The identification of the transcriptional regulator CRP in Aeromonas hydrophila JMP636 and its involvement in amylase production and the 'acidic toxicity' effect

Aims: The physiological examination of amylase production by Aeromonas hydrophila JMP636 and identification of the mechanism of regulation. Methods and Results: Aeromonas hydrophila JMP636 was grown with single, then dual carbon sources; the growth cycle was followed and amylase activity throughout was monitored. The levels of cAMP, a known secondary messenger for the regulatory gene crp, were also examined. Amylase activity was regulated by catabolite repression. Physiological studies revealed that JMP636 exhibited both diauxic growth, with two carbon sources, and the 'acid toxicity' effect on glucose. The crp gene was cloned, expressed and inactivated from the JMP636 chromosome. Catabolite repression of amylase production and the 'acid toxicity' effect both require crp and were linked to cAMP levels. Conclusions: Regulation of amylase production was predicted to follow the model CRP-mediated cAMP-dependent Escherichia coli catabolite regulation system. Significance and Impact of the Study: This work provides an understanding of the physiology of the opportunistic pathogen Aer. hydrophila through identification of the mechanism of catabolite repression of amylase production and the existence of crp within this cell. It also provides a broader knowledge of global gene regulation and suggests regulatory mechanisms of other Aer. hydrophila gene/s.

Functional analysis of the post-transcriptional regulator RsmA reveals a novel RNA-binding site.

The RsmA family of RNA-binding proteins are global post-transcriptional regulators that mediate extensive changes in gene expression in bacteria. They bind to, and affect the translation rate of target mRNAs, a function that is further modulated by one or more, small, untranslated competitive regulatory RNAs. To gain new insights into the nature of this protein/RNA interaction, we used X-ray crystallography to solve the structure of the Yersinia enterocolitica RsmA homologue. RsmA consists of a dimeric beta barrel from which two alpha helices are projected. From structure-based alignments of the RsmA protein family from diverse bacteria, we identified key amino acid residues likely to be involved in RNA-binding. Site-specific mutagenesis revealed that arginine at position 44, located at the N terminus of the alpha helix is essential for biological activity in vivo and RNA-binding in vitro. Mutation of this site affects swarming motility, exoenzyme and secondary metabolite production in the human pathogen Pseudomonas aeruginosa, carbon metabolism in Escherichia coli, and hydrogen cyanide production in the plant beneficial strain Pseudomonas fluorescens CHA0. R44A mutants are also unable to interact with the small untranslated RNA, RsmZ. Thus, although possessing a motif similar to the KH domain of some eukaryotic RNA-binding proteins, RsmA differs substantially and incorporates a novel class of RNA-binding site.

p21WAF1/Cip1 is a negative transcriptional regulator of Wnt4 expression downstream of Notch1 activation.

In keratinocytes, the cyclin/CDK inhibitor p21(WAF1/Cip1) is a direct transcriptional target of Notch1 activation; loss of either the p21 or Notch1 genes expands stem cell populations and facilitates tumor development. The Notch1 tumor-suppressor function was associated with down-regulation of Wnt signaling. Here, we show that suppression of Wnt signaling by Notch1 activation is mediated, at least in part, by down-modulation of Wnts gene expression. p21 is a negative regulator of Wnts transcription downstream of Notch1 activation, independently of effects on the cell cycle. More specifically, expression of the Wnt4 gene is under negative control of endogenous p21 both in vitro and in vivo. p21 associates with the E2F-1 transcription factor at the Wnt4 promoter and causes curtailed recruitment of c-Myc and p300, and histone hypoacetylation at this promoter. Thus, p21 acts as a selective negative regulator of transcription and links the Notch and Wnt signaling pathways in keratinocyte growth control.

