Global regulation of food supply by Pseudomonas putida DOT-T1E

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.

Different phenanthrene degraders between free-cell mediated and biochar-immobilization assisted soil bioaugmentation as identified by RNA-based stable isotope probing (RNA-SIP)

Bioaugmentation (BA) is an effective approach to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soils, and biochar is frequently used to enhance PAH degradation performance. In this study, phenanthrene (PHE) degradation behavior and active degraders in a petroleum-contaminated soil were investigated and compared between free-cell mediated and biochar-immobilization assisted bioaugmentation. Biochar-immobilization assisted bioaugmentation (BA-IPB) introduced PHE degraders immobilized on biochar and effectively promoted PHE degradation, achieving higher PHE removal efficiencies within 24 h (~58 %) than free-cell mediated bioaugmentation (BA-FPB, ~39 %). Soil microbial community structure significantly changed in both BA-FPB and BA-IPB treatments. Through RNA-stable isotope probing (SIP), 14 and 11 bacterial lineages responsible for in situ PHE degradation were identified in BA-FPB and BA-IPB treatments, respectively. ASV_17 in BA-FPB treatment was Rhodococcus in the exogenous bacterial mixture; in contrast, none of exogenous bacteria were involved in PHE degradation in BA-IPB treatment. Methylobacterium (ASV_186), Xanthomonas (ASV_41), Kroppenstedtia (ASV_205), Scopulibacillus (ASV_243), Bautia (ASV_356), and Lactobacillus (ASV_376) were identified as PHE degraders for the first time. Our findings expanded the knowledge of the active PHE degraders and underlying mechanisms in bioaugmentation process, and suggested biochar-immobilization assisted bioaugmentation as a promising strategy for the bioremediation of PAH contaminated soils.

Melanin production by Pseudomonas sp. and in silico comparative analysis of tyrosinase gene sequences

Background

Melanin finds enormous applications in different industries for its unique photoprotective and anti-oxidant properties. Due to its emerging demand, scientific researchers are putting efforts to unravel more microorganisms with a potential of producing melanin on large scale. Hence, the present study was aimed at the isolation of extracellular melanin producing microorganisms from lime quarries of Karnataka, India. Besides this, the tyrosinase gene governing melanin synthesis in different organisms were compared in silico to understand its evolutionary aspects.

Material and methods

Melanin producing microorganisms were screened on tyrosine gelatin beef extract agar medium. Potential isolate was explored for submerged production of melanin in broth containing L-tyrosine. Melanin was characterized by UV-Vis spectroscopy, thin layer and high performance liquid chromatographic techniques. Antibacterial activity of melanin was performed by agar well assay. Comparative tyrosinase gene sequence analysis was performed by using Geneious 2021.1 trial version software.

Results

Pseudomonas otitidis DDB2 was found to be potential for melanin production. No antibacterial activity was exerted by the melanin against tested pathogens. The in silico studies showed that the common central domain of tyrosinase protein sequence of selected Pseudomonas sps. exhibited 100% identity with the common central domain of Homo sapiens tyrosinase (NP_000363.1).

Conclusions

Our study shows the production of melanin in good quantities by the isolate Pseudomonas otitidis DDB2 which can be explored for scale-up process. Since the melanin formed is of eumelanin type and the tyrosinase gene sequence of several Pseudomonas sp. showed relatedness to humans, this molecule may be further developed for sunscreen formulations.

Phylogenetic analysis and population structure of Pseudomonas alloputida

The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida. Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7^T to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic diversity and its potential for biotechnological applications.

Synthesis of aromatic amino acids from 2G lignocellulosic substrates

Pseudomonas putida is a highly solvent‐resistant microorganism and useful chassis for the production of value‐added compounds from lignocellulosic residues, in particular aromatic compounds that are made from phenylalanine. The use of these agricultural residues requires a two‐step treatment to release the components of the polysaccharides of cellulose and hemicellulose as monomeric sugars, the most abundant monomers being glucose and xylose. Pan‐genomic studies have shown that Pseudomonas putida metabolizes glucose through three convergent pathways to yield 6‐phosphogluconate and subsequently metabolizes it through the Entner–Doudoroff pathway, but the strains do not degrade xylose. The valorization of both sugars is critical from the point of view of economic viability of the process. For this reason, a P. putida strain was endowed with the ability to metabolize xylose via the xylose isomerase pathway, by incorporating heterologous catabolic genes that convert this C5 sugar into intermediates of the pentose phosphate cycle. In addition, the open reading frame T1E_2822, encoding glucose dehydrogenase, was knocked‐out to avoid the production of the dead‐end product xylonate. We generated a set of DOT‐T1E‐derived strains that metabolized glucose and xylose simultaneously in culture medium and that reached high cell density with generation times of around 100 min with glucose and around 300 min with xylose. The strains grew in 2G hydrolysates from diluted acid and steam explosion pretreated corn stover and sugarcane straw. During growth, the strains metabolized > 98% of glucose, > 96% xylose and > 85% acetic acid. In 2G hydrolysates P. putida 5PL, a DOT‐T1E derivative strain that carries up to five independent mutations to avoid phenylalanine metabolism, accumulated this amino acid in the medium. We constructed P. putida 5PLΔgcd (xylABE) that produced up to 250 mg l⁻¹ of phenylalanine when grown in 2G pretreated corn stover or sugarcane straw. These results support as a proof of concept the potential of P. putida as a chassis for 2G processes.

