Sodium Lactate Negatively Regulates Shewanella putrefaciens CN32 Biofilm Formation via a Three-Component Regulatory System (LrbS-LrbA-LrbR)

Screening and functional characterization of isocitrate lyase AceA in the biofilm formation of Vibrio alginolyticus

Biofilm is a well-known sessile lifestyle for bacterial pathogens, but a little is known about the mechanism on biofilm formation in Vibrio alginolyticus. In this study, we screened V. alginolyticus strains with strong biofilm formation ability from coastal seawater. The antibiotic resistance of the biofilm cells (BFs) was higher than that of the planktonic cells (PTs). To study the genes and pathways involved in biofilm formation, we performed transcriptome analysis of the BFs and PTs of V. alginolyticus R9. A total of 685 differentially expressed genes (DEGs) were upregulated, and 517 DEGs were downregulated in the BFs. The upregulated DEGs were significantly enriched in several pathways including glyoxylate and dicarboxylate metabolism, while the downregulated genes were significantly enriched in the flagellar assembly pathways. The key gene involved in glyoxylate shunt, aceA, was cloned, and ΔaceA mutant was constructed to determine the function of AceA in carbon source utilization, biofilm formation, and virulence. Real-time reverse transcription PCR showed that the expression of aceA was higher at the mature stage but lower at the disperse stage of biofilm formation, and the expression of the flagellar related genes was upregulated in ΔaceA. This is the first study to illustrate the global gene expression profile during the biofilm formation of V. alginolyticus, and isocitrate lyase AceA, the key enzyme involved in glyoxylate shunt, was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the late stage.IMPORTANCEBiofilms pose serious public problems, not only protecting the cells in it from environmental hazard but also affecting the composition and abundance of bacteria, algae, fungi, and protozoa. The important opportunistic pathogen Vibrio alginolyticus is extremely ubiquitously present in seawater, and it also exhibited a strong ability to form biofilm; thus, investigation on the biofilm formation of V. alginolyticus at molecular level is fundamental for the deeper exploration of the environmental concerns arose by biofilm. In this study, transcriptome analysis of biofilm cells (BFs) and planktonic cells (PTs) from V. alginolyticus was performed and AceA was screened to play an important role in biofilm formation. AceA was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the disperse stage. This method was helpful to further understand the ability and mechanism of V. alginolyticus biofilm formation and provide clues for prevention of V. alginolyticus infection.

The global regulation of c-di-GMP and cAMP in bacteria

Nucleotide second messengers are highly versatile signaling molecules that regulate a variety of key biological processes in bacteria. The best-studied examples are cyclic AMP (cAMP) and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), which both act as global regulators. Global regulatory frameworks of c-di-GMP and cAMP in bacteria show several parallels but also significant variances. In this review, we illustrate the global regulatory models of the two nucleotide second messengers, compare the different regulatory frameworks between c-di-GMP and cAMP, and discuss the mechanisms and physiological significance of cross-regulation between c-di-GMP and cAMP. c-di-GMP responds to numerous signals dependent on a great number of metabolic enzymes, and it regulates various signal transduction pathways through its huge number of effectors with varying activities. In contrast, due to the limited quantity, the cAMP metabolic enzymes and its major effector are regulated at different levels by diverse signals. cAMP performs its global regulatory function primarily by controlling the transcription of a large number of genes via cAMP receptor protein (CRP) in most bacteria. This review can help us understand how bacteria use the two typical nucleotide second messengers to effectively coordinate and integrate various physiological processes, providing theoretical guidelines for future research.

Regulating bacterial biofilms in food and biomedicine: unraveling mechanisms and Innovating strategies

Bacterial biofilm has brought a lot of intractable problems in food and biomedicine areas. Conventional biofilm control mainly focuses on inactivation and removal of biofilm. However, with robust construction and enhanced resistance, the established biofilm is extremely difficult to eradicate. According to the mechanism of biofilm development, biofilm formation can be modulated by intervening in the key factors and regulatory systems. Therefore, regulation of biofilm formation has been proposed as an alternative way for effective biofilm control. This review aims to provide insights into the regulation of biofilm formation in food and biomedicine. The underlying mechanisms for early-stage biofilm establishment are summarized based on the key factors and correlated regulatory networks. Recent developments and applications of novel regulatory strategies such as anti/pro-biofilm agents, nanomaterials, functionalized surface materials and physical strategies are also discussed. The current review indicates that these innovative methods have contributed to effective biofilm control in a smart, safe and eco-friendly way. However, standard methodology for regulating biofilm formation in practical use is still missing. As biofilm formation in real-world systems could be far more complicated, further studies and interdisciplinary collaboration are still needed for simulation and experiments in the industry and other open systems.

