Genetics of bacterial alginate: alginate genes distribution, organization and biosynthesis in bacteria

Structural basis for the minimal bifunctional alginate epimerase AlgE3 from Azotobacter chroococcum

Among the epimerases specific to alginate, some of them in Azotobacter genera convert β-d-mannuronic acid to α-l-guluronic acid but also have lyase activity to degrade alginate. The remarkable characteristics of these epimerases make it a promising enzyme for tailoring alginates to meet specific demands. Here, we determined the structure of the bifunctional mannuronan C-5 epimerase AlgE3 from Azotobacter chroococcum (AcAlgE3) in complex with several mannuronic acid oligomers as well as in apo form, which allowed us to elucidate the binding manner of each mannuronic acid oligomer, and the structural plasticity, which is dependent on calcium ions. Moreover, a comprehensive analysis of the lyase activity profiles of AcAlgE3 combined with structural characteristics explained the preference for different chain length oligomers.

In vitro effects of alginate lyase SG4 + produced by Paenibacillus lautus alone and combined with antibiotics on biofilm formation by mucoid Pseudomonas aeruginosa

Alginate is a major extra polymeric substance in the biofilm formed by mucoid Pseudomonas aeruginosa. It is the main proven perpetrator of lung infections in patients suffering from cystic fibrosis. Alginate lyases are very important in the treatment of cystic fibrosis. This study evaluated the role of standalone and in conjugation, effect of alginate lyase of SG4 + isolated from Paenibacillus lautus in enhancing in vitro bactericidal activity of gentamicin and amikacin on mucoid P. aeruginosa. Using Response Surface Methodology (RSM) alginate lyase SG4 + production was optimized in shake flask and there 8.49-fold enhancement in enzyme production. In fermenter, maximum growth (10.15 mg/ml) and alginate lyase (1.46 International Units) production, 1.71-fold was increased using Central Composite Design (CCD). Further, fermentation time was reduced from 48 to 20 h. To the best of our knowledge this is the first report in which CCD was used for fermenter studies to optimize alginate lyase production. The Km and Vmax of purified enzyme were found to be 2.7 mg/ml and 0.84 mol/ml-min, respectively. The half-life (t 1/2) of purified alginate lyase SG4 + at 37 °C was 180 min. Alginate lyase SG4 + in combination with gentamicin and amikacin eradiated 48.4- 52.3% and 58- 64.6%, alginate biofilm formed by P. aeruginosa strains, respectively. The study proves that alginate lyase SG4 + has excellent exopolysaccharide disintegrating ability and may be useful in development of potent therapeutic agent to treat P. aeruginosa biofilms.

Exploring Pseudomonas syringae pv. tomato biofilm-like aggregate formation in susceptible and PTI-responding Arabidopsis thaliana

Bacterial biofilm-like aggregates have been observed in plants, but their role in pathogenicity is underinvestigated. In the present study, we observed that extracellular DNA and polysaccharides colocalized with green fluorescent protein (GFP)-expressing Pseudomonas syringae pv. tomato (Pst) aggregates in Arabidopsis leaves, suggesting that Pst aggregates are biofilms. GFP-expressing Pst, Pst ΔalgU ΔmucAB (Pst algU mutant), and Pst ΔalgD ΔalgU ΔmucAB (Pst algU algD mutant) were examined to explore the roles of (1) alginate, a potential biofilm component; (2) Pst AlgU, thought to regulate alginate biosynthesis and some type III secretion system effector genes; and (3) intercellular salicylic acid (SA) accumulation during pathogen-associated molecular pattern-triggered immunity (PTI). Pst formed extensive aggregates in susceptible plants, whereas aggregate numbers and size were reduced in Pst algU and Pst algD algU mutants, and both multiplied poorly in planta, suggesting that aggregate formation contributes to Pst success in planta. However, in SA-deficient sid2-2 plants, Pst algD algU mutant multiplication and aggregate formation were partially restored, suggesting plant-produced SA contributes to suppression of Pst aggregate formation. Pst algD algU mutants formed fewer and smaller aggregates than Pst algU mutants, suggesting both AlgU and AlgD contribute to Pst aggregate formation. Col-0 plants accumulated low levels of SA in response to Pst and both mutants (Pst algU and Pst algD algU), suggesting the regulatory functions of AlgU are not involved in suppressing SA-mediated plant defence. Plant PTI was associated with highly reduced Pst aggregate formation and accumulation of intercellular SA in flg22-induced PTI-responding wild-type Col-0, but not in PTI-incompetent fls2, suggesting intercellular SA accumulation by Arabidopsis contributes to suppression of Pst biofilm-like aggregate formation during PTI.