PCAF regulates the stability of the transcriptional regulator and cyclin-dependent kinase inhibitor p27Kip1

P27(Kip1) (p27) is a member of the Cip/Kip family of cyclin-dependent kinase inhibitors. Recently, a new function of p27 as transcriptional regulator has been reported. It has been shown that p27 regulates the expression of target genes mostly involved in splicing, cell cycle, respiration and translation. We report here that p27 directly binds to the transcriptional coactivator PCAF by a region including amino acids 91-120. PCAF associates with p27 through its catalytic domain and acetylates p27 at lysine 100. Our data showed that overexpression of PCAF induces the degradation of p27 whereas in contrast, the knockdown of PCAF stabilizes the protein. A p27 mutant in which K100 was substituted by arginine (p27-K100R) cannot be acetylated by PCAF and has a half-life much higher than that of p27WT. Moreover, p27-K100R remains stable along cell-cycle progression. Ubiquitylation assays and the use of proteasome inhibitors indicate that PCAF induces p27 degradation via proteasome. We also observed that knockdown of skp2 did not affect the PCAF induced degradation of p27. In conclusion, our data suggest that the p27 acetylation by PCAF regulates its stability.

Genomic roles of the HCF transcriptional regulator in "Drosophila"

Abstract : Transcriptional regulation is the result of a combination of positive and negative effectors, such as transcription factors, cofactors and chromatin modifiers. During my thesis project I studied chromatin association, and transcriptional and cell cycle regulatory functions of dHCF, the Drosophila homologue of the human protein HCF-1 (host cell factor-1). The human and Drosophila HCF proteins are synthesized as large polypeptides that are cleaved into two subunits (HCFN and HCFC), which remain associated with one another by non covalent interactions. Studies in mammalian cells over the past 20 years have been devoted to understanding the cellular functions of HCF-1 and have revealed that it is a key regulator of transcription and cell cycle regulation. In human cells, HCF-1 interacts with the histone methyltransferase Set1/Ash2 and MLL/Ash2 complexes and the histone deacetylase Sin3 complex, which are involved in transcriptional activation and repression, respectively. HCF-1 is also recruited to promoters to regulate G1 -to-S phase progression during the cell cycle by the activator transcription factors E2F1 and E2F3, and by the repressor transcription factor E2F4. HCF-1 protein structure and these interactions between HCP-1 and E2F transcriptional regulator proteins are also conserved in Drosophila. In this doctoral thesis, I use proliferating Drosophila SL2 cells to study both the genomic-binding sites of dHCF, using a combination of chromatin immunoprecipitation and ultra high throughput sequencing (ChIP-seq) analysis, and dHCF regulated genes, employing RNAi and microarray expression analysis. I show that dHCF is bound to over 7500 chromosomal sites in proliferating SL2 cells, and is located at +-200 bp relative to the transcriptional start sites of about 30% of Drosophila genes. There is also a direct relationship between dHCF promoter association and promoter- associated transcriptional activity. Thus, dHCF binding levels at promoters correlated directly with transcriptional activity. In contrast, expression studies showed that dHCF appears to be involved in both transcriptional activation and repression. Analysis of dHCF-binding sites identified nine dHCF-associated motifs, four of them linked dHCF to (i) two insulator proteins, GAGA and BEAF, (ii) the E-box motif, and (iii) a degenerated TATA-box. The dHCF-associated motifs allowed the organization of the dHCF-bound genes into five biological processes: differentiation, cell cycle and gene expression, regulation of endocytosis, and cellular localization. I further show that different mechanisms regulate dHCF association with chromatin. Despite that after dHCF cleavage the dHCFN and dHCFC subunits remain associated, the two subunits showed different affinities for chromatin and differential binding to a set of tested promoters, suggesting that dHCF could target specific promoters through each of the two subunits. Moreover, in addition to the interaction between dHCF and E2F transcription factors, the dHCF binding pattern is correlated with dE2F2 genomic 4 distribution. I show that dE2F factors are necessary for recruitment of dHCF to the promoter of a set of dHCF regulated genes. Therefore dHCF, as in mammals, is involved in regulation of G1 to S phase progression in collaboration with the dE2Fs transcription factors. In addition, gene expression arrays