Role of MicroRNA Modulation in the Interferon-α/Ribavirin Suppression of HIV-1 In Vivo.

BACKGROUND Interferon-α (IFN-α) treatment suppresses HIV-1 viremia and reduces the size of the HIV-1 latent reservoir. Therefore, investigation of the molecular and immunologic effects of IFN-α may provide insights that contribute to the development of novel prophylactic, therapeutic and curative strategies for HIV-1 infection. In this study, we hypothesized that microRNAs (miRNAs) contribute to the IFN-α-mediated suppression of HIV-1. To inform the development of novel miRNA-based antiretroviral strategies, we investigated the effects of exogenous IFN-α treatment on global miRNA expression profile, HIV-1 viremia, and potential regulatory networks between miRNAs and cell-intrinsic anti-HIV-1 host factors in vivo. METHODS Global miRNA expression was examined in longitudinal PBMC samples obtained from seven HIV/HCV-coinfected, antiretroviral therapy-naïve individuals before, during, and after pegylated interferon-α/ribavirin therapy (IFN-α/RBV). We implemented novel hybrid computational-empirical approaches to characterize regulatory networks between miRNAs and anti-HIV-1 host restriction factors. RESULTS miR-422a was the only miRNA significantly modulated by IFN-α/RBV in vivo (p<0.0001, paired t test; FDR<0.037). Our interactome mapping revealed extensive regulatory involvement of miR-422a in p53-dependent apoptotic and pyroptotic pathways. Based on sequence homology and inverse expression relationships, 29 unique miRNAs may regulate anti-HIV-1 restriction factor expression in vivo. CONCLUSIONS The specific reduction of miR-422a is associated with exogenous IFN-α treatment, and likely contributes to the IFN-α suppression of HIV-1 through the enhancement of anti-HIV-1 restriction factor expression and regulation of genes involved in programmed cell death. Moreover, our regulatory network analysis presents additional candidate miRNAs that may be targeted to enhance anti-HIV-1 restriction factor expression in vivo.

Nonsense-mediated mRNA decay (NMD) restricts replication of mammalian RNA viruses

A genome-wide siRNA screen against host factors that affect the infection of Semliki Forest virus (SFV), a positive-strand (+)RNA virus, revealed that components of the nonsense-mediated mRNA decay (NMD) pathway restrict early, post-entry steps of the infection cycle. In HeLa cells and primary human fibroblasts, knockdown of UPF1, SMG5 and SMG7 leads to increased levels of viral proteins and RNA and to higher titers of released virus. The inhibitory effect of NMD was stronger when the efficiency of virus replication was impaired by mutations or deletions in the replicase proteins. Accordingly, impairing NMD resulted in a more than 20-fold increased production of these attenuated viruses. Our data suggest that intrinsic features of genomic and sub-genomic viral mRNAs, most likely the extended 3'-UTR length, make them susceptible to NMD. The fact that SFV replication is entirely cytoplasmic strongly suggests that degradation of the viral RNA occurs through the exon junction complex (EJC)-independent mode of NMD. Collectively, our findings uncover a new biological function for NMD as an intrinsic barrier to the translation of early viral proteins and the amplification of (+)RNA viruses in animal cells. Thus, in addition to its role in mRNA surveillance and post-transcriptional gene regulation, NMD also contributes to protect cells from RNA viruses.

Human Urinary Composition Controls Siderocalin's Antibacterial Activity.

During Escherichia coli urinary tract infections, cells in the human urinary tract release the antimicrobial protein siderocalin (SCN; also known as lipocalin 2, neutrophil gelatinase-associated lipocalin/NGAL, or 24p3). SCN can interfere with E. coli iron acquisition by sequestering ferric iron complexes with enterobactin, the conserved E. coli siderophore. Here we find that human urinary constituents can reverse this relationship, instead making enterobactin critical for overcoming SCN-mediated growth restriction. Urinary control of SCN activity exhibits wide ranging individual differences. We used these differences to identify elevated urinary pH and aryl metabolites as key biochemical host factors controlling urinary SCN activity. These aryl metabolites are well-known products of intestinal microbial metabolism. Together, these results identify an innate antibacterial immune interaction that is critically dependent upon individualistic chemical features of human urine.

