Fabrizio Bolognese

Complex Transcriptional Effects of p63 Isoforms: Identification of Novel Activation and Repression Domains†

ABSTRACT p63 is a transcription factor structurally related to the p53 tumor suppressor. The C-terminal region differs from p53s in that it contains a sterile alpha motif (SAM) domain and is subject to multiple alternative splicings. The N-terminal region is present in the transactivation (TA) and ΔN configurations, with the latter lacking the transcriptional activation domain 1. Single amino acid substitutions and frameshift mutations of p63 cause the human ankyloblepharon ectodermal dysplasia clefting (AEC) or ectrodactyly ectodermal dysplasia and facial clefting (EEC) syndromes. We have systematically compared the activities of the wild-type p63 isoforms and of the natural mutants in activation and repression assays on three promoters modulated by p53. We found that p63 proteins with an altered SAM domain or no SAM domain—the β isoforms, the EEC frameshift mutant, and the missense AEC mutations—all showed a distinctly higher level of activation of the MDM2 promoter and decreased repression on the HSP70 promoter. Fusion of SAM to the GAL4 DNA-binding domain repressed a heterologous promoter. A second activation domain, TA2, corresponding to exons 11 to 12, was uncovered by comparing the activation of ΔN isoforms on natural promoters and in GAL4 fusion systems. In colony formation assays, the AEC mutants, but not the EEC frameshift, were consistently less efficient in suppressing growth, in both the TA version and the ΔN version, with respect to their p63α counterparts. These data highlight the modularity of p63, identifying the SAM domain as a dominant transcriptional repression module and indicating that the AEC and EEC frameshift mutants are characterized by a subversion of the p63 transcriptional potential.

The cyclin B2 promoter depends on NF-Y, a trimer whose CCAAT-binding activity is cell-cycle regulated

Cyclin B2 is a regulator of p34cdc2 kinase, involved in G2/M progression of the cell cycle, whose gene is strictly regulated at the transcriptional level in cycling cells. The mouse promoter was cloned and three conserved CCAAT boxes were found. In this study, we analysed the mechanisms leading to activation of the cyclin B2 CCAAT boxes: a combination of (i) genomic footprinting, (ii) transfections with single, double and triple mutants, (iii) EMSAs with nuclear extracts, antibodies and NF-Y recombinant proteins and (iv) transfections with an NF-YA dominant negative mutant established the positive role of the three CCAAT sequences and proved that NF-Y plays a crucial role in their activation. NF-Y, an ubiquitous trimer containing histone fold subunits, activates several other promoters regulated during the cell cycle. To analyse the levels of NF-Y subunits in the different phases of the cycle, we separated MEL cells by elutriation, obtaining fractions >80% pure. The mRNA and protein levels of the histone-fold containing NF-YB and NF-YC were invariant, whereas the NF-YA protein, but not its mRNA, was maximal in mid-S and decreased in G2/M. EMSA confirmed that the CCAAT-binding activity followed the amount of NF-YA, indicating that this subunit is limiting within the NF-Y complex, and suggesting that post-transcriptional mechanisms regulate NF-YA levels. Our results support a model whereby fine tuning of this activator is important for phase-specific transcription of CCAAT-containing promoters.

Functional consequences of mutations in CDKL5, an X-linked gene involved in infantile spasms and mental retardation.

Mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have been identified in patients with Rett syndrome, West syndrome, and X-linked infantile spasms sharing the common features of generally intractable early seizures and mental retardation. Disease-causing mutations are distributed in both the catalytic domain and in the large COOH terminus. In this report, we examine the functional consequences of some Rett mutations of CDKL5 together with some synthetically designed derivatives useful to underline the functional domains of the protein. The mutated CDKL5 derivatives have been subjected to in vitro kinase assays and analyzed for phosphorylation of the TEY (Thr-Glu-Tyr) motif within the activation loop, their subcellular localization, and the capacity of CDKL5 to interact with itself. Whereas wild-type CDKL5 autophosphorylates and mediates the phosphorylation of the methyl-CpG-binding protein 2 (MeCP2) in vitro, Rett-mutated proteins show both impaired and increased catalytic activity suggesting that a tight regulation of CDKL5 is required for correct brain functions. Furthermore, we show that CDKL5 can self-associate and mediate the phosphorylation of its own TEY (Thr-Glu-Tyr) motif. Eventually, we show that the COOH terminus regulates CDKL5 properties; in particular, it negatively influences the catalytic activity and is required for its proper sub-nuclear localization. We propose a model in which CDKL5 phosphorylation is required for its entrance into the nucleus whereas a portion of the COOH-terminal domain is responsible for a stable residency in this cellular compartment probably through protein-protein interactions.