reveal that dHCF could indirectly regulate cell cycle progression by promoting expression of genes involved in gene expression and protein synthesis, and inhibiting expression of genes involved in cell-cell adhesion. Therefore, dHCF is an evolutionary conserved protein, which binds to many specific sites of the Drosophila genome via interaction with DNA of chromatin-binding proteins to regulate the expression of genes involved in many different cellular functions. Résumé : La regulation de la transcription est le résultat des effets positifs et négatifs des facteurs de transcription, cofacteurs et protéines effectrices qui modifient la chromatine. Pendant mon projet de thèse, j'ai étudié l'association a la chromatine, ainsi que la régulation de la transcription et du cycle cellulaire par dHCF, l'homologue chez la drosophile de la protéine humaine HCF-1 (host cell factor-1). Chez 1'humain et la V drosophile, les deux protéines HCF sont synthétisées sous la forme d'un long polypeptide, qui est ensuite coupé en deux sous-unités au centre de la protéine. Les deux sous-unités restent associées ensemble grâce a des interactions non-covalentes. Des études réalisées pendant les 20 dernières années ont permit d'établir que HCF-l et un facteur clé dans la régulation de la transcription et du cycle cellulaire. Dans les cellules humaines, HCF-1 active et réprime la transcription en interagissant avec des complexes de protéines qui activent la transcription en méthylant les histones (HMT), comme par Set1/Ash2 et MLL/Ash2, et d'autres complexes qui répriment la transcription et sont responsables de la déacétylation des histones (HDAC) comme la protéine Sin3. HCF-l est aussi recruté aux promoteurs par les activateurs de la transcription E2F l et E2F3a, et par le répresseur de la transcription E2F4 pour réguler la transition entre les phases G1 et S du cycle cellulaire. La structure de HCF-1 et les interactions entre HCF-l et les régulateurs de la transcription sont conservées chez la drosophile. Pendant ma these j'ai utilisé les cellules de la drosophile, SL2 en culture, pour étudier les endroits de liaisons de HCF-l à la chromatine, grâce a immunoprecipitation de la chromatine et du séquençage de l'ADN massif ainsi que les gènes régulés par dHCF 3 grâce a la technique de RNAi et des microarrays. Mes résultats on montré que dHCF se lie à environ 7565 endroits, et estimé a 1200 paire de bases autour des sites d'initiation de la transcription de 30% des gènes de la drosophile. J 'ai observe une relation entre dHCF et le niveau de la transcription. En effet, le niveau de liaison dHCF au promoteur corrèle avec l'activité de la transcription. Cependant, mes études d'expression ont montré que dHCF est implique dans le processus d'activation et mais aussi de répression de la transcription. L'analyse des séquences d'ADN liées par dHCF a révèle neuf motifs, quatre de ces motifs ont permis d'associer dl-ICF a deux protéines isolatrices GAGA et BEAF, au motif pour les E-boxes et a une TATA-box dégénérée. Les neuf motifs associes à dHCF ont permis d'associer les gènes lies par dHCF au promoteur a cinq processus biologiques: différentiation, cycle cellulaire, expression de gènes, régulation de l'endocytosis et la localisation cellulaire, J 'ai aussi montré qu'il y a plusieurs mécanismes qui régulent l'association de dHCF a la chromatine, malgré qu'après clivage, les deux sous-unites dHCFN and dHCFC, restent associées, elles montrent différentes affinités pour la chromatine et lient différemment un group de promoteurs, les résultats suggèrent que dHCF peut se lier aux promoteurs en utilisant chacune de ses sous-unitées. En plus de l'association de dHCF avec les facteurs de transcription dE2F s, la distribution de dHCF sur le génome corrèle avec celle du facteur de transcription dE2F2. J'ai aussi montré que les dE2Fs sont nécessaires pour le recrutement de dHCF aux promoteurs d'un sous-groupe de gènes régules par dHCF. Mes résultats ont aussi montré que chez la drosophile comme chez les humains, dl-ICF est implique dans la régulation de la progression de la phase G1 a la phase S du cycle cellulaire en collaboration avec dE2Fs. D'ailleurs, les arrays d'expression ont suggéré que dHCF pourrait réguler le cycle cellulaire de façon indirecte en activant l'expression de gènes impliqués dans l'expression génique et la synthèse de protéines, et en inhibant l'expression de gènes impliqués dans l'adhésion cellulaire. En conclusion, dHCF est une protéine, conservée dans l'évolution, qui se lie spécifiquement a beaucoup d'endroits du génome de Drosophile, grâce à l'interaction avec d'autres protéines, pour réguler l'expression des gènes impliqués dans plusieurs fonctions cellulaires.

