scholarly journals Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Otto Pulkkinen ◽  
Ralf Metzler
Keyword(s):  
Gene Regulation ◽  
Response Times ◽  
Bacterial Gene ◽  
Enzyme Reactions ◽  
Single Enzyme

A kinetic analysis of coupled sequential enzyme reactions

2018 ◽  
Author(s):  
Justin Eilertsen ◽  
Santiago Schnell
Keyword(s):  
Enzyme Assay ◽  
Sequential Reaction ◽  
Enzyme Reactions ◽  
Indicator Reaction ◽  
Single Substrate ◽  
Complex Sequences ◽  
Catalyzed Reactions ◽  
Enzyme Catalyzed Reactions ◽  
Single Enzyme

<div>As a case study, we consider a coupled enzyme assay of sequential enzyme reactions obeying the Michaelis--Menten reaction mechanism. The sequential reaction consists of a single-substrate, single-enzyme non-observable reaction followed by another single-substrate, single-enzyme observable reaction (indicator reaction). In this assay, the product of the non-observable reaction becomes the substrate of the indicator reaction. A mathematical analysis of the reaction kinetics is performed, and it is found that after an initial fast transient, the sequential reaction is described by a pair of interacting Michaelis--Menten equations. Timescales that approximate the respective lengths of the indicator and non-observable reactions, as well as conditions for the validity of the Michaelis--Menten equations are derived. The theory can be extended to deal with more complex sequences of enzyme catalyzed reactions.</div>

A kinetic analysis of coupled sequential enzyme reactions

2018 ◽  
Author(s):  
Justin Eilertsen ◽  
Santiago Schnell
Keyword(s):  
Enzyme Assay ◽  
Sequential Reaction ◽  
Enzyme Reactions ◽  
Indicator Reaction ◽  
Single Substrate ◽  
Complex Sequences ◽  
Catalyzed Reactions ◽  
Enzyme Catalyzed Reactions ◽  
Single Enzyme

<div>As a case study, we consider a coupled enzyme assay of sequential enzyme reactions obeying the Michaelis-Menten reaction mechanism. The sequential reaction consists of a single-substrate, single enzyme non-observable reaction followed by another single-substrate, single enzyme observable reaction (indicator reaction). In this assay, the product of the non-observable reaction becomes the substrate of the indicator reaction. A mathematical analysis of the reaction kinetics is performed, and it is found that after an initial fast transient, the sequential reaction is described by a pair of interacting Michaelis-Menten equations. Timescales that approximate the respective lengths of the indicator and non-observable reactions, as well as conditions for the validity of the Michaelis-Menten equations are derived. The theory can be extended to deal with more complex sequences of enzyme catalyzed reactions.</div>

scholarly journals In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions

2019 ◽  
Author(s):  
Tatsuya Nobori ◽  
Yiming Wang ◽  
Jingni Wu ◽  
Sara Christina Stolze ◽  
Yayoi Tsuda ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Pseudomonas Syringae ◽  
Protein Level ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Bacterial Pathogen ◽  
Bacterial Virulence ◽  
In Planta ◽  
Bacterial Gene ◽  
Global Food Security

AbstractUnderstanding how gene expression is regulated in plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a foliar bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana and identified a number of bacterial processes influenced by plant immunity at the mRNA and the protein level. We found instances of both concordant and discordant regulation of bacterial mRNAs and proteins. Notably, the tip component of bacterial type III secretion system was selectively suppressed by the plant salicylic acid pathway at the protein level, suggesting protein-level targeting of the bacterial virulence system by plant immunity. Furthermore, gene co-expression analysis illuminated previously unknown gene regulatory modules underlying bacterial virulence and their regulatory hierarchy. Collectively, the integrated in planta bacterial omics approach provides molecular insights into multiple layers of bacterial gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in controlling pathogens.

Biophysical Approaches to Bacterial Gene Regulation by Riboswitches

2016 ◽  
pp. 157-191 ◽  
Author(s):  
Cibran Perez-Gonzalez ◽  
Jonathan P. Grondin ◽  
Daniel A. Lafontaine ◽  
J. Carlos Penedo
Keyword(s):  
Gene Regulation ◽  
Bacterial Gene

Lies and deception in bacterial gene regulation: the roles of nucleic acid decoys

2014 ◽  
Vol 92 (4) ◽  
pp. 641-647 ◽  
Author(s):  
Yvonne Göpel ◽  
Boris Görke
Keyword(s):  
Gene Regulation ◽  
Nucleic Acid ◽  
Bacterial Gene

scholarly journals Who turned on the lights?: What the regulation of bacterial bioluminescence tells us about this and other bacterial group behaviours

2013 ◽  
Vol 35 (5) ◽  
pp. 18-23 ◽  
Author(s):  
Eric V. Stabb ◽  
Zomary Flores-Cruz
Keyword(s):  
Gene Regulation ◽  
Group Activity ◽  
Bacterial Group ◽  
Bacterial Gene ◽  
Bioluminescent Bacteria ◽  
Regulatory Decision ◽  
Bacterial Bioluminescence ◽  
Regulatory Circuits ◽  
Pheromone Signalling

Luminescence produced by organisms, or ‘bioluminescence’, holds a distinct fascination for humankind, and the study of bacterial bioluminescence has a long history in the field of microbiology. Advances in our understanding of bacterial bioluminescence have in many ways paralleled advances in the field as a whole. Intriguingly, studies of bioluminescent bacteria led to a seminal discovery in bacterial gene regulation and behaviour, because for bacteria, bioluminescence is a group activity. Bioluminescent bacteria communicate using pheromones, and as a result the regulatory decision to induce bioluminescence is only made if a group of bacteria has achieved a dense enough population to allow the build-up of pheromone. More recently, it has become clear that there are complex regulatory circuits governing not only luminescence, but also pheromone signalling itself. These additional layers of regulation pose new questions such as what are bacteria really saying to each other? Understanding regulation may also help answer ancient questions including, what use is luminescence?

Kinetics of Single-Enzyme Reactions on Vesicles: Role of Substrate Aggregation

2015 ◽  
Vol 10 (02) ◽  
pp. 69-83 ◽  
Author(s):  
Vladimir P. Zhdanov
Keyword(s):  
Lipid Membranes ◽  
Lipid Vesicles ◽  
Enzymatic Reactions ◽  
Enzyme Dynamics ◽  
Special Issue ◽  
Enzyme Reactions ◽  
And Function ◽  
Single Enzyme

Enzymatic reactions occurring in vivo on lipid membranes can be influenced by various factors including macromolecular crowding in general and substrate aggregation in particular. In academic studies, the role of these factors can experimentally be clarified by tracking single-enzyme kinetics occurring on individual lipid vesicles. To extend the conceptual basis for such experiments, we analyze herein the corresponding kinetics mathematically with emphasis on the role of substrate aggregation. In general, the aggregation may occur on different length scales. Small aggregates may e.g. contain a few proteins or peptides while large aggregates may be mesoscopic as in the case of lipid domains which can be formed in the membranes composed of different lipids. We present a kinetic model describing comprehensively the effect of aggregation of the former type on the dependence of the reaction rate on substrate membrane concentration. The results obtained with physically reasonable parameters indicate that the aggregation-related deviations from the conventional Michaelis–Menten kinetics may be appreciable. [Formula: see text]Special Issue Comments: This theoretical article is focused on single-enzyme reactions occurring in parallel with substrate aggregation on individual vesicles. This subject is related to a few Special Issue articles concerning enzyme dynamics6,7 and function8 and mathematical aspects of stochastic kinetics.9

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