DNA-SIP identification of phenanthrene-degrading bacteria undergoing bioaugmentation and natural attenuation in petroleum-contaminated soil

DNA-stable isotope probing (SIP) with ¹³C labeled phenanthrene (PHE) as substrate was used to identify specific bacterial degraders during natural attenuation (NA) and bioaugmentation (BA) in petroleum contaminated soil. BA, with the addition of a bacterial suspension mixture named GZ, played a significant role in PHE degradation with a higher PHE removal rate (∼90%) than that of NA (∼80%) during the first 3 days, and remarkably altered microbial communities. Of the five strains introduced in BA, only two genera, particularly, Ochrobactrum, Rhodococcus were extensively responsible for PHE-degradation. Six (Bacillus sp., Acinetobacter sp., Xanthomonas sp., Conexibacter sp., Acinetobacter sp. and Staphylococcus sp.) and seven (Ochrobactrum sp., Rhodococcus sp., Alkanindiges sp., Williamsia sp., Sphingobium sp., Gillisia sp. and Massilia sp.) bacteria responsible for PHE degradation were identified in NA and BA treatments, respectively. This study reports for the first time the association of Xanthomonas sp., Williamsia sp., and Gillisia sp. to PHE degradation.

Whole Genome Sequencing and Tn5-Insertion Mutagenesis of Pseudomonas taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease

The Gram-negative bacterium Pseudomonas taiwanensis is a novel bacterium that uses shrimp shell waste as its sole sources of carbon and nitrogen. It is a versatile bacterium with potential for use in biological control, with activities including toxicity toward insects, fungi, and the rice pathogen Xanthomonas oryzae pv.oryzae (Xoo). In this study, the complete 5.08-Mb genome sequence of P. taiwanensis CMS was determined by a combination of NGS/Sanger sequencing and optical mapping. Comparison of optical maps of seven Pseudomonas species showed that P. taiwanensis is most closely related to P. putida KT 2400. We screened a total of 11,646 individual Tn5-transponson tagged strains to identify genes that are involved in the production and regulation of the iron-chelator pyoverdine in P. taiwanensis, which is a key anti-Xoo factor. Our results indicated that the two-component system (TCS) EnvZ/OmpR plays a positive regulatory role in the production of pyoverdine, whereas the sigma factor RpoS functions as a repressor. The knowledge of the molecular basis of the regulation of pyoverdine by P. taiwanensis provided herein will be useful for its development for use in biological control, including as an anti-Xoo agent.

Enabling anoxic acetate assimilation by electrode-driven respiration in the obligate aerobe, Pseudomonas putida

This study examined the obligate aerobe, Pseudomonas putida, using acetate as the sole carbon and energy source, and respiration via an anode as the terminal electron acceptor under anoxic conditions. P. putida showed significantly different acetate assimilation in a closed-circuit microbial fuel cell (CC-MFC) compared to an open circuit MFC (OC-MFC). More than 72% (2.6 mmol) of acetate was consumed during 84 hrs in the CC-MFC in contrast to the no acetate consumption observed in the OC-MFC. The CC-MFC produced 150 μA (87 C) from acetate metabolization. Electrode-based respiration reduced the NADH/NAD⁺ ratio anaerobically, which is similar to the aerobic condition. The CC-MFC showed significantly higher acetyl-CoA synthetase activity than the OC-MFC (0.028 vs. 0.001 μmol/min/mg), which was comparable to the aerobic condition (circa 60%). Overall, electrode-based respiration enables P. putida to metabolize acetate under anoxic conditions and provide a platform to regulate the bacterial redox balance without oxygen.

