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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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Chong TN, Panjalingam M, Saurabh S, Shapiro L. Phosphatase to kinase switch of a critical enzyme contributes to timing of cell differentiation. mBio 2024; 15:e0212523. [PMID: 38055339 PMCID: PMC10790692 DOI: 10.1128/mbio.02125-23] [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: 08/08/2023] [Accepted: 10/20/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE The process of cell differentiation is highly regulated in both prokaryotic and eukaryotic organisms. The aquatic bacterium, Caulobacter crescentus, undergoes programmed cell differentiation from a motile swarmer cell to a stationary stalked cell with each cell cycle. This critical event is regulated at multiple levels. Kinase activity of the bifunctional enzyme, PleC, is limited to a brief period when it initiates the molecular signaling cascade that results in cell differentiation. Conversely, PleC phosphatase activity is required for pili formation and flagellar rotation. We show that PleC is localized to the flagellar pole by the scaffold protein, PodJ, which is known to suppress PleC kinase activity in vitro. PleC mutants that are unable to bind PodJ have increased kinase activity in vivo, resulting in premature differentiation. We propose a model in which PodJ regulation of PleC's enzymatic activity contributes to the robust timing of cell differentiation during the Caulobacter cell cycle.
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Affiliation(s)
- Trisha N. Chong
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Mayura Panjalingam
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Saumya Saurabh
- Department of Chemistry, New York University, New York, New York, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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3
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Louis G, Cherry P, Michaux C, Rahuel-Clermont S, Dieu M, Tilquin F, Maertens L, Van Houdt R, Renard P, Perpete E, Matroule JY. A cytoplasmic chemoreceptor and reactive oxygen species mediate bacterial chemotaxis to copper. J Biol Chem 2023; 299:105207. [PMID: 37660909 PMCID: PMC10579534 DOI: 10.1016/j.jbc.2023.105207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023] Open
Abstract
Chemotaxis is a widespread strategy used by unicellular and multicellular living organisms to maintain their fitness in stressful environments. We previously showed that bacteria can trigger a negative chemotactic response to a copper (Cu)-rich environment. Cu ion toxicity on bacterial cell physiology has been mainly linked to mismetallation events and reactive oxygen species (ROS) production, although the precise role of Cu-generated ROS remains largely debated. Here, using inductively coupled plasma optical emission spectrometry on cell fractionates, we found that the cytoplasmic Cu ion content mirrors variations of the extracellular Cu ion concentration. ROS-sensitive fluorescent probe and biosensor allowed us to show that the increase of cytoplasmic Cu ion content triggers a dose-dependent oxidative stress, which can be abrogated by superoxide dismutase and catalase overexpression. The inhibition of ROS production in the cytoplasm not only improves bacterial growth but also impedes Cu chemotaxis, indicating that ROS derived from cytoplasmic Cu ions mediate the control of bacterial chemotaxis to Cu. We also identified the Cu chemoreceptor McpR, which binds Cu ions with low affinity, suggesting a labile interaction. In addition, we demonstrate that the cysteine 75 and histidine 99 within the McpR sensor domain are key residues in Cu chemotaxis and Cu coordination. Finally, we discovered that in vitro both Cu(I) and Cu(II) ions modulate McpR conformation in a distinct manner. Overall, our study provides mechanistic insights on a redox-based control of Cu chemotaxis, indicating that the cellular redox status can play a key role in bacterial chemotaxis.
