Abstract: Advancement in proteome analytical techniques and the development of protein databases have been helping to understand the physiology and subtle molecular mechanisms behind biofilm formation in bacteria. This review is to highlight how the evolving proteomic approaches have revealed fundamental molecular processes underlying the formation and regulation of bacterial biofilms. Based on the survey of research reports available on differential expression of proteins in biofilms of bacterial from wide range of environments, four important cellular processes viz. metabolism, motility, transport and stress response that contribute to formation of bacterial biofilms are discussed. This review might answer how proteins related to these cellular processes contribute significantly in stabilizing biofilms of different bacteria in diverse environmental conditions. Graphical Abstract: [Figure not available: see fulltext.]. © 2018, Springer Nature B.V.

Rani C

Department of Electrical Engineering

School of Electrical Engineering

Vellore Campus

Babu S

Department of Biotechnology

School of Bio Sciences and Technology

Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

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VIT University

World Journal of Microbiology and Biotechnology

Pseudomonas aeruginosa is a pathogenic biofilm forming bacteria which exist in wide range of environments such as water, soil and human body. In an earlier study, we used a system biology approach based analysis of biofilm forming genes of P. aeruginosa and their possible role in TiO2 nanoparticle binding. The major protein of P. aeruginosa targeted by TiO2 was found to be KatA, a major catalase required for H2O2 resistance and acute virulence and the direct interacting protein partners of KatA were found to be DnaK, Hfq, RpoA and RpoS. To understand the protein-protein physical interaction characteristic of these key proteins involved in biofilm related processes, homology modeling, docking and molecular dynamic simulation were performed. For all these proteins, physical and chemical properties, amino acid composition, nest and cleft analysis were performed using online tools. The interactions between TiO2NPs-KatA and four protein-protein complexes such as KatA-DnaK, KatA-Hfq, KatA-RpoA and KatA-RpoS were studied. Our results indicate that all four key proteins and TiO2NPs can have stable complexation with KatA. The study has given enough clues to understand the interaction of TiO2NPs with P. aeruginosa biofilm in natural environment. Further investigations could lead to development of TiO2NPs based therapeutic and sanitary interventions to combat this pathogenic bacterium.

Journal of Theoretical Biology

Insights into the interaction of key biofilm proteins in Pseudomonas aeruginosa PAO1 with TiO2 nanoparticle: An in silico analysis

A systems biology approach was used to study all the biofilm related genes of P. aeruginosa PAO1, and the interaction of titanium dioxide (TiO2) anatase with biofilm related proteins. Among the 71 genes, the interactions of all the nodal pairs were extracted by STRING 10.5 database. The inter-relationship among these genes was predicted by constructing complete PPI network and visualized in Cytoscape v 3.4.0. Total number of nodes of the network was found to be 335 and edges were 795. The network was further investigated for its clusters and the best cluster was further analyzed for the hub proteins which significantly contribute in cross-regulation of the biofilm related process. The hub proteins were identified based on four topological parameters of degree, closeness, betweeness and radiality. Four major hub proteins of P. aeruginosa PAO1 were identified to be algD, gacS, rpoS and rpoN which were common in all the hubs. Further, we have also elucidated the probable mechanism of TiO2 interaction with P. aeruginosa PAO1 at molecular level. Using STITCH server, the major target gene of TiO2 was identified as katA which also appeared commonly in our main dataset and this gene has been focused for the further study because of its unique common appearance in gene–gene network as well as gene-anatase network. The direct interacting partners of katA were found to be dnaK, hfq, rpoS and rpoA. Based on these findings and available gene regulatory information, probable TiO2 interacting cascade has been represented. This in silico study of P. aeruginosa PAO1 biofilm genes and the interaction of protein products with TiO2 might be significant to understand the perspective pathogenic resistance as well as the toxicity research pertaining to nanoparticles. © 2018 Elsevier B.V.

Gene

Cross-regulatory network in Pseudomonas aeruginosa biofilm genes and TiO 2 anatase induced molecular perturbations in key proteins unraveled by a systems biology approach

Metagenomic analysis of biofilm forming bacteria in environmental samples remains challenging due to the non-availability of gene sequences of most of the uncultivable bacteria. Sequences of Pseudomonas aeruginosa PAO1-UW genes involved either directly or indirectly in biofilm formation were analyzed using BLASTn to obtain matching sequences from different strain, species and genus. Conserved regions in the functional domain of the amino acid sequences were used to design common primers for direct PCR analysis of freshwater metagenomes. Seven key genes such as aceA, clpP, typA, cbrA, phoR, rpoS and gacA involved in biofilm formation were validated. The ortholog genes belonged to wide range of Pseudomonas sp. indicating the diversity of biofilm genes and the conservation of protein functional domains. The approach would also help in analyzing the expression of biofilm genes in different bacteria of freshwater systems for monitoring toxic contaminations such as organic or inorganic pollutants. © 2017 Elsevier Inc.

Fulltext

Genomics

Gene-centric metegenome analysis reveals diversity of Pseudomonas aeruginosa biofilm gene orthologs in fresh water ecosystem

International Journal of Food Microbiology

Corrigendum to “Proteomic and genetics insights on the response of the bacteriocinogenic Lactobacillus sakei CRL1862 during biofilm formation on stainless steel surface at 10 °C” [Int. J. Food Microbiol. 258 (2017), 18–27]

Biotechnology for Biofuels

Meta-proteomic analysis of protein expression distinctive to electricity-generating biofilm communities in air-cathode microbial fuel cells

Microorganisms

Comparing the Recombinant Protein Production Potential of Planktonic and Biofilm Cells

Environmental proteomic studies: closer step to understand bacterial biofilms

Journal	Data powered by TypesetWorld Journal of Microbiology and Biotechnology
Publisher	Data powered by TypesetSpringer Science and Business Media LLC
ISSN	0959-3993
Open Access	No