NPAS2 as a transcriptional regulator of non-rapid eye movement sleep: genotype and sex interactions.

Because the transcription factor neuronal Per-Arnt-Sim-type signal-sensor protein-domain protein 2 (NPAS2) acts both as a sensor and an effector of intracellular energy balance, and because sleep is thought to correct an energy imbalance incurred during waking, we examined NPAS2's role in sleep homeostasis using npas2 knockout (npas2-/-) mice. We found that, under conditions of increased sleep need, i.e., at the end of the active period or after sleep deprivation (SD), NPAS2 allows for sleep to occur at times when mice are normally awake. Lack of npas2 affected electroencephalogram activity of thalamocortical origin; during non-rapid eye movement sleep (NREMS), activity in the spindle range (10-15 Hz) was reduced, and within the delta range (1-4 Hz), activity shifted toward faster frequencies. In addition, the increase in the cortical expression of the NPAS2 target gene period2 (per2) after SD was attenuated in npas2-/- mice. This implies that NPAS2 importantly contributes to the previously documented wake-dependent increase in cortical per2 expression. The data also revealed numerous sex differences in sleep; in females, sleep need accumulated at a slower rate, and REMS loss was not recovered after SD. In contrast, the rebound in NREMS time after SD was compromised only in npas2-/- males. We conclude that NPAS2 plays a role in sleep homeostasis, most likely at the level of the thalamus and cortex, where NPAS2 is abundantly expressed.

Transcriptional regulator PRDM12 is essential for human pain perception.

Pain perception has evolved as a warning mechanism to alert organisms to tissue damage and dangerous environments. In humans, however, undesirable, excessive or chronic pain is a common and major societal burden for which available medical treatments are currently suboptimal. New therapeutic options have recently been derived from studies of individuals with congenital insensitivity to pain (CIP). Here we identified 10 different homozygous mutations in PRDM12 (encoding PRDI-BF1 and RIZ homology domain-containing protein 12) in subjects with CIP from 11 families. Prdm proteins are a family of epigenetic regulators that control neural specification and neurogenesis. We determined that Prdm12 is expressed in nociceptors and their progenitors and participates in the development of sensory neurons in Xenopus embryos. Moreover, CIP-associated mutants abrogate the histone-modifying potential associated with wild-type Prdm12. Prdm12 emerges as a key factor in the orchestration of sensory neurogenesis and may hold promise as a target for new pain therapeutics.

CztR, a LysR-Type Transcriptional Regulator Involved in Zinc Homeostasis and Oxidative Stress Defense in Caulobacter crescentus

Caulobacter crescentus is a free-living alphaproteobacterium that has 11 predicted LysR-type transcriptional regulators (LTTRs). Previously, a C. crescentus mutant strain with a mini-Tn5lacZ transposon inserted into a gene encoding an LTTR was isolated; this mutant was sensitive to cadmium. In this work, a mutant strain with a deletion was obtained, and the role of this LTTR (called CztR here) was evaluated. The transcriptional start site of this gene was determined by primer extension analysis, and its promoter was cloned in front of a lacZ reporter gene. beta-Galactosidase activity assays, performed with the wild-type and mutant strains, indicated that this gene is 2-fold induced when cells enter stationary phase and that it is negatively autoregulated. Moreover, this regulator is essential for the expression of the divergent cztA gene at stationary phase, in minimal medium, and in response to zinc depletion. This gene encodes a hypothetical protein containing 10 predicted transmembrane segments, and its expression pattern suggests that it encodes a putative zinc transporter. The cztR strain was also shown to be sensitive to superoxide (generated by paraquat) and to hydrogen peroxide but not to tert-butyl hydroperoxide. The expression of katG and ahpC, but not that of the superoxide dismutase genes, was increased in the cztR mutant. A model is proposed to explain how CztR binding to the divergent regulatory regions could activate cztA expression and repress its own transcription.