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Affiliation(s)
- Gwennaëlle Louis
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Pauline Cherry
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Namur Research Institute for Life Sciences (NARILIS) and Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | | | - Marc Dieu
- MaSUN, Mass Spectrometry Facility, University of Namur, Namur, Belgium
| | - Françoise Tilquin
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Laurens Maertens
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Patricia Renard
- MaSUN, Mass Spectrometry Facility, University of Namur, Namur, Belgium
| | - Eric Perpete
- Laboratoire de Chimie Physique des Biomolécules, Namur Research Institute for Life Sciences (NARILIS) and Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Jean-Yves Matroule
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
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4
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Shu R, Yuan C, Liu B, Song Y, Hou L, Ren P, Wang H, Cui C. PAS Domain-Containing Chemoreceptors Influence the Signal Sensing and Intestinal Colonization of Vibrio cholerae. Genes (Basel) 2022; 13:genes13122224. [PMID: 36553491 PMCID: PMC9777591 DOI: 10.3390/genes13122224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Bacterial chemotaxis is the phenomenon in which bacteria migrate toward a more favorable niche in response to chemical cues in the environment. The methyl-accepting chemotaxis proteins (MCPs) are the principal sensory receptors of the bacterial chemotaxis system. Aerotaxis is a special form of chemotaxis in which oxygen serves as the signaling molecule; the process is dependent on the aerotaxis receptors (Aer) containing the Per-Arnt-Sim (PAS) domain. Over 40 MCPs are annotated on the genome of Vibrio cholerae; however, little is known about their functions. We investigated six MCPs containing the PAS domain in V. cholerae El Tor C6706, namely aer2, aer3, aer4, aer5, aer6, and aer7. Deletion analyses of each aer homolog gene indicated that these Aer receptors are involved in aerotaxis, chemotaxis, biofilm formation, and intestinal colonization. Swarming motility assay indicated that the aer2 gene was responsible for sensing the oxygen gradient independent of the other five homologs. When bile salts and mucin were used as chemoattractants, each Aer receptor influenced the chemotaxis differently. Biofilm formation was enhanced by overexpression of the aer6 and aer7 genes. Moreover, deletion of the aer2 gene resulted in better bacterial colonization of the mutant in adult mice; however, virulence gene expression was unaffected. These data suggest distinct roles for different Aer homologs in V. cholerae physiology.
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Affiliation(s)
- Rundong Shu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chaoqun Yuan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bojun Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Song
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Leqi Hou
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Panpan Ren
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (H.W.); (C.C.); Tel.: +86-25-84396645 (H.W.)
| | - Chunhong Cui
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (H.W.); (C.C.); Tel.: +86-25-84396645 (H.W.)
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5
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Bacteria-on-a-bead: probing the hydrodynamic interplay of dynamic cell appendages during cell separation. Commun Biol 2022; 5:1093. [PMID: 36241769 PMCID: PMC9568603 DOI: 10.1038/s42003-022-04026-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/23/2022] [Indexed: 11/08/2022] Open
Abstract
Surface attachment of bacteria is the first step of biofilm formation and is often mediated and coordinated by the extracellular appendages, flagellum and pili. The model organism Caulobacter crescentus undergoes an asymmetric division cycle, giving rise to a motile "swarmer cell" and a sessile "stalked cell", which is attached to the surface. In the highly polarized predivisional cell, pili and flagellum, which are assembled at the pole opposite the stalk, are both activated before and during the process of cell separation. We explored the interplay of flagellum and active pili by growing predivisional cells on colloidal beads, creating a bacteria-on-a-bead system. Using this set-up, we were able to simultaneously visualize the bacterial motility and analyze the dynamics of the flagellum and pili during cell separation. The observed activities of flagellum and pili at the new cell pole of the predivisional cell result in a cooperating interplay of the appendages during approaching and attaching to a surface. Even in presence of a functioning flagellum, pili are capable of surface attachment and keeping the cell in position. Moreover, while flagellar rotation decreases the average attachment time of a single pilus, it increases the overall attachment rate of pili in a synergetic manner.
