Design of orthogonal regulatory systems for modulating gene expression in plants

2020 ◽  
Vol 16 (8) ◽  
pp. 857-865 ◽  
Author(s):  
Michael S. Belcher ◽  
Khanh M. Vuu ◽  
Andy Zhou ◽  
Nasim Mansoori ◽  
Amanda Agosto Ramos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Systems

scholarly journals Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage λ-Infected Escherichia coli Cells

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 1633-1648 ◽  
Author(s):  
Adam Arkin ◽  
John Ross ◽  
Harley H McAdams
Keyword(s):  
Gene Expression ◽  
Kinetic Model ◽  
Kinetic Analysis ◽  
Molecular Level ◽  
Host Responses ◽  
Statistical Thermodynamic ◽  
Regulatory Systems ◽  
Regulatory Circuit ◽  
Phenotype Selection ◽  
Decision Circuit

Abstract Fluctuations in rates of gene expression can produce highly erratic time patterns of protein production in individual cells and wide diversity in instantaneous protein concentrations across cell populations. When two independently produced regulatory proteins acting at low cellular concentrations competitively control a switch point in a pathway, stochastic variations in their concentrations can produce probabilistic pathway selection, so that an initially homogeneous cell population partitions into distinct phenotypic subpopulations. Many pathogenic organisms, for example, use this mechanism to randomly switch surface features to evade host responses. This coupling between molecular-level fluctuations and macroscopic phenotype selection is analyzed using the phage λ lysis-lysogeny decision circuit as a model system. The fraction of infected cells selecting the lysogenic pathway at different phage:cell ratios, predicted using a molecular-level stochastic kinetic model of the genetic regulatory circuit, is consistent with experimental observations. The kinetic model of the decision circuit uses the stochastic formulation of chemical kinetics, stochastic mechanisms of gene expression, and a statistical-thermodynamic model of promoter regulation. Conventional deterministic kinetics cannot be used to predict statistics of regulatory systems that produce probabilistic outcomes. Rather, a stochastic kinetic analysis must be used to predict statistics of regulatory outcomes for such stochastically regulated systems.

scholarly journals Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1176
Author(s):  
Ivan Tsers ◽  
Vladimir Gorshkov ◽  
Natalia Gogoleva ◽  
Olga Parfirova ◽  
Olga Petrova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Cell Wall ◽  
Soft Rot ◽  
Regulatory Elements ◽  
Plant Responses ◽  
Gene Promoters ◽  
Rna Seq ◽  
Induced Plant Responses ◽  
Regulatory Systems ◽  
Genome Level

Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological events in Pba-infected plants and to reveal novel potential molecular “players” in plant–Pba interactions, an original functional gene classification was performed. The classifications present in various databases were merged, enriched by “missed” genes, and divided into subcategories. Particular changes in plant cell wall-related processes, perturbations in hormonal and other regulatory systems, and alterations in primary, secondary, and redox metabolism were elucidated in terms of gene expression. Special attention was paid to the prediction of transcription factors (TFs) involved in the disease’s development. Herewith, gene expression was analyzed within the predicted TF regulons assembled at the whole-genome level based on the presence of particular cis-regulatory elements (CREs) in gene promoters. Several TFs, whose regulons were enriched by differentially expressed genes, were considered to be potential master regulators of Pba-induced plant responses. Differential regulation of genes belonging to a particular multigene family and encoding cognate proteins was explained by the presence/absence of the particular CRE in gene promoters.

scholarly journals Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut

Cell ◽  
2017 ◽  
Vol 169 (3) ◽  
pp. 547-558.e15 ◽  
Author(s):  
Bentley Lim ◽  
Michael Zimmermann ◽  
Natasha A. Barry ◽  
Andrew L. Goodman
Keyword(s):  
Gene Expression ◽  
Regulatory Systems

scholarly journals Biodegradation of Tetralin: Genomics, Gene Function and Regulation

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 339 ◽  
Author(s):  
Belén Floriano ◽  
Eduardo Santero ◽  
Francisca Reyes-Ramírez
Keyword(s):  
Gene Expression ◽  
Current Knowledge ◽  
Gene Clusters ◽  
Sole Source ◽  
Regulatory Elements ◽  
Catabolic Pathway ◽  
Regulatory Systems ◽  
Biochemical Genetic ◽  
Complex Regulation ◽  
Rhodococcus Sp

