ScmR, a Global Regulator of Gene Expression, Quorum Sensing, pH Homeostasis, and Virulence in Burkholderia thailandensis

Repurposing promethazine hydrochloride to inhibit biofilm formation against Burkholderia thailandensis

Melioidosis is a severe infectious disease caused by Burkholderia pseudomallei, an intracellular pathogen with a high mortality rate and significant antibiotic resistance. The high mortality rate and resistance to antibiotics have drawn considerable attention from researchers studying melioidosis. This study evaluated the effects of various concentrations (75, 50, and 25 µg/mL) of promethazine hydrochloride (PTZ), a potent antihistamine, on biofilm formation and lipase activity after 24 h of exposure to B. thailandensis E264. A concentration-dependent decrease in both biofilm biomass and lipase activity was observed. RT-PCR analysis revealed that PTZ treatment not only made the biofilm structure loose but also reduced the expression of btaR1, btaR2, btaR3, and scmR. Single gene knockouts of quorum sensing (QS) receptor proteins (∆btaR1, ∆btaR2, and ∆btaR3) were successfully constructed. Deletion of btaR1 affected biofilm formation in B. thailandensis, while deletion of btaR2 and btaR3 led to reduced lipase activity. Molecular docking and biological performance results demonstrated that PTZ inhibits biofilm formation and lipase activity by suppressing the expression of QS-regulated genes. This study found that repositioning PTZ reduced biofilm formation in B. thailandensis E264, suggesting a potential new approach for combating melioidosis.

Driving mechanism of different nutrient conditions on microbial mediated nitrate reduction in magnetite-present river infiltration zone

Significant research is focused on the ability of riparian zones to reduce groundwater nitrate contamination. Owing to the extremely high redox activity of nitrate, naturally existing electron donors, such as organic matter and iron minerals, are crucial in facilitating nitrate reduction in the riparian zone. Here, we examined the coexistence of magnetite, an iron mineral, and nitrate, a frequently observed coexisting system in sediments, to investigate nitrate reduction features at various C/N ratios and evaluate the response of microbial communities to these settings. Additionally, we aimed to use this information as a foundation for examining the effect of nutritional conditions on the nitrate reduction process in magnetite-present environments. These results emphasise the significance of organic matter in enabling dissimilatory nitrate reduction to ammonium (DNRA) and enhancing the connection between nitrate reduction and iron in sedimentary environments. In the later phases of nitrate reduction, nitrogen fixation was the prevailing process in low-carbon environments, whereas high-carbon environments tended to facilitate the breakdown of organic nitrogen. High-throughput sequencing analysis revealed a robust association between C/N ratios and alterations in microbial community composition, providing insights into notable modifications in essential functioning microorganisms. The nitrogen-fixing bacterium Ralstonia is more abundant in ecosystems with scarce organic matter. In contrast, in settings rich in organic matter, microorganisms, such as Acinetobacter and Clostridia, which may produce ammonia, play crucial roles. Moreover, the population of iron bacteria grows in such an environment. Hence, this study proposes that C/N ratios can influence Fe(II)/Fe(III) conversions and simultaneously affect the process of nitrate reduction by shaping the composition of specific microbial communities.

AHL-Based Quorum Sensing Regulates the Biosynthesis of a Variety of Bioactive Molecules in Bacteria

Bacteria are social microorganisms that use communication systems known as quorum sensing (QS) to regulate diverse cellular behaviors including the production of various secreted molecules. Bacterial secondary metabolites are widely studied for their bioactivities including antibiotic, antifungal, antiparasitic, and cytotoxic compounds. Besides playing a crucial role in natural bacterial niches and intermicrobial competition by targeting neighboring organisms and conferring survival advantages to the producer, these bioactive molecules may be of prime interest to develop new antimicrobials or anticancer therapies. This review focuses on bioactive compounds produced under acyl homoserine lactone-based QS regulation by Gram-negative bacteria that are pathogenic to humans and animals, including the Burkholderia, Serratia, Pseudomonas, Chromobacterium, and Pseudoalteromonas genera. The synthesis, regulation, chemical nature, biocidal effects, and potential applications of these identified toxic molecules are presented and discussed in light of their role in microbial interactions.