Enteroaggregative Escherichia coli as a cause of acute diarrhea

Enteroaggregative Escherichia coli (EAEC) are considered an important emerging enteric and food-borne pathogen. The groups importantly affected by EAEC include international travelers, children in the developing world, and patients with HIV infection. EAEC does not commonly cause diarrheal illness in all hosts. ^ The reasons for the observed clinical variation in EAEC infection are multifactorial and are dependant on the pathogen, the inoculum ingested and the host susceptibility. A major obstacle in identifying the mechanism of pathogenesis for EAEC is the heterogeneity in virulence of strains. No EAEC virulence gene is consistently present in all diarrheagenic strains. However, a recent report suggests that a package of plasmid borne and chromosomal virulence factors are under the control of the described transcriptional activator aggR. Although the exact inoculum required for EAEC diarrheal illness is not known, a volunteer study has shown that oral ingestion of 10 10 cfu of virulent EAEC elicited diarrhea. Ongoing studies are being conducted to better define the exact infectious dose. There are also host factors associated with increased susceptibility of persons to diarrheal illness with EAEC. ^ The following three manuscripts: (1) review EAEC as an emerging enteric pathogen; (2) identify EAEC as a cause of acute diarrhea among different subpopulations worldwide; (3) identify virulence characteristics and the molecular epidemiology of EAEC isolates among travelers with diarrheal illness and describe the pathogenesis of EAEC infection. ^

Immune response to hepatitis B vaccination in drug using populations: A systematic review and meta-regression analysis

Hepatitis B virus (HBV) is a significant cause of liver diseases and related complications worldwide. Both injecting and non-injecting drug users are at increased risk of contracting HBV infection. Scientific evidence suggests that drug users have subnormal response to HBV vaccination and the seroprotection rates are lower than that in the general population; potentially due to vaccine factors, host factors, or both. The purpose of this systematic review is to examine the rates of seroprotection following HBV vaccination in drug using populations and to conduct a meta-analysis to identify the factors associated with varying seroprotection rates. Seroprotection is defined as developing an anti-HBs antibody level of ≥ 10 mIU/ml after receiving the HBV vaccine. Original research articles were searched using online databases and reference lists of shortlisted articles. HBV vaccine intervention studies reporting seroprotection rates in drug users and published in English language during or after 1989 were eligible. Out of 235 citations reviewed, 11 studies were included in this review. The reported seroprotection rates ranged from 54.5 – 97.1%. Combination vaccine (HAV and HBV) (Risk ratio 12.91, 95% CI 2.98-55.86, p = 0.003), measurement of anti-HBs with microparticle immunoassay (Risk ratio 3.46, 95% CI 1.11-10.81, p = 0.035) and anti-HBs antibody measurement at 2 months after the last HBV vaccine dose (RR 4.11, 95% CI 1.55-10.89, p = 0.009) were significantly associated with higher seroprotection rates. Although statistically nonsignificant, the variables mean age>30 years, higher prevalence of anti-HBc antibody and anti-HIV antibody in the sample population, and current drug use (not in drug rehabilitation treatment) were strongly associated with decreased seroprotection rates. Proportion of injecting drug users, vaccine dose and accelerated vaccine schedule were not predictors of heterogeneity across studies. Studies examined in this review were significantly heterogeneous (Q = 180.850, p = 0.000) and factors identified should be considered when comparing immune response across studies. The combination vaccine showed promising results; however, its effectiveness compared to standard HBV vaccine needs to be examined systematically. Immune response in DUs can possibly be improved by the use of bivalent vaccines, booster doses, and improving vaccine completion rates through integrated public programs and incentives.^

