scholarly journals Transcriptional Profiling of Caulobacter crescentus during Growth on Complex and Minimal Media

2004 ◽  
Vol 186 (5) ◽  
pp. 1448-1461 ◽  
Author(s):  
Alison K. Hottes ◽  
Maliwan Meewan ◽  
Desiree Yang ◽  
Naomi Arana ◽  
Pedro Romero ◽  
...  
Keyword(s):  
Carbon Source ◽  
Mutational Analysis ◽  
Caulobacter Crescentus ◽  
Transcriptional Profiling ◽  
Transport Systems ◽  
Specific Expression ◽  
Induced Expression ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Minimal Media

ABSTRACT Microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium Caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (PYE) and minimal salts medium with glucose or xylose as the carbon source. Nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. The differentially expressed genes included many encoding transport systems, most notably diverse TonB-dependent outer membrane channels of unknown substrate specificity. Amino acid degradation pathways constituted the largest class of genes induced in PYE. In contrast, many of the genes upregulated in minimal media encoded enzymes for synthesis of amino acids, including incorporation of ammonia and sulfate into glutamate and cysteine. Glucose availability induced expression of genes encoding enzymes of the Entner-Doudoroff pathway, which was demonstrated here through mutational analysis to be essential in C. crescentus for growth on glucose. Xylose induced expression of genes encoding several hydrolytic exoenzymes as well as an operon that may encode a novel pathway for xylose catabolism. A conserved DNA motif upstream of many xylose-induced genes was identified and shown to confer xylose-specific expression. Xylose is an abundant component of xylan in plant cell walls, and the microarray data suggest that in addition to serving as a carbon source for growth of C. crescentus, this pentose may be interpreted as a signal to produce enzymes associated with plant polymer degradation.

Staphylococcus aureus Efflux Pumps and Tolerance to Ciprofloxacin and Chlorhexidine following Induction by Mupirocin

2021 ◽  
Author(s):  
Q.C. Truong-Bolduc ◽  
Y. Wang ◽  
J. L. Reedy ◽  
J.M. Vyas ◽  
D.C. Hooper
Keyword(s):  
Staphylococcus Aureus ◽  
Efflux Pumps ◽  
Induced Expression ◽  
Expression Of Genes ◽  
Genes Encoding

Mupirocin induced expression of genes encoding efflux pumps NorA and MepA as well as a YFP fluorescence reporter of NorA. Mupirocin exposure also produced reduced susceptibility to pump substrates ciprofloxacin and chlorhexidine, a change that was dependent on intact norA and mepA , respectively.

scholarly journals Differential Regulation of High-Affinity Phosphate Transport Systems of Mycobacterium smegmatis: Identification of PhnF, a Repressor of the phnDCE Operon

2007 ◽  
Vol 190 (4) ◽  
pp. 1335-1343 ◽  
Author(s):  
Susanne Gebhard ◽  
Gregory M. Cook
Keyword(s):  
Mycobacterium Smegmatis ◽  
Constitutive Expression ◽  
Phosphate Transport ◽  
Phosphate Limitation ◽  
Transport Systems ◽  
New Members ◽  
High Affinity ◽  
Expression Of Genes ◽  
Two Component ◽  
Genes Encoding

ABSTRACT The uptake of phosphate into the cell via high-affinity, phosphate-specific transport systems has been studied with several species of mycobacteria. All of these species have been shown to contain several copies of such transport systems, which are synthesized in response to phosphate limitation. However, the mechanisms leading to the expression of the genes encoding these transporters have not been studied. This study reports on the investigation of the regulation of the pstSCAB and the phnDCE operons of Mycobacterium smegmatis. The phn locus contains an additional gene, phnF, encoding a GntR-like transcriptional regulator. Expression analyses of a phnF deletion mutant demonstrated that PhnF acts as a repressor of the phnDCE operon but does not affect the expression of pstSCAB. The deletion of pstS, which is thought to cause the constitutive expression of genes regulated by the two-component system SenX3-RegX3, led to the constitutive expression of the transcriptional fusions pstS-lacZ, phnD-lacZ, and phnF-lacZ, suggesting that phnDCE and phnF are conceivably new members of the SenX3-RegX3 regulon of M. smegmatis. Two presumptive binding sites for PhnF in the intergenic region between phnD and phnF were identified and shown to be required for the repression of phnD and phnF, respectively. We propose a model in which the transcription of pstSCAB is controlled by the two-component SenX3-RegX3 system, while phnDCE and phnF are subject to dual control by SenX3-RegX3 and PhnF.