Interaction between the inner nuclear membrane lamin B receptor and the heterochromatic methyl binding protein, MeCP2.

The nuclear membrane has an important role for the dynamic regulation of the genome, besides the well-established cytoskeletal function. The nuclear lamina is emerging as an important player in the organization of the position and functional state of interphase chromosomes. Epigenetic modifications such as DNA methylation and histone modifications are required for genome reprogramming during development, tissue-specific gene expression and global gene silencing. The Methyl-CpG binding protein MeCP2 binds methyl-CpG dinucleotides in the mammalian genome and functions as a transcriptional repressor in vivo by interacting with Sin3A, thereby recruiting histone deacetylases (HDAC). MeCP2 also mediates the formation of higher-order chromatin structures contributing to determine the architectural organization of the nucleus. In this paper, we show that MeCP2 interacts in vitro and in vivo with the inner nuclear membrane protein LBR and that the unstructured aminoacidic sequence linking the MBD and TRD domains of MeCP2 is responsible for this association. The formation of an LBR-MeCP2 protein complex might help providing a molecular explanation to the distribution of part of the heterochromatin at the nuclear periphery linked to inner membrane.

Evolution of catabolic pathways and metabolic versatility in Pseudomonas stutzeri OX1.

Pseudomonas stutzeri OX1 is able to degrade toluene and ortho-xylene via the direct oxygenation of the aromatic ring. The genetic studies carried out suggest that the genes coding for the monooxygenase involved in the early steps of this catabolic route have been acquired by gene transfer. P. stutzeri OX1 is also potentially able to utilize meta- and para-xylene as growth substrates. These two isomers are metabolized through a different pathway (TOL pathway). Both catabolic routes can be activated or inactivated by means of genomic rearrangements. The relevance of such recombination mechanisms in the evolution and the adaptability of P. stutzeri is discussed.

Pigments influence the tolerance of Pseudomonas aeruginosa PAO1 to photodynamically induced oxidative stress

Pseudomonas aeruginosa is an opportunistic pathogen known to be resistant to different classes of antibiotics and disinfectants. P. aeruginosa also displays a certain degree of tolerance to photodynamic therapy (PDT), an alternative antimicrobial approach exploiting a photo-oxidative stress induced by exogenous photosensitizers and visible light. To evaluate whether P. aeruginosa pigments can contribute to its relative tolerance to PDT, we analysed the response to this treatment of isogenic transposon mutants of P. aeruginosa PAO1 with altered pigmentation. In general, in the presence of pigments a higher tolerance to PDT-induced photo-oxidative stress was observed. Hyperproduction of pyomelanin makes the cells much more tolerant to stress caused by either radicals or singlet oxygen generated by different photosensitizers upon photoactivation. Phenazines, pyocyanin and phenazine-1-carboxylic acid, produced in different amounts depending on the cultural conditions, are able to counteract both types of PDT-elicited reactive oxygen species. Hyperproduction of pyoverdine, caused by a mutation in a quorum-sensing gene, rendered P. aeruginosa more tolerant to a photosensitizer that generates mainly singlet oxygen, although in this case the observed tolerance to photo-oxidative stress cannot be exclusively attributed to the presence of the pigment.

Honey-sensitive Pseudomonas aeruginosa mutants are impaired in catalase A

The antimicrobial power of honey seems to be ascribable to several factors, including oxidative and osmotic stress. The aim of this study was to find genetic determinants involved in the response to honey stress in the opportunistic pathogen Pseudomonas aeruginosa, chosen as model micro-organism. A library of transposon mutants of P. aeruginosa PAO1 was constructed and only four mutants unable to grow in presence of fir honeydew honey were selected. All four mutants were impaired in the major H2O2-scavenging enzyme catalase A (KatA). The knockout of katA gene caused sensitivity, as expected, not only to hydrogen peroxide but also to different types of honey including Manuka GMO 220 honey. Genetic complementation, as well as the addition of PAO1 supernatant containing extracellular catalase, restored tolerance to honey stress in all the mutants. As P. aeruginosa PAO1 catalase KatA copes with H2O2 stress, it is conceivable that the antimicrobial activity of honey is, at least partially, due to the presence of hydrogen peroxide in honey or the ability of honey to induce production of hydrogen peroxide. The katA-deficient mutants could be used as tester micro-organisms to compare the power of different types of natural and curative honeys in eliciting oxidative stress mediated by hydrogen peroxide.

