scholarly journals The “Jack-of-all-Trades” Flagellum From Salmonella and E. coli Was Horizontally Acquired From an Ancestral β-Proteobacterium

2021 ◽  
Vol 12 ◽  
Author(s):  
Josie L. Ferreira ◽  
Izaak Coleman ◽  
Max L. Addison ◽  
Tobias Zachs ◽  
Bonnie L. Quigley ◽  
...  
Keyword(s):  
General Purpose ◽  
Gut Bacteria ◽  
E Coli ◽  
Flagellar Motors ◽  
Subtomogram Averaging

The γ-proteobacteria are a group of diverse bacteria including pathogenic Escherichia, Salmonella, Vibrio, and Pseudomonas species. The majority swim in liquids with polar, sodium-driven flagella and swarm on surfaces with lateral, non-chemotactic flagella. Notable exceptions are the enteric Enterobacteriaceae such as Salmonella and E. coli. Many of the well-studied Enterobacteriaceae are gut bacteria that both swim and swarm with the same proton-driven peritrichous flagella. How different flagella evolved in closely related lineages, however, has remained unclear. Here, we describe our phylogenetic finding that Enterobacteriaceae flagella are not native polar or lateral γ-proteobacterial flagella but were horizontally acquired from an ancestral β-proteobacterium. Using electron cryo-tomography and subtomogram averaging, we confirmed that Enterobacteriaceae flagellar motors resemble contemporary β-proteobacterial motors and are distinct to the polar and lateral motors of other γ-proteobacteria. Structural comparisons support a model in which γ-proteobacterial motors have specialized, suggesting that acquisition of a β-proteobacterial flagellum may have been beneficial as a general-purpose motor suitable for adjusting to diverse conditions. This acquisition may have played a role in the development of the enteric lifestyle.

scholarly journals Gut Microbiota Prevents Sugar Alcohol-Induced Diarrhea

Nutrients ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 2029
Author(s):  
Kouya Hattori ◽  
Masahiro Akiyama ◽  
Natsumi Seki ◽  
Kyosuke Yakabe ◽  
Koji Hase ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Bacteria ◽  
Food Science ◽  
Sugar Alcohol ◽  
Processed Food ◽  
Phosphotransferase System ◽  
Sugar Alcohols ◽  
E Coli ◽  
The Family ◽  
Rdna Analysis

While poorly-absorbed sugar alcohols such as sorbitol are widely used as sweeteners, they may induce diarrhea in some individuals. However, the factors which determine an individual’s susceptibility to sugar alcohol-induced diarrhea remain unknown. Here, we show that specific gut bacteria are involved in the suppression of sorbitol-induced diarrhea. Based on 16S rDNA analysis, the abundance of Enterobacteriaceae bacteria increased in response to sorbitol consumption. We found that Escherichia coli of the family Enterobacteriaceae degraded sorbitol and suppressed sorbitol-induced diarrhea. Finally, we showed that the metabolism of sorbitol by the E. coli sugar phosphotransferase system helped suppress sorbitol-induced diarrhea. Therefore, gut microbiota prevented sugar alcohol-induced diarrhea by degrading sorbitol in the gut. The identification of the gut bacteria which respond to and degrade sugar alcohols in the intestine has implications for microbiome science, processed food science, and public health.

scholarly journals TheDynamopackage for tomography and subtomogram averaging: components forMATLAB, GPU computing and EC2 Amazon Web Services

2017 ◽  
Vol 73 (6) ◽  
pp. 478-487 ◽  
Author(s):  
Daniel Castaño-Díez
Keyword(s):  
Software Maintenance ◽  
Gpu Computing ◽  
Computing Time ◽  
Three Dimensional ◽  
Middle Layer ◽  
General Purpose ◽  
Single Node ◽  
Subtomogram Averaging ◽  
Particle Extraction ◽  
High Level

