Organization and transcription of the principal sigma gene (rpoDA) of Pseudomonas aeruginosa PAO1: involvement of a sigma 32-like RNA polymerase in rpoDA gene expression

Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures

Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some key P. aeruginosa PAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products.

Regulation of the Pseudomonas aeruginosa toxA, regA and ptxR genes by the iron-starvation sigma factor PvdS under reduced levels of oxygen

The level of environmental oxygen (EO) within various Pseudomonas aeruginosa infection sites is low (microaerobic), and this can affect the production of different virulence factors. Expression of the toxA gene, encoding exotoxin A (ETA), is regulated by regA, ptxR and pvdS. Moreover, the iron-starvation sigma factor PvdS directs the transcription of pyoverdine siderophore genes (e.g. pvdD). DNA-protein binding analysis using recombinant PvdS showed that the PvdS-RNA polymerase holoenzyme complex specifically bound the toxA, regA and ptxR promoter regions. All three promoters contain a PvdS-binding site, the iron-starvation box. To determine the relationship between these different genes and PvdS, we conducted a comparative analysis of toxA, regA, ptxR and pvdD transcription throughout the growth cycle of wild-type P. aeruginosa and its pvdS mutant in iron-deficient medium under aerobic-shaking (A-sh) and microaerobic-static (M-st) conditions. Under both EO conditions, optimal toxA, regA and pvdD expression and pyoverdine production required PvdS, while ptxR expression was moderately dependent on PvdS only under A-sh conditions. Expression of regA, pvdD and pyoverdine production in wild-type P. aeruginosa was significantly lower under M-st in comparison with A-sh conditions, while the opposite was observed for toxA and ptxR. Although low, the level of toxA expression and ETA production in the pvdS mutant were higher under M-st than under A-sh conditions. Transcription of pvdS and PvdS expression were also reduced by low EO. We propose that the regulation of toxA expression under aerobic conditions primarily involves PvdS, while an additional EO-responsive regulator(s) besides PvdS is required under low EO levels. Thus, PvdS may control the transcription of the ptxR, regA and toxA genes, and respond to EO by acting at different levels of the toxA regulatory cascade.

Involvement of AlgQ in transcriptional regulation of pyoverdine genes in Pseudomonas aeruginosa PAO1

In response to iron limitation, Pseudomonas aeruginosa produces the fluorescent siderophore pyoverdine. Transcription of pyoverdine biosynthetic (pvd) genes is driven by the iron starvation sigma factor PvdS, which is negatively regulated by the Fur-Fe(II) holorepressor. We studied the effect of AlgQ, the Escherichia coli Rsd orthologue, on pyoverdine production by P. aeruginosa PAO1. AlgQ is a global regulatory protein which activates alginate, ppGpp, and inorganic polyphosphate synthesis through a cascade involving nucleoside diphosphate kinase (Ndk). AlgQ is also capable of interacting with region 4 of RpoD. In a reconstituted E. coli system, PvdS-dependent transcription from the pvdA promoter was doubled by the multicopy algQ gene. The P. aeruginosa DeltaalgQ mutant exhibited a moderate but reproducible reduction in pyoverdine production compared with wild-type PAO1, as a result of a decline in transcription of pvd genes. PvdS expression was not affected by the algQ mutation. Single-copy algQ fully restored pyoverdine production and expression of pvd genes in the DeltaalgQ mutant, while ndk did not. An increased intracellular concentration of RpoD mimicked the DeltaalgQ phenotype, whereas PvdS overexpression suppressed the algQ mutation. E. coli rsd could partially substitute for algQ in transcriptional modulation of pvd genes. We propose that AlgQ acts as an anti-sigma factor for RpoD, eliciting core RNA polymerase recruitment by PvdS and transcription initiation at pvd promoters. AlgQ provides a link between the pyoverdine and alginate regulatory networks. These systems have similarities in responsiveness and physiological function: both depend on alternative sigma factors, respond to nutrient starvation, and act as virulence determinants for P. aeruginosa.

