 10-day feast/famine cycles for 900 days. Population-level analysis revealed that compared to populations evolving to 1-day cycles, 10-day populations evolved increased biofilm density, higher parallelism in mutational targets, and increased mutation rates. As previous investigations of evolution in structured environments have identified biofilm formation as the earliest observable phenotype associated with diversification of ecotypes, we revived cultures midway through the evolutionary process and conducted additional genomic, transcriptional, and phenotypic analyses of clones isolated from these evolving populations. We found not only that 10-day feast/famine cycles support multiple ecotypes but also that these ecotypes exhibit cooperative behavior. Consistent with the black queen hypothesis, or evolution of cooperation by gene loss, transcriptomic evidence suggests the evolution of bidirectional cross-feeding behaviors based on essential resources. These results provide insight into how analogous cooperative relationships may emerge in natural microbial communities. IMPORTANCE Despite regular feast and famine conditions representing an environmental pressure that is commonly encountered by microbial communities, the evolutionary outcomes of repeated cycles of feast and famine have been less studied. By experimentally evolving initially isogenic Escherichia coli populations to 10-day feast/famine cycles, we observed rapid diversification into ecotypes with evidence of bidirectional cross-feeding on costly resources and frequency-dependent fitness. Although unidirectional cross-feeding has been repeatedly observed to evolve in laboratory culture, most investigations of bidirectional cooperative behaviors in microbial populations have been conducted in engineered communities. This work demonstrates the de novo evolution of black queen relationships in a microbial population originating from a single ancestor, providing a model for investigation of the eco-evolutionary processes leading to mutualistic cooperation.
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Zhang Z, Zhou K, Tran D, Saier M. Insertion Sequence (IS) Element-Mediated Activating Mutations of the Cryptic Aromatic β-Glucoside Utilization ( BglGFB) Operon Are Promoted by the Anti-Terminator Protein (BglG) in Escherichia coli. Int J Mol Sci 2022; 23:ijms23031505. [PMID: 35163427 PMCID: PMC8836124 DOI: 10.3390/ijms23031505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 01/24/2023] Open
Abstract
The cryptic β-glucoside GFB (bglGFB) operon in Escherichia coli (E. coli) can be activated by mutations arising under starvation conditions in the presence of an aromatic β-glucoside. This may involve the insertion of an insertion sequence (IS) element into a "stress-induced DNA duplex destabilization" (SIDD) region upstream of the operon promoter, although other types of mutations can also activate the bgl operon. Here, we show that increased expression of the bglG gene, encoding a well-characterized transcriptional antiterminator, dramatically increases the frequency of both IS-mediated and IS-independent Bgl+ mutations occurring on salicin- and arbutin-containing agar plates. Both mutation rates increased with increasing levels of bglG expression but IS-mediated mutations were more prevalent at lower BglG levels. Mutations depended on the presence of both BglG and an aromatic β-glucoside, and bglG expression did not influence IS insertion in other IS-activated operons tested. The N-terminal mRNA-binding domain of BglG was essential for mutational activation, and alteration of BglG's binding site in the mRNA nearly abolished Bgl+ mutant appearances. Increased bglG expression promoted residual bgl operon expression in parallel with the increases in mutation rates. Possible mechanisms are proposed explaining how BglG enhances the frequencies of bgl operon activating mutations.
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A New Sugar for an Old Phage: a c-di-GMP-Dependent Polysaccharide Pathway Sensitizes Escherichia coli for Bacteriophage Infection. mBio 2021; 12:e0324621. [PMID: 34903045 PMCID: PMC8669472 DOI: 10.1128/mbio.03246-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Bacteriophages are ubiquitous parasites of bacteria and major drivers of bacterial ecology and evolution. Despite an ever-growing interest in their biotechnological and therapeutic applications, detailed knowledge of the molecular mechanisms underlying phage-host interactions remains scarce. Here, we show that bacteriophage N4 exploits a novel surface glycan (NGR) as a receptor to infect its host Escherichia coli. We demonstrate that this process is regulated by the second messenger c-di-GMP and that N4 infection is specifically stimulated by the diguanylate cyclase DgcJ, while the phosphodiesterase PdeL effectively protects E. coli from N4-mediated killing. PdeL-mediated protection requires its catalytic activity to reduce c-di-GMP and includes a secondary role as a transcriptional repressor. We demonstrate that PdeL binds to and represses the promoter of the wec operon, which encodes components of the enterobacterial common antigen (ECA) exopolysaccharide pathway. However, only the acetylglucosamine epimerase WecB but none of the other ECA components is required for N4 infection. Based on this, we postulate that NGR is an N-acetylmannosamine-based carbohydrate polymer that is produced and exported to the cell surface of E. coli in a c-di-GMP-dependent manner, where it serves as a receptor for N4. This novel carbohydrate pathway is conserved in E. coli and other bacterial pathogens, serves as the primary receptor for various bacteriophages, and is induced at elevated temperature and by specific amino acid-based nutrients. These studies provide an entry point into understanding how bacteria use specific regulatory mechanisms to balance costs and benefits of highly conserved surface structures.
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Li B, Hou C, Ju X, Feng Y, Ye ZQ, Xiao Y, Gu M, Fu C, Wei C, You C. Gain of Spontaneous clpX Mutations Boosting Motility via Adaption to Environments in Escherichia coli. Front Bioeng Biotechnol 2021; 9:772397. [PMID: 34900963 PMCID: PMC8652233 DOI: 10.3389/fbioe.2021.772397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022] Open
Abstract
Motility is finely regulated and is crucial to bacterial processes including colonization and biofilm formation. There is a trade-off between motility and growth in bacteria with molecular mechanisms not fully understood. Hypermotile Escherichia coli could be isolated by evolving non-motile cells on soft agar plates. Most of the isolates carried mutations located upstream of the flhDC promoter region, which upregulate the transcriptional expression of the master regulator of the flagellum biosynthesis, FlhDC. Here, we identified that spontaneous mutations in clpX boosted the motility of E. coli largely, inducing several folds of changes in swimming speed. Among the mutations identified, we further elucidated the molecular mechanism underlying the ClpXV78F mutation on the regulation of E. coli motility. We found that the V78F mutation affected ATP binding to ClpX, resulting in the inability of the mutated ClpXP protease to degrade FlhD as indicated by both structure modeling and in vitro protein degradation assays. Moreover, our proteomic data indicated that the ClpXV78F mutation elevated the stability of known ClpXP targets to various degrees with FlhD as one of the most affected. In addition, the specific tag at the C-terminus of FlhD being recognized for ClpXP degradation was identified. Finally, our transcriptome data characterized that the enhanced expression of the motility genes in the ClpXV78F mutations was intrinsically accompanied by the reduced expression of stress resistance genes relating to the reduced fitness of the hypermotile strains. A similar pattern was observed for previously isolated hypermotile E. coli strains showing high expression of flhDC at the transcriptional level. Hence, clpX appears to be a hot locus comparable to the upstream of the flhDC promoter region evolved to boost bacterial motility, and our finding provides insight into the reduced fitness of the hypermotile bacteria.
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Affiliation(s)
- Bingyu Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China.,Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chaofan Hou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
| | - Xian Ju
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
| | - Yong Feng
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
| | - Zhi-Qiang Ye
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yunzhu Xiao
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
| | - Mingyao Gu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen, China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chaoliang Wei
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen, China
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University, Shenzhen, China
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15
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Mattingly HH, Kamino K, Machta BB, Emonet T. Escherichia coli chemotaxis is information limited. NATURE PHYSICS 2021; 17:1426-1431. [PMID: 35035514 PMCID: PMC8758097 DOI: 10.1038/s41567-021-01380-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/10/2021] [Indexed: 05/08/2023]
Abstract
Organisms acquire and use information from their environment to guide their behaviour. However, it is unclear whether this information quantitatively limits their behavioural performance. Here, we relate information to the ability of Escherichia coli to navigate up chemical gradients, the behaviour known as chemotaxis. First, we derive a theoretical limit on the speed with which cells climb gradients, given the rate at which they acquire information. Next, we measure cells' gradient-climbing speeds and the rate of information acquisition by their chemotaxis signaling pathway. We find that E. coli make behavioural decisions with much less than the one bit required to determine whether they are swimming up-gradient. Some of this information is irrelevant to gradient climbing, and some is lost in communication to behaviour. Despite these limitations, E. coli climb gradients at speeds within a factor of two of the theoretical bound. Thus, information can limit the performance of an organism, and sensory-motor pathways may have evolved to efficiently use information acquired from the environment.