Inflammatory Breast Cancer: The Immune Perspective

Inflammatory breast cancer (IBC) is the most insidious form of locally advanced disease. Although rare and less than 2% of all breast cancer, IBC is responsible for up to 10% of all breast cancer deaths. Despite the name, very little is known about the role of inflammation or immune mediators in IBC. Therefore, we analyzed blood samples from IBC patients and non-IBC patients, as well as healthy donor controls to establish an IBC-specific profile of peripheral blood leukocyte phenotype and function of T cells and dendritic cells and serum inflammatory cytokines. Emerging evidence suggests that host factors in the microenviromement may interact with underlying IBC genetics to promote the aggressive nature of the tumor. An integral part of the metastatic process involves epithelial to mesenchymal transition (EMT) where primary breast cancer cells gain motility and stem cell-like features that allow distant seeding. Interestingly, the IBC consortium microarray data found no clear evidence for EMT in IBC tumor tissues. It is becoming increasingly evident that inflammatory factors can induce EMT. However, it is unknown if EMT-inducing soluble factors secreted by activated immune cells in the IBC microenvironment canπ account for the absence of EMT in studies of the tumor cells themselves. We hypothesized that soluble factors from immune cells are capable of inducing EMT in IBC. We tested the ability of immune conditioned media to induce EMT in IBC cells. We found that soluble factors from activated immune cells are able to induce the expression of EMT-related factors in IBC cells along with increased migration and invasion. Specifically, the pro-inflammatory cytokines TNF-α, IL-6 and TGF-β were able to induce EMT and blocking these factors in conditioned media abated the induction of EMT. Surprisingly, unique to IBC cells, this process was related to increased levels of E-cadherin expression and adhesion, reminiscent of the characteristic tightly packed tumor emboli seen in IBC samples. This data offers insight into the unique pathology of IBC by suggesting that tumor immune interactions in the tumor microenvironment contribute to the aggressive nature of IBC implying that immune induced inflammation can be a novel therapeutic target. Specifically, we showed that soluble factors secreted by activated immune cells are capable of inducing EMT in IBC cells and may mediate the persistent E-cadherin expression observed in IBC. This data suggests that immune mediated inflammation may contribute to the highly aggressive nature of IBC and represents a potential therapeutic target that warrants further investigation.

Caracterización de la necrosis sistémica inducida por la interacción sinérgica entre el Virus X de la patata y potyvirus en Nicotiana benthamiana

