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Blanco-Romero E, Durán D, Garrido-Sanz D, Redondo-Nieto M, Martín M, Rivilla R. Adaption of Pseudomonas ogarae F113 to the Rhizosphere Environment-The AmrZ-FleQ Hub. Microorganisms 2023; 11:microorganisms11041037. [PMID: 37110460 PMCID: PMC10146422 DOI: 10.3390/microorganisms11041037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Motility and biofilm formation are two crucial traits in the process of rhizosphere colonization by pseudomonads. The regulation of both traits requires a complex signaling network that is coordinated by the AmrZ-FleQ hub. In this review, we describe the role of this hub in the adaption to the rhizosphere. The study of the direct regulon of AmrZ and the phenotypic analyses of an amrZ mutant in Pseudomonas ogarae F113 has shown that this protein plays a crucial role in the regulation of several cellular functions, including motility, biofilm formation, iron homeostasis, and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) turnover, controlling the synthesis of extracellular matrix components. On the other hand, FleQ is the master regulator of flagellar synthesis in P. ogarae F113 and other pseudomonads, but its implication in the regulation of multiple traits related with environmental adaption has been shown. Genomic scale studies (ChIP-Seq and RNA-Seq) have shown that in P. ogarae F113, AmrZ and FleQ are general transcription factors that regulate multiple traits. It has also been shown that there is a common regulon shared by the two transcription factors. Moreover, these studies have shown that AmrZ and FleQ form a regulatory hub that inversely regulate traits such as motility, extracellular matrix component production, and iron homeostasis. The messenger molecule c-di-GMP plays an essential role in this hub since its production is regulated by AmrZ and it is sensed by FleQ and required for its regulatory role. This regulatory hub is functional both in culture and in the rhizosphere, indicating that the AmrZ-FleQ hub is a main player of P. ogarae F113 adaption to the rhizosphere environment.
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Affiliation(s)
- Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
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2
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Bacteria phototaxis optimizer. Neural Comput Appl 2023. [DOI: 10.1007/s00521-023-08391-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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3
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Nsamela A, Garcia Zintzun AI, Montenegro-Johnson TD, Simmchen J. Colloidal Active Matter Mimics the Behavior of Biological Microorganisms-An Overview. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202685. [PMID: 35971193 DOI: 10.1002/smll.202202685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/18/2022] [Indexed: 06/15/2023]
Abstract
This article provides a review of the recent development of biomimicking behaviors in active colloids. While the behavior of biological microswimmers is undoubtedly influenced by physics, it is frequently guided and manipulated by active sensing processes. Understanding the respective influences of the surrounding environment can help to engineering the desired response also in artificial swimmers. More often than not, the achievement of biomimicking behavior requires the understanding of both biological and artificial microswimmers swimming mechanisms and the parameters inducing mechanosensory responses. The comparison of both classes of microswimmers provides with analogies in their dependence on fuels, interaction with boundaries and stimuli induced motion, or taxis.
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Affiliation(s)
- Audrey Nsamela
- Chair of Physical Chemistry, TU Dresden, 01069, Dresden, Germany
- Elvesys SAS, 172 Rue de Charonne, Paris, 75011, France
| | | | | | - Juliane Simmchen
- Chair of Physical Chemistry, TU Dresden, 01069, Dresden, Germany
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4
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Ji F, Wu Y, Pumera M, Zhang L. Collective Behaviors of Active Matter Learning from Natural Taxes Across Scales. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203959. [PMID: 35986637 DOI: 10.1002/adma.202203959] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Taxis orientation is common in microorganisms, and it provides feasible strategies to operate active colloids as small-scale robots. Collective taxes involve numerous units that collectively perform taxis motion, whereby the collective cooperation between individuals enables the group to perform efficiently, adaptively, and robustly. Hence, analyzing and designing collectives is crucial for developing and advancing microswarm toward practical or clinical applications. In this review, natural taxis behaviors are categorized and synthetic microrobotic collectives are discussed as bio-inspired realizations, aiming at closing the gap between taxis strategies of living creatures and those of functional active microswarms. As collective behaviors emerge within a group, the global taxis to external stimuli guides the group to conduct overall tasks, whereas the local taxis between individuals induces synchronization and global patterns. By encoding the local orientations and programming the global stimuli, various paradigms can be introduced for coordinating and controlling such collective microrobots, from the viewpoints of fundamental science and practical applications. Therefore, by discussing the key points and difficulties associated with collective taxes of different paradigms, this review potentially offers insights into mimicking natural collective behaviors and constructing intelligent microrobotic systems for on-demand control and preassigned tasks.
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Affiliation(s)
- Fengtong Ji
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, 999077, China
| | - Yilin Wu
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, 999077, China
| | - Martin Pumera
- Faculty of Electrical Engineering and Computer Science, VSB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava, 70800, Czech Republic
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Li Zhang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, 999077, China
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5
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Dubay MM, Acres J, Riekeles M, Nadeau JL. Recent advances in experimental design and data analysis to characterize prokaryotic motility. J Microbiol Methods 2023; 204:106658. [PMID: 36529156 DOI: 10.1016/j.mimet.2022.106658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Bacterial motility plays a key role in important cell processes such as chemotaxis and biofilm formation, but is challenging to quantify due to the small size of the individual microorganisms and the complex interplay of biological and physical factors that influence motility phenotypes. Swimming, the first type of motility described in bacteria, still remains largely unquantified. Light microscopy has enabled qualitative characterization of swimming patterns seen in different strains, such as run and tumble, run-reverse-flick, run and slow, stop and coil, and push and pull, which has allowed for elucidation of the underlying physics. However, quantifying these behaviors (e.g., identifying run distances and speeds, turn angles and behavior by surfaces or cell-cell interactions) remains a challenging task. A qualitative and quantitative understanding of bacterial motility is needed to bridge the gap between experimentation, omics analysis, and bacterial motility theory. In this review, we discuss the strengths and limitations of how phase contrast microscopy, fluorescence microscopy, and digital holographic microscopy have been used to quantify bacterial motility. Approaches to automated software analysis, including cell recognition, tracking, and track analysis, are also discussed with a view to providing a guide for experimenters to setting up the appropriate imaging and analysis system for their needs.
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Affiliation(s)
- Megan Marie Dubay
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Jacqueline Acres
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Max Riekeles
- Astrobiology Group, Center of Astronomy and Astrophysics, Technical University Berlin, Hardenbergstraße 36A, 10623 Berlin, Germany
| | - Jay L Nadeau
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America.
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6
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Maschmann Z, Chandrasekaran S, Chua TK, Crane BR. Interdomain Linkers Regulate Histidine Kinase Activity by Controlling Subunit Interactions. Biochemistry 2022; 61:2672-2686. [PMID: 36321948 PMCID: PMC10134573 DOI: 10.1021/acs.biochem.2c00326] [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] [Indexed: 11/06/2022]
Abstract
Bacterial chemoreceptors regulate the cytosolic multidomain histidine kinase CheA through largely unknown mechanisms. Residue substitutions in the peptide linkers that connect the P4 kinase domain to the P3 dimerization and P5 regulatory domain affect CheA basal activity and activation. To understand the role that these linkers play in CheA activity, the P3-to-P4 linker (L3) and P4-to-P5 linker (L4) were extended and altered in variants of Thermotoga maritima (Tm) CheA. Flexible extensions of the L3 and L4 linkers in CheA-LV1 (linker variant 1) allowed for a well-folded kinase domain that retained wild-type (WT)-like binding affinities for nucleotide and normal interactions with the receptor-coupling protein CheW. However, CheA-LV1 autophosphorylation activity registered ∼50-fold lower compared to WT. Neither a WT nor LV1 dimer containing a single P4 domain could autophosphorylate the P1 substrate domain. Autophosphorylation activity was rescued in variants with extended L3 and L4 linkers that favor helical structure and heptad spacing. Autophosphorylation depended on linker spacing and flexibility and not on sequence. Pulse-dipolar electron-spin resonance (ESR) measurements with spin-labeled adenosine 5'-triphosphate (ATP) analogues indicated that CheA autophosphorylation activity inversely correlated with the proximity of the P4 domains within the dimers of the variants. Despite their separation in primary sequence and space, the L3 and L4 linkers also influence the mobility of the P1 substrate domains. In all, interactions of the P4 domains, as modulated by the L3 and L4 linkers, affect domain dynamics and autophosphorylation of CheA, thereby providing potential mechanisms for receptors to regulate the kinase.
