Comparing the Recombinant Protein Production Potential of Planktonic and Biofilm Cells

Engineering Escherichia coli Biofilms for Curcumin Production

Biofilms are emerging platforms for the production of valuable compounds. The present study is the first to assess the capacity of Escherichia coli biofilms to produce curcumin through the expression of a biosynthetic pathway involving three genes: 4-coumarate-CoA ligase (4CL), diketide-CoA synthase (DCS), and curcumin synthase (CURS). The effects of chemical induction with isopropyl β-d-1-thiogalactopyranoside (IPTG) and ferulic acid (FA), and the incubation temperature on biofilm formation and curcumin production were evaluated. Biofilms were formed in 12-well microtiter plates over three days and then induced with 1 mM IPTG and FA at 2 or 8 mM. After induction, the samples were incubated for two days at 26 or 30 °C. Total and culturable planktonic and biofilm cells, as well as biofilm thickness and volumetric and specific curcumin production, were assessed on days 3, 4, and 5. The results demonstrated that biofilms produced up to 10-fold higher curcumin levels (0.9-2.2 fg·cell-1) than their planktonic counterparts (0.1-0.3 fg·cell-1). The highest specific curcumin production (2.2 fg·cell-1) was achieved using 8 mM FA. However, no significant differences in curcumin production were observed between the induced samples incubated at the tested temperatures. These results validated the potential of biofilm systems for expressing a complete exogenous biosynthetic pathway using metabolic engineering, particularly for curcumin production.

The enhanced expression of genes encoding diguanylate cyclases under cold stress contributes to the adhesion and biofilm formation of Shewanella putrefaciens WS13

Shewanella putrefaciens is a special spoilage bacterium of seafood during cold storage, which is easy to form biofilm and bring serious hazard to the seafood quality. Life cycle of biofilm starts after bacterial adhesion, which is essential for the formation and development of biofilm. As a ubiquitous second messenger in bacteria, c-di-GMP regulates the conversion between bacterial planktonic state and biofilm state. In this study, the adhesion and biofilm formation of S. putrefaciens WS13 under 4°C were compared to those under 30°C. Atom force microscope and scanning electron microscope were used to study the bacterial adhesion. Biofilm was analyzed by Fourier transform infrared spectroscopy, Bradford assay and phenol-sulfuric acid method. High-performance liquid chromatographic-tandem mass spectrometric and quantitative real-time PCR were applied to study c-di-GMP level and genes encoding diguanylate cyclases in cells, respectively. Results showed that the swarming mobility of S. putrefaciens WS13 was weaker under 4°C, however, the adhesive force under 4°C was 4–5 times higher than that under 30°C. Biofilm biomass, extracellular polysaccharides and extracellular proteins were 2.5 times, 3 times, and 1.6 times more than those under 30°C, respectively, but biofilm composition formed under both temperatures were similar. c-di-GMP level in S. putrefaciens WS13 under 30°C was no more than half of that in the corresponding growth stage under 4°C. Quantitative real-time PCR analysis also showed that the expression of genes encoding diguanylate cyclases were significantly enhanced under 4°C than that under 30°C. S. putrefaciens WS13 adapted to the cold stress by enhancing the expression of genes encoding diguanylate cyclases to promote bacterial adhesion and biofilm formation. This study provides a theoretical foundation for the research on the cold adaptation mechanism of specific spoilage bacteria of seafood based on c-di-GMP, and also provides a new idea to control seafood quality from the perspective of microbial molecular biology.

Advances on Bacterial and Fungal Biofilms for the Production of Added-Value Compounds

Simple Summary

The production of bio-based materials, including organic acids, antibiotics, enzymes, ethanol, and hydrogen, is generally done by the cultivation of suspended cells rather than using immobilized cells. However, several studies suggest the application of productive biofilms as a reliable alternative for biocatalysis, with many advantages over suspended-growth systems. This review gives an overview of the breakthrough in the application of biofilm platforms for the sustainable production of valuable compounds, with particular insight into the latest advances in the production of recombinant proteins. Productive biofilms are shown to improve production rates and product yields, demonstrating great potential for industrial applications.

Abstract

In recent years, abundant research has been performed on biofilms for the production of compounds with biotechnological and industrial relevance. The use of biofilm platforms has been seen as a compelling approach to producing fine and bulk chemicals such as organic acids, alcohols, and solvents. However, the production of recombinant proteins using this system is still scarce. Biofilm reactors are known to have higher biomass density, operational stability, and potential for long-term operation than suspended cell reactors. In addition, there is an increasing demand to harness industrial and agricultural wastes and biorefinery residues to improve process sustainability and reduce production costs. The synthesis of recombinant proteins and other high-value compounds is mainly achieved using suspended cultures of bacteria, yeasts, and fungi. This review discusses the use of biofilm reactors for the production of recombinant proteins and other added-value compounds using bacteria and fungi.

