scholarly journals Global Regulation of Gene Expression and Cell Differentiation in Caulobacter crescentus in Response to Nutrient Availability

2009 ◽  
Vol 192 (3) ◽  
pp. 819-833 ◽  
Author(s):  
Jennifer C. England ◽  
Barrett S. Perchuk ◽  
Michael T. Laub ◽  
James W. Gober
Keyword(s):  
Gene Expression ◽  
Nitrogen Limitation ◽  
Caulobacter Crescentus ◽  
Regulation Of Gene Expression ◽  
Fixed Time ◽  
Natural Environments ◽  
Swarmer Cell ◽  
Regulatory Strategies ◽  
Time Period ◽  
Regulated Gene Expression

ABSTRACT In a developmental strategy designed to efficiently exploit and colonize sparse oligotrophic environments, Caulobacter crescentus cells divide asymmetrically, yielding a motile swarmer cell and a sessile stalked cell. After a relatively fixed time period under typical culture conditions, the swarmer cell differentiates into a replicative stalked cell. Since differentiation into the stalked cell type is irreversible, it is likely that environmental factors such as the availability of essential nutrients would influence the timing of the decision to abandon motility and adopt a sessile lifestyle. We measured two different parameters in nutrient-limited chemostat cultures, biomass concentration and the ratio of nonstalked to stalked cells, over a range of flow rates and found that nitrogen limitation significantly extended the swarmer cell life span. The transcriptional profiling experiments described here generate the first comprehensive picture of the global regulatory strategies used by an oligotroph when confronted with an environment where key macronutrients are sparse. The pattern of regulated gene expression in nitrogen- and carbon-limited cells shares some features in common with most copiotrophic organisms, but critical differences suggest that Caulobacter, and perhaps other oligotrophs, have evolved regulatory strategies to deal distinctly with their natural environments. We hypothesize that nitrogen limitation extends the swarmer cell lifetime by delaying the onset of a sequence of differentiation events, which when initiated by the correct combination of external environmental cues, sets the swarmer cell on a path to differentiate into a stalked cell within a fixed time period.

scholarly journals Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

2016 ◽  
Vol 113 (40) ◽  
pp. E5952-E5961 ◽  
Author(s):  
Dante P. Ricci ◽  
Michael D. Melfi ◽  
Keren Lasker ◽  
David L. Dill ◽  
Harley H. McAdams ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Binding Sites ◽  
Cell Cycle Progression ◽  
Target Genes ◽  
Caulobacter Crescentus ◽  
Regulation Of Gene Expression ◽  
Cycle Progression ◽  
Swarmer Cell ◽  
Sequence Recognition

Faithful cell cycle progression in the dimorphic bacteriumCaulobacter crescentusrequires spatiotemporal regulation of gene expression and cell pole differentiation. We discovered an essential DNA-associated protein, GapR, that is required forCaulobactergrowth and asymmetric division. GapR interacts with adenine and thymine (AT)-rich chromosomal loci, associates with the promoter regions of cell cycle-regulated genes, and shares hundreds of recognition sites in common with known master regulators of cell cycle-dependent gene expression. GapR target loci are especially enriched in binding sites for the transcription factors GcrA and CtrA and overlap with nearly all of the binding sites for MucR1, a regulator that controls the establishment of swarmer cell fate. Despite constitutive synthesis, GapR accumulates preferentially in the swarmer compartment of the predivisional cell. Homologs of GapR, which are ubiquitous among the α-proteobacteria and are encoded on multiple bacteriophage genomes, also accumulate in the predivisional cell swarmer compartment when expressed inCaulobacter. TheEscherichia colinucleoid-associated protein H-NS, like GapR, selectively associates with AT-rich DNA, yet it does not localize preferentially to the swarmer compartment when expressed exogenously inCaulobacter, suggesting that recognition of AT-rich DNA is not sufficient for the asymmetric accumulation of GapR. Further, GapR does not silence the expression of H-NS target genes when expressed inE. coli, suggesting that GapR and H-NS have distinct functions. We propose thatCaulobacterhas co-opted a nucleoid-associated protein with high AT recognition to serve as a mediator of cell cycle progression.

scholarly journals Analysis of the Polar Flagellar Gene System ofVibrio parahaemolyticus