Catalase A is involved in the response to photooxidative stress in Pseudomonas aeruginosa

BACKGROUND Pseudomonas aeruginosa is the etiological agent of systemic and skin infections that are often difficult to treat. Photodynamic therapy (PDT) and, more recently, phototherapy (PT), are emerging among antimicrobial treatments to be combined with antibiotics. Visible light, either alone or combined with a photosensitizer (PS), elicits photooxidative stress that induces microbial death. The response of bacteria to phototherapy seems to involve the antioxidant machinery. This study relies on the effects of detoxifying catalase A (KatA) in response to PDT and PT-induced photooxidative stress. METHODS The photo- and photodynamic inactivation experiments have been targeted at P. aeruginosa PAO1 and its isogenic derivative katA- mutant. The microorganisms were irradiated by a wide-spectrum halogen-tungsten lamp or light-emitting diodes (LEDs). Two photosensitizers, Tetrakis-(1-methyl-4-pyridyl)-21H, 23porphine, tetra-p-tosylate (TMPyP) porphyrin and Toluidine Blue O (TBO), were applied as part of the photodynamic approach. RESULTS P. aeruginosa katA- mutant was more sensitive than wild-type strain PAO1 to wide-spectrum light and blue LED (464 nm) treatments. The complementation of KatA, in katA- mutant, restored the light response of wild-type PAO1. Upon TBO treatment and irradiation by visible light (halogen lamp or LED), the sensitivity of katA- mutant was significant higher (p = 0.028 and p = 0.045, respectively) than that of the PAO1 strain. CONCLUSIONS This study provides the first description of KatA in the response to photooxidative stress induced by photo- and photodynamic therapy.

Anti-Pseudomonas activity of 3-nitro-4-phenylfuroxan

Pseudomonas aeruginosa is a microorganism that is well adapted to both clinical and industrial settings, where it can form adherent communities that are difficult to eradicate. New anti-Pseudomonas compounds and strategies are necessary, as the current antimicrobial approaches for the inhibition of biofilm formation and, above all, the eradication of formed biofilms are ineffective. Compounds that belong to the furoxan family, which are well-known NO donors, have recently been shown to display anti-Pseudomonas activity. The present study investigates three furoxan compounds that are substituted at the hetero-ring with electron-withdrawing groups (NO2, CN, CONH2) for their effects on P. aeruginosa PAO1 growth and biofilm formation/dispersal. Of the furoxans tested, only 3-nitro-4-phenylfuroxan (KN455) inhibited the growth of suspended P. aeruginosa PAO1 cultures. Furthermore, KN455 inhibited the formation of both younger and older biofilms with very high yields and thus proved itself to be toxic to planktonic subpopulations. It also displayed moderate eradicating power. The activity of KN455 does not appear to be related to its capacity to release small amounts of NO. Interestingly, the isomer 4-nitro-3-phenylfuroxan (KN454), included for comparison, displayed a comparable antibiofilm rate, but did not show the same antimicrobial activity against suspended cells and planktonic subpopulations. While hypotheses as to the mechanism of action have been formulated, further investigations are necessary to shed light onto the antimicrobial activity of this furoxan.

Blue light enhances the antimicrobial activity of honey against Pseudomonas aeruginosa

Pseudomonas aeruginosa may be isolated from skin wounds of burn patients, bedsore and diabetic ulcers. The healing of wounds is often impaired by the intrinsic antibiotic resistance, the tolerance to many antimicrobials and the ability to form biofilm of this opportunistic pathogen. Finding new topical treatments to combine with antibiotics is thus essential. Among natural products, the antimicrobial properties of honeys have been known for millennia. In this study honey and visible light have been combined to control the growth of P. aeruginosa PAO1. The irradiation by a broad spectrum light source of bacteria inoculated onto 2 % w/v fir and forest honeydew (HD) honeys caused a killing effect that the honeys alone or the light alone did not show. This antimicrobial activity was light energy-dose and honey-concentration dependent. Among the tested honeys, the fir and forest HD honeys were the most efficient ones. In particular, the irradiation by blue LED (λmax = 466 nm) yielded good rates of killing, that were significantly higher in comparison to irradiation alone and honey alone. Interestingly, a similar effect was obtained by plating bacteria on blue LED pre-irradiated HD honeys. The combined use of honey and blue light was also successful in inhibiting the biofilm formation of P. aeruginosa. The blue LED irradiation of PAO1 administered with 10 % w/v forest HD honey significantly enhanced the inhibition of biofilm formation in comparison to dark incubated honey.