1
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Hatstat AK, Kormos R, Xu V, Du G, Liu L, Zhang SQ, DeGrado WF. A Designed Zn 2+ Sensor Domain Transmits Binding Information to Transmembrane Histidine Kinases. J Am Chem Soc 2025. [PMID: 40388352 DOI: 10.1021/jacs.5c02273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2025]
Abstract
Generating stimulus-responsive allosteric signaling de novo is a significant challenge in protein design. In natural systems like bacterial histidine kinases (HKs), signal transduction occurs when ligand binding initiates a signal that is amplified across biological membranes over long distances to induce large-scale rearrangements and phosphorylation relays. Here, we ask whether our understanding of protein design and multidomain, intramolecular signaling has progressed sufficiently to enable engineering of a HK with tunable de novo components. We generated de novo metal-binding sensor domains and substituted them for the native sensor domain of a transmembrane HK, affording chimeras that transduce signals initiated from a de novo sensor. Signaling depended on the designed sensor's stability and the interdomain linker's phase and length. These results show the usefulness of de novo design to elucidate the biochemical mechanisms and principles of transmembrane signaling.
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Affiliation(s)
- A Katherine Hatstat
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-9001, United States
- The Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
| | - Rian Kormos
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-9001, United States
- The Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
- Biophysics Graduate Program, University of California, San Francisco, California 94158-9001, United States
| | - Vee Xu
- Biotechnology Program, City College of San Francisco, San Francisco, California 94112, United States
| | - Guoming Du
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lijun Liu
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - Shao-Qing Zhang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-9001, United States
- The Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
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2
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Liu J, Wang Y, Zhou Y, Wang X, Bi S. Functional characterization of the methyl-accepting chemotaxis proteins RS10830 and RS10815 in Xanthomonas oryzae pv. oryzicola. Int J Biol Macromol 2025; 306:141800. [PMID: 40054815 DOI: 10.1016/j.ijbiomac.2025.141800] [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: 12/17/2024] [Revised: 03/03/2025] [Accepted: 03/04/2025] [Indexed: 05/11/2025]
Abstract
Xanthomonas oryzae pv. oryzicola (Xoc) causes the economically important leaf streak disease in rice. Chemotaxis plays a role in the entry and colonization of some phytopathogens within the host. However, the physiological function and ligand specificity of Xoc methyl-accepting chemotaxis proteins (MCPs) are not well defined. In this study, we show that the transmembrane MCP ACU12_RS10830 (RS10830) binds L-malic acid and L-tartaric acid, whereas the transmembrane MCP ACU12_RS10815 (RS10815) binds ethanolamine, methylamine, ethylamine, ethylenediamine, amylamine, and tyramine, to elicit attractant responses. The chemotactic responses mediated by the sensory domains of RS10830 and RS10815 were also observed for the chimeric receptors in Escherichia coli. Furthermore, the RS10830 and RS10815-mediated positive chemotaxis of Xoc RS105 correlated with the promoting effects of their ligands on bacterial growth and virulence in rice. To the best of our knowledge, this is the first report on the function of Xoc MCPs in virulence and signaling molecules of the Xoc chemotaxis system. RS10830 is the first L-tartaric acid-binding MCP reported in bacteria.
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Affiliation(s)
- Jinye Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yuxin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yuying Zhou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xue Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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Edelmann DB, Jakob AM, Wilson LG, Colin R, Brandt D, Eck F, Kalinowski J, Thormann KM. Role of a single MCP in evolutionary adaptation of Shewanella putrefaciens for swimming in planktonic and structured environments. Appl Environ Microbiol 2025; 91:e0022925. [PMID: 40130843 PMCID: PMC12016497 DOI: 10.1128/aem.00229-25] [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: 01/28/2025] [Accepted: 02/21/2025] [Indexed: 03/26/2025] Open
Abstract
Bacteria can adapt to their environments by changing phenotypic traits by mutations. However, improving one trait often results in the deterioration of another one, a trade-off that limits the degree of adaptation. The gammaproteobacterium Shewanella putrefaciens CN-32 has an elaborate motility machinery comprising two distinct flagellar systems and an extensive chemotaxis array with 36 methyl-accepting chemotaxis sensor proteins (MCPs). In this study, we performed experimental selection on S. putrefaciens for increased spreading through a porous environment. We readily obtained a mutant that showed a pronounced increase in covered distance. This phenotype was almost completely caused by a deletion of 24 bp from the chromosome, which leads to a moderately enhanced production of a single MCP. Accordingly, chemotaxis assays under free-swimming conditions and cell tracking in soft agar showed that the mutation improved navigation through nutritional gradients. In contrast, further increased levels of the MCP negatively affected spreading. The study demonstrates how moderate differences in the abundance of a single MCP can lead to an efficient upgrade of chemotaxis in specific environments at a low expense of cellular resources.IMPORTANCEExperimental evolution experiments have been used to determine the trade-offs occurring in specific environments. Several studies that have used the spreading behavior of bacteria in structured environments identified regulatory mutants that increase the swimming speed of the cells. While this results in a higher chemotaxis drift, the growth fitness decreases as the higher swimming speed requires substantial cellular resources. Here we show that rapid chemotaxis adaptation can also be achieved by modifying the chemotaxis signal input at a low metabolic cost for the cell.
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Affiliation(s)
- Daniel B. Edelmann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Anna M. Jakob
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | | | - Rémy Colin
- Max Planck Institute for Terrestrial Microbiology, and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - David Brandt
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Frederik Eck
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Kai M. Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
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4
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Chen H, Chen C, Zhao H, Wei Y, Wang P, Wu LF, Song T. Synergistic mechanism of magneto-optical sensing mediated by magnetic response protein Amb0994 and LOV-like protein Amb2291 in Magnetospirillum magneticum AMB-1. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2025; 265:113124. [PMID: 39954315 DOI: 10.1016/j.jphotobiol.2025.113124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 01/27/2025] [Accepted: 02/11/2025] [Indexed: 02/17/2025]
Abstract
Magnetotactic bacteria (MTB), known for their precision in navigating along magnetic fields, also exhibit light-sensitive behaviors. In Magnetospirillum magneticum AMB-1, the photoreceptor Amb2291 is involved in phototaxis regulation and magnetosome synthesis, particularly under oxidative stress. The magnetoreceptor Amb0994 modulates flagellar activity in response to magnetic field changes. Our study used a magneto-optical system to analyze the U-turn motility of north-seeking AMB-1 wild type (WT), amb2291 and amb0994 mutants under reversed magnetic fields and controlled light conditions. The results showed that WT strains consistently executed U-turns in response to magnetic fields, regardless of light variations. The diameters of U-turn of amb0994 mutant were smaller than those of the WT control. When illuminated with blue light in a direction opposite to the magnetic field, Δamb0994 exhibited slower U-turns with diameters similar to WT. In contrast, the Δamb2291 strain exhibited exaggerated U-turn movements under blue light, characterized by larger movement diameters and times compared to the WT, particularly whatever the light propagation direction is the same or opposite to the magnetic field in the initial state of motility. Gene expression analysis revealed that long-term exposure to blue light and magnetic fields led to a significant upregulation of amb2291 in Δamb0994 mutant strains and amb0994 in Δamb2291 mutant strains. These indicate a potential cooperative role of amb2291 and amb0994 in modulating bacterial motility under blue light. This research enhances our understanding of photoreception in MTB and its impact on magnetotaxis, shedding light on how environmental factors interact with microorganisms.
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Affiliation(s)
- Haitao Chen
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China; France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
| | - Changyou Chen
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China; France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
| | - Haoyu Zhao
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China; France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China; School of Electronics, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Wei
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China; France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China; School of Electronics, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pingping Wang
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China; France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
| | - Long-Fei Wu
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS, F-13402 Marseille, France; Aix Marseille University, CNRS, LCB, F-13402 Marseille, France
| | - Tao Song
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China; France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China; School of Electronics, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Nicolaou K, Passmore JB, Kapitein LC, Mulder BM, Berger F. Behind the scenes of cellular organization: Quantifying spatial phenotypes of puncta structures with statistical models including random fields. Mol Biol Cell 2025; 36:ar22. [PMID: 39785704 PMCID: PMC11974956 DOI: 10.1091/mbc.e24-10-0461] [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: 10/29/2024] [Revised: 12/19/2024] [Accepted: 01/02/2025] [Indexed: 01/12/2025] Open
Abstract
The cellular interior is a spatially complex environment shaped by nontrivial stochastic and biophysical processes. Within this complexity, spatial organizational principles-also called spatial phenotypes-often emerge with functional implications. However, identifying and quantifying these phenotypes in the stochastic intracellular environment is challenging. To overcome this challenge for puncta, we discuss the use of inference of point-process models that link the density of points to other imaged structures and a random field that captures hidden processes. We apply these methods to simulated data and multiplexed immunofluorescence images of Vero E6 cells. Our analysis suggests that peroxisomes are likely to be found near the perinuclear region, overlapping with the endoplasmic reticulum, and located within a distance of 1 µm to mitochondria. Moreover, the random field captures a hidden variation of the mean density in the order of 15 µm. This length scale could provide critical information for further developing mechanistic hypotheses and models. By using spatial statistical models including random fields, we add a valuable perspective to cell biology.
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Affiliation(s)
- Kyriacos Nicolaou
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
- Centre for Complex Systems Studies, Utrecht University, 3584 CE Utrecht, The Netherlands
| | - Josiah B. Passmore
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Bela M. Mulder
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
- Institute AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Florian Berger
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
- Centre for Complex Systems Studies, Utrecht University, 3584 CE Utrecht, The Netherlands
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6
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Li SY, He C, Valades-Cruz CA, Zhang CC, Yang Y. Phototactic signaling network in rod-shaped cyanobacteria: A study on Synechococcus elongatus UTEX 3055. Microbiol Res 2025; 292:127967. [PMID: 39637757 DOI: 10.1016/j.micres.2024.127967] [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: 08/26/2024] [Revised: 11/03/2024] [Accepted: 11/03/2024] [Indexed: 12/07/2024]
Abstract
Light-controlled motility is advantageous for photosynthetic prokaryotes to better survive in environment with constantly changing light conditions. For cyanobacteria, light is both an energy source for photosynthesis and a stress factor. Consequently, some cyanobacteria evolved the ability to control type-IV pili (T4P)-mediated surface motility using a chemotaxis-like system in response to light signals. Extensive studies on the mechanism of phototaxis has been conducted in the spherical Synechocystis sp. PCC 6803 and the filamentous strain Nostoc punctiforme, while less is explored in rod-shaped cyanobacteria such as Synechococcus species. In this study, we investigated the phototaxis pathway in the unicellular rod-shaped cyanobacterium Synechococcus elongatus UTEX 3055, which exhibits bidirectional phototaxis using a single tax1 operon, in contrast to more complex and multiple gene clusters revealed in Synechocystis sp. PCC 6803. Results obtained by protein-protein interaction assays and protein subcellular localization experiments indicated that proteins encoded by the tax1 operon form large clusters that asymmetrically distributed both between the two poles and within the same pole. In vitro phosphorylation assays and site-directed mutations of conserved phosphorylation sites in PixLSe, PixGSe and PixHSe demonstrate that PixLSe acts as a histidine kinase, and PixGSe and PixHSe as response regulators for signal transduction. We further show that PixGSe and PixHSe are recruited to cell poles via interactions with the N-terminal region of PixLSe. While phosphotransfer reactions in this signaling pathway are critical for phototactic signaling, the two response regulators appear to play different roles in the control of phototaxis. This study provides a framework for further investigation into the complex phototactic signaling network in rod-shaped cyanobacteria with clearly defined cell poles in contrast to round shaped Synechocystis species with virtual cells poles through light-lensing effect.