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Affiliation(s)
- Zachary Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
| | - Siddarth Chandrasekaran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
- National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca NY 1485
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
- National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca NY 1485
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7
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Maschmann ZA, Chua TK, Chandrasekaran S, Ibáñez H, Crane BR. Redox properties and PAS domain structure of the Escherichia coli energy sensor Aer indicate a multistate sensing mechanism. J Biol Chem 2022; 298:102598. [PMID: 36252616 PMCID: PMC9668731 DOI: 10.1016/j.jbc.2022.102598] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
The Per-Arnt-Sim (PAS; named for the representative proteins: Period, Aryl hydrocarbon receptor nuclear translocator protein and Single-minded) domain of the dimeric Escherichia coli aerotaxis receptor Aer monitors cellular respiration through a redox-sensitive flavin adenine dinucleotide (FAD) cofactor. Conformational shifts in the PAS domain instigated by the oxidized FAD (FADOX)/FAD anionic semiquinone (FADASQ) redox couple traverse the HAMP (histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and kinase control domains of the Aer dimer to regulate CheA kinase activity. The PAS domain of Aer is unstable and has not been previously purified. Here, residue substitutions that rescue FAD binding in an FAD binding-deficient full-length Aer variant were used in combination to stabilize the Aer PAS domain. We solved the 2.4 Å resolution crystal structure of this variant, Aer-PAS-GVV, and revealed a PAS fold that contains distinct features associated with FAD-based redox sensing, such as a close contact between the Arg115 side chain and N5 of the isoalloxazine ring and interactions of the flavin with the side chains of His53 and Asn85 that are poised to convey conformational signals from the cofactor to the protein surface. In addition, we determined the FADox/FADASQ formal potentials of Aer-PAS-GVV and full-length Aer reconstituted into nanodiscs. The Aer redox couple is remarkably low at -289.6 ± 0.4 mV. In conclusion, we propose a model for Aer energy sensing based on the low potential of Aer-PAS-FADox/FADASQ couple and the inability of Aer-PAS to bind to the fully reduced FAD hydroquinone.
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Affiliation(s)
- Zachary A Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | | | - Héctor Ibáñez
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.
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8
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Joshi H, Prakash MK. Using Atomistic Simulations to Explore the Role of Methylation and ATP in Chemotaxis Signal Transduction. ACS OMEGA 2022; 7:27886-27895. [PMID: 35990422 PMCID: PMC9386827 DOI: 10.1021/acsomega.2c00792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
A bacterial chemotaxis mechanism is activated when nutrients bind to surface receptors. The sequence of intra- and interprotein events in this signal cascade from the receptors to the eventual molecular motors has been clearly identified. However, the atomistic details remain elusive, as in general may be expected of intraprotein signal transduction pathways, especially when fibrillar proteins are involved. We performed atomistic calculations of the methyl accepting chemoprotein (MCP)-CheA-CheW multidomain complex from Escherichia coli, simulating the methylated and unmethylated conditions in the chemoreceptors and the ATP-bound and apo conditions of the CheA. Our results indicate that these atomistic simulations, especially with one of the two force fields we tried, capture several relevant features of the downstream effects, such as the methylation favoring an intermediate structure that is more toward a dipped state and increases the chance of ATP hydrolysis. The results thus suggest the sensitivity of the model to reflect the nutrient signal response, a nontrivial validation considering the complexity of the system, encouraging even more detailed studies on the thermodynamic quantification of the effects and the identification of the signaling networks.
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9
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Gupta R, Yuan J, Lele PP. Bacterial Proprioception: Can a Bacterium Sense Its Movement? Front Microbiol 2022; 13:928408. [PMID: 35875555 PMCID: PMC9302961 DOI: 10.3389/fmicb.2022.928408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The evolution of the bacterial flagellum gave rise to motility and repurposing of a signaling network, now termed the chemotaxis network, enabled biasing of cell movements. This made it possible for the bacterium to seek out favorable chemical environments. To enable chemotaxis, the chemotaxis network sensitively detects extracellular chemical stimuli and appropriately modulates flagellar functions. Additionally, the flagellar motor itself is capable of detecting mechanical stimuli and adapts its structure and function in response, likely triggering a transition from planktonic to surface-associated lifestyles. Recent work has shown a link between the flagellar motor's response to mechanical stimuli and the chemotactic output. Here, we elaborate on this link and discuss how it likely helps the cell sense and adapt to changes in its swimming speeds in different environments. We discuss the mechanism whereby the motor precisely tunes its chemotaxis output under different mechanical loads, analogous to proprioception in higher order organisms. We speculate on the roles bacterial proprioception might play in a variety of phenomena including the transition to surface-associated lifestyles such as swarming and biofilms.
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Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei, China
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
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10
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Poddar H, Heyes DJ, Zhang S, Hardman SJ, Sakuma M, Scrutton NS. An unusual light-sensing function for coenzyme B 12 in bacterial transcription regulator CarH. Methods Enzymol 2022; 668:349-372. [PMID: 35589201 DOI: 10.1016/bs.mie.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coenzyme B12 is one of the most complex cofactors found in nature and synthesized de novo by certain groups of bacteria. Although its use in various enzymatic reactions is well characterized, only recently an unusual light-sensing function has been ascribed to coenzyme B12. It has been reported that the coenzyme B12 binding protein CarH, found in the carotenoid biosynthesis pathway of several thermostable bacteria, binds to the promoter region of DNA and suppresses transcription. To overcome the harmful effects of light-induced damage in the cells, CarH releases DNA in the presence of light and promotes transcription and synthesis of carotenoids, thereby working as a photoreceptor. CarH is able to achieve this by exploiting the photosensitive nature of the CoC bond between the adenosyl moiety and the cobalt atom in the coenzyme B12 molecule. Extensive structural and spectroscopy studies provided a mechanistic understanding of the molecular basis of this unique light-sensitive reaction. Most studies on CarH have used the ortholog from the thermostable bacterium Thermus thermophilus, due to the ease with which it can be expressed and purified in high quantities. In this chapter we give an overview of this intriguing class of photoreceptors and report a step-by-step protocol for expression, purification and spectroscopy experiments (both static and time-resolved techniques) employed in our laboratory to study CarH from T. thermophilus. We hope the contents of this chapter will be of interest to the wider coenzyme B12 community and apprise them of the potential and possibilities of using coenzyme B12 as a light-sensing probe in a protein scaffold.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Shaowei Zhang
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Samantha J Hardman
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom.
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11
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Sharan P, Xiao Z, Mancuso V, Uspal WE, Simmchen J. Upstream Rheotaxis of Catalytic Janus Spheres. ACS NANO 2022; 16:4599-4608. [PMID: 35230094 DOI: 10.1021/acsnano.1c11204] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fluid flow is ubiquitous in many environments that form habitats for microorganisms. Therefore, it is not surprising that both biological and artificial microswimmers show responses to flows that are determined by the interplay of chemical and physical factors. In particular, to deepen the understanding of how different systems respond to flows, it is crucial to comprehend the influence played by swimming pattern. The tendency of organisms to navigate up or down the flow is termed rheotaxis. Early theoretical studies predicted a positive rheotactic response for puller-type spherical Janus micromotors. However, recent experimental studies have focused on pusher-type Janus particles, finding that they exhibit cross-stream migration in externally applied flows. To study the response to the flow of swimmers with a qualitatively different flow pattern, we introduce Cu@SiO2 micromotors that swim toward their catalytic cap. On the basis of experimental observations, and supported by flow field calculations using a model for self-electrophoresis, we hypothesize that they behave effectively as a puller-type system. We investigate the effect of externally imposed flow on these spherically symmetrical Cu@SiO2 active Janus colloids, and we indeed observe a steady upstream directional response. Through a simple squirmer model for a puller, we recover the major experimental observations. Additionally, the model predicts a "jumping" behavior for puller-type micromotors at high flow speeds. Performing additional experiments at high flow speeds, we capture this phenomenon, in which the particles "roll" with their swimming axes aligned to the shear plane, in addition to being dragged downstream by the fluid flow.
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Affiliation(s)
- Priyanka Sharan
- Physical Chemistry, TU Dresden, Zellescher Weg 19, Dresden 01069, Germany
| | - Zuyao Xiao
- Physical Chemistry, TU Dresden, Zellescher Weg 19, Dresden 01069, Germany
| | - Viviana Mancuso
- Department of Mechanical Engineering, University of Hawai'i at Ma̅noa, Honolulu 96822, Hawaii, United States
| | - William E Uspal
- Department of Mechanical Engineering, University of Hawai'i at Ma̅noa, Honolulu 96822, Hawaii, United States
| | - Juliane Simmchen
- Physical Chemistry, TU Dresden, Zellescher Weg 19, Dresden 01069, Germany
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12
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Ranjbaran M, Carciofi BAM, Datta AK. Engineering modeling frameworks for microbial food safety at various scales. Compr Rev Food Sci Food Saf 2021; 20:4213-4249. [PMID: 34486219 DOI: 10.1111/1541-4337.12818] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/25/2021] [Indexed: 11/27/2022]
Abstract
The landscape of mathematical model-based understanding of microbial food safety is wide and deep, covering interdisciplinary fields of food science, microbiology, physics, and engineering. With rapidly growing interest in such model-based approaches that increasingly include more fundamental mechanisms of microbial processes, there is a need to build a general framework that steers this evolutionary process by synthesizing literature spread over many disciplines. The framework proposed here shows four interconnected, complementary levels of microbial food processes covering sub-cellular scale, microbial population scale, food scale, and human population scale (risk). A continuum of completely mechanistic to completely empirical models, widely-used and emerging, are integrated into the framework; well-known predictive microbiology modeling being a part of this spectrum. The framework emphasizes fundamentals-based approaches that should get enriched over time, such as the basic building blocks of microbial population scale processes (attachment, migration, growth, death/inactivation and communication) and of food processes (e.g., heat and moisture transfer). A spectrum of models are included, for example, microbial population modeling covers traditional predictive microbiology models to individual-based models and cellular automata. The models are shown in sufficient quantitative detail to make obvious their coupling, or their integration over various levels. Guidelines to combine sub-processes over various spatial and time scales into a complete interdisciplinary and multiphysics model (i.e., a system) are provided, covering microbial growth/inactivation/transport and physical processes such as fluid flow and heat transfer. As food safety becomes increasingly predictive at various scales, this synthesis should provide its roadmap. This big picture and framework should be futuristic in driving novel research and educational approaches.
