scholarly journals Diversity in Chemotaxis Mechanisms among the Bacteria and Archaea

2004 ◽  
Vol 68 (2) ◽  
pp. 301-319 ◽  
Author(s):  
Hendrik Szurmant ◽  
George W. Ordal
Keyword(s):  
Response Regulator ◽  
Bacterial Chemotaxis ◽  
Two Component System ◽  
E Coli ◽  
Cellular Processes ◽  
Intracellular Signal ◽  
The One ◽  
Chemotaxis System ◽  
Hydrolysis Of ◽  
Insight Into

SUMMARY The study of chemotaxis describes the cellular processes that control the movement of organisms toward favorable environments. In bacteria and archaea, motility is controlled by a two-component system involving a histidine kinase that senses the environment and a response regulator, a very common type of signal transduction in prokaryotes. Most insights into the processes involved have come from studies of Escherichia coli over the last three decades. However, in the last 10 years, with the sequencing of many prokaryotic genomes, it has become clear that E. coli represents a streamlined example of bacterial chemotaxis. While general features of excitation remain conserved among bacteria and archaea, specific features, such as adaptational processes and hydrolysis of the intracellular signal CheY-P, are quite diverse. The Bacillus subtilis chemotaxis system is considerably more complex and appears to be similar to the one that existed when the bacteria and archaea separated during evolution, so that understanding this mechanism should provide insight into the variety of mechanisms used today by the broad sweep of chemotactic bacteria and archaea. However, processes even beyond those used in E. coli and B. subtilis have been discovered in other organisms. This review emphasizes those used by B. subtilis and these other organisms but also gives an account of the mechanism in E. coli.

scholarly journals Cellular Stoichiometry of Chemotaxis Proteins in Sinorhizobium meliloti

2020 ◽  
Vol 202 (14) ◽  
Author(s):  
Timofey D. Arapov ◽  
Rafael Castañeda Saldaña ◽  
Amanda L. Sebastian ◽  
W. Keith Ray ◽  
Richard F. Helm ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Sinorhizobium Meliloti ◽  
Response Regulator ◽  
Bacterial Chemotaxis ◽  
Adaptor Proteins ◽  
Molar Ratio ◽  
Content Type ◽  
Chemotaxis Proteins ◽  
Chemotaxis System

ABSTRACT Chemotaxis systems enable microbes to sense their immediate environment, moving toward beneficial stimuli and away from those that are harmful. In an effort to better understand the chemotaxis system of Sinorhizobium meliloti, a symbiont of the legume alfalfa, the cellular stoichiometries of all ten chemotaxis proteins in S. meliloti were determined. A combination of quantitative immunoblot and mass spectrometry revealed that the protein stoichiometries in S. meliloti varied greatly from those in Escherichia coli and Bacillus subtilis. To compare protein ratios to other systems, values were normalized to the central kinase CheA. All S. meliloti chemotaxis proteins exhibited increased ratios to various degrees. The 10-fold higher molar ratio of adaptor proteins CheW1 and CheW2 to CheA might result in the formation of rings in the chemotaxis array that consist of only CheW instead of CheA and CheW in a 1:1 ratio. We hypothesize that the higher ratio of CheA to the main response regulator CheY2 is a consequence of the speed-variable motor in S. meliloti, instead of a switch-type motor. Similarly, proteins involved in signal termination are far more abundant in S. meliloti, which utilizes a phosphate sink mechanism based on CheA retrophosphorylation to inactivate the motor response regulator versus CheZ-catalyzed dephosphorylation as in E. coli and B. subtilis. Finally, the abundance of CheB and CheR, which regulate chemoreceptor methylation, was increased compared to CheA, indicative of variations in the adaptation system of S. meliloti. Collectively, these results mark significant differences in the composition of bacterial chemotaxis systems. IMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti contributes greatly to host-plant growth by fixing atmospheric nitrogen. The provision of nitrogen as ammonium by S. meliloti leads to increased biomass production of its legume host alfalfa and diminishes the use of environmentally harmful chemical fertilizers. To better understand the role of chemotaxis in host-microbe interaction, a comprehensive catalogue of the bacterial chemotaxis system is vital, including its composition, function, and regulation. The stoichiometry of chemotaxis proteins in S. meliloti has very few similarities to the systems in Escherichia coli and Bacillus subtilis. In addition, total amounts of proteins are significantly lower. S. meliloti exhibits a chemotaxis system distinct from known models by incorporating new proteins as exemplified by the phosphate sink mechanism.

