Design of Novel Relaxase Substrates Based on Rolling Circle Replicases for Bioconjugation to DNA Nanostructures

During bacterial conjugation and rolling circle replication, HUH endonucleases, respectively known as relaxases and replicases, form a covalent bond with ssDNA when they cleave their target sequence (nic site). Both protein families show structural similarity but limited amino acid identity. Moreover, the organization of the inverted repeat (IR) and the loop that shape the nic site differs in both proteins. Arguably, replicases cleave their target site more efficiently, while relaxases exert more biochemical control over the process. Here we show that engineering a relaxase target by mimicking the replicase target, results in enhanced formation of protein-DNA covalent complexes. Three widely different relaxases, which belong to MOBF, MOBQ and MOBP families, can properly cleave DNA sequences with permuted target sequences. Collaterally, the secondary structure that the permuted targets acquired within a supercoiled plasmid DNA resulted in poor conjugation frequencies underlying the importance of relaxase accessory proteins in conjugative DNA processing. Our results reveal that relaxase and replicase targets can be interchangeable in vitro. The new Rep substrates provide new bioconjugation tools for the design of sophisticated DNA-protein nanostructures.This work was financed by grants BFU2014-55534-C2-1-P from the Spanish Ministry of Economy and Competitiveness and 612146/FP7-ICT- 2013 and 282004/FP7-HEALTH.2011.2.3.1-2 from the European Union Seventh Framework Programme to FC and grant BFU2014-55534-C2-2-P from the Spanish Ministry of Economy and Competitiveness to GM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Effect of viral storm in patients admitted to intensive care units with severe COVID-19 in Spain: a multicentre, prospective, cohort study

Background: The contribution of the virus to the pathogenesis of severe COVID-19 is still unclear. We aimed to evaluate associations between viral RNA load in plasma and host response, complications, and deaths in critically ill patients with COVID-19. Methods: We did a prospective cohort study across 23 hospitals in Spain. We included patients aged 18 years or older with laboratory-confirmed SARS-CoV-2 infection who were admitted to an intensive care unit between March 16, 2020, and Feb 27, 2021. RNA of the SARS-CoV-2 nucleocapsid region 1 (N1) was quantified in plasma samples collected from patients in the first 48 h following admission, using digital PCR. Patients were grouped on the basis of N1 quantity: VIR-N1-Zero (2747 N1 copies per mL). The primary outcome was all-cause death within 90 days after admission. We evaluated odds ratios (ORs) for the primary outcome between groups using a logistic regression analysis. Findings: 1068 patients met the inclusion criteria, of whom 117 had insufficient plasma samples and 115 had key information missing. 836 patients were included in the analysis, of whom 403 (48%) were in the VIR-N1-Low group, 283 (34%) were in the VIR-N1-Storm group, and 150 (18%) were in the VIR-N1-Zero group. Overall, patients in the VIR-N1-Storm group had the most severe disease: 266 (94%) of 283 patients received invasive mechanical ventilation (IMV), 116 (41%) developed acute kidney injury, 180 (65%) had secondary infections, and 148 (52%) died within 90 days. Patients in the VIR-N1-Zero group had the least severe disease: 81 (54%) of 150 received IMV, 34 (23%) developed acute kidney injury, 47 (32%) had secondary infections, and 26 (17%) died within 90 days (OR for death 0·30, 95% CI 0·16-0·55; p<0·0001, compared with the VIR-N1-Storm group). 106 (26%) of 403 patients in the VIR-N1-Low group died within 90 days (OR for death 0·39, 95% CI 0·26-0·57; p<0·0001, compared with the VIR-N1-Storm group). Interpretation: The presence of a so-called viral storm is associated with increased all-cause death in patients admitted to the intensive care unit with severe COVID-19. Preventing this viral storm could help to reduce poor outcomes. Viral storm could be an enrichment marker for treatment with antivirals or purification devices to remove viral components from the blood.This work was supported by grants from the Instituto de Salud Carlos III (FONDO-COVID19, COV20/00110, CIBERES, 06/06/0028; AT), Proyectos de Investigación en Salud (PI19/00590; JFB-M), Miguel Servet (CP20/00041; DdG-C), Sara Borrell (CD018/0123; APT), and Predoctorales de Formación en Investigación en Salud (FI20/00278; AdF). We also received funds from Programa de Donaciones Estar Preparados, UNESPA (Madrid, Spain), and from the Canadian Institutes of Health Research (CIHR OV2–170357; DJK and JFB-M), Research Nova Scotia, Li-Ka Shing Foundation (DJK), and finally by a Research Grant 2020 from ESCMID (APT). COV20/00110, PI19/00590, CP20/00041, CD018/0123, FI20/00278 were co-funded by European Regional Development Fund and European Social Fund (A way to make Europe, and Investing in your future). We thank the IRB-Lleida Biobank 119 (B.0000682) and Plataforma Biobancos PT17/0015/0027 in Lleida, the Hospital Clinic Barcelona (HCB)-IDIBAPS biobank in Barcelona, and the National DNA Bank and the Hospital Universitario de Salamanca biobank (both in Salamanca) for their logistical support with sample processing and storage. We are indebted to the Fundació Glòria Soler for its contribution and support to the COVIDBANK of HCBIDIBAPS Biobank. This work was not supported by any pharmaceutical company or other agency.S

