Transcriptional Regulation Microorganisms respond to their environment by altering gene expression, whether activating multiple pathways to change the composition of the cellular membrane, inducing biosynthetic operons to metabolize available alternative energy sources, or repressing the synthesis of membrane transport proteins when exposed to toxic compounds. Researchers are using GeneChip expression arrays to visualize the global changes in gene expression and thereby elucidate the pathways employed by the microorganism as it adjusts to changes in environmental conditions.
In Escherichia coli most carbohydrate catabolic genes are regulated by substrate-specific induction (e.g. lactose) or by global systems like carbon catabolite repression, which blocks expression of alternative carbon utilization pathways when glucose, the preferred carbon source, is present. This mechanism conserves cellular resources by preventing the synthesis of enzymes and transporters needed to metabolize unavailable carbon sources. Recently, Liu et al. used GeneChip E. coli Arrays to investigate how E. coli coordinates carbohydrate catabolic gene expression when grown on six different carbon sources of varying quality. They observed a strikingly similar and hierarchical pattern of increased gene expression among the different substrates as growth rate declined. Specifically, the number of up-regulated genes was inversely proportional with growth rate, far exceeding the number of down-regulated genes, and that those genes expressed at high growth rates are a subset of those expressed at low growth rates. Further, genes for unavailable carbon sources are progressively induced as carbon source quality decreases, along with the genes for cell motility. Their data imply that as carbon source quality decreases, rather than conserve energy, E. coli induces expression of multiple metabolic and cell motility operons to forage for and utilize new growth substrates.
The chronic pneumonia caused by Pseudomonas aeruginosa is the leading cause of mortality in Cystic Fibrosis patients. Alginate, an exopolysaccharide that conveys the mucoid phenotype to P. aeruginosa, insulates the bacterium from the killing mechanisms of phagocytes and prevents phagocytosis by neutrophils and macrophages. Alginate production is controlled by the transcriptional regulator AlgR. To determine whether AlgR regulates genes other than those involved in alginate biosynthesis, Lizewski et al. used the GeneChip P. aeruginosa Array to compare the gene expression profiles of the wild-type lab strain PAO1 with that of an AlgR-deletion strain under logarithmic and stationary growth conditions. They found that under logarithmic growth conditions, AlgR activated 58 genes, but repressed 37 others as compared to the deletion mutant, while under stationary growth conditions, AlgR activated 45 genes, but repressed 14. These results demonstrate
that AlgR does regulate other genes in P. aeruginosa, both positively and negatively, some of which are involved in increased virulence and pilus production.
Rhodobacter sphaeroides, a phototrophic proteobacterium, is capable of metabolizing single-carbon compounds such as carbon dioxide or methanol, producing molecular hydrogen, and detoxifying metal oxides and oxyanions. It derives energy through aerobic respiration, anoxygenic photosynthesis, anaerobic respiration, or fermentation, depending upon the environmental conditions. Pappas et al. used GeneChip CustomExpress Arrays to compare the gene expression profiles of R. sphaeroides grown under three different conditions; aerobic, anaerobic in the dark, and anaerobic photosynthesis. Of 4,292 putative genes identified in R. sphaeroides, they found 233 whose expression was increased in response to the absence of oxygen, while the expression of 305 others was repressed, regardless of the light conditions. The expression of another 122 increased in the presence of light, while 5 others were repressed, regardless of oxygen conditions. Their data demonstrate that 20%-35% of the genes exhibit significant
changes in expression under these three growth conditions, indicating that massive changes in gene expression are required to adapt to diverse environmental changes.
The bacterium Caulobacter crescentus is known for its ability to live in low-nutrient environments, a characteristic of heavy metal-contaminated sites, making it an interesting candidate for use in bioremediation and subsequent environmental restoration. Hu et al. used GeneChip CustomExpress Arrays to identify the pathways responding to heavy-metal toxicity in C. crescentus cells exposed to four heavy metals: chromium, cadmium, selenium, and uranium. They observed four genes whose expression was increased when cells were exposed to each of the metals, but only one of those, sodA (superoxide dismutase), has a known function, which is to remove superoxide radicals generated upon exposure to heavy metals. Exposure to cadmium increased expression of multiple efflux pump systems to lower intracellular cadmium concentration, while exposure to chromium resulted in decreased expression of a sulfate transporter to reduce nonspecific uptake of chromium. Exposure to selenium resulted in increased expression
of a subset of those seen with exposure to cadmium and chromium. However, expose to uranium resulted in increased expression of a different group of genes, which may explain the high tolerance of C. crescentus to uranium through the formation of extracellular calcium-uranium-phosphate precipitates. Finally, they also identified several antisense transcripts that were differentially regulated in response to heavy metal exposure, demonstrating the need to interrogate both strands of the genome.
Bacterial lipoproteins are unique proteins modified with glyceryl groups at their amino-terminal cysteine residues, comprising a major constituent of the cellular membrane of E. coli. Brokx et al. used GeneChip E. coli Arrays to analyze the global changes in the expression of lipoprotein mRNAs in E. coli MG1655 cells under three different growth conditions; aerobic, anaerobic, and anaerobic with potassium nitrate as an alternative electron acceptor, to better understand the changes in the composition of the cell envelope. Of 96 lipoprotein genes studied, 21 were not expressed under either growth condition, while 10 were expressed under one of the three growth conditions, 5 were expressed under two of the growth conditions, and 60 were expressed under all three. Further, 64 genes were expressed under aerobic conditions, but the expression of 14 others increased under anaerobic conditions, allowing a genome-wide view of the changes in cellular membrane composition under two common, but very
different, growth conditions.
References
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Liu, M. et al. Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J. Biol. Chem.280: 15921-15927 (2005).
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Lizewski, S.E. et al. Identification of AlgR-regulated genes in Pseudomonas aeruginosa by use of microarrays. J. Bacteriol.186: 5672-5684 (2004).
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Pappas, C.T. et al. Construction and validation of the Rhodobacter sphaeroides 2.4.1 DNA microarray: Transcriptome flexibility at diverse growth modes J. Bacteriol.186: 4748-4758 (2004).
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Hu P, et al. Whole-Genome Transcriptional Analysis of Heavy Metal Stresses in Caulobacter crescentus. J. Bacteriol.187: 8437-8449 (2005).
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Brokx, S.J. et al. Genome-wide analysis of lipoprotein expression in Escherichia coli MG1655. J. Bacteriol.186: 3254-3258 (2004).
Related Scientific Publications
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Mashburn, L. et al. Staphylococcus aureus Serves as an Iron Source for Pseudomonas aeruginosa during In Vivo Coculture. J. Bacteriol.187: 554-566 (2005).
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Soupene, E. et al. Physiological Studies of Escherichia coli Strain MG1655: Growth Defects and Apparent Cross-Regulation of Gene Expression. J. Bacteriol.185: 5611-5626 (2003).
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Schembri, M. et al. Global gene expression in Escherichia coli biofilms. Mol. Microbiol.48: 253-267(2003).
Microorganisms respond to their environment by altering gene expression, whether activating multiple pathways to change the composition of the cellular membrane, inducing biosynthetic operons to metabolize available alternative energy sources, or repressing the synthesis of membrane transport proteins when exposed to toxic compounds. Researchers are using GeneChip expression arrays to visualize the global changes in gene expression and thereby elucidate the pathways employed by the microorganism as it adjusts to changes in environmental conditions.
The bacterium Caulobacter crescentus is known for its ability to live in low-nutrient environments, a characteristic of heavy metal-contaminated sites, making it an interesting candidate for use in bioremediation and subsequent environmental restoration. Hu et al. used 