Tetralin (1,2,3,4-tetrahydonaphthalene) is a recalcitrant compound that consists of an aromatic and an alicyclic ring. It is found in crude oils, produced industrially from naphthalene or anthracene, and widely used as an organic solvent. Its toxicity is due to the alteration of biological membranes by its hydrophobic character and to the formation of toxic hydroperoxides. Two unrelated bacteria, Sphingopyxis granuli strain TFA and Rhodococcus sp. strain TFB were isolated from the same niche as able to grow on tetralin as the sole source of carbon and energy. In this review, we provide an overview of current knowledge on tetralin catabolism at biochemical, genetic and regulatory levels in both strains. Although they share the same biodegradation strategy and enzymatic activities, no evidences of horizontal gene transfer between both bacteria have been found. Moreover, the regulatory elements that control the expression of the gene clusters are completely different in each strain. A special consideration is given to the complex regulation discovered in TFA since three regulatory systems, one of them involving an unprecedented communication between the catabolic pathway and the regulatory elements, act together at transcriptional and posttranscriptional levels to optimize tetralin biodegradation gene expression to the environmental conditions.

scholarly journals Characterization of NorR Protein, a Multifunctional Regulator of norA Expression in Staphylococcus aureus

2003 ◽  
Vol 185 (10) ◽  
pp. 3127-3138 ◽  
Author(s):  
Que Chi Truong-Bolduc ◽  
Xiamei Zhang ◽  
David C. Hooper
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Efflux Pump ◽  
Protein A ◽  
Protein Overexpression ◽  
Wild Type ◽  
Liquid Media ◽  
Cell Surface Properties ◽  
Regulatory Systems

ABSTRACT We characterized a Staphylococcus aureus norA gene expression regulator, NorR, initially identified from its binding to the norA promoter. The norR gene was 444 bp in length, located ∼7 kb upstream from the norA gene, and encoded a predicted 17.6-kDa protein. Overexpression of norR in wild-type S. aureus strain ISP794 led to a fourfold decrease in sensitivity to quinolones and ethidium bromide and an increase in the level of norA transcripts, suggesting that NorR acts as a positive regulator of norA expression. Overexpression of norR in sarA and agr mutants did not alter quinolone sensitivity or levels of norA transcription, indicating that the presence of these two global regulatory systems is necessary for NorR to affect the expression of norA. Insertion and disruption of norR in ISP794 increased resistance to quinolones by 4- to 16-fold but had no effect on norA transcription, suggesting that NorR acts as a repressor for another unidentified efflux pump or pumps. These mutants also exhibited an exaggerated clumping phenotype in liquid media, which was complemented fully by a plasmid-encoded norR gene. Collectively, these results indicate that NorR is a multifunctional regulator, affecting cell surface properties as well as the expression of NorA and likely other multidrug resistance efflux pumps.

scholarly journals Cyclic di-GMP-Mediated Regulation of Gene Transfer and Motility in Rhodobacter capsulatus

2019 ◽  
Vol 202 (2) ◽  
Author(s):  
Purvikalyan Pallegar ◽  
Lourdes Peña-Castillo ◽  
Evan Langille ◽  
Mark Gomelsky ◽  
Andrew S. Lang
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Rhodobacter Capsulatus ◽  
Heterologous Gene Expression ◽  
Second Messenger ◽  
Site Directed Mutagenesis ◽  
Flagellar Motility ◽  
Content Type ◽  
Regulatory Systems ◽  
Transfer Agents

