Decoding the proteomic changes involved in the biofilm formation of Enterococcus faecalis SK460 to elucidate potential biofilm determinants

Abstract

Background Enterococcus faecalis is a major clinically relevant nosocomial bacterial pathogen frequently isolated from polymicrobial infections. The biofilm forming ability of E. faecalis attributes a key role in its virulence and drug resistance. Biofilm cells are phenotypically and metabolically different from their planktonic counterparts and many aspects involved in E. faecalis biofilm formation are yet to be elucidated. The strain E. faecalis SK460 used in the present study is esp (Enterococcal surface protein) and fsr (two-component signal transduction system) negative non-gelatinase producing strong biofilm former isolated from a chronic diabetic foot ulcer patient. We executed a label-free quantitative proteomic approach to elucidate the differential protein expression pattern at planktonic and biofilm stages of SK460 to come up with potential determinants associated with Enterococcal biofilm formation. Results The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of proteomic data revealed that biofilm cells expressed higher levels of proteins which are associated with glycolysis, amino acid biosynthesis, biosynthesis of secondary metabolites, microbial metabolism in diverse environments and stress response factors. Besides these basic survival pathways, LuxS-mediated quorum sensing, arginine metabolism, rhamnose biosynthesis, pheromone and adhesion associated proteins were found to be upregulated during the biofilm transit from planktonic stages. The selected subsets were validated by quantitative real-time PCR. In silico functional interaction analysis revealed that the genes involved in upregulated pathways pose a close molecular interaction thereby coordinating the regulatory network to thrive as a biofilm community. Conclusions The present study describes the first report of the quantitative proteome analysis of an esp and fsr negative non gelatinase producing E. faecalis . Proteome analysis evidenced enhanced expression of glycolytic pathways, stress response factors, LuxS quorum signaling system, rhamnopolysaccharide synthesis and pheromone associated proteins in biofilm phenotype. We also pointed out the relevance of LuxS quorum sensing and pheromone associated proteins in the biofilm development of E. faecalis which lacks the Fsr quorum signaling system. These validated biofilm determinants can act as potential inhibiting targets in Enterococcal infections. Electronic supplementary material The online version of this article (10.1186/s12866-019-1527-2) contains supplementary material, which is available to authorized users.

Metabolic Shift of an Isogenic Strain of Enterococcus faecalis 14, Deficient in Its Own Bacteriocin Synthesis, as Revealed by a Transcriptomic Analysis

“…In this study, we provide a new insight and show that the bacteriocinogenic E. faecalis 14, genetically modified and thus deprived of its bacteriocin production, has increased its biofilm formation ability ( Figure 5 ). Interestingly, this form of cellular organization can enhance the bacterial persistence and resistance to environmental stress [ 39 , 40 , 41 ], which correlates with our own observations ( Figure 2 , lines 24–35). Moreover, the involvement of enzymes such as NADH peroxidase Npx, lactate dehydrogenase as well as the general stress protein Gls24, in the response to oxidative stress, has already been demonstrated in E. faecalis [ 42 , 43 , 44 ].…”

“…The lack of bacteriocin and enhancement of other putative virulence mechanisms caused this strain to undergo metabolic reorganization. In this respect, different mechanisms have been described in bacteria to explain the relationship between biofilm formation and the metabolic reprogramming [ 41 , 48 , 49 ]. This would probably explain the elevated in vitro growth rate observed in the Δ bac mutant, which is accompanied by overexpression of genes involved in the glycolysis, tagatose, glycerol, and arginine pathways ( Figure 2 , lines 36–57).…”

Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum

“…Agmatinase (SpeB) was found in 75.8% of DPANN genomes, and ornithine decarboxylase (SpeC) was detected in 31.7% of Woesearchaeota , 20.0% of Aenigmarchaeota , 19.0% of Nanoarchaeota , and 16.9% of Pacearchaeota . Arginine deiminase (ArcA, the key enzyme of the arginine deiminase pathway), which produces ammonia as a by-product of acid stress resistance ( 68 , 69 ), was found in 28.6% of Micrarchaeota . In addition, ∼56.6% of Micrarchaeota and ∼63.2% of Parvarchaeota possessed the ability to produce spermidine and spermine from agmatine.…”

Quorum Sensing System-Regulated Proteins Affect the Spoilage Potential of Co-cultured Acinetobacter johnsonii and Pseudomonas fluorescens From Spoiled Bigeye Tuna (Thunnus obesus) as Determined by Proteomic Analysis

“…A label-free quantitative proteomic approach has been applied to analyze the differential protein expression of Enterococcus faecalis SK460 to determine potential factors related to enterococcal biofilm formation. The results of this study showed that the related protein in the relevance of LuxS QS and pheromone in the biofilm development of E. faecalis was due to the Fsr being lacking in QS (Suryaletha et al, 2019). Based on proteomic analysis, a total of 338 vesicular proteins of Pseudomonas aeruginosa were identified with high confidence by LC-MS/MS analysis.…”