Temporal Hierarchy and Context-Dependence of Quorum Sensing Signal in Pseudomonas aeruginosa

The Gram-negative bacterium Pseudomonas aeruginosa can cause infections in a broad range of hosts including plants, invertebrates and mammals and is an important source of nosocomial infections in humans. We were interested in how differences in the bacteria's nutritional environment impact bacterial communication and virulence factor production. We grew P. aeruginosa in 96 different conditions in BIOLOG Gen III plates and assayed quorum sensing (QS) signaling over the course of growth. We also quantified pyocyanin and biofilm production and the impact of sub-inhibitory exposure to tobramycin. We found that while 3-oxo-C12 homoserine lactone remained the dominant QS signal to be produced, timing of PQS production differed between media types. Further, whether cells grew predominantly as biofilms or planktonic cells was highly context dependent. Our data suggest that understanding the impact of the nutritional environment on the bacterium can lead to valuable insights into the link between bacterial physiology and pathology.

What makes another life possible in bacteria? Global regulators as architects of bacterial biofilms

Biofilm structures are the main mode of evolutionary reproductive adaptation of bacteria, and even these features alone, are sufficient to make them the focus of genetic and physiological studies. As this life form is a multicellular-like life form coordinated by genetic and physiological programming, it is quite different from the planktonic form. In bacterial biofilms, which are often composed of more than one species in nature, there is a clear division of labor, nutrient channels, and a language (signaling) established between the cells forming the biofilm. On the other hand, biofilms, especially formed by pathogens, cause important industrial and clinical problems due to their high resistance to environmental stress conditions. Obtaining new data on the molecular basis of bacterial evolution and understanding the intra- and inter-species ecosystem relations in this context, as well as finding permanent solutions to the serious problems they create, are directly related to a detailed understanding of the genetic regulation of bacterial biofilm structures. Today, it is becoming increasingly certain that environmental signals effective in the transition from planktonic form to biofilm form and their receptor/response molecules are generally managed by similar systems and global regulator molecules in bacteria. In this sense; Besides the quorum sensing (QS) systems, cyclic adenosine monophosphate-catabolite suppressor protein (cAMP-CRP) and bis-(3'-5') cyclic dimeric guanosine monophosphate (c-di-GMP) signaling molecules are of critical importance. In this review article, current information on bacterial biofilms is summarized and interpreted based on this framework.

RclS Sensor Kinase Modulates Virulence of Pseudomonas capeferrum

Signal transduction systems are the key players of bacterial adaptation and survival. The orthodox two-component signal transduction systems perceive diverse environmental stimuli and their regulatory response leads to cellular changes. Although rarely described, the unorthodox three-component systems are also implemented in the regulation of major bacterial behavior such as the virulence of clinically relevant pathogen P. aeruginosa. Previously, we described a novel three-component system in P. capeferrum WCS358 (RclSAR) where the sensor kinase RclS stimulates the intI1 transcription in stationary growth phase. In this study, using rclS knock-out mutant, we identified RclSAR regulon in P. capeferrum WCS358. The RNA sequencing revealed that activity of RclSAR signal transduction system is growth phase dependent with more pronounced regulatory potential in early stages of growth. Transcriptional analysis emphasized the role of RclSAR in global regulation and indicated the involvement of this system in regulation of diverse cellular activities such as RNA binding and metabolic and biocontrol processes. Importantly, phenotypic comparison of WCS358 wild type and ΔrclS mutant showed that RclS sensor kinase contributes to modulation of antibiotic resistance, production of AHLs and siderophore as well as host cell adherence and cytotoxicity. Finally, we proposed the improved model of interplay between RclSAR, RpoS and LasIR regulatory systems in P. capeferrum WCS358.

Inhibition of citral nanoemulsion to growth, spoilage ability and AI-2/luxS quorum sensing system of Shewanella putrefaciens CN-32: A study on bacteriostasis from in vitro culture and gene expression analysis

Objectives

The bacteriostatic effects of a citral nanoemulsion against Shewanella putrefaciens CN-32 (SHP CN-32) were investigated using in vitro culture and gene expression analysis, for building a potential application in spoilage microorganism control and aquatic products quality maintenance.

Materials and Methods

The SHP CN-32 was treated by prepared citral nanoemulsion when the minimal inhibitory concentration (MIC) was verified. The growth curve, membrane integrity, scanning electron microscope (SEM) observation, biofilm formation and quorum sensing (QS) signaling molecule AI-2 content were evaluated in different MIC treatment groups (0 MIC to 1.00 MIC). The gene expression status of SHP CN-32 in 0 MIC group and 0.50 MIC group were compared using transcriptome sequencing and quantitative PCR.

Results

The in vitro culture revealed that the citral nanoemulsion could inhibit the growth of SHP CN-32 with MIC of about 200 μg/ml. Images from membrane integrity, SEM and biofilm formation suggested significant biological structure damage in bacteria after treatment. Meanwhile, the quorum sensing (QS) signaling molecule AI-2 content showed a decline following the rise of treatment concentration. Transcriptome sequencing and quantitative PCR revealed that the majority genes related diversified functional metabolic pathways of SHP CN-32 were down-regulated at varying degree.