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Affiliation(s)
- H H Mattingly
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - K Kamino
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - B B Machta
- Department of Physics, Yale University
- Systems Biology Institute, West Campus, Yale University
| | - T Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
- Department of Physics, Yale University
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16
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Stabryla LM, Johnston KA, Diemler NA, Cooper VS, Millstone JE, Haig SJ, Gilbertson LM. Role of bacterial motility in differential resistance mechanisms of silver nanoparticles and silver ions. NATURE NANOTECHNOLOGY 2021; 16:996-1003. [PMID: 34155383 DOI: 10.1038/s41565-021-00929-w] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 05/14/2021] [Indexed: 05/27/2023]
Abstract
Unlike conventional antimicrobials, the study of bacterial resistance to silver nanoparticles (AgNPs) remains in its infancy and the mechanism(s) through which it evolves are limited and inconclusive. The central question remains whether bacterial resistance is driven by the AgNPs, released Ag(I) ions or a combination of these and other factors. Here, we show a specific resistance in an Escherichia coli K-12 MG1655 strain to subinhibitory concentrations of AgNPs, and not Ag(I) ions, as indicated by a statistically significant greater-than-twofold increase in the minimum inhibitory concentration occurring after eight repeated passages that was maintained after the AgNPs were removed and reintroduced. Whole-population genome sequencing identified a cusS mutation associated with the heritable resistance that possibly increased silver ion efflux. Finally, we rule out the effect of particle aggregation on resistance and suggest that the mechanism of resistance may be enhanced or mediated by flagellum-based motility.
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Affiliation(s)
- Lisa M Stabryla
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
| | | | - Nathan A Diemler
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jill E Millstone
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah-Jane Haig
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leanne M Gilbertson
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
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17
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Responsive core-shell DNA particles trigger lipid-membrane disruption and bacteria entrapment. Nat Commun 2021; 12:4743. [PMID: 34362911 PMCID: PMC8346484 DOI: 10.1038/s41467-021-24989-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
Biology has evolved a variety of agents capable of permeabilizing and disrupting lipid membranes, from amyloid aggregates, to antimicrobial peptides, to venom compounds. While often associated with disease or toxicity, these agents are also central to many biosensing and therapeutic technologies. Here, we introduce a class of synthetic, DNA-based particles capable of disrupting lipid membranes. The particles have finely programmable size, and self-assemble from all-DNA and cholesterol-DNA nanostructures, the latter forming a membrane-adhesive core and the former a protective hydrophilic corona. We show that the corona can be selectively displaced with a molecular cue, exposing the 'sticky' core. Unprotected particles adhere to synthetic lipid vesicles, which in turn enhances membrane permeability and leads to vesicle collapse. Furthermore, particle-particle coalescence leads to the formation of gel-like DNA aggregates that envelop surviving vesicles. This response is reminiscent of pathogen immobilisation through immune cells secretion of DNA networks, as we demonstrate by trapping E. coli bacteria.
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18
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The Nutrient and Energy Pathway Requirements for Surface Motility of Nonpathogenic and Uropathogenic Escherichia coli. J Bacteriol 2021; 203:JB.00467-20. [PMID: 33782053 PMCID: PMC8117529 DOI: 10.1128/jb.00467-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Uropathogenic E. coli (UPEC) is the causative pathogen for most uncomplicated urinary tract infections. Motility is likely to contribute to these infections, and E. coli possesses flagella-dependent swimming motility, flagella-dependent surface motility (often called swarming), and the recently observed pili-dependent surface motility. Surface motility has not been extensively studied, but for the strains that have been tested nonpathogenic E. coli (NPEC) lab strains use pili, NPEC hypermotile derivatives of these lab strains use flagella, and UPEC strains use flagella. Using a representative of these three types of strains, we showed differences in the nutritional and pathway requirements for surface motility with respect to the glucose concentration, the glycolytic pathway utilized, acetogenesis, and the TCA cycle. In addition, glucose controlled flagella synthesis for the NPEC strain, but not for the hypermotile NPEC variant or the UPEC strain. The requirements for surface motility are likely to reflect major metabolic differences between strains for the pathways and regulation of energy metabolism.IMPORTANCEUrinary tract infections (UTIs) are one of the most common bacterial infections and are an increasing burden on the healthcare system because of recurrence and antibiotic resistance (1, 2). The most common uropathogen is E. coli (3, 4), which is responsible for about 80-90% of community acquired UTIs and 40-50% of nosocomial acquired UTIs (2). Virulence requires both pili and flagella, and either appendage can contribute to surface motility, although surface motility of uropathogenic E. coli has not been examined. We found different appendage, nutrient and pathway requirements for surface motility of a nonpathogenic E. coli lab strain and a uropathogenic E. coli We propose that these differences are the result of differences in the pathways and regulation of energy metabolism.
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19
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Leyn SA, Zlamal JE, Kurnasov OV, Li X, Elane M, Myjak L, Godzik M, de Crecy A, Garcia-Alcalde F, Ebeling M, Osterman AL. Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance. Microb Genom 2021; 7. [PMID: 33945454 PMCID: PMC8209735 DOI: 10.1099/mgen.0.000553] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding the dynamics and mechanisms of acquired drug resistance across major classes of antibiotics and bacterial pathogens is of critical importance for the optimization of current anti-infective therapies and the development of novel ones. To systematically address this challenge, we developed a workflow combining experimental evolution in a morbidostat continuous culturing device with deep genomic sequencing of population samples collected in time series. This approach was applied to the experimental evolution of six populations of Escherichia coli BW25113 towards acquiring resistance to triclosan (TCS), an antibacterial agent in various consumer products. This study revealed the rapid emergence and expansion (up to 100% in each culture within 4 days) of missense mutations in the fabI gene, encoding enoyl-acyl carrier protein reductase, the known TCS molecular target. A follow-up analysis of isolated clones showed that distinct amino acid substitutions increased the drug IC90 in a 3-16-fold range, reflecting their proximity to the TCS-binding site. In contrast to other antibiotics, efflux-upregulating mutations occurred only rarely and with low abundance. Mutations in several other genes were detected at an earlier stage of evolution. Most notably, three distinct amino acid substitutions were mapped in the C-terminal periplasmic domain of CadC protein, an acid stress-responsive transcriptional regulator. While these mutations do not confer robust TCS resistance, they appear to play a certain, yet unknown, role in adaptation to relatively low drug pressure. Overall, the observed evolutionary trajectories suggest that the FabI enzyme is the sole target of TCS (at least up to the ~50 µm level), and amino acid substitutions in the TCS-binding site represent the main mechanism of robust TCS resistance in E. coli. This model study illustrates the potential utility of the established morbidostat-based approach for uncovering resistance mechanisms and target identification for novel drug candidates with yet unknown mechanisms of action.
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Affiliation(s)
- Semen A Leyn
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jaime E Zlamal
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Oleg V Kurnasov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Xiaoqing Li
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Marinela Elane
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lourdes Myjak
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Mikolaj Godzik
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Fernando Garcia-Alcalde
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center, Basel, Switzerland
| | - Martin Ebeling
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Basel, Switzerland
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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20
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Ziegler M, Zieringer J, Takors R. Transcriptional profiling of the stringent response mutant strain E. coli SR reveals enhanced robustness to large-scale conditions. Microb Biotechnol 2021; 14:993-1010. [PMID: 33369128 PMCID: PMC8085953 DOI: 10.1111/1751-7915.13738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/05/2022] Open
Abstract
In large-scale fed-batch production processes, microbes are exposed to heterogeneous substrate availability caused by long mixing times. Escherichia coli, the most common industrial host for recombinant protein production, reacts by recurring accumulation of the alarmone ppGpp and energetically wasteful transcriptional strategies. Here, we compare the regulatory responses of the stringent response mutant strain E. coli SR and its parent strain E. coli MG1655 to repeated nutrient starvation in a two-compartment scale-down reactor. Our data show that E. coli SR can withstand these stress conditions without a ppGpp-mediated stress response maintaining fully functional ammonium uptake and biomass formation. Furthermore, E. coli SR exhibited a substantially reduced short-term transcriptional response compared to E. coli MG1655 (less than half as many differentially expressed genes). E. coli SR proceeded adaptation via more general SOS response pathways by initiating negative regulation of transcription, translation and cell division. Our results show that locally induced stress responses propagating through the bioreactor do not result in cyclical induction and repression of genes in E. coli SR, but in a reduced and coordinated response, which makes it potentially suitable for large-scale production processes.
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Affiliation(s)
- Martin Ziegler
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Julia Zieringer
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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21
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Mori M, Zhang Z, Banaei‐Esfahani A, Lalanne J, Okano H, Collins BC, Schmidt A, Schubert OT, Lee D, Li G, Aebersold R, Hwa T, Ludwig C. From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions. Mol Syst Biol 2021; 17:e9536. [PMID: 34032011 PMCID: PMC8144880 DOI: 10.15252/msb.20209536] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data-independent acquisition proteomics (DIA/SWATH) together with a novel protein inference algorithm (xTop). We used this workflow to accurately quantify absolute protein abundances in Escherichia coli for > 2,000 proteins over > 60 growth conditions, including nutrient limitations, non-metabolic stresses, and non-planktonic states. The resulting high-quality dataset of protein mass fractions allowed us to characterize proteome responses from a coarse (groups of related proteins) to a fine (individual) protein level. Hereby, a plethora of novel biological findings could be elucidated, including the generic upregulation of low-abundant proteins under various metabolic limitations, the non-specificity of catabolic enzymes upregulated under carbon limitation, the lack of large-scale proteome reallocation under stress compared to nutrient limitations, as well as surprising strain-dependent effects important for biofilm formation. These results present valuable resources for the systems biology community and can be used for future multi-omics studies of gene regulation and metabolic control in E. coli.