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Affiliation(s)
- Mohsen Ranjbaran
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Bruno A M Carciofi
- Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianopolis, SC, Brazil
| | - Ashim K Datta
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
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13
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Knights HE, Jorrin B, Haskett TL, Poole PS. Deciphering bacterial mechanisms of root colonization. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:428-444. [PMID: 33538402 PMCID: PMC8651005 DOI: 10.1111/1758-2229.12934] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 05/07/2023]
Abstract
Bacterial colonization of the rhizosphere is critical for the establishment of plant-bacteria interactions that represent a key determinant of plant health and productivity. Plants influence bacterial colonization primarily through modulating the composition of their root exudates and mounting an innate immune response. The outcome is a horizontal filtering of bacteria from the surrounding soil, resulting in a gradient of reduced bacterial diversity coupled with a higher degree of bacterial specialization towards the root. Bacteria-bacteria interactions (BBIs) are also prevalent in the rhizosphere, influencing bacterial persistence and root colonization through metabolic exchanges, secretion of antimicrobial compounds and other processes. Traditionally, bacterial colonization has been examined under sterile laboratory conditions that mitigate the influence of BBIs. Using simplified synthetic bacterial communities combined with microfluidic imaging platforms and transposon mutagenesis screening approaches, we are now able to begin unravelling the molecular mechanisms at play during the early stages of root colonization. This review explores the current state of knowledge regarding bacterial root colonization and identifies key tools for future exploration.
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Affiliation(s)
| | - Beatriz Jorrin
- Department of Plant SciencesUniversity of OxfordOxfordOX1 3RBUK
| | | | - Philip S. Poole
- Department of Plant SciencesUniversity of OxfordOxfordOX1 3RBUK
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14
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Lingam M. Theoretical Constraints Imposed by Gradient Detection and Dispersal on Microbial Size in Astrobiological Environments. ASTROBIOLOGY 2021; 21:813-830. [PMID: 33902321 DOI: 10.1089/ast.2020.2392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages such as facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by organisms endowed with motility is possibly beneficial in related contexts. Hence, the connections between information acquisition, motility, and microbial size are explored from an explicitly astrobiological standpoint. By using prior theoretical models, the constraints on organism size imposed by gradient detection and motility are elucidated in the form of simple heuristic scaling relations. It is argued that environments such as alkaline hydrothermal vents, which are distinguished by the presence of steep gradients, might be conducive to the existence of "small" microbes (with radii of ≳0.1 μm) in principle, when only the above two factors are considered; other biological functions (e.g., metabolism and genetic exchange) could, however, regulate the lower bound on microbial size and elevate it. The derived expressions are potentially applicable to a diverse array of settings, including those entailing solvents other than water; for example, the lakes and seas of Titan. The article concludes with a brief exposition of how this formalism may be of practical and theoretical value to astrobiology.
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Science, Florida Institute of Technology, Melbourne, Florida, USA
- Institute for Theory and Computation, Harvard University, Cambridge, Massachusetts, USA
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15
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de Pina LC, da Silva FSH, Galvão TC, Pauer H, Ferreira RBR, Antunes LCM. The role of two-component regulatory systems in environmental sensing and virulence in Salmonella. Crit Rev Microbiol 2021; 47:397-434. [PMID: 33751923 DOI: 10.1080/1040841x.2021.1895067] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Adaptation to environments with constant fluctuations imposes challenges that are only overcome with sophisticated strategies that allow bacteria to perceive environmental conditions and develop an appropriate response. The gastrointestinal environment is a complex ecosystem that is home to trillions of microorganisms. Termed microbiota, this microbial ensemble plays important roles in host health and provides colonization resistance against pathogens, although pathogens have evolved strategies to circumvent this barrier. Among the strategies used by bacteria to monitor their environment, one of the most important are the sensing and signalling machineries of two-component systems (TCSs), which play relevant roles in the behaviour of all bacteria. Salmonella enterica is no exception, and here we present our current understanding of how this important human pathogen uses TCSs as an integral part of its lifestyle. We describe important aspects of these systems, such as the stimuli and responses involved, the processes regulated, and their roles in virulence. We also dissect the genomic organization of histidine kinases and response regulators, as well as the input and output domains for each TCS. Lastly, we explore how these systems may be promising targets for the development of antivirulence therapeutics to combat antibiotic-resistant infections.
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Affiliation(s)
- Lucindo Cardoso de Pina
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Biociências, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação Ciência para o Desenvolvimento, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Teca Calcagno Galvão
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Heidi Pauer
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil
| | | | - L Caetano M Antunes
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil.,Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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16
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Guo J, Hu X, Gao Z, Li G, Fu F, Shang X, Liang Z, Shan Y. Global transcriptomic response of Listeria monocytogenes exposed to Fingered Citron (Citrus medica L. var. sarcodactylis Swingle) essential oil. Food Res Int 2021; 143:110274. [PMID: 33992374 DOI: 10.1016/j.foodres.2021.110274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/15/2020] [Accepted: 02/23/2021] [Indexed: 11/26/2022]
Abstract
Listeria monocytogenes, which could cause severe disease of listeriosis, is one of the most concerned foodborne pathogens worldwide. Citrus medica L. var. sarcodactylis Swingle (Fingered Citron) is one of the citrus species cultivated in south China. Here, we investigated the efficacy of Fingered Citron essential oil (FCEO) against L. monocytogenes and explored the response of L. monocytogenes in the presence of FCEO using genome-wide transcriptome analysis. FCEO exhibited strong anti-listeria activity and obvious alterations of cell morphology were observed by scanning electron microscopy and transmission electron microscopy. Moreover, GO analysis demonstrated many potential cell responses, including metabolic process, cellular process, single-organism process, cell part, membrane, catalytic activity, binding, and transporter activity. KEGG analysis suggests that L. monocytogenes respond and adapt by (1) increasing motility through the enhancement of flagella rotation; (2) promoting cell tumbles and re-orientating to escape from FCEO; (3) enhancing the uptake of carbohydrates from environment to gain more energy; (4) changing the uptake of several metallic cations, including iron, zinc, cobalt, and nickel. Our research contributes to the understanding of the adaptive responses of L. monocytogenes exposed to FCEO and provides novel insights for finding new targets of anti-listeria therapy.
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Affiliation(s)
- Jiajing Guo
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China
| | - Xiao Hu
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China
| | - Zhipeng Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan Province, China.
| | - Gaoyang Li
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China
| | - Fuhua Fu
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China
| | - Xuebo Shang
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China
| | - Zengenni Liang
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China
| | - Yang Shan
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China.
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17
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Deshpande A, Ouldridge TE. Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration. BIOLOGICAL CYBERNETICS 2020; 114:653-668. [PMID: 33044662 DOI: 10.1007/s00422-020-00846-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Enzymes are central to both metabolism and information processing in cells. In both cases, an enzyme's ability to accelerate a reaction without being consumed in the reaction is crucial. Nevertheless, enzymes are transiently sequestered when they bind to their substrates; this sequestration limits activity and potentially compromises information processing and signal transduction. In this article, we analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, while maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies of the enzyme-substrate and enzyme-product reaction intermediates minimize the fraction of enzymes sequestered in complexes, while sustaining a certain minimal flux? Under reasonable biophysical assumptions, we find that the optimal design will saturate the bound on the minimal flux and reflects a basic trade-off in catalytic operation. If both binding free energies are too high, there is low sequestration, but the effective progress of the reaction is hampered. If both binding free energies are too low, there is high sequestration, and the reaction flux may also be suppressed in extreme cases. The optimal binding free energies are therefore neither too high nor too low, but in fact moderate. Moreover, the optimal difference in substrate and product binding free energies, which contributes to the thermodynamic driving force of the reaction, is in general strongly constrained by the intrinsic free-energy difference between products and reactants. Both the strategies of using a negative binding free-energy difference to drive the catalyst-bound reaction forward and of using a positive binding free-energy difference to enhance detachment of the product are limited in their efficacy.