Conclusion

A significant bacteriostasis of citral nanoemulsion against Shewanella putrefaciens CN-32 (SHP CN-32) were verified via the results of growth inhibition, structural destruction, signal molecular decrease and gene expression down-regulation of strains. These synergies significantly affect the characteristic expression of SHP CN-32, revealing the application potential as bacteriostat, QS inhibitor and preservative in aquatic products.

Fnr Negatively Regulates Prodigiosin Synthesis in Serratia sp. ATCC 39006 During Aerobic Fermentation

The well-known Crp/Fnr family regulator Fnr has long been recognized as an oxygen sensor to regulate multiple biological processes, including the switch between aerobic/anaerobic metabolism, nitrogen fixation, bioluminescence, infection, and virulence. In most cases, Fnr was found to be active under anaerobic conditions. However, its role in aerobic antibiotic metabolism has not yet been revealed. In this research, we report that in the model organism, Serratia sp. ATCC 39006, Fnr (Ser39006_013370) negatively regulates prodigiosin production by binding to the spacer between the −10 and −35 region in the promoter of prodigiosin biosynthetic gene cluster under aerobic conditions. Fnr was also shown to modulate the anti-bacterial activity and motility by regulating pathway-specific regulatory genes, indicating that Fnr acts as a global regulator in Serratia sp. ATCC 39006. For the first time, we describe that Fnr regulates antibiotic synthesis in the presence of oxygen, which expands the known physiological functions of Fnr and benefits the further investigation of this important transcriptional regulator.

L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation

L-arabinose inducible promoters are commonly used in gene expression analysis. However, nutrient source and availability also play a role in biofilm formation; therefore, L-arabinose metabolism could impact biofilm development. In this study we examined the impact of L-arabinose on Salmonella enterica serovar Typhimurium (S. Typhimurium) biofilm formation. Using mutants impaired for the transport and metabolism of L-arabinose, we showed that L-arabinose metabolism negatively impacts S. Typhimurium biofilm formation in vitro. When L-arabinose metabolism is abrogated, biofilm formation returned to baseline levels. However, without the ability to import extracellular L-arabinose, biofilm formation significantly increased. Using RNA-Seq we identified several gene families involved in these different phenotypes including curli expression, amino acid synthesis, and L-arabinose metabolism. Several individual candidate genes were tested for their involvement in the L-arabinose-mediated biofilm phenotypes, but most played no significant role. Interestingly, in the presence of L-arabinose the diguanylate cyclase gene adrA was downregulated in wild type S. Typhimurium. Meanwhile cyaA, encoding an adenylate cyclase, was downregulated in an L-arabinose transport mutant. Using an IPTG-inducible plasmid to deplete c-di-GMP via vieA expression, we were able to abolish the increased biofilm phenotype seen in the transport mutant. However, the mechanism by which the L-arabinose import mutant forms significantly larger biofilms remains to be determined. Regardless, these data suggest that L-arabinose metabolism influences intracellular c-di-GMP levels and therefore biofilm formation. These findings are important when considering the use of an L-arabinose inducible promoter in biofilm conditions.

Lactate-induced dispersal of Neisseria meningitidis microcolonies is mediated by changes in cell density and pilus retraction and is influenced by temperature change

Neisseria meningitidis is the etiologic agent of meningococcal meningitis and sepsis. Initial colonization of meningococci to the upper respiratory tract epithelium is crucial for disease development. The colonization occurs in several steps and expression of type IV pili (Tfp) is essential for both attachment and microcolony formation of encapsulated bacteria. Previously, we have shown that host-derived lactate induces synchronized dispersal of meningococcal microcolonies. In this study, we demonstrated that lactate-induced dispersal is dependent on bacterial concentration but not on the quorum sensing system autoinducer-2 or the two-component systems NarP/NarQ, PilR/PilS, NtrY/NtrX, and MisR/MisS. Further, there were no changes in expression of genes related to assembly, elongation, retraction, and modification of Tfp throughout the time course of lactate induction. By using pilT and pptB mutants, however, we found that lactate-induced dispersal was dependent on PilT-retraction but not on phosphoglycerol-modification of Tfp even though the PptB activity was important for preventing re-aggregation post-dispersal. Furthermore, protein synthesis was required for lactate-induced dispersal. Finally, we found that at a lower temperature, lactate-induced dispersal was delayed and unsynchronized, and bacteria reformed microcolonies. We conclude that lactate-induced microcolony dispersal is dependent on bacterial concentration, PilT-dependent Tfp retraction, and protein synthesis and influenced by environmental temperature.