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6
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Bouvard J, Douarche C, Mergaert P, Auradou H, Moisy F. Direct measurement of the aerotactic response in a bacterial suspension. Phys Rev E 2022; 106:034404. [PMID: 36266851 DOI: 10.1103/physreve.106.034404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/29/2022] [Indexed: 06/16/2023]
Abstract
Aerotaxis is the ability of motile cells to navigate toward oxygen. A key question is the dependence of the aerotactic velocity with the local oxygen concentration c. Here we combine simultaneous bacteria tracking and local oxygen concentration measurements using Ruthenium encapsulated in micelles to characterize the aerotactic response of Burkholderia contaminans, a motile bacterium ubiquitous in the environment. In our experiments, an oxygen gradient is produced by the bacterial respiration in a sealed glass capillary permeable to oxygen at one end, producing a bacterial band traveling toward the oxygen source. We compute the aerotactic response χ(c) both at the population scale, from the drift velocity in the bacterial band, and at the bacterial scale, from the angular modulation of the run times. Both methods are consistent with a power-law χ∝c^{-2}, in good agreement with existing models based on the biochemistry of bacterial membrane receptors.
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Affiliation(s)
- J Bouvard
- Université Paris-Saclay, CNRS, FAST, 91405, Orsay, France
| | - C Douarche
- Université Paris-Saclay, CNRS, FAST, 91405, Orsay, France
| | - P Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - H Auradou
- Université Paris-Saclay, CNRS, FAST, 91405, Orsay, France
| | - F Moisy
- Université Paris-Saclay, CNRS, FAST, 91405, Orsay, France
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7
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Abstract
Cholera disease is caused by Vibrio cholerae infecting the lining of the small intestine and results in severe diarrhea. V. cholerae’s swimming motility is known to play a crucial role in pathogenicity and may aid the bacteria in crossing the intestinal mucus barrier to reach sites of infection, but the exact mechanisms are unknown. The cell can be either pushed or pulled by its single polar flagellum, but there is no consensus on the resulting repertoire of motility behaviors. We use high-throughput three-dimensional (3D) bacterial tracking to observe V. cholerae swimming in buffer, in viscous solutions of the synthetic polymer PVP, and in mucin solutions that may mimic the host environment. We perform a statistical characterization of its motility behavior on the basis of large 3D trajectory data sets. We find that V. cholerae performs asymmetric run-reverse-flick motility, consisting of a sequence of a forward run, reversal, and a shorter backward run, followed by a turn by approximately 90°, called a flick, preceding the next forward run. Unlike many run-reverse-flick swimmers, V. cholerae’s backward runs are much shorter than its forward runs, resulting in an increased effective diffusivity. We also find that the swimming speed is not constant but subject to frequent decreases. The turning frequency in mucin matches that observed in buffer. Run-reverse-flick motility and speed fluctuations are present in all environments studied, suggesting that these behaviors also occur in natural aquatic habitats as well as the host environment. IMPORTANCE Cholera disease produces vomiting and severe diarrhea and causes approximately 100,000 deaths per year worldwide. The disease is caused by the bacterium Vibrio cholerae colonizing the lining of the small intestine. V. cholerae’s ability to swim is known to increase its infectivity, but the underlying mechanisms are not known. One possibility is that swimming aids in crossing the protective mucus barrier that covers the lining of the small intestine. Our work characterizing how V. cholerae swims in environments that mimic properties of the host environment may advance the understanding of how motility contributes to infection.
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8
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Grognot M, Taute KM. A multiscale 3D chemotaxis assay reveals bacterial navigation mechanisms. Commun Biol 2021; 4:669. [PMID: 34083715 PMCID: PMC8175578 DOI: 10.1038/s42003-021-02190-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 05/07/2021] [Indexed: 12/18/2022] Open
Abstract
How motile bacteria navigate environmental chemical gradients has implications ranging from health to climate science, but the underlying behavioral mechanisms are unknown for most species. The well-studied navigation strategy of Escherichia coli forms a powerful paradigm that is widely assumed to translate to other bacterial species. This assumption is rarely tested because of a lack of techniques capable of bridging scales from individual navigation behavior to the resulting population-level chemotactic performance. Here, we present such a multiscale 3D chemotaxis assay by combining high-throughput 3D bacterial tracking with microfluidically created chemical gradients. Large datasets of 3D trajectories yield the statistical power required to assess chemotactic performance at the population level, while simultaneously resolving the underlying 3D navigation behavior for every individual. We demonstrate that surface effects confound typical 2D chemotaxis assays, and reveal that, contrary to previous reports, Caulobacter crescentus breaks with the E. coli paradigm.