2000 ◽  
Vol 182 (13) ◽  
pp. 3693-3704 ◽  
Author(s):  
Yun-Kyeong Kim ◽  
Linda L. McCarter
Keyword(s):  
Gene Expression ◽  
Caulobacter Crescentus ◽  
Regulation Of Gene Expression ◽  
Enteric Bacteria ◽  
Polar Flagellum ◽  
Flagellar Gene ◽  
Swarmer Cell ◽  
Gene System ◽  
Genotypic Analysis ◽  
Insight Into

ABSTRACT Vibrio parahaemolyticus has dual flagellar systems adapted for locomotion under different circumstances. A single, sheathed polar flagellum propels the swimmer cell in liquid environments. Numerous unsheathed lateral flagella move the swarmer cell over surfaces. The polar flagellum is produced continuously, whereas the synthesis of lateral flagella is induced under conditions that impede the function of the polar flagellum, e.g., in viscous environments or on surfaces. Thus, the organism possesses two large gene networks that orchestrate polar and lateral flagellar gene expression and assembly. In addition, the polar flagellum functions as a mechanosensor controlling lateral gene expression. In order to gain insight into the genetic circuitry controlling motility and surface sensing, we have sought to define the polar flagellar gene system. The hierarchy of regulation appears to be different from the polar system of Caulobacter crescentus or the peritrichous system of enteric bacteria but is pertinent to many Vibrio andPseudomonas species. The gene identity and organization of 60 potential flagellar and chemotaxis genes are described. Conserved sequences are defined for two classes of polar flagellar promoters. Phenotypic and genotypic analysis of mutant strains with defects in swimming motility coupled with primer extension analysis of flagellar and chemotaxis transcription provides insight into the polar flagellar organelle, its assembly, and regulation of gene expression.

scholarly journals A toxin-antitoxin system associated transcription factor of Caulobacter crescentus can influence cell cycle-regulated gene expression during the SOS response

2020 ◽  
Author(s):  
Koyel Ghosh ◽  
Kamilla Ankær Brejndal ◽  
Clare L. Kirkpatrick
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Dna Damage ◽  
Transcription Factor ◽  
Caulobacter Crescentus ◽  
Sos Response ◽  
Cell Cycle Gene ◽  
Regulated Gene Expression ◽  
Cell Cycle Gene Expression

AbstractToxin-antitoxin (TA) systems are widespread in bacterial chromosomes but their functions remain enigmatic. Although many are transcriptionally upregulated by stress conditions, it is unclear what role they play in cellular responses to stress and to what extent the role of a given TA system homologue varies between different bacterial species. In this work we investigate the role of the DNA damage-inducible TA system HigBA of Caulobacter crescentus in the SOS response and discover that in addition to the toxin HigB affecting cell cycle gene expression through inhibition of the master regulator CtrA, HigBA possesses a transcription factor third component, HigC, which both auto-regulates the TA system and acts independently of it. Through HigC, the system exerts downstream effects on antibiotic (ciprofloxacin) resistance and cell cycle gene expression. HigB and HigC had inverse effects on cell cycle gene regulation, with HigB reducing and HigC increasing the expression of CtrA-dependent promoters. Neither HigBA nor HigC had any effect on formation of persister cells in response to ciprofloxacin. Rather, their role in the SOS response appears to be as transcriptional and post-transcriptional regulators of cell cycle-dependent gene expression, transmitting the status of the SOS response as a regulatory input into the cell cycle control network via CtrA.ImportanceAlmost all bacteria respond to DNA damage by upregulating a set of genes that helps them to repair and recover from the damage, known as the SOS response. The set of genes induced during the SOS response varies between species, but frequently includes toxin-antitoxin systems. However, it is unknown what the consequence of inducing these systems is, and whether they provide any benefit to the cells. We show here that the DNA damage-induced TA system HigBA of the asymmetrically dividing bacterium Caulobacter crescentus affects the cell cycle regulation of this bacterium. HigBA also has a transcription factor encoded immediately downstream of it, named here HigC, which controls expression of the TA system and potentially other genes as well. Therefore, this work identifies a new role for TA systems in the DNA damage response, distinct from non-specific stress tolerance mechanisms which had been proposed previously.

