Analysis of Gene Expression in Escherichia coli in Response to Changes of Growth-Limiting Nutrient in Chemostat Cultures

Abstract

Studies of steady-state metabolic fluxes in.8% of a total of 4,071 genes investigated, especially those involved in amino acid metabolism, central carbon and energy metabolism, transport system and cell envelope, were observed to be differentially expressed between the two nutrient-limited cultures. One important characteristic of E. coli grown under nutrient limitation was its capacity to scavenge carbon or nitrogen from the medium through elevating the expression of the corresponding transport and assimilation genes. The number of differentially expressed genes in faster-growing cells (specific growth rate of 0.55 h ؊1 ), however, decreased to below half of that in slow-growing cells, which could be explained by diverse transcriptional responses to the growth rate under different nutrient limitations. Independent of the growth rate, 92 genes were identified as being differentially expressed. Genes tightly related to the culture conditions were highlighted, some of which may be used to characterize nutrient-limited growth.Microorganisms are capable of varying their metabolic fluxes and sizes of intermediate pools over a wide range in response to changes in environmental conditions. These metabolic responses are usually studied in chemostat cultures, where growth conditions can be well controlled. By designing the composition of the feeding medium carefully, growth in chemostats may be limited by a single or multiple nutrients. Carbon limitation is the most widely used type and has been applied to investigate cell metabolism (9,17,18,30,37), metabolic differences among knockout mutants (11,30,38), metabolic reaction models (7), and so on. Growth in carbondeficient medium may be regarded as limiting energy or catabolism. On the other hand, although energy generation rates are high in carbon-replete cultures, cell yields are usually low, resulting in anabolism limitation and overflow metabolism (9, 18, 23). Other nutrient-limited chemostat cultures include limitation of the nitrogen source, phosphorus, or sulfur, among which nitrogen limitation is the most frequently studied (9, 18, 30, 37). Growth, metabolism and energetics in chemostat cultures under carbon-limited and nitrogen-limited conditions have been investigated for Saccharomyces cerevisiae, Bacillus subtilis, and other microorganisms (5,9,13,17,18). For Escherichia coli, the influences of nutrient limitation on metabolic responses has been investigated in recent studies by using information on isotopomer distribution (11,30). Metabolic changes and kinetic properties during the transition from glucose-excess to glucose-limited growth conditions have also been studied (37).Recently, we developed the method of flux ratio analysis (30) to identify central reaction networks and obtained reliable metabolic fluxes in wild-type W3110 and some knockout mutants of Escherichia coli grown in either glucose-limited or ammonia-limited chemostats (16,38). Steady-state flux information suggested remarkable metabolic alterations in these strains in response to changes of...

Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

“…For example, transcript levels for genes for a number of ribosomal proteins, such as rplL and rpsC, were approximately 20-fold lower during growth on sediments. Transcript levels for protein synthesis genes are typically lower in microorganisms growing at slower growth rates (Gonzalez et al, 2002;Hua et al, 2004;Boccazzi et al, 2005). Thus, these results are consistent with the fact that G. uraniireducens grows sevenfold slower on sediments relative to fumarate (DE Holmes, manuscript in preparation).…”

Escherichia coli YqhD Exhibits Aldehyde Reductase Activity and Protects from the Harmful Effect of Lipid Peroxidation-derived Aldehydes

“…TBAR determination suggested that lipid peroxidation does not occur in this condition, indicating that toxic YqhD substrates are not generated (unpublished results). 5 Transcription activation of the yqhD gene has been observed in cells treated with the oxidant Curvularia haloperoxidase system (23) when exposed to cold shock (21) or when grown in a limited-nutrient medium (22). Here we demonstrate that yqhD is also induced in cells exposed to conditions favoring lipid peroxidation, as are treatments with the ROS elicitors K 2 TeO 3 , H 2 O 2 , or paraquat or with the membrane lipid-peroxidating compound t-BOOH.…”

“…Based mainly on the bound coenzyme, NADP(OH) 2 , they proposed a putative relationship between YqhD and oxidative stress. Genomic and proteomic studies have shown that YqhD is expressed in E. coli after exposure to stress conditions such as cold shock (21), nutrient starving (22), and oxidative stress generated by the Curvularia peroxidase system (23). YqhD has several features similar to AdhE, an alcohol/aldehyde dehydrogenase involved in fermentative metabolism in E. coli for which an antioxidant function under aerobic conditions has been proposed (24).…”

TrgI, toluene repressed gene I, a novel gene involved in toluene-tolerance in Pseudomonas putida S12

“…Saccharomyces cerevisiae (Boer et al 2003;Wu et al 2004) and E. coli (Hua et al 2004). This phenomenon should be considered when studying the effects of a chemical effector such as toluene at the transcriptome level.…”