Cloning, mapping and characterization of the Pseudomonas aeruginosa hemL gene

Blue laser light inhibits biofilm formation in vitro and in vivo by inducing oxidative stress

Resolution of bacterial infections is often hampered by both resistance to conventional antibiotic therapy and hiding of bacterial cells inside biofilms, warranting the development of innovative therapeutic strategies. Here, we report the efficacy of blue laser light in eradicating Pseudomonas aeruginosa cells, grown in planktonic state, agar plates and mature biofilms, both in vitro and in vivo, with minimal toxicity to mammalian cells and tissues. Results obtained using knock-out mutants point to oxidative stress as a relevant mechanism by which blue laser light exerts its anti-microbial effect. Finally, the therapeutic potential is confirmed in a mouse model of skin wound infection. Collectively, these data set blue laser phototherapy as an innovative approach to inhibit bacterial growth and biofilm formation, and thus as a realistic treatment option for superinfected wounds.

Kinemage of action - proposed reaction mechanism of glutamate-1-semialdehyde aminomutase at an atomic level

Glutamate-1-semialdehyde aminomutase (GSAM), a key enzyme in tetrapyrrole cofactor biosynthesis, performs a unique transamination on a single substrate. The substrate, glutamate-1-semialdehyde (GSA), undergoes a reaction that exchanges the position of an amine and a carbonyl group to produce 5-aminolevulinic acid (ALA). This transamination reaction is unique in the fact that is does not require an external cofactor to act as a nitrogen donor or acceptor in this transamination reaction. One of the other remarkable features of the catalytic mechanism is the release free in the enzyme active site of the intermediate 4,5-diaminovaleric acid (DAVA). The action of a gating loop prevents the escape of DAVA from the active site. In a MD simulation approach, using snapshots provided by X-ray crystallography and protein crystal absorption spectrometry data, the individual catalytic steps in this unique intramolecular transamination have been elucidated.

A large gene cluster encoding peptide synthetases and polyketide synthases is involved in production of siderophores and oxidative stress response in the cyanobacterium Anabaena sp. strain PCC 7120

Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are necessary for the production of a variety of secondary metabolites, such as siderophores involved in iron acquisition. In response to iron limitation, the cyanobacterium Anabaena sp. strain PCC 7120 synthesizes several siderophores. The chromosome of this organism contains a large gene cluster of 76 kb with 24 open-reading frames from all2658 to all2635, including those that encode seven NRPSs and two PKSs. The function of this gene cluster was unknown, and one possibility could be the synthesis of siderophores. These genes were indeed activated under conditions of iron limitation. One mutant, MDelta41-49, bearing a large deletion of 43.4 kb in this gene cluster, synthesized considerably less siderophores and contained less iron as compared with the wild type. Its growth rate was similar to the wild type in the presence of iron, but was reduced when iron became limiting. Two other mutants, MDelta44-45 and MDelta47-49, lacking either all2644 and all2645, or all2647, all2648 and all2649 respectively, produced more siderophores than MDelta41-49, but less than the wild type. These genes were also activated under oxidative stress conditions to which MDelta41-49 was highly sensitive, consistent with the importance of iron in oxidative stress response. We propose that this gene cluster is involved in the synthesis of siderophores in Anabaena sp. PCC 7120 and plays an important role in defence against oxidative stress.