Los virus de plantas pueden causar enfermedades severas que conllevan serias pérdidas económicas a nivel mundial. Además, en la naturaleza son comunes las infecciones simultáneas con distintos virus que conducen a la exacerbación de los síntomas de enfermedad, fenómeno al que se conoce como sinergismo viral. Una de las sintomatologías más severas causadas por los virus en plantas susceptibles es la necrosis sistémica (NS), que incluso puede conducir a la muerte del huésped. Este fenotipo ha sido comparado en ocasiones con la respuesta de resistencia de tipo HR, permitiendo establecer una serie de paralelismos entre ambos tipos de respuesta que sugieren que la NS producida en interacciones compatibles sería el resultado de una respuesta hipersensible sistémica (SHR). Sin embargo, los mecanismos moleculares implicados en el desarrollo de la NS, su relación con procesos de defensa antiviral o su relevancia biológica aún no son bien entendidos, al igual que tampoco han sido estudiados los cambios producidos en la planta a escala genómica en infecciones múltiples que muestran sinergismo en patología. En esta tesis doctoral se han empleado distintas aproximaciones de análisis de expresión génica, junto con otras técnicas genéticas y bioquímicas, en el sistema modelo de Nicotiana benthamiana para estudiar la NS producida por la infección sinérgica entre el Virus X de la patata (PVX) y diversos potyvirus. Se han comparado los cambios producidos en el huésped a nivel genómico y fisiológico entre la infección doble con PVX y el Virus Y de la patata (PVY), y las infecciones simples con PVX o PVY. Además, los cambios transcriptómicos y hormonales asociados a la infección con la quimera viral PVX/HC‐Pro, que reproduce los síntomas del sinergismo entre PVX‐potyvirus, se han comparado con aquellos producidos por otros dos tipos de muerte celular, la PCD ligada a una interacción incompatible y la PCD producida por la disfunción del proteasoma. Por último, técnicas de genética reversa han permitido conocer la implicación de factores del huésped, como las oxilipinas, en el desarrollo de la NS asociada al sinergismo entre PVXpotyvirus. Los resultados revelan que, respecto a las infecciones con solo uno de los virus, la infección doble con PVX‐PVY produce en el huésped diferencias cualitativas además de cuantitativas en el perfil transcriptómico relacionado con el metabolismo primario. Otros cambios en la expresión génica, que reflejan la activación de mecanismos de defensa, correlacionan con un fuerte estrés oxidativo en las plantas doblemente infectadas que no se detecta en las infecciones simples. Además, medidas en la acumulación de determinados miRNAs implicados en diversos procesos celulares muestran como la infección doble altera de manera diferencial tanto la acumulación de estos miRNAs como su funcionalidad, lo cual podría estar relacionado con los cambios en el transcriptoma, así como con la sintomatología de la infección. La comparación a nivel transcriptómico y hormonal entre la NS producida por PVX/HC‐Pro y la interacción incompatible del Virus del mosaico del tabaco en plantas que expresan el gen N de resistencia (SHR), muestra que la respuesta en la interacción compatible es similar a la que se produce durante la SHR, si bien se presenta de manera retardada en el tiempo. Sin embargo, los perfiles de expresión de genes de defensa y de respuesta a hormonas, así como la acumulación relativa de ácido salicílico (SA), ácido jasmonico (JA) y ácido abscísico, en la interacción compatible son más semejantes a la respuesta PCD producida por la disfunción del proteasoma que a la interacción incompatible. Estos datos sugieren una contribución de la interferencia sobre la funcionalidad del proteasoma en el incremento de la patogenicidad, observado en el sinergismo PVX‐potyvirus. Por último, los resultados obtenidos al disminuir la expresión de 9‐LOX, α‐DOX1 y COI1, relacionados con la síntesis o con la señalización de oxilipinas, y mediante la aplicación exógena de JA y SA, muestran la implicación del metabolismo de las oxilipinas en el desarrollo de la NS producida por la infección sinérgica entre PVXpotyvirus en N. benthamiana. Además, estos resultados indican que la PCD asociada a esta infección, al igual que ocurre en interacciones incompatibles, no contiene necesariamente la acumulación viral, lo cual indica que necrosis e inhibición de la multiplicación viral son procesos independientes. ABSTRACT Plant viruses cause severe diseases that lead to serious economic losses worldwide. Moreover, simultaneous infections with several viruses are common in nature leading to exacerbation of the disease symptoms. This phenomenon is known as viral synergism. Systemic necrosis (SN) is one of the most severe symptoms caused by plant viruses in susceptible plants, even leading to death of the host. This phenotype has been compared with the hypersensitive response (HR) displayed by resistant plants, and some parallelisms have been found between both responses, which suggest that SN induced by compatible interactions could be the result of a systemic hypersensitive response (SHR). However, the molecular mechanisms involved in the development of SN, its relationship with antiviral defence processes and its biological relevance are still unknown. Furthermore, the changes produced in plants by mixed infections that cause synergistic pathological effects have not been studied in a genome‐wide scale. In this doctoral thesis different approaches have been used to analyse gene expression, together with other genetic and biochemical techniques, in the model plant Nicotiana benthamiana, in order to study the SN produced by the synergistic infection of Potato virus X (PVX) with several potyviruses. Genomic and physiological changes produced in the host by double infection with PVX and Potato virus Y (PVY), and by single infection with PVX or PVY have been compared. In addition, transcriptional and hormonal changes associated with infection by the chimeric virus PVX/HC‐Pro, which produces synergistic symptoms similar to those caused by PVX‐potyvirus, have been compared with those produced by other types of cell death. These types of cell death are: PCD associated with an incompatible interaction, and PCD produced by proteasome disruption. Finally, reverse genetic techniques have revealed the involvement of host factors, such as oxylipins, in the development of SN associated with PVX‐potyvirus synergism. The results revealed that compared with single infections, double infection with PVX‐PVY produced qualitative and quantitative differences in the transcriptome profile, mainly related to primary metabolism. Other changes in gene expression, which reflected the activation of defence mechanisms, correlated with a severe oxidative stress in doubly infected plants that was undetected in single infections. Additionally, accumulation levels of several miRNAs involved in different cellular processes were measured, and the results showed that double infection not only produced the greatest variations in miRNA accumulation levels but also in miRNA functionality. These variations could be related with transcriptomic changes and the symptomatology of the infection. Transcriptome and hormone level comparisons between SN induced by PVX/HCPro and the incompatible interaction produced by Tobacco mosaic virus in plants expressing the N resistance gene (SHR), showed some similarities between both responses, even though the compatible interaction appeared retarded in time. Nevertheless, the expression profiles of both defence‐related genes and hormoneresponsive genes, as well as the relative accumulation of salicylic acid (SA), jasmonic acid (JA) and abscisic acid in the compatible interaction are more similar to the PCD response produced by proteasome disruption. These data suggest that interference with proteasome functionality contributes to the increase in pathogenicity associated with PVX‐potyvirus synergism. Finally, the results obtained by reducing the expression of 9‐LOX, α‐DOX1 and COI1, related with synthesis or signalling of oxylipins, and by applying exogenously JA and SA, revealed that oxylipin metabolism is involved in the development of SN induced by PVX‐potyvirus synergistic infections in N. benthamiana. Moreover, these results also indicated that PVX‐potyvirus associated PCD does not necessarily restrict viral accumulation, as is also the case in incompatible interactions. This indicates that both necrosis and inhibition of viral multiplication are independent processes.