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Affiliation(s)
- Abhishek Deshpande
- Department of Mathematics, University of Wisconin Madison, Madison, 53706, WI, United States of America
| | - Thomas E Ouldridge
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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18
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Yang RS, Chen YT. Flagellation of Shewanella oneidensis Impacts Bacterial Fitness in Different Environments. Curr Microbiol 2020; 77:1790-1799. [PMID: 32328750 DOI: 10.1007/s00284-020-01999-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 04/15/2020] [Indexed: 10/24/2022]
Abstract
Flagella occur on many prokaryotes, which primarily propel cells to move from detrimental to favorable environments. A variety of species-specific flagellation patterns have been identified. Although it is presumed that for each of these flagellated microorganisms, an evolutionarily fixed flagellation pattern is favored under the normal living conditions, direct evidence is lacking. Here, we use Shewanella oneidensis, a rod-shaped Gram-negative bacterium with a monotrichous polar flagellum (MR-1, the wild-type), as a research model. The investigation has been enabled by multiple mutants with diverse flagellation patterns that had been generated by removing FlhF and FlhG proteins that control flagellar location and number, respectively. Growth assays, as a measure of fitness, revealed that the wild-type strain predominated in spreading on swim plates and in pellicles which form at the air-liquid interface. However, under the pellicles where oxygen is limited, both aflagellated and monotrichous lateral strains showed similar increase in fitness, whereas strains with multiple flagella were less competitive. Moreover, under shaking culturing conditions, the aflagellated strain outcompeted all other strains, including the wild-type, suggesting that cells devoid of flagella would be more likely enriched upon agitation. Overall, these data support the presumption that the monotrichous polar flagellum, as evolutionarily fixed in the wild-type strain, is optimal for the growth fitness of S. oneidensis over any other mutants under most test conditions. However, upon specific changes of environmental conditions, another form could come to predominate. These findings provide insight into the impacts of flagellation patterns and function on bacterial adaptation to differing environments.
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Affiliation(s)
- Ri-Sheng Yang
- Microbiology and Immunology Laboratory, College of Life Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, 310053, Zhejiang, China
| | - Yi-Tao Chen
- Microbiology and Immunology Laboratory, College of Life Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, 310053, Zhejiang, China.
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19
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Kenney LJ, Anand GS. EnvZ/OmpR Two-Component Signaling: An Archetype System That Can Function Noncanonically. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0001-2019. [PMID: 32003321 PMCID: PMC7192543 DOI: 10.1128/ecosalplus.esp-0001-2019] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Indexed: 01/09/2023]
Abstract
Two-component regulatory systems represent the major paradigm for signal transduction in prokaryotes. The simplest systems are composed of a sensor kinase and a response regulator. The sensor is often a membrane protein that senses a change in environmental conditions and is autophosphorylated by ATP on a histidine residue. The phosphoryl group is transferred onto an aspartate of the response regulator, which activates the regulator and alters its output, usually resulting in a change in gene expression. In this review, we present a historical view of the archetype EnvZ/OmpR two-component signaling system, and then we provide a new view of signaling based on our recent experiments. EnvZ responds to cytoplasmic signals that arise from changes in the extracellular milieu, and OmpR acts canonically (requiring phosphorylation) to regulate the porin genes and noncanonically (without phosphorylation) to activate the acid stress response. Herein, we describe how insights gleaned from stimulus recognition and response in EnvZ are relevant to nearly all sensor kinases and response regulators.
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Affiliation(s)
- Linda J Kenney
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Mechanobiology Institute, T-Lab, National University of Singapore, Singapore
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore
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20
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Paithankar KS, Enderle M, Wirthensohn DC, Miller A, Schlesner M, Pfeiffer F, Rittner A, Grininger M, Oesterhelt D. Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation. Acta Crystallogr F Struct Biol Commun 2019; 75:576-585. [PMID: 31475924 PMCID: PMC6718144 DOI: 10.1107/s2053230x19010896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/04/2019] [Indexed: 12/15/2022] Open
Abstract
Archaea are motile by the rotation of the archaellum. The archaellum switches between clockwise and counterclockwise rotation, and movement along a chemical gradient is possible by modulation of the switching frequency. This modulation involves the response regulator CheY and the archaellum adaptor protein CheF. In this study, two new crystal forms and protein structures of CheY are reported. In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection.
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Affiliation(s)
- Karthik Shivaji Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Mathias Enderle
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - David C. Wirthensohn
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Arthur Miller
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Schlesner
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Dieter Oesterhelt
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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21
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Muok AR, Briegel A, Crane BR. Regulation of the chemotaxis histidine kinase CheA: A structural perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183030. [PMID: 31374212 DOI: 10.1016/j.bbamem.2019.183030] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023]
Abstract
Bacteria sense and respond to their environment through a highly conserved assembly of transmembrane chemoreceptors (MCPs), the histidine kinase CheA, and the coupling protein CheW, hereafter termed "the chemosensory array". In recent years, great strides have been made in understanding the architecture of the chemosensory array and how this assembly engenders sensitive and cooperative responses. Nonetheless, a central outstanding question surrounds how receptors modulate the activity of the CheA kinase, the enzymatic output of the sensory system. With a focus on recent advances, we summarize the current understanding of array structure and function to comment on the molecular mechanism by which CheA, receptors and CheW generate the high sensitivity, gain and dynamic range emblematic of bacterial chemotaxis. The complexity of the chemosensory arrays has motivated investigation with many different approaches. In particular, structural methods, genetics, cellular activity assays, nanodisc technology and cryo-electron tomography have provided advances that bridge length scales and connect molecular mechanism to cellular function. Given the high degree of component integration in the chemosensory arrays, we ultimately aim to understand how such networked molecular interactions generate a whole that is truly greater than the sum of its parts. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.
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Affiliation(s)
- Alise R Muok
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, United States of America.
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22
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Balaraman P, Plettner E. Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1). Biochim Biophys Acta Gen Subj 2018; 1863:304-312. [PMID: 30391161 DOI: 10.1016/j.bbagen.2018.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 11/29/2022]
Abstract
The camphor-degrading microorganism, Pseudomonas putida strain ATCC 17453, is an aerobic, gram-negative soil bacterium that uses camphor as its sole carbon and energy source. The genes responsible for the catabolic degradation of camphor are encoded on the extra-chromosomal CAM plasmid. A monooxygenase, cytochrome P450cam, mediates hydroxylation of camphor to 5-exo-hydroxycamphor as the first and committed step in the camphor degradation pathway, requiring a dioxygen molecule (O2) from air. Under low O2 levels, P450cam catalyzes the production of borneol via an unusual reduction reaction. We have previously shown that borneol downregulates the expression of P450cam. To understand the function of P450cam and the consequences of down-regulation by borneol under low O2 conditions, we have studied chemotaxis of camphor induced and non-induced P. putida strain ATCC 17453. We have tested camphor, borneol, oxidized camphor metabolites and known bacterial attractants (d)-glucose, (d) - and (l)-glutamic acid for their elicitation chemotactic behavior. In addition, we have used 1-phenylimidazole, a P450cam inhibitor, to investigate if P450cam plays a role in the chemotactic ability of P. putida in the presence of camphor. We found that camphor, a chemoattractant, became toxic and chemorepellent when P450cam was inhibited. We have also evaluated the effect of borneol on chemotaxis and found that the bacteria chemotaxed away from camphor in the presence of borneol. This is the first report of the chemotactic behaviour of P. putida ATCC 17453 and the essential role of P450cam in this process.
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Affiliation(s)
- Priyadarshini Balaraman
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Erika Plettner
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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23
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Information Theoretical Study of Cross-Talk Mediated Signal Transduction in MAPK Pathways. ENTROPY 2017. [DOI: 10.3390/e19090469] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Optimal information transfer and stochastic resonance in collective decision making. SWARM INTELLIGENCE 2017. [DOI: 10.1007/s11721-017-0136-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Taxis of Artificial Swimmers in a Spatio-Temporally Modulated Activation Medium. ENTROPY 2017. [DOI: 10.3390/e19030097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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26
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Novak EA, Sekar P, Xu H, Moon KH, Manne A, Wooten RM, Motaleb MA. The Borrelia burgdorferi CheY3 response regulator is essential for chemotaxis and completion of its natural infection cycle. Cell Microbiol 2016; 18:1782-1799. [PMID: 27206578 PMCID: PMC5116424 DOI: 10.1111/cmi.12617] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/14/2016] [Accepted: 05/06/2016] [Indexed: 12/12/2022]
Abstract
Borrelia burgdorferi possesses a sophisticated and complex chemotaxis system, but how the organism utilizes this system in its natural enzootic life cycle is poorly understood. Of the three CheY chemotaxis response regulators in B. burgdorferi, we found that only deletion of cheY3 resulted in an altered motility and significantly reduced chemotaxis phenotype. Although ΔcheY3 maintained normal densities in unfed ticks, their numbers were significantly reduced in fed ticks compared with the parental or cheY3-complemented spirochetes. Importantly, mice fed upon by the ΔcheY3-infected ticks did not develop a persistent infection. Intravital confocal microscopy analyses discovered that the ΔcheY3 spirochetes were motile within skin, but appeared unable to reverse direction and perform the characteristic backward-forward motility displayed by the parental strain. Subsequently, the ΔcheY3 became 'trapped' in the skin matrix within days of inoculation, were cleared from the skin needle-inoculation site within 96 h post-injection and did not disseminate to distant tissues. Interestingly, although ΔcheY3 cells were cleared within 96 h post-injection, this attenuated infection elicited significant levels of B. burgdorferi-specific IgM and IgG. Taken together, these data demonstrate that cheY3-mediated chemotaxis is crucial for motility, dissemination and viability of the spirochete both within and between mice and ticks.