scholarly journals Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH

2020 ◽  
Vol 48 (7) ◽  
pp. 3776-3788 ◽  
Author(s):  
Ang Gao ◽  
Nikita Vasilyev ◽  
Abhishek Kaushik ◽  
Wenqian Duan ◽  
Alexander Serganov
Keyword(s):  
Rna Processing ◽  
Reaction Rates ◽  
Growth Conditions ◽  
Rna Degradation ◽  
Nudix Hydrolase ◽  
X Ray ◽  
E Coli ◽  
Cellular Processes ◽  
Protein Factor ◽  
Hydrolysis Of

Abstract All enzymes face a challenge of discriminating cognate substrates from similar cellular compounds. Finding a correct substrate is especially difficult for the Escherichia coli Nudix hydrolase RppH, which triggers 5′-end-dependent RNA degradation by removing orthophosphate from the 5′-diphosphorylated transcripts. Here we show that RppH binds and slowly hydrolyzes NTPs, NDPs and (p)ppGpp, which each resemble the 5′-end of RNA. A series of X-ray crystal structures of RppH-nucleotide complexes, trapped in conformations either compatible or incompatible with hydrolysis, explain the low reaction rates of mononucleotides and suggest two distinct mechanisms for their hydrolysis. While RppH adopts the same catalytic arrangement with 5′-diphosphorylated nucleotides as with RNA, the enzyme hydrolyzes 5′-triphosphorylated nucleotides by extending the active site with an additional Mg2+ cation, which coordinates another reactive nucleophile. Although the average intracellular pH minimizes the hydrolysis of nucleotides by slowing their reaction with RppH, they nevertheless compete with RNA for binding and differentially inhibit the reactivity of RppH with triphosphorylated and diphosphorylated RNAs. Thus, E. coli RppH integrates various signals, such as competing non-cognate substrates and a stimulatory protein factor DapF, to achieve the differential degradation of transcripts involved in cellular processes important for the adaptation of bacteria to different growth conditions.

scholarly journals Swimming Escherichia coli explore the environment by Lévy walk

2021 ◽  
Author(s):  
Haiyan Huo ◽  
Rui He ◽  
Rongjing Zhang ◽  
Junhua Yuan
Keyword(s):  
Random Walk ◽  
Response Regulator ◽  
Bacterial Chemotaxis ◽  
Random Fluctuation ◽  
Aqueous Environment ◽  
E Coli ◽  
Lévy Walk ◽  
Diffusion Characteristics ◽  
Levy Walk ◽  
Run Lengths

E. coli cells swim in aqueous environment in a random walk of alternating runs and tumbles. The diffusion characteristics of this random walk remains unclear. Here, by tracking the swimming of wildtype cells in a 3d homogeneous environment, we found that their trajectories are super diffusive, consistent with Lévy walk behavior. For comparison, we tracked the swimming of mutant cells that lack the chemotaxis signaling noise (the steady-state fluctuation of the concentration of the chemotaxis response regulator CheY-P), and found that their trajectories are normal diffusive. Therefore, wildtype E. coli cells explore the environment by Lévy walk, which originates from the chemotaxis signaling noise. This Lévy walk pattern enhances their efficiency in environmental exploration. Importance E. coli cells explore the environment in a random walk of alternating runs and tumbles. By tracking the 3d trajectories of E. coli cells in aqueous environment, we find that their trajectories are super diffusive, with a power-law shape for the distribution of run lengths, which is characteristics of Lévy walk. We further show that this Lévy walk behavior is due to the random fluctuation of the output level of the bacterial chemotaxis pathway, and it enhances the efficiency of the bacteria in exploring the environment.