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Affiliation(s)
- Shang-Yu Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenliu He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
| | - Cesar Augusto Valades-Cruz
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, PR China.
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China.
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7
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Vo L, Avgidis F, Mattingly HH, Edmonds K, Burger I, Balasubramanian R, Shimizu TS, Kazmierczak BI, Emonet T. Nongenetic adaptation by collective migration. Proc Natl Acad Sci U S A 2025; 122:e2423774122. [PMID: 39970001 PMCID: PMC11874451 DOI: 10.1073/pnas.2423774122] [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: 11/14/2024] [Accepted: 01/17/2025] [Indexed: 02/21/2025] Open
Abstract
Cell populations must adjust their phenotypic composition to adapt to changing environments. One adaptation strategy is to maintain distinct phenotypic subsets within the population and to modulate their relative abundances via gene regulation. Another strategy involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. We found that the migrating populations became enriched with high-performing swimming phenotypes in each environment, allowing the populations to adapt without requiring mutations or gene regulation. This adaptation is dynamic and rapid, reversing in a few doubling times when migration ceases. By measuring the chemoreceptor abundance distributions during migration toward different attractants, we demonstrated that adaptation acts on multiple chemotaxis-related traits simultaneously. These measurements are consistent with a general mechanism in which adaptation results from a balance between cell growth generating diversity and collective migration eliminating underperforming phenotypes. Thus, collective migration enables cell populations with continuous, multidimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions.
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Affiliation(s)
- Lam Vo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | - Fotios Avgidis
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Center for Living Systems, AMOLF Institute, Amsterdam1098 XG, The Netherlands
| | - Henry H. Mattingly
- Center for Computational Biology, Flatiron Institute, New York City, NY10010
| | - Karah Edmonds
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | - Isabel Burger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | - Ravi Balasubramanian
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | - Thomas S. Shimizu
- Center for Living Systems, AMOLF Institute, Amsterdam1098 XG, The Netherlands
| | | | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Department of Physics, Yale University, New Haven, CT06511
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8
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Ruan S, He R, Liang Y, Zhang R, Yuan J. Phosphorylation-Dependent Dispersion of the Response Regulator in Bacterial Chemotaxis. J Mol Biol 2025; 437:168920. [PMID: 39710331 DOI: 10.1016/j.jmb.2024.168920] [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: 07/29/2024] [Revised: 12/11/2024] [Accepted: 12/18/2024] [Indexed: 12/24/2024]
Abstract
Protein phosphorylation is a fundamental cellular regulatory mechanism that governs the activation and deactivation of numerous proteins. In two-component signaling transduction pathways, the phosphorylation of response regulator proteins and their subsequent diffusion play pivotal roles in signal transmission. However, the impact of protein phosphorylation on their dispersion properties remains elusive. In this study, using the response regulator CheY in bacterial chemotaxis as a model, we performed comprehensive measurements of the spatial distributions and diffusion characteristics of CheY and phosphorylated CheY through single-molecule tracking within live cells. We discovered that phosphorylation significantly enhances diffusion and mitigates the constraining influence of the cell membrane on these proteins. Moreover, we observed that ATP-dependent fluctuations also promote protein diffusion and reduce the restraining effect of the cell membrane. These findings highlight important effects of phosphorylation beyond protein activation.
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Affiliation(s)
- Shirui Ruan
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rui He
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Yixin Liang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rongjing Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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9
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McQuillen R, Perez AJ, Yang X, Bohrer CH, Smith EL, Chareyre S, Tsui HCT, Bruce KE, Hla YM, McCausland JW, Winkler ME, Goley ED, Ramamurthi KS, Xiao J. Light-dependent modulation of protein localization and function in living bacteria cells. Nat Commun 2024; 15:10746. [PMID: 39737933 PMCID: PMC11685620 DOI: 10.1038/s41467-024-54974-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 11/22/2024] [Indexed: 01/01/2025] Open
Abstract
Most bacteria lack membrane-enclosed organelles and rely on macromolecular scaffolds at different subcellular locations to recruit proteins for specific functions. Here, we demonstrate that the optogenetic CRY2-CIB1 system from Arabidopsis thaliana can be used to rapidly direct proteins to different subcellular locations with varying efficiencies in live Escherichia coli cells, including the nucleoid, the cell pole, the membrane, and the midcell division plane. Such light-induced re-localization can be used to rapidly inhibit cytokinesis in actively dividing E. coli cells. We further show that CRY2-CIBN binding kinetics can be modulated by green light, adding a new dimension of control to the system. Finally, we test this optogenetic system in three additional bacterial species, Bacillus subtilis, Caulobacter crescentus, and Streptococcus pneumoniae, providing important considerations for this system's applicability in bacterial cell biology.
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Affiliation(s)
- Ryan McQuillen
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amilcar J Perez
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher H Bohrer
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Erika L Smith
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Kevin E Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Yin Mon Hla
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Joshua W McCausland
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Erin D Goley
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Xiao
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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10
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Raghunandanan S, Zhang K, Zhang Y, Priya R, Sze CW, Lou Y, Lynch MJ, Crane BR, Kaplan MH, Li C, Yang XF. MCP5, a methyl-accepting chemotaxis protein regulated by both the Hk1-Rrp1 and Rrp2-RpoN-RpoS pathways, is required for the immune evasion of Borrelia burgdorferi. PLoS Pathog 2024; 20:e1012327. [PMID: 39775665 PMCID: PMC11723614 DOI: 10.1371/journal.ppat.1012327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 01/10/2025] [Accepted: 12/04/2024] [Indexed: 01/11/2025] Open
Abstract
Borrelia (or Borreliella) burgdorferi, the causative agent of Lyme disease, is a motile and invasive zoonotic pathogen adept at navigating between its arthropod vector and mammalian host. While motility and chemotaxis are well known to be essential for its enzootic cycle, the role of each methyl-accepting chemotaxis proteins (MCPs) in the infectious cycle of B. burgdorferi remains unclear. In this study, we show that mcp5, a gene encoding one of the most abundant MCPs in B. burgdorferi, is differentially expressed in response to environmental signals and at distinct stages of the pathogen's enzootic cycle. Notably, mcp5 expression is regulated by the Hk1-Rrp1 and Rrp2-RpoN-RpoS pathways, two key regulatory pathways that are critical for the spirochete's colonization of the tick vector and mammalian host, respectively. Infection experiments with an mcp5 mutant revealed that spirochetes lacking MCP5 were unable to establish infections in either C3H/HeN mice or Severe Combined Immunodeficiency (SCID) mice, which are deficient in adaptive immunity, underscoring MCP5's critical role in mammalian infection. However, the mcp5 mutant was able to establish infection and disseminate in NOD SCID Gamma (NSG) mice, which are deficient in both adaptive and most innate immune responses, suggesting that MCP5 plays an important role in evading host innate immunity. Moreover, NK cell depletion in C3H and SCID mice restored the infectivity of the mcp5 mutant, further highlighting MCP5's role in evading NK cell-associated immunity. Co-culture assays with NK cells and macrophages revealed that the mcp5 mutant enhanced interferon-gamma production by NK cells. In the tick vector, the mcp5 mutants survived feeding but failed to transmit to mice. These findings reveal that MCP5, regulated by both the Rrp1 and Rrp2 pathways, is critical for establishing infection in mammalian hosts by evading NK cell-mediated host innate immunity and is important for the transmission of spirochetes from ticks to mammalian hosts. This work provides a foundation for further elucidation of chemotactic signals sensed by MCP5 that facilitate B. burgdorferi in evading host defenses.
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Affiliation(s)
- Sajith Raghunandanan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Kai Zhang
- Department of Oral Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Yan Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Raj Priya
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Ching Wooen Sze
- Department of Oral Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Michael J. Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Mark H. Kaplan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Chunhao Li
- Department of Oral Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - X. Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
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11
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Vo L, Avgidis F, Mattingly HH, Edmonds K, Burger I, Balasubramanian R, Shimizu TS, Kazmierczak BI, Emonet T. Non-genetic adaptation by collective migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573956. [PMID: 38260286 PMCID: PMC10802332 DOI: 10.1101/2024.01.02.573956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cell populations must adjust their phenotypic composition to adapt to changing environments. One adaptation strategy is to maintain distinct phenotypic subsets within the population and to modulate their relative abundances via gene regulation. Another strategy involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. We found that the migrating populations became enriched with high-performing swimming phenotypes in each environment, allowing the populations to adapt without requiring mutations or gene regulation. This adaptation is dynamic and rapid, reversing in a few doubling times when migration ceases. By measuring the chemoreceptor abundance distributions during migration towards different attractants, we demonstrated that adaptation acts on multiple chemotaxis-related traits simultaneously. These measurements are consistent with a general mechanism in which adaptation results from a balance between cell growth generating diversity and collective migration eliminating under-performing phenotypes. Thus, collective migration enables cell populations with continuous, multi-dimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions. Significance statement Conventional cell adaptation mechanisms, like gene regulation and stochastic phenotypic switching, act swiftly but are limited to a few traits, while mutation-driven adaptations unfold slowly. By quantifying phenotypic diversity during bacterial collective migration, we discovered an adaptation mechanism that rapidly and reversibly adjusts multiple traits simultaneously. By balancing the generation of diversity through growth with the loss of phenotypes unable to keep up, this process tunes the phenotypic composition of migrating populations to the environments they traverse, without gene regulation or mutations. Given the prevalence of collective migration in microbes, cancers, and embryonic development, non-genetic adaptation through collective migration may be a universal mechanism for populations to navigate diverse environments, offering insights into broader applications across various fields.