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Affiliation(s)
- Elizabeth A. Novak
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Padmapriya Sekar
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine, Toledo, Ohio, USA
| | - Hui Xu
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ki Hwan Moon
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Akarsh Manne
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - R. Mark Wooten
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine, Toledo, Ohio, USA
| | - Md. A. Motaleb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
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27
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Unluturk BD, Balasubramaniam S, Akyildiz IF. The Impact of Social Behavior on the Attenuation and Delay of Bacterial Nanonetworks. IEEE Trans Nanobioscience 2016; 15:959-969. [PMID: 27849547 DOI: 10.1109/tnb.2016.2627081] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Molecular communication (MC) is a new paradigm for developing communication systems that exchanges information through the transmission and reception of molecules. One proposed model for MC is using bacteria to carry information encoded into DNA plasmids, and this is termed bacterial nanonetworks. However, a limiting factor in the models that have been studied so far is the environment considered only in ideal conditions with a single population. This is far from realistic in natural environments, where bacteria coexist in multiple populations of same and different species, resulting in a very complex social community. This complex community has social interactions that include cooperation, cheating, as well as competition. In this paper, the effects of these social interactions on the information delivery in bacterial nanonetworks are studied in terms of delay, attenuation and data rate. The numerical results show that the cooperative behavior of bacteria improves the performance of delay and attenuation leading to a higher data rate, and this performance can be degraded once their behavior switches towards cheating. The competitive social behavior shows that the performance can degrade delay as well as attenuation leading to slower data rates, as the population with the encoded DNA plasmids are prevented from reaching the receiver. The analysis of social interactions between the bacteria will pave the way for efficient design of bacterial nanonetworks enabling applications such as intrabody sensing, drug delivery, and environmental control against pollution and biological hazards.
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28
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A Chemotaxis Receptor Modulates Nodulation during the Azorhizobium caulinodans-Sesbania rostrata Symbiosis. Appl Environ Microbiol 2016; 82:3174-84. [PMID: 26994081 DOI: 10.1128/aem.00230-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/14/2016] [Indexed: 01/02/2023] Open
Abstract
UNLABELLED Azorhizobium caulinodans ORS571 is a free-living nitrogen-fixing bacterium which can induce nitrogen-fixing nodules both on the root and the stem of its legume host Sesbania rostrata This bacterium, which is an obligate aerobe that moves by means of a polar flagellum, possesses a single chemotaxis signal transduction pathway. The objective of this work was to examine the role that chemotaxis and aerotaxis play in the lifestyle of the bacterium in free-living and symbiotic conditions. In bacterial chemotaxis, chemoreceptors sense environmental changes and transmit this information to the chemotactic machinery to guide motile bacteria to preferred niches. Here, we characterized a chemoreceptor of A. caulinodans containing an N-terminal PAS domain, named IcpB. IcpB is a soluble heme-binding protein that localized at the cell poles. An icpB mutant strain was impaired in sensing oxygen gradients and in chemotaxis response to organic acids. Compared to the wild-type strain, the icpB mutant strain was also affected in the production of extracellular polysaccharides and impaired in flocculation. When inoculated alone, the icpB mutant induced nodules on S. rostrata, but the nodules formed were smaller and had reduced N2-fixing activity. The icpB mutant failed to nodulate its host when inoculated competitively with the wild-type strain. Together, the results identify chemotaxis and sensing of oxygen by IcpB as key regulators of the A. caulinodans-S. rostrata symbiosis. IMPORTANCE Bacterial chemotaxis has been implicated in the establishment of various plant-microbe associations, including that of rhizobial symbionts with their legume host. The exact signal(s) detected by the motile bacteria that guide them to their plant hosts remain poorly characterized. Azorhizobium caulinodans ORS571 is a diazotroph that is a motile and chemotactic rhizobial symbiont of Sesbania rostrata, where it forms nitrogen-fixing nodules on both the roots and the stems of the legume host. We identify here a chemotaxis receptor sensing oxygen in A. caulinodans that is critical for nodulation and nitrogen fixation on the stems and roots of S. rostrata These results identify oxygen sensing and chemotaxis as key regulators of the A. caulinodans-S. rostrata symbiosis.
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29
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Fedi S, Barberi TT, Nappi MR, Sandri F, Booth S, Turner RJ, Attimonelli M, Cappelletti M, Zannoni D. The Role of cheA Genes in Swarming and Swimming Motility of Pseudomonas pseudoalcaligenes KF707. Microbes Environ 2016; 31:169-72. [PMID: 27151656 PMCID: PMC4912153 DOI: 10.1264/jsme2.me15164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A genome analysis of Pseudomonas pseudoalcaligenes KF707, a PCBs degrader and metal-resistant soil microorganism, revealed the presence of two novel gene clusters named che2 and che3, which were predicted to be involved in chemotaxis-like pathways, in addition to a che1 gene cluster. We herein report that the histidine kinase coding genes, cheA2 and cheA3, have no role in swimming or chemotaxis in P. pseudoalcaligenes KF707, in contrast to cheA1. However, the cheA1 and cheA2 genes were both necessary for cell swarming, whereas the cheA3 gene product had a negative effect on the optimal swarming phenotype of KF707 cells.
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Affiliation(s)
- Stefano Fedi
- Department of Pharmacy and Biotechnology, University of Bologna
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30
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The antimicrobial polymer PHMB enters cells and selectively condenses bacterial chromosomes. Sci Rep 2016; 6:23121. [PMID: 26996206 PMCID: PMC4800398 DOI: 10.1038/srep23121] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/29/2016] [Indexed: 11/08/2022] Open
Abstract
To combat infection and antimicrobial resistance, it is helpful to elucidate drug mechanism(s) of action. Here we examined how the widely used antimicrobial polyhexamethylene biguanide (PHMB) kills bacteria selectively over host cells. Contrary to the accepted model of microbial membrane disruption by PHMB, we observed cell entry into a range of bacterial species, and treated bacteria displayed cell division arrest and chromosome condensation, suggesting DNA binding as an alternative antimicrobial mechanism. A DNA-level mechanism was confirmed by observations that PHMB formed nanoparticles when mixed with isolated bacterial chromosomal DNA and its effects on growth were suppressed by pairwise combination with the DNA binding ligand Hoechst 33258. PHMB also entered mammalian cells, but was trapped within endosomes and excluded from nuclei. Therefore, PHMB displays differential access to bacterial and mammalian cellular DNA and selectively binds and condenses bacterial chromosomes. Because acquired resistance to PHMB has not been reported, selective chromosome condensation provides an unanticipated paradigm for antimicrobial action that may not succumb to resistance.
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Transmembrane protein sorting driven by membrane curvature. Nat Commun 2015; 6:8728. [PMID: 26522943 PMCID: PMC4632190 DOI: 10.1038/ncomms9728] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 09/25/2015] [Indexed: 12/22/2022] Open
Abstract
The intricate structure of prokaryotic and eukaryotic cells depends on the ability to target proteins to specific cellular locations. In most cases, we have a poor understanding of the underlying mechanisms. A typical example is the assembly of bacterial chemoreceptors at cell poles. Here we show that the classical chemoreceptor TlpA of Bacillus subtilis does not localize according to the consensus stochastic nucleation mechanism but accumulates at strongly curved membrane areas generated during cell division. This preference was confirmed by accumulation at non-septal curved membranes. Localization appears to be an intrinsic property of the protein complex and does not rely on chemoreceptor clustering, as was previously shown for Escherichia coli. By constructing specific amino-acid substitutions, we demonstrate that the preference for strongly curved membranes arises from the curved shape of chemoreceptor trimer of dimers. These findings demonstrate that the intrinsic shape of transmembrane proteins can determine their cellular localization. The accumulation of chemoreceptor proteins at bacterial poles is thought to depend on their clustering into arrays. Strahl et al. show that in Bacillus subtilis, the chemoreceptor TlpA uses high membrane curvature as a spatial cue for polar localization, through the intrinsic curvature sensitivity of the receptor complex.