Regulation of glycogen metabolism by the CRE-1, RCO-1 and RCM-1 proteins in Neurospora crassa. The role of CRE-1 as the central transcriptional regulator

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The transcriptional regulator megakaryoblastic leukemia-1 mediates serum response factor-independent activation of tenascin-C transcription by mechanical stress

The extracellular matrix protein tenascin-C (TNC) is up-regulated in processes influenced by mechanical stress, such as inflammation, tissue remodeling, wound healing, and tumorigenesis. Cyclic strain-induced TNC expression depends on RhoA-actin signaling, the pathway that regulates transcriptional activity of serum response factor (SRF) by its coactivator megakaryoblastic leukemia-1 (MKL1). Therefore, we tested whether MKL1 controls TNC transcription. We demonstrate that overexpression of MKL1 strongly induces TNC expression in mouse NIH3T3 fibroblasts and normal HC11 and transformed 4T1 mammary epithelial cells. Part of the induction was dependant on SRF and a newly identified atypical CArG box in the TNC promoter. Another part was independent of SRF but required the SAP domain of MKL1. An MKL1 mutant incapable of binding to SRF still strongly induced TNC, while induction of the SRF target c-fos was abolished. Cyclic strain failed to induce TNC in MKL1-deficient but not in SRF-deficient fibroblasts, and strain-induced TNC expression strongly depended on the SAP domain of MKL1. Promoter-reporter and chromatin immunoprecipitation experiments unraveled a SAP-dependent, SRF-independent interaction of MKL1 with the proximal promoter region of TNC, attributing for the first time a functional role to the SAP domain of MKL1 in regulating gene expression.

Localization of a putative transcriptional regulator (ATRX) at pericentromeric heterochromatin and the short arms of acrocentric chromosomes

ATRX is a member of the SNF2 family of helicase/ATPases that is thought to regulate gene expression via an effect on chromatin structure and/or function. Mutations in the hATRX gene cause severe syndromal mental retardation associated with α-thalassemia. Using indirect immunofluorescence and confocal microscopy we have shown that ATRX protein is associated with pericentromeric heterochromatin during interphase and mitosis. By coimmunofluorescence, ATRX localizes with a mouse homologue of the Drosophila heterochromatic protein HP1 in vivo, consistent with a previous two-hybrid screen identifying this interaction. From the analysis of a trap assay for nuclear proteins, we have shown that the localization of ATRX to heterochromatin is encoded by its N-terminal region, which contains a conserved plant homeodomain-like finger and a coiled-coil domain. In addition to its association with heterochromatin, at metaphase ATRX clearly binds to the short arms of human acrocentric chromosomes, where the arrays of ribosomal DNA are located. The unexpected association of a putative transcriptional regulator with highly repetitive DNA provides a potential explanation for the variability in phenotype of patients with identical mutations in the ATRX gene.

LXRα functions as a cAMP-responsive transcriptional regulator of gene expression

LXRα is a member of a nuclear receptor superfamily that regulates transcription. LXRα forms a heterodimer with RXRα, another member of this family, to regulate the expression of cholesterol 7α-hydroxylase by means of binding to the DR4-type cis-element. Here, we describe a function for LXRα as a cAMP-responsive regulator of renin and c-myc gene transcriptions by the interaction with a specific cis-acting DNA element, CNRE (an overlapping cAMP response element and a negative response element). Our previous studies showed that renin gene expression is regulated by cAMP, at least partly, through the CNRE sequence in its 5′-flanking region. This sequence is also found in c-myc and several other genes. Based on our cloning results using the yeast one-hybrid system, we discovered that the mouse homologue of human LXRα binds to the CNRE and demonstrated that it binds as a monomer. To define the function of LXRα on gene expression, we transfected the renin-producing renal As4.1 cells with LXRα expression plasmid. Overexpression of LXRα in As4.1 cells confers cAMP inducibility to reporter constructs containing the renin CNRE. After stable transfection of LXRα, As4.1 cells show a cAMP-inducible up-regulation of renin mRNA expression. In parallel experiments, we demonstrated that LXRα can also bind to the homologous CNRE in the c-myc promoter. cAMP promotes transcription through c-myc/CNRE:LXRα interaction in LXRα transiently transfected cells and increases c-myc mRNA expression in stably transfected cells. Identification of LXRα as a cAMP-responsive nuclear modulator of renin and c-myc expression not only has cardiovascular significance but may have generalized implication in the regulation of gene transcription.