Effect of viral storm in patients admitted to intensive care units with severe COVID-19 in Spain: a multicentre, prospective, cohort study

Background: The contribution of the virus to the pathogenesis of severe COVID-19 is still unclear. We aimed to evaluate associations between viral RNA load in plasma and host response, complications, and deaths in critically ill patients with COVID-19. Methods: We did a prospective cohort study across 23 hospitals in Spain. We included patients aged 18 years or older with laboratory-confirmed SARS-CoV-2 infection who were admitted to an intensive care unit between March 16, 2020, and Feb 27, 2021. RNA of the SARS-CoV-2 nucleocapsid region 1 (N1) was quantified in plasma samples collected from patients in the first 48 h following admission, using digital PCR. Patients were grouped on the basis of N1 quantity: VIR-N1-Zero ([removed]2747 N1 copies per mL). The primary outcome was all-cause death within 90 days after admission. We evaluated odds ratios (ORs) for the primary outcome between groups using a logistic regression analysis. Findings: 1068 patients met the inclusion criteria, of whom 117 had insufficient plasma samples and 115 had key information missing. 836 patients were included in the analysis, of whom 403 (48%) were in the VIR-N1-Low group, 283 (34%) were in the VIR-N1-Storm group, and 150 (18%) were in the VIR-N1-Zero group. Overall, patients in the VIR-N1-Storm group had the most severe disease: 266 (94%) of 283 patients received invasive mechanical ventilation (IMV), 116 (41%) developed acute kidney injury, 180 (65%) had secondary infections, and 148 (52%) died within 90 days. Patients in the VIR-N1-Zero group had the least severe disease: 81 (54%) of 150 received IMV, 34 (23%) developed acute kidney injury, 47 (32%) had secondary infections, and 26 (17%) died within 90 days (OR for death 0·30, 95% CI 0·16–0·55; p<0·0001, compared with the VIR-N1-Storm group). 106 (26%) of 403 patients in the VIR-N1-Low group died within 90 days (OR for death 0·39, 95% CI 0·26–0·57; p[removed]11 página

Clustering COVID-19 ARDS patients through the first days of ICU admission. An analysis of the CIBERESUCICOVID Cohort

Background Acute respiratory distress syndrome (ARDS) can be classified into sub-phenotypes according to different inflammatory/clinical status. Prognostic enrichment was achieved by grouping patients into hypoinflammatory or hyperinflammatory sub-phenotypes, even though the time of analysis may change the classification according to treatment response or disease evolution. We aimed to evaluate when patients can be clustered in more than 1 group, and how they may change the clustering of patients using data of baseline or day 3, and the prognosis of patients according to their evolution by changing or not the cluster.Methods Multicenter, observational prospective, and retrospective study of patients admitted due to ARDS related to COVID-19 infection in Spain. Patients were grouped according to a clustering mixed-type data algorithm (k-prototypes) using continuous and categorical readily available variables at baseline and day 3.Results Of 6205 patients, 3743 (60%) were included in the study. According to silhouette analysis, patients were grouped in two clusters. At baseline, 1402 (37%) patients were included in cluster 1 and 2341(63%) in cluster 2. On day 3, 1557(42%) patients were included in cluster 1 and 2086 (57%) in cluster 2. The patients included in cluster 2 were older and more frequently hypertensive and had a higher prevalence of shock, organ dysfunction, inflammatory biomarkers, and worst respiratory indexes at both time points. The 90-day mortality was higher in cluster 2 at both clustering processes (43.8% [n = 1025] versus 27.3% [n = 383] at baseline, and 49% [n = 1023] versus 20.6% [n = 321] on day 3). Four hundred and fifty-eight (33%) patients clustered in the first group were clustered in the second group on day 3. In contrast, 638 (27%) patients clustered in the second group were clustered in the first group on day 3.Conclusions During the first days, patients can be clustered into two groups and the process of clustering patients may change as they continue to evolve. This means that despite a vast majority of patients remaining in the same cluster, a minority reaching 33% of patients analyzed may be re-categorized into different clusters based on their progress. Such changes can significantly impact their prognosis

