ICETh1 & ICETh2, two mobile genetic elements coordinated in Thermus thermophilus transjugation

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 13-12-2019Esta tesis tiene embargado el acceso al texto completo hasta el 13-06-2021Horizontal Gene Transfer (HGT) is considered one of the most important sources of bacterial evolution. In the thermophilic bacterium Thermus thermophilus, the transjugation mechanism has been described as a highly efficient HGT system. This mechanism consists in the transfer of DNA from a donor to a recipient cell, being necessary the machinery for DNA donation in the donor and the transformation machinery in the recipient cell. In the strain HB27 of this organism, two small Integrative and Conjugative Elements (ICEs), have been discovered and we show how they coordinate their activities in the transjugation process. ICETh1 encodes the machinery necessary for DNA donation, where the translocase TdtA is essential, as it is probably the most important protein in this process. However, accessory proteins such as the nuclease NurA and the restrictase Tth111II are also relevant for this event, likely processing DNA prior to its transfer mediated by TdtA. Any locus in the genome can be transferred to a recipient cell; however, the ICEThs show a higher transfer rate. We have shown that ICETh1 is not capable by itself to excise or integrate in the chromosome. This process is dependent on a specialized excision/integration module encoded in ICETh2, a second mobile element that can excise and integrate both ICEThs in their respective sites despite being catalyzed by a single enzyme These ICEThs seem to exhibit a higher excision rate and apparently replicate under stress conditions produced by UV or in the absence of the primase/polymerase PrimPol encoded by ICETh2. Autonomous replication of both ICEThs, even when it is not clear, could be driven by a TOPRIM-domain homologue protein. A Toxin-Antitoxin (TA) system could assure the presence of ICETh1 in the cell population via post-segregational killing. Additionally, the possibility exists that the TOPRIM-domain homologue, encoded in ICETh2, could be required for some cellular function promoting somehow the maintenance of ICETh1 and, to a lesser extent of ICETh2. Furthermore, in this work it is proposed a retro-transfer model for DNA transjugation in which DNA fragments, apart from the ICEThs themselves, can be transferred to a recipient cell in which they integrate. Then, with the intervention of ICETh1 transjugation machinery, DNA fragments from the recipient cell could be transferred back in the opposite direction to the original donor, followed by integration, generating mosaicism in the progeny.Tengo que agradecer también la financiación aportada por el ministerio de ciencia (antiguamente MINECO)

ICETh1 and ICETh2, two interdependent mobile genetic elements in Thermus thermophilus transjugation.

Cell to cell DNA transfer between Thermus thermophilus, or transjugation, requires the natural competence apparatus (NCA) of the recipient cell and a DNA donation machinery in the donor. In T. thermophilus HB27, two mobile genetic elements with functional similarities to Integrative and Conjugative Elements (ICEs) coexist, ICETh1 encoding the DNA transfer apparatus and ICETh2, encoding a putative replication module. Here, we demonstrate that excision and integration of both elements depend on a single tyrosine recombinase encoded by ICETh2, and that excision is not required but improves the transfer of these elements to a recipient cell. These findings along with previous results suggest that ICETh1 and ICETh2 depend on each other for spreading among T. thermophilus by transjugation.post-print1,28 M

Approche théorique, analytique et réflexive sur l’enseignement du FLE

Le rôle de l’enseignant a énormément évolué ces dernières décennies grâce à différents facteurs : le passage de la société industrielle à la société de l’information, l’apparition des TICE et l’évolution des méthodologies avec l’apparition de l’approche communicative et de la perspective actionnelle. Ainsi, les rôles des acteurs de la classe changent profondément parce que les apprenants deviennent les responsables de leur processus d’apprentissage et le professeur devient à son tour un guide et un facilitateur de cet apprentissage. Ce mémoire fin de master vise à décrire cette évolution du rôle de l’enseignant et à faire un bilan de notre formation à travers une analyse critique et réflexif de trois activités réalisées tout au long du master : la programmation annuelle, l’unité didactique et la tâche finale complexe. De cette manière, nous établissons dans un premier temps un cadre théorique sur le rôle actuel de l’enseignant. Dans un deuxième temps, nous justifions le choix des activités à analyser pour ensuite, dans un troisième temps, analyser leur processus d’élaboration. Dans un quatrième temps, nous analysons d’un point de vue critique les relations qui existent entre les trois activités choisies. Finalement, nous fournissons une conclusion générale et certaines propositions d’avenir qui pourraient améliorer la formation de master.<br /