Transcription analysis of rpoH in Pseudomonas putida

We previously determined the complete DNA sequence of the rpoH gene encoding the heat-shock sigma factor (sigmaH) of Pseudomonas putida. In the present study, the transcriptional start sites of rpoH were determined to be 41 nucleotides (T1), 153 nucleotides (T2) and 157 nucleotides (T3) upstream from the translational start codon (AUG) of rpoH by rapid amplification of cDNA 5'-ends. Based on the locations of T2 and T3, a sigma70-type promoter (P2) was determined to be located in the open reading frame region of upstream ftsX in addition to the sigmaE-type promoter (P1; DNA Res. 6 (1999) 241). In the in vitro transcription assay with reconstituted RNA polymerases (Esigma70, EsigmaE, EsigmaH and EsigmaS) of Pseudomonas aeruginosa, EsigmaE transcribed rpoH from T1 and Esigma(70) transcribed it from T2 and T3. In both cases, the level of transcription was higher at 42 degrees C than at 30 degrees C. No transcript was detected when EsigmaH or EsigmaS was used. These results indicate that EsigmaE and Esigma70 recognize P1 promoter and P2 promoter, respectively, and also prove that the synthesis of rpoH mRNA is inducible upon heat shock.

In vitro transcription system using reconstituted RNA polymerase (Esigma(70), Esigma(H), Esigma(E) and Esigma(S)) of Pseudomonas aeruginosa

We have developed an in vitro transcription system for Pseudomonas aeruginosa genes, using RNA polymerase (RNAP) holoenzyme reconstituted with purified sigma protein and RNAP core enzyme. The RNAP core enzyme was directly purified from P. aeruginosa PAO1 cells. The sigma factors of P. aeruginosa (sigma(70), sigma(H), sigma(E) and sigma(S)) were prepared in a hexa-histidine tagged form, which were expressed in Escherichia coli and purified using a HisTrap Chelating column. The RNAP holoenzyme reconstituted from core enzyme with each sigma factor recognized correctly each of the cognate promoters. This system will be useful for the promoter analysis of many genes in P. aeruginosa.

In vitro transcription analysis of rpoD in Pseudomonas aeruginosa PAO1

The rpoD gene encoding the principal sigma factor (sigma(70)) of Pseudomonas aeruginosa is transcribed from two promoters, P(C) and P(HS). The sequence of P(C) is similar to the Escherichia coli sigma(70) consensus promoter sequence and that of P(HS) is similar to the E. coli sigma(H) consensus promoter sequence. Synthesis of rpoD mRNA from P(C) is constitutive under both steady-state and heat-shock growth conditions, while that of P(HS) is transiently induced upon heat-shock. To gain a better understanding of the regulation of rpoD expression, we examined in vitro transcription of rpoD using two RNA polymerases (Esigma(70) and Esigma(H), containing sigma(70) and sigma(H), respectively) purified from P. aeruginosa. DNase I footprinting analysis showed specific bindings of Esigma(70) and Esigma(H) to P(C) and P(HS) promoter regions, respectively. In the in vitro runoff transcription assay, Esigma(H) transcribed the template from P(HS) both at 30 degrees C and 42 degrees C but not from P(C). However, Esigma(70) transcribed rpoD not only from P(C) both at 30 degrees C and 42 degrees C but also from P(HS) at 42 degrees C.

Transcription of the groESL operon in Pseudomonas aeruginosa PAO1

Northern hybridization and S1 nuclease mapping demonstrated that the groES and groEL genes in Pseudomonas aeruginosa were transcribed as a bicistronic mRNA of 2.2 kb. Two transcription start sites and a transcription termination site were mapped. Overlapping consensus sequences for sigma 32- and sigma 70-dependent promoters were found in the upstream region of groES. Levels of groESL-specific mRNA were increased about 2-fold upon heat shock. This response differs from the dramatic enhancement (more than 10-fold) of groESL transcription after heat shock observed in other bacterial species.

A novel genetic organization: the leuA-rpoD1 locus in the cyanobacterium Microcystis aeruginosa K-81

We cloned and sequenced the region upstream of rpoD1, which encodes a principal sigma factor in the cyanobacterium Microcystis aeruginosa K-81. An open reading frame (orf1, 1599 bp) was discovered, the deduced amino-acid sequence of which (533 aa, 58, 016 Da) exhibits homology to another bacterial leuA gene product, 2-isopropylmalate synthase. The leuA (orf1) gene specifically complemented an E. coli leuA mutant. The 5'-upstream region of leuA did not contain possible leader peptide or stem-loop structures for attenuation. These findings indicate that the genetic structure of the leuA-rpoD1 locus in M. aeruginosa K-81 significantly differs from those of known leuA and rpoD loci found in other bacteria.