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Affiliation(s)
- Matteo Mori
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
| | - Zhongge Zhang
- Section of Molecular BiologyDivision of Biological SciencesUniversity of California at San DiegoLa JollaCAUSA
| | - Amir Banaei‐Esfahani
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Jean‐Benoît Lalanne
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Hiroyuki Okano
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
| | - Ben C Collins
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- School of Biological SciencesQueen's University of BelfastBelfastUK
| | | | - Olga T Schubert
- Department of Human GeneticsUniversity of California, Los AngelesLos AngelesCAUSA
| | - Deok‐Sun Lee
- School of Computational SciencesKorea Institute for Advanced StudySeoulKorea
| | - Gene‐Wei Li
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Ruedi Aebersold
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Faculty of ScienceUniversity of ZurichZurichSwitzerland
| | - Terence Hwa
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
- Section of Molecular BiologyDivision of Biological SciencesUniversity of California at San DiegoLa JollaCAUSA
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS)Technical University of Munich (TUM)FreisingGermany
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22
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Abstract
Isogenic microbial populations in constant and homogeneous environments can display remarkable levels of phenotypic diversity. Quantitative understanding of how such diversity is generated and maintained in populations is, however, experimentally and theoretically challenging. We focus on the swimming behavior of Escherichia coli as a model system of phenotypic diversity and show that, despite temporal changes in behavior that each individual undergoes, significant differences between individuals persist throughout most of their lifetimes. While the behavior of even closely related bacteria can be remarkably different, the behavioral variations produced by nongenetic mechanisms are inherited across generations. The general experimental and theoretical framework developed here can be applied to study quantitative aspects of phenotypic diversity in many biological systems. Isogenic populations often display remarkable levels of phenotypic diversity even in constant, homogeneous environments. Such diversity results from differences between individuals (“nongenetic individuality”) as well as changes during individuals’ lifetimes (“changeability”). Yet, studies that capture and quantify both sources of diversity are scarce. Here we measure the swimming behavior of hundreds of Escherichia coli bacteria continuously over two generations and use a model-independent method for quantifying behavior to show that the behavioral space of E. coli is low-dimensional, with variations occurring mainly along two independent and interpretable behavioral traits. By statistically decomposing the diversity in these two traits, we find that individuality is the main source of diversity, while changeability makes a smaller but significant contribution. Finally, we show that even though traits of closely related individuals can be remarkably different, they exhibit positive correlations across generations that imply nongenetic inheritance. The model-independent experimental and theoretical framework developed here paves the way for more general studies of microbial behavioral diversity.
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23
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Galvanin A, Vogt LM, Grober A, Freund I, Ayadi L, Bourguignon-Igel V, Bessler L, Jacob D, Eigenbrod T, Marchand V, Dalpke A, Helm M, Motorin Y. Bacterial tRNA 2'-O-methylation is dynamically regulated under stress conditions and modulates innate immune response. Nucleic Acids Res 2020; 48:12833-12844. [PMID: 33275131 PMCID: PMC7736821 DOI: 10.1093/nar/gkaa1123] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022] Open
Abstract
RNA modifications are a well-recognized way of gene expression regulation at the post-transcriptional level. Despite the importance of this level of regulation, current knowledge on modulation of tRNA modification status in response to stress conditions is far from being complete. While it is widely accepted that tRNA modifications are rather dynamic, such variations are mostly assessed in terms of total tRNA, with only a few instances where changes could be traced to single isoacceptor species. Using Escherichia coli as a model system, we explored stress-induced modulation of 2'-O-methylations in tRNAs by RiboMethSeq. This analysis and orthogonal analytical measurements by LC-MS show substantial, but not uniform, increase of the Gm18 level in selected tRNAs under mild bacteriostatic antibiotic stress, while other Nm modifications remain relatively constant. The absence of Gm18 modification in tRNAs leads to moderate alterations in E. coli mRNA transcriptome, but does not affect polysomal association of mRNAs. Interestingly, the subset of motility/chemiotaxis genes is significantly overexpressed in ΔTrmH mutant, this corroborates with increased swarming motility of the mutant strain. The stress-induced increase of tRNA Gm18 level, in turn, reduced immunostimulation properties of bacterial tRNAs, which is concordant with the previous observation that Gm18 is a suppressor of Toll-like receptor 7 (TLR7)-mediated interferon release. This documents an effect of stress induced modulation of tRNA modification that acts outside protein translation.
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Affiliation(s)
- Adeline Galvanin
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Lea-Marie Vogt
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Antonia Grober
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, 01307 Dresden, Germany
| | - Isabel Freund
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Ruprecht-Karls University Heidelberg, 69117 Heidelberg, Germany
| | - Lilia Ayadi
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Valerie Bourguignon-Igel
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Larissa Bessler
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Dominik Jacob
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Tatjana Eigenbrod
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Ruprecht-Karls University Heidelberg, 69117 Heidelberg, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Alexander Dalpke
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, 01307 Dresden, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
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24
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Kinosita Y, Ishida T, Yoshida M, Ito R, Morimoto YV, Goto K, Berry RM, Nishizaka T, Sowa Y. Distinct chemotactic behavior in the original Escherichia coli K-12 depending on forward-and-backward swimming, not on run-tumble movements. Sci Rep 2020; 10:15887. [PMID: 32985511 PMCID: PMC7522084 DOI: 10.1038/s41598-020-72429-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/27/2020] [Indexed: 11/21/2022] Open
Abstract
Most motile bacteria are propelled by rigid, helical, flagellar filaments and display distinct swimming patterns to explore their favorable environments. Escherichia coli cells have a reversible rotary motor at the base of each filament. They exhibit a run-tumble swimming pattern, driven by switching of the rotational direction, which causes polymorphic flagellar transformation. Here we report a novel swimming mode in E. coli ATCC10798, which is one of the original K-12 clones. High-speed tracking of single ATCC10798 cells showed forward and backward swimming with an average turning angle of 150°. The flagellar helicity remained right-handed with a 1.3 μm pitch and 0.14 μm helix radius, which is consistent with the feature of a curly type, regardless of motor switching; the flagella of ATCC10798 did not show polymorphic transformation. The torque and rotational switching of the motor was almost identical to the E. coli W3110 strain, which is a derivative of K-12 and a wild-type for chemotaxis. The single point mutation of N87K in FliC, one of the filament subunits, is critical to the change in flagellar morphology and swimming pattern, and lack of flagellar polymorphism. E. coli cells expressing FliC(N87K) sensed ascending a chemotactic gradient in liquid but did not spread on a semi-solid surface. Based on these results, we concluded that a flagellar polymorphism is essential for spreading in structured environments.
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Affiliation(s)
- Yoshiaki Kinosita
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan.
- Department of Physics, University of Oxford, Park load, Oxford, OX1 3PU, UK.
- Molecular Physiology Laboratory, RIKEN, Wako, Japan.
| | - Tsubasa Ishida
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, 184-8584, Japan
| | - Myu Yoshida
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, 184-8584, Japan
| | - Rie Ito
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, 184-8584, Japan
| | - Yusuke V Morimoto
- Department of Physics and Information Technology, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Kazuki Goto
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Richard M Berry
- Department of Physics, University of Oxford, Park load, Oxford, OX1 3PU, UK
| | - Takayuki Nishizaka
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Yoshiyuki Sowa
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, 184-8584, Japan.
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25
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Bacterial flagellar motor as a multimodal biosensor. Methods 2020; 193:5-15. [PMID: 32640316 DOI: 10.1016/j.ymeth.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/04/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023] Open
Abstract
Bacterial Flagellar Motor is one of nature's rare rotary molecular machines. It enables bacterial swimming and it is the key part of the bacterial chemotactic network, one of the best studied chemical signalling networks in biology, which enables bacteria to direct its movement in accordance with the chemical environment. The network can sense down to nanomolar concentrations of specific chemicals on the time scale of seconds. Motor's rotational speed is linearly proportional to the electrochemical gradients of either proton or sodium driving ions, while its direction is regulated by the chemotactic network. Recently, it has been discovered that motor is also a mechanosensor. Given these properties, we discuss the motor's potential to serve as a multifunctional biosensor and a tool for characterising and studying the external environment, the bacterial physiology itself and single molecular motor biophysics.