DisA Limits RecG Activities at Stalled or Reversed Replication Forks

The DNA damage checkpoint protein DisA and the branch migration translocase RecG are implicated in the preservation of genome integrity in reviving haploid Bacillus subtilis spores. DisA synthesizes the essential cyclic 3′, 5′-diadenosine monophosphate (c-di-AMP) second messenger and such synthesis is suppressed upon replication perturbation. In vitro, c-di-AMP synthesis is suppressed when DisA binds DNA structures that mimic stalled or reversed forks (gapped forks or Holliday junctions [HJ]). RecG, which does not form a stable complex with DisA, unwinds branched intermediates, and in the presence of a limiting ATP concentration and HJ DNA, it blocks DisA-mediated c-di-AMP synthesis. DisA pre-bound to a stalled or reversed fork limits RecG-mediated ATP hydrolysis and DNA unwinding, but not if RecG is pre-bound to stalled or reversed forks. We propose that RecG-mediated fork remodeling is a genuine in vivo activity, and that DisA, as a molecular switch, limits RecG-mediated fork reversal and fork restoration. DisA and RecG might provide more time to process perturbed forks, avoiding genome breakage.This work was supported by the Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación (MCIU/AEI)/FEDER PGC2018-097054-B-I00 to S.A. and J.C.A

Integrative and Conjugative Element ICETh1 Functions as a Pangenomic DNA Capture Module in Thermus thermophilus.

Transjugation is an unconventional conjugation mechanism in Thermus thermophilus (Tth) that involves the active participation of both mating partners, encompassing a DNA secretion system (DSS) in the donor and an active natural competence apparatus (NCA) in the recipient cells. DSS is encoded within an integrative and conjugative element (ICETh1) in the strain Tth HB27, whereas the NCA is constitutively expressed in both mates. Previous experiments suggested the presence of multiple origins of transfer along the genome, which could generate genomic mosaicity among the progeny. Here, we designed transjugation experiments between two closely related strains of Tth with highly syntenic genomes, containing enough single nucleotide polymorphisms to allow precise parenthood analysis. Individual clones from the progeny were sequenced, revealing their origin as derivatives of our ICETh1-containing intended “donor” strain (HB27), which had acquired separate fragments from the genome of the ICETh1-free HB8 cells, which are our intended recipient. Due to the bidirectional nature of transjugation, only assays employing competence-defective HB27 derivatives as donors allowed the recovery of HB8-derived progeny. These results show a preference for a retrotransfer mechanism in transjugation in ICETh1-bearing strains, supporting an inter-strain gene-capture function for ICETh1. This function could benefit the donor-capable host by facilitating the acquisition of adaptive traits from external sources, ultimately increasing the open pangenome of Thermus, maximizing the potential repertoire of physiological and phenotypical traits related to adaptation and speciation.post-print11136 K

A thermostable DNA primase-polymerase from a mobilegenetic element involved in defence againstenvironmental DNA.

Primase-polymerases (Ppol) are one of the few enzymes able to start DNA synthesis on ssDNA templates. The role of Thermus thermophilus HB27 Ppol, encoded along a putative helicase (Hel) within a mobile genetic element (ICETh2), has been studied. A mutant lacking Ppol showed no effects on the replication of the element. Also, no apparent differences in the sensitivity to DNA damaging agents and other stressors or morphological changes in the mutant cells were detected. However, the mutants lacking Ppol showed an increase in two to three orders of magnitude in their transformation efficiency with plasmids and genomic DNA acquired from the environment (eDNA), independently of its origin and G + C content. In contrast, no significant differences with the wild type were detected when the cells received the DNA from other T. thermophilus partners in conjugation-like mating experiments. The similarities of this behaviour with that shown by mutants lacking the Argonaute (ThAgo) protein suggests a putative partnership Ppol-ThAgo in the DNA–DNA interference mechanism of defence, although other eDNA defence mechanisms independent of ThAgo cannot be discarded.post-print697 K

Epigenetic Landscape in Blood Leukocytes Following Ketosis and Weight Loss Induced by a Very Low Calorie Ketogenic Diet (VLCKD) in Patients with Obesity

Background: The molecular mechanisms underlying the potential health benefits of a ketogenic diet are unknown and could be mediated by epigenetic mechanisms. Objective: To identify the changes in the obesity-related methylome that are mediated by the induced weight loss or are dependent on ketosis in subjects with obesity underwent a very-low calorie ketogenic diet (VLCKD). Methods: Twenty-one patients with obesity (n ¼ 12 women, 47.9 ± 1.02 yr, 33.0 ± 0.2 kg/m2 ) after 6 months on a VLCKD and 12 normal weight volunteers (n ¼ 6 women, 50.3 ± 6.2 yrs, 22.7 ± 1.5 kg/m2 ) were studied. Data from the Infinium MethylationEPIC BeadChip methylomes of blood leukocytes were obtained at time points of ketotic phases (basal, maximum ketosis, and out of ketosis) during VLCKD (n ¼ 10) and at baseline in volunteers (n ¼ 12). Results were further validated by pyrosequencing in representative cohort of patients on a VLCKD (n ¼ 18) and correlated with gene expression. Results: After weight reduction by VLCKD, differences were found at 988 CpG sites (786 unique genes). The VLCKD altered methylation levels in patients with obesity had high resemblance with those from normal weight volunteers and was concomitant with a downregulation of DNA methyltransferases (DNMT)1, 3a and 3b. Most of the encoded genes were involved in metabolic processes, protein metabolism, and muscle, organ, and skeletal system development. Novel genes representing the top scoring associated events were identified, including ZNF331, FGFRL1 (VLCKD-induced weight loss) and CBFA2T3, C3orf38, JSRP1, and LRFN4 (VLCKD-induced ketosis). Interestingly, ZNF331 and FGFRL1 were validated in an independent cohort and inversely correlated with gene expression. Conclusions: The beneficial effects of VLCKD therapy on obesity involve a methylome more suggestive of normal weight that could be mainly mediated by the VLCKD-induced ketosis rather than weight loss.This work was supported by the PronoKal Group® and grants from the Fondo de Investigacion Sanitaria as well as PI17/01287, PI20/00628 and PI20/00650 research projects and CIBERobn from the Instituto de Salud Carlos III (ISCIII)-Subdireccion General de Evaluacion y Fomento de la Investigación; Fondo Europeo de Desarrollo Regional (FEDER) Ana B Crujeiras is funded by a research contract “Miguel Servet” (CP17/00088) from the ISCIII, co-financed by the European Regional Development Fund (FEDER) and Xunta de Galicia-GAIN (IN607B2020). The funding source had no involvement in the study design or interpretation of the result