Dynamois a package for the processing of tomographic data. As a tool for subtomogram averaging, it includes different alignment and classification strategies. Furthermore, its data-management module allows experiments to be organized in groups of tomograms, while offering specialized three-dimensional tomographic browsers that facilitate visualization, location of regions of interest, modelling and particle extraction in complex geometries. Here, a technical description of the package is presented, focusing on its diverse strategies for optimizing computing performance.Dynamois built upon mbtools (middle layer toolbox), a general-purposeMATLABlibrary for object-oriented scientific programming specifically developed to underpinDynamobut usable as an independent tool. Its structure intertwines a flexibleMATLABcodebase with precompiled C++ functions that carry the burden of numerically intensive operations. The package can be delivered as a precompiled standalone ready for execution without aMATLABlicense. Multicore parallelization on a single node is directly inherited from the high-level parallelization engine provided forMATLAB, automatically imparting a balanced workload among the threads in computationally intense tasks such as alignment and classification, but also in logistic-oriented tasks such as tomogram binning and particle extraction.Dynamosupports the use of graphical processing units (GPUs), yielding considerable speedup factors both for nativeDynamoprocedures (such as the numerically intensive subtomogram alignment) and procedures defined by the user through itsMATLAB-based GPU library for three-dimensional operations. Cloud-based virtual computing environments supplied with a pre-installed version ofDynamocan be publicly accessed through the Amazon Elastic Compute Cloud (EC2), enabling users to rent GPU computing time on a pay-as-you-go basis, thus avoiding upfront investments in hardware and longterm software maintenance.

scholarly journals 3P150 Measurement of rotational behavior of flagellar motors in E. coli induced by caged serine(Molecular motor,The 48th Annual Meeting of the Biophysical Society of Japan)

2010 ◽  
Vol 50 (supplement2) ◽  
pp. S171
Author(s):  
Yu Kikuchi ◽  
Hajime Hukuoka ◽  
Yuichi Inoue ◽  
Hiroto Takahashi ◽  
Takahiro Muraoka ◽  
...  
Keyword(s):  
Annual Meeting ◽  
Molecular Motor ◽  
Rotational Behavior ◽  
E Coli ◽  
Flagellar Motors ◽  
Biophysical Society

scholarly journals Gut bacteria regulate the pathogenesis of Huntington's disease in Drosophila

2021 ◽  
Author(s):  
Anjalika Chongtham ◽  
Jung Hyun Yoo ◽  
Theodore M Chin ◽  
Ngozi D Akingbesote ◽  
Ainul Huda ◽  
...  
Keyword(s):  
Huntington's Disease ◽  
Huntington’S Disease ◽  
Fruit Fly ◽  
Gut Bacteria ◽  
Protective Effects ◽  
Human Gut ◽  
E Coli ◽  
Disease Phenotypes ◽  
Opposing Effects ◽  
Transgenic Drosophila

Changes in the composition of gut microbiota are implicated in the pathogenesis of several neurodegenerative disorders. Here, we investigated whether gut bacteria affect the hallmarks of Huntington's disease (HD) in transgenic Drosophila melanogaster (fruit fly) models expressing human full-length or N-terminal fragments of mutant huntingtin (HTT) protein, here referred to as HD flies. We find that elimination of commensal gut bacteria by antibiotics reduces the aggregation of amyloidogenic N-terminal fragments of HTT and delays the development of motor defects. Conversely, colonization of HD flies with Escherichia coli (E. coli), a known pathobiont of human gut, accelerates HTT aggregation, aggravates immobility and shortens life span. Similar to antibiotics, treatment of HD flies with compounds such as luteolin, a flavone, or crocin a beta-carotenoid, ameliorates disease phenotypes and promotes survival. Crocin prevents colonization of E. coli in the HD flies gut and alters the levels of commensal bacteria, which may be linked to its protective effects. The opposing effects of E. coli and crocin on HTT aggregation, motor defects and survival in transgenic Drosophila support the involvement of gut-brain networks in the pathogenesis of HD.

scholarly journals Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold

2016 ◽  
Vol 113 (13) ◽  
pp. E1917-E1926 ◽  
Author(s):  
Morgan Beeby ◽  
Deborah A. Ribardo ◽  
Caitlin A. Brennan ◽  
Edward G. Ruby ◽  
Grant J. Jensen ◽  
...  
Keyword(s):  
Protein Scaffold ◽  
Related Family ◽  
Flagellar Motors ◽  
Torque Generation ◽  
High Torque ◽  
Protein Components ◽  
Subtomogram Averaging ◽  
First Time ◽  
Sequential Assembly

Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, fromCampylobacterandVibriospecies. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes.