Combined physical and genetic map of the Pseudomonas putida KT2440 chromosome

A combined physical and genetic map of the Pseudomonas putida KT2440 genome was constructed from data obtained by pulsed-field gel electrophoresis techniques (PFGE) and Southern hybridization. Circular genome size was estimated at 6.0 Mb by adding the sizes of 19 SwaI, 9 PmeI, 6 PacI, and 6 I-CeuI fragments. A complete physical map was achieved by combining the results of (i) analysis of PFGE of the DNA fragments resulting from digestion of the whole genome with PmeI, SwaI, I-CeuI, and PacI as well as double digestion with combinations of these enzymes and (ii) Southern hybridization analysis of the whole wild-type genome digested with different enzymes and hybridized against a series of probes obtained as cloned genes from different pseudomonads of rRNA group I and Escherichia coli, as P. putida DNA obtained by PCR amplification based on sequences deposited at the GenBank database, and by labeling of macrorestriction fragments of the P. putida genome eluted from agarose gels. As an alternative, 10 random mini-Tn5-Km mutants of P. putida KT2440 were used as a source of DNA, and the band carrying the mini-Tn5 in each mutant was identified after PFGE of a series of complete chromosomal digestions and hybridization with the kanamycin resistance gene of the mini-Tn5 as a probe. We established a circular genome map with an average resolution of 160 kb. Among the 63 genes located on the genetic map were key markers such as oriC, 6 rrn loci (rnnA to -F), recA, ftsZ, rpoS, rpoD, rpoN, and gyrB; auxotrophic markers; and catabolic genes for the metabolism of aromatic compounds. The genetic map of P. putida KT2440 was compared to those of Pseudomonas aeruginosa PAO1 and Pseudomonas fluorescens SBW25. The chromosomal backbone revealed some similarity in gene clustering among the three pseudomonads but differences in physical organization, probably as a result of intraspecific rearrangements.

Regulation of Pseudomonas aeruginosa hemF and hemN by the dual action of the redox response regulators Anr and Dnr

The oxidative decarboxylation of coproporphyrinogen III catalysed by an oxygen-dependent oxidase (HemF) and an oxygen-independent dehydrogenase (HemN) is one of the key regulatory points of haem biosynthesis in Pseudomonas aeruginosa. To investigate the oxygen-dependent regulation of hemF and hemN, the corresponding genes were cloned from the P. aeruginosa chromosome. Recognition sequences for the Fnr-type transcriptional regulator Anr were detected -44.5 bp from the 5' end of the hemF mRNA transcript and at an optimal distance of -41.5 bp with respect to the transcriptional start of hemN. An approximately 10-fold anaerobic induction of hemN gene expression was mediated by the dual action of Anr and a second Fnr-type regulator, Dnr. Regulation by both proteins required the Anr recognition sequence. Surprisingly, aerobic expression of hemN was dependent only on Anr. An anr mutant did not contain detectable amounts of hemN mRNA and accumulated coproporphyrin III both aerobically and anaerobically, indicating the importance of HemN for aerobic and anaerobic haem formation. Mutation of hemN and hemF did not abolish aerobic or anaerobic growth, indicating the existence of an additional HemN-type enzyme, which was termed HemZ. Expression of hemF was induced approximately 20-fold during anaerobic growth and, as was found for hemN, both Anr and Dnr were required for anaerobic induction. Paradoxically, oxygen is necessary for HemF catalysis, suggesting the existence of an additional physiological function for the P. aeruginosa HemF protein.

Cell biology and molecular basis of denitrification

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

The dnaK operon of Bacillus subtilis is heptacistronic

In 1992, we described the cloning and sequencing of the dnaK locus of Bacillus subtilis which, together with transcriptional studies, implied a tetracistronic structure of the operon consisting of the genes hrcA, grpE, dnaK, and dnaJ. We have repeated the Northern blot analysis, this time using riboprobes instead of oligonucleotides, and have detected a heat-inducible 8-kb transcript, suggesting the existence of additional heat shock genes downstream of dnaJ. Cloning and sequencing of that region revealed the existence of three novel heat shock genes named orf35, orf28, and orf50, extending the tetra- into a heptacistronic operon. This is now the largest dnaK operon to be described to date. The three new genes are transcribed as a part of the entire dnaK operon (8.0-kb heptacistronic heat-inducible transcript) and as part of a suboperon starting at an internal vegetative promoter immediately upstream of dnaJ (4.3-kb tetracistronic non-heat-inducible transcript). In addition, the Northern blot analysis detected several processing products of these two primary transcripts. To demonstrate the existence of the internal promoter, a DNA fragment containing this putative promoter structure was inserted upstream of a promoterless bgaB gene, resulting in the synthesis of beta-galactosidase. Challenging this transcriptional fusion with various stress factors did not result in the activation of this promoter. To assign a biological function to the three novel genes, they have each been inactivated by the insertion of a cat cassette. All of the mutants were viable, and furthermore, these genes are (i) not essential for growth at high temperatures, (ii) not involved in the regulation of the heat shock response, and (iii) sporulation proficient. Blocking transcription of the suboperon from the upstream heat-inducible promoter did not impair growth and viability at high temperatures.