The Influence of Nutrient Medium Composition on Escherichia coli Biofilm Development and Heterologous Protein Expression

In the present study, the effects of different nutrient media on the development of Escherichia coli biofilms and the production of a heterologous protein were examined. E. coli JM109(DE3) cells transformed with pFM23 plasmid carrying the gene for enhanced green fluorescent protein (eGFP) expression were used. Cells were grown in two different culture media, Lysogenic Broth (LB) and M9ZB, in a flow cell system for 10 days. Epifluorescence microscopy, fluorimetry, and a high-performance liquid chromatography (HPLC) method based on hydrophobic interaction chromatography (HIC) were used to assess bacterial growth, plasmid copy number (PCN), and eGFP production in both planktonic and biofilm cells. The results showed that biofilm development was favored in M9ZB medium when compared with LB. However, the number of eGFP-expressing cells was higher in LB for both planktonic and sessile states (two-fold and seven-fold, respectively). In addition, the PCN in biofilm cells was slightly higher when using LB medium (on average, 29 plasmids per cell versus 20 plasmids per cell in M9ZB), and higher plasmid stability was observed in biofilms formed in LB compared to their planktonic counterparts. Hence, E. coli biofilms grown in LB enhanced both plasmid stability and capacity to produce the model heterologous protein when compared to M9ZB.

Assessing the Biofilm Formation Capacity of the Wine Spoilage Yeast Brettanomyces bruxellensis through FTIR Spectroscopy

Brettanomyces bruxellensis is a wine spoilage yeast known to colonize and persist in production cellars. However, knowledge on the biofilm formation capacity of B. bruxellensis remains limited. The present study investigated the biofilm formation of 11 B. bruxellensis strains on stainless steel coupons after 3 h of incubation in an aqueous solution. FTIR analysis was performed for both planktonic and attached cells, while comparison of the obtained spectra revealed chemical groups implicated in the biofilm formation process. The increased region corresponding to polysaccharides and lipids clearly discriminated the obtained spectra, while the absorption peaks at the specific wavenumbers possibly reveal the presence of β-glucans, mannas and ergosterol. Unsupervised clustering and supervised classification were employed to identify the important wavenumbers of the whole spectra. The fact that all the metabolic fingerprints of the attached versus the planktonic cells were similar within the same cell phenotype class and different between the two phenotypes, implies a clear separation of the cell phenotype; supported by the results of the developed classification model. This study represents the first to succeed at applying a non-invasive technique to reveal the metabolic fingerprint implicated in the biofilm formation capacity of B. bruxellensis, underlying the homogenous mechanism within the yeast species.

Analysing the Initial Bacterial Adhesion to Evaluate the Performance of Antifouling Surfaces

The aim of this work was to study the initial events of Escherichia coli adhesion to polydimethylsiloxane, which is critical for the development of antifouling surfaces. A parallel plate flow cell was used to perform the initial adhesion experiments under controlled hydrodynamic conditions (shear rates ranging between 8 and 100/s), mimicking biomedical scenarios. Initial adhesion studies capture more accurately the cell-surface interactions as in later stages, incoming cells may interact with the surface but also with already adhered cells. Adhesion rates were calculated and results shown that after some time (between 5 and 9 min), these rates decreased (by 55% on average), from the initial values for all tested conditions. The common explanation for this decrease is the occurrence of hydrodynamic blocking, where the area behind each adhered cell is screened from incoming cells. This was investigated using a pair correlation map from which two-dimensional histograms showing the density probability function were constructed. The results highlighted a lower density probability (below 4.0 × 10⁻⁴) of the presence of cells around a given cell under different shear rates irrespectively of the radial direction. A shadowing area behind the already adhered cells was not observed, indicating that hydrodynamic blocking was not occurring and therefore it could not be the cause for the decreases in cell adhesion rates. Afterward, cell transport rates from the bulk solution to the surface were estimated using the Smoluchowski-Levich approximation and values in the range of 80–170 cells/cm².s were obtained. The drag forces that adhered cells have to withstand were also estimated and values in the range of 3–50 × 10⁻¹⁴ N were determined. Although mass transport increases with the flow rate, drag forces also increase and the relative importance of these factors may change in different conditions. This work demonstrates that adjustment of operational parameters in initial adhesion experiments may be required to avoid hydrodynamic blocking, in order to obtain reliable data about cell-surface interactions that can be used in the development of more efficient antifouling surfaces.

Special Issue: Recombinant Protein Expression in Microorganisms

Microorganisms are widely used in industrial biotechnology as cell factories for the sustainable production of a wide range of compounds and chemicals [...].

Recombinant protein expression in biofilms

Biofilm research is usually focused on the prevention or control of biofilm formation. Recently, the significance of the biofilm mode of growth in biotechnological applications received increased attention. Since biofilm reactors show many advantages over suspended cell reactors, especially in their higher biomass density and operational stability, bacterial biofilms have emerged as an interesting approach for the expression of specific proteins. Despite the potential of biofilm systems, recombinant protein production using biofilms has been scarcely investigated for the past 25 years. Our group has demonstrated that E. coli biofilms were able to produce a model recombinant protein, the enhanced green fluorescent protein (eGFP), at much higher levels than their planktonic counterparts. Even without optimization of cultivation conditions, an attractive productivity was obtained, indicating that biofilm cultures can be used as an alternative form of high cell density cultivation (HCDC). E. coli remains one of the favorite hosts for recombinant protein production and it has been successfully used in metabolic engineering for the synthesis of high value products. This review presents the advantages and concerns of using biofilms for the production of recombinant proteins and summarizes the different biofilm systems which have been described for this purpose. The relative advantages and disadvantages of the four microbial hosts tested for recombinant protein production in biofilms (two bacteria and two filamentous fungi) are also discussed.

Environmental proteomic studies: closer step to understand bacterial biofilms

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.