scholarly journals In situ reprogramming of gut bacteria by oral delivery

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Bryan B. Hsu ◽  
Isaac N. Plant ◽  
Lorena Lyon ◽  
Frances M. Anastassacos ◽  
Jeffrey C. Way ◽  
...  
Keyword(s):  
Oral Delivery ◽  
Multidisciplinary Approach ◽  
Gut Bacteria ◽  
Release Mechanism ◽  
Bacterial Gene ◽  
E Coli ◽  
Bacterial Gene Expression ◽  
Bacterial Function

Abstract Abundant links between the gut microbiota and human health indicate that modification of bacterial function could be a powerful therapeutic strategy. The inaccessibility of the gut and inter-connections between gut bacteria and the host make it difficult to precisely target bacterial functions without disrupting the microbiota and/or host physiology. Herein we describe a multidisciplinary approach to modulate the expression of a specific bacterial gene within the gut by oral administration. We demonstrate that an engineered temperate phage λ expressing a programmable dCas9 represses a targeted E. coli gene in the mammalian gut. To facilitate phage administration while minimizing disruption to host processes, we develop an aqueous-based encapsulation formulation with a microbiota-based release mechanism and show that it facilitates oral delivery of phage in vivo. Finally we combine these technologies and show that bacterial gene expression in the mammalian gut can be precisely modified in situ with a single oral dose.

scholarly journals In situ reprogramming of gut bacteria by oral delivery

2020 ◽  
Author(s):  
Bryan B. Hsu ◽  
Isaac N. Plant ◽  
Lorena Lyon ◽  
Frances M. Anastassacos ◽  
Jeffrey C. Way ◽  
...  
Keyword(s):  
Oral Delivery ◽  
Multidisciplinary Approach ◽  
Gut Bacteria ◽  
Release Mechanism ◽  
Bacterial Gene ◽  
E Coli ◽  
Bacterial Gene Expression ◽  
Bacterial Function

AbstractAbundant links between the gut microbiota and human health indicate that the modification of bacterial function could be a powerful therapeutic strategy. The inaccessibility of the gut and inter-connections between gut bacteria and the host make it difficult to precisely target bacterial functions without disrupting the microbiota and/or host physiology. Herein we describe a multidisciplinary approach to modulate the expression of a specific bacterial gene within the gut by oral administration. We first demonstrate that an engineered temperate phage λ expressing a programmable dCas9 represses a targeted E. coli gene in the mammalian gut. To facilitate phage administration while minimizing disruption to host processes, we develop an aqueous-based encapsulation formulation with a microbiota-based release mechanism and show that it facilitates the oral delivery of phage in vivo. Finally we combine these technologies and show that bacterial gene expression in the mammalian gut can be precisely modified in situ with a single oral dose.

scholarly journals Effect of Intracellular pH on Rotational Speed of Bacterial Flagellar Motors

2003 ◽  
Vol 185 (4) ◽  
pp. 1190-1194 ◽  
Author(s):  
Tohru Minamino ◽  
Yasuo Imae ◽  
Fumio Oosawa ◽  
Yuji Kobayashi ◽  
Kenji Oosawa
Keyword(s):  
Swimming Speed ◽  
Rotational Speed ◽  
Potassium Acetate ◽  
Flagellar Motor ◽  
Weak Acids ◽  
E Coli ◽  
Rotation Rates ◽  
Ph Values ◽  
Flagellar Motors ◽  
External Ph

ABSTRACT Weak acids such as acetate and benzoate, which partially collapse the transmembrane proton gradient, not only mediate pH taxis but also impair the motility of Escherichia coli and Salmonella at an external pH of 5.5. In this study, we examined in more detail the effect of weak acids on motility at various external pH values. A change of external pH over the range 5.0 to 7.8 hardly affected the swimming speed of E. coli cells in the absence of 34 mM potassium acetate. In contrast, the cells decreased their swimming speed significantly as external pH was shifted from pH 7.0 to 5.0 in the presence of 34 mM acetate. The total proton motive force of E. coli cells was not changed greatly by the presence of acetate. We measured the rotational rate of tethered E. coli cells as a function of external pH. Rotational speed decreased rapidly as the external pH was decreased, and at pH 5.0, the motor stopped completely. When the external pH was returned to 7.0, the motor restarted rotating at almost its original level, indicating that high intracellular proton (H+) concentration does not irreversibly abolish flagellar motor function. Both the swimming speeds and rotation rates of tethered cells of Salmonella also decreased considerably when the external pH was shifted from pH 7.0 to 5.5 in the presence of 20 mM benzoate. We propose that the increase in the intracellular proton concentration interferes with the release of protons from the torque-generating units, resulting in slowing or stopping of the motors.