Lethal paralysis of Caenorhabditis elegans by Pseudomonas aeruginosa

Identification of host factors that interact with pathogens is crucial to an understanding of infectious disease, but direct screening for host mutations to aid in this task is not feasible in mammals. The nematode Caenorhabditis elegans is a genetically tractable alternative for investigating the pathogenic bacterium Pseudomonas aeruginosa. A P. aeruginosa toxin, produced at high cell density under control of the quorum-sensing regulators LasR and RhlR, rapidly and lethally paralyzes C. elegans. Loss-of-function mutations in C. elegans egl-9, a gene required for normal egg laying, confer strong resistance to the paralysis. Thus, activation of EGL-9 or of a pathway that includes it may lead to the paralysis. The molecular identity of egl-9 was determined by transformation rescue and DNA sequencing. A mammalian homologue of EGL-9 is expressed in tissues in which exposure to P. aeruginosa could have clinical effects.

Isolation and characterization of powdery mildew-resistant Arabidopsis mutants

A compatible interaction between a plant and a pathogen is the result of a complex interplay between many factors of both plant and pathogen origin. Our objective was to identify host factors involved in this interaction. These factors may include susceptibility factors required for pathogen growth, factors manipulated by the pathogen to inactivate or avoid host defenses, or negative regulators of defense responses. To this end, we identified 20 recessive Arabidopsis mutants that do not support normal growth of the powdery mildew pathogen, Erysiphe cichoracearum. Complementation analyses indicated that four loci, designated powdery mildew resistant 1–4 (pmr1–4), are defined by this collection. These mutants do not constitutively accumulate elevated levels of PR1 or PDF1.2 mRNA, indicating that resistance is not simply due to constitutive activation of the salicylic acid- or ethylene- and jasmonic acid-dependent defense pathways. Further Northern blot analyses revealed that some mutants accumulate higher levels of PR1 mRNA than wild type in response to infection by powdery mildew. To test the specificity of the resistance, the pmr mutants were challenged with other pathogens including Pseudomonas syringae, Peronospora parasitica, and Erysiphe orontii. Surprisingly, one mutant, pmr1, was susceptible to E. orontii, a very closely related powdery mildew, suggesting that a very specific resistance mechanism is operating in this case. Another mutant, pmr4, was resistant to P. parasitica, indicating that this resistance is more generalized. Thus, we have identified a novel collection of mutants affecting genes required for a compatible interaction between a plant and a biotrophic pathogen.