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26
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Toyotake Y, Nishiyama M, Yokoyama F, Ogawa T, Kawamoto J, Kurihara T. A Novel Lysophosphatidic Acid Acyltransferase of Escherichia coli Produces Membrane Phospholipids with a cis-vaccenoyl Group and Is Related to Flagellar Formation. Biomolecules 2020; 10:E745. [PMID: 32403425 PMCID: PMC7277886 DOI: 10.3390/biom10050745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/02/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023] Open
Abstract
Lysophosphatidic acid acyltransferase (LPAAT) introduces fatty acyl groups into the sn-2 position of membrane phospholipids (PLs). Various bacteria produce multiple LPAATs, whereas it is believed that Escherichia coli produces only one essential LPAAT homolog, PlsC-the deletion of which is lethal. However, we found that E. coli possesses another LPAAT homolog named YihG. Here, we show that overexpression of YihG in E. coli carrying a temperature-sensitive mutation in plsC allowed its growth at non-permissive temperatures. Analysis of the fatty acyl composition of PLs from the yihG-deletion mutant (∆yihG) revealed that endogenous YihG introduces the cis-vaccenoyl group into the sn-2 position of PLs. Loss of YihG did not affect cell growth or morphology, but ∆yihG cells swam well in liquid medium in contrast to wild-type cells. Immunoblot analysis showed that FliC was highly expressed in ∆yihG cells, and this phenotype was suppressed by expression of recombinant YihG in ∆yihG cells. Transmission electron microscopy confirmed that the flagellar structure was observed only in ∆yihG cells. These results suggest that YihG has specific functions related to flagellar formation through modulation of the fatty acyl composition of membrane PLs.
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Affiliation(s)
- Yosuke Toyotake
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Masayoshi Nishiyama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
| | - Fumiaki Yokoyama
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
| | - Takuya Ogawa
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
| | - Jun Kawamoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
| | - Tatsuo Kurihara
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; (Y.T.); (M.N.); (F.Y.); (T.O.); (J.K.)
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Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress. PLoS Genet 2020; 16:e1008649. [PMID: 32163413 PMCID: PMC7093028 DOI: 10.1371/journal.pgen.1008649] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 03/24/2020] [Accepted: 02/04/2020] [Indexed: 11/19/2022] Open
Abstract
Unicellular organisms have the prevalent challenge to survive under oxidative stress of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). ROS are present as by-products of photosynthesis and aerobic respiration. These reactive species are even employed by multicellular organisms as potent weapons against microbes. Although bacterial defences against lethal and sub-lethal oxidative stress have been studied in model bacteria, the role of fluctuating H2O2 concentrations remains unexplored. It is known that sub-lethal exposure of Escherichia coli to H2O2 results in enhanced survival upon subsequent exposure. Here we investigate the priming response to H2O2 at physiological concentrations. The basis and the duration of the response (memory) were also determined by time-lapse quantitative proteomics. We found that a low level of H2O2 induced several scavenging enzymes showing a long half-life, subsequently protecting cells from future exposure. We then asked if the phenotypic resistance against H2O2 alters the evolution of resistance against oxygen stress. Experimental evolution of H2O2 resistance revealed faster evolution and higher levels of resistance in primed cells. Several mutations were found to be associated with resistance in evolved populations affecting different loci but, counterintuitively, none of them was directly associated with scavenging systems. Our results have important implications for host colonisation and infections where microbes often encounter reactive oxygen species in gradients. Throughout evolution, bacteria were exposed to reactive oxygen species and evolved the ability to scavenge toxic oxygen radicals. Furthermore, multicellular organisms evolved the ability to produce such oxygen species directed against pathogens. Recent studies also suggest that ROS such as H2O2 play an important role during host gut colonisation by its microbiota. Traditionally, experiments with different antimicrobials have been carried out using fixed concentrations while in nature, including in intra-host environments, microbes are more likely to experience this type of stress in steps or gradients. Here we show that bacteria treated with sub-lethal concentrations of H2O2 (priming) survive far better than non-treated cells when they subsequently encounter a higher concentration. We also found that the 'priming' response has a protective role from lethal mutagenesis. This protection is provided by long-lived proteins that, upon priming, remain at a high level for several generations as determined by time-lapse LC-mass spectrometry. Bacteria that were primed evolved H2O2 resistance faster and to a higher level. Moreover, mutations that increase resistance to H2O2, as determined by whole-genome sequencing (WGS), do not occur in known scavenger encoding genes but in loci coding for other functions, at least in E. coli.
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Cheng L, Min D, Liu DF, Zhu TT, Wang KL, Yu HQ. Deteriorated biofilm-forming capacity and electroactivity of Shewanella oneidnsis MR-1 induced by insertion sequence (IS) elements. Biosens Bioelectron 2020; 156:112136. [PMID: 32174561 DOI: 10.1016/j.bios.2020.112136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/17/2022]
Abstract
Shewanella oneidensis MR-1, a model species of exoelectrogenic bacteria (EEB), has been widely applied in bioelectrochemical systems. Biofilms of EEB grown on electrodes are essential in governing the current output and power density of bioelectrochemical systems. The MR-1 genome is exceptionally dynamic due to the existence of a large number of insertion sequence (IS) elements. However, to date, the impacts of IS elements on the biofilm-forming capacity of EEB and performance of bioelectrochemical systems remain unrevealed. Herein, we isolated a non-motile mutant (NMM) with biofilm-deficient phenotype from MR-1. We found that the insertion of an ISSod2 element into the flrA (encoding the master regulator for flagella synthesis and assembly) of MR-1 resulted in the non-motile and biofilm-deficient phenotypes in NMM cells. Notably, such a variant was readily confused with the wild-type strain because there were no obvious differences in growth rates and colonial morphologies between the two strains. However, the reduced biofilm formation on the electrodes and the deteriorated performances of bioelectrochemical systems and Cr(VI) immobilization for the strain NMM were observed. Given the wide distribution of IS elements in EEB, appropriate cultivation and preservation conditions should be adopted to reduce the likelihood that IS elements-mediated mutation occurs in EEB. These findings reveal the negative impacts of IS elements on the biofilm-forming capacity of EEB and performance of bioelectrochemical systems and suggest that great attention should be given to the actual physiological states of EEB before their applications.
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Affiliation(s)
- Lei Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China.
| | - Ting-Ting Zhu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Kai-Li Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei, 230026, China.
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Kim JM, Garcia-Alcala M, Balleza E, Cluzel P. Stochastic transcriptional pulses orchestrate flagellar biosynthesis in Escherichia coli. SCIENCE ADVANCES 2020; 6:eaax0947. [PMID: 32076637 PMCID: PMC7002133 DOI: 10.1126/sciadv.aax0947] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 11/22/2019] [Indexed: 05/28/2023]
Abstract
The classic picture of flagellum biosynthesis in Escherichia coli, inferred from population measurements, depicts a deterministic program where promoters are sequentially up-regulated and are maintained steadily active throughout exponential growth. However, complex regulatory dynamics at the single-cell level can be masked by bulk measurements. Here, we discover that in individual E. coli cells, flagellar promoters are stochastically activated in pulses. These pulses are coordinated within specific classes of promoters and comprise "on" and "off" states, each of which can span multiple generations. We demonstrate that in this pulsing program, the regulatory logic of flagellar assembly dictates which promoters skip pulses. Surprisingly, pulses do not require specific transcriptional or translational regulation of the flagellar master regulator, FlhDC, but instead appears to be essentially governed by an autonomous posttranslational circuit. Our results suggest that even topologically simple transcriptional networks can generate unexpectedly rich temporal dynamics and phenotypic heterogeneities.
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Affiliation(s)
- J. Mark Kim
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Mayra Garcia-Alcala
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Enrique Balleza
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Philippe Cluzel
- Department of Molecular and Cellular Biology, Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
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Reassessing the Role of the Type II MqsRA Toxin-Antitoxin System in Stress Response and Biofilm Formation: mqsA Is Transcriptionally Uncoupled from mqsR. mBio 2019; 10:mBio.02678-19. [PMID: 31848281 PMCID: PMC6918082 DOI: 10.1128/mbio.02678-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Toxin-antitoxin (TA) systems are broadly distributed modules whose biological roles remain mostly unknown. The mqsRA system is a noncanonical TA system in which the toxin and antitoxins genes are organized in operon but with the particularity that the toxin gene precedes that of the antitoxin. This system was shown to regulate global processes such as resistance to bile salts, motility, and biofilm formation. In addition, the MqsA antitoxin was shown to be a master regulator that represses the transcription of the csgD, cspD, and rpoS global regulator genes, thereby displaying a pleiotropic regulatory role. Here, we identified two promoters located in the toxin sequence driving the constitutive expression of mqsA, allowing thereby excess production of the MqsA antitoxin compared to the MqsR toxin. Our results show that both antitoxin-specific and operon promoters are not regulated by stresses such as amino acid starvation, oxidative shock, or bile salts. Moreover, we show that the MqsA antitoxin is not a global regulator as suggested, since the expression of csgD, cspD and rpoS is similar in wild-type and ΔmqsRA mutant strains. Moreover, these two strains behave similarly in terms of biofilm formation and sensitivity to oxidative stress or bile salts.IMPORTANCE There is growing controversy regarding the role of chromosomal toxin-antitoxin systems in bacterial physiology. mqsRA is a peculiar toxin-antitoxin system, as the gene encoding the toxin precedes that of the antitoxin. This system was previously shown to play a role in stress response and biofilm formation. In this work, we identified two promoters specifically driving the constitutive expression of the antitoxin, thereby decoupling the expression of antitoxin from the toxin. We also showed that mqsRA contributes neither to the regulation of biofilm formation nor to the sensitivity to oxidative stress and bile salts. Finally, we were unable to confirm that the MqsA antitoxin is a global regulator. Altogether, our data are ruling out the involvement of the mqsRA system in Escherichia coli regulatory networks.