scholarly journals Roles of Charged Residues of Rotor and Stator in Flagellar Rotation: Comparative Study using H+-Driven and Na+-Driven Motors in Escherichia coli

2006 ◽  
Vol 188 (4) ◽  
pp. 1466-1472 ◽  
Author(s):  
Toshiharu Yakushi ◽  
Junghoon Yang ◽  
Hajime Fukuoka ◽  
Michio Homma ◽  
David F. Blair
Keyword(s):  
Escherichia Coli ◽  
Comparative Study ◽  
Electrostatic Interactions ◽  
General Feature ◽  
Flagellar Motor ◽  
Motor Patterns ◽  
E Coli ◽  
Flagellar Motors ◽  
Charged Residues ◽  
Flagellar Rotation

ABSTRACT In Escherichia coli, rotation of the flagellar motor has been shown to depend upon electrostatic interactions between charged residues of the stator protein MotA and the rotor protein FliG. These charged residues are conserved in the Na+-driven polar flagellum of Vibrio alginolyticus, but mutational studies in V. alginolyticus suggested that they are relatively unimportant for motor rotation. The electrostatic interactions detected in E. coli therefore might not be a general feature of flagellar motors, or, alternatively, the V. alginolyticus motor might rely on similar interactions but incorporate additional features that make it more robust against mutation. Here, we have carried out a comparative study of chimeric motors that were resident in E. coli but engineered to use V. alginolyticus stator components, rotor components, or both. Charged residues in the V. alginolyticus rotor and stator proteins were found to be essential for motor rotation when the proteins functioned in the setting of the E. coli motor. Patterns of synergism and suppression in rotor/stator double mutants indicate that the V. alginolyticus proteins interact in essentially the same way as their counterparts in E. coli. The robustness of the rotor-stator interface in V. alginolyticus is in part due to the presence of additional charged residues in PomA but appears mainly due to other factors, because an E. coli motor using both rotor and stator components from V. alginolyticus remained sensitive to mutation. Motor function in V. alginolyticus may be enhanced by the proteins MotX and MotY.

scholarly journals Roles of Charged Residues in the C-Terminal Region of PomA, a Stator Component of the Na+-Driven Flagellar Motor

2008 ◽  
Vol 190 (10) ◽  
pp. 3565-3571 ◽  
Author(s):  
Madoka Obara ◽  
Toshiharu Yakushi ◽  
Seiji Kojima ◽  
Michio Homma
Keyword(s):  
Electrostatic Interactions ◽  
Intramolecular Interactions ◽  
The Other ◽  
Flagellar Motor ◽  
Wild Type ◽  
Mutant Proteins ◽  
E Coli ◽  
Flagellar Motors ◽  
Charged Residues ◽  
Suppressor Analysis

ABSTRACT Bacterial flagellar motors use specific ion gradients to drive their rotation. It has been suggested that the electrostatic interactions between charged residues of the stator and rotor proteins are important for rotation in Escherichia coli. Mutational studies have indicated that the Na+-driven motor of Vibrio alginolyticus may incorporate interactions similar to those of the E. coli motor, but the other electrostatic interactions between the rotor and stator proteins may occur in the Na+-driven motor. Thus, we investigated the C-terminal charged residues of the stator protein, PomA, in the Na+-driven motor. Three of eight charge-reversing mutations, PomA(K203E), PomA(R215E), and PomA(D220K), did not confer motility either with the motor of V. alginolyticus or with the Na+-driven chimeric motor of E. coli. Overproduction of the R215E and D220K mutant proteins but not overproduction of the K203E mutant protein impaired the motility of wild-type V. alginolyticus. The R207E mutant conferred motility with the motor of V. alginolyticus but not with the chimeric motor of E. coli. The motility with the E211K and R232E mutants was similar to that with wild-type PomA in V. alginolyticus but was greatly reduced in E. coli. Suppressor analysis suggested that R215 may participate in PomA-PomA interactions or PomA intramolecular interactions to form the stator complex.

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