The dabABC operon is a marker of C4-alkylated monobactam biosynthesis and responsible for (2S,3R)-diaminobutyrate production

Non-ribosomal peptide synthetases (NRPSs) assemble metabolites of medicinal and commercial value. Both serine and threonine figure prominently in these processes and separately can be converted to the additional NRPS building blocks 2,3-diaminopropionate (Dap) and 2,3-diaminobutyrate (Dab). Here we bring extensive bioinformatics, in vivo and in vitro experimentation to compose a unified view of the biosynthesis of these widely distributed non-canonical amino acids that both derive by pyridoxal-mediated β-elimination of the activated O-phosphorylated substrates followed by β-addition of an amine donor. By examining monobactam biosynthesis in Pseudomonas and in Burkholderia species where it is silent, we show that (2S,3R)-Dab synthesis depends on an l-threonine kinase (DabA), a β-replacement reaction with l-aspartate (DabB) and an argininosuccinate lyase-like protein (DabC). The growing clinical importance of monobactams to both withstand Ambler Class B metallo-β-lactamases and retain their antibiotic activity make reprogrammed precursor and NRPS synthesis of modified monobactams a feasible and attractive goal.

Adaptive mechanism of the marine bacterium Pseudomonas sihuiensis-BFB-6S towards pCO2 variation: Insights into synthesis of extracellular polymeric substances and physiochemical modulation

Marine bacteria can adapt to various extreme environments by the production of extracellular polymeric substances (EPS). Throughout this investigation, impact of variable pCO2 levels on the metabolic activity and physiochemical modulation in EPS matrix of marine bacterium Pseudomonas sihuiensis - BFB-6S was evaluated using a fluorescence microscope, excitation-emission matrix (EEM), 2D-Fourier transform infrared correlation spectroscopy (2D-ATR-FTIR-COS), FT-NMR and TGA-DSC. From the results at higher pCO2 levels, there was a substantial reduction in EPS production by 58-62.8 % (DW). In addition to the biochemical composition of EPS, reduction in carbohydrates (8.7-47.6 %), protein (7.1-91.5 %), and lipids (16.9-68.6 %) content were observed at higher pCO2 levels. Functional discrepancies of fluorophores (tyrosine and tryptophan-like) in EPS, speckled differently in response to variable pCO2. The 2D-ATR-FTIR-COS analysis revealed functional amides (CN, CC, CO bending, -NH bending in amines) of EPS were preferentially altered, which led to the domination of polysaccharides relevant functional groups at higher pCO2. 1H NMR analysis of EPS confirmed the absence of chemical signals from H-C-COOH of proteins, α, β anomeric protons, and acetyl group relevant region at higher pCO2 levels. These findings can contribute new insights into the influence of pCO2 on the adaptation of marine microbes in future ocean acidification scenarios.

A membrane protein of the rice pathogen Burkholderia glumae required for oxalic acid secretion and quorum sensing

Bacterial panicle blight is caused by Burkholderia glumae and results in damage to rice crops worldwide. Virulence of B. glumae requires quorum sensing (QS)-dependent synthesis and export of toxoflavin, responsible for much of the damage to rice. The DedA family is a conserved membrane protein family found in all bacterial species. B. glumae possesses a member of the DedA family, named DbcA, which we previously showed is required for toxoflavin secretion and virulence in a rice model of infection. B. glumae secretes oxalic acid as a "common good" in a QS-dependent manner to combat toxic alkalinization of the growth medium during the stationary phase. Here, we show that B. glumae ΔdbcA fails to secrete oxalic acid, leading to alkaline toxicity and sensitivity to divalent cations, suggesting a role for DbcA in oxalic acid secretion. B. glumae ΔdbcA accumulated less acyl-homoserine lactone (AHL) QS signalling molecules as the bacteria entered the stationary phase, probably due to nonenzymatic inactivation of AHL at alkaline pH. Transcription of toxoflavin and oxalic acid operons was down-regulated in ΔdbcA. Alteration of the proton motive force with sodium bicarbonate also reduced oxalic acid secretion and expression of QS-dependent genes. Overall, the data show that DbcA is required for oxalic acid secretion in a proton motive force-dependent manner, which is critical for QS of B. glumae. Moreover, this study supports the idea that sodium bicarbonate may serve as a chemical for treatment of bacterial panicle blight.

