[Show abstract][Hide abstract] ABSTRACT: Hsp70s are important cancer chaperones that act upstream of Hsp90 and exhibit independent anti-apoptotic activities. To develop chemical tools for the study of human Hsp70, we developed a homology model that unveils a previously unknown allosteric site located in the nucleotide binding domain of Hsp70. Combining structure-based design and phenotypic testing, we discovered a previously unknown inhibitor of this site, YK5. In cancer cells, this compound is a potent and selective binder of the cytosolic but not the organellar human Hsp70s and has biological activity partly by interfering with the formation of active oncogenic Hsp70/Hsp90/client protein complexes. YK5 is a small molecule inhibitor rationally designed to interact with an allosteric pocket of Hsp70 and represents a previously unknown chemical tool to investigate cellular mechanisms associated with Hsp70.
[Show abstract][Hide abstract] ABSTRACT: DNAJA1 (DJA1/Hdj2) and DNAJA2 (DJA2) are the major J domain partners of human Hsp70/Hsc70 chaperones. Although they have overall similarity with the well-characterized Type I co-chaperones from yeast and bacteria, they are biologically distinct and their functional mechanisms poorly characterized. We identified DJA2-specific activities in luciferase folding and repression of HERG trafficking, that depended on its expression levels in cells. Mutations in particular internal domains of DJA2 abolished these effects. Using purified proteins, we addressed the mechanistic defects. A mutant lacking the region between the zinc finger motifs (DJA2-m2) was able to bind substrate similar to wild-type but was incapable of releasing substrate during its transfer to Hsc70. The equivalent mutation in DJA1 also abolished its substrate release. A DJA2 mutant (DJA-221), that had its C-terminal dimerization region replaced by that of DJA1, was inactive but retained its ability to release substrate. The release mechanism required the J domain and ATP hydrolysis by Hsc70, although the nucleotide dependence diverged between DJA2 and DJA1. Limited proteolysis suggested further conformational differences between the two wild-type co-chaperones and the mutants. Our results demonstrate an essential role of specific DJA domains in the folding mechanism of Hsc70.
[Show abstract][Hide abstract] ABSTRACT: Transcription-induced hypernegative supercoiling is a hallmark of Escherichia coli topoisomerase I (topA) mutants. However, its physiological significance has remained unclear. Temperature downshift of a mutant yielded transient
growth arrest and a parallel increase in hypernegative supercoiling that was more severe with lower temperature. Both properties
were alleviated by overexpression of RNase HI. While ribosomes in extracts showed normal activity when obtained during growth
arrest, mRNA on ribosomes was reduced for fis and shorter for crp, polysomes were much less abundant relative to monosomes, and protein synthesis rate dropped, as did the ratio of large to
small proteins. Altered processing and degradation of lacA and fis mRNA was also observed. These data are consistent with truncation of mRNA during growth arrest. These effects were not affected
by a mutation in the gene encoding RNase E, indicating that this endonuclease is not involved in the abnormal mRNA processing.
They were also unaffected by spectinomycin, an inhibitor of protein synthesis, which argued against induction of RNase activity.
In vitro transcription revealed that R-loop formation is more extensive on hypernegatively supercoiled templates. These results
allow us, for the first time, to present a model by which hypernegative supercoiling inhibits growth. In this model, the introduction
of hypernegative supercoiling by gyrase facilitates degradation of nascent RNA; overproduction of RNase HI limits the accumulation
of hypernegative supercoiling, thereby preventing extensive RNA degradation.