scholarly journals Differential Effects of Mild and Severe Cucumber mosaic virus Strains in the Perturbation of MicroRNA-Regulated Gene Expression in Tomato Map to the 3′ Sequence of RNA 2

2009 ◽  
Vol 22 (10) ◽  
pp. 1239-1249 ◽  
Author(s):  
Fabrizio Cillo ◽  
Tiziana Mascia ◽  
Marco M. Pasciuto ◽  
Donato Gallitelli
Keyword(s):  
Gene Expression ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Regulation Of Gene Expression ◽  
Mitochondrial Rna ◽  
Leaf Morphogenesis ◽  
Developmental Defects ◽  
Mild Phenotype ◽  
Mirna Pathway ◽  
Regulated Gene Expression

Viral infections interfere with the microRNA (miRNA)-mediated regulation of gene expression, determining developmental defects. In tomato leaves, the accumulation levels of six miRNA species and their target transcripts corresponding to transcription factors with roles in plant development and leaf morphogenesis and two genes involved in the short RNA processing, DCL1 and AGO1, were significantly enhanced upon infection with the severe strain Cucumber mosaic virus (CMV)-Fny, while that of AGO4 was reduced. In plants harboring the infection of the mild strain CMV-LS, the effects on miRNA pathway were reduced, although AGO1, DCL1, and NAC1 also were shown to overaccumulate during infections exhibiting a mild phenotype. The use of the recombinant strain CMV-Fny(LS2b), in which the 3′-terminal region of CMV-Fny RNA 2, including the 2b coding sequence, was replaced with the corresponding region of CMV-LS RNA 2, provided evidence that the exchanged region was implicated in the perturbation of miRNA metabolism. In tomato plants infected with CMV-Fny supporting the ameliorative satellite (sat)RNA variant Tfn-satRNA, the symptomless phenotype correlated, with the exception of NAC1 upregulation, with the absence of effects on mitochondrial RNA and miRNA expression. Some of the aspects of miRNA pathway perturbation described were peculiar to CMV–tomato interactions and involved in the etiology of the disease phenotype elicited in this host.

scholarly journals Temporal Regulation of Genes Encoding the Flagellar Proximal Rod in Caulobacter crescentus

2001 ◽  
Vol 183 (2) ◽  
pp. 725-735 ◽  
Author(s):  
Charles H. Boyd ◽  
James W. Gober
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Developmental Stages ◽  
Caulobacter Crescentus ◽  
Response Regulator ◽  
Class Ii ◽  
Class Iii ◽  
Swarmer Cell ◽  
Sequencing Project

ABSTRACT The gram-negative bacterium Caulobacter crescentus has a life cycle that includes two distinct and separable developmental stages, a motile swarmer phase and a sessile stalked phase. The cell cycle-controlled biogenesis of the single polar flagellum of the swarmer cell is the best-studied aspect of this developmental program. The flagellar regulon is arranged into a rigid trans-acting hierarchy of gene expression in which successful expression of early genes is required for the expression of genes that are later in the hierarchy and in which the order of gene expression mirrors the order of assembly of gene products into the completed flagellum. TheflgBC-fliE genes were identified as a result of the C. crescentus genome sequencing project and encode the homologues of two flagellar proximal rod proteins, FlgB and FlgC, and one conserved protein, FliE, that is of unknown function. Footprint assays on a DNA fragment containing the operon promoter as well as in vivo mutant suppressor analysis of promoter mutations indicate that this operon is controlled by the cell cycle response regulator CtrA, which with ς70 is responsible for regulating transcription of other early flagellar genes in C. crescentus. Promoter analysis, timing of expression, and epistasis experiments place these genes outside of the flagellar regulatory hierarchy; they are expressed in class II mutants, andflgB deletions do not prevent class III gene expression. This operon is also unusual in that it is expressed from a promoter that is divergent from the class II operon containing fliP, which encodes a member of the flagellum-specific protein export apparatus.

scholarly journals Comparison of gene expression patterns of Kappaphycus alvarezii (Rhodophyta, Solieriaceae) under different light wavelengths and CO2 enrichment

2017 ◽  
Author(s):  
Thien Vun Yee ◽  
Kenneth Francis Rodrigues ◽  
Clemente Michael Wong Vui Ling ◽  
Wilson Yong Thau Lym
Keyword(s):  
Gene Expression ◽  
Carbon Fixation ◽  
Kappaphycus Alvarezii ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
Molecular Evidence ◽  
Limited Information ◽  
Metabolic Pattern ◽  
Regulated Gene Expression