Psychrotrophic Bacteria Equipped with Virulence and Colonization Traits Populate the Ice Cream Manufacturing Environment

Several microbial taxa have been associated with food processing facilities, and they might resist by attaching on tools and equipment even after sanitation procedures, producing biofilms that adhere to the surfaces and might embed other microorganisms, including spoilers and pathogens. There is increasing evidence that these communities can be transferred to the final product. To explore the microbial contamination routes in a facility producing ice creams, we collected foods and environmental swabs from industrial surfaces of equipment and tools and performed taxonomic and functional analyses of the microbial DNA extracted from the environmental samples. Our results suggest that complex communities dominated by psychrotrophic bacteria (e.g., Pseudomonas and Acinetobacter spp.) inhabit the food processing environment, and we demonstrate that these communities might be transferred from the surfaces to the products. Functional analysis performed on environmental samples highlighted the presence of several genes linked to antimicrobial resistance and adherence on abiotic surfaces; such genes were more abundant on food contact (FC) than on other surfaces. Metagenome-assembled genomes (MAGs) of Pseudomonas stutzeri showed genes linked with biofilm formation and motility, which are surely linked to colonizing capabilities in the processing lines. The study highlights clear potential advantages of applying microbiome mapping in the food industry for source tracking of microbial contamination and for planning appropriate ad hoc sanitization strategies. IMPORTANCE Several microbial species might permanently establish in food processing facilities, thus contributing to food loss. In fact, food contact surfaces might transfer microorganisms to intermediates and products, potentially representing a hazard to human health. In this work, we provide evidence of the existence of complex microbial communities overcoming sanitation in an ice cream-producing facility. These communities harbored several genes that could potentially lead to attachment to surfaces and antimicrobial resistance. Also, prediction of routes of contamination showed that several potential spoilage taxa might end up in the final product. Importantly, in this work, we show that mapping the environmental microbiome is a high-resolution technique that might help food business operators ensure food quality and safety through detection of potentially hazardous microorganisms.

Revisiting ESKAPE Pathogens: virulence, resistance, and combating strategies focusing on quorum sensing

The human-bacterial association is long-known and well-established in terms of both augmentations of human health and attenuation. However, the growing incidents of nosocomial infections caused by the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) call for a much deeper understanding of these organisms. Adopting a holistic approach that includes the science of infection and the recent advancements in preventing and treating infections is imperative in designing novel intervention strategies against ESKAPE pathogens. In this regard, this review captures the ingenious strategies commissioned by these master players, which are teamed up against the defenses of the human team, that are equally, if not more, versatile and potent through an analogy. We have taken a basketball match as our analogy, dividing the human and bacterial species into two teams playing with the ball of health. Through this analogy, we make the concept of infectious biology more accessible.

Alginate: Enhancement Strategies for Advanced Applications

Alginate is an excellent biodegradable and renewable material that is already used for a broad range of industrial applications, including advanced fields, such as biomedicine and bioengineering, due to its excellent biodegradable and biocompatible properties. This biopolymer can be produced from brown algae or a microorganism culture. This review presents the principles, chemical structures, gelation properties, chemical interactions, production, sterilization, purification, types, and alginate-based hydrogels developed so far. We present all of the advanced strategies used to remarkably enhance this biopolymer's physicochemical and biological characteristics in various forms, such as injectable gels, fibers, films, hydrogels, and scaffolds. Thus, we present here all of the material engineering enhancement approaches achieved so far in this biopolymer in terms of mechanical reinforcement, thermal and electrical performance, wettability, water sorption and diffusion, antimicrobial activity, in vivo and in vitro biological behavior, including toxicity, cell adhesion, proliferation, and differentiation, immunological response, biodegradation, porosity, and its use as scaffolds for tissue engineering applications. These improvements to overcome the drawbacks of the alginate biopolymer could exponentially increase the significant number of alginate applications that go from the paper industry to the bioprinting of organs.

Genome analysis of alginate synthesizing Pseudomonas aeruginosa strain SW1 isolated from degraded seaweeds

Pseudomonas aeruginosa strain SW1 is an aerobic, motile, Gram-negative, and rod-shaped bacterium isolated from degraded seaweeds. Based on the 16S rRNA gene sequence and MALDI TOF analysis, strain SW1 exhibits 100% similarity to P. aeruginosa DSM 50,071, its closest phylogenetic neighbor. The complete genome of strain SW1 consists of a single circular chromosome with 23,258,857 bp (G + C content of 66%), including 6734 protein-coding sequences, 8 rRNA, and 63 tRNA sequences. The genome of the P. aeruginosa SW1 contains at least 27 genes for the biosynthesis of alginate and other exopolysaccharide involved in biofilm formation. KAAS and GO analysis and functional annotation by COG and CAZymes are consistent with the biosynthesis of alginate. In addition, the presence of antimicrobial resistance, multi-efflux operon, and antibiotic inactivation genes indicate a pathogenic potential similar to strain DSM50071. The high-quality genome and associated annotation provide a starting point to exploit the potential for P. aeruginosa to produce alginate.