Selectively enhanced contextual fear conditioning in mice lacking the transcriptional regulator CCAAT/enhancer binding protein δ

CCAAT/enhancer binding protein δ (C/EBPδ) is a transcriptional regulator implicated in the hepatic acute phase response and in adipogenic and myeloid cell differentiation. We found that C/EBPδ is widely expressed in the peripheral and central nervous systems, including neurons of the hippocampal formation, indicating a role in neural functions. To examine the role of C/EBPδ in vivo, we generated mice with a targeted deletion of the C/EBPδ gene. This mutation does not interfere with normal embryonic and postnatal development. Performance in a battery of behavioral tests indicates that basic neurological functions are normal. Furthermore, performance in a Morris water maze task suggests that C/EBPδ mutant mice have normal spatial learning. However, in the contextual and auditory-cue-conditioned fear task, C/EBPδ null mice displayed significantly more conditioned freezing to the test context than did wild-type controls, but equivalent conditioning to the auditory cue. These data demonstrate a selectively enhanced contextual fear response in mice carrying a targeted genomic mutation and implicate C/EBPδ in the regulation of a specific type of learning and memory.

The quorum-sensing transcriptional regulator TraR requires its cognate signaling ligand for protein folding, protease resistance, and dimerization

Complexes between the quorum-sensing regulator TraR and its inducing ligand autoinducer (AAI) are soluble in Escherichia coli, whereas apo-TraR is almost completely insoluble. Here we show that the lack of soluble TraR is due in large part to rapid proteolysis, inasmuch as apo-TraR accumulated to high levels in an E. coli strain deficient in Clp and Lon proteases. In pulse labeling experiments, AAI protected TraR against proteolysis only when it was added before the radiolabel. This observation indicates that TraR proteins can productively bind AAI only during their own synthesis on polysomes, whereas fully synthesized apo-TraR proteins are not functional AAI receptors. Purified apo-TraR was rapidly degraded by trypsin to oligopeptides, whereas TraR–AAI complexes were more resistant to trypsin and were cleaved at discrete interdomain linkers, indicating that TraR requires AAI to attain its mature tertiary structure. TraR–AAI complexes eluted from a gel filtration column as dimers and bound DNA as dimers. In contrast, apo-TraR was monomeric, and incubation with AAI under a variety of conditions did not cause dimerization. We conclude that AAI is critical for the folding of nascent TraR protein into its mature tertiary structure and that full-length apo-TraR cannot productively bind AAI and is consequently targeted for rapid proteolysis.

RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: A negative feedback circuit

The RPN4 (SON1, UFD5) protein of the yeast Saccharomyces cerevisiae is required for normal levels of intracellular proteolysis. RPN4 is a transcriptional activator of genes encoding proteasomal subunits. Here we show that RPN4 is required for normal levels of these subunits. Further, we demonstrate that RPN4 is extremely short-lived (t1/2 ≈2 min), that it directly interacts with RPN2, a subunit of the 26S proteasome, and that rpn4Δ cells are perturbed in their cell cycle. The degradation signal of RPN4 was mapped to its N-terminal region, outside the transcription–activation domains of RPN4. The ability of RPN4 to augment the synthesis of proteasomal subunits while being metabolically unstable yields a negative feedback circuit in which the same protein up-regulates the proteasome production and is destroyed by the assembled active proteasome.