Ingeniería de relaxasas para el ensamblaje de múltiples proteínas sobre nanoestructuras de ADN

ABSTRACT: In the last decade, nanostructures made from DNA have been created with any imaginable shape. For the application of these DNA-based nanostructures (DNA origamis) in biomedicine, new approaches are required for covalent coupling of proteins to DNA. In this thesis, we focused in the application of relaxases for site-specific covalent conjugation of proteins to single stranded DNA extensions on DNA origamis. Relaxases are involved in DNA processing for bacterial conjugation, which is a process of DNA transfer from a donor to a recipient cell. Relaxases are capable of forming a covalent phosphotyrosine bond with specific DNA sequences. Three of the four relaxases investigated, TrwCR388 TraIR100 and MobAR1162, showed good binding performance to DNA origamis with high specificity and orthogonality. We have also studied the relaxases as a new tool for polymerization of single and double stranded DNA (dsDNA), or even polymerization of DNA origamis. Our goal was also the improvement of the reaction performed by relaxases. For this purpose, we have modified the recognition sequence of relaxases with secondary structures mimicking the stem-loop recognized and cleaved by replicases. We have also used substrates with a permutation between the nic site and the inverted repeat (reverse conformation), and also substrates with dsDNA around the nic site. We found that the percentage of covalent complexes with TrwCR388 improved significantly with these substrates but not all the evaluated relaxases increased the yield. These studies have helped to gain more insight into the application of relaxases in the field of biotechnology.RESUMEN: En la última década se han conseguido construir nanoestructuras de ADN (origamis de ADN) con cualquier forma imaginable. Para la aplicación de estos origamis de ADN en biomedicina, se requieren nuevos métodos para conseguir unir proteínas covalentemente al ADN. En esta tesis, hemos explorado la capacidad de las relaxasas para unirse de forma programada sobre nanoestructuras hechas de ADN ya que estas enzimas, implicadas en la transferencia de ADN plasmídico de una célula donadora a una célula receptora, son capaces de formar un enlace covalente fosfotirosina con secuencias específicas de ADN. Tres de las cuatro relaxasas investigadas, TrwCR388, TraIR100 y MobAR1162, mostraron un buen rendimiento de unión a origamis, con una alta especificad y ortogonalidad. También hemos estudiado las relaxasas como una nueva herramienta de polimerización de ADN sencillo, doble o incluso de origamis de ADN. Nuestro objetivo también ha sido la mejora de la reacción de las relaxasas. Para aumentar la actividad, hemos modificado la secuencia de reconocimiento de las relaxasas imitando la conformación de horquilla que reconocen las replicasas. También hemos utilizado una conformación en la que se han permutado el sitio nic y la repetición invertida (conformación inversa), e incluso con doble cadena después del sitio nic. Encontramos que el porcentaje de complejos covalentes mejoraba significativamente con TrwCR388 pero no todas las relaxasas evaluadas lo incrementaban. Estos estudios han servido para ampliar el potencial de las relaxasas como herramientas biotecnológicas.Esta Tesis ha sido financiada con las siguientes ayudas: -BACTOCOM (FP7-ICT-2009-4-248919) -EMBO Short Term Fellowship (ASTF 141-2012) -COBRA Project (270371) -PLASMWIRES (FP7-ICT-2013-10-612146) - Volkswagen Stiftung (Az.86 395-1