Identification of IAA-regulated genes in Pseudomonas syringae pv. tomato strain DC3000

The auxin indole-3-acetic acid (IAA) is a plant hormone that not only regulates plant growth and development but also plays important roles in plant-microbe interactions. We previously reported that IAA alters expression of several virulence-related genes in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000 (PtoDC3000). To learn more about the impact of IAA on regulation of PtoDC3000 gene expression we performed a global transcriptomic analysis of bacteria grown in culture, in the presence or absence of exogenous IAA. We observed that IAA repressed expression of genes involved in the Type III secretion (T3S) system and motility and promoted expression of several known and putative transcriptional regulators. Several of these regulators are orthologs of factors known to regulate stress responses and accordingly expression of several stress response-related genes was also upregulated by IAA. Similar trends in expression for several genes were also observed by RT-qPCR. Using an Arabidopsis thaliana auxin receptor mutant that accumulates elevated auxin, we found that many of the P. syringae genes regulated by IAA in vitro were also regulated by auxin in planta. Collectively the data indicate that IAA modulates many aspects of PtoDC3000 biology, presumably to promote both virulence and survival under stressful conditions, including those encountered in or on plant leaves. IMPORTANCE Indole-3-acetic acid (IAA), a form of the plant hormone auxin, is used by many plant-associated bacteria as a cue to sense the plant environment. Previously, we showed that IAA can promote disease in interactions between the plant pathogen Pseudomonas syringae strain PtoDC000 and one of its hosts, Arabidopsis thaliana. However, the mechanisms by which IAA impacts the biology of PtoDC3000 and promotes disease are not well understood. Here we demonstrate that IAA is a signal molecule that regulates gene expression in PtoDC3000. The presence of exogenous IAA affects expression of over 700 genes in the bacteria, including genes involved in Type III secretion and genes involved in stress response. This work offers insight into the roles of auxin promoting pathogenesis.

Bacterial Extracellular Polymers: A Review

Prokaryotic microbial cells especially bacteria are highly emphases for their exopolysaccharides (EPS) production. EPS are the higher molecular weight natural extracellular compounds observe at the surface of the bacterial cells. Nowadays bacterial EPS represent rapidly emerging as new and industrially important biomaterials because it having tremendous physical and chemical properties with novel functionality. Due to its industrial demand as well as research studies the different extraction processes have been discovered to remove the EPS from the microbial biofilm. The novelties of EPS are also based on the microbial habitat conditions such as higher temperature, lower temperature, acidic, alkaliphilic, saline, etc. Based on its chemical structure they can be homopolysaccharide or heteropolysaccharide. EPSs have a wide range of applications in various industries such as food, textile, pharmaceutical, heavy metal recovery, agriculture, etc. So, this review focus on the understanding of the structure, different extraction processes, biosynthesis and genetic engineering of EPS as well as their desirable biotechnological applications.

Heterogenous Susceptibility to R-Pyocins in Populations of Pseudomonas aeruginosa Sourced from Cystic Fibrosis Lungs

Bacteriocins are proteinaceous antimicrobials produced by bacteria that are active against other strains of the same species. R-type pyocins are phage tail-like bacteriocins produced by Pseudomonas aeruginosa Due to their antipseudomonal activity, R-pyocins have potential as therapeutics in infection. P. aeruginosa is a Gram-negative opportunistic pathogen and is particularly problematic for individuals with cystic fibrosis (CF). P. aeruginosa organisms from CF lung infections develop increasing resistance to antibiotics, making new treatment approaches essential. P. aeruginosa populations become phenotypically and genotypically diverse during infection; however, little is known of the efficacy of R-pyocins against heterogeneous populations. R-pyocins vary by subtype (R1 to R5), distinguished by binding to different residues on the lipopolysaccharide (LPS). Each type varies in killing spectrum, and each strain produces only one R-type. To evaluate the prevalence of different R-types, we screened P. aeruginosa strains from the International Pseudomonas Consortium Database (IPCD) and from our biobank of CF strains. We found that (i) R1-types were the most prevalent R-type among strains from respiratory sources, (ii) a large number of strains lack R-pyocin genes, and (iii) isolates collected from the same patient have the same R-type. We then assessed the impact of intrastrain diversity on R-pyocin susceptibility and found a heterogenous response to R-pyocins within populations, likely due to differences in the LPS core. Our work reveals that heterogeneous populations of microbes exhibit variable susceptibility to R-pyocins and highlights that there is likely heterogeneity in response to other types of LPS-binding antimicrobials, including phage.IMPORTANCE R-pyocins have potential as alternative therapeutics against Pseudomonas aeruginosa in chronic infection; however, little is known about the efficacy of R-pyocins in heterogeneous bacterial populations. P. aeruginosa is known to become resistant to multiple antibiotics and to evolve phenotypic and genotypic diversity over time; thus, it is particularly difficult to eradicate in chronic cystic fibrosis (CF) lung infections. In this study, we found that P. aeruginosa populations from CF lungs maintain the same R-pyocin genotype but exhibit heterogeneity in susceptibility to R-pyocins from other strains. Our findings suggest there is heterogeneity in response to other types of LPS-binding antimicrobials, such as phage, highlighting the necessity of further studying the potential of LPS-binding antimicrobial particles as alternative therapies in chronic infections.