Genome-Wide Analysis of Sugar Transporters Identifies the gtsA Gene for Glucose Transportation in Pseudomonas stutzeri A1501

Pseudomonas stutzeri A1501 possesses an extraordinary number of transporters which confer this rhizosphere bacterium with the sophisticated ability to metabolize various carbon sources. However, sugars are not a preferred carbon source for P. stutzeri A1501. The P. stutzeri A1501 genome has been sequenced, allowing for the homology-based in silico identification of genes potentially encoding sugar-transport systems by using established microbial sugar transporters as a template sequence. Genomic analysis revealed that there were 10 sugar transporters in P. stutzeri A1501, most of which belong to the ATP-binding cassette (ABC) family (5/10); the others belong to the phosphotransferase system (PTS), major intrinsic protein (MIP) family, major facilitator superfamily (MFS) and the sodium solute superfamily (SSS). These systems might serve for the import of glucose, galactose, fructose and other types of sugar. Growth analysis showed that the only effective medium was glucose and its corresponding metabolic system was relatively complete. Notably, the loci of glucose metabolism regulatory systems HexR, GltR/GtrS, and GntR were adjacent to the transporters ABC^MalEFGK, ABC^GtsABCD, and ABC^MtlEFGK, respectively. Only the ABC^GtsABCD expression was significantly upregulated under both glucose-sufficient and -limited conditions. The predicted structure and mutant phenotype data of the key protein GtsA provided biochemical evidence that P. stutzeri A1501 predominantly utilized the ABC^GtsABCD transporter for glucose uptake. We speculate that gene absence and gene diversity in P. stutzeri A1501 was caused by sugar-deficient environmental factors and hope that this report can provide guidance for further analysis of similar bacterial lifestyles.

Functional metagenomic exploration identifies novel prokaryotic copper resistance genes from the soil microbiome

Functional metagenomics is a premise-free approach for exploring metal resistance genes, enabling more profound effects on the development of bioremediation tools than pure culture based selection. Six soil metagenomic libraries were screened for copper (Cu) resistance genes in the current study through conventional functional genomics. Clones from the six metagenomic libraries were randomly selected from solid medium supplied with Cu, resulting in 411 Cu resistance clones. Thirty-five clones with the strongest Cu resistance were sequenced and 12 unique sequences harboring 25 putative open reading frames were obtained. It is inferred by bioinformatic analysis that putative genes carried by these recombinant plasmids probably function in the pathways of responding to Cu stress, including energy metabolism, integral components of membrane, ion transport/chelation, protein/amino acid metabolism, carbohydrate/fatty acid metabolism, signal transduction and DNA binding. The sequenced clones were re-transformed into Escherichia coli strain DH5α, and the host's biomass and the metal sorption under Cu stress were subsequently determined. The results showed that the biomass of eight of the clones was significantly increased, whereas four of them were significantly reduced. A negative correlation (R = 0.86) was found between the biomass and Cu sorption capacity. The 12 positive clones were further transferred into a Cu-sensitive E. coli strain (ΔCopA), among which nine restored the host's Cu resistance substantially. The Cu resistant genes explored in this study by functional metagenomics possess a potential capacity for developing novel bioremediation strategies, and the findings imply a vast diversity of microbial Cu resistance genetic factors in soil yet to be discovered.

The biotechnological potential of marine bacteria in the novel lineage of Pseudomonas pertucinogena

Marine habitats represent a prolific source for molecules of biotechnological interest. In particular, marine bacteria have attracted attention and were successfully exploited for industrial applications. Recently, a group of Pseudomonas species isolated from extreme habitats or living in association with algae or sponges were clustered in the newly established Pseudomonas pertucinogena lineage. Remarkably for the predominantly terrestrial genus Pseudomonas, more than half (9) of currently 16 species within this lineage were isolated from marine or saline habitats. Unlike other Pseudomonas species, they seem to have in common a highly specialized metabolism. Furthermore, the marine members apparently possess the capacity to produce biomolecules of biotechnological interest (e.g. dehalogenases, polyester hydrolases, transaminases). Here, we summarize the knowledge regarding the enzymatic endowment of the marine Pseudomonas pertucinogena bacteria and report on a genomic analysis focusing on the presence of genes encoding esterases, dehalogenases, transaminases and secondary metabolites including carbon storage compounds.

The versatility of Pseudomonas putida in the rhizosphere environment

This article addresses the lifestyle of Pseudomonas and focuses on how Pseudomonas putida can be used as a model system for biotechnological processes in agriculture, and in the removal of pollutants from soils. In this chapter we aim to show how a deep analysis using genetic information and experimental tests has helped to reveal insights into the lifestyle of Pseudomonads. Pseudomonas putida is a Plant Growth Promoting Rhizobacteria (PGPR) that establishes commensal relationships with plants. The interaction involves a series of functions encoded by core genes which favor nutrient mobilization, prevention of pathogen development and efficient niche colonization. Certain Pseudomonas putida strains harbor accessory genes that confer specific biodegradative properties and because these microorganisms can thrive on the roots of plants they can be exploited to remove pollutants via rhizoremediation, making the consortium plant/Pseudomonas a useful tool to combat pollution.