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Abstract
Bacterial chemotaxis, the directed movement of cells along gradients of chemoattractants, is among the best-characterized subjects in molecular biology1-10, but much less is known about its physiological roles11. It is commonly seen as a starvation response when nutrients run out, or as an escape response from harmful situations12-16. Here we identify an alternative role of chemotaxis by systematically examining the spatiotemporal dynamics of Escherichia coli in soft agar12,17,18. Chemotaxis in nutrient-replete conditions promotes the expansion of bacterial populations into unoccupied territories well before nutrients run out in the current environment. Low levels of chemoattractants act as aroma-like cues in this process, establishing the direction and enhancing the speed of population movement along the self-generated attractant gradients. This process of navigated range expansion spreads faster and yields larger population gains than unguided expansion following the canonical Fisher-Kolmogorov dynamics19,20 and is therefore a general strategy to promote population growth in spatially extended, nutrient-replete environments.
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Rapid Accumulation of Motility-Activating Mutations in Resting Liquid Culture of Escherichia coli. J Bacteriol 2019; 201:JB.00259-19. [PMID: 31285239 DOI: 10.1128/jb.00259-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
Expression of motility genes is a potentially beneficial but costly process in bacteria. Interestingly, many isolate strains of Escherichia coli possess motility genes but have lost the ability to activate them under conditions in which motility is advantageous, raising the question of how they respond to these situations. Through transcriptome profiling of strains in the E. coli single-gene knockout Keio collection, we noticed drastic upregulation of motility genes in many of the deletion strains compared to levels in their weakly motile parent strain (BW25113). We show that this switch to a motile phenotype is not a direct consequence of the genes deleted but is instead due to a variety of secondary mutations that increase the expression of the major motility regulator, FlhDC. Importantly, we find that this switch can be reproduced by growing poorly motile E. coli strains in nonshaking liquid medium overnight but not in shaking liquid medium. Individual isolates after the nonshaking overnight incubations acquired distinct mutations upstream of the flhDC operon, including different insertion sequence (IS) elements and, to a lesser extent, point mutations. The rapidity with which genetic changes sweep through the populations grown without shaking shows that poorly motile strains can quickly adapt to a motile lifestyle by genetic rewiring.IMPORTANCE The ability to tune gene expression in times of need outside preordained regulatory networks is an essential evolutionary process that allows organisms to survive and compete. Here, we show that upon overnight incubation in liquid medium without shaking, populations of largely nonmotile Escherichia coli bacteria can rapidly accumulate mutants that have constitutive motility. This effect contributes to widespread secondary mutations in the single-gene knockout library, the Keio collection. As a result, 49/71 (69%) of the Keio strains tested exhibited various degrees of motility, whereas their parental strain is poorly motile. These observations highlight the plasticity of gene expression even in the absence of preexisting regulatory programs and should raise awareness of procedures for handling laboratory strains of E. coli.
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Krasnopeeva E, Lo CJ, Pilizota T. Single-Cell Bacterial Electrophysiology Reveals Mechanisms of Stress-Induced Damage. Biophys J 2019; 116:2390-2399. [PMID: 31174851 PMCID: PMC6588726 DOI: 10.1016/j.bpj.2019.04.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/06/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023] Open
Abstract
An electrochemical gradient of protons, or proton motive force (PMF), is at the basis of bacterial energetics. It powers vital cellular processes and defines the physiological state of the cell. Here, we use an electric circuit analogy of an Escherichia coli cell to mathematically describe the relationship between bacterial PMF, electric properties of the cell membrane, and catabolism. We combine the analogy with the use of bacterial flagellar motor as a single-cell "voltmeter" to measure cellular PMF in varied and dynamic external environments (for example, under different stresses). We find that butanol acts as an ionophore and functionally characterize membrane damage caused by the light of shorter wavelengths. Our approach coalesces noninvasive and fast single-cell voltmeter with a well-defined mathematical framework to enable quantitative bacterial electrophysiology.
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Affiliation(s)
- Ekaterina Krasnopeeva
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Chien-Jung Lo
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan, Republic of China
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
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Zhi S, Banting G, Stothard P, Ashbolt NJ, Checkley S, Meyer K, Otto S, Neumann NF. Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater. WATER RESEARCH 2019; 156:208-222. [PMID: 30921537 DOI: 10.1016/j.watres.2019.03.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 03/12/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
We previously demonstrated the existence of naturalized strains of E. coli in wastewater and herein perform an in-depth comparative whole genome analysis of these strains (n = 17). Fourteen of the Canadian E. coli strains, isolated from geographically separated wastewater treatment plants, were virtually identical at the core genome and were ≥96% similar at the whole genome level, suggesting clonal-relatedness among these isolates. Remarkably, these strains were shown to be extremely similar to the genome of an E. coli isolated from wastewater in Switzerland, suggesting a global distribution of these strains. The genomes of three other Canadian wastewater strains were more diverse but very similar to the genomes of E. coli isolates collected from U.S. wastewater samples. Based on maximum likelihood phylogenetic analysis, wastewater strains from Canada, the U.S. and Switzerland formed a clade separate from other known enteric phylogroups (i.e., A, B1, B2, D, E) and the cryptic clades. All Canadian, Swiss and U.S. wastewater strains possessed a common SNP biomarker pattern across their genomes, and a sub-population (i.e., 14 Canadian and 1 Swiss strain) also possessed a previously identified wastewater-specific marker known as uspC-IS30-flhDC element. Biochemical heat mapping of 518 categories of genes recapitulated phylogeny, with wastewater strains phenotypically clustering separately from enteric and cryptic clades. Wastewater strains were enriched for stress-response genes (i.e., nutrient acquisition/deprivation, DNA repair, oxidative stress, and UV resistance) - elements reflective of their environmental survival challenges. Wastewater strains were shown to carry a plethora of known antibiotic resistance (AR) genes, the patterns of which were remarkably similar among all Canadian, U.S. and Swiss wastewater strains. Virulence gene composition was also similar among all the wastewater strains, with an abundant representation of virulence genes commonly associated with urinary pathogenic E. coli (UPEC) as well as enterohemorrhagic (EHEC) E. coli. The remarkable degree of similarity between all wastewater strains from Canada, Switzerland and the U.S. suggests the evolution and global-dissemination of water treatment-resistant clone of E. coli. These finding, along with others, raise some important concerns about the potential for emergence of E. coli pathotypes resistant to water-treatment.
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Affiliation(s)
- Shuai Zhi
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada
| | - Graham Banting
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada
| | - Paul Stothard
- Faculty of Agricultural, Life and Environmental Sciences, 1400 College Plaza, University of Alberta, Edmonton, Alberta, Canada
| | - Nicholas J Ashbolt
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada
| | - Sylvia Checkley
- Faculty of Veterinary Medicine, Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Kelsey Meyer
- Faculty of Veterinary Medicine, Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Simon Otto
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada
| | - Norman F Neumann
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada.
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Lai JYH, Zhang H, Chiang MHY, Lun CHI, Zhang R, Lau SCK. The putative functions of lysogeny in mediating the survivorship of Escherichia coli in seawater and marine sediment. FEMS Microbiol Ecol 2019; 94:4780272. [PMID: 29293955 DOI: 10.1093/femsec/fix187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 12/25/2017] [Indexed: 01/07/2023] Open
Abstract
Escherichia coli colonizes various body parts of animal hosts as a commensal and a pathogen. It can also persist in the external environment in the absence of fecal pollution. It remains unclear how this species has evolved to adapt to such contrasting habitats. Lysogeny plays pivotal roles in the diversification of the phenotypic and ecologic characters of E. coli as a symbiont. We hypothesized that lysogeny could also confer fitness to survival in the external environment. To test this hypothesis, we used the induced phages of an E. coli strain originating from marine sediment to infect a fecal E. coli strain to obtain an isogenic lysogen of the latter. The three strains were tested for survivorship in microcosms of seawater, marine sediment and sediment interstitial water as well as swimming motility, glycogen accumulation, biofilm formation, substrate utilization and stress resistance. The results indicate that lysogenic infection led to tractable changes in many of the ecophysiological attributes tested. Particularly, the lysogen had better survivorship in the microcosms and had a substrate utilization profile resembling the sediment strain more than the wild type fecal strain. Our findings provide new insights into the understanding of how E. coli survives in the natural environment.