AlgU, a Conserved Sigma Factor Regulating Abiotic Stress Tolerance and Promoting Virulence in Pseudomonas syringae

Pseudomonas syringae can rapidly deploy specialized functions to deal with abiotic and biotic stresses. Host niches pose specific sets of environmental challenges driven, in part, by immune defenses. Bacteria use a "just-in-time" strategy of gene regulation, meaning that they only produce the functions necessary for survival as needed. Extracytoplasmic function (ECF) sigma factors transduce a specific set of environmental signals and change gene expression patterns by altering RNA polymerase promoter specificity, to adjust bacterial physiology, structure, or behavior, singly or in combination, to improve chances of survival. The broadly conserved ECF sigma factor AlgU affects virulence in both animal and plant pathogens. Pseudomonas syringae AlgU controls expression of more than 800 genes, some of which contribute to suppression of plant immunity and bacterial fitness in plants. This review discusses AlgU activation mechanisms, functions controlled by AlgU, and how these functions contribute to P. syringae survival in plants.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. 2021.

Biofilms by bacterial human pathogens: Clinical relevance - development, composition and regulation - therapeutical strategies

Notably, bacterial biofilm formation is increasingly recognized as a passive virulence factor facilitating many infectious disease processes. In this review we will focus on bacterial biofilms formed by human pathogens and highlight their relevance for diverse diseases. Along biofilm composition and regulation emphasis is laid on the intensively studied biofilms of Vibrio cholerae, Pseudomonas aeruginosa and Staphylococcus spp., which are commonly used as biofilm model organisms and therefore contribute to our general understanding of bacterial biofilm (patho-)physiology. Finally, therapeutical intervention strategies targeting biofilms will be discussed.

In Silico Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria Pseudomonas fluorescens F113 and Other Pseudomonads

Biofilms are complex structures that are crucial during host-bacteria interaction and colonization. Bacteria within biofilms are surrounded by an extracellular matrix (ECM) typically composed of proteins, polysaccharides, lipids, and DNA. Pseudomonads contain a variety of ECM components, some of which have been extensively characterized. However, neither the ECM composition of plant-associated pseudomonads nor their phylogenetic distribution within the genus has been so thoroughly studied. In this work, we use in silico methods to describe the ECM composition of Pseudomonas fluorescens F113, a plant growth-promoting rhizobacteria and model for rhizosphere colonization. These components include the polysaccharides alginate, poly-N-acetyl-glucosamine (PNAG) and levan; the adhesins LapA, MapA and PsmE; and the functional amyloids in Pseudomonas. Interestingly, we identified novel components: the Pseudomonas acidic polysaccharide (Pap), whose presence is limited within the genus; and a novel type of Flp/Tad pilus, partially different from the one described in P. aeruginosa. Furthermore, we explored the phylogenetic distribution of the most relevant ECM components in nearly 600 complete Pseudomonas genomes. Our analyses show that Pseudomonas populations contain a diverse set of gene/gene clusters potentially involved in the formation of their ECMs, showing certain commensal versus pathogen lifestyle specialization.

Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides

Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential "soil glue" producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.

Pseudomonas savastanoi Two-Component System RhpRS Switches between Virulence and Metabolism by Tuning Phosphorylation State and Sensing Nutritional Conditions