Metabolite profiling of the cold adaptation of Pseudomonas putida KT2440 and cold-sensitive mutants

Free-living bacteria such as Pseudomonas putida are frequently exposed to temperature shifts and non-optimal growth conditions. We compared the transcriptome and metabolome of the cold adaptation of P. putida KT2440 and isogenic cold-sensitive transposon mutants carrying transposons in their cbrA, cbrB, pcnB, vacB, and bipA genes. Pseudomonas putida changes the mRNA expression of about 43% of all annotated open reading frames during this initial phase of cold adaptation, but only a small number of 6-93 genes were differentially expressed at 10°C between the wild-type strain and the individual mutants. The spectrum of metabolites underwent major changes during cold adaptation particularly in the mutants. Both the KT2440 strain and the mutants increased the levels of the most abundant sugars and amino acids which were more pronounced in the cold-sensitive mutants. All mutants depleted their pools for core metabolites of aromatic and sugar metabolism, but increased their pool of polar amino acids which should be advantageous to cope with the cold stress.

Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species

The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.

Aldehyde dehydrogenase diversity in bacteria of the Pseudomonas genus

Aldehyde dehydrogenases (ALDHs) comprise one of the most ancient protein superfamilies widely distributed in the three domains of life. Their members have been extensively studied in animals and plants, sorted out in different ALDH protein families and their participation in a broad variety of metabolic pathways has been documented. Paradoxically, no systematic studies comprising ALDHs from bacteria have been performed so far. Among bacteria, the genus Pseudomonas occupies numerous ecological niches, and is one of the most complex bacterial genera with the largest number of known species. For these reasons, we selected Pseudomonas as a paradigm to analyze the diversity of ALDHs in bacteria. With this aim, complete Pseudomonas genome sequences and annotations were retrieved from NCBI's RefSeq genome database. The 258 Pseudomonas strains belong to 46 different species, along with 23 with no species designation. The genomes of these Pseudomonas contain from 3,315 to 6,825 annotated protein coding genes. A total of 6,510 ALDH sequences were found in the selected Pseudomonas, with a median of 24 ALDH-coding genes per strain (by comparison humans possess only 19 different ALDH loci). Pseudomonas saudiphocaensis possesses the lowest number of aldh genes (9), while Pseudomonas pseudoalcaligenes KF707 NBRC110670 possesses the maximum number of aldh genes (49). The ALDHs found in Pseudomonas can be sorted out into 42 protein families, with a predominance of 14 families, which contained 76% of all ALDHs found. In this regard, it is important to note that many Pseudomonas genomes have multiple aldh genes coding for proteins belonging to the same family. Given that all strains contained members of families ALDH4, ALDH5, ALDH6, ALDH14, ALDH18 and ALDH27, we consider these families to be part of the core Pseudomonas genome.

Regulation of carbohydrate degradation pathways in Pseudomonas involves a versatile set of transcriptional regulators

Bacteria of the genus Pseudomonas are widespread in nature. In the last decades, members of this genus, especially Pseudomonas aeruginosa and Pseudomonas putida, have acquired great interest because of their interactions with higher organisms. Pseudomonas aeruginosa is an opportunistic pathogen that colonizes the lung of cystic fibrosis patients, while P. putida is a soil bacterium able to establish a positive interaction with the plant rhizosphere. Members of Pseudomonas genus have a robust metabolism for amino acids and organic acids as well as aromatic compounds; however, these microbes metabolize a very limited number of sugars. Interestingly, they have three-pronged metabolic system to generate 6-phosphogluconate from glucose suggesting an adaptation to efficiently consume this sugar. This review focuses on the description of the regulatory network of glucose utilization in Pseudomonas, highlighting the differences between P. putida and P. aeruginosa. Most interestingly, It is highlighted a functional link between glucose assimilation and exotoxin A production in P. aeruginosa. The physiological relevance of this connection remains unclear, and it needs to be established whether a similar relationship is also found in other bacteria.

Identification and elucidation of in vivo function of two alanine racemases from Pseudomonas putida KT2440

The genome of Pseudomonas putida KT2440 contains two open reading frames (ORFs), PP_3722 and PP_5269, that encode proteins with a Pyridoxal phosphate binding motif and a high similarity to alanine racemases. Alanine racemases play a key role in the biosynthesis of D-alanine, a crucial amino acid in the peptidoglycan layer. For these ORFs, we generated single and double mutants and found that inactivation of PP_5269 resulted in D-alanine auxotrophy, while inactivation of PP_3722 did not. Furthermore, as expected, the PP_3722/PP_5269 double mutant was a strict auxotroph for D-alanine. These results indicate that PP_5269 is an alr allele and that it is the essential alanine racemase in P. putida. We observed that the PP_5269 mutant grew very slowly, while the double PP_5269/PP_3722 mutant did not grow at all. This suggests that PP_3722 may replace PP_5269 in vivo. In fact, when the ORF encoding PP_3772 was cloned into a wide host range expression vector, ORF PP_3722 successfully complemented P. putida PP_5269 mutants. We purified both proteins to homogeneity and while they exhibit similar K_M values, the V_max of PP_5269 is fourfold higher than that of PP_3722. Here, we propose that PP_5269 and PP_3722 encode functional alanine racemases and that these genes be named alr-1 and alr-2 respectively.