Journal of bacteriology 10/2008; 190(22):7346-56. DOI:10.1128/JB.00680-08 · 2.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Gyrase-mediated hypernegative supercoiling is one manifestation of R-loop formation, a phenomenon that is normally suppressed by topoisomerase I (topA) in Escherichia coli. Overproduction of RNase HI (rnhA), an enzyme that removes the RNA moiety of R-loops, prevents hypernegative supercoiling and allows growth of topA null mutants. We previously showed that topA and rnhA null mutations are incompatible. We now report that such mutants were viable when RNase HI or topoisomerase III was expressed from a plasmid-borne gene. Surprisingly, DNA of topA null mutants became relaxed rather than hypernegatively supercoiled following depletion of RNase HI activity. This result failed to correlate with the cellular concentration of gyrase or topoisomerase IV (the other relaxing enzyme in the cell) or with transcription-induced supercoiling. Rather, intracellular DNA relaxation in the absence of RNase HI was related to inhibition of gyrase activity both in vivo and in extracts. Cells lacking topA and rnhA also exhibited properties consistent with segregation defects. Overproduction of topoisomerase III, an enzyme that can carry out DNA decatenation, corrected the segregation defects without restoring supercoiling activity. Collectively these data reveal (i) the existence of a cellular response to loss of RNase HI that counters the supercoiling activity of gyrase, and (ii) supercoiling-independent segregation defects due to loss of RNase HI from topA null mutants. Thus RNase HI plays a more central role in DNA topology than previously thought.
[Show abstract][Hide abstract] ABSTRACT: It has long been known that Escherichia coli cells deprived of topoisomerase I (topA null mutants) do not grow. Because mutations reducing DNA gyrase activity and, as a consequence, negative supercoiling, occur to compensate for the loss of topA function, it has been assumed that excessive negative supercoiling is somehow involved in the growth inhibition of topA null mutants. However, how excess negative supercoiling inhibits growth is still unknown. We have previously shown that the overproduction of RNase HI, an enzyme that degrades the RNA portion of an R-loop, can partially compensate for the growth defects because of the absence of topoisomerase I. In this article, we have studied the effects of gyrase reactivation on the physiology of actively growing topA null cells. We found that growth immediately and almost completely ceases upon gyrase reactivation, unless RNase HI is overproduced. Northern blot analysis shows that the cells have a significantly reduced ability to accumulate full-length mRNAs when RNase HI is not overproduced. Interestingly, similar phenotypes, although less severe, are also seen when bacterial cells lacking RNase HI activity are grown and treated in the same way. All together, our results suggest that excess negative supercoiling promotes the formation of R-loops, which, in turn, inhibit RNA synthesis.
[Show abstract][Hide abstract] ABSTRACT: DNA supercoiling and topoisomerases have long been known to affect transcription initiation. In many studies, topA mutants were used to perturb chromosomal supercoiling. Although such studies clearly revealed that supercoiling could significantly affect gene expression, they did not tell much about the essential function(s) of DNA topoisomerase I, encoded by topA. Indeed, the topA mutants used in these studies were growing relatively well, although this gene is normally essential for growth. These mutants were either carrying a topA allele with enough residual activity to permit growth, or if deleted for the topA gene, they were carrying a compensatory mutation allowing them to grow. We have recently used a set of isogenic strains carrying a conditional gyrB mutation that allowed us to study the real effects of losing topoisomerase I activity on cell physiology. The results of our work show that an essential function of topoisomerase I is related to transcription, more precisely to inhibit R-loop formation. This is in agreement with a series of biochemical studies that revealed a role for topoisomerase I in inhibiting R-loop formation during transcription in the presence of DNA gyrase. In addition, our studies may have revealed an important role for DNA supercoiling in modulating gene expression, not only at the level of transcription initiation but also during elongation. In this paper, we will first discuss global and local supercoiling, then we will address the topic of R-loop formation and finally, we will review the subject of hypersupercoiling and R-loop formation in gene expression. Whenever possible, we will try to make correlations with growth phenotypes, since such correlations reveal the essential function of DNA topoisomerase I.
Frontiers in Bioscience 02/2003; 8:d210-21. · 3.52 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: "Mémoire présenté à la faculté des études supérieures En vue de l'obtention du grade de Maître ès science (M.Sc.) En microbiologie et immunologie" Thèse (M. Sc.)--Université de Montréal, 2004. Microfilm du manuscrit.
