Gene expression analysis of monospecies Salmonella Typhimurium biofilms using Differential Fluorescence Induction

Hermans, Kim; Nguyen, Tran; Roberfroid, Stefanie; Schoofs, Geert; Verhoeven, Tine; Coster, David De; Vanderleyden, Jos; Keersmaecker, Sigrid C. J. De

doi:10.1016/j.mimet.2011.01.012

Cited by 17 publications

(22 citation statements)

References 74 publications

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“…The expression levels of csgB and csgD in TSB increased markedly by days 5 and 7 of incubation, in keeping with the development of a mature biofilm. However, csgB and csgD of biofilm cells grown in MTLB showed higher expression at 3 days incubation than that at 7 days, the finding was also observed in another RTqPCR analysis (Hermans et al, 2011). The gene csgD regulates the multi-cellular behavior of Salmonella cells, since csgD regulated the synthesis of curli and cellulose by a complex regulatory network, involving motility, cell aggregation, virulence, survival and biofilm formation (Jonas et al, 2007;White et al, 2010).…”

Section: Discussionsupporting

confidence: 61%

Effect of growth media on gene expression levels in Salmonella Typhimurium biofilm formed on stainless steel surface

et al. 2016

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Section: Discussionsupporting

confidence: 61%

Effect of growth media on gene expression levels in Salmonella Typhimurium biofilm formed on stainless steel surface

et al. 2016

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“…Furthermore, the local microenvironment that results from being embedded in a self-produced matrix would result in the induction of numerous pathways associated with stress tolerance and nutrient scavenging. In addition to this hypothesis, we also identified S. Typhimurium genes involved in surface and transport properties to be up-regulated during biofilm growth (Hermans et al, 2011). Together, this suggests that homeostasis of the extracellular matrix is an important property during biofilm formation.…”

Section: Biofilm Formation Coincides With a Global Metabolic Shiftsupporting

confidence: 54%

“…Since RpoS is also an important regulator of Salmonella biofilm formation (see previous section), a potential link between Salmonella biofilm formation and the cpx system seems reasonable. Interestingly and further confirming this link, in a recent study using the differential fluorescence induction (DFI) single cell approach to study S. Typhimurium biofilm formation we identified cpxP, the alkaline-induced periplasmic chaperone that inhibits the CpxA autokinase function (Danese & Silhavy, 1998), as being up-regulated under Salmonella biofilm formation conditions (Hermans et al, 2011).…”

Section: Complex Regulation Of Csgd Expression By Trans (Ompr Ihf Hmentioning

confidence: 54%

“…We, however, recently noticed that polyamine uptake and biosynthesis mutants have altered biofilm formation (Hermans et al, unpublished results). In addition, we also identified genes encoding an ABC transporter involved in putrescine uptake (potFGHI) to be upregulated under S. Typhimurium biofilm conditions (Hermans et al, 2011). As the CsgD regulon did not reveal any gene targets linked to global carbon flux and relatively few related to stress resistance, the authors hypothesized that the primary role of CsgD is to control the aggregation process, while the induction of gluconeogenesis is a consequence of the metabolic demand of polysaccharide production at the onset of biofilm formation, rather than elaboration of a defined genetic program.…”

Section: Biofilm Formation Coincides With a Global Metabolic Shiftmentioning

confidence: 99%

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Salmonella biofilms: An overview on occurrence, structure, regulation and eradication

Steenackers

Hermans

Vanderleyden

et al. 2012

Food Research International

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462

341

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“…Overall, the sequences of the clones characterized in this study reveal that SIGEX is capable of recovering genes that are functionally related to the chemical used for their induction. While the literature has focused on the high-throughput nature of FCM and its ability to rapidly analyze millions of clones (14,15), another substantial advantage, i.e., single-cell analysis of gene expression (34,49), has often been overlooked. Single-cell analysis improves the detection of differences between populations having unusual distributions of gene expression.…”

Section: Discussionmentioning

confidence: 99%

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil

Meier

Paterson

Lambert

2016

Appl Environ Microbiol

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Metagenomics allows the study of genes related to xenobiotic degradation in a culture-independent manner, but many of these studies are limited by the lack of genomic context for metagenomic sequences. This study combined a phenotypic screen known as substrate-induced gene expression (SIGEX) with whole-metagenome shotgun sequencing. SIGEX is a high-throughput promoter-trap method that relies on transcriptional activation of a green fluorescent protein (GFP) reporter gene in response to an inducing compound and subsequent fluorescence-activated cell sorting to isolate individual inducible clones from a metagenomic DNA library. We describe a SIGEX procedure with improved library construction from fragmented metagenomic DNA and improved flow cytometry sorting procedures. We used SIGEX to interrogate an aromatic hydrocarbon (AH)-contaminated soil metagenome. The recovered clones contained sequences with various degrees of similarity to genes (or partial genes) involved in aromatic metabolism, for example, nahG (salicylate oxygenase) family genes and their respective upstream nahR regulators. To obtain a broader context for the recovered fragments, clones were mapped to contigs derived from de novo assembly of shotgun-sequenced metagenomic DNA which, in most cases, contained complete operons involved in aromatic metabolism, providing greater insight into the origin of the metagenomic fragments. A comparable set of contigs was generated using a significantly less computationally intensive procedure in which assembly of shotgun-sequenced metagenomic DNA was directed by the SIGEX-recovered sequences. This methodology may have broad applicability in identifying biologically relevant subsets of metagenomes (including both novel and known sequences) that can be targeted computationally by in silico assembly and prediction tools.T he massive influx of novel sequence data derived from nextgeneration sequencing (NGS) technologies, in the context of both individual genomes (1) and metagenomes (2, 3), has far outstripped efforts to link those sequences to specific organisms and biological functions (4). Techniques such as quantitative PCR (qPCR) (5), microarrays (6), clone libraries (7), and stable-isotope probing (8) have been used successfully to identify organisms potentially involved in biodegradation. Substrate-induced gene expression (SIGEX) was proposed as a method for uncovering novel catabolic operons from metagenomes (9-12). SIGEX is a promoter trap method based on single-cell sorting of clones from a plasmid library using flow cytometry (FCM), where metagenomic clones of interest are identified by the increased expression of a downstream fluorescent reporter gene in the presence, but not in the absence, of an inducing compound. SIGEX was initially perceived as having great potential for mining genes from metagenomic samples in a high-throughput manner, without requiring prior knowledge of the sequences being screened for (13-15). However, SIGEX, and metagenomic promoter traps in general, has not lived up to this pote...

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Gene expression analysis of monospecies Salmonella Typhimurium biofilms using Differential Fluorescence Induction

Cited by 17 publications

References 74 publications

Effect of growth media on gene expression levels in Salmonella Typhimurium biofilm formed on stainless steel surface

Effect of growth media on gene expression levels in Salmonella Typhimurium biofilm formed on stainless steel surface

Salmonella biofilms: An overview on occurrence, structure, regulation and eradication

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil

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