Global gene expression in Escherichia coli biofilms

Abstract

SummaryIt is now apparent that microorganisms undergo significant changes during the transition from planktonic to biofilm growth. These changes result in phenotypic adaptations that allow the formation of highly organized and structured sessile communities, which possess enhanced resistance to antimicrobial treatments and host immune defence responses. Escherichia coli has been used as a model organism to study the mechanisms of growth within adhered communities. In this study, we use DNA microarray technology to examine the global gene expression profile of E. coli during sessile growth compared with planktonic growth. Genes encoding proteins involved in adhesion (type 1 fimbriae) and, in particular, autoaggregation (Antigen 43) were highly expressed in the adhered population in a manner that is consistent with current models of sessile community development. Several novel gene clusters were induced upon the transition to biofilm growth, and these included genes expressed under oxygen-limiting conditions, genes encoding (putative) transport proteins, putative oxidoreductases and genes associated with enhanced heavy metal resistance. Of particular interest was the observation that many of the genes altered in expression have no current defined function. These genes, as well as those induced by stresses relevant to biofilm growth such as oxygen and nutrient limitation, may be important factors that trigger enhanced resistance mechanisms of sessile communities to antibiotics and hydrodynamic shear forces.

Microtoming coupled to microarray analysis to evaluate the spatial metabolic status of Geobacter sulfurreducens biofilms

“…Genes specifically expressed during biofilm formation in response to environmental conditions or specific mutations have been identified (Whiteley et al, 2001;Schembri et al, 2003;Stanley et al, 2003;Zhu and Mekalanos, 2003), but these studies on whole biofilms lacked the spatial resolution that may be necessary to account for the heterogeneity in metabolic states that can be expected in biofilms (Stewart and Franklin, 2008). Introducing reporters that express unstable green fluorescent proteins can provide insight into the expression of individual genes throughout biofilms (Sternberg et al, 1999;Teal et al, 2006;Stewart and Franklin, 2008).…”

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

“…Other significantly downregulated transcripts, whose presence was previously linked to stress response in Shewanella (Qiu et al, 2005;McLean et al, 2008), encoded lambda-like bacteriophage proteins and the LrgAB system that controls autolysis via modulating murein hydrolase activity (Groicher et al, 2000). Notably, this coincided with transcriptional upregulation of several surface attachment factors (pilA, pilM, pilXWV, bpfA and csgA) of Shewanella W3-18-1, which are typically associated with biofilm lifestyle (Schembri et al, 2003;Beloin and Ghigo, 2005).…”

Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)

“…Several poorly characterized genes were also induced on deletion of yncC including ynhG (4.6-fold), which was repressed in E. coli MG1655 biofilms (Schembri et al, 2003), ybiM (6.5-fold), which was induced by AI-2 in E. coli W3110 (DeLisa et al, 2001b), yqjC (4.6-fold), which was repressed by AI-2 in E. coli W3110 (DeLisa et al, 2001b) and yahO (5.7-fold), which was induced by MqsR expression in E. coli MG1655 (González Barrios et al, 2006).…”

“…Hundreds of genes are differentially expressed during this biofilm development process (Schembri et al, 2003;Beloin et al, 2004;Ren et al, 2004a) and bacterial signaling such as quorum and metabolite sensing and catabolite repression are involved in this process (Jackson et al, 2002;Stanley and Lazazzera, 2004;Camilli and Bassler, 2006).…”