Versatility and Complexity: Common and Uncommon Facets of LysR-Type Transcriptional Regulators

LysR-type transcriptional regulators (LTTRs) form one of the largest families of bacterial regulators. They are widely distributed and contribute to all aspects of metabolism and physiology. Most are homotetramers, with each subunit composed of an N-terminal DNA-binding domain followed by a long helix connecting to an effector-binding domain. LTTRs typically bind DNA in the presence or absence of a small-molecule ligand (effector). In response to cellular signals, conformational changes alter DNA interactions, contact with RNA polymerase, and sometimes contact with other proteins. Many are dual-function repressor-activators, although different modes of regulation may occur at multiple promoters. This review presents an update on the molecular basis of regulation, the complexity of regulatory schemes, and applications in biotechnology and medicine. The abundance of LTTRs reflects their versatility and importance. While a single regulatory model cannot describe all family members, a comparison of similarities and differences provides a framework for future study.

Sustainable rhamnolipids production in the next decade - Advancing with Burkholderia thailandensis as a potent biocatalytic strain

Rhamnolipids are one of the most promising eco-friendly green glycolipids for bio-replacements of commercially available fossil fuel-based surfactants. However, the current industrial biotechnology practices cannot meet the required standards due to the low production yields, expensive biomass feedstocks, complicated processing, and opportunistic pathogenic nature of the conventional rhamnolipid producer strains. To overcome these problems, it has become important to realize non-pathogenic producer substitutes and high-yielding strategies supporting biomass-based production. We hereby review the inherent characteristics of Burkholderia thailandensis E264 which favor its competence towards such sustainable rhamnolipid biosynthesis. The underlying biosynthetic networks of this species have unveiled unique substrate specificity, carbon flux control and rhamnolipid congener profile. Acknowledging such desirable traits, the present review provides critical insights towards metabolism, regulation, upscaling, and applications of B. thailandensis rhamnolipids. Identification of their unique and naturally inducible physiology has proved to be beneficial for achieving previously unmet redox balance and metabolic flux requirements in rhamnolipids production. These developments in part are targeted by the strategic optimization of B. thailandensis valorizing low-cost substrates ranging from agro-industrial byproducts to next generation (waste) fractions. Accordingly, safer bioconversions can propel the industrial rhamnolipids in advanced biorefinery domains to promote circular economy, reduce carbon footprint and increased applicability as both social and environment friendly bioproducts.

Transitioning from Soil to Host: Comparative Transcriptome Analysis Reveals the Burkholderia pseudomallei Response to Different Niches

Burkholderia pseudomallei, a soil and water saprophyte, is responsible for the tropical human disease melioidosis. A hundred years since its discovery, there is still much to learn about B. pseudomallei proteins that are essential for the bacterium's survival in and interaction with the infected host, as well as their roles within the bacterium's natural soil habitat. To address this gap, bacteria grown under conditions mimicking the soil environment were subjected to transcriptome sequencing (RNA-seq) analysis. A dual RNA-seq approach was used on total RNA from spleens isolated from a B. pseudomallei mouse infection model at 5 days postinfection. Under these conditions, a total of 1,434 bacterial genes were induced, with 959 induced in the soil environment and 475 induced in bacteria residing within the host. Genes encoding metabolism and transporter proteins were induced when the bacteria were present in soil, while virulence factors, metabolism, and bacterial defense mechanisms were upregulated during active infection of mice. On the other hand, capsular polysaccharide and quorum-sensing pathways were inhibited during infection. In addition to virulence factors, reactive oxygen species, heat shock proteins, siderophores, and secondary metabolites were also induced to assist bacterial adaptation and survival in the host. Overall, this study provides crucial insights into the transcriptome-level adaptations which facilitate infection by soil-dwelling B. pseudomallei. Targeting novel therapeutics toward B. pseudomallei proteins required for adaptation provides an alternative treatment strategy given its intrinsic antimicrobial resistance and the absence of a vaccine. IMPORTANCE Burkholderia pseudomallei, a soil-dwelling bacterium, is the causative agent of melioidosis, a fatal infectious disease of humans and animals. The bacterium has a large genome consisting of two chromosomes carrying genes that encode proteins with important roles for survival in diverse environments as well as in the infected host. While a general mechanism of pathogenesis has been proposed, it is not clear which proteins have major roles when the bacteria are in the soil and whether the same proteins are key to successful infection and spread. To address this question, we grew the bacteria in soil medium and then in infected mice. At 5 days postinfection, bacteria were recovered from infected mouse organs and their gene expression was compared against that of bacteria grown in soil medium. The analysis revealed a list of genes expressed under soil growth conditions and a different set of genes encoding proteins which may be important for survival, replication, and dissemination in an infected host. These proteins are a potential resource for understanding the full adaptation mechanism of this pathogen. In the absence of a vaccine for melioidosis and with treatment being reliant on combinatorial antibiotic therapy, these proteins may be ideal targets for designing antimicrobials to treat melioidosis.