scholarly journals Regulation of ABCA1 and ABCG1 gene expression in the intraabdominal adipose tissue

2016 ◽  
Vol 62 (3) ◽  
pp. 283-289 ◽  
Author(s):  
V.V. Miroshnikova ◽  
A.A. Panteleeva ◽  
E.A. Bazhenova ◽  
E.P. Demina ◽  
T.S. Usenko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Cholesterol Metabolism ◽  
Nuclear Factor ◽  
Specific Expression ◽  
Protein Levels ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
And Control

Tissue specific expression of genes encoding cholesterol transporters ABCA1 and ABCG1 as well as genes encoding the most important transcriptional regulators of adipogenesis – LXRa, LXRb, PPARg and RORa has been investigated in intraabdominal adipose tissue (IAT) samples.A direct correlation between the content of ABCA1 and ABCG1 proteins with RORa protein level (r=0.480, p<0.05; r=0.435, p<0.05, respectively) suggests the role of the transcription factor RORa in the regulation of IAT ABCA1 and ABCG1 protein levels. ABCA1 and ABCG1 gene expression positively correlated with obesity indicators such as body mass index (BMI) (r=0.522, p=0.004; r=0.594, p=0.001, respectively) and waist circumference (r=0.403, p=0.033; r=0.474, p=0.013, respectively). The development of obesity is associated with decreased IAT levels of RORa and LXRb mRNA (p=0.016 and p=0.002, respectively). These data suggest that the nuclear factor RORa can play a significant role in the regulation of cholesterol metabolism and control IAT expression of ABCA1 and ABCG1, while the level of IAT LXRb gene expression may be an important factor associated with the development of obesity.

scholarly journals Differential transcription of expanded gene families in central carbon metabolism of Streptomyces coelicolor A3(2)

2019 ◽  
Author(s):  
Jana K Schniete ◽  
Richard Reumerman ◽  
Leena Kerr ◽  
Nicholas P Tucker ◽  
Iain S Hunter ◽  
...  
Keyword(s):  
Carbon Source ◽  
Streptomyces Coelicolor ◽  
Carbon Sources ◽  
Gene Families ◽  
Gene Clusters ◽  
Central Carbon Metabolism ◽  
Rna Seq ◽  
Enzymatic Function ◽  
Expression Of Genes ◽  
Genes Encoding

AbstractBackgroundStreptomycete bacteria are prolific producers of specialised metabolites, many of which have clinically relevant bioactivity. A striking feature of their genomes is the expansion of gene families that encode the same enzymatic function. Genes that undergo expansion events, either by horizontal gene transfer or duplication, can have a range of fates: genes can be lost, or they can undergo neo-functionalisation or sub-functionalisation. To test whether expanded gene families in Streptomyces exhibit differential expression, an RNA-Seq approach was used to examine cultures of wild-type Streptomyces coelicolor grown with either glucose or tween as the sole carbon source.ResultsRNA-Seq analysis showed that two-thirds of genes within expanded gene families show transcriptional differences when strains were grown on tween compared to glucose. In addition, expression of specialised metabolite gene clusters (actinorhodin, isorenieratane, coelichelin and a cryptic NRPS) was also influenced by carbon source.ConclusionsExpression of genes encoding the same enzymatic function had transcriptional differences when grown on different carbon sources. This transcriptional divergence enables partitioning to function under different physiological conditions. These approaches can inform metabolic engineering of industrial Streptomyces strains and may help develop cultivation conditions to activate the so-called silent biosynthetic gene clusters.

scholarly journals Pseudomonas aeruginosa Uses Multiple Pathways To Acquire Iron during Chronic Infection in Cystic Fibrosis Lungs

2013 ◽  
Vol 81 (8) ◽  
pp. 2697-2704 ◽  
Author(s):  
Anna F. Konings ◽  
Lois W. Martin ◽  
Katrina J. Sharples ◽  
Louise F. Roddam ◽  
Roger Latham ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Iron Uptake ◽  
Transport Systems ◽  
Ferrous Ions ◽  
Content Type ◽  
Bacterial Physiology ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Uptake Mechanisms