Specific Gene Loci of Clinical Pseudomonas putida Isolates

Pseudomonas putida are ubiquitous inhabitants of soils and clinical isolates of this species have been seldom described. Clinical isolates show significant variability in their ability to cause damage to hosts because some of them are able to modulate the host’s immune response. In the current study, comparisons between the genomes of different clinical and environmental strains of P. putida were done to identify genetic clusters shared by clinical isolates that are not present in environmental isolates. We show that in clinical strains specific genes are mostly present on transposons, and that this set of genes exhibit high identity with genes found in pathogens and opportunistic pathogens. The set of genes prevalent in P. putida clinical isolates, and absent in environmental isolates, are related with survival under oxidative stress conditions, resistance against biocides, amino acid metabolism and toxin/antitoxin (TA) systems. This set of functions have influence in colonization and survival within human tissues, since they avoid host immune response or enhance stress resistance. An in depth bioinformatic analysis was also carried out to identify genetic clusters that are exclusive to each of the clinical isolates and that correlate with phenotypical differences between them, a secretion system type III-like was found in one of these clinical strains, a determinant of pathogenicity in Gram-negative bacteria.

Interspecies signalling: Pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance

In Gram-negative bacteria, multidrug efflux pumps are responsible for the extrusion of chemicals that are deleterious for growth. Some of these efflux pumps are induced by endogenously produced effectors, while abiotic or biotic signals induce the expression of other efflux pumps. In Pseudomonas putida, the TtgABC efflux pump is the main antibiotic extrusion system that respond to exogenous antibiotics through the modulation of the expression of this operon mediated by TtgR. The plasmid-encoded TtgGHI efflux pump in P. putida plays a minor role in antibiotic resistance in the parental strain; however, its role is critical in isogenic backgrounds deficient in TtgABC. Expression of ttgGHI is repressed by the TtgV regulator that recognizes indole as an effector, although P. putida does not produce indole itself. Because indole is not produced by Pseudomonas, the indole-dependent antibiotic resistance seems to be part of an antibiotic resistance programme at the community level. Pseudomonas putida recognizes indole added to the medium or produced by Escherichia coli in mixed microbial communities. Transcriptomic analyses revealed that the indole-specific response involves activation of 43 genes and repression of 23 genes. Indole enhances not only the expression of the TtgGHI pump but also a set of genes involved in iron homeostasis, as well as genes for amino acid catabolism. In a ttgABC-deficient P. putida, background ampicillin and other bactericidal compounds lead to cell death. Co-culture of E. coli and P. putida ΔttgABC allowed growth of the P. putida mutant in the presence of ampicillin because of induction of the indole-dependent efflux pump.

The biology of habitat dominance; can microbes behave as weeds?

Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard-wired to behave in a vigorous and ecologically aggressive manner. These 'microbial weeds' are able to dominate the communities that develop in fertile but uncolonized--or at least partially vacant--habitats via traits enabling them to out-grow competitors; robust tolerances to habitat-relevant stress parameters and highly efficient energy-generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat-specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp., Salinibacter ruber and Haloquadratum walsbyi. Some microbes, such as Escherichia coli, Mycobacterium smegmatis and Pseudoxylaria spp., exhibit characteristics of both weed and non-weed species. We propose that the concept of nonweeds represents a 'dustbin' group that includes species such as Synodropsis spp., Polypaecilum pisce, Metschnikowia orientalis, Salmonella spp., and Caulobacter crescentus. We show that microbial weeds are conceptually distinct from plant weeds, microbial copiotrophs, r-strategists, and other ecophysiological groups of microorganism. Microbial weed species are unlikely to emerge from stationary-phase or other types of closed communities; it is open habitats that select for weed phenotypes. Specific characteristics that are common to diverse types of open habitat are identified, and implications of weed biology and open-habitat ecology are discussed in the context of further studies needed in the fields of environmental and applied microbiology.

Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome

Pseudomonas putida DOT-T1E is an organic solvent tolerant strain capable of degrading aromatic hydrocarbons. Here we report the DOT-T1E genomic sequence (6 394 153 bp) and its metabolic atlas based on the classification of enzyme activities. The genome encodes for at least 1751 enzymatic reactions that account for the known pattern of C, N, P and S utilization by this strain. Based on the potential of this strain to thrive in the presence of organic solvents and the subclasses of enzymes encoded in the genome, its metabolic map can be drawn and a number of potential biotransformation reactions can be deduced. This information may prove useful for adapting desired reactions to create value-added products. This bioengineering potential may be realized via direct transformation of substrates, or may require genetic engineering to block an existing pathway, or to re-organize operons and genes, as well as possibly requiring the recruitment of enzymes from other sources to achieve the desired transformation.