The Global Regulator MftR Controls Virulence and Siderophore Production in Burkholderia thailandensis

Bacterial pathogens face iron limitation in a host environment. To overcome this challenge, they produce siderophores, small iron-chelating molecules.

Extracytoplasmic Function Sigma Factors Governing Production of the Primary Siderophores in Pathogenic Burkholderia Species

Bacteria respond to changing environments by modulating their gene expression programs. One of the mechanisms by which this may be accomplished is by substituting the primary σ factor with an alternative σ factor belonging to the family of extracytoplasmic function (ECF) σ factors. ECF σ factors are activated only in presence of specific signals, and they direct the RNA polymerase (RNAP) to transcribe a defined subset of genes. One condition, which may trigger the activation of an ECF σ factor, is iron limitation. To overcome iron starvation, bacteria produce and secrete siderophores, which chelate iron and facilitate its cellular uptake. In the genus Burkholderia, which includes several serious human pathogens, uptake of iron is critical for virulence, and expression of biosynthetic gene clusters encoding proteins involved in synthesis and transport of the primary siderophores are under control of an ECF σ factor. This review summarizes mechanisms involved in regulation of these gene clusters, including the role of global transcriptional regulators. Since siderophore-mediated iron acquisition is important for virulence, interference with this process constitutes a viable approach to the treatment of bacterial infections.

Methodological tools to study species of the genus Burkholderia

Bacteria belonging to the Burkholderia genus are extremely versatile and diverse. They can be environmental isolates, opportunistic pathogens in cystic fibrosis, immunocompromised or chronic granulomatous disease patients, or cause disease in healthy people (e.g., Burkholderia pseudomallei) or animals (as in the case of Burkholderia mallei). Since the genus was separated from the Pseudomonas one in the 1990s, the methodological tools to study and characterize these bacteria are evolving fast. Here we reviewed the techniques used in the last few years to update the taxonomy of the genus, to study gene functions and regulations, to deepen the knowledge on the drug resistance which characterizes these bacteria, and to elucidate their mechanisms to establish infections. The availability of these tools significantly impacts the quality of research on Burkholderia and the choice of the most appropriated is fundamental for a precise characterization of the species of interest.

Key points

• Updated techniques to study the genus Burkholderia were reviewed.

• Taxonomy, genomics, assays, and animal models were described.

• A comprehensive overview on recent advances in Burkholderia studies was made.

An updated overview on the regulatory circuits of polyhydroxyalkanoates synthesis

Polyhydroxyalkanoates (PHA) are a promising and sustainable alternative to the petroleum‐based synthetic plastics. Regulation of PHA synthesis is receiving considerable importance as engineering the regulatory factors might help developing strains with improved PHA‐producing abilities. PHA synthesis is dedicatedly regulated by a number of regulatory networks. They tightly control the PHA content, granule size and their distribution in cells. Most PHA‐accumulating microorganisms have multiple regulatory networks that impart a combined effect on PHA metabolism. Among them, several factors ranging from global to specific regulators, have been identified and characterized till now. This review is an attempt to categorically summarize the diverse regulatory circuits that operate in some important PHA‐producing microorganisms. However, in several organisms, the detailed mechanisms involved in the regulation of PHA synthesis is not well‐explored and hence further research is needed. The information presented in this review might help researcher to identify the prevailing research gaps in PHA regulation.