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12
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Tao Y, Mu J, Peng L, Yang JL, Liang X. Chemotaxis gene of a bacterium impacts larval settlement and metamorphosis in the marine mussel Mytilus coruscus via c-di-GMP controlling extracellular protein production. BIOFOULING 2024; 40:882-892. [PMID: 39540578 DOI: 10.1080/08927014.2024.2423806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 10/22/2024] [Accepted: 10/25/2024] [Indexed: 11/16/2024]
Abstract
Bacterial chemotaxis enhances bacterial adaptation to the environment and is important for biofilm formation. Biofilms play a key role in inducing larval settlement and metamorphosis in many marine invertebrates. However, the specific mechanisms by which bacterial chemotaxis influences larval settlement and metamorphosis in mussels remain unknown. The findings indicate that the absence of the chemotaxis gene cheW resulted in reduced motility of Pseudoalteromonas marina, accompanied by an increase in c-di-GMP content. The ΔcheW strain exhibited a higher capacity for biofilm formation compared to the wild-type strain. The extracellular protein content of the ΔcheW strain exhibited a significant 77% reduction, specifically in the flagellin content. The inducing activity of ΔcheW was reduced by 56% compared to the wild-type strain. This study highlights that the deficiency of the chemotaxis gene cheW inhibited larval settlement and metamorphosis in mussels through c-di-GMP regulation of extracellular protein production. It provides a novel ecological function of bacterial chemotaxis in regulating the larval settlement and metamorphosis of marine invertebrates.
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Affiliation(s)
- Yu Tao
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai Ocean University, Shanghai, China
| | - Jiayi Mu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai Ocean University, Shanghai, China
| | - Lihua Peng
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai Ocean University, Shanghai, China
| | - Jin-Long Yang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai Ocean University, Shanghai, China
| | - Xiao Liang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-Culture of Aquaculture Animals, Shanghai Ocean University, Shanghai, China
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13
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Hatstat AK, Kormos R, Xu V, DeGrado WF. A designed Zn 2+ sensor domain transmits binding information to transmembrane histidine kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.30.621206. [PMID: 39553995 PMCID: PMC11565981 DOI: 10.1101/2024.10.30.621206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Generating stimulus-responsive, allosteric signaling de novo is a significant challenge in protein design. In natural systems like bacterial histidine kinases (HKs), signal transduction occurs when ligand binding initiates a signal that is amplified across biological membranes over long distances to induce large-scale rearrangements and phosphorylation relays. Here, we ask whether our understanding of protein design and multi-domain, intramolecular signaling has progressed sufficiently to enable engineering of a HK with tunable de novo components. We generated de novo metal-binding sensor domains and substituted them for the native sensor domain of a transmembrane HK, affording chimeras that transduce signals initiated from a de novo sensor. Signaling depended on the designed sensor's stability and the interdomain linker's phase and length. These results show the usefulness of de novo design to elucidate biochemical mechanisms and principles for design of new signaling systems.
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14
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Wang Y, Zhang R, Mathivanan K, Zhang Y, Yang L, Guan F, Duan J. Proteomics and EPS Compositional Analysis Reveals Desulfovibrio bisertensis SY-1 Induced Corrosion on Q235 Steel by Biofilm Formation. MATERIALS (BASEL, SWITZERLAND) 2024; 17:5060. [PMID: 39459765 PMCID: PMC11509735 DOI: 10.3390/ma17205060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 10/01/2024] [Accepted: 10/09/2024] [Indexed: 10/28/2024]
Abstract
Microorganisms that exist in the seawater form microbial biofilms on materials used in marine construction, especially on metal surfaces submerged in seawater, where they form biofilms and cause severe corrosion. Biofilms are mainly composed of bacteria and their secreted polymeric substances. In order to understand how biofilms promote metal corrosion, planktonic and biofilm cells of Desulfovibrio bizertensis SY-1 (D. bizertensis) from Q235 steel were collected and analyzed as to their intracellular proteome and extracellular polymeric substances (EPS). The intracellular proteome analysis showed that the cellular proteins were strongly regulated in biofilm cells compared to planktonic cells, e.g., along with flagellar proteins, signaling-related proteins were significantly increased, whereas energy production and conversion proteins and DNA replication proteins were significantly regulated. The up-and-down regulation of proteins revealed that biofilm formation by bacteria on metal surfaces is affected by flagellar and signaling proteins. A significant decrease in DNA replication proteins indicated that DNA is no longer replicated and transcribed in mature biofilms, thus reducing energy consumption. Quantitative analysis and lectin staining of the biofilm on the metal's surface revealed that the bacteria secreted a substantial amount of EPS when they began to attach to the surface, and proteins dominated the main components of EPS. Further, the infrared analysis showed that the secondary structure of the proteins in the EPS of the biofilm was mainly dominated by β-sheet and 3-turn helix, which may help to enhance the adhesion of EPS. The functional groups of EPS analyzed using XPS showed that the C element of EPS in the biofilm mainly existed in the form of combinations with N. Furthermore, the hydroxyl structure in the EPS extracted from the biofilm had a stronger hydrogen bonding effect, which could maintain the stability of the EPS structure and biofilm. The study results revealed that D. bizertensis regulates the metabolic pathways and their secreted EPS structure to affect biofilm formation and cause metal corrosion, which has a certain reference significance for the study of the microbially influenced corrosion (MIC) mechanism.
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Affiliation(s)
- Yanan Wang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (K.M.); (Y.Z.); (L.Y.); (F.G.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruiyong Zhang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (K.M.); (Y.Z.); (L.Y.); (F.G.)
- Guangxi Key Laboratory of Marine Environmental Science, Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, Nanning 530007, China
| | - Krishnamurthy Mathivanan
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (K.M.); (Y.Z.); (L.Y.); (F.G.)
| | - Yimeng Zhang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (K.M.); (Y.Z.); (L.Y.); (F.G.)
| | - Luhua Yang
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (K.M.); (Y.Z.); (L.Y.); (F.G.)
| | - Fang Guan
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (K.M.); (Y.Z.); (L.Y.); (F.G.)
- Guangxi Key Laboratory of Marine Environmental Science, Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, Nanning 530007, China
| | - Jizhou Duan
- Key Laboratory of Advanced Marine Materials, Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (K.M.); (Y.Z.); (L.Y.); (F.G.)
- Guangxi Key Laboratory of Marine Environmental Science, Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, Nanning 530007, China
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15
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Baillou R, Ranft J. Nonequilibrium cluster-cluster aggregation in the presence of anchoring sites. Phys Rev E 2024; 110:034410. [PMID: 39425304 DOI: 10.1103/physreve.110.034410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 08/15/2024] [Indexed: 10/21/2024]
Abstract
Nonequilibrium cluster-cluster aggregation of particles diffusing in or at the cell membrane has been hypothesized to lead to domains of finite size in different biological contexts, such as lipid rafts, cell adhesion complexes, or postsynaptic domains in neurons. In this scenario, the desorption of particles balances a continuous flux to the membrane, imposing a cutoff on possible aggregate sizes and giving rise to a stationary size distribution. Here, we investigate the case of nonequilibrium cluster-cluster aggregation in two dimensions where diffusing particles and/or clusters remain fixed in space at specific anchoring sites, which should be particularly relevant for synapses but may also be present in other biological or physical systems. Using an effective mean-field description of the concentration field around anchored clusters, we derive an expression for their average size as a function of parameters such as the anchoring site density. We furthermore propose and solve appropriate rate equations that allow us to predict the size distributions of both diffusing and fixed clusters. We confirm our results with particle-based simulations and discuss potential implications for biological and physical systems.
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16
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Fu R, Feng H. Deciphering Bacterial Chemorepulsion: The Complex Response of Microbes to Environmental Stimuli. Microorganisms 2024; 12:1706. [PMID: 39203548 PMCID: PMC11357200 DOI: 10.3390/microorganisms12081706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/16/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
Bacterial motility relying on flagella is characterized by several modes, including swimming, swarming, twitching, and gliding. This motility allows bacteria to adapt remarkably well to hostile environments. More than 50% of bacteria naturally contain flagella, which are crucial for bacterial chemotaxis motility. Chemotaxis can be either positive, where bacteria move towards a chemical source, or negative, known as chemorepulsion, where bacteria move away from the source. Although much is known about the mechanisms driving chemotaxis towards attractants, the molecular mechanisms underlying chemorepulsion remain elusive. Chemotaxis plays an important role in the colonization of the rhizosphere by rhizobacteria. Recently, researchers have systematically studied the identification and recognition mechanisms of chemoattractants. However, the mechanisms underlying chemorepellents remain unclear. Systematically sorting and analyzing research on chemorepellents could significantly enhance our understanding of how these compounds help probiotics evade harmful environments or drive away pathogens.
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Affiliation(s)
- Ruixin Fu
- School of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China;
| | - Haichao Feng
- College of Agriculture, Henan University, Kaifeng 475004, China
- Food Laboratory of Zhongyuan, Henan University, Luohe 462300, China
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17
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Raghunandanan S, Zhang K, Zhang Y, Sze CW, Priya R, Luo Y, Lynch MJ, Crane BR, Li C, Yang XF. MCP5, a methyl-accepting chemotaxis protein regulated by both the Hk1-Rrp1 and Rrp2-RpoN-RpoS pathways, is required for the immune evasion of Borrelia burgdorferi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598185. [PMID: 38915556 PMCID: PMC11195095 DOI: 10.1101/2024.06.10.598185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Borrelia (or Borreliella) burgdorferi, the causative agent of Lyme disease, is a motile and invasive zoonotic pathogen, adept at navigating between its arthropod vector and mammalian host. While motility and chemotaxis are well established as essential for its enzootic cycle, the function of methyl-accepting chemotaxis proteins (MCPs) in the infectious cycle of B. burgdorferi remains unclear. In this study, we demonstrate that MCP5, one of the most abundant MCPs in B. burgdorferi, is differentially expressed in response to environmental signals as well as at different stages of the pathogen's enzootic cycle. Specifically, the expression of mcp5 is regulated by the Hk1-Rrp1 and Rrp2-RpoN-RpoS pathways, which are critical for the spirochete's colonization of the tick vector and mammalian host, respectively. Infection experiments with an mcp5 mutant revealed that spirochetes lacking MCP5 could not establish infections in either C3H/HeN mice or Severe Combined Immunodeficiency (SCID) mice, which are defective in adaptive immunity, indicating the essential role of MCP5 in mammalian infection. However, the mcp5 mutant could establish infection and disseminate in NOD SCID Gamma (NSG) mice, which are deficient in both adaptive and most innate immune responses, suggesting a crucial role of MCP5 in evading host innate immunity. In the tick vector, the mcp5 mutants survived feeding but failed to transmit to mice, highlighting the importance of MCP5 in transmission. Our findings reveal that MCP5, regulated by the Rrp1 and Rrp2 pathways, is critical for the establishment of infection in mammalian hosts by evading host innate immunity and is important for the transmission of spirochetes from ticks to mammalian hosts, underscoring its potential as a target for intervention strategies.