A common muscarinic pathway for diapause recovery in the distantly related nematode species Caenorhabditis elegans and Ancylostoma caninum

Converging TGF-β and insulin-like neuroendocrine signaling pathways regulate whether Caenorhabditis elegans develops reproductively or arrests at the dauer larval stage. We examined whether neurotransmitters act in the dauer entry or recovery pathways. Muscarinic agonists promote recovery from dauer arrest induced by pheromone as well as by mutations in the TGF-β pathway. Dauer recovery in these animals is inhibited by the muscarinic antagonist atropine. Muscarinic agonists do not induce dauer recovery of either daf-2 or age-1 mutant animals, which have defects in the insulin-like signaling pathway. These data suggest that a metabotropic acetylcholine signaling pathway activates an insulin-like signal during C. elegans dauer recovery. Analogous and perhaps homologous cholinergic regulation of mammalian insulin release by the autonomic nervous system has been noted. In the parasitic nematode Ancylostoma caninum, the dauer larval stage is the infective stage, and recovery to the reproductive stage normally is induced by host factors. Muscarinic agonists also induce and atropine potently inhibits in vitro recovery of A. caninum dauer arrest. We suggest that host or parasite insulin-like signals may regulate recovery of A. caninum and could be potential targets for antihelminthic drugs.

A mutant allele of essential, general translation initiation factor DED1 selectively inhibits translation of a viral mRNA

Positive-strand RNA virus genomes are substrates for translation, RNA replication, and encapsidation. To identify host factors involved in these functions, we used the ability of brome mosaic virus (BMV) RNA to replicate in yeast. We report herein identification of a mutation in the essential yeast gene DED1 that inhibited BMV RNA replication but not yeast growth. DED1 encodes a DEAD (Asp-Glu-Ala-Asp)-box RNA helicase required for translation initiation of all yeast mRNAs. Inhibition of BMV RNA replication by the mutant DED1 allele (ded1–18) resulted from inhibited expression of viral polymerase-like protein 2a, encoded by BMV RNA2. Inhibition of RNA2 translation was selective, with no effect on general cellular translation or translation of BMV RNA1-encoded replication factor 1a, and was independent of p20, a cellular antagonist of DED1 function in translation. Inhibition of RNA2 translation in ded1–18 yeast required the RNA2 5′ noncoding region (NCR), which also conferred a ded1–18-specific reduction in expression on a reporter gene mRNA. Comparison of the similar RNA1 and RNA2 5′ NCRs identified a 31-nucleotide RNA2-specific region that was required for the ded1–18-specific RNA2 translation block and attenuated RNA2 translation in wild-type yeast. Further comparisons and RNA structure predictions suggest a modular arrangement of replication and translation signals in RNA1 and RNA2 5′ NCRs that appears conserved among bromoviruses. The 5′ attenuator and DED1 dependence of RNA2 suggest that, despite its divided genome, BMV regulates polymerase translation relative to other replication factors, just as many single-component RNA viruses use translational read-through and frameshift mechanisms to down-regulate polymerase. The results show that a DEAD-box helicase can selectively activate translation of a specific mRNA and may provide a paradigm for translational regulation by other members of the ubiquitous DEAD-box RNA helicase family.

TOM1, an Arabidopsis gene required for efficient multiplication of a tobamovirus, encodes a putative transmembrane protein

Host-encoded factors play an important role in virus multiplication, acting in concert with virus-encoded factors. However, information regarding the host factors involved in this process is limited. Here we report the map-based cloning of an Arabidopsis thaliana gene, TOM1, which is necessary for the efficient multiplication of tobamoviruses, positive-strand RNA viruses infecting a wide variety of plants. The TOM1 mRNA is suggested to encode a 291-aa polypeptide that is predicted to be a multipass transmembrane protein. The Sos recruitment assay supported the hypothesis that TOM1 is associated with membranes, and in addition, that TOM1 interacts with the helicase domain of tobamovirus-encoded replication proteins. Taken into account that the tobamovirus replication complex is associated with membranes, we propose that TOM1 participates in the in vivo formation of the replication complex by serving as a membrane anchor.