AbstractTranscriptomes associated with the process of photosynthesis and carbon fixation have offered insights into the mechanism of gene regulation in terrestrial plants, however limited information is available as far as macroalgae are concerned. Intertidal red alga, Kappaphycus alvarezii is exposed to different wavelengths of light in their lives as light quantity and quality changes at different depths in seawater. This investigation aims to study the underlying mechanisms associated with photosynthesis and carbon fixation under specific light qualities and CO2 enrichment. Light regulation of gene expression has not been previously described for red algae. By using next generation sequencing, transcriptome profiling of K. alvarezii generated 76,871 qualified transcripts with a mean length of 979bp and a N50 length of 1,707bp and 55.83% transcripts were annotated on the basis of function. Blue, green and red light all have demonstrated roles in modulating light responses, such as changes in gene expression. Here we analysed the effects of light regulation on four selected photosynthesis aspects (light-harvesting complex, phycobilisomes, photosystems and photoreceptors). We observed that light-regulated gene expression in this species is not a single light response and different light qualities are transduced to regulate the same metabolic pattern. The carbon fixation pathway was analysed and key genes encoding enzymes involved in the carbon fixation pathway such as ppc, pepc, prk, pgk, ppdk, provided that unequivocal molecular evidence that most of the C3 and C4 pathway genes were actively transcribed in K. alvarezii. In addition to this the CO2 induced transcriptome suggested the possibility of shifting carbon metabolism pathway after acclimation to increased level of CO2. Impact of CO2 enrichment on the cultures has provided new insight into the response to rising CO2.

scholarly journals Vibrio parahaemolyticus ScrC Modulates Cyclic Dimeric GMP Regulation of Gene Expression Relevant to Growth on Surfaces

2007 ◽  
Vol 190 (3) ◽  
pp. 851-860 ◽  
Author(s):  
Rosana B. R. Ferreira ◽  
Luis Caetano M. Antunes ◽  
E. Peter Greenberg ◽  
Linda L. McCarter
Keyword(s):  
Gene Expression ◽  
Vibrio Parahaemolyticus ◽  
Capsular Polysaccharide ◽  
Dominant Role ◽  
Regulation Of Gene Expression ◽  
Diguanylate Cyclase ◽  
Swarming Motility ◽  
Swarmer Cell ◽  
High Concentrations ◽  
Mutant Phenotypes

ABSTRACT In Vibrio parahaemolyticus, scrC participates in controlling the decision to be a highly mobile swarmer cell or a more adhesive, biofilm-proficient cell type. scrC mutants display decreased swarming motility over surfaces and enhanced capsular polysaccharide production. ScrC is a cytoplasmic membrane protein that contains both GGDEF and EAL conserved protein domains. These domains have been shown in many organisms to respectively control the formation and degradation of the small signaling nucleotide cyclic dimeric GMP (c-di-GMP). The scrC gene is part of the three-gene scrABC operon. Here we report that this operon influences the cellular nucleotide pool and that c-di-GMP levels inversely modulate lateral flagellar and capsular polysaccharide gene expression. High concentrations of this nucleotide prevent swarming and promote adhesiveness. Further, we demonstrate that ScrC has intrinsic diguanylate cyclase and phosphodiesterase activities, and these activities are controlled by ScrAB. Specifically, ScrC acts to form c-di-GMP in the absence of ScrA and ScrB; whereas ScrC acts to degrade c-di-GMP in the presence of ScrA and ScrB. The scrABC operon is specifically induced by growth on a surface, and the analysis of mutant phenotypes supports a model in which the phosphodiesterase activity of ScrC plays a dominant role during surface translocation and in biofilms.

scholarly journals Coherent feedforward regulation of gene expression byCaulobacterσTand GsrN during hyperosmotic stress

2018 ◽  
Author(s):  
Matthew Z. Tien ◽  
Benjamin J. Stein ◽  
Sean Crosson
Keyword(s):  
Gene Expression ◽  
Protein Expression ◽  
Cell Survival ◽  
Caulobacter Crescentus ◽  
Regulation Of Gene Expression ◽  
Hyperosmotic Stress ◽  
Transcriptional Level ◽  
Stem Loop ◽  
General Stress ◽  
Gene Expression Control