Impaired purine homeostasis plays a primary role in trimethoprim-mediated induction of virulence genes in Burkholderia thailandensis

One of the most commonly prescribed antibiotics against Burkholderia infections is co-trimoxazole, a cocktail of trimethoprim and sulfamethoxazole. Trimethoprim elicits an upregulation of the mal gene cluster, which encodes proteins involved in synthesis of the cytotoxic polyketide malleilactone; trimethoprim does so by increasing expression of the malR gene, which encodes the activator MalR. We report that B. thailandensis grown on trimethoprim exhibited increased virulence against Caenorhabditis elegans. This enhanced virulence correlated with an increase in expression of the mal gene cluster. Notably, inhibition of xanthine dehydrogenase by addition of allopurinol led to similar upregulation of malA and malR, with addition of trimethoprim or allopurinol also resulting in an equivalent intracellular accumulation of xanthine. Xanthine is a ligand for the transcription factor MftR that leads to attenuated DNA binding, and we show using chromatin immunoprecipitation that MftR binds directly to malR. Our gene expression data suggest that malR expression is repressed by both MftR and by a separate transcription factor, which also responds to a metabolite that accumulates on exposure to trimethoprim. Since allopurinol elicits a similar increase in malR/malA expression as trimethoprim, we suggest that impaired purine homeostasis plays a primary role in trimethoprim-mediated induction of malR and in turn malA.

Secondary metabolites from the Burkholderia pseudomallei complex: structure, ecology, and evolution

Bacterial secondary metabolites play important roles in promoting survival, though few have been carefully studied in their natural context. Numerous gene clusters code for secondary metabolites in the genomes of members of the Bptm group, made up of three closely related species with distinctly different lifestyles: the opportunistic pathogen Burkholderia pseudomallei, the non-pathogenic saprophyte Burkholderia thailandensis, and the host-adapted pathogen Burkholderia mallei. Several biosynthetic gene clusters are conserved across two or all three species, and this provides an opportunity to understand how the corresponding secondary metabolites contribute to survival in different contexts in nature. In this review, we discuss three secondary metabolites from the Bptm group: bactobolin, malleilactone (and malleicyprol), and the 4-hydroxy-3-methyl-2-alkylquinolines, providing an overview of each of their biosynthetic pathways and insight into their potential ecological roles. Results of studies on these secondary metabolites provide a window into how secondary metabolites contribute to bacterial survival in different environments, from host infections to polymicrobial soil communities.

Quorum Sensing Controls Both Rhamnolipid and Polyhydroxyalkanoate Production in Burkholderia thailandensis Through ScmR Regulation

Rhamnolipids are surface-active agents of microbial origin used as alternatives to synthetic surfactants. Burkholderia thailandensis is a non-pathogenic rhamnolipid-producing bacterium that could represent an interesting candidate for use in commercial processes. However, current bioprocesses for rhamnolipid production by this bacterium are not efficient enough, mainly due to low yields. Since regulation of rhamnolipid biosynthesis in B. thailandensis remains poorly understood, identifying new regulatory factors could help increase the production of these valuable metabolites. We performed a random transposon mutagenesis screening to identify genes directing rhamnolipid production in B. thailandensis E264. The most efficient rhamnolipid producer we identified harbored an inactivating transposon insertion in the scmR gene, which was recently described to encode as a secondary metabolite regulator in B. thailandensis. We investigated the impact of scmR loss on rhamnolipid biosynthesis and cell growth. Because biosynthesis of rhamnolipids and polyhydroxyalkanoates (PHAs) could share the same pool of lipid precursors, we also investigate the effect of ScmR on PHA production. We found that production of both rhamnolipids and PHAs are modulated by ScmR during the logarithmic growth phase and demonstrate that ScmR downregulates the production of rhamnolipids by affecting the expression of both rhl biosynthetic operons. Furthermore, our results indicate that PHA biosynthesis is reduced in the scmR- mutant, as ScmR promotes the transcription of the phaC and phaZ genes. By studying the relationship between ScmR and quorum sensing (QS) regulation we reveal that QS acts as an activator of scmR transcription. Finally, we pinpoint the QS-3 system as being involved in the regulation of rhamnolipid and PHA biosynthesis. We conclude that ScmR negatively affects rhamnolipid production, whereas it positively impacts PHAs biosynthesis. This could provide an interesting approach for future strain engineering, leading to improved yields of these valuable metabolites.