The hemA gene encoding glutamyl-tRNA reductase from the archaeon Methanobacterium thermoautotrophicum strain Marburg

In archaea the first general tetrapyrrole precursor 5-aminolevulinic acid (ALA) is formed via the tRNA-dependent five-carbon pathway from glutamate. We have cloned the hemA gene encoding the central enzyme of the pathway glutamyl-tRNA reductase from the methanogenic archaeon Methanobacterium thermoautotrophicum by complementation of an Escherichia coli hemA mutant to ALA prototrophy. An 1194 bp open reading frame that encodes a 398 amino acid polypeptide with the calculated M, 44,509 was detected. The deduced amino acid sequence showed 20-35% amino acid identity to bacterial HemAs with the highest identity score to the Pseudomonas aeruginosa HemA. An identity of approximately 22% was found to plant HemAs. Glutamyl-tRNA reductase activity was shown for the M. thermoautotrophicum HemA after overexpression in E. coli and partial purification. The enzymatic reaction catalyzed by the partially purified enzyme revealed a temperature optimum of 65 degrees C at an optimal pH of 7.0. The reductase utilized preferentially NADPH for the reduction of the activated carboxyl group. The presence of ATP and GTP showed no obvious influence on catalysis.

Comparative genome mapping of Pseudomonas aeruginosa PAO with P. aeruginosa C, which belongs to a major clone in cystic fibrosis patients and aquatic habitats

A physical and genetic map was constructed for Pseudomonas aeruginosa C. Mainly, two-dimensional methods were used to place 47 SpeI, 8 PacI, 5 SwaI, and 4 I-CeuI sites onto the 6.5-Mb circular chromosome. A total of 21 genes, including the rrn operons and the origin of replication, were located on the physical map. Comparison of the physical and genetic map of strain C with that of the almost 600-kb-smaller genome of P. aeruginosa reference strain PAO revealed conservation of gene order between the two strains. A large-scale mosaic structure which was due to insertions of blocks of new genetic elements which had sizes of 23 to 155 kb and contained new SpeI sites was detected in the strain C chromosome. Most of these insertions were concentrated in three locations: two are congruent with the ends of the region rich in biosynthetic genes, and the third is located in the proposed region of the replication terminus. In addition, three insertions were scattered in the region rich in biosynthetic genes. The arrangement of the rrn operons around the origin of replication was conserved in C, PAO, and nine other examined independent strains.

H+ extrusion and organic-acid synthesis in N2 -fixing symbioses involving vascular plants

An analysis of published data suggests that the N₂ -fixing symbiotic vascular plants extrude more H⁺ per unit N fixed than would be expected from data on the same genotypes growing on NH₄ ⁺ if the plants had the same chemical composition when grown on the two N sources. The H⁺ /N ratio with urea as the N source is similar to that with N₂ . The higher H⁺ /N ratio and higher organic acid/N ratio with N₂ or urea as N source implies higher whole-plant energy and water costs per unit of biomass and, ultimately, inclusive fitness, produced. The rhizosphere acidification resulting from H⁺ extrusion may serve to change rhizosphere pH to some 'optimal' value, and to increase the availability of such limiting resources as P, Mo and Fe which are especially needed in diazotrophy. Data in the literature are consistent with these possibilities in the few cases examined. Within the plant, data on xylem and phloem sap composition in conjunction with shoot composition, of diazotrophically-growing legumes suggest that shoot acid-base homoiostasis can be maintained via the import of appropriate solutes in the xylem and the export of appropriate solutes in the phloem. Acid-base regulation of the nodules in the absence of any H⁺ exchange with their environment can also probably be explained in terms of the solutes supplied in the phloem and exported in the xylem. This conclusion is based on data in the literature on the composition of stem phloem sap and of xylem sap exuding from detached nodules of diazotrophic vascular plants. These considerations do not exclude the possibility of net H⁺ efflux from nodules fixing N₂ in contact with an aqueous medium. The limited data available are consistent with extrusion of some of the H⁺ generated in nodules as an alternative to their neutralization by metabolism of organic anions entering in the phloem. Such H⁺ extrusion by nodules could aid in their acquisition of Fe from the medium, albeit not always at a phase in the life or the nodule when there is a net requirement for Fe.