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Affiliation(s)
| | - Katja M Taute
- Rowland Institute at Harvard University, Cambridge, MA, USA.
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9
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Antani JD, Sumali AX, Lele TP, Lele PP. Asymmetric random walks reveal that the chemotaxis network modulates flagellar rotational bias in Helicobacter pylori. eLife 2021; 10:63936. [PMID: 33493107 PMCID: PMC7834020 DOI: 10.7554/elife.63936] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
The canonical chemotaxis network modulates the bias for a particular direction of rotation in the bacterial flagellar motor to help the cell migrate toward favorable chemical environments. How the chemotaxis network in Helicobacter pylori modulates flagellar functions is unknown, which limits our understanding of chemotaxis in this species. Here, we determined that H. pylori swim faster (slower) whenever their flagella rotate counterclockwise (clockwise) by analyzing their hydrodynamic interactions with bounding surfaces. This asymmetry in swimming helped quantify the rotational bias. Upon exposure to a chemo-attractant, the bias decreased and the cells tended to swim exclusively in the faster mode. In the absence of a key chemotaxis protein, CheY, the bias was zero. The relationship between the reversal frequency and the rotational bias was unimodal. Thus, H. pylori’s chemotaxis network appears to modulate the probability of clockwise rotation in otherwise counterclockwise-rotating flagella, similar to the canonical network.
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Affiliation(s)
- Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Anita X Sumali
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Tanmay P Lele
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77840, College Station, TX 77840, United States.,Department of Translational Medical Sciences, Texas A&M University, Houston, TX 77030, United States
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
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10
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R Cerqueira F, Vasconcelos ATR. OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5989499. [PMID: 33206960 PMCID: PMC7673341 DOI: 10.1093/database/baaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/11/2020] [Accepted: 07/27/2020] [Indexed: 11/14/2022]
Abstract
Small open reading frames (ORFs) have been systematically disregarded by automatic genome annotation. The difficulty in finding patterns in tiny sequences is the main reason that makes small ORFs to be overlooked by computational procedures. However, advances in experimental methods show that small proteins can play vital roles in cellular activities. Hence, it is urgent to make progress in the development of computational approaches to speed up the identification of potential small ORFs. In this work, our focus is on bacterial genomes. We improve a previous approach to identify small ORFs in bacteria. Our method uses machine learning techniques and decoy subject sequences to filter out spurious ORF alignments. We show that an advanced multivariate analysis can be more effective in terms of sensitivity than applying the simplistic and widely used e-value cutoff. This is particularly important in the case of small ORFs for which alignments present higher e-values than usual. Experiments with control datasets show that the machine learning algorithms used in our method to curate significant alignments can achieve average sensitivity and specificity of 97.06% and 99.61%, respectively. Therefore, an important step is provided here toward the construction of more accurate computational tools for the identification of small ORFs in bacteria.