Relaxase engineering for multiprotein assembly on DNA nanostructures

Memoria presentada por Sandra Sagredo de Pedro para la obtención del grado de Doctor.[EN]: In the last decade, nanostructures made from DNA have been created with any imaginable shape. For the application of these DNA-based nanostructures (DNA origamis) in biomedicine, new approaches are required for covalent coupling of proteins to DNA. In this thesis, we focused in the application of relaxases for site-specific covalent conjugation of proteins to single stranded DNA extensions on DNA origamis. Relaxases are involved in DNA processing for bacterial conjugation, which is a process of DNA transfer from a donor to a recipient cell. Relaxases are capable of forming a covalent phosphotyrosine bond with specific DNA sequences. Three of the four relaxases investigated, TrwCR388 TraIR100 and MobAR1162, showed good binding performance to DNA origamis with high specificity and orthogonality. We have also studied the relaxases as a new tool for polymerization of single and double stranded DNA (dsDNA), or even polymerization of DNA origamis. Our goal was also the improvement of the reaction performed by relaxases. For this purpose, we have modified the recognition sequence of relaxases with secondary structures mimicking the stem-loop recognized and cleaved by replicases. We have also used substrates with a permutation between the nic site and the inverted repeat (reverse conformation), and also substrates with dsDNA around the nic site. We found that the percentage of covalent complexes with TrwCR388 improved significantly with these substrates but not all the evaluated relaxases increased the yield. These studies have helped to gain more insight into the application of relaxases in the field of biotechnology.[ES]: En la última década se han conseguido construir nanoestructuras de ADN (origamis de ADN) con cualquier forma imaginable. Para la aplicación de estos origamis de ADN en biomedicina, se requieren nuevos métodos para conseguir unir proteínas covalentemente al ADN. En esta tesis, hemos explorado la capacidad de las relaxasas para unirse de forma programada sobre nanoestructuras hechas de ADN ya que estas enzimas, implicadas en la transferencia de ADN plasmídico de una célula donadora a una célula receptora, son capaces de formar un enlace covalente fosfotirosina con secuencias específicas de ADN. Tres de las cuatro relaxasas investigadas, TrwCR388, TraIR100 y MobAR1162, mostraron un buen rendimiento de unión a origamis, con una alta especificad y ortogonalidad. También hemos estudiado las relaxasas como una nueva herramienta de polimerización de ADN sencillo, doble o incluso de origamis de ADN. Nuestro objetivo también ha sido la mejora de la reacción de las relaxasas. Para aumentar la actividad, hemos modificado la secuencia de reconocimiento de las relaxasas imitando la conformación de horquilla que reconocen las replicasas. También hemos utilizado una conformación en la que se han permutado el sitio nic y la repetición invertida (conformación inversa), e incluso con doble cadena después del sitio nic. Encontramos que el porcentaje de complejos covalentes mejoraba significativamente con TrwCR388 pero no todas las relaxasas evaluadas lo incrementaban. Estos estudios han servido para ampliar el potencial de las relaxasas como herramientas biotecnológicas.Esta Tesis ha sido financiada con las siguientes ayudas: -BACTOCOM (FP7-ICT-2009-4-248919); -EMBO Short Term Fellowship (ASTF 141-2012); -COBRA Project (270371); -PLASMWIRES (FP7-ICT-2013-10-612146); - Volkswagen Stiftung (Az.86 395-1).Peer Reviewe

Relaxing relaxases: deregulation of the nic-cleavage reaction for biotechnological applications

Trabajo presentado al "22nd IUBMB" y "37th FEBS" from "Single Molecules to Systems Biology" celebrado en Sevilla del 4 al 9 de septiembre de 2012.Peer Reviewe

Out-of-Plane Aptamer Functionalization of RNA Three-Helix Tiles

Co-transcriptionally folding RNA nanostructures have great potential as biomolecular scaffolds, which can be used to organize small molecules or proteins into spatially ordered assemblies. Here, we develop an RNA tile composed of three parallel RNA double helices, which can associate into small hexagonal assemblies via kissing loop interactions between its two outer helices. The inner RNA helix is modified with an RNA motif found in the internal ribosome entry site (IRES) of the hepatitis C virus (HCV), which provides a 90&#176; bend. This modification is used to functionalize the RNA structures with aptamers pointing perpendicularly away from the tile plane. We demonstrate modifications with the fluorogenic malachite green and Spinach aptamers as well with the protein-binding PP7 and streptavidin aptamers. The modified structures retain the ability to associate into larger assemblies, representing a step towards RNA hybrid nanostructures extending in three dimensions

Novel designs for DNA substrates of model single-Y relaxases.

<p>(A) SDS-PAGE of MobA_R_RSF1010 with its targets. 7 μM MobA_R was incubated with 15 μM of different oligonucleotides. Lane 1, MobA_R. Lanes 2 and 3, wt oligonucleotide WQ(30+7) and a substrate that lacks the upper-hairpin nucleotides of the IR WQ(23+7). Lanes 4, 5 and 6, Rep-like oligonucleotides HQ(16+16),HQ(16+19) and HQ(16+22), respectively. Lanes 7, 8 and 9 reverse substrates RQ(8+28), RQ(8+34) and RQ(8+40). Lane 10, molecular weight ladder. (B) SDS-PAGE of TraI_R_RP4 with its targets. 1.5 μM TraI_R was incubated with 15 μM of different oligonucleotides. Lane 1, TraI_R; lane 2, wt substrate WP(15+6); lane 3, wt substrate WP(24+8); lane 4, reverse substrate RP(8+24) and lane 5, Rep-like substrate HP(14+14). Molecular weight ladder is shown on Lane 6. Bar graphs with the quantification of covalent complexes are shown below the SDS-PAGE gels. Data showed mean±s.d. of three independent experiments.</p

Cleavage activity of TrwC_R on different oligonucleotides.

<p>Cleavage activity of TrwC_R on different oligonucleotides.</p