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Affiliation(s)
- Sajith Raghunandanan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Kai Zhang
- Department of Oral Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, 23298
| | - Yan Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China, 325035
| | - Ching Wooen Sze
- Department of Oral Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, 23298
| | - Raj Priya
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Yongliang Luo
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China, 325035
| | - Michael J Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chunhao Li
- Department of Oral Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, 23298
| | - X. Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
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18
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Andrews SS, Kochen M, Smith L, Feng S, Wiley HS, Sauro HM. Signal integration and integral feedback control with biochemical reaction networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591337. [PMID: 38746178 PMCID: PMC11092504 DOI: 10.1101/2024.04.26.591337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Biochemical reaction networks perform a variety of signal processing functions, one of which is computing the integrals of signal values. This is often used in integral feedback control, where it enables a system's output to respond to changing inputs, but to then return exactly back to some pre-determined setpoint value afterward. To gain a deeper understanding of how biochemical networks are able to both integrate signals and perform integral feedback control, we investigated these abilities for several simple reaction networks. We found imperfect overlap between these categories, with some networks able to perform both tasks, some able to perform integration but not integral feedback control, and some the other way around. Nevertheless, networks that could either integrate or perform integral feedback control shared key elements. In particular, they included a chemical species that was neutrally stable in the open loop system (no feedback), meaning that this species does not have a unique stable steady-state concentration. Neutral stability could arise from zeroth order decay reactions, binding to a partner that was produced at a constant rate (which occurs in antithetic control), or through a long chain of covalent cycles. Mathematically, it arose from rate equations for the reaction network that were underdetermined when evaluated at steady-state.
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19
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Kannaiah S, Goldberger O, Alam N, Barnabas G, Pozniak Y, Nussbaum-Shochat A, Schueler-Furman O, Geiger T, Amster-Choder O. MinD-RNase E interplay controls localization of polar mRNAs in E. coli. EMBO J 2024; 43:637-662. [PMID: 38243117 PMCID: PMC10897333 DOI: 10.1038/s44318-023-00026-9] [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: 02/03/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
The E. coli transcriptome at the cell's poles (polar transcriptome) is unique compared to the membrane and cytosol. Several factors have been suggested to mediate mRNA localization to the membrane, but the mechanism underlying polar localization of mRNAs remains unknown. Here, we combined a candidate system approach with proteomics to identify factors that mediate mRNAs localization to the cell poles. We identified the pole-to-pole oscillating protein MinD as an essential factor regulating polar mRNA localization, although it is not able to bind RNA directly. We demonstrate that RNase E, previously shown to interact with MinD, is required for proper localization of polar mRNAs. Using in silico modeling followed by experimental validation, the membrane-binding site in RNase E was found to mediate binding to MinD. Intriguingly, not only does MinD affect RNase E interaction with the membrane, but it also affects its mode of action and dynamics. Polar accumulation of RNase E in ΔminCDE cells resulted in destabilization and depletion of mRNAs from poles. Finally, we show that mislocalization of polar mRNAs may prevent polar localization of their protein products. Taken together, our findings show that the interplay between MinD and RNase E determines the composition of the polar transcriptome, thus assigning previously unknown roles for both proteins.
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Affiliation(s)
- Shanmugapriya Kannaiah
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA.
| | - Omer Goldberger
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Georgina Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Pathology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yair Pozniak
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100001, Rehovot, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
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20
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Oh D, Liu X, Sheetz MP, Kenney LJ. Small, Dynamic Clusters of Tir-Intimin Seed Actin Polymerization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302580. [PMID: 37649226 DOI: 10.1002/smll.202302580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/26/2023] [Indexed: 09/01/2023]
Abstract
The understanding of actin pedestal formation by enteropathogenic Escherichia coli (EPEC) relies mainly on static ensemble information obtained from cell lysates. Here, the dynamic nature of signaling components on the subsecond timescale, which resemble phase condensates, is demonstrated. Unlike in vitro phase condensates, transfected intimin receptor (Tir) and downstream component form clusters 200 nm in diameter that are spaced ≈500 nm on average, indicating cellular regulation. On supported lipid bilayers with diffusive intimin, Tir-expressing fibroblasts formed Tir-intimin clusters even without Tir tyrosines, although Tir tyrosine phosphorylation is necessary for actin polymerization from clusters. Single-molecule tracking showed that Tir is diffusive in the clusters and exchanges with Tir in the plasma membrane. Further, Nck and N-WASP bind to the clusters and exchange with cytoplasmic molecules. Tir has a similar cluster lifetime to Nck, but longer than that of N-WASP. Actin polymerization from the clusters requires N-WASP binding, involved Arp2/3 activation, and stabilized N-WASP clusters. These dynamic properties are distinct from larger in vitro systems and do not depend significantly upon crosslinking. Thus, Tir-intimin clusters in the plasma membrane are limited in size by exchange and enhance signaling needed for actin polymerization that enables strong and stable bacterial attachment to host cells.
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Affiliation(s)
- Dongmyung Oh
- Mechanobiology Institute, National University of Singapore, bukit timah, 117411, Singapore
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Xuyao Liu
- Mechanobiology Institute, National University of Singapore, bukit timah, 117411, Singapore
| | - Michael P Sheetz
- Mechanobiology Institute, National University of Singapore, bukit timah, 117411, Singapore
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Linda J Kenney
- Mechanobiology Institute, National University of Singapore, bukit timah, 117411, Singapore
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
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21
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Plotkin BJ, Halkyard S, Spoolstra E, Micklo A, Kaminski A, Sigar IM, Konaklieva MI. The Role of the Insulin/Glucose Ratio in the Regulation of Pathogen Biofilm Formation. BIOLOGY 2023; 12:1432. [PMID: 37998031 PMCID: PMC10669081 DOI: 10.3390/biology12111432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
During the management of patients in acute trauma the resulting transient hyperglycemia is treated by administration of insulin. Since the effect of insulin, a quorum sensing compound, together with glucose affects biofilm formation in a concentration-specific manner, we hypothesize that the insulin/glucose ratio over the physiologic range modulates biofilm formation potentially influencing the establishment of infection through biofilm formation. METHODS A variety of Gram-positive and Gram-negative bacteria were grown in peptone (1%) yeast nitrogen base broth overnight in 96-well plates with various concentrations of glucose and insulin. Biofilm formation was determined by the crystal violet staining procedure. Expression of insulin binding was determined by fluorescent microscopy (FITC-insulin). Controls were buffer alone, insulin alone, and glucose alone. RESULTS Overall, maximal biofilm levels were measured at 220 mg/dL of glucose, regardless of insulin concentration (10, 100, 200 µU/mL) of the organism tested. In general, insulin with glucose over the range of 160-180 mg/dL exhibited a pattern of biofilm suppression. However, either above or below this range, the presence of insulin in combination with glucose significantly modulated (increase or decrease) biofilm formation in a microbe-specific pattern. This modulation appears for some organisms to be reflective of the glucose-regulated intrinsic expression of bacterial insulin receptor expression. CONCLUSION Insulin at physiologic levels (normal and hyperinsulinemic) in combination with glucose can affect biofilm formation in a concentration-specific and microbe-specific manner. These findings may provide insight into the importance of co-regulation of the insulin/glucose ratio in patient management.
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Affiliation(s)
- Balbina J. Plotkin
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL 60515, USA; (S.H.); (E.S.); (A.M.); (A.K.); (I.M.S.)
| | - Scott Halkyard
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL 60515, USA; (S.H.); (E.S.); (A.M.); (A.K.); (I.M.S.)
| | - Emily Spoolstra
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL 60515, USA; (S.H.); (E.S.); (A.M.); (A.K.); (I.M.S.)
| | - Amanda Micklo
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL 60515, USA; (S.H.); (E.S.); (A.M.); (A.K.); (I.M.S.)
| | - Amber Kaminski
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL 60515, USA; (S.H.); (E.S.); (A.M.); (A.K.); (I.M.S.)
| | - Ira M. Sigar
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL 60515, USA; (S.H.); (E.S.); (A.M.); (A.K.); (I.M.S.)
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22
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Yue C, Zhang C, Zhang R, Yuan J. Tethered particle motion of the adaptation enzyme CheR in bacterial chemotaxis. iScience 2023; 26:107950. [PMID: 37817931 PMCID: PMC10561060 DOI: 10.1016/j.isci.2023.107950] [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: 05/09/2023] [Revised: 07/25/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
Bacteria perform chemotactic adaptation by sequential modification of multiple modifiable sites on chemoreceptors through stochastic action of tethered adaptation enzymes (CheR and CheB). To study the molecular kinetics of this process, we measured the response to different concentrations of MeAsp for the Tar-only Escherichia coli strain. We found a strong dependence of the methylation rate on the methylation level and established a new mechanism of adaptation kinetics due to tethered particle motion of the methylation enzyme CheR. Experiments with various lengths of the C-terminal flexible chain in the Tar receptor further validated this mechanism. The tethered particle motion resulted in a CheR concentration gradient that ensures encounter-rate matching of the sequential modifiable sites. An analytical model of multisite catalytic reaction showed that this enables robustness of methylation to fluctuations in receptor activity or cell-to-cell variations in the expression of adaptation enzymes and reduces the variation in methylation level among individual receptors.