ABSTRACTPseudomonas aeruginosachronically infects the lungs of more than 80% of adult patients with cystic fibrosis (CF) and is a major contributor to the progression of disease pathology.P. aeruginosarequires iron for growth and has multiple iron uptake systems that have been studied in bacteria grown in laboratory culture. The purpose of this research was to determine which of these are active during infection in CF. RNA was extracted from 149 sputum samples obtained from 23 CF patients. Reverse transcription–quantitative real-time PCR (RT-qPCR) was used to measure the expression ofP. aeruginosagenes encoding transport systems for the siderophores pyoverdine and pyochelin, for heme, and for ferrous ions. Expression ofP. aeruginosagenes could be quantified in 89% of the sputum samples. Expression of genes associated with siderophore-mediated iron uptake was detected in most samples but was at low levels in some samples, indicating that other iron uptake mechanisms are active. Expression of genes encoding heme transport systems was also detected in most samples, indicating that heme uptake occurs during infection in CF.feoBexpression was detected in all sputum samples, implying an important role for ferrous ion uptake byP. aeruginosain CF. Our data show that multipleP. aeruginosairon uptake mechanisms are active in chronic CF infection and that RT-qPCR of RNA extracted from sputum provides a powerful tool for investigating bacterial physiology during infection in CF.

scholarly journals Comparison of Metabolome and Transcriptome of Flavonoid Biosynthesis Pathway in a Purple-Leaf Tea Germplasm Jinmingzao and a Green-Leaf Tea Germplasm Huangdan reveals Their Relationship with Genetic Mechanisms of Color Formation

2020 ◽  
Vol 21 (11) ◽  
pp. 4167
Author(s):  
Xuejin Chen ◽  
Pengjie Wang ◽  
Yucheng Zheng ◽  
Mengya Gu ◽  
Xinying Lin ◽  
...  
Keyword(s):  
Economic Value ◽  
Flavonoid Biosynthesis ◽  
Green Leaf ◽  
Future Research ◽  
Anthocyanin Content ◽  
Leaf Color ◽  
Specific Expression ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Purple Leaf

Purple-leaf tea is a phenotype with unique color because of its high anthocyanin content. The special flavor of purple-leaf tea is highly different from that of green-leaf tea, and its main ingredient is also of economic value. To probe the genetic mechanism of the phenotypic characteristics of tea leaf color, we conducted widely targeted metabolic and transcriptomic profiling. The metabolites in the flavonoid biosynthetic pathway of purple- and green-leaf tea were compared, and results showed that phenolic compounds, including phenolic acids, flavonoids, and tannins, accumulated in purple-leaf tea. The high expression of genes related to flavonoid biosynthesis (e.g., PAL and LAR) exhibits the specific expression of biosynthesis and the accumulation of these metabolites. Our result also shows that two CsUFGTs were positively related to the accumulation of anthocyanin. Moreover, genes encoding transcription factors that regulate flavonoids were identified by coexpression analysis. These results may help to identify the metabolic factors that influence leaf color differentiation and provide reference for future research on leaf color biology and the genetic improvement of tea.

scholarly journals Identification of Genes Required for Recycling Reducing Power during Photosynthetic Growth

2005 ◽  
Vol 187 (15) ◽  
pp. 5249-5258 ◽  
Author(s):  
Christine L. Tavano ◽  
Angela M. Podevels ◽  
Timothy J. Donohue
Keyword(s):  
Carbon Source ◽  
Calvin Cycle ◽  
Photosynthetic Apparatus ◽  
Reducing Power ◽  
Global Gene Expression ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Glycolate Metabolism ◽  
Global Gene Expression Analysis ◽  
Photoheterotrophic Growth

ABSTRACT Photosynthetic organisms have the unique ability to transform light energy into reducing power. We study the requirements for photosynthesis in the α-proteobacterium Rhodobacter sphaeroides. Global gene expression analysis found that ∼50 uncharacterized genes were regulated by changes in light intensity and O2 tension, similar to the expression of genes known to be required for photosynthetic growth of this bacterium. These uncharacterized genes included RSP4157 to -4159, which appeared to be cotranscribed and map to plasmid P004. A mutant containing a polar insertion in RSP4157, CT01, was able to grow via photosynthesis under autotrophic conditions using H2 as an electron donor and CO2 as a carbon source. However, CT01 was unable to grow photoheterotrophically in a succinate-based medium unless compounds that could be used to recycle reducing power (the external electron acceptor dimethyl sulfoxide (DMSO) or CO2) were provided. This suggests that the insertion in RSP4157 caused a defect in recycling reducing power during photosynthetic growth when a fixed carbon source was present. CT01 had decreased levels of RNA for genes encoding putative glycolate degradation functions. We found that exogenous glycolate also rescued photoheterotrophic growth of CT01, leading us to propose that CO2 produced from glycolate metabolism can be used by the Calvin cycle to recycle reducing power generated in the photosynthetic apparatus. The ability of glycolate, CO2, or DMSO to support photoheterotrophic growth of CT01 suggests that one or more products of RSP4157 to -4159 serve a previously unknown role in recycling reducing power under photosynthetic conditions.

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