Funding Information Work in our laboratory was supported by Fondo Social Europeo and Fondos FEDER from the European Union, through several projects (BIO2010-17227, Consolider-Ingenio CSD2007-00005, Excelencia 2007 CVI-3010, Excelencia 2011 CVI-7391 and EXPLORA BIO2011-12776-E).

Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1

Pseudomonas putida BIRD-1 is a plant growth-promoting rhizobacterium whose genome size is 5.7 Mbp. It adheres to plant roots and colonizes the rhizosphere to high cell densities even in soils with low moisture. This property is linked to its ability to synthesize trehalose, since a mutant deficient in the synthesis of trehalose exhibited less tolerance to desiccation than the parental strain. The genome of BIRD-1 encodes a wide range of proteins that help it to deal with reactive oxygen stress generated in the plant rhizosphere. BIRD-1 plant growth-promoting rhizobacteria properties derive from its ability to enhance phosphorous and iron solubilization and to produce phytohormones. BIRD-1 is capable of solubilizing insoluble inorganic phosphate forms through acid production. The genome of BIRD-1 encodes at least five phosphatases related to phosphorous solubilization, one of them being a phytase that facilitates the utilization of phytic acid, the main storage form of phosphorous in plants. Pyoverdine is the siderophore produced by this strain, a mutant that in the FvpD siderophore synthase failed to grow on medium without supplementary iron, but the mutant was as competitive as the parental strain in soils because it captures the siderophores produced by other microbes. BIRD-1 overproduces indole-3-acetic acid through convergent pathways.

Exploring the optimal strategy to predict essential genes in microbes

Accurately predicting essential genes is important in many aspects of biology, medicine and bioengineering. In previous research, we have developed a machine learning based integrative algorithm to predict essential genes in bacterial species. This algorithm lends itself to two approaches for predicting essential genes: learning the traits from known essential genes in the target organism, or transferring essential gene annotations from a closely related model organism. However, for an understudied microbe, each approach has its potential limitations. The first is constricted by the often small number of known essential genes. The second is limited by the availability of model organisms and by evolutionary distance. In this study, we aim to determine the optimal strategy for predicting essential genes by examining four microbes with well-characterized essential genes. Our results suggest that, unless the known essential genes are few, learning from the known essential genes in the target organism usually outperforms transferring essential gene annotations from a related model organism. In fact, the required number of known essential genes is surprisingly small to make accurate predictions. In prokaryotes, when the number of known essential genes is greater than 2% of total genes, this approach already comes close to its optimal performance. In eukaryotes, achieving the same best performance requires over 4% of total genes, reflecting the increased complexity of eukaryotic organisms. Combining the two approaches resulted in an increased performance when the known essential genes are few. Our investigation thus provides key information on accurately predicting essential genes and will greatly facilitate annotations of microbial genomes.

Involvement of the global Crp regulator in cyclic AMP-dependent utilization of aromatic amino acids by Pseudomonas putida

The phhAB operon encodes a phenylalanine hydroxylase involved in the conversion of L-phenylalanine into L-tyrosine in Pseudomonas putida. The phhAB promoter is transcribed by RNA polymerase sigma-70 and is unusual in that the specific regulator PhhR acts as an enhancer protein that binds to two distant upstream sites (-75 to -92 and -132 to -149). There is an integration host factor (IHF) binding site that overlaps the proximal PhhR box, and, consequently, IHF acts as an inhibitor of transcription. Use of L-phenylalanine is compromised in a crp-deficient background due to reduced expression from the phhAB promoter. Electrophoretic mobility shift assays and DNase I footprinting assays reveal that Crp binds at a site centered at -109 only in the presence of cyclic AMP (cAMP). We show, using circular permutation analysis, that the simultaneous binding of Crp/cAMP and PhhR bends DNA to bring positive regulators and RNA polymerase into close proximity. This nucleoprotein complex promotes transcription from phhA only in response to L-phenylalanine.

The Crp regulator of Pseudomonas putida: evidence of an unusually high affinity for its physiological effector, cAMP

Although the genome of Pseudomonas putida KT2440 encodes an orthologue of the crp gene of Escherichia coli (encoding the cAMP receptor protein), the regulatory scope of this factor seems to be predominantly co-opted in this bacterium for controlling non-metabolic functions. In order to investigate the reasons for such a functional divergence in otherwise nearly identical proteins, the Crp regulator of P. putida (Crp(P. putida)) was purified to apparent homogeneity and subject to a battery of in vitro assays aimed at determining its principal physicochemical properties. Analytical ultracentrifugation indicated effector-free Crp(P. putida) to be a dimer in solution that undergoes a significant change in its hydrodynamic shape in the presence of cAMP. Such a conformational transition was confirmed by limited proteolysis of the protein in the absence or presence of the inducer. Thermodynamic parameters calculated by isothermal titration calorimetry revealed a tight cAMP-Crp(P. putida) association with an apparent K(D) of 22.5 ± 2.8 nM, i.e. much greater affinity than that reported for the E. coli's counterpart. The regulator also bound cGMP, but with a K(D) = 2.6 ± 0.3 µM. An in vitro transcription system was then set up with purified P. putida's RNA polymerase for examining the preservation of the correct protein-protein architecture that makes Crp to activate target promoters. These results, along with cognate gel retardation assays indicated that all basic features of the reference Crp(E. coli) protein are kept in the P. putida's counterpart, albeit operating under a different set of parameters, the extraordinarily high affinity for cAMP being the most noticeable.