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Affiliation(s)
- Caijuan Yue
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chi Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rongjing Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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23
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Salar S, Ball NE, Baaziz H, Nix JC, Sobe RC, Compton KK, Zhulin IB, Brown AM, Scharf BE, Schubot FD. The structural analysis of the periplasmic domain of Sinorhizobium meliloti chemoreceptor McpZ reveals a novel fold and suggests a complex mechanism of transmembrane signaling. Proteins 2023; 91:1394-1406. [PMID: 37213073 PMCID: PMC10524373 DOI: 10.1002/prot.26510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/23/2023]
Abstract
Chemotaxis is a fundamental process whereby bacteria seek out nutrient sources and avoid harmful chemicals. For the symbiotic soil bacterium Sinorhizobium meliloti, the chemotaxis system also plays an essential role in the interaction with its legume host. The chemotactic signaling cascade is initiated through interactions of an attractant or repellent compound with chemoreceptors or methyl-accepting chemotaxis proteins (MCPs). S. meliloti possesses eight chemoreceptors to mediate chemotaxis. Six of these receptors are transmembrane proteins with periplasmic ligand-binding domains (LBDs). The specific functions of McpW and McpZ are still unknown. Here, we report the crystal structure of the periplasmic domain of McpZ (McpZPD) at 2.7 Å resolution. McpZPD assumes a novel fold consisting of three concatenated four-helix bundle modules. Through phylogenetic analyses, we discovered that this helical tri-modular domain fold arose within the Rhizobiaceae family and is still evolving rapidly. The structure, offering a rare view of a ligand-free dimeric MCP-LBD, reveals a novel dimerization interface. Molecular dynamics calculations suggest ligand binding will induce conformational changes that result in large horizontal helix movements within the membrane-proximal domains of the McpZPD dimer that are accompanied by a 5 Å vertical shift of the terminal helix toward the inner cell membrane. These results suggest a mechanism of transmembrane signaling for this family of MCPs that entails both piston-type and scissoring movements. The predicted movements terminate in a conformation that closely mirrors those observed in related ligand-bound MCP-LBDs.
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Affiliation(s)
- Safoura Salar
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Nicolas E. Ball
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Hiba Baaziz
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jay C. Nix
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Richard C. Sobe
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - K. Karl Compton
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Igor B. Zhulin
- Department of Microbiology & Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210
| | - Anne M. Brown
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Birgit E. Scharf
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Florian D. Schubot
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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24
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Raza MR, George JE, Kumari S, Mitra MK, Paul D. Anomalous diffusion of E. coli under microfluidic confinement and chemical gradient. SOFT MATTER 2023; 19:6446-6457. [PMID: 37606542 DOI: 10.1039/d3sm00286a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
We report a two-layer microfluidic device to study the combined effect of confinement and chemical gradient on the motility of wild-type E. coli. We track individual E. coli in 50 μm and 10 μm wide microchannels, with a channel height of 2 μm, to generate quasi-2D conditions. We find that contrary to expectations, bacterial trajectories are superdiffusive even in the absence of a chemical (glucose) gradient. The superdiffusive behaviour becomes more pronounced upon introducing a chemical gradient or strengthening the lateral confinement. Run length distributions for weak lateral confinement in the absence of chemical gradients follow an exponential distribution. Both confinement and chemoattraction induce deviations from this behaviour, with the run length distributions approaching a power-law form under these conditions. Both confinement and chemoattraction suppress large-angle tumbles as well. Our results suggest that wild-type E. coli modulates both its runs and tumbles in a similar manner under physical confinement and chemical gradient. Our findings have implications for understanding how bacteria modulate their motility behaviour in natural habitats.
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Affiliation(s)
- Md Ramiz Raza
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Jijo Easo George
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Savita Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Mithun K Mitra
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Debjani Paul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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25
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Irazoki O, Ter Beek J, Alvarez L, Mateus A, Colin R, Typas A, Savitski MM, Sourjik V, Berntsson RPA, Cava F. D-amino acids signal a stress-dependent run-away response in Vibrio cholerae. Nat Microbiol 2023; 8:1549-1560. [PMID: 37365341 PMCID: PMC10390336 DOI: 10.1038/s41564-023-01419-6] [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: 01/03/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
To explore favourable niches while avoiding threats, many bacteria use a chemotaxis navigation system. Despite decades of studies on chemotaxis, most signals and sensory proteins are still unknown. Many bacterial species release D-amino acids to the environment; however, their function remains largely unrecognized. Here we reveal that D-arginine and D-lysine are chemotactic repellent signals for the cholera pathogen Vibrio cholerae. These D-amino acids are sensed by a single chemoreceptor MCPDRK co-transcribed with the racemase enzyme that synthesizes them under the control of the stress-response sigma factor RpoS. Structural characterization of this chemoreceptor bound to either D-arginine or D-lysine allowed us to pinpoint the residues defining its specificity. Interestingly, the specificity for these D-amino acids appears to be restricted to those MCPDRK orthologues transcriptionally linked to the racemase. Our results suggest that D-amino acids can shape the biodiversity and structure of complex microbial communities under adverse conditions.
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Affiliation(s)
- Oihane Irazoki
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Laura Alvarez
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology, and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden.
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26
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Heuermann D, Döll S, Schweneker D, Feuerstein U, Gentsch N, von Wirén N. Distinct metabolite classes in root exudates are indicative for field- or hydroponically-grown cover crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122285. [PMID: 37089658 PMCID: PMC10118039 DOI: 10.3389/fpls.2023.1122285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Introduction Plants release a large variety of metabolites via their roots to shape physico-chemical soil properties and biological processes in the rhizosphere. While hydroponic growth conditions facilitate accessibility of the root system and recovery of root exudates, the natural soil environment can alter root metabolism and exudate secretion, raising the question to what extent the quantity and composition of root exudates released in hydroponic growth systems reflect those recovered from soil-grown roots. Methods Using a root washing method, we sampled root exudates from four field-grown cover crop species with wide taxonomic distance, namely white mustard, lacy phacelia, bristle oat, and Egyptian clover. A set of primary metabolites and secondary metabolites were analysed in a targeted and untargeted LC-MS-based approach, respectively, for comparison with exudates obtained from hydroponically cultured plants. Results and discussion We found that hydroponically cultivated plants released a larger amount of total carbon, but that the recovery of total carbon was not indicative for the diversity of metabolites in root exudates. In the field, root exudates from phacelia and clover contained 2.4 to 3.8 times more secondary metabolites, whereas carbon exudation in hydroponics was 5- to 4-fold higher. The composition of the set of metabolites identified using the untargeted approach was much more distinct among all species and growth conditions than that of quantified primary metabolites. Among secondary metabolite classes, the presence of lipids and lipid-like molecules was highly indicative for field samples, while the release of a large amount of phenylpropanoids, organoheterocyclic compounds or benzenoids was characteristic for clover, mustard or oat, respectively, irrespective of the cultivation condition. However, at the compound level the bulk of released metabolites was specific for cultivation conditions in every species, which implies that hydroponically sampled root exudates poorly reflect the metabolic complexity of root exudates recovered from field-grown plants.
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Affiliation(s)
- Diana Heuermann
- Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Seeland, Germany
| | - Stefanie Döll
- Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Dörte Schweneker
- Deutsche Saatveredelung Aktiengesellschaft (AG), Asendorf, Germany
| | - Ulf Feuerstein
- Deutsche Saatveredelung Aktiengesellschaft (AG), Asendorf, Germany
| | - Norman Gentsch
- Institute of Soil Science, Leibniz Universität Hannover, Hannover, Germany
| | - Nicolaus von Wirén
- Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Seeland, Germany
- *Correspondence: Nicolaus von Wirén,
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27
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Li X, Shim S, Hardin KR, Vanaja KG, Song H, Levchenko A, Ming GL, Zheng JQ. Signal amplification in growth cone gradient sensing by a double negative feedback loop among PTEN, PI(3,4,5)P 3 and actomyosin. Mol Cell Neurosci 2022; 123:103772. [PMID: 36055521 PMCID: PMC9856701 DOI: 10.1016/j.mcn.2022.103772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 01/24/2023] Open
Abstract
Axon guidance during neural wiring involves a series of precisely controlled chemotactic events by the motile axonal tip, the growth cone. A fundamental question is how neuronal growth cones make directional decisions in response to extremely shallow gradients of guidance cues with exquisite sensitivity. Here we report that nerve growth cones possess a signal amplification mechanism during gradient sensing process. In neuronal growth cones of Xenopus spinal neurons, phosphatidylinositol-3,4,5-trisphosphate (PIP3), an important signaling molecule in chemotaxis, was actively recruited to the up-gradient side in response to an external gradient of brain-derived neurotrophic factor (BDNF), resulting in an intracellular gradient with approximate 30-fold amplification of the input. Furthermore, a reverse gradient of phosphatase and tensin homolog (PTEN) was induced by BDNF within the growth cone and the increased PTEN activity at the down-gradient side is required for the amplification of PIP3 signals. Mechanistically, the establishment of both positive PIP3 and reverse PTEN gradients depends on the filamentous actin network. Together with computational modeling, our results revealed a double negative feedback loop among PTEN, PIP3 and actomyosin for signal amplification, which is essential for gradient sensing of neuronal growth cones in response to diffusible cues.
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Affiliation(s)
- Xiong Li
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Sangwoo Shim
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Department of Cell Biology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
| | - Katherine R Hardin
- Department of Cell Biology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
| | - Kiran G Vanaja
- Department of Biomedical Engineering and Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Andre Levchenko
- Department of Biomedical Engineering and Yale Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Guo-Li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - James Q Zheng
- Department of Cell Biology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA.
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28
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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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29
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Zhang Y, Mao G, Liu R, Zhou X, Bartlam M, Wang Y. Transcriptome Profiling of Stenotrophomonas sp. Strain WZN-1 Reveals Mechanisms of 2,2',4,4'-Tetrabromodiphenyl Ether (BDE-47) Biotransformation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11288-11299. [PMID: 35881891 DOI: 10.1021/acs.est.2c00197] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The brominated flame retardant 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) is extensively used, stable, and difficult to degrade in the environment. The existence of BDE-47 could pose a certain risk to the environment and human health. However, the biotransformation mechanisms of BDE-47 by microorganisms remain unclear. In this study, aerobic degradation of BDE-47 by Stenotrophomonas sp. strain WZN-1 and transcriptome analysis were carried out. BDE-47 degradation by Stenotrophomonas sp. strain WZN-1 was mainly through the biological action of intracellular enzymes via the route of debromination and hydroxylation. The results of the transcriptome sequencing indicated the differentially expressed genes were related to transport, metabolism, and stress response. The key processes involved the microbial transmembrane transportation of BDE-47, energy anabolism, synthesis, and metabolism of functional enzymes, stress response, and other biological processes of gene regulation. In particular, bacterial chemotaxis played a potential role in biodegradation of BDE-47 by Stenotrophomonas sp. strain WZN-1. This study provides the first insights into the biotransformation of Stenotrophomonas sp. strain WZN-1 to BED-47 stress and shows potential for application in remediation of polluted environments.