Analysis of the rpoD gene encoding the principal sigma factor of Pseudomonas putida

The gene (rpoD) encoding the principal sigma factor of Pseudomonas putida (Pp) was cloned and sequenced. The amino-acid sequence deduced from the nucleotide sequence of rpoD contained sequences with significant similarity to the conserved region of the principal sigma factors. In vivo transcriptional analyses revealed that the Pp rpoD is transcribed as a monocistronic mRNA of 2.1 kb and that the transcription of rpoD is under control of the heat-shock (HS) response. The transcription start point (tsp) of the gene was determined and found to be different depending on either normal growth (at 30 degrees C) or HS (at 42 degrees C) conditions. The possible promoter sequences for the principal (sigma 70) and the HS RNA polymerase of Pseudomonas were located in the upstream region of the tsp.

Characterization of heat-shock response of the marine bacterium Vibrio harveyi

We have investigated heat-shock response in a marine bacterium Vibrio harveyi. We have found that 39 degrees C was the highest temperature at which V. harveyi was able to grow steadily. A shift from 30 degrees C to 39 degrees C caused increased synthesis of at least 10 proteins, as judged by SDS-PAGE, with molecular masses of 90, 70, 58, 41, 31, 27, 22, 15, 14.5 and 14kDa. The 70, 58, 41 and 14.5 kDa proteins were immunologically homologous to DnaK, GroEL, DnaJ and GroES heat-shock proteins of Escherichia coli, respectively. V. harveyi GroES protein had a lower molecular mass (14.5 kDa) than E. coli GroES, migrating in SDS-PAGE as 15kDa protein. We showed that a protein of approximately 43 kDa, immunologically reactive with antiserum against E. coli sigma 32 subunit (sigma 32) of RNA polymerase, was induced by heat-shock and co-purified with V. harveyi RNA polymerase. These results suggest that the 43 kDa protein is a heat-shock sigma protein of V. harveyi. Preparation containing the V. harveyi sigma 32 homologue, supplemented with core RNA polymerase of E. coli, was able to transcribe heat-shock promoters of E. coli in vitro.

Cloning and primary sequence of the rpoH gene from Pseudomonas aeruginosa

A DNA fragment from Pseudomonas aeruginosa containing the rpoH gene encoding the heat-shock sigma factor sigma 32 has been cloned and sequenced. The gene is expressed in Escherichia coli and complements an rpoH- strain. An open reading frame encoding 284 amino acids shows 61% identity and 78% similarity to the RpoH protein of Escherichia coli.

Cloning, analysis and expression of an rpoS homologue gene from Pseudomonas aeruginosa PAO1

A homologue of the rpoS gene of Escherichia coli was cloned from Pseudomonas aeruginosa PAO1 by hybridization with an oligodeoxyribonucleotide probe designed from an amino-acid stretch conserved among the principal sigma factors of eubacteria. Two open reading frames, the pcm gene and the orf-297 of unknown function, were found in the upstream region of rpoS, and in the same order as in E. coli. The rpoS gene of P. aeruginosa was expressed in E. coli and complemented the catalase deficiency of the rpoS mutant of E. coli. The RpoS protein of P. aeruginosa was identified by Western blot analysis in both P. aeruginosa (Pa) and the transformed E. coli. Levels of RpoS of Pa increased drastically at the onset of the stationary growth phase.

Transcription of the principal sigma-factor genes, rpoD and rpoS, in Pseudomonas aeruginosa is controlled according to the growth phase

The rpoS gene encodes the second principal sigma factor of RNA polymerase in stationary-phase cells in Escherichia coli. We examined the transcription of Pseudomonas aeruginosa rpoS as to the growth of cells. The results of quantitative S1 nuclease mapping of rpoS and rpoD, encoding the principal sigma factor, indicated that the transcription of rpoS is induced in stationary-phase cells, whereas that of rpoD is induced in exponential-phase cells. By high-resolution S1 nuclease mapping, the 5'- and 3'-ends of rpoS mRNA were determined. The results indicated that rpoS is transcribed as a monocistronic mRNA. The sequence preceding the 5' end of rpoS mRNA showed poor homology to the consensus sequences of the previously known promoters. P. aeruginosa rpoS was not transcribed in E. coli. By in vitro transcription assaying, P. aeruginosa rpoS was shown to be transcribed by the RNA polymerase fraction containing the principal sigma (sigma 70)-RNA polymerase of P. aeruginosa.