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Opposite and Coordinated Rotation of Amphitrichous Flagella Governs Oriented Swimming and Reversals in a Magnetotactic Spirillum. J Bacteriol 2015; 197:3275-82. [PMID: 26240070 DOI: 10.1128/jb.00172-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/30/2015] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Current knowledge regarding the mechanism that governs flagellar motor rotation in response to environmental stimuli stems mainly from the study of monotrichous and peritrichous bacteria. Little is known about how two polar flagella, one at each cell pole of the so-called amphitrichous bacterium, are coordinated to steer the swimming. Here we fluorescently labeled the flagella of Magnetospirillum magneticum AMB-1 cells and took advantage of the magnetically controllable swimming of this bacterium to investigate flagellar rotation in moving cells. We identified three motility behaviors (runs, tumbles, and reversals) and two characteristic fluorescence patterns likely corresponding to flagella rotating in opposite directions. Each AMB-1 locomotion mode was systematically associated with particular flagellar patterns at the poles which led us to conclude that, while cell runs are allowed by the asymmetrical rotation of flagellar motors, their symmetrical rotation triggers cell tumbling. Our observations point toward a precise coordination of the two flagellar motors which can be temporarily unsynchronized during tumbling. IMPORTANCE Motility is essential for bacteria to search for optimal niches and survive. Many bacteria use one or several flagella to explore their environment. The mechanism by which bipolarly flagellated cells coordinate flagellar rotation is poorly understood. We took advantage of the genetic amenability and magnetically controlled swimming of the spirillum-shaped magnetotactic bacterium Magnetospirillum magneticum AMB-1 to correlate cell motion with flagellar rotation. We found that asymmetric rotation of the flagella (counterclockwise at the lagging pole and clockwise at the leading pole) enables cell runs whereas symmetric rotation triggers cell tumbling. Taking into consideration similar observations in spirochetes, bacteria possessing bipolar ribbons of periplasmic flagella, we propose a conserved motility paradigm for spirillum-shaped bipolarly flagellated bacteria.
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Maity AK, Chaudhury P, Banik SK. Role of relaxation time scale in noisy signal transduction. PLoS One 2015; 10:e0123242. [PMID: 25955500 PMCID: PMC4425683 DOI: 10.1371/journal.pone.0123242] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 02/28/2015] [Indexed: 11/18/2022] Open
Abstract
Intra-cellular fluctuations, mainly triggered by gene expression, are an inevitable phenomenon observed in living cells. It influences generation of phenotypic diversity in genetically identical cells. Such variation of cellular components is beneficial in some contexts but detrimental in others. To quantify the fluctuations in a gene product, we undertake an analytical scheme for studying few naturally abundant linear as well as branched chain network motifs. We solve the Langevin equations associated with each motif under the purview of linear noise approximation and derive the expressions for Fano factor and mutual information in close analytical form. Both quantifiable expressions exclusively depend on the relaxation time (decay rate constant) and steady state population of the network components. We investigate the effect of relaxation time constraints on Fano factor and mutual information to indentify a time scale domain where a network can recognize the fluctuations associated with the input signal more reliably. We also show how input population affects both quantities. We extend our calculation to long chain linear motif and show that with increasing chain length, the Fano factor value increases but the mutual information processing capability decreases. In this type of motif, the intermediate components act as a noise filter that tune up input fluctuations and maintain optimum fluctuations in the output. For branched chain motifs, both quantities vary within a large scale due to their network architecture and facilitate survival of living system in diverse environmental conditions.
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Affiliation(s)
| | | | - Suman K Banik
- Department of Chemistry, Bose Institute, Kolkata, India
- * E-mail:
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Halang P, Vorburger T, Steuber J. Serine 26 in the PomB subunit of the flagellar motor is essential for hypermotility of Vibrio cholerae. PLoS One 2015; 10:e0123518. [PMID: 25874792 PMCID: PMC4398553 DOI: 10.1371/journal.pone.0123518] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/19/2015] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae is motile by means of its single polar flagellum which is driven by the sodium-motive force. In the motor driving rotation of the flagellar filament, a stator complex consisting of subunits PomA and PomB converts the electrochemical sodium ion gradient into torque. Charged or polar residues within the membrane part of PomB could act as ligands for Na+, or stabilize a hydrogen bond network by interacting with water within the putative channel between PomA and PomB. By analyzing a large data set of individual tracks of swimming cells, we show that S26 located within the transmembrane helix of PomB is required to promote very fast swimming of V. cholerae. Loss of hypermotility was observed with the S26T variant of PomB at pH 7.0, but fast swimming was restored by decreasing the H+ concentration of the external medium. Our study identifies S26 as a second important residue besides D23 in the PomB channel. It is proposed that S26, together with D23 located in close proximity, is important to perturb the hydration shell of Na+ before its passage through a constriction within the stator channel.
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Affiliation(s)
- Petra Halang
- Institute of Microbiology, University of Hohenheim (Stuttgart), Stuttgart, Germany
| | - Thomas Vorburger
- Institute of Microbiology, University of Hohenheim (Stuttgart), Stuttgart, Germany
- * E-mail: (TV); (JS)
| | - Julia Steuber
- Institute of Microbiology, University of Hohenheim (Stuttgart), Stuttgart, Germany
- * E-mail: (TV); (JS)
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Hiremath G, Hyakutake A, Yamamoto K, Ebisawa T, Nakamura T, Nishiyama SI, Homma M, Kawagishi I. Hypoxia-induced localization of chemotaxis-related signaling proteins inVibrio cholerae. Mol Microbiol 2015; 95:780-90. [DOI: 10.1111/mmi.12887] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Geetha Hiremath
- Research Center for Micro-Nano Technology; Hosei University; Koganei Tokyo 184-8584 Japan
| | - Akihiro Hyakutake
- Division of Biological Science; Graduate School of Science; Nagoya University; Chikusa-ku Nagoya 464-8602 Japan
| | - Kentaro Yamamoto
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
| | - Tatsuaki Ebisawa
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
| | - Tomoyuki Nakamura
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
| | - So-ichiro Nishiyama
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
| | - Michio Homma
- Division of Biological Science; Graduate School of Science; Nagoya University; Chikusa-ku Nagoya 464-8602 Japan
| | - Ikuro Kawagishi
- Research Center for Micro-Nano Technology; Hosei University; Koganei Tokyo 184-8584 Japan
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
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Plasmid-encoded MCP is involved in virulence, motility, and biofilm formation of Cronobacter sakazakii ATCC 29544. Infect Immun 2014; 83:197-204. [PMID: 25332122 DOI: 10.1128/iai.02633-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to elucidate the function of the plasmid-borne mcp (methyl-accepting chemotaxis protein) gene, which plays pleiotropic roles in Cronobacter sakazakii ATCC 29544. By searching for virulence factors using a random transposon insertion mutant library, we identified and sequenced a new plasmid, pCSA2, in C. sakazakii ATCC 29544. An in silico analysis of pCSA2 revealed that it included six putative open reading frames, and one of them was mcp. The mcp mutant was defective for invasion into and adhesion to epithelial cells, and the virulence of the mcp mutant was attenuated in rat pups. In addition, we demonstrated that putative MCP regulates the motility of C. sakazakii, and the expression of the flagellar genes was enhanced in the absence of a functional mcp gene. Furthermore, a lack of the mcp gene also impaired the ability of C. sakazakii to form a biofilm. Our results demonstrate a regulatory role for MCP in diverse biological processes, including the virulence of C. sakazakii ATCC 29544. To the best of our knowledge, this study is the first to elucidate a potential function of a plasmid-encoded MCP homolog in the C. sakazakii sequence type 8 (ST8) lineage.
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Acemoglu A, Yesilyurt S. Effects of geometric parameters on swimming of micro organisms with single helical flagellum in circular channels. Biophys J 2014; 106:1537-47. [PMID: 24703315 DOI: 10.1016/j.bpj.2014.01.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/23/2014] [Accepted: 01/29/2014] [Indexed: 11/29/2022] Open
Abstract
We present a computational fluid dynamics (CFD) model for the swimming of micro organisms with a single helical flagellum in circular channels. The CFD model is developed to obtain numerical solutions of Stokes equations in three dimensions, validated with experiments reported in literature, and used to analyze the effects of geometric parameters, such as the helical radius, wavelength, radii of the channel and the tail and the tail length on forward and lateral swimming velocities, rotation rates, and the efficiency of the swimmer. Optimal shapes for the speed and the power efficiency are reported. Effects of Brownian motion and electrostatic interactions are excluded to emphasize the role of hydrodynamic forces on lateral velocities and rotations on the trajectory of swimmers. For thin flagella, as the channel radius decreases, forward velocity and the power efficiency of the swimmer decreases as well; however, for thick flagella, there is an optimal radius of the channel that maximizes the velocity and the efficiency depending on other geometric parameters. Lateral motion of the swimmer is suppressed as the channel is constricted below a critical radius, for which the magnitude of the lateral velocity reaches a maximum. Results contribute significantly to the understanding of the swimming of bacteria in micro channels and capillary tubes.