AbstractGsrN is a conserved small RNA that is under transcriptional control of the general stress sigma factor, σT, and that functions as a post-transcriptional regulator ofCaulobacter crescentussurvival under multiple stress conditions. We have defined features of GsrN structure that determine survival under hyperosmotic stress, and have applied transcriptomic and proteomic methods to identify regulatory targets of GsrN under hyperosmotic conditions. The 5’ end of GsrN, which includes a conserved cytosine-rich stem loop structure, is necessary for cell survival after osmotic upshock. GsrN both activates and represses gene expression in this stress condition. Expression of an uncharacterized open reading frame predicted to encode a glycine-zipper protein,osrP, is strongly activated by GsrN. Our data support a model in which GsrN physically interacts withosrPmRNA through its 5’ C-rich stem loop to enhance OsrP protein expression. We conclude thatsigT,gsrN, andosrPform a coherent feedforward loop in which σTactivatesgsrNandosrPtranscription during stress, and GsrN activates OsrP protein expression at the post-transcriptional level. This study delineates transcriptional and post-transcriptional layers ofCaulobactergene expression control during hyperosmotic stress, uncovers a new regulatory target of GsrN, and defines a coherent feedforward motif in theCaulobacterGSR regulatory network.ImportanceBacteria inhabit diverse niches, and must adapt their physiology to constant environmental fluctuations. A major response to environmental perturbation is to change gene expression.Caulobacterand other alphaproteobacteria initiate a complex gene expression program known as the general stress response (GSR) under conditions including oxidative stress, osmotic stress, and nutrient limitation. The GSR enables cell survival in these environments. Understanding how bacteria survive stress requires that we dissect gene expression responses, such as the GSR, at the molecular level. This study is significant as it defines transcriptional and post-transcriptional layers of gene expression regulation in response to hyperosmotic stress. We further provide evidence that coherent feedforward motifs influence the system properties of theCaulobacterGSR pathway.

scholarly journals Functional Analysis of Haplotypes and Promoter Activity at the 5’ Region of the ADH7 Gene

2021 ◽  
Author(s):  
Kuo Zeng ◽  
Ya Li ◽  
Meng Gao ◽  
Yong-ping Liu ◽  
Feng-ling Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Cell Lines ◽  
Fluorescence Intensity ◽  
Regulation Of Gene Expression ◽  
Regulatory Region ◽  
Luciferase Reporter ◽  
Relative Fluorescence Intensity ◽  
Hek 293 ◽  
Regulated Gene Expression

Abstract Background: The function of the 5’ regulatory region and the role of the different SNP loci have not been well characterized. This study investigated the effect of several ADH7 haplotypes on the regulation of gene expression in vitro and the functional sequences in the 5’ regulatory region of ADH7. Three SNPs (rs17537595, rs2851028, and rs2654847) and four different haplotypes (T-C-T, T-T-T, C-T-T, T-C-A) were identified by cloning and sequencing. Methods: Effects of 4 different haplotypes and 8 truncated fragments of 5’ regulatory region on ADH7 gene expression were detected using a dual-luciferase reporter assay system. All recombinant plasmids were transfected into HEK-293, U87, and SH-SY5Y cells, respectively, and their relative fluorescence intensity was measured.Results: In HEK-293, U87, and SH-SY5Y cell lines, the relative fluorescence intensity of haplotype T-C-T was significantly higher than that of haplotype T-T-T, C-T-T, and T-C-A. Additionally, we found that regions from -83 to -310bp (ATG, +1), -560 to -768bp , and -987bp to -1203bp up-regulated gene expression. In contrast, the region from -768 to -987bp down-regulated gene expression. The gene expression of regions from -1203 to -1369bp and -1369 to -1626bp was down-regulated in U87 and SH-SY5Y cell lines, but the trend was opposite in HEK-293 cell line. The region from -310 to -560bp up-regulated gene expression in SH-SY5Y cell line, but down-regulated gene expression in HEK-293 and U87 cell lines.Conclusions: This study has shown that the polymorphisms of ADH7 5’ regulatory region play an important role in the regulation of gene expression.

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