Pseudomonas savastanoi uses a type III secretion system (T3SS) to invade host plants. Our previous studies have demonstrated that a two-component system (TCS), RhpRS, enables P. savastanoi to coordinate the T3SS gene expression, which depends on the phosphorylation state of RhpR under different environmental conditions. Orthologues of RhpRS are distributed in a wide range of bacterial species, indicating a general regulatory mechanism. How RhpRS uses external signals and the phosphorylation state to exercise its regulatory functions remains unknown. We performed chromatin immunoprecipitation sequencing (ChIP-seq) assays to identify the specific binding sites of RhpR and RhpR^D70A in either King's B medium (KB [a T3SS-inhibiting medium]) or minimal medium (MM [a T3SS-inducing medium]). We identified 125 KB-dependent binding sites and 188 phosphorylation-dependent binding sites of RhpR. In KB, RhpR directly and positively regulated cytochrome c ₅₅₀ production (via ccmA) and alcohol dehydrogenase activity (via adhB) but negatively regulated anthranilate synthase activity (via trpG) and protease activity (via hemB). In addition, phosphorylated RhpR (RhpR-P) directly and negatively regulated the T3SS (via hrpR and hopR1), swimming motility (via flhA), c-di-GMP levels (via PSPPH_2590), and biofilm formation (via algD). It positively regulated twitching motility (via fimA) and lipopolysaccharide production (via PSPPH_2653). Our transcriptome sequencing (RNA-seq) analyses identified 474 and 840 new genes that were regulated by RhpR in KB and MM, respectively. We showed nutrient-rich conditions allowed RhpR to directly regulate multiple metabolic pathways of P. savastanoi and phosphorylation enabled RhpR to specifically control virulence and the cell envelope. The action of RhpRS switched between virulence and regulation of multiple metabolic pathways by tuning its phosphorylation and sensing environmental signals in KB, respectively.IMPORTANCE The plant pathogen Pseudomonas savastanoi invades host plants through a type III secretion system, which is strictly regulated by a two-component system called RhpRS. The orthologues of RhpRS are widely distributed in the bacterial kingdom. The master regulator RhpR specifically depends on the phosphorylation state to regulate the majority of the virulence-related genes. Under nutrient-rich conditions, it modulates many important metabolic pathways, which consist of one-fifth of the genome. We propose that RhpRS uses phosphorylation- and nutrition-dependent mechanisms to switch between regulating virulence and metabolism, and this functionality is widely conserved among bacterial species.

Interaction of gentamicin sulfate with alginate and consequences on the physico-chemical properties of alginate-containing biofilms

BACKGROUND

Alginate is one of the main extracellular polymeric substances (EPS) in biofilms of Cystic Fibrosis (CF) patients suffering from pulmonary infections. Gentamicin sulfate (GS) can strongly bind to alginate resulting in loss of pharmacological activity; however neither the mechanism nor its repercussion is fully understood. In this study, we investigated how GS modifies the alginate macromolecular network and its microenvironment.

MATERIAL AND METHODS

Alginate gels of two different compositions (either enriched in guluronate units (G) or enriched in mannuronate units (M)) were crosslinked with Ca²⁺ and exposed to GS at varying times and concentrations. The complexes formed were characterized via turbidimetry, mechanical tests, swelling assay, calorimetry techniques, nuclear magnetic resonance, Ca²⁺ displacement, macromolecular probe diffusion and pH alteration.

RESULTS

In presence of GS, the alginate network and its environment undergo a tremendous reorganization in terms of gel density, stiffness, diffusion property, presence and state of the water molecules. We noted that the intensity of those alterations is directly dependent on the polysaccharide motif composition (ratio M/G).

CONCLUSION

Our results underline the importance of alginate as biofilm component, its pernicious role during antibiotherapy and could represent a potential macromolecular target to improve anti-infectious therapies.

Genetic, structural and pharmacological characterization of polymannuronate synthesized by algG mutant indigenous soil bacterium Pseudomonas aeruginosa CMG1421

AIMS

It was aimed to study the genetic, structural and pharmacological characteristics of polymannuronate synthesized by Pseudomonas aeruginosa CMG1421.

METHODS AND RESULTS

Synthesis was analysed by transmission electron microscopy, FT/IR, ¹ H-NMR and gel permeation chromatography followed by in vitro bioassays. Colony PCR followed by sequence analysis was employed for screening of structural genes. FT/IR analysis indicated the presence of hydroxyl, carboxyl and O-acetyl groups linked to mannuronate. ¹ H-NMR analysis indicated M-M bond characteristics for mannuronic acid residues. The average relative molecular weight was found in range of 20 000-250 000 Da. The amplified DNA fragments were identified as 16S rRNA, algD, alg8, alg44, algG, algE and algX genes showing 99-100% homology with those of P. aeruginosa. However, in algG there were transition mutations of adenine and cytosine at nucleotide position 766 and 769, and 878 and 881 respectively. Polymannuronate and its oligomannuronates respectively showed moderate and significant antioxidant, anti-inflammatory, anti-obesity and antidiabetic activities.

CONCLUSIONS

Alginate synthesized by ∆algG mutant P. aeruginosa CMG1421 was bioactive and solely consists of acetylated d-mannuronates.