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Analyzing the modification of the Shewanella oneidensis MR-1 flagellar filament. PLoS One 2013; 8:e73444. [PMID: 24039942 PMCID: PMC3765264 DOI: 10.1371/journal.pone.0073444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/22/2013] [Indexed: 11/19/2022] Open
Abstract
The unsheathed flagellar filament of Shewanella oneidensis MR-1 is composed of two highly homologous flagellins, FlaA, and the major structural unit, FlaB. We identified a gene cluster, SO_3261-SO_3265 (now sfmABCDE), that is required for the formation of a fully functional filament and for motility. The predicted function of the corresponding gene products strongly indicated a role in flagellin modification. Accordingly, loss of sfmABCDE results in a significant mass shift of both FlaA and FlaB. Mass spectroscopy analysis and single residue substitutions identified five serine residues in both flagellins that are modified via O-linkage. Modeling of the flagellin structures strongly suggests that at least four of the modified residues are exposed to the filament's surface. However, none of the five serine residues solely is crucial for function and assembly. Structural analysis of the flagellin modification revealed that it likely contains a nonulosonic acid (274 Da) linked to each glycosylated serine. The putative nonulosonic acid is further substituted with a 236 Da moiety which can carry additional methyl groups (250 Da, 264 Da). In addition, at least 5 lysine residues in FlaB and one in FlaA were found to be methylated. Based on homology comparisons we suggest that smfABCDE is required for species-specific flagellin modification in S. oneidensis MR-1.
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Maity AK, Bandyopadhyay A, Chattopadhyay S, Chaudhuri JR, Metzler R, Chaudhury P, Banik SK. Quantification of noise in bifunctionality-induced post-translational modification. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:032716. [PMID: 24125303 DOI: 10.1103/physreve.88.032716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 03/07/2013] [Indexed: 06/02/2023]
Abstract
We present a generic analytical scheme for the quantification of fluctuations due to bifunctionality-induced signal transduction within the members of a bacterial two-component system. The proposed model takes into account post-translational modifications in terms of elementary phosphotransfer kinetics. Sources of fluctuations due to autophosphorylation, kinase, and phosphatase activity of the sensor kinase have been considered in the model via Langevin equations, which are then solved within the framework of linear noise approximation. The resultant analytical expression of phosphorylated response regulators are then used to quantify the noise profile of biologically motivated single and branched pathways. Enhancement and reduction of noise in terms of extra phosphate outflux and influx, respectively, have been analyzed for the branched system. Furthermore, the role of fluctuations of the network output in the regulation of a promoter with random activation-deactivation dynamics has been analyzed.
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Affiliation(s)
- Alok Kumar Maity
- Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
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40
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Xu X, Chen HL. Adaptive computational chemotaxis based on field in bacterial foraging optimization. Soft comput 2013. [DOI: 10.1007/s00500-013-1089-4] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Inoue K, Tsukamoto T, Sudo Y. Molecular and evolutionary aspects of microbial sensory rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:562-77. [PMID: 23732219 DOI: 10.1016/j.bbabio.2013.05.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 02/03/2023]
Abstract
Retinal proteins (~rhodopsins) are photochemically reactive membrane-embedded proteins, with seven transmembrane α-helices which bind the chromophore retinal (vitamin A aldehyde). They are widely distributed through all three biological kingdoms, eukarya, bacteria and archaea, indicating the biological significance of the retinal proteins. Light absorption by the retinal proteins triggers a photoisomerization of the chromophore, leading to the biological function, light-energy conversion or light-signal transduction. This article reviews molecular and evolutionary aspects of the light-signal transduction by microbial sensory receptors and their related proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Tsukamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Yuki Sudo
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan; Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan; Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, Japan.
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Voegel TM, Doddapaneni H, Cheng DW, Lin H, Stenger DC, Kirkpatrick BC, Roper MC. Identification of a response regulator involved in surface attachment, cell-cell aggregation, exopolysaccharide production and virulence in the plant pathogen Xylella fastidiosa. MOLECULAR PLANT PATHOLOGY 2013; 14:256-264. [PMID: 23186359 PMCID: PMC6638743 DOI: 10.1111/mpp.12004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Xylella fastidiosa, the causal agent of Pierce's disease of grapevine, possesses several two-component signal transduction systems that allow the bacterium to sense and respond to changes in its environment. Signals are perceived by sensor kinases that autophosphorylate and transfer the phosphate to response regulators (RRs), which direct an output response, usually by acting as transcriptional regulators. In the X. fastidiosa genome, 19 RRs were found. A site-directed knockout mutant in one unusual RR, designated XhpT, composed of a receiver domain and a histidine phosphotransferase output domain, was constructed. The resulting mutant strain was analysed for changes in phenotypic traits related to biofilm formation and gene expression using microarray analysis. We found that the xhpT mutant was altered in surface attachment, cell-cell aggregation, exopolysaccharide (EPS) production and virulence in grapevine. In addition, this mutant had an altered transcriptional profile when compared with wild-type X. fastidiosa in genes for several biofilm-related traits, such as EPS production and haemagglutinin adhesins.
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Affiliation(s)
- Tanja M Voegel
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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Jeong KW, Ko H, Lee SA, Hong E, Ko S, Cho HS, Lee W, Kim Y. Backbone dynamics of an atypical orphan response regulator protein, Helicobacter pylori 1043. Mol Cells 2013; 35:158-65. [PMID: 23456337 PMCID: PMC3887898 DOI: 10.1007/s10059-013-2303-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 12/13/2012] [Accepted: 12/17/2012] [Indexed: 01/19/2023] Open
Abstract
An atypical orphan response regulator protein, HP1043 (HP-RR) in Helicobacter pylori, is proven to be essential for cell growth and does not require the well known phosphorelay scheme. HP-RR was identified as a symmetric dimer with two functional domains, an N-terminal regulatory domain (HP-RR(r)) and a C-terminal effector domain (HP-RR(e)). HP-RR is a new class of response regulator, as a phosphorylation-independent regulator. Previously, we have presented a detailed three-dimensional structure of HP-RR using NMR spectroscopy and X-ray crystallography. In this study, in order to understand the functional importance of flexibilities in HP-RR(r) and HP-RR(e), T1, T2, heteronuclear NOE experiments have been performed and backbone dynamics of HP-RR(r) and HP-RR(e) were investigated. HP-RR(r) is a symmetric dimer and the interface region, α4-β5-α5 of dimer, showed high rigidity (high S (2) values). Site of rearrangements associated with phosphorylation of HP-RR(r) (Ser(75): R ex = 3.382, Ile(95): R ex = 5.228) showed slow chemical exchanges. HP-RR(e) is composed of three α-helices flanked on two sides by anti-parallel β-sheets. Low order parameters as well as conformational exchanges in the centers of loop regions known as the DNA binding site and transcription site of HP-RR(e) suggested that flexibility of HP-RR(e) is essential for interaction with DNA. In conclusion, backbone dynamics information for HP-RR implies that structural flexibilities in HP-RR(r) are necessary for the phosphorylation site and the dynamic nature of HP-RR(e) is essential for the regulation of interaction between protein and DNA.
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Affiliation(s)
- Ki-Woong Jeong
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Institute of SMART Biotechnology, Konkuk University, Seoul 143-701,
Korea
| | - Hyunsook Ko
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Institute of SMART Biotechnology, Konkuk University, Seoul 143-701,
Korea
| | - Sung-Ah Lee
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Institute of SMART Biotechnology, Konkuk University, Seoul 143-701,
Korea
| | | | | | | | | | - Yangmee Kim
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Institute of SMART Biotechnology, Konkuk University, Seoul 143-701,
Korea
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Ditty JL, Williams KM, Keller MM, Chen GY, Liu X, Parales RE. Integrating grant-funded research into the undergraduate biology curriculum using IMG-ACT. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:16-23. [PMID: 23382122 DOI: 10.1002/bmb.20662] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Indexed: 06/01/2023]
Abstract
It has become clear in current scientific pedagogy that the emersion of students in the scientific process in terms of designing, implementing, and analyzing experiments is imperative for their education; as such, it has been our goal to model this active learning process in the classroom and laboratory in the context of a genuine scientific question. Toward this objective, the National Science Foundation funded a collaborative research grant between a primarily undergraduate institution and a research-intensive institution to study the chemotactic responses of the bacterium Pseudomonas putida F1. As part of the project, a new Bioinformatics course was developed in which undergraduates annotate relevant regions of the P. putida F1 genome using Integrated Microbial Genomes Annotation Collaboration Toolkit, a bioinformatics interface specifically developed for undergraduate programs by the Department of Energy Joint Genome Institute. Based on annotations of putative chemotaxis genes in P. putida F1 and comparative genomics studies, undergraduate students from both institutions developed functional genomics research projects that evolved from the annotations. The purpose of this study is to describe the nature of the NSF grant, the development of the Bioinformatics lecture and wet laboratory course, and how undergraduate student involvement in the project that was initiated in the classroom has served as a springboard for independent undergraduate research projects.
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Affiliation(s)
- Jayna L Ditty
- Department of Biology, University of St. Thomas, St. Paul, MN, USA.