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Affiliation(s)
- Fabio R Cerqueira
- Department of Production Engineering, Universidade Federal Fluminense, Rua Domingos Silvério s/n, Petrópolis, 25 650-050, Rio de Janeiro, Brazil.,Graduate Program in Computer Science, Universidade Federal de Viçosa, 36570-900, Minas Gerais, Brazil
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11
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Role of Caulobacter Cell Surface Structures in Colonization of the Air-Liquid Interface. J Bacteriol 2019; 201:JB.00064-19. [PMID: 31010900 DOI: 10.1128/jb.00064-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/15/2019] [Indexed: 01/17/2023] Open
Abstract
In aquatic environments, Caulobacter spp. can be found at the boundary between liquid and air known as the neuston. I report an approach to study temporal features of Caulobacter crescentus colonization and pellicle biofilm development at the air-liquid interface and have defined the role of cell surface structures in this process. At this interface, C. crescentus initially forms a monolayer of cells bearing a surface adhesin known as the holdfast. When excised from the liquid surface, this monolayer strongly adheres to glass. The monolayer subsequently develops into a three-dimensional structure that is highly enriched in clusters of stalked cells known as rosettes. As this pellicle film matures, it becomes more cohesive and less adherent to a glass surface. A mutant strain lacking a flagellum does not efficiently reach the surface, and strains lacking type IV pili exhibit defects in organization of the three-dimensional pellicle. Strains unable to synthesize the holdfast fail to accumulate at the boundary between air and liquid and do not form a pellicle. Phase-contrast images support a model whereby the holdfast functions to trap C. crescentus cells at the air-liquid boundary. Unlike the holdfast, neither the flagellum nor type IV pili are required for C. crescentus to partition to the air-liquid interface. While it is well established that the holdfast enables adherence to solid surfaces, this study provides evidence that the holdfast has physicochemical properties that allow partitioning of nonmotile mother cells to the air-liquid interface and facilitate colonization of this microenvironment.IMPORTANCE In aquatic environments, the boundary at the air interface is often highly enriched with nutrients and oxygen. Colonization of this niche likely confers a significant fitness advantage in many cases. This study provides evidence that the cell surface adhesin known as a holdfast enables Caulobacter crescentus to partition to and colonize the air-liquid interface. Additional surface structures, including the flagellum and type IV pili, are important determinants of colonization and biofilm formation at this boundary. Considering that holdfast-like adhesins are broadly conserved in Caulobacter spp. and other members of the diverse class Alphaproteobacteria, these surface structures may function broadly to facilitate colonization of air-liquid boundaries in a range of ecological contexts, including freshwater, marine, and soil ecosystems.
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12
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Jashnsaz H, Anderson GG, Pressé S. Statistical signatures of a targeted search by bacteria. Phys Biol 2017; 14:065002. [PMID: 28809162 DOI: 10.1088/1478-3975/aa84ea] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Chemoattractant gradients are rarely well-controlled in nature and recent attention has turned to bacterial chemotaxis toward typical bacterial food sources such as food patches or even bacterial prey. In environments with localized food sources reminiscent of a bacterium's natural habitat, striking phenomena-such as the volcano effect or banding-have been predicted or expected to emerge from chemotactic models. However, in practice, from limited bacterial trajectory data it is difficult to distinguish targeted searches from an untargeted search strategy for food sources. Here we use a theoretical model to identify statistical signatures of a targeted search toward point food sources, such as prey. Our model is constructed on the basis that bacteria use temporal comparisons to bias their random walk, exhibit finite memory and are subject to random (Brownian) motion as well as signaling noise. The advantage with using a stochastic model-based approach is that a stochastic model may be parametrized from individual stochastic bacterial trajectories but may then be used to generate a very large number of simulated trajectories to explore average behaviors obtained from stochastic search strategies. For example, our model predicts that a bacterium's diffusion coefficient increases as it approaches the point source and that, in the presence of multiple sources, bacteria may take substantially longer to locate their first source giving the impression of an untargeted search strategy.
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Affiliation(s)
- Hossein Jashnsaz
- Department of Physics, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, IN 46202, United States of America
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13
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Colin R, Sourjik V. Emergent properties of bacterial chemotaxis pathway. Curr Opin Microbiol 2017; 39:24-33. [PMID: 28822274 DOI: 10.1016/j.mib.2017.07.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 07/27/2017] [Indexed: 11/17/2022]
Abstract
The chemotaxis pathway of Escherichia coli is the most studied sensory system in prokaryotes. The highly conserved general architecture of this pathway consists of two modules which mediate signal transduction and adaptation. The signal transduction module detects and amplifies changes in environmental conditions and rapidly transmits these signals to control bacterial swimming behavior. The adaptation module gradually resets the activity and sensitivity of the first module after initial stimulation and thereby enables the temporal comparisons necessary for bacterial chemotaxis. Recent experimental and theoretical work has unraveled multiple quantitative features emerging from the interplay between these two modules. This has laid the groundwork for rationalization of these emerging properties in the context of the evolutionary optimization of the chemotactic behavior.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-strasse 16, 35043 Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-strasse 16, 35043 Marburg, Germany.