SIGNIFICANCE AND IMPACT OF THE STUDY

We investigated biocompatible, nonimmunogenic and nontoxic pharmacological agents for treatment and attenuation of degenerative, inflammatory, autoimmune disease, and metabolic disorders such as obesity and diabetes.

Critical review of EPS production, synthesis and composition for sludge flocculation

Extracellular polymeric substances (EPS) produced by microorganisms represent biological macromolecules with unfathomable potentials and they are required to be explored further for their potential application as a bioflocculant in various wastewater sludge treatment. Although several studies already exist on biosynthetic pathways of different classical biopolymers like alginate and xanthan, no dedicated studies are available for EPS in sludge. This review highlights the EPS composition, functionality, and biodegradability for its potential use as a carbon source for production of other metabolites. Furthermore, the effect of various extraction methods (physical and chemical) on compositional, structural, physical and functional properties of microbial EPS has been addressed. The vital knowledge of the effect of extraction method on various important attributes of EPS can help to choose the suitable extraction method depending upon the intended use of EPS. The possible use of different molecular biological techniques for enhanced production of desired EPS was summarized.

Screening of Alginate Lyase-Producing Bacteria and Optimization of Media Compositions for Extracellular Alginate Lyase Production

Background:

Alginate is a linear polysaccharide consisting of guluronate (polyG) and mannuronate (polyM) subunits.

Methods:

In the initial screening of alginate-degrading bacteria from soil, 10 isolates were able to grow on minimal medium containing alginate. The optimization of cell growth and alginate lyase (algL) production was carried out by the addition of 0.8% alginate and 0.2-0.3 M NaCl to the culture medium. Of 10 isolates, one was selected based on its fast growth rate on minimal 9 medium containing 0.4% sodium alginate. The selected bacterium, identified based on morphological and biochemical characteristics, as well as 16S rDNA sequence data, was confirmed to be an isolate belonging to the genus Bacillus and designated as Bacillus sp. TAG8.

Results:

The results showed the ability of Bacillus sp. TAG8 in utilizing alginate as a sole carbon source. Bacillus sp. TAG8 growth and algL production were augmented with an increase in sodium alginate concentration and also by the addition of 0.2-0.3 M NaCl. Molecular analysis of TAG8 algL gene showed 99% sequence identity with algL of Pseudomonasaeruginosa PAO1. The algL produced by Bacillus sp. TAG8 cleaved both polyM and polyG blocks in alginate molecule, as well as acetylated alginate residues, confirming the bifunctionality of the isolated lyase.

Conclusion:

The identification of novel algL genes from microbial communities constitutes a new approach for exploring lyases with specific activity against bacterial alginates and may thus contribute to the eradication of persistent biofilms from clinical samples.

The effect of alginate lyase on the gentamicin resistance of Pseudomonas aeruginosa in mucoid biofilms

AIMS

Pseudomonas aeruginosa can secrete large amounts of alginate during chronic infections and this has been associated with high resistance to antibiotics. The major aim of this study was to investigate whether degradation of extracellular alginate by alginate lyase would increase the sensitivity of Ps. aeruginosa to gentamicin, an aminoglycoside antibiotic.

METHODS AND RESULTS

Degradation of alginate from Ps. aeruginosa was monitored using a spectrometric assay. Alginate lyase depolymerized alginate, but calcium and zinc cations at concentrations found in the cystic fibrosis lung reduced enzyme activity. Biofilms formed on agar were partially degraded by alginate lyase, but staining with crystal violet showed that the biomass of biofilms grown in liquid was not significantly affected by the enzyme. Viability testing showed that the sensitivity to gentamicin of biofilm bacteria and of bacteria released from biofilms was unaffected by alginate lyase.

CONCLUSIONS

Our results show that at least under the conditions used here alginate lyase does not affect gentamicin resistance of Ps. aeruginosa.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study indicates that alginate does not contribute to resistance to gentamicin and so does not provide support for the concept of treating patients with alginate lyase in order to increase the antibiotic sensitivity of Ps. aeruginosa.

Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria

Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.

Bacterial exopolysaccharides: biosynthesis pathways and engineering strategies

Bacteria produce a wide range of exopolysaccharides which are synthesized via different biosynthesis pathways. The genes responsible for synthesis are often clustered within the genome of the respective production organism. A better understanding of the fundamental processes involved in exopolysaccharide biosynthesis and the regulation of these processes is critical toward genetic, metabolic and protein-engineering approaches to produce tailor-made polymers. These designer polymers will exhibit superior material properties targeting medical and industrial applications. Exploiting the natural design space for production of a variety of biopolymer will open up a range of new applications. Here, we summarize the key aspects of microbial exopolysaccharide biosynthesis and highlight the latest engineering approaches toward the production of tailor-made variants with the potential to be used as valuable renewable and high-performance products for medical and industrial applications.