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Affiliation(s)
- Jennifer Yuet Ha Lai
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Hao Zhang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Miranda Hei Yin Chiang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Clare Hau In Lun
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Rui Zhang
- Institute of Marine Microbes and Ecospheres, and State Key Laboratory of Marine Environmental Science, Xiamen University, People's Republic of China
| | - Stanley Chun Kwan Lau
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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Green CA, Kamble NS, Court EK, Bryant OJ, Hicks MG, Lennon C, Fraser GM, Wright PC, Stafford GP. Engineering the flagellar type III secretion system: improving capacity for secretion of recombinant protein. Microb Cell Fact 2019; 18:10. [PMID: 30657054 PMCID: PMC6337784 DOI: 10.1186/s12934-019-1058-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/08/2019] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Many valuable biopharmaceutical and biotechnological proteins have been produced in Escherichia coli, however these proteins are almost exclusively localised in the cytoplasm or periplasm. This presents challenges for purification, i.e. the removal of contaminating cellular constituents. One solution is secretion directly into the surrounding media, which we achieved via the 'hijack' of the flagellar type III secretion system (FT3SS). Ordinarily flagellar subunits are exported through the centre of the growing flagellum, before assembly at the tip. However, we exploit the fact that in the absence of certain flagellar components (e.g. cap proteins), monomeric flagellar proteins are secreted into the supernatant. RESULTS We report the creation and iterative improvement of an E. coli strain, by means of a modified FT3SS and a modular plasmid system, for secretion of exemplar proteins. We show that removal of the flagellin and HAP proteins (FliC and FlgKL) resulted in an optimal prototype. We next developed a high-throughput enzymatic secretion assay based on cutinase. This indicated that removal of the flagellar motor proteins, motAB (to reduce metabolic burden) and protein degradation machinery, clpX (to boost FT3SS levels intracellularly), result in high capacity secretion. We also show that a secretion construct comprising the 5'UTR and first 47 amino acidsof FliC from E. coli (but no 3'UTR) achieved the highest levels of secretion. Upon combination, we show a 24-fold improvement in secretion of a heterologous (cutinase) enzyme over the original strain. This improved strain could export a range of pharmaceutically relevant heterologous proteins [hGH, TrxA, ScFv (CH2)], achieving secreted yields of up to 0.29 mg L-1, in low cell density culture. CONCLUSIONS We have engineered an E. coli which secretes a range of recombinant proteins, through the FT3SS, to the extracellular media. With further developments, including cell culture process strategies, we envision further improvement to the secreted titre of recombinant protein, with the potential application for protein production for biotechnological purposes.
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Affiliation(s)
- Charlotte A Green
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK.,Sustainable Process Technologies, Chemical and Environmental Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nitin S Kamble
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Elizabeth K Court
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Owain J Bryant
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Matthew G Hicks
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK
| | - Christopher Lennon
- FUJIFILM Diosynth Biotechnologies, Belasis Avenue, Stockton-on-Tees, Billingham, TS23 1LH, UK
| | - Gillian M Fraser
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Phillip C Wright
- School of Engineering, The Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle, NE1 7RU, UK
| | - Graham P Stafford
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, S10 2TA, UK.
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Cross Talk between MarR-Like Transcription Factors Coordinates the Regulation of Motility in Uropathogenic Escherichia coli. Infect Immun 2018; 86:IAI.00338-18. [PMID: 30275009 PMCID: PMC6246914 DOI: 10.1128/iai.00338-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/16/2018] [Indexed: 01/19/2023] Open
Abstract
The MarR-like protein PapX represses the transcription of the flagellar master regulator genes flhDC in uropathogenic Escherichia coli (UPEC), the primary cause of uncomplicated urinary tract infections (UTIs). PapX is encoded by the pap operon, which also encodes the adherence factors termed P fimbriae. The MarR-like protein PapX represses the transcription of the flagellar master regulator genes flhDC in uropathogenic Escherichia coli (UPEC), the primary cause of uncomplicated urinary tract infections (UTIs). PapX is encoded by the pap operon, which also encodes the adherence factors termed P fimbriae. Both adherence and motility are critical for productive colonization of the urinary tract. However, the mechanisms involved in coordinating the transition between adherence and motility are not well characterized. UPEC strain CFT073 carries both papX and a homolog, focX, located in the foc operon encoding F1C fimbriae. In this study, we characterized the dose effects of “X” genes on flagellar gene expression and cross talk between focX and papX. We found that both FocX and PapX repress flhD transcription. However, we determined that the ΔpapX mutant was hypermotile, while the loss of focX did not affect motility. We further investigated this phenotype and found that FocX functions as a repressor of papX. Additionally, we identified a proximal independent promoter upstream of both focX and papX and assessed the expression of focX and papX during culture in human urine and on LB agar plates compared to LB medium. Finally, we characterized the contributions of PapX and FocX to fitness in the ascending murine model of UTI and observed a subtle, but not statistically significant, fitness defect in colonization of the kidneys. Altogether, these results expand our understanding of the impact of carrying multiple X genes on the coordinated regulation of motility and adherence in UPEC.
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Caby M, Bontemps-Gallo S, Gruau P, Delrue B, Madec E, Lacroix JM. The EnvZ-OmpR Two-Component Signaling System Is Inactivated in a Mutant Devoid of Osmoregulated Periplasmic Glucans in Dickeya dadantii. Front Microbiol 2018; 9:2459. [PMID: 30425688 PMCID: PMC6218677 DOI: 10.3389/fmicb.2018.02459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/25/2018] [Indexed: 12/04/2022] Open
Abstract
Osmoregulated periplasmic glucans (OPGs) are general constituents of alpha-, beta-, and gamma-Proteobacteria. This polymer of glucose is required for full virulence of many pathogens including Dickeya dadantii (D. dadantii). The phytopathogenic enterobacterium D. dadantii causes soft-rot disease in a wide range of plants. An OPG-defective mutant is impaired in environment sensing. We previously demonstrated that (i) fluctuation of OPG concentration controlled the activation level of the RcsCDB system, and (ii) RcsCDB along with EnvZ/OmpR controlled the mechanism of OPG succinylation. These previous data lead us to explore whether OPGs are required for other two-component systems. In this study, we demonstrate that inactivation of the EnvZ/OmpR system in an OPG-defective mutant restores full synthesis of pectinase but only partial virulence. Unlike for the RcsCDB system, the EnvZ-OmpR system is not controlled by OPG concentration but requires OPGs for proper activation.
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Affiliation(s)
- Marine Caby
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR CNRS 8576, Université des Sciences et Technologies de Lille, Université de Lille, Lille, France
| | - Sébastien Bontemps-Gallo
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR CNRS 8576, Université des Sciences et Technologies de Lille, Université de Lille, Lille, France
| | - Peggy Gruau
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR CNRS 8576, Université des Sciences et Technologies de Lille, Université de Lille, Lille, France
| | | | - Edwige Madec
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR CNRS 8576, Université des Sciences et Technologies de Lille, Université de Lille, Lille, France
| | - Jean-Marie Lacroix
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR CNRS 8576, Université des Sciences et Technologies de Lille, Université de Lille, Lille, France
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Zakaria MA, Mohd Yusoff MZ, Zakaria MR, Hassan MA, Wood TK, Maeda T. Pseudogene product YqiG is important for pflB expression and biohydrogen production in Escherichia coli BW25113. 3 Biotech 2018; 8:435. [PMID: 30306004 DOI: 10.1007/s13205-018-1461-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/24/2018] [Indexed: 01/08/2023] Open
Abstract
Pseudogenes in the Escherichia coli genome are assumed to be non-functional. In this study, Keio collection BW25113∆yqiG and YqiG-producing strain (BW25113/pCA24N-YqiG) were used to evaluate the importance of pseudogene yqiG in hydrogen metabolism. Our results show pseudogene protein YqiG was identified as an essential protein in the production of biohydrogen from glucose. The mutant yqiG decreased biohydrogen production from 37 µmol mg-1 protein to 6 µmol mg-1 protein compared to the wild-type strain, and glucose consumption was reduced by 80%. Through transcriptional analysis, we found that the yqiG mutation represses pflB transcription tenfold; pflB encodes pyruvate-formate lyase, one of the key enzymes in the anaerobic metabolism of E. coli. Moreover, production of YqiG stimulated glycolysis and increased biohydrogen productivity 1.5-fold compared to that of the wild-type strain. Thus, YqiG is important for the central glycolysis reaction and is able to influence hydrogen metabolism activity in E. coli.