The Complex Rcs Regulatory Cascade

2018 ◽  
Vol 72 (1) ◽  
pp. 111-139 ◽  
Author(s):  
Erin Wall ◽  
Nadim Majdalani ◽  
Susan Gottesman
Keyword(s):  
Response Regulator ◽  
Two Component System ◽  
Regulatory Cascade ◽  
Outer Membrane Lipoprotein ◽  
Two Component ◽  
Membrane Lipoprotein ◽  
Inner Membrane Protein ◽  
Insight Into ◽  
System Paradigm

RcsB, a response regulator of the FixJ/NarL family, is at the center of a complex network of regulatory inputs and outputs. Cell surface stress is sensed by an outer membrane lipoprotein, RcsF, which regulates interactions of the inner membrane protein IgaA, lifting negative regulation of a phosphorelay. In vivo evidence supports a pathway in which histidine kinase RcsC transfers phosphate to phosphotransfer protein RcsD, resulting in phosphorylation of RcsB. RcsB acts either alone or in combination with RcsA to positively regulate capsule synthesis and synthesis of small RNA (sRNA) RprA as well as other genes, and to negatively regulate motility. RcsB in combination with other FixJ/NarL auxiliary proteins regulates yet other functions, independent of RcsB phosphorylation. Proper expression of Rcs and its targets is critical for success of Escherichia coli commensal strains, for proper development of biofilm, and for virulence in some pathogens. New understanding of how the Rcs phosphorelay works provides insight into the flexibility of the two-component system paradigm.

scholarly journals Conserved Network of Proteins Essential for Bacterial Viability

2009 ◽  
Vol 191 (15) ◽  
pp. 4732-4749 ◽  
Author(s):  
Jennifer I. Handford ◽  
Bérengère Ize ◽  
Grant Buchanan ◽  
Gareth P. Butland ◽  
Jack Greenblatt ◽  
...  
Keyword(s):  
Response Regulator ◽  
Model Organism ◽  
Growth Conditions ◽  
Cell Ultrastructure ◽  
System Response ◽  
Two Component System ◽  
E Coli ◽  
Conditional Expression ◽  
Two Hybrid

ABSTRACT The yjeE, yeaZ, and ygjD genes are highly conserved in the genomes of eubacteria, and ygjD orthologs are also found throughout the Archaea and eukaryotes. In this study, we have constructed conditional expression strains for each of these genes in the model organism Escherichia coli K12. We show that each gene is essential for the viability of E. coli under laboratory growth conditions. Growth of the conditional strains under nonpermissive conditions results in dramatic changes in cell ultrastructure. Deliberate repression of the expression of yeaZ results in cells with highly condensed nucleoids, while repression of yjeE and ygjD expression results in at least a proportion of very enlarged cells with an unusual peripheral distribution of DNA. Each of the three conditional expression strains can be complemented by multicopy clones harboring the rstA gene, which encodes a two-component-system response regulator, strongly suggesting that these proteins are involved in the same essential cellular pathway. The results of bacterial two-hybrid experiments show that YeaZ can interact with both YjeE and YgjD but that YgjD is the preferred interaction partner. The results of in vitro experiments indicate that YeaZ mediates the proteolysis of YgjD, suggesting that YeaZ and YjeE act as regulators to control the activity of this protein. Our results are consistent with these proteins forming a link between DNA metabolism and cell division.

scholarly journals A transcriptome study of the QseEF two-component system and the QseG membrane protein in enterohaemorrhagic Escherichia coli O157 : H7

Microbiology ◽  
2010 ◽  
Vol 156 (4) ◽  
pp. 1167-1175 ◽  
Author(s):  
Nicola C. Reading ◽  
David Rasko ◽  
Alfredo G. Torres ◽  
Vanessa Sperandio
Keyword(s):  
Escherichia Coli ◽  
Membrane Protein ◽  
Response Regulator ◽  
Two Component System ◽  
E Coli ◽  
Enterohaemorrhagic Escherichia Coli ◽  
Component Systems ◽  
Two Component ◽  
Two Component Systems ◽  
Type Iii Secretion Effector