A Pseudomonas fluorescens type 6 secretion system is related to mucoidy, motility and bacterial competition

BACKGROUND

Pseudomonas fluorescens strain MFE01 secretes in abundance two Hcp proteins (haemolysin co-regulated proteins) Hcp1 and Hcp2, characteristic of a functional type 6 secretion system. Phenotypic studies have shown that MFE01 has antibacterial activity against a wide range of competitor bacteria, including rhizobacteria and clinically relevant bacteria. Mutagenesis of the hcp2 gene abolishes or reduces, depending on the target strain, MFE01 antibacterial activity. Hcp1, encoded by hcp1, may also be involved in bacterial competition. We therefore assessed the contribution of Hcp1 to competition of P. fluorescens MFE01 with other bacteria, by studying MFE01 mutants in various competitive conditions.

RESULTS

Mutation of hcp1 had pleiotropic effects on the MFE01 phenotype. It affected mucoidy of the strain and its motility and was associated with the loss of flagella, which were restored by introduction of plasmid expressing hcp1. The hcp1 mutation had no effect on bacterial competition during incubation in solid medium. MFE01 was able to sequester another P. fluorescens strain, MFN1032, under swimming conditions. The hcp2 mutant but not the hcp1 mutant conserved this ability. In competition assays on swarming medium, MFE01 impaired MFN1032 swarming and displayed killing activity. The hcp2 mutant, but not the hcp1 mutant, was able to reduce MFN1032 swarming. The hcp1 and hcp2 mutations each abolished killing activity in these conditions.

CONCLUSION

Our findings implicate type 6 secretion of Hcp1 in mucoidy and motility of MFE01. Our study is the first to establish a link between a type 6 secretion system and flagellin and mucoidy. Hcp1 also appears to contribute to limiting the motility of prey cells to facilitate killing mediated by Hcp2. Inhibition of motility associated with an Hcp protein has never been described. With this work, we illustrate the importance and versatility of type 6 secretion systems in bacterial adaptation and fitness.

Plant growth promoting characterization of indigenous Azotobacteria isolated from soils in Iran

It has been well known that the bacteria of the genus Azotobacter, in addition to the beneficial N(2)-fixing activity, are able to improve plant growth by a number of direct and indirect mechanisms. To identify this potential in indigenous azotobacteria, the efficiency of 17 isolates of Azotobacter from the rhizosphere of wheat and barley plants cultivated in salt- and/or drought-affected soils in Iran were evaluated for their ability to dissolve inorganic and organic phosphates, siderophore secretion, indole acetic acid (IAA) production; and protease, chitinase, and ACC deaminase (ACCD) activities. First, they were biochemically characterized and one isolate (strain) was identified by 16S rDNA sequencing. Eight isolates were designated as Azotobacter vinelandii and the remaining isolates were identified as A. chroococcum. All isolates hydrolyzed the organic and inorganic phosphate compounds and effectively produced IAA. Fifteen isolates produced siderophore, but only one isolate showed protease activity which is being reported for the first time in relation to Azotobacter. None of the 17 isolates was capable of producing ACCD or chitinase. However, polymerase chain reaction amplification of the ACCD coding genes, by the use of the gene-specific primers, indicated that not all contain the ACCD gene. The standard screening methods with slight modifications, especially in the case of ACCD assay, were applied. The results showed that the use of specific screening methods, modified according to bacterial nutritional requirements, are the efficient methods for precise evaluation of the plant growth promoting rhizobacteria activity.

Co-evolution with lytic phage selects for the mucoid phenotype of Pseudomonas fluorescens SBW25

The effects of co-evolution with lytic phage on bacterial virulence-related traits are largely unknown. In this study we investigate the incidence of the mucoid phenotype of the bacterium Pseudomonas fluorescens SBW25 in response to co-evolution with the lytic phage phi2 (φ2). The mucoid phenotype of Pseudomonas spp. is due to overproduction of alginate and is a considerable virulence factor contributing to the intractability of infections most notably in cystic fibrosis (CF) lung, but also in pathogenic infections of plants. Our data show that this phenotype can evolve as an adaptive response to phage predation and is favoured under specific abiotic conditions, in particular a homogenous spatial structure and a high rate of nutrient replacement. The mucoid phenotype remains partially sensitive to phage infection, which facilitates 'apparent competition' with phage-sensitive competitors, partially offsetting the costs of alginate production. Although P. fluorescens SBW25 is not a pathogen, several key characteristics typical of Pseudomonas aeruginosa clinical isolates from CF lung were noted, including loss of motility on mucoid conversion and a high rate of spontaneous reversion to the wild-type phenotype. Although the genetic mechanisms of this phenotype remain unknown, they do not include mutations at many of the commonly reported loci implicated in mucoid conversion, including mucA and algU. These data not only further our understanding of the potential role phage have in the ecology and evolution of bacteria virulence in both natural and clinical settings, but also highlight the need to consider both biotic and abiotic variables if bacteriophages are to be used therapeutically.