Lagging strand replication of rolling-circle plasmids: Specific recognition of the ssoA-type origins in different gram-positive bacteria

Many bacterial plasmids replicate by a rolling-circle mechanism that involves the generation of single-stranded DNA (ssDNA) intermediates. Replication of the lagging strand of such plasmids initiates from their single strand origin (sso). Many different types of ssos have been identified. One group of ssos, termed ssoA, which have conserved sequence and structural features, function efficiently only in their natural hosts in vivo. To study the host specificity of sso sequences, we have analyzed the functions of two closely related ssoAs belonging to the staphylococcal plasmid pE194 and the streptococcal plasmid pLS1 in Staphylococcus aureus. The pLS1 ssoA functioned poorly in vivo in S. aureus as evidenced by accumulation of high levels of ssDNA but supported efficient replication in vitro in staphylococcal extracts. These results suggest that one or more host factors that are present in sufficient quantities in S. aureus cell-free extracts may be limiting in vivo. Mapping of the initiation points of lagging strand synthesis in vivo and in vitro showed that DNA synthesis initiates from specific sites within the pLS1 ssoA. These results demonstrate that specific initiation of replication can occur from the pLS1 ssoA in S. aureus although it plays a minimal role in lagging strand synthesis in vivo. Therefore, the poor functionality of the pLS1 in vivo in a nonnative host is caused by the low efficiency rather than a lack of specificity of the initiation process. We also have identified ssDNA promoters and mapped the primer RNAs synthesized by the S. aureus and Bacillus subtilis RNA polymerases from the pE194 and pLS1 ssoAs. The S. aureus RNA polymerase bound more efficiently to the native pE194 ssoA as compared with the pLS1 ssoA, suggesting that the strength of RNA polymerase–ssoA interaction may play a major role in the functionality of the ssoA sequences in Gram-positive bacteria.

Chromosomal transposition of a Tc1/mariner-like element in mouse embryonic stem cells

Mouse has become an increasingly important organism for modeling human diseases and for determining gene function in a mammalian context. Unfortunately, transposon-tagged mutagenesis, one of the most valuable tools for functional genomics, still is not available in this organism. On the other hand, it has long been speculated that members of the Tc1/mariner-like elements may be less dependent on host factors and, hence, can be introduced into heterologous organisms. However, this prediction has not been realized in mice. We report here the chromosomal transposition of the Sleeping Beauty (SB) element in mouse embryonic stem cells, providing evidence that it can be used as an in vivo mutagen in mice.

Handoff from recombinase to replisome: Insights from transposition

Bacteriophage Mu replicates as a transposable element, exploiting host enzymes to promote initiation of DNA synthesis. The phage-encoded transposase MuA, assembled into an oligomeric transpososome, promotes transfer of Mu ends to target DNA, creating a fork at each end, and then remains tightly bound to both forks. In the transition to DNA synthesis, the molecular chaperone ClpX acts first to weaken the transpososome's interaction with DNA, apparently activating its function as a molecular matchmaker. This activated transpososome promotes formation of a new nucleoprotein complex (prereplisome) by yet unidentified host factors [Mu replication factors (MRFα2)], which displace the transpososome in an ATP-dependent reaction. Primosome assembly proteins PriA, PriB, DnaT, and the DnaB–DnaC complex then promote the binding of the replicative helicase DnaB on the lagging strand template of the Mu fork. PriA helicase plays an important role in opening the DNA duplex for DnaB binding, which leads to assembly of DNA polymerase III holoenzyme to form the replisome. The MRFα2 transition factors, assembled into a prereplisome, not only protect the fork from action by nonspecific host enzymes but also appear to aid in replisome assembly by helping to activate PriA's helicase activity. They consist of at least two separable components, one heat stable and the other heat labile. Although the MRFα2 components are apparently not encoded by currently known homologous recombination genes such as recA, recF, recO, and recR, they may fulfill an important function in assembling replisomes on arrested replication forks and products of homologous strand exchange.