QseE is a sensor kinase that responds to epinephrine, sulfate and phosphate. QseE constitutes a two-component signalling system together with the QseF σ 54-dependent response regulator. Encoded within the same operon as qseEF is the qseG gene, which encodes a membrane protein involved in the translocation of a type III secretion effector protein of enterohaemorrhagic Escherichia coli (EHEC) into epithelial cells. The qseEGF genes also form an operon with the glnB gene, which encodes the E. coli nitrogen sensor PII protein. Here we report a transcriptome analysis comparing qseE, qseF andqseG single mutants with the wild-type strain. This study revealed that the proteins encoded by these genes play a modest but significant role in iron uptake. Although QseEFG regulate genes involved in nitrogen utilization, these proteins do not play a notable role in nitrogen metabolism. In addition, QseEFG regulate transcription of the rcsBC and phoPQ two-component systems, linking several signal transduction pathways. The similarity of the microarray profiles of these mutants also indicates that these proteins work together. These data indicate that QseEFG are involved in the regulation of virulence and metabolism in EHEC.

scholarly journals The Escherichia coli BarA-UvrY Two-Component System Is Needed for Efficient Switching between Glycolytic and Gluconeogenic Carbon Sources

2003 ◽  
Vol 185 (3) ◽  
pp. 843-853 ◽  
Author(s):  
Anna-Karin Pernestig ◽  
Dimitris Georgellis ◽  
Tony Romeo ◽  
Kazushi Suzuki ◽  
Henrik Tomenius ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Response Regulator ◽  
Carbon Sources ◽  
Regulation System ◽  
Wild Type ◽  
Two Component System ◽  
Kinase Gene ◽  
Component System ◽  
E Coli ◽  
Two Component

ABSTRACT The Escherichia coli BarA and UvrY proteins were recently demonstrated to constitute a novel two-component system, although its function has remained largely elusive. Here we show that mutations in the sensor kinase gene, barA, or the response regulator gene, uvrY, in uropathogenic E. coli drastically affect survival in long-term competition cultures. Using media with gluconeogenic carbon sources, the mutants have a clear growth advantage when competing with the wild type, but using media with carbon sources feeding into the glycolysis leads to a clear growth advantage for the wild type. Results from competitions with mutants in the carbon storage regulation system, CsrA/B, known to be a master switch between glycolysis and gluconeogenesis, led us to propose that the BarA-UvrY two-component system controls the Csr system. Taking these results together, we propose the BarA-UvrY two-component system is crucial for efficient adaptation between different metabolic pathways, an essential function for adaptation to a new environment.

scholarly journals The KdpD Sensor Kinase of Escherichia coli Responds to Several Distinct Signals To Turn on Expression of the Kdp Transport System

2015 ◽  
Vol 198 (2) ◽  
pp. 212-220 ◽  
Author(s):  
Wolfgang Epstein
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Transport System ◽  
Kinase Activity ◽  
Response Regulator ◽  
Sensor Kinase ◽  
Monovalent Cations ◽  
Two Component System ◽  
Content Type ◽  
E Coli

ABSTRACTKdp, one of three saturable K+uptake systems inEscherichia coli, is the system with the highest affinity for K+and the only one whose expression is strongly controlled by medium K+concentration. Expression is controlled by a two-component system of KdpD, the sensor kinase, and KdpE, the response regulator. There is general agreement that expression occurs when the growth rate of cells begins to become limited by K+availability. How K+limitation results in expression has been controversial. Studying the roles of the major components of the growth medium shows that KdpD senses at least two distinct signals inside the cell, those of Na+and NH4+, and it probably senses other monovalent cations in the cell. KdpD does not sense turgor.IMPORTANCEThe expression of the Kdp K+transport system ofE. colioccurs when cells become limited in their growth rate by the availability of K+. Cells sense limited K+and try to compensate by taking up other monovalent cations, particularly Na+and NH4+. These cations are sensed in the cytoplasm by the KdpD response regulator, presumably to stimulate its kinase activity. It is shown that KdpD does not sense turgor, as was suggested earlier.