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Affiliation(s)
- Yadi Zhang
- Key Laboratory Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, 300350, China
| | - Guannan Mao
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research,Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruidan Liu
- Key Laboratory Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, 300350, China
| | - Xinzhu Zhou
- Key Laboratory Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, 300350, China
| | - Mark Bartlam
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, 300071, China
| | - Yingying Wang
- Key Laboratory Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, 300350, China
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30
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Zhao X, Ford RM. Escherichia coli chemotaxis to competing stimuli in a microfluidic device with a constant gradient. Biotechnol Bioeng 2022; 119:2564-2573. [PMID: 35716141 DOI: 10.1002/bit.28161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/20/2022] [Accepted: 06/08/2022] [Indexed: 11/07/2022]
Abstract
In natural systems bacteria are exposed to many chemical stimulants; some attract chemotactic bacteria as they promote survival, while others repel bacteria because they inhibit survival. When faced with a mixture of chemoeffectors, it is not obvious which direction the population will migrate. Predicting this direction requires an understanding of how bacteria process information about their surroundings. We used a multiscale mathematical model to relate molecular level details of their two-component signaling system to the probability that an individual cell changes its swimming direction to the chemotactic velocity of a bacterial population. We used a microfluidic device designed to maintain a constant chemical gradient to compare model predictions to experimental observations. We obtained parameter values for the multiscale model of Escherichia coli chemotaxis to individual stimuli, α-methylaspartate and nickel ion, separately. Then without any additional fitting parameters, we predicted bacteria response to chemoeffector mixtures. Migration of E. coli toward α-methylaspartate was modulated by adding increasing concentrations of nickel ion. Thus, the migration direction was controlled by the relative concentrations of competing chemoeffectors in a predictable way. This study demonstrated the utility of a multiscale model to predict the migration direction of bacteria in the presence of competing chemoeffectors. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xueying Zhao
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
| | - Roseanne M Ford
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
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31
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Yue G, Liu Q. Cooperative Target Tracking Algorithm based on Massive Beacon Coordinates System in Directional Molecular Communication. IEEE Trans Nanobioscience 2022; 21:405-415. [PMID: 35380965 DOI: 10.1109/tnb.2022.3164835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
As nanotechnology advances, it is possible to build nanomachines to conduct tasks on the nano-scale. Since the EM wave, the traditional communication medium does not apply in nano-scale, Molecular Communication (MC) has been recently given increasing attention for its excellent biocompatibility and low energy consumption within the human body. Diffusion channel-based MC(DbMC) is mainly studied in the aquatic environment. However, due to the randomness of diffusion, DbMC suffers high losses, low propagation speed, and limited communication range. Directional Molecular Communication(DMC) is proposed by introducing chemotaxis. DMC can significantly improve the efficiency of molecular communication because it keeps molecules moving along a predetermined path. It is particularly suitable in the scenario of target tracking related to some applications such as drug delivery. In this paper, we have proposed a novel massive beacon coordinates system model to aid target tracking. Beacons in this system navigate nanomachines, and the beacon system can uniquely determine their position coordinates. Each nanomachine carries a lot of bacteria carrier (E.coli) to share information. Information is encoded in DNA molecules and transferred to other nanomachines by bacteria carriers. With the help of bacteria carriers, nanomachines can share their current position information with others to realize cooperated fast target tracking. We have evaluated its performance in target tracking through simulation by comparison with the diffusion-based model. Some key factors that may influence target tracking are also taken into consideration.
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32
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Sengupta K, Hivarkar SS, Palevich N, Chaudhary PP, Dhakephalkar PK, Dagar SS. Genomic architecture of three newly isolated unclassified Butyrivibrio species elucidate their potential role in the rumen ecosystem. Genomics 2022; 114:110281. [DOI: 10.1016/j.ygeno.2022.110281] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/31/2022] [Indexed: 11/25/2022]
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33
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Mou F, Xie Q, Liu J, Che S, Bahmane L, You M, Guan J. ZnO-based micromotors fueled by CO 2: the first example of self-reorientation-induced biomimetic chemotaxis. Natl Sci Rev 2021; 8:nwab066. [PMID: 34876993 PMCID: PMC8645024 DOI: 10.1093/nsr/nwab066] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/08/2021] [Accepted: 04/11/2021] [Indexed: 12/18/2022] Open
Abstract
Synthetic chemotactic micro/nanomotors are envisioned to actively ‘seek out’ targets by following specific chemicals, but they are mainly powered by bioincompatible fuels and only show pseudochemotaxis (or advanced chemokinesis) due to their weak self-reorientation capabilities. Here we demonstrate that synthetic ZnO-based Janus micromotors can be powered by the alternative biocompatible fuel of CO2, and further provide the first example of self-reorientation-induced biomimetic chemotaxis using them. The ZnO-based micromotors are highly sensitive to dissolved CO2 in water, which enables the corrosion of ZnO to continuously occur by providing H+ through hydration. Thus, they can autonomously move even in water exposed to air based on self-diffusiophoresis. Furthermore, they can sense the local CO2 gradient and perform positive chemotaxis by self-reorientations under the phoretic torque. Our discovery opens a gate to developing intelligent micro/nanomotors powered by, and sensitive to, biocompatible atmospheric or endogenous gaseous chemicals for biomedical and environmental applications.
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Affiliation(s)
- Fangzhi Mou
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - Qi Xie
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - Jianfeng Liu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - Shengping Che
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - Lamya Bahmane
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - Ming You
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - Jianguo Guan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
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Colin R, Ni B, Laganenka L, Sourjik V. Multiple functions of flagellar motility and chemotaxis in bacterial physiology. FEMS Microbiol Rev 2021; 45:fuab038. [PMID: 34227665 PMCID: PMC8632791 DOI: 10.1093/femsre/fuab038] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model bacteria. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
| | - Bin Ni
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
- College of Resources and Environmental Science, National Academy of Agriculture Green Development, China Agricultural University, Yuanmingyuan Xilu No. 2, Beijing 100193, China
| | - Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
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Dynamics of the Two Stator Systems in the Flagellar Motor of Pseudomonas aeruginosa Studied by a Bead Assay. Appl Environ Microbiol 2021; 87:e0167421. [PMID: 34524895 DOI: 10.1128/aem.01674-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a robust bead assay for studying flagellar motor behavior of Pseudomonas aeruginosa. Using this assay, we studied the dynamics of the two stator systems in the flagellar motor. We found that the two sets of stators function differently, with MotAB stators providing higher total torque and MotCD stators ensuring more stable motor speed. The motors in wild-type cells adjust the stator compositions according to the environment, resulting in an optimal performance in environmental exploration compared to that of mutants with one set of stators. The bead assay we developed in this investigation can be further used to study P. aeruginosa chemotaxis at the level of a single cell using the motor behavior as the chemotaxis output. IMPORTANCE Cells of Pseudomonas aeruginosa possess a single polar flagellum, driven by a rotatory motor powered by two sets of torque-generating units (stators). We developed a robust bead assay for studying the behavior of the flagellar motor in P. aeruginosa, by attaching a microsphere to shortened flagellar filament and using it as an indicator of motor rotation. Using this assay, we revealed the dynamics of the two stator systems in the flagellar motor and found that the motors in wild-type cells adjust the stator compositions according to the environment, resulting in an optimal performance in environmental exploration compared to that of mutants with one set of stators.
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Seco EM, Fernández LÁ. Efficient markerless integration of genes in the chromosome of probiotic E. coli Nissle 1917 by bacterial conjugation. Microb Biotechnol 2021; 15:1374-1391. [PMID: 34755474 PMCID: PMC9049610 DOI: 10.1111/1751-7915.13967] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 01/30/2023] Open
Abstract
The probiotic strain Escherichia coli Nissle 1917 (EcN) is a common bacterial chassis in synthetic biology developments for therapeutic applications given its long track record of safe administration in humans. Chromosomal integration of the genes of interest (GOIs) in the engineered bacterium offers significant advantages in genetic stability and to control gene dose, but common methodologies relying on the transformation of EcN are inefficient. In this work, we implement in EcN the use of bacterial conjugation in combination with markerless genome engineering to efficiently insert multiple GOIs at different loci of EcN chromosome, leaving no antibiotic resistance genes, vector sequences or scars in the modified bacterium. The resolution of cointegrants that leads to markerless insertion of the GOIs requires expression of I-SceI endonuclease and its efficiency is enhanced by λ Red proteins. We show the potential of this strategy by integrating different genes encoding fluorescent and bioluminescent reporters (i.e. GFP, mKate2, luxCDABE) both individually and sequentially. We also demonstrate its application for gene deletions in EcN (ΔflhDC) and to replace the endogenous regulation of chromosomal locus (i.e. flhDC) by heterologous regulatory elements (e.g. tetR-Ptet) in order to have an ectopic control of gene expression in EcN with an external inducer to alter bacterial behaviour (e.g. flagellar motility). Whole-genome sequencing confirmed the introduction of the designed modifications without off-target alterations in the genome. This straightforward approach accelerates the generation of multiple modifications in EcN chromosome for the generation of living bacterial therapeutics.
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Affiliation(s)
- Elena M Seco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, Madrid, 28049, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, Madrid, 28049, Spain
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Ryzhykau YL, Vlasov AV, Orekhov PS, Rulev MI, Rogachev AV, Vlasova AD, Kazantsev AS, Verteletskiy DP, Skoi VV, Brennich ME, Pernot P, Murugova TN, Gordeliy VI, Kuklin AI. Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II-transducer complex. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1386-1400. [PMID: 34726167 DOI: 10.1107/s2059798321009542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/14/2021] [Indexed: 01/14/2023]
Abstract
Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII-NpHtrII) was performed. The influence of the polydispersity of NpSRII-NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.
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Affiliation(s)
- Yury L Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Philipp S Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Maksim I Rulev
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Andrey V Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Anastasia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Alexander S Kazantsev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Dmitry P Verteletskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Vadim V Skoi
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Martha E Brennich
- Synchrotron Crystallography Team, EMBL Grenoble Outstation, 38042 Grenoble, France
| | - Petra Pernot
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Tatiana N Murugova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Alexander I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
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The Only Chemoreceptor Encoded by che Operon Affects the Chemotactic Response of Agrobacterium to Various Chemoeffectors. Microorganisms 2021; 9:microorganisms9091923. [PMID: 34576817 PMCID: PMC8466855 DOI: 10.3390/microorganisms9091923] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 12/16/2022] Open
Abstract
Chemoreceptor (also called methyl-accepting chemotaxis protein, MCP) is the leading signal protein in the chemotaxis signaling pathway. MCP senses and binds chemoeffectors, specifically, and transmits the sensed signal to downstream proteins of the chemotaxis signaling system. The genome of Agrobacterium fabrum (previously, tumefaciens) C58 predicts that a total of 20 genes can encode MCP, but only the MCP-encoding gene atu0514 is located inside the che operon. Hence, the identification of the exact function of atu0514-encoding chemoreceptor (here, named as MCP514) will be very important for us to understand more deeply the chemotaxis signal transduction mechanism of A. fabrum. The deletion of atu0514 significantly decreased the chemotactic migration of A. fabrum in a swim plate. The test of atu0514-deletion mutant (Δ514) chemotaxis toward single chemicals showed that the deficiency of MCP514 significantly weakened the chemotactic response of A. fabrum to four various chemicals, sucrose, valine, citric acid and acetosyringone (AS), but did not completely abolish the chemotactic response. MCP514 was localized at cell poles although it lacks a transmembrane (TM) region and is predicted to be a cytoplasmic chemoreceptor. The replacement of residue Phe328 showed that the helical structure in the hairpin subdomain of MCP514 is a direct determinant for the cellular localization of MCP514. Single respective replacements of key residues indicated that residues Asn336 and Val353 play a key role in maintaining the chemotactic function of MCP514.