The ColRS system is essential for the hunger response of glucose-growing Pseudomonas putida

Background

The survival of bacteria largely depends on signaling systems that coordinate cell responses to environmental cues. Previous studies on the two-component ColRS signal system in Pseudomonas putida revealed a peculiar subpopulation lysis phenotype of colR mutant that grows on solid glucose medium. Here, we aimed to clarify the reasons for the lysis of bacteria.

Results

We present evidence that the lysis defect of P. putida colR mutant is linked to hunger response. A subpopulation prone to lysis was located in the periphery of bacterial cultures growing on solid medium. Cell lysis was observed in glucose-limiting, but not in glucose-rich conditions. Furthermore, lysis was also alleviated by exhaustion of glucose from the medium which was evidenced by a lower lysis of central cells compared to peripheral ones. Thus, lysis takes place at a certain glucose concentration range that most probably provides bacteria a hunger signal. An analysis of membrane protein pattern revealed several hunger-induced changes in the bacterial outer membrane: at glucose limitation the amount of OprB1 channel protein was significantly increased whereas that of OprE was decreased. Hunger-induced up-regulation of OprB1 correlated in space and time with the lysis of the colR mutant, indicating that hunger response is detrimental to the colR-deficient bacteria. The amount of OprB1 is controlled post-transcriptionally and derepression of OprB1 in glucose-limiting medium depends at least partly on the carbon catabolite regulator protein Crc. The essentiality of ColR in hunger response can be bypassed by reducing the amount of certain outer membrane proteins. In addition to depletion of OprB1, the lysis defect of colR mutant can be suppressed by the down-regulation of OprF levels and the hindering of SecB-dependent protein secretion.

Conclusions

We show that Pseudomonas putida growing on solid glucose medium adapts to glucose limitation through up-regulation of the sugar channel protein OprB1 that probably allows enhanced acquisition of a limiting nutrient. However, to survive such hunger response bacteria need signalling by the ColRS system. Hence, the ColRS system should be considered a safety factor in hunger response that ensures the welfare of the cell membrane during the increased expression of certain membrane proteins.

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.

Characterization of the RND family of multidrug efflux pumps: in silico to in vivo confirmation of four functionally distinct subgroups

We have developed a generalized profile that identifies members of the root-nodulation-cell-division (RND) family of efflux pumps and classifies them into four functional subfamilies. According to Z-score values, efflux pumps can be grouped by their metabolic function, thus making it possible to distinguish pumps involved in antibiotic resistance (group 1) from those involved in metal resistance (group 3). In silico data regarding efflux pumps in group 1 were validated after identification of RND efflux pumps in a number of environmental microbes that were isolated as resistant to ethidium bromide. Analysis of the Pseudomonas putida KT2440 genome identified efflux pumps in all groups. A collection of mutants in efflux pumps and a screening platform consisting of 50 drugs were created to assign a function to the efflux pumps. We validated in silico data regarding efflux pumps in groups 1 and 3 using 9 different mutants. Four mutants belonging to group 2 were found to be more sensitive than the wild-type to oxidative stress-inducing agents such as bipyridyl and methyl viologen. The two remaining mutants belonging to group 4 were found to be more sensitive than the parental to tetracycline and one of them was particularly sensitive to rubidium and chromate. By effectively combining in vivo data with generalized profiles and gene annotation data, this approach allowed the assignment, according to metabolic function, of both known and uncharacterized RND efflux pumps into subgroups, thereby providing important new insight into the functions of proteins within this family.

Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida

The genome of the soil bacterium Pseudomonas putida KT2440 encodes singular orthologues of genes crp (encoding the catabolite repression protein, Crp) and cyaA (adenylate cyclase) of Escherichia coli. The levels of cAMP formed by P. putida cells were below detection with a Dictyostelium biosensor in vivo. The cyaA(P. putida) gene was transcribed in vivo but failed to complement the lack of maltose consumption of a cyaA mutant of E. coli, thereby indicating that cyaA(P. putida) was poorly translated or rendered non-functional in the heterologous host. Yet, generation of cAMP by CyaA(P. putida) could be verified by expressing the cyaA(P. putida) gene in a hypersensitive E. coli strain. On the other hand, the crp(P. putida) gene restored the metabolic capacities of an equivalent crp mutant of E. coli, but not in a double crp/cyaA strain, suggesting that the ability to regulate such functions required cAMP. In order to clarify the breadth of the Crp/cAMP system in P. putida, crp and cyaA mutants were generated and passed through a battery of phenotypic tests for recognition of gross metabolic properties and stress-endurance abilities. These assays revealed that the loss of each gene led in most (but not all) cases to the same phenotypic behaviour, indicating a concerted functionality. Unexpectedly, none of the mutations affected the panel of carbon compounds that can be used by P. putida as growth substrates, the mutants being impaired only in the use of various dipeptides as N sources. Furthermore, the lack of crp or cyaA had little influence on the gross growth fingerprinting of the cells. The poor physiological profile of the Crp-cAMP system of P. putida when compared with E. coli exposes a case of regulatory exaptation, i.e. the process through which a property evolved for a particular function is co-opted for a new use.

Sensing of environmental signals: classification of chemoreceptors according to the size of their ligand binding regions

Central to the different forms of taxis are methyl-accepting chemotaxis proteins (MCPs). The increasing number of genome sequences reveals that MCPs differ enormously in sequence, topology and genomic abundance. This work is a one-by-one bioinformatic analysis of the almost-totality of MCP genes available and a classification of motile bacteria according to their lifestyle. On average, motile archaea have 6.7 MCP genes per genome whereas motile bacteria have more than twice as much. We show that the number of MCPs per genome depends on bacterial lifestyle and metabolic diversity, but weakly on genome size. Signal perception at an MCP occurs at the N-terminal ligand binding region (LBR). Here we show that around 88% of MCPs possess an LBR that remains un-annotated in SMART. MCPs can be classified into two clusters according to the size of the LBR. Cluster I receptors have an LBR between 120 and 210 amino acids whereas cluster II receptors have larger LBRs of 220-299 amino acids. There is evidence that suggests that some cluster II LBRs are composed of two cluster I LBRs. Further evidence indicates that other cluster II LBRs might harbour novel sensor domains. Cluster II receptors are dominant in archaea whereas cluster I receptors are prevalent in bacteria. MCPs can be classified into six different receptor topologies and this work contains a first estimation of the relative abundance of different receptor topologies in bacteria and archaea. Topologies involving extracytoplasmic sensing are prevalent in bacteria whereas topologies with cytosolic signal recognition are abundant in archaea.

Catabolite repression of the TodS/TodT two-component system and effector-dependent transphosphorylation of TodT as the basis for toluene dioxygenase catabolic pathway control

The TodS/TodT two-component system of Pseudomonas putida regulates the expression of the toluene dioxygenase (tod) operon for the metabolism of toluene, benzene, and ethylbenzene. The sensor kinase TodS has a complex domain arrangement containing two functional modules, each harboring a sensor and an autokinase domain separated by a receiver domain. The TodT protein is the cognate response regulator that activates transcription of the toluene dioxygenase (TOD) pathway genes at the P(todX) promoter. We report in this study that the todST operon is transcribed from a main promoter and that the +1 initiation point is located 31 nucleotides upstream from the A of the first ATG codon and is preceded by a -10/-35 canonical promoter. Expression from P(todS) is under catabolite control, and in cells growing with glucose, the level of expression from this promoter is reduced, which in turn translates to low levels of the TodS/TodT regulators and results in a decrease of transcription from the P(todX) promoter. Thus, the main underlying regulatory mechanisms of the tod structural genes are at the levels of catabolite repression control from P(todS) and transcription activation, mediated by the TodT response regulator through a regulatory cascade in which the effector enhances autophosphorylation of TodS by ATP, with subsequent transphosphorylation of TodT.

Carbon catabolite repression in Pseudomonas : optimizing metabolic versatility and interactions with the environment

Metabolically versatile free-living bacteria have global regulation systems that allow cells to selectively assimilate a preferred compound among a mixture of several potential carbon sources. This process is known as carbon catabolite repression (CCR). CCR optimizes metabolism, improving the ability of bacteria to compete in their natural habitats. This review summarizes the regulatory mechanisms responsible for CCR in the bacteria of the genus Pseudomonas, which can live in many different habitats. Although the information available is still limited, the molecular mechanisms responsible for CCR in Pseudomonas are clearly different from those of Enterobacteriaceae or Firmicutes. An understanding of the molecular mechanisms underlying CCR is important to know how metabolism is regulated and how bacteria degrade compounds in the environment. This is particularly relevant for compounds that are degraded slowly and accumulate, creating environmental problems. CCR has a major impact on the genes involved in the transport and metabolism of nonpreferred carbon sources, but also affects the expression of virulence factors in several bacterial species, genes that are frequently directed to allow the bacterium to gain access to new sources of nutrients. Finally, CCR has implications in the optimization of biotechnological processes such as biotransformations or bioremediation strategies.