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Affiliation(s)
- Muhammad Azman Zakaria
- 1Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Mohd Zulkhairi Mohd Yusoff
- 1Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- 2Laboratory of Biopolymer and Derivatives, Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Mohd Rafein Zakaria
- 1Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- 2Laboratory of Biopolymer and Derivatives, Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Mohd Ali Hassan
- 1Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Thomas K Wood
- 3Department of Chemical Engineering and Biochemistry and Molecular Biology, Pennsylvania State University, 161 Fenske Laboratory, University Park, PA 16802 USA
| | - Toshinari Maeda
- 4Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0196 Japan
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40
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Leaman EJ, Geuther BQ, Behkam B. Quantitative Investigation of the Role of Intra-/Intercellular Dynamics in Bacterial Quorum Sensing. ACS Synth Biol 2018; 7:1030-1042. [PMID: 29579377 DOI: 10.1021/acssynbio.7b00406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacteria utilize diffusible signals to regulate population density-dependent coordinated gene expression in a process called quorum sensing (QS). While the intracellular regulatory mechanisms of QS are well-understood, the effect of spatiotemporal changes in the population configuration on the sensitivity and robustness of the QS response remains largely unexplored. Using a microfluidic device, we quantitatively characterized the emergent behavior of a population of swimming E. coli bacteria engineered with the lux QS system and a GFP reporter. We show that the QS activation time follows a power law with respect to bacterial population density, but this trend is disrupted significantly by microscale variations in population configuration and genetic circuit noise. We then developed a computational model that integrates population dynamics with genetic circuit dynamics to enable accurate (less than 7% error) quantitation of the bacterial QS activation time. Through modeling and experimental analyses, we show that changes in spatial configuration of swimming bacteria can drastically alter the QS activation time, by up to 22%. The integrative model developed herein also enables examination of the performance robustness of synthetic circuits with respect to growth rate, circuit sensitivity, and the population's initial size and spatial structure. Our framework facilitates quantitative tuning of microbial systems performance through rational engineering of synthetic ribosomal binding sites. We have demonstrated this through modulation of QS activation time over an order of magnitude. Altogether, we conclude that predictive engineering of QS-based bacterial systems requires not only the precise temporal modulation of gene expression (intracellular dynamics) but also accounting for the spatiotemporal changes in population configuration (intercellular dynamics).
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Affiliation(s)
- Eric J. Leaman
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Brian Q. Geuther
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Bahareh Behkam
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
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41
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Sartori P, Chiarello E, Jayaswal G, Pierno M, Mistura G, Brun P, Tiribocchi A, Orlandini E. Wall accumulation of bacteria with different motility patterns. Phys Rev E 2018; 97:022610. [PMID: 29548231 DOI: 10.1103/physreve.97.022610] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Indexed: 06/08/2023]
Abstract
We systematically investigate the role of different swimming patterns on the concentration distribution of bacterial suspensions confined between two flat walls, by considering wild-type motility Escherichia coli and Pseudomonas aeruginosa, which perform Run and Tumble and Run and Reverse patterns, respectively. The experiments count motile bacteria at different distances from the bottom wall. In agreement with previous studies, an accumulation of motile bacteria close to the walls is observed. Different wall separations, ranging from 100 to 250μm, are tested. The concentration profiles result to be independent on the motility pattern and on the walls' separation. These results are confirmed by numerical simulations, based on a collection of self-propelled dumbbells-like particles interacting only through steric interactions. The good agreement with the simulations suggests that the behavior of the investigated bacterial suspensions is determined mainly by steric collisions and self-propulsion, as well as hydrodynamic interactions.
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Affiliation(s)
- Paolo Sartori
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Enrico Chiarello
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Gaurav Jayaswal
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Matteo Pierno
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Giampaolo Mistura
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Paola Brun
- Dipartimento di Medicina Molecolare, Università di Padova, via Gabelli 63, 35121 Padova PD, Italy
| | - Adriano Tiribocchi
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova and INFN, via Marzolo 8, 35131 Padova PD, Italy
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova and INFN, via Marzolo 8, 35131 Padova PD, Italy
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42
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Ni B, Ghosh B, Paldy FS, Colin R, Heimerl T, Sourjik V. Evolutionary Remodeling of Bacterial Motility Checkpoint Control. Cell Rep 2017; 18:866-877. [PMID: 28122238 PMCID: PMC5289928 DOI: 10.1016/j.celrep.2016.12.088] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/16/2016] [Accepted: 12/27/2016] [Indexed: 11/21/2022] Open
Abstract
Regulatory networks play a central role in the relationship between genotype and phenotype in all organisms. However, the mechanisms that underpin the evolutionary plasticity of these networks remain poorly understood. Here, we used experimental selection for enhanced bacterial motility in a porous environment to explore the adaptability of one of the most complex networks known in bacteria. We found that the resulting phenotypic changes are mediated by adaptive mutations in several functionally different proteins, including multiple components of the flagellar motor. Nevertheless, this evolutionary adaptation could be explained by a single mechanism, namely remodeling of the checkpoint regulating flagellar gene expression. Supported by computer simulations, our findings suggest that the specific “bow-tie” topology of the checkpoint facilitates evolutionary tuning of the cost-benefit trade-off between motility and growth. We propose that bow-tie regulatory motifs, which are widespread in cellular networks, play a general role in evolutionary adaptation. Multiple mutations enhance swimming behavior under selection A universal trade-off relationship between motility and growth is observed Checkpoint remodeling provides a mechanism of evolutionary adaptation Bow-tie topology facilitates evolvability of the motility network
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Affiliation(s)
- Bin Ni
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Bhaswar Ghosh
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Ferencz S Paldy
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg 35043, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany.
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43
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Abstract
Bacterial motility, and in particular repulsion or attraction toward specific chemicals, has been a subject of investigation for over 100 years, resulting in detailed understanding of bacterial chemotaxis and the corresponding sensory network in many bacterial species. For Escherichia coli most of the current understanding comes from the experiments with low levels of chemotactically active ligands. However, chemotactically inactive chemical species at concentrations found in the human gastrointestinal tract produce significant changes in E. coli's osmotic pressure and have been shown to lead to taxis. To understand how these nonspecific physical signals influence motility, we look at the response of individual bacterial flagellar motors under stepwise changes in external osmolarity. We combine these measurements with a population swimming assay under the same conditions. Unlike for chemotactic response, a long-term increase in swimming/motor speeds is observed, and in the motor rotational bias, both of which scale with the osmotic shock magnitude. We discuss how the speed changes we observe can lead to steady-state bacterial accumulation.
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44
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Involvement of Two-Component Signaling on Bacterial Motility and Biofilm Development. J Bacteriol 2017; 199:JB.00259-17. [PMID: 28533218 DOI: 10.1128/jb.00259-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Two-component signaling is a specialized mechanism that bacteria use to respond to changes in their environment. Nonpathogenic strains of Escherichia coli K-12 harbor 30 histidine kinases and 32 response regulators, which form a network of regulation that integrates many other global regulators that do not follow the two-component signaling mechanism, as well as signals from central metabolism. The output of this network is a multitude of phenotypic changes in response to changes in the environment. Among these phenotypic changes, many two-component systems control motility and/or the formation of biofilm, sessile communities of bacteria that form on surfaces. Motility is the first reversible attachment phase of biofilm development, followed by a so-called swim or stick switch toward surface organelles that aid in the subsequent phases. In the mature biofilm, motility heterogeneity is generated by a combination of evolutionary and gene regulatory events.
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45
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Plague GR, Boodram KS, Dougherty KM, Bregg S, Gilbert DP, Bakshi H, Costa D. Transposable Elements Mediate Adaptive Debilitation of Flagella in Experimental Escherichia coli Populations. J Mol Evol 2017. [PMID: 28646326 DOI: 10.1007/s00239-017-9797-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although insertion sequence (IS) elements are generally considered genomic parasites, they can mediate adaptive genetic changes in bacterial genomes. We discovered that among 12 laboratory-evolved Escherichia coli populations, three had experienced at least six different IS1-mediated deletions of flagellar genes. These deletions all involved the master flagellar regulator flhDC, and as such completely incapacitate motility. Two lines of evidence strongly suggest that these deletions were adaptive in our evolution experiment: (1) parallel evolution in three independent populations is highly unlikely just by chance, and (2) one of these deletion mutations swept to fixation within ~1000 generations, which is over two million times faster than expected if this deletion was instead selectively neutral and thus evolving by genetic drift. Because flagella are energetically expensive to synthesize and operate, we suspect that debilitating their construction conferred a fitness advantage in our well-stirred evolution experiment. These findings underscore the important role that IS elements can play in mediating adaptive loss-of-function mutations in bacteria.