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14
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Abstract
Swimming bacteria exhibit a repertoire of motility patterns, in which persistent motion is interrupted by turning events. What are the statistical properties of such random walks? If some particular instances have long been studied, the general case where turning times do not follow a Poisson process has remained unsolved. We present a generic extension of the continuous time random walks formalism relying on operators and noncommutative calculus. The approach is first applied to a unimodal model of bacterial motion. We examine the existence of a minimum in velocity correlation function and discuss the maximum of diffusivity at an optimal value of rotational diffusion. The model is then extended to bimodal patterns and includes as particular cases all swimming strategies: run-and-tumble, run-stop, run-reverse and run-reverse-flick. We characterize their velocity correlation functions and investigate how bimodality affects diffusivity. Finally, the wider applicability of the method is illustrated by considering curved trajectories and Lévy walks. Our results are relevant for intermittent motion of living beings, be they swimming micro-organisms or crawling cells.
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Affiliation(s)
- François Detcheverry
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
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Menolascina F, Rusconi R, Fernandez VI, Smriga S, Aminzare Z, Sontag ED, Stocker R. Logarithmic sensing in Bacillus subtilis aerotaxis. NPJ Syst Biol Appl 2017; 3:16036. [PMID: 28725484 PMCID: PMC5516866 DOI: 10.1038/npjsba.2016.36] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/13/2016] [Accepted: 10/05/2016] [Indexed: 11/09/2022] Open
Abstract
Aerotaxis, the directed migration along oxygen gradients, allows many microorganisms to locate favorable oxygen concentrations. Despite oxygen's fundamental role for life, even key aspects of aerotaxis remain poorly understood. In Bacillus subtilis, for example, there is conflicting evidence of whether migration occurs to the maximal oxygen concentration available or to an optimal intermediate one, and how aerotaxis can be maintained over a broad range of conditions. Using precisely controlled oxygen gradients in a microfluidic device, spanning the full spectrum of conditions from quasi-anoxic to oxic (60 n mol/l-1 m mol/l), we resolved B. subtilis' 'oxygen preference conundrum' by demonstrating consistent migration towards maximum oxygen concentrations ('monotonic aerotaxis'). Surprisingly, the strength of aerotaxis was largely unchanged over three decades in oxygen concentration (131 n mol/l-196 μ mol/l). We discovered that in this range B. subtilis responds to the logarithm of the oxygen concentration gradient, a rescaling strategy called 'log-sensing' that affords organisms high sensitivity over a wide range of conditions. In these experiments, high-throughput single-cell imaging yielded the best signal-to-noise ratio of any microbial taxis study to date, enabling the robust identification of the first mathematical model for aerotaxis among a broad class of alternative models. The model passed the stringent test of predicting the transient aerotactic response despite being developed on steady-state data, and quantitatively captures both monotonic aerotaxis and log-sensing. Taken together, these results shed new light on the oxygen-seeking capabilities of B. subtilis and provide a blueprint for the quantitative investigation of the many other forms of microbial taxis.
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Affiliation(s)
- Filippo Menolascina
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Scotland, UK.,SynthSys-Centre for Synthetic and Systems Biology, The University of Edinburgh, Scotland, UK
| | - Roberto Rusconi
- Ralph M Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Zurich, Switzerland
| | - Vicente I Fernandez
- Ralph M Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Zurich, Switzerland
| | - Steven Smriga
- Ralph M Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Zurich, Switzerland
| | - Zahra Aminzare
- The Program in Applied and Computational Mathematics, Princeton, NJ, USA
| | - Eduardo D Sontag
- Department of Mathematics, Hill Center Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Roman Stocker
- Ralph M Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Zurich, Switzerland
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