The Cyclic AMP Receptor Protein, Crp, Is Required for the Decolorization of Acid Yellow 36 in Shewanella putrefaciens CN32

Shewanella shows good application potentials in the decolorization and detoxification of azo dye wastewater. However, the molecular mechanism of decolorization is still lacking. In this study, it was found that Shewanella putrefaciens CN32 exhibited good decolorization ability to various azo dyes, and a global regulatory protein cAMP receptor protein (Crp) was identified to be required for the decolorization of acid yellow 36 (AY) by constructing a transposon mutant library. Then, the molecular mechanism of AY decolorization regulated by Crp was further investigated. RT-qPCR and electrophoretic mobility shift assay (EMSA) results showed that Crp was able to directly bind to the promoter region of the cymA gene and promote its expression. Riboflavin acting as an electron shuttle could accelerate the AY decolorization efficiency of S. putrefaciens CN32 wild-type (WT) but did not show a promoting effect to Δcrp mutant and ΔcymA mutant, further confirming that Crp promotes the decolorization through regulating electron transport chains. Moreover, the mutant with cymA overexpression could slightly enhance the AY decolorization efficiency compared with the WT strain. In addition, it was found that MtrA, MtrB, and MtrC partially contribute to the electron transfer from CymA to dye molecules, and other main electron transport chains need to be identified in future experiments. This study revealed the molecular mechanism of a global regulator Crp regulating the decolorization of azo dye, which is helpful in understanding the relationship between the decolorization and other metabolic processes in S. putrefaciens CN32.

The Regulation of Bacterial Biofilm Formation by cAMP-CRP: A Mini-Review

Biofilms are communities of microorganisms that live in a self-produced extracellular matrix in order to survive in hostile environments. Second messengers, such as c-di-GMP and cAMP, participate in the regulation of biofilm formation. c-di-GMP is a major molecule that is involved in modulating the bacterial transition between a planktonic lifestyle and biofilm formation. Aside from regulating carbon catabolism repression in most bacteria, cAMP has also been found to mediate biofilm formation in many bacteria. Although the underlying mechanisms of biofilm formation mediated by cAMP-CRP have been well-investigated in several bacteria, the regulatory pathways of cAMP-CRP are still poorly understood compared to those of c-di-GMP. Moreover, some bacteria appear to form biofilm in response to changes in carbon source type or concentration. However, the relationship between the carbon metabolisms and biofilm formation remains unclear. This mini-review provides an overview of the cAMP-CRP-regulated pathways involved in biofilm formation in some bacteria. This information will benefit future investigations of the underlying mechanisms that connect between biofilm formation with nutrient metabolism, as well as the cross-regulation between multiple second messengers.

Two-Component Signal Transduction Systems: A Major Strategy for Connecting Input Stimuli to Biofilm Formation

Biofilms are multicellular communities of microbes that are encased within an extracellular matrix. Environmental factors induce bacteria to form biofilm. Bacteria have several regulatory mechanisms in response to environmental changes, and the two-component signal transduction system (TCS) is a major strategy in connecting changes in input signals to changes in cellular physiological output. The TCS employs multiple mechanisms such as cross-regulation, to integrate and coordinate various input stimuli to control biofilm formation. In this mini-review, we demonstrate the roles of TCS on biofilm formation, illustrating these input signals and modulation modes, which may be utilized by future investigations in elucidating the regulatory signals and underlying the mechanisms of biofilm formation.

Decolorization and detoxification of water-insoluble Sudan dye by Shewanella putrefaciens CN32 co-cultured with Bacillus circulans BWL1061

Effluents loaded with various synthetic dyes are considered as a huge burden to the surrounding ecosystems. Sudan dyes are relatively difficult to decolorize due to its water-insolubility. In the present study, the strain Shewanella putrefaciens CN32 was firstly applied to decolorize Sudan dyes under the anaerobic condition, and the physicochemical parameters on the decolorization were optimized. The results demonstrated that the suitable decolorization condition was temperature 26 °C, initial pH 7.0-8.0 and NaCl concentrations 0-20 g/L. Electron competitive acceptors including nitrite, nitrate, dimethyl sulphoxide and oxygen could cause the significant inhibition to the decolorization of Sudan dyes. Biosurfactant rhamnolipid played a positive role in enhancing the decolorization of Sudan I. The co-culture of S. putrefaciens CN32 and Bacillus circulans BWL1061 is reported for the first time to accelerate the decolorization through improving the synergistic effect of enzymatic degradation and biological reductive effect. The highest decolorization of 90.23% to Sudan I was achieved within 108 h, suggesting that co-culture technique has a good potential in the treatment of dyeing wastewater. Furthermore, the microbial toxicity tests indicated that the toxicity of Sudan I to Escherichia coli BL21 and Bacillus subtilis 168 was obviously decreased after the decolorization.