[Show abstract][Hide abstract] ABSTRACT: Des variations importantes du surenroulement de l’ADN peuvent être générées durant la phase d’élongation de la transcription selon le modèle du « twin supercoiled domain ». Selon ce modèle, le déplacement du complexe de transcription génère du surenroulement positif à l’avant, et du surenroulement négatif à l’arrière de l’ARN polymérase. Le rôle essentiel de la topoisomérase I chez Escherichia coli est de prévenir l’accumulation de ce surenroulement négatif générée durant la transcription. En absence de topoisomérase I, l’accumulation de ce surenroulement négatif favorise la formation de R-loops qui ont pour conséquence d’inhiber la croissance bactérienne. Les R-loops sont des hybrides ARN-ADN qui se forment entre l’ARN nouvellement synthétisé et le simple brin d’ADN complémentaire. Dans les cellules déficientes en topoisomérase I, des mutations compensatoires s’accumulent dans les gènes qui codent pour la gyrase, réduisant le niveau de surenroulement négatif du chromosome et favorisant la croissance. Une des ces mutations est une gyrase thermosensible qui s’exprime à 37 °C. La RNase HI, une enzyme qui dégrade la partie ARN d’un R-loop, peut aussi restaurer la croissance en absence de topoisomérase I lorsqu’elle est produite en très grande quantité par rapport à sa concentration physiologique. En présence de topoisomérase I, des R-loops peuvent aussi se former lorsque la RNase HI est inactive. Dans ces souches mutantes, les R-loops induisent la réponse SOS et la réplication constitutive de l’ADN (cSDR). Dans notre étude, nous montrons comment les R-loops formés en absence de topoisomérase I ou RNase HI peuvent affecter négativement la croissance des cellules. Lorsque la topoisomérase I est inactivée, l’accumulation d’hypersurenroulement négatif conduit à la formation de nombreux R-loops, ce qui déclenche la dégradation de l’ARN synthétisé. Issus de la dégradation de l’ARNm de pleine longueur, des ARNm incomplets et traductibles s’accumulent et causent l’inhibition de la synthèse protéique et de la croissance. Le processus par lequel l’ARN est dégradé n’est pas encore complètement élucidé, mais nos résultats soutiennent fortement que la RNase HI présente en concentration physiologique est responsable de ce phénotype. Chose importante, la RNase E qui est l’endoribonuclease majeure de la cellule n’est pas impliquée dans ce processus, et la dégradation de l’ARN survient avant son action. Nous montrons aussi qu’une corrélation parfaite existe entre la concentration de RNase HI, l’accumulation d’hypersurenroulement négatif et l’inhibition de la croissance bactérienne. Lorsque la RNase HI est en excès, l’accumulation de surenroulement négatif est inhibée et la croissance n’est pas affectée. L’inverse se produit Lorsque la RNase HI est en concentration physiologique. En limitant l’accumulation d’hypersurenroulement négatif, la surproduction de la RNase HI prévient alors la dégradation de l’ARN et permet la croissance. Quand la RNase HI est inactivée en présence de topoisomérase I, les R-loops réduisent le niveau d’expression de nombreux gènes, incluant des gènes de résistance aux stress comme rpoH et grpE. Cette inhibition de l’expression génique n’est pas accompagnée de la dégradation de l’ARN contrairement à ce qui se produit en absence de topoisomérase I. Dans le mutant déficient en RNase HI, la diminution de l’expression génique réduit la concentration cellulaire de différentes protéines, ce qui altère négativement le taux de croissance et affecte dramatiquement la survie des cellules exposées aux stress de hautes températures et oxydatifs. Une inactivation de RecA, le facteur essentiel qui déclenche la réponse SOS et le cSDR, ne restaure pas l’expression génique. Ceci démontre que la réponse SOS et le cSDR ne sont pas impliqués dans l’inhibition de l’expression génique en absence de RNase HI. La croissance bactérienne qui est inhibée en absence de topoisomérase I, reprend lorsque l’excès de surenroulement négatif est éliminé. En absence de RNase HI et de topoisomérase I, le surenroulement négatif est très relaxé. Il semble que la réponse cellulaire suite à la formation de R-loops, soit la relaxation du surenroulement négatif. Selon le même principe, des mutations compensatoires dans la gyrase apparaissent en absence de topoisomérase I et réduisent l’accumulation de surenroulement négatif. Ceci supporte fortement l’idée que le surenroulement négatif joue un rôle primordial