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Abedini D, Jaupitre S, Bouwmeester H, Dong L. Metabolic interactions in beneficial microbe recruitment by plants. Curr Opin Biotechnol 2021; 70:241-247. [PMID: 34237663 DOI: 10.1016/j.copbio.2021.06.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 12/26/2022]
Abstract
During millions of years of evolution, land plants and microorganisms have established elaborate partnerships. Microbes play essential roles in plant fitness and help plants cope with environmental challenges. Vice versa, plants provide the microbes with a niche and food. In the soil, a complex network of interactions mediated by metabolic signals drives the relationship between plants and microbes. Here, we review the roles of metabolic signaling in the plant-microbiome interaction. We discuss how plant-produced small molecules are involved in the recruitment of the microbiome. Also the microbial partners in this relationship use small molecules, such as quorum sensing molecules and volatiles for intra-species and inter-species communication. We give an overview of the regulation of the biosynthesis, secretion and perception of both plant and microbial small molecules and discuss the examples of biotechnological approaches to engineer the plant-microbiome interaction by targeting these metabolic dialogues. Ultimately, an improved understanding of the plant-microbiome interaction and engineering possibilities will pave the way to a more sustainable agriculture.
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Affiliation(s)
- Davar Abedini
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sébastien Jaupitre
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Harro Bouwmeester
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Lemeng Dong
- Plant Hormone Biology Group, Green Life Sciences Cluster, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere. Genes (Basel) 2021; 12:genes12040535. [PMID: 33917127 PMCID: PMC8067831 DOI: 10.3390/genes12040535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 11/19/2022] Open
Abstract
Soil fertility is a function of the level of organic and inorganic substances present in the soil, and it influences the activities of soil-borne microbes, plant growth performance and a host of other beneficial ecological functions. In this metagenomics study, we evaluated the response of maize microbial functional gene diversity involved in chemotaxis, antibiotics, siderophores, and antifungals producing genes within the rhizosphere of maize plants under compost, inorganic fertilizer, and unfertilized conditions. The results show that fertilization treatments at higher compost manure and lower inorganic fertilizer doses as well as maize plants itself in the unfertilized soil through rhizosphere effects share similar influences on the abundance of chemotaxis, siderophores, antifungal, and antibiotics synthesizing genes present in the samples, while higher doses of inorganic fertilizer and lower compost manure treatments significantly repress these genes. The implication is for a disease suppressive soil to be achieved, soil fertilization with high doses of compost manure fertilizer treatments as well as lower inorganic fertilizer should be used to enrich soil fertility and boost the abundance of chemotaxis and disease suppressive genes. Maize crops also should be planted sole or intercropped with other crops to enhance the rhizosphere effect of these plants in promoting the expression and abundance of these beneficial genes in the soil.
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Tian M, Zhang C, Zhang R, Yuan J. Collective motion enhances chemotaxis in a two-dimensional bacterial swarm. Biophys J 2021; 120:1615-1624. [PMID: 33636168 DOI: 10.1016/j.bpj.2021.02.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/20/2021] [Accepted: 02/10/2021] [Indexed: 02/05/2023] Open
Abstract
In a dilute liquid environment in which cell-cell interaction is negligible, flagellated bacteria, such as Escherichia coli, perform chemotaxis by biased random walks alternating between run-and-tumble. In a two-dimensional crowded environment, such as a bacterial swarm, the typical behavior of run-and-tumble is absent, and this raises the question whether and how bacteria can perform chemotaxis in a swarm. Here, by examining the chemotactic behavior as a function of the cell density, we showed that chemotaxis is surprisingly enhanced because of cell crowding in a bacterial swarm, and this enhancement is correlated with increase in the degree of cell body alignment. Cells tend to form clusters that move collectively in a swarm with increased effective run length, and we showed analytically that this resulted in increased drift velocity toward attractants. We also explained the enhancement by stochastically simulating bacterial chemotaxis in a swarm. We found that cell crowding in a swarm enhances chemotaxis if the cell-cell interactions used in the simulation induce cell-cell alignment, but it impedes chemotaxis if the interactions are collisions that randomize cell moving direction. Therefore, collective motion in a bacterial swarm enhances chemotaxis.
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Affiliation(s)
- Maojin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Chi Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Rongjing Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China.
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China.
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Kreling V, Falcone FH, Kehrenberg C, Hensel A. Campylobacter sp.: Pathogenicity factors and prevention methods-new molecular targets for innovative antivirulence drugs? Appl Microbiol Biotechnol 2020; 104:10409-10436. [PMID: 33185702 PMCID: PMC7662028 DOI: 10.1007/s00253-020-10974-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 08/24/2020] [Accepted: 10/21/2020] [Indexed: 02/08/2023]
Abstract
Infections caused by bacterial species from the genus Campylobacter are one of the four main causes of strong diarrheal enteritis worldwide. Campylobacteriosis, a typical food-borne disease, can range from mild symptoms to fatal illness. About 550 million people worldwide suffer from campylobacteriosis and lethality is about 33 million p.a. This review summarizes the state of the current knowledge on Campylobacter with focus on its specific virulence factors. Using this knowledge, multifactorial prevention strategies can be implemented to reduce the prevalence of Campylobacter in the food chain. In particular, antiadhesive strategies with specific adhesion inhibitors seem to be a promising concept for reducing Campylobacter bacterial load in poultry production. Antivirulence compounds against bacterial adhesion to and/or invasion into the host cells can open new fields for innovative antibacterial agents. Influencing chemotaxis, biofilm formation, quorum sensing, secretion systems, or toxins by specific inhibitors can help to reduce virulence of the bacterium. In addition, the unusual glycosylation of the bacterium, being a prerequisite for effective phase variation and adaption to different hosts, is yet an unexplored target for combating Campylobacter sp. Plant extracts are widely used remedies in developing countries to combat infections with Campylobacter. Therefore, the present review summarizes the use of natural products against the bacterium in an attempt to stimulate innovative research concepts on the manifold still open questions behind Campylobacter towards improved treatment and sanitation of animal vectors, treatment of infected patients, and new strategies for prevention. KEY POINTS: • Campylobacter sp. is a main cause of strong enteritis worldwide. • Main virulence factors: cytolethal distending toxin, adhesion proteins, invasion machinery. • Strong need for development of antivirulence compounds.
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Affiliation(s)
- Vanessa Kreling
- Institute of Pharmaceutical Biology and Phytochemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Franco H Falcone
- Institute of Parasitology, University of Gießen, Schubertstraße 81, 35392, Gießen, Germany
| | - Corinna Kehrenberg
- Institute of Veterinary Food Science, University of Gießen, Frankfurterstraße 81, 35392, Gießen, Germany
| | - Andreas Hensel
- Institute of Pharmaceutical Biology and Phytochemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany.
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Khan F, Tabassum N, Pham DTN, Oloketuyi SF, Kim YM. Molecules involved in motility regulation in Escherichia coli cells: a review. BIOFOULING 2020; 36:889-908. [PMID: 33028083 DOI: 10.1080/08927014.2020.1826939] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
The initial colonization of the host organism by commensal, probiotic, and pathogenic Escherichia coli strains is an important step in the development of infections and biofilms. Sensing and colonization of host cell surfaces are governed by flagellar and fimbriae/pili appendages, respectively. Biofilm formation confers great advantages on pathogenic E. coli cells such as protection against the host immune system, antimicrobial agents, and several environmental stress factors. The transition from planktonic to sessile physiological states involves several signaling cascades and factors responsible for the regulation of flagellar motility in E. coli cells. These regulatory factors have thus become important targets to control pathogenicity. Hence, attenuation of flagellar motility is considered a potential therapy against pathogenic E. coli. The present review describes signaling pathways and proteins involved in direct or indirect regulation of flagellar motility. Furthermore, application strategies for antimotility natural or synthetic compounds are discussed also.
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Affiliation(s)
- Fazlurrahman Khan
- Institute of Food Science, Pukyong National University, Busan, Republic of Korea
| | - Nazia Tabassum
- Industrial Convergence Bionix Engineering, Pukyong National University, Busan, Republic of Korea
| | - Dung Thuy Nguyen Pham
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | | | - Young-Mog Kim
- Institute of Food Science, Pukyong National University, Busan, Republic of Korea
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
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Hong S, Choi SH, Park J, Yoo H, Oh JY, Hwang E, Yoon DH, Kim S. Sensory Adaptation and Neuromorphic Phototransistors Based on CsPb(Br 1-xI x) 3 Perovskite and MoS 2 Hybrid Structure. ACS NANO 2020; 14:9796-9806. [PMID: 32628447 DOI: 10.1021/acsnano.0c01689] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sensory adaptation is an essential part of biological neural systems for sustaining human life. Using the light-induced halide phase segregation of CsPb(Br1-xIx)3 perovskite, we introduce neuromorphic phototransistors that emulate human sensory adaptation. The phototransistor based on a hybrid structure of perovskite and transition-metal dichalcogenide (TMD) emulates the sensory adaptation in response to a continuous light stimulus, similar to the neural system. The underlying mechanism for the sensory adaptation is the halide segregation of the mixed halide perovskites. The phase separation under visible-light illumination leads to the segregation of I and Br into separate iodide- and bromide-rich domains, significantly changing the photocurrent in the phototransistors. The devices are reversible upon the removal of the light stimulation, resulting in near-complete recovery of the photosensitivity before the phase segregation (sensitivity recovery of 96.65% for 5 min rest time). The proposed phototransistor based on the perovskite-TMD hybrid structure can be applied to other neuromorphic devices such as neuromorphic photonic devices, intelligent sensors, and selective light-detecting image sensors.