"I am feeling tension in my whole body": An experimental phenomenological study of empathy for pain

Introduction: Traditionally, empathy has been studied from two main perspectives: the theory-theory approach and the simulation theory approach. These theories claim that social emotions are fundamentally constituted by mind states in the brain. In contrast, classical phenomenology and recent research based on enactive theories consider empathy as the basic process of contacting others’ emotional experiences through direct bodily perception and sensation. Objective: This study aims to enrich knowledge of the empathic experience of pain by using an experimental phenomenological method. Method: Implementing an experimental paradigm used in affective neuroscience, we exposed 28 healthy adults to a video of sportspersons suffering physical accidents while practicing extreme sports. Immediately after watching the video, each participant underwent a phenomenological interview to gather data on embodied, multi-layered dimensions (bodily sensations, emotions, and motivations) and temporal aspects of empathic experience. We also performed quantitative analyses of the phenomenological categories. Results: Experiential access to the other person’s painful experience involves four main-themes. Bodily resonance: participants felt a multiplicity of bodily, affective, and kinesthetic sensations. Attentional focus: some participants centered their attention more on their own personal discomfort and sensations of rejection, while others on the pain and suffering experienced by the sportspersons. Kinesthetic motivation: some participants experienced the feeling in their bodies to avoid or escape from watching the video, while others experienced the need to help the sportspersons avoid suffering any injury while practicing extreme sports. Temporality of experience: participants witnessed temporal fluctuations in their experiences, bringing intensity changes in their bodily resonance, attentional focus, and kinesthetic motivation. Finally, two experiential structures were found: one structure is self-centered empathic experience, characterized by bodily resonance, attentional focus centered on the participant’s own experience of seeing the sportsperson suffering, and self-protective kinesthetic motivation; the other structure is other-centered empathic experience, characterized by bodily resonance, attentional focus centered on the sportsperson, and prosocial kinesthetic motivation to help them. Discussion: We show how phenomenological data may contribute to comprehending empathy for pain in social neuroscience. In addition, we address the phenomenological aspect of the enactive approach to the three dimensions of embodiment of human consciousness, especially the intersubjective dimension. Also, based on our results, we suggest an extension of the enactive theory for non-interactive social experience

The Transcription Factor ArcA Modulates Salmonella’s Metabolism in Response to Neutrophil Hypochlorous Acid-Mediated Stress

Indexación: ScopusSalmonella Typhimurium, a bacterial pathogen with high metabolic plasticity, can adapt to different environmental conditions; these traits enhance its virulence by enabling bacterial survival. Neutrophils play important roles in the innate immune response, including the production of microbicidal reactive oxygen species (ROS). In addition, the myeloperoxidase in neutrophils catalyzes the formation of hypochlorous acid (HOCl), a highly toxic molecule that reacts with essential biomolecules, causing oxidative damage including lipid peroxidation and protein carbonylation. The bacterial response regulator ArcA regulates adaptive responses to oxygen levels and influences the survival of Salmonella inside phagocytic cells. Here, we demonstrate by whole transcriptomic analyses that ArcA regulates genes related to various metabolic pathways, enabling bacterial survival during HOCl-stress in vitro. Also, inside neutrophils, ArcA controls the transcription of several metabolic pathways by downregulating the expression of genes related to fatty acid degradation, lysine degradation, and arginine, proline, pyruvate, and propanoate metabolism. ArcA also upregulates genes encoding components of the oxidative pathway. These results underscore the importance of ArcA in ATP generation inside the neutrophil phagosome and its participation in bacterial metabolic adaptations during HOCl stress. © Copyright © 2019 Pardo-Esté, Castro-Severyn, Krüger, Cabezas, Briones, Aguirre, Morales, Baquedano, Sulbaran, Hidalgo, Meneses, Poblete-Castro, Castro-Nallar, Valvano and Saavedra.https://www.frontiersin.org/articles/10.3389/fmicb.2019.02754/ful