dans la formation de R-loop. La régulation du surenroulement négatif de l’ADN est donc une tâche essentielle pour la cellule. Elle favorise notamment l’expression génique optimale durant la croissance et l’exposition aux stress, en limitant la formation de R-loops. La topoisomérase I et la RNase HI jouent un rôle important et complémentaire dans ce processus. Important fluctuations of DNA supercoiling occur during transcription in the frame of the “twin supercoiled domain” model. In this model, transcription elongation generates negative and positive supercoiling respectively, upstream and downstream of the moving RNA polymerase. The major role of bacterial topoisomerase I is to prevent the accumulation of transcription-induced negative supercoiling. In its absence, the accumulation of negative supercoiling triggers R-loop formation which inhibits bacterial growth. R-loops are DNA/RNA hybrids formed during transcription when the nascent RNA hybridizes with the template strand thus, leaving the non-template strand single stranded. In cells lacking DNA topoisomerase I, a constant and selective pressure for the acquisition of compensatory mutations in gyrase genes reduces the negative supercoiling level of the chromosome and allows growth. One of these mutations is a thermosensitive gyrase expressed at 37 °C. The overexpression of RNase HI, an enzyme that degrades the RNA moiety of an R-loop, is also able to correct growth inhibition in absence of topoisomerase I. In the presence of topoisomerase I, R-loops can also form when RNase HI is lacking. In these mutants, R-loop formation induces SOS and constitutive stable DNA replication (cSDR). In our study, we show how R-loops formed in cells lacking topoisomerase I or RNase HI can affect bacterial growth. When topoisomerase I is inactivated, the accumulation of hypernegative supercoiling inhibits growth by causing extensive R-loop formation which, in turn, can lead to RNA degradation. As a result of RNA degradation, the accumulation of truncated and functional mRNA instead of full length ones, is responsible for protein synthesis inhibition that alters bacterial growth. The mechanism by which RNA is degraded is not completely clear but our results strongly suggest that RNase HI is involved in this process. More importantly, the major endoribonuclease, RNase E, is not involved in RNA degradation because RNA is degraded before its action. We show also that there is a perfect correlation between RNase HI concentration, the accumulation of hypernegative supercoiling and bacterial growth inhibition. When RNase HI is in excess, no accumulation of hypernegative supercoiling and growth inhibition are observed. The opposite is true when RNase HI is at its wild type level. By preventing the accumulation of hypernegative supercoiling, the overproduction of RNase HI inhibits extensive R-loop formation and RNA degradation, thus, allowing growth. In absence of RNase HI (rnhA) and in presence of topoisomerase I, R-loops are also responsible for an inhibition in gene expression, including stress genes such as rpoH and grpE. The inhibition of gene expression is not related to RNA degradation as seen in absence of topoisomerase I but it is rather related to a reduction in gene expression. In absence of RNase HI, the diminution of genes expression is responsible for a reduction in the cellular level of proteins, which negatively affects bacterial growth and bacterial survival to heat shock and oxydative stress. Additional mutations in RecA, the protein that activates SOS and cSDR after R-loop formation in rnhA, do not correct this phenotype in rnhA. Thus, SOS and cSDR are not directly involved in the inhibition of gene expression in the absence of RNase HI. In absence of topoisomerase I, growth inhibition resumes when hypernegative supercoiling is reduced. When compared to wild type strains, DNA is very relaxed in absence of RNase HI and topoisomerase I. It seems that R-loop formation induces the relaxation of negatively supercoiled DNA. All this strongly supports the idea that negative supercoiling plays an important role in R-loop formation. Finally, our work shows how essential negative supercoiling regulation is for cell physiology. By preventing R-loop formation, regulation of negative supercoiling allows optimal gene expression, which is crucial for cellular growth and for stress survival. Both topoisomerase I and RNase HI play an important and complementary role in this process.