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Affiliation(s)
- Seongin Hong
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Seung Hee Choi
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Jongsun Park
- School of Electrical Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Hocheon Yoo
- Department of Electronic Engineering, Gachon University, 1342 Seongnam-daero, Seongnam 13120, Korea
| | - Joo Youn Oh
- Department of Ophthalmology, Seoul National University College of Medicine, 103, Daehak-ro, Jongno-gu, Seoul 03080, South Korea
- Laboratory of Ocular Regenerative Medicine and Immunology, Biomedical Research Institute, Seoul National University Hospital, 101, Daehak-ro, Jongno-gu, Seoul 03080, South Korea
| | - Euyheon Hwang
- SKKU Advanced Institute of Nanotechnology (SAINT) and Department of Nano Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Dae Ho Yoon
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Sunkook Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
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Duggal Y, Fontaine BM, Dailey DM, Ning G, Weinert EE. RNase I Modulates Escherichia coli Motility, Metabolism, and Resistance. ACS Chem Biol 2020; 15:1996-2004. [PMID: 32551492 DOI: 10.1021/acschembio.0c00390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria are constantly adapting to their environment by sensing extracellular factors that trigger production of intracellular signaling molecules, known as second messengers. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified in Escherichia coli and have emerged as possible novel signaling molecules. 2',3'-cNMPs are produced through endonucleolytic cleavage of short RNAs by the T2 endoribonuclease, RNase I; however, the physiological roles of RNase I remain unclear. Our transcriptomic analysis suggests that RNase I is involved in modulating numerous cellular processes, including nucleotide metabolism, motility, acid sensitivity, metal homeostasis, and outer membrane morphology. Through a combination of deletion strain and inhibitor studies, we demonstrate that RNase I plays a previously unknown role in E. coli stress resistance by affecting pathways that are part of the defense mechanisms employed by bacteria when introduced to external threats, including antibiotics. Thus, this work provides insight into the emerging roles of RNase I in bacterial signaling and physiology and highlights the potential of RNase I as a target for antibacterial adjuvants.
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Affiliation(s)
- Yashasvika Duggal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Benjamin M. Fontaine
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Deanna M. Dailey
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Gang Ning
- Microscopy Facility, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Emily E. Weinert
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Arapov TD, Saldaña RC, Sebastian AL, Ray WK, Helm RF, Scharf BE. Cellular Stoichiometry of Chemotaxis Proteins in Sinorhizobium meliloti. J Bacteriol 2020; 202:e00141-20. [PMID: 32393521 PMCID: PMC7317046 DOI: 10.1128/jb.00141-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/05/2020] [Indexed: 11/20/2022] Open
Abstract
Chemotaxis systems enable microbes to sense their immediate environment, moving toward beneficial stimuli and away from those that are harmful. In an effort to better understand the chemotaxis system of Sinorhizobium meliloti, a symbiont of the legume alfalfa, the cellular stoichiometries of all ten chemotaxis proteins in S. meliloti were determined. A combination of quantitative immunoblot and mass spectrometry revealed that the protein stoichiometries in S. meliloti varied greatly from those in Escherichia coli and Bacillus subtilis To compare protein ratios to other systems, values were normalized to the central kinase CheA. All S. meliloti chemotaxis proteins exhibited increased ratios to various degrees. The 10-fold higher molar ratio of adaptor proteins CheW1 and CheW2 to CheA might result in the formation of rings in the chemotaxis array that consist of only CheW instead of CheA and CheW in a 1:1 ratio. We hypothesize that the higher ratio of CheA to the main response regulator CheY2 is a consequence of the speed-variable motor in S. meliloti, instead of a switch-type motor. Similarly, proteins involved in signal termination are far more abundant in S. meliloti, which utilizes a phosphate sink mechanism based on CheA retrophosphorylation to inactivate the motor response regulator versus CheZ-catalyzed dephosphorylation as in E. coli and B. subtilis Finally, the abundance of CheB and CheR, which regulate chemoreceptor methylation, was increased compared to CheA, indicative of variations in the adaptation system of S. meliloti Collectively, these results mark significant differences in the composition of bacterial chemotaxis systems.IMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti contributes greatly to host-plant growth by fixing atmospheric nitrogen. The provision of nitrogen as ammonium by S. meliloti leads to increased biomass production of its legume host alfalfa and diminishes the use of environmentally harmful chemical fertilizers. To better understand the role of chemotaxis in host-microbe interaction, a comprehensive catalogue of the bacterial chemotaxis system is vital, including its composition, function, and regulation. The stoichiometry of chemotaxis proteins in S. meliloti has very few similarities to the systems in Escherichia coli and Bacillus subtilis In addition, total amounts of proteins are significantly lower. S. meliloti exhibits a chemotaxis system distinct from known models by incorporating new proteins as exemplified by the phosphate sink mechanism.
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Affiliation(s)
- Timofey D Arapov
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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Yang CY, Erickstad M, Tadrist L, Ronan E, Gutierrez E, Wong-Ng J, Groisman A. Aggregation Temperature of Escherichia coli Depends on Steepness of the Thermal Gradient. Biophys J 2020; 118:2816-2828. [PMID: 32348719 DOI: 10.1016/j.bpj.2020.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/14/2020] [Accepted: 02/03/2020] [Indexed: 11/30/2022] Open
Abstract
Bacterial chemotaxis, the directed migration of bacteria in a gradient of chemoattractant, is one of the most well-studied and well-understood processes in cell biology. On the other hand, bacterial thermotaxis, the directed migration of bacteria in a gradient of temperature, is understood relatively poorly, with somewhat conflicting reports by different groups. One of the reasons for that is the relative technical difficulty of the generation of well-defined gradients of temperature that are sufficiently steep to elicit readily detectable thermotaxis. Here, we used a specially designed microfluidic device to study thermotaxis of Escherichia coli in a broad range of thermal gradients with a high rate of data collection. We found that in shallow temperature gradients with narrow temperature ranges, E. coli tended to aggregate near a sidewall of the gradient channel at either the lowest or the highest temperature. On the other hand, in sufficiently steep gradients with wide temperature ranges, E. coli aggregated at intermediate temperatures, with maximal cell concentrations found away from the sidewalls. We observed this intermediate temperature aggregation in a motility buffer that did not contain any major chemoattractants of E. coli, in contradiction to some previous reports, which suggested that this type of aggregation required the presence of at least one major chemoattractant in the medium. Even more surprisingly, the aggregation temperature strongly depended on the gradient steepness, decreasing by ∼10° as the steepness was increased from 27 to 53°C/mm. Our experiments also highlight the fact that assessments of thermal gradients by changes in fluorescence of temperature-sensitive fluorescent dyes need to account for thermophoresis of the dyes.
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Affiliation(s)
- Chih-Yu Yang
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Michael Erickstad
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Loïc Tadrist
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Edward Ronan
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Edgar Gutierrez
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Jérôme Wong-Ng
- Department of Physics, University of California, San Diego, La Jolla, California.
| | - Alex Groisman
- Department of Physics, University of California, San Diego, La Jolla, California.
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Wang R, Chen Q, Zhang R, Yuan J. Measurement of the Internal Frictional Drag of the Bacterial Flagellar Motor by Fluctuation Analysis. Biophys J 2020; 118:2718-2725. [PMID: 32392462 DOI: 10.1016/j.bpj.2020.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 11/26/2022] Open
Abstract
The bacterial flagellar motor generates the torque that drives the rotation of bacterial flagellar filaments. The torque it generates depends sensitively on the frictional viscous drag on the motor, which includes the frictional viscous drag on the filaments (external load) and the internal frictional viscous drag on the rotor (internal load). The internal load was roughly estimated previously by modeling it as a sphere of a radius of 20 nm rotating in a lipid of viscosity of 100 cp but was never measured experimentally. Here, we measured the internal load by fluctuation analysis of the motor velocity traces. A similar approach should be applicable to other molecular motors.
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Affiliation(s)
- Renjie Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, China; Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiaopeng Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, China; Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Rongjing Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, China; Department of Physics, University of Science and Technology of China, Hefei, Anhui, China.
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, China; Department of Physics, University of Science and Technology of China, Hefei, Anhui, China.
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A programmable chemical computer with memory and pattern recognition. Nat Commun 2020; 11:1442. [PMID: 32188858 PMCID: PMC7080730 DOI: 10.1038/s41467-020-15190-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/20/2020] [Indexed: 11/08/2022] Open
Abstract
Current computers are limited by the von Neumann bottleneck, which constrains the throughput between the processing unit and the memory. Chemical processes have the potential to scale beyond current computing architectures as the processing unit and memory reside in the same space, performing computations through chemical reactions, yet their lack of programmability limits them. Herein, we present a programmable chemical processor comprising of a 5 by 5 array of cells filled with a switchable oscillating chemical (Belousov-Zhabotinsky) reaction. Each cell can be individually addressed in the 'on' or 'off' state, yielding more than 2.9 × 1017 chemical states which arise from the ability to detect distinct amplitudes of oscillations via image processing. By programming the array of interconnected BZ reactions we demonstrate chemically encoded and addressable memory, and we create a chemical Autoencoder for pattern recognition able to perform the equivalent of one million operations per second.
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Liu Y, Feng H, Fu R, Zhang N, Du W, Shen Q, Zhang R. Induced root-secreted D-galactose functions as a chemoattractant and enhances the biofilm formation of Bacillus velezensis SQR9 in an McpA-dependent manner. Appl Microbiol Biotechnol 2019; 104:785-797. [PMID: 31813049 DOI: 10.1007/s00253-019-10265-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/09/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022]
Abstract
Chemotaxis towards root exudates and subsequent biofilm formation are very important for root colonization and for providing the beneficial functions of plant growth-promoting rhizobacteria (PGPRs). In this study, in comparison with other root-secreted compounds, D-galactose in the root exudates of cucumber was found to be a strong chemoattractant at the concentration of 1 μM for Bacillus velezensis SQR9. Chemotaxis assays with methyl-accepting chemotaxis proteins (MCPs) deletion strains demonstrated that McpA was solely responsible for chemotaxis towards D-galactose. Interestingly, D-galactose significantly enhanced the biofilm formation of SQR9 in an McpA-dependent manner. Further experiment showed that D-galactose also enhanced root colonization by SQR9. In addition, the secretion of D-galactose by cucumber roots could be induced by inoculation with SQR9, indicating that D-galactose may be an important signal in the interaction between plant and SQR9. These findings suggested that the root-secreted D-galactose was a signal, the secretion of which was induced by the beneficial bacteria, and which in turn induced colonization of the bacteria.
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Affiliation(s)
- Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Haichao Feng
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ruixin Fu
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Nan Zhang
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Qirong Shen
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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