Produção de alginato por microrganismos

O alginato é um copolímero linear constituído de unidades de ácidos α-L-gulurônicos e β-D-manurônicos e é extensamente utilizado devido as suas propriedades espessantes, estabilizantes e gelificantes. Estas características fazem com que este biopolímero encontre aplicações na indústria de alimentos, na indústria têxtil e de papel, em cosméticos e na área farmacêutica e médica. Atualmente para este conjunto de aplicações sua principal fonte são algas marrons, entretanto, o alginato pode ser obtido a partir de biossíntese, utilizando-se microrganismos do gênero Pseudomonas e Azotobacter. A produção bacteriana de alginato apresenta-se como uma alternativa interessante e sua produção por microrganismos, além de possibilitar a produção de biopolímeros de alta qualidade com características específicas e pré-determinadas, irá diminuir o impacto ambiental nas regiões em que as algas marinhas das quais é extraído são coletadas. Nos últimos anos, vários estudos relacionados à produção de alginato por microrganismos foram realizados com o objetivo de avaliar sua produção e rota metabólica de biossíntese, para caracterizar o material produzido e para determinar as potencialidades de aplicação deste novo material. O rápido desenvolvimento de aplicações do alginato na área médica e farmacêutica, bem como a descoberta de propriedades imunológicas únicas deste material tem aumentado o interesse no desenvolvimento de processos para produzi-lo. Neste artigo são abordados aspectos relacionados à produção e as características do alginato bacteriano e também reportadas às potencialidades e aplicações inovadoras nas quais este material vem sendo utilizado.

Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung

Pseudomonas aeruginosa, the leading cause of morbidity and mortality in people with cystic fibrosis (CF), adapts for survival in the CF lung through both mutation and gene expression changes. Frequent clonal strains such as the Australian Epidemic Strain-1 (AES-1), have increased ability to establish infection in the CF lung and to superimpose and replace infrequent clonal strains. Little is known about the factors underpinning these properties. Analysis has been hampered by lack of expression array templates containing CF-strain specific genes. We sequenced the genome of an acute infection AES-1 isolate from a CF infant (AES-1R) and constructed a non-redundant micro-array (PANarray) comprising AES-1R and seven other sequenced P. aeruginosa genomes. The unclosed AES-1R genome comprised 6.254Mbp and contained 6957 putative genes, including 338 not found in the other seven genomes. The PANarray contained 12,543 gene probe spots; comprising 12,147 P. aeruginosa gene probes, 326 quality-control probes and 70 probes for non-P. aeruginosa genes, including phage and plant genes. We grew AES-1R and its isogenic pair AES-1M, taken from the same patient 10.5 years later and not eradicated in the intervening period, in our validated artificial sputum medium (ASMDM) and used the PANarray to compare gene expression of both in duplicate. 675 genes were differentially expressed between the isogenic pairs, including upregulation of alginate, biofilm, persistence genes and virulence-related genes such as dihydroorotase, uridylate kinase and cardiolipin synthase, in AES-1M. Non-PAO1 genes upregulated in AES-1M included pathogenesis-related (PAGI-5) genes present in strains PACS2 and PA7, and numerous phage genes. Elucidation of these genes' roles could lead to targeted treatment strategies for chronically infected CF patients.

Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

BACKGROUND

Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored.

RESULTS

In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits.

CONCLUSIONS

Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate nutritional status cues with the regulation of traits that are of ecological, industrial and clinical importance.

Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes

Azotobacter vinelandii is a soil bacterium related to the Pseudomonas genus that fixes nitrogen under aerobic conditions while simultaneously protecting nitrogenase from oxygen damage. In response to carbon availability, this organism undergoes a simple differentiation process to form cysts that are resistant to drought and other physical and chemical agents. Here we report the complete genome sequence of A. vinelandii DJ, which has a single circular genome of 5,365,318 bp. In order to reconcile an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes, A. vinelandii is specialized in terms of its complement of respiratory proteins. It is able to produce alginate, a polymer that further protects the organism from excess exogenous oxygen, and it has multiple duplications of alginate modification genes, which may alter alginate composition in response to oxygen availability. The genome analysis identified the chromosomal locations of the genes coding for the three known oxygen-sensitive nitrogenases, as well as genes coding for other oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and formate dehydrogenase. These findings offer new prospects for the wider application of A. vinelandii as a host for the production and characterization of oxygen-sensitive proteins.