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Schürg T, Brandt U, Adis C, Fleissner A. The Saccharomyces cerevisiae BEM1 homologue in Neurospora crassa promotes co-ordinated cell behaviour resulting in cell fusion. Mol Microbiol 2012; 86:349-66. [PMID: 22906237 DOI: 10.1111/j.1365-2958.2012.08197.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2012] [Indexed: 12/24/2022]
Abstract
Directed growth or movement is a common feature of microbial development and propagation. In polar growing filamentous fungi, directed growth requires the interaction of signal sensing machineries with factors controlling polarity and cell tip extension. In Neurospora crassa an unusual mode of cell-cell signalling mediates mutual attraction of germinating spores, which subsequently fuse. During directed growth of the two fusion partners, the cells co-ordinately alternate between two physiological stages, probably associated with signal sending and receiving. Here, we show that the Saccharomyces cerevisiae BEM1 homologue in N. crassa is essential for the robust and efficient functioning of this MAP kinase-based signalling system. BEM1 localizes to growing hyphal tips suggesting a conserved function as a polarity component. In the absence of BEM1, activation of MAK-2, a MAP kinase essential for germling fusion, is strongly reduced and delayed. Germling interactions become highly instable and successful fusion is greatly reduced. In addition, BEM1 is actively recruited around the forming fusion pore, suggesting potential functions after cell-cell contact has been established. By genetically dissecting the contribution of BEM1 to additional various polarization events, we also obtained first hints that BEM1 might function in different protein complexes controlling polarity and growth direction.
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Affiliation(s)
- Timo Schürg
- Institut für Genetik, Technische Universität, Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
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Hatzios SK, Ringgaard S, Davis BM, Waldor MK. Studies of dynamic protein-protein interactions in bacteria using Renilla luciferase complementation are undermined by nonspecific enzyme inhibition. PLoS One 2012; 7:e43175. [PMID: 22905225 PMCID: PMC3419657 DOI: 10.1371/journal.pone.0043175] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 07/20/2012] [Indexed: 12/13/2022] Open
Abstract
The luciferase protein fragment complementation assay is a powerful tool for studying protein-protein interactions. Two inactive fragments of luciferase are genetically fused to interacting proteins, and when these two proteins interact, the luciferase fragments can reversibly associate and reconstitute enzyme activity. Though this technology has been used extensively in live eukaryotic cells, split luciferase complementation has not yet been applied to studies of dynamic protein-protein interactions in live bacteria. As proof of concept and to develop a new tool for studies of bacterial chemotaxis, fragments of Renilla luciferase (Rluc) were fused to the chemotaxis-associated response regulator CheY3 and its phosphatase CheZ in the enteric pathogen Vibrio cholerae. Luciferase activity was dependent on the presence of both CheY3 and CheZ fusion proteins, demonstrating the specificity of the assay. Furthermore, enzyme activity was markedly reduced in V. cholerae chemotaxis mutants, suggesting that this approach can measure defects in chemotactic signaling. However, attempts to measure changes in dynamic CheY3-CheZ interactions in response to various chemoeffectors were undermined by nonspecific inhibition of the full-length luciferase. These observations reveal an unexpected limitation of split Rluc complementation that may have implications for existing data and highlight the need for great caution when evaluating small molecule effects on dynamic protein-protein interactions using the split luciferase technology.
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Affiliation(s)
- Stavroula K. Hatzios
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Simon Ringgaard
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Brigid M. Davis
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
- * E-mail:
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Mlp24 (McpX) of Vibrio cholerae implicated in pathogenicity functions as a chemoreceptor for multiple amino acids. Infect Immun 2012; 80:3170-8. [PMID: 22753378 DOI: 10.1128/iai.00039-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The chemotaxis of Vibrio cholerae, the causative agent of cholera, has been implicated in pathogenicity. The bacterium has more than 40 genes for methyl-accepting chemotaxis protein (MCP)-like proteins (MLPs). In this study, we found that glycine and at least 18 L-amino acids, including serine, arginine, asparagine, and proline, serve as attractants to the classical biotype strain O395N1. Based on the sequence comparison with Vibrio parahaemolyticus, we speculated that at least 17 MLPs of V. cholerae may mediate chemotactic responses. Among them, Mlp24 (previously named McpX) is required for the production of cholera toxin upon mouse infection. mlp24 deletion strains of both classical and El Tor biotypes showed defects in taxis toward several amino acids, which were complemented by the expression of Mlp24. These amino acids enhanced methylation of Mlp24. Serine, arginine, asparagine, and proline were shown to bind directly to the periplasmic fragment of Mlp24. The structural information of its closest homolog, Mlp37, predicts that Mlp24 has two potential ligand-binding pockets per subunit, the membrane distal of which was suggested, by mutational analyses, to be involved in sensing of amino acids. These results suggest that Mlp24 is a chemoreceptor for multiple amino acids, including serine, arginine, and asparagine, which were previously shown to stimulate the expression of several virulence factors, implying that taxis toward a set of amino acids plays critical roles in pathogenicity of V. cholerae.
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Melton ED, Schmidt C, Kappler A. Microbial Iron(II) Oxidation in Littoral Freshwater Lake Sediment: The Potential for Competition between Phototrophic vs. Nitrate-Reducing Iron(II)-Oxidizers. Front Microbiol 2012; 3:197. [PMID: 22666221 PMCID: PMC3364526 DOI: 10.3389/fmicb.2012.00197] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 05/14/2012] [Indexed: 11/13/2022] Open
Abstract
The distribution of neutrophilic microbial iron oxidation is mainly determined by local gradients of oxygen, light, nitrate and ferrous iron. In the anoxic top part of littoral freshwater lake sediment, nitrate-reducing and phototrophic Fe(II)-oxidizers compete for the same e− donor; reduced iron. It is not yet understood how these microbes co-exist in the sediment and what role they play in the Fe cycle. We show that both metabolic types of anaerobic Fe(II)-oxidizing microorganisms are present in the same sediment layer directly beneath the oxic-anoxic sediment interface. The photoferrotrophic most probable number counted 3.4·105 cells·g−1 and the autotrophic and mixotrophic nitrate-reducing Fe(II)-oxidizers totaled 1.8·104 and 4.5·104 cells·g−1 dry weight sediment, respectively. To distinguish between the two microbial Fe(II) oxidation processes and assess their individual contribution to the sedimentary Fe cycle, littoral lake sediment was incubated in microcosm experiments. Nitrate-reducing Fe(II)-oxidizing bacteria exhibited a higher maximum Fe(II) oxidation rate per cell, in both pure cultures and microcosms, than photoferrotrophs. In microcosms, photoferrotrophs instantly started oxidizing Fe(II), whilst nitrate-reducing Fe(II)-oxidizers showed a significant lag-phase during which they probably use organics as e− donor before initiating Fe(II) oxidation. This suggests that they will be outcompeted by phototrophic Fe(II)-oxidizers during optimal light conditions; as phototrophs deplete Fe(II) before nitrate-reducing Fe(II)-oxidizers start Fe(II) oxidation. Thus, the co-existence of the two anaerobic Fe(II)-oxidizers may be possible due to a niche space separation in time by the day-night cycle, where nitrate-reducing Fe(II)-oxidizers oxidize Fe(II) during darkness and phototrophs play a dominant role in Fe(II) oxidation during daylight. Furthermore, metabolic flexibility of Fe(II)-oxidizing microbes may play a paramount role in the conservation of the sedimentary Fe cycle.
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Affiliation(s)
- E D Melton
- Geomicrobiology, Centre for Applied Geosciences, University of Tübingen Tübingen, Germany
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Park S, Crane BR. Structural insight into the low affinity between Thermotoga maritima CheA and CheB compared to their Escherichia coli/Salmonella typhimurium counterparts. Int J Biol Macromol 2011; 49:794-800. [PMID: 21816169 PMCID: PMC3204391 DOI: 10.1016/j.ijbiomac.2011.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 07/19/2011] [Accepted: 07/19/2011] [Indexed: 01/07/2023]
Abstract
CheA-mediated CheB phosphorylation and the subsequent CheB-mediated demethylation of the chemoreceptors are important steps required for the bacterial chemotactic adaptation response. Although Escherichia coli CheB has been reported to interact with CheA competitively against CheY, we have observed that Thermotoga maritima CheB has no detectable CheA-binding. By determining the CheY-like domain crystal structure of T. maritima CheB, and comparing against the T. maritima CheY and Salmonella typhimurium CheB structures, we propose that the two consecutive glutamates in the β4/α4 loop of T. maritima CheB that is absent in T. maritima CheY and in E. coli/S. typhimurium CheB may be one factor contributing to the low CheA affinity.
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Affiliation(s)
- SangYoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul, Korea,To whom correspondence should be addressed: SangYoun Park, PhD, School of Systems Biomedical Science, College of Natural Sciences, Soongsil University, 511 Sangdo-Dong, Dongjak-Gu, Seoul 156-743, Korea, Phone: 82-2-820-0456, Fax: 82-2-824-4383,
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
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50
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Armitano J, Baraquet C, Michotey V, Méjean V, Jourlin-Castelli C. The chemical-in-μwell: a high-throughput technique for identifying solutes eliciting a chemotactic response in motile bacteria. Res Microbiol 2011; 162:934-8. [DOI: 10.1016/j.resmic.2011.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 02/18/2011] [Indexed: 10/18/2022]
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