scholarly journals Adaptability of non-genetic diversity in bacterial chemotaxis

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Nicholas W Frankel ◽  
William Pontius ◽  
Yann S Dufour ◽  
Junjiajia Long ◽  
Luis Hernandez-Nunez ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Environmental Variability ◽  
Bacterial Chemotaxis ◽  
Chemotaxis Model ◽  
Clonal Population ◽  
Multiple Systems ◽  
E Coli ◽  
Protein Levels ◽  
Trade Offs ◽  
Chemotaxis System

Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an alternative, or even evolutionary stepping-stone, to switching between multiple systems. We hypothesized that mutations in gene regulation could lead to heritable control of chemotactic diversity. By simulating foraging and colonization of E. coli using a single-cell chemotaxis model, we found that different environments selected for different behaviors. The resulting trade-offs show that populations facing diverse environments would ideally diversify behaviors when time for navigation is limited. We show that advantageous diversity can arise from changes in the distribution of protein levels among individuals, which could occur through mutations in gene regulation. We propose experiments to test our prediction that chemotactic diversity in a clonal population could be a selectable trait that enables adaptation to environmental variability.

The Effects of Amines on the Esterase Activities of Thrombin and Thrombokinase and on Several Clotting Tests

1974 ◽  
Vol 31 (02) ◽  
pp. 309-318
Author(s):  
Phyllis S Roberts ◽  
Raphael M Ottenbrite ◽  
Patricia B Fleming ◽  
James Wigand
Keyword(s):  
Choline Chloride ◽  
Polymerization Process ◽  
Ammonium Bromide ◽  
Bovine Thrombin ◽  
One Stage ◽  
Human Proteins ◽  
Rate Of Hydrolysis ◽  
The One ◽  
Hydrolysis Of Esters ◽  
Hydrolysis Of

Summary1. Choline chloride, 0.1 M (in 0.25 M Tris. HCl buffer, pH 7.4 or 8.0, 37°), doubles the rate of hydrolysis of TAME by bovine thrombokinase but has no effect on the hydrolysis of this ester by either human or bovine thrombin. Only when 1.0 M or more choline chloride is present is the hydrolysis of BAME by thrombokinase or thrombin weakly inhibited. Evidence is presented that shows that these effects are due to the quaternary amine group.2. Tetramethyl ammonium bromide or chloride has about the same effects on the hydrolysis of esters by these enzymes as does choline chloride but tetra-ethyl, -n.propyl and -n.butyl ammonium bromides (0.1 M) are stronger accelerators of the thrombokinase-TAME reaction and they also accelerate, but to a lesser degree, the thrombin-TAME reaction. In addition, they inhibit the hydrolysis of BAME by both enzymes. Their effects on these reactions, however, do not follow any regular order. The tetraethyl compound is the strongest accelerator of the thrombokinase-TAME reaction but the tetra-ethyl and -butyl compounds are the strongest accelerators of the thrombin-TAME reaction. The ethyl and propyl compounds are the best (although weak) inhibitors of the thrombokinase-BAME and the propyl compound of the thrombin-BAME reactions.3. Tetra-methyl, -ethyl, -n.propyl and -n.butyl ammonium bromides (0.01 M) inhibit the clotting of fibrinogen by thrombin (bovine and human proteins) at pH 7.4, imidazole or pH 6.1, phosphate buffers and they also inhibit, but to a lesser degree, a modified one-stage prothrombin test. In all cases the inhibition increases regularly as the size of the alkyl group increases from methyl to butyl. Only the ethyl com pound (0.025 M but not 0.01 M), however, significantly inhibits the polymerization of bovine fibrin monomers. It was concluded that inhibition of the fibrinogen-thrombin and the one-stage tests by the quaternary amines is not due to any effect of the com pounds on the polymerization process but probably due to inhibition of thrombin’s action on fibrinogen by the quaternary amines.

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