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Affiliation(s)
- Gordon R Plague
- Department of Biology, State University of New York at Potsdam, Potsdam, NY, 13676, USA.
| | | | - Kevin M Dougherty
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Sandar Bregg
- Department of Biology, State University of New York at Potsdam, Potsdam, NY, 13676, USA.,Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Daniel P Gilbert
- Department of Biology, State University of New York at Potsdam, Potsdam, NY, 13676, USA.,School of Engineering Lab, Clarkson University, Potsdam, NY, USA
| | - Hira Bakshi
- Department of Biology, State University of New York at Potsdam, Potsdam, NY, 13676, USA
| | - Daniel Costa
- Department of Biology, State University of New York at Potsdam, Potsdam, NY, 13676, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
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46
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Novel genes associated with enhanced motility of Escherichia coli ST131. PLoS One 2017; 12:e0176290. [PMID: 28489862 PMCID: PMC5425062 DOI: 10.1371/journal.pone.0176290] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 04/07/2017] [Indexed: 12/20/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the cause of ~75% of all urinary tract infections (UTIs) and is increasingly associated with multidrug resistance. This includes UPEC strains from the recently emerged and globally disseminated sequence type 131 (ST131), which is now the dominant fluoroquinolone-resistant UPEC clone worldwide. Most ST131 strains are motile and produce H4-type flagella. Here, we applied a combination of saturated Tn5 mutagenesis and transposon directed insertion site sequencing (TraDIS) as a high throughput genetic screen and identified 30 genes associated with enhanced motility of the reference ST131 strain EC958. This included 12 genes that repress motility of E. coli K-12, four of which (lrhA, ihfA, ydiV, lrp) were confirmed in EC958. Other genes represented novel factors that impact motility, and we focused our investigation on characterisation of the mprA, hemK and yjeA genes. Mutation of each of these genes in EC958 led to increased transcription of flagellar genes (flhD and fliC), increased expression of the FliC flagellin, enhanced flagella synthesis and a hyper-motile phenotype. Complementation restored all of these properties to wild-type level. We also identified Tn5 insertions in several intergenic regions (IGRs) on the EC958 chromosome that were associated with enhanced motility; this included flhDC and EC958_1546. In both of these cases, the Tn5 insertions were associated with increased transcription of the downstream gene(s), which resulted in enhanced motility. The EC958_1546 gene encodes a phage protein with similarity to esterase/deacetylase enzymes involved in the hydrolysis of sialic acid derivatives found in human mucus. We showed that over-expression of EC958_1546 led to enhanced motility of EC958 as well as the UPEC strains CFT073 and UTI89, demonstrating its activity affects the motility of different UPEC strains. Overall, this study has identified and characterised a number of novel factors associated with enhanced UPEC motility.
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47
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Moura de Sousa J, Balbontín R, Durão P, Gordo I. Multidrug-resistant bacteria compensate for the epistasis between resistances. PLoS Biol 2017; 15:e2001741. [PMID: 28419091 PMCID: PMC5395140 DOI: 10.1371/journal.pbio.2001741] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/21/2017] [Indexed: 01/02/2023] Open
Abstract
Mutations conferring resistance to antibiotics are typically costly in the absence of the drug, but bacteria can reduce this cost by acquiring compensatory mutations. Thus, the rate of acquisition of compensatory mutations and their effects are key for the maintenance and dissemination of antibiotic resistances. While compensation for single resistances has been extensively studied, compensatory evolution of multiresistant bacteria remains unexplored. Importantly, since resistance mutations often interact epistatically, compensation of multiresistant bacteria may significantly differ from that of single-resistant strains. We used experimental evolution, next-generation sequencing, in silico simulations, and genome editing to compare the compensatory process of a streptomycin and rifampicin double-resistant Escherichia coli with those of single-resistant clones. We demonstrate that low-fitness double-resistant bacteria compensate faster than single-resistant strains due to the acquisition of compensatory mutations with larger effects. Strikingly, we identified mutations that only compensate for double resistance, being neutral or deleterious in sensitive or single-resistant backgrounds. Moreover, we show that their beneficial effects strongly decrease or disappear in conditions where the epistatic interaction between resistance alleles is absent, demonstrating that these mutations compensate for the epistasis. In summary, our data indicate that epistatic interactions between antibiotic resistances, leading to large fitness costs, possibly open alternative paths for rapid compensatory evolution, thereby potentially stabilizing costly multiple resistances in bacterial populations. Antibiotics target essential cellular functions, such as translation or cell wall biogenesis, and bacteria can become resistant to antibiotics by acquiring mutations in genes encoding those functions. This causes most drug-resistance mutations to be detrimental in the absence of the drug. However, bacteria can reduce this handicap by acquiring additional mutations, known as compensatory mutations. Compensatory evolution is crucial for the maintenance and dissemination of antibiotic resistances in bacterial populations. While compensation for single resistances has been extensively studied, compensatory evolution of multidrug-resistant bacteria remains unexplored. Importantly, interactions between resistance mutations are frequent, and this may cause compensation of multidrug-resistant bacteria to differ significantly from that of single-resistant strains. By comparing compensation of single- and double-drug–resistant E. coli, we found that double-drug–resistant bacteria compensate faster than single-drug–resistant strains. This is due to the acquisition of compensatory mutations with larger effects and possibly driven by the large fitness cost of double-drug resistance. Strikingly, we identified mutations that compensate specifically for the interaction between drug resistances, since they are beneficial only for double-drug–resistant bacteria and in conditions in which the interaction between resistances occurs. In summary, our data indicate that certain interactions between antibiotic-resistance mutations can open alternative paths for rapid compensatory evolution, thereby potentially stabilizing multiple drug resistances in bacterial populations.
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Affiliation(s)
| | | | - Paulo Durão
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
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48
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Vandecraen J, Chandler M, Aertsen A, Van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 2017; 43:709-730. [PMID: 28407717 DOI: 10.1080/1040841x.2017.1303661] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism. The direct consequence of IS transposition is the insertion of one DNA sequence into another. This event can result in gene inactivation as well as in modulation of neighbouring gene expression. The latter is usually mediated by de-repression or by the introduction of a complete or partial promoter located within the element. Furthermore, transcription and transposition of IS are affected by host factors and in some cases by environmental signals offering the host an adaptive strategy and promoting genetic variability to withstand the environmental challenges.
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Affiliation(s)
- Joachim Vandecraen
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium.,b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Michael Chandler
- c Laboratoire de Microbiologie et Génétique Moléculaires, Centre national de la recherche scientifique , Toulouse , France
| | - Abram Aertsen
- b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Rob Van Houdt
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium
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49
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Zhang Z, Kukita C, Humayun MZ, Saier MH. Environment-directed activation of the Escherichia coliflhDC operon by transposons. MICROBIOLOGY-SGM 2017; 163:554-569. [PMID: 28100305 DOI: 10.1099/mic.0.000426] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The flagellar system in Escherichia coli K12 is expressed under the control of the flhDC-encoded master regulator FlhDC. Transposition of insertion sequence (IS) elements to the upstream flhDC promoter region up-regulates transcription of this operon, resulting in a more rapid motility. Wang and Wood (ISME J 2011;5:1517-1525) provided evidence that insertion of IS5 into upstream activating sites occurs at higher rates in semi-solid agar media in which swarming behaviour is allowed as compared with liquid or solid media where swarming cannot occur. We confirm this conclusion and show that three IS elements, IS1, IS3 and IS5, transpose to multiple upstream sites within a 370 bp region of the flhDC operon control region. Hot spots for IS insertion correlate with positions of stress-induced DNA duplex destabilization (SIDD). We show that IS insertion occurs at maximal rates in 0.24 % agar, with rates decreasing dramatically with increasing or decreasing agar concentrations. In mixed cultures, we show that these mutations preferentially arise from the wild-type parent at frequencies of up to 3×10-3 cell-1 day-1 when the inoculated parental and co-existing IS-activated mutant cells are entering the stationary growth phase. We rigorously show that the apparent increased mutation frequencies cannot be accounted for by increased swimming or by increased growth under the selective conditions used. Thus, our data are consistent with the possibility that appropriate environmental conditions, namely those that permit but hinder flagellar rotation, result in the activation of a mutational pathway that involves IS element insertion upstream of the flhDC operon.
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Affiliation(s)
- Zhongge Zhang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Chika Kukita
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - M Zafri Humayun
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07101-1709, USA
| | - Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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50
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Growth rate control of flagellar assembly in Escherichia coli strain RP437. Sci Rep 2017; 7:41189. [PMID: 28117390 PMCID: PMC5259725 DOI: 10.1038/srep41189] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/12/2016] [Indexed: 01/10/2023] Open
Abstract
The flagellum is a rotary motor that enables bacteria to swim in liquids and swarm over surfaces. Numerous global regulators control flagellar assembly in response to cellular and environmental factors. Previous studies have also shown that flagellar assembly is affected by the growth-rate of the cell. However, a systematic study has not yet been described under controlled growth conditions. Here, we investigated the effect of growth rate on flagellar assembly in Escherichia coli using steady-state chemostat cultures where we could precisely control the cell growth-rate. Our results demonstrate that flagellar abundance correlates with growth rate, where faster growing cells produce more flagella. They also demonstrate that this growth-rate dependent control occurs through the expression of the flagellar master regulator, FlhD4C2. Collectively, our results demonstrate that motility is intimately coupled to the growth-rate of the cell.
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