ABSTRACT Gene transfer agents (GTAs) are bacteriophage-like particles produced by several bacterial and archaeal lineages that contain small pieces of the producing cells’ genomes that can be transferred to other cells in a process similar to transduction. One well-studied GTA is RcGTA, produced by the alphaproteobacterium Rhodobacter capsulatus. RcGTA gene expression is regulated by several cellular regulatory systems, including the CckA-ChpT-CtrA phosphorelay. The transcription of multiple other regulator-encoding genes is affected by the response regulator CtrA, including genes encoding putative enzymes involved in the synthesis and hydrolysis of the second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP). To investigate whether c-di-GMP signaling plays a role in RcGTA production, we disrupted the CtrA-affected genes potentially involved in this process. We found that disruption of four of these genes affected RcGTA gene expression and production. We performed site-directed mutagenesis of key catalytic residues in the GGDEF and EAL domains responsible for diguanylate cyclase (DGC) and c-di-GMP phosphodiesterase (PDE) activities and analyzed the functions of the wild-type and mutant proteins. We also measured RcGTA production in R. capsulatus strains where intracellular levels of c-di-GMP were altered by the expression of either a heterologous DGC or a heterologous PDE. This adds c-di-GMP signaling to the collection of cellular regulatory systems controlling gene transfer in this bacterium. Furthermore, the heterologous gene expression and the four gene disruptions had similar effects on R. capsulatus flagellar motility as found for gene transfer, and we conclude that c-di-GMP inhibits both RcGTA production and flagellar motility in R. capsulatus. IMPORTANCE Gene transfer agents (GTAs) are virus-like particles that move cellular DNA between cells. In the alphaproteobacterium Rhodobacter capsulatus, GTA production is affected by the activities of multiple cellular regulatory systems, to which we have now added signaling via the second messenger dinucleotide molecule bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP). Similar to the CtrA phosphorelay, c-di-GMP also affects R. capsulatus flagellar motility in addition to GTA production, with lower levels of intracellular c-di-GMP favoring increased flagellar motility and gene transfer. These findings further illustrate the interconnection of GTA production with global systems of regulation in R. capsulatus, providing additional support for the notion that the production of GTAs has been maintained in this and related bacteria because it provides a benefit to the producing organisms.

scholarly journals Developmental Control of Stress Stimulons inStreptomyces coelicolor Revealed by Statistical Analyses of Global Gene Expression Patterns

2000 ◽  
Vol 182 (17) ◽  
pp. 4979-4986 ◽  
Author(s):  
J. Vohradsky ◽  
X.-M. Li ◽  
G. Dale ◽  
M. Folcher ◽  
L. Nguyen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Physiological Stress ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Statistical Analyses ◽  
Developmental Control ◽  
Salt Shock ◽  
Developmental Program ◽  
Regulatory Systems

ABSTRACT Stress-induced regulatory networks coordinated with a procaryotic developmental program were revealed by two-dimensional gel analyses of global gene expression. Four developmental stages were identified by their distinctive protein synthesis patterns using principal component analysis. Statistical analyses focused on five stress stimulons (induced by heat, cold, salt, ethanol, or antibiotic shock) and their synthesis during development. Unlike other bacteria, for which various stresses induce expression of similar sets of protein spots, inStreptomyces coelicolor heat, salt, and ethanol stimulons were composed of independent sets of proteins. This suggested independent control by different physiological stress signals and their corresponding regulatory systems. These stress proteins were also under developmental control. Cluster analysis of stress protein synthesis profiles identified 10 different developmental patterns or “synexpression groups.” Proteins induced by cold, heat, or salt shock were enriched in three developmental synexpression groups. In addition, certain proteins belonging to the heat and salt shock stimulons were coregulated during development. Thus, stress regulatory systems controlling these stimulons were implicated as integral parts of the developmental program. This correlation suggested that thermal shock and salt shock stress response regulatory systems either allow the cell to adapt to stresses associated with development or directly control the developmental program.

scholarly journals Quorum sensing, virulence and secondary metabolite production in plant soft-rotting bacteria

2007 ◽  
Vol 362 (1483) ◽  
pp. 1165-1183 ◽  
Author(s):  
Anne M.L Barnard ◽  
Steven D Bowden ◽  
Tom Burr ◽  
Sarah J Coulthurst ◽  
Rita E Monson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quorum Sensing ◽  
Plant Cell Wall ◽  
Antibiotic Production ◽  
Dependent Manner ◽  
Virulence Determinants ◽  
Cell Wall Degrading Enzymes ◽  
Acylhomoserine Lactone ◽  
Autoinducer 2 ◽  
Regulatory Systems

Quorum sensing describes the ability of bacteria to sense their population density and respond by modulating gene expression. In the plant soft-rotting bacteria, such as Erwinia , an arsenal of plant cell wall-degrading enzymes is produced in a cell density-dependent manner, which causes maceration of plant tissue. However, quorum sensing is central not only to controlling the production of such destructive enzymes, but also to the control of a number of other virulence determinants and secondary metabolites. Erwinia synthesizes both N -acylhomoserine lactone (AHL) and autoinducer-2 types of quorum sensing signal, which both play a role in regulating gene expression in the phytopathogen. We review the models for AHL-based regulation of carbapenem antibiotic production in Erwinia . We also discuss the importance of quorum sensing in the production and secretion of virulence determinants by Erwinia , and its interplay with other regulatory systems.

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