scholarly journals The archaeal Ced system imports DNA

2016 ◽  
Vol 113 (9) ◽  
pp. 2496-2501 ◽  
Author(s):  
Marleen van Wolferen ◽  
Alexander Wagner ◽  
Chris van der Does ◽  
Sonja-Verena Albers
Keyword(s):  
Uv Light ◽  
Transmembrane Protein ◽  
Dna Transfer ◽  
Dna Double Strand Breaks ◽  
Chromosomal Dna ◽  
Bacterial Dna ◽  
Strand Breaks ◽  
Domains Of Life ◽  
Membrane Bound ◽  
First Time

The intercellular transfer of DNA is a phenomenon that occurs in all domains of life and is a major driving force of evolution. Upon UV-light treatment, cells of the crenarchaeal genus Sulfolobus express Ups pili, which initiate cell aggregate formation. Within these aggregates, chromosomal DNA, which is used for the repair of DNA double-strand breaks, is exchanged. Because so far no clear homologs of bacterial DNA transporters have been identified among the genomes of Archaea, the mechanisms of archaeal DNA transport have remained a puzzling and underinvestigated topic. Here we identify saci_0568 and saci_0748, two genes from Sulfolobus acidocaldarius that are highly induced upon UV treatment, encoding a transmembrane protein and a membrane-bound VirB4/HerA homolog, respectively. DNA transfer assays showed that both proteins are essential for DNA transfer between Sulfolobus cells and act downstream of the Ups pili system. Our results moreover revealed that the system is involved in the import of DNA rather than the export. We therefore propose that both Saci_0568 and Saci_0748 are part of a previously unidentified DNA importer. Given the fact that we found this transporter system to be widely spread among the Crenarchaeota, we propose to name it the Crenarchaeal system for exchange of DNA (Ced). In this study we have for the first time to our knowledge described an archaeal DNA transporter.

scholarly journals End-resection at DNA double-strand breaks in the three domains of life

2013 ◽  
Vol 41 (1) ◽  
pp. 314-320 ◽  
Author(s):  
John K. Blackwood ◽  
Neil J. Rzechorzek ◽  
Sian M. Bray ◽  
Joseph D. Maman ◽  
Luca Pellegrini ◽  
...  
Keyword(s):  
Dna Repair ◽  
Homologous Recombination ◽  
Strand Break ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Homologous Chromosomes ◽  
Domains Of Life ◽  
Strand Invasion ◽  
End Resection

During DNA repair by HR (homologous recombination), the ends of a DNA DSB (double-strand break) must be resected to generate single-stranded tails, which are required for strand invasion and exchange with homologous chromosomes. This 5′–3′ end-resection of the DNA duplex is an essential process, conserved across all three domains of life: the bacteria, eukaryota and archaea. In the present review, we examine the numerous and redundant helicase and nuclease systems that function as the enzymatic analogues for this crucial process in the three major phylogenetic divisions.

scholarly journals Natural Competence Is a Major Mechanism for Horizontal DNA Transfer in the Oral Pathogen Porphyromonas gingivalis

mBio ◽  
2012 ◽  
Vol 3 (1) ◽  
Author(s):  
Gena D. Tribble ◽  
Todd W. Rigney ◽  
Doan-Hieu V. Dao ◽  
Cindy T. Wong ◽  
Jennifer E. Kerr ◽  
...  
Keyword(s):  
Porphyromonas Gingivalis ◽  
Dna Transfer ◽  
Extracellular Dna ◽  
Minor Role ◽  
Chromosomal Dna ◽  
Natural Competence ◽  
Content Type ◽  
A Minor ◽  
First Time

ABSTRACTPorphyromonas gingivalisis a Gram-negative anaerobe that resides exclusively in the human oral cavity. Long-term colonization byP. gingivalisrequires the bacteria to evade host immune responses while adapting to the changing host physiology and alterations in the composition of the oral microflora. The genetic diversity ofP. gingivalisappears to reflect the variability of its habitat; however, little is known about the molecular mechanisms generating this diversity. Previously, our research group established that chromosomal DNA transfer occurs betweenP. gingivalisstrains. In this study, we examine the role of putative DNA transfer genes in conjugation and transformation and demonstrate that natural competence mediated bycomFis the dominant form of chromosomal DNA transfer, with transfer by a conjugation-like mechanism playing a minor role. Our results reveal that natural competence mechanisms are present in multiple strains ofP. gingivalis, and DNA uptake is not sensitive to DNA source or modification status. Furthermore, extracellular DNA was observed for the first time inP. gingivalisbiofilms and is predicted to be the major DNA source for horizontal transfer and allelic exchange between strains. We propose that exchange of DNA in plaque biofilms by a transformation-like process is of major ecological importance in the survival and persistence ofP. gingivalisin the challenging oral environment.IMPORTANCEP. gingivaliscolonizes the oral cavities of humans worldwide. The long-term persistence of these bacteria can lead to the development of chronic periodontitis and host morbidity associated with tooth loss.P. gingivalisis a genetically diverse species, and this variability is believed to contribute to its successful colonization and survival in diverse human hosts, as well as evasion of host immune defenses and immunization strategies. We establish here that natural competence is the major driving force behindP. gingivalisDNA exchange and that conjugative DNA transfer plays a minor role. Furthermore, we reveal for the first time the presence of extracellular DNA inP. gingivalisbiofilms, which is most likely the source of DNA exchanged between strains within dental plaque. These studies expand our understanding of the mechanisms used by this important member of the human oral flora to transition its relationship with the host from a commensal to a pathogenic relationship.

scholarly journals A rod conformation of the Pyrococcus furiosus Rad50 coiled coil

2020 ◽  
Author(s):  
Young-Min Soh ◽  
Jerome Basquin ◽  
Stephan Gruber
Keyword(s):  
Pyrococcus Furiosus ◽  
Coiled Coil ◽  
Vital Role ◽  
Coiled Coils ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Dimerization Domain ◽  
Strand Breaks ◽  
Domains Of Life ◽  
Bacterial Homolog

AbstractThe Rad50-Mre11 nuclease complex plays a vital role in DNA repair in all domains of life. It recognizes and processes DNA double-strand breaks. Rad50 proteins fold into an extended structure with a ~20-60 nm long coiled coil connecting a globular ABC ATPase domain with a zinc hook dimerization domain. A published structure of an archaeal Rad50 zinc hook shows coiled coils pointing away from each other. Here we present the crystal structure of an alternate conformation displaying co-aligned coiled coils. Archaeal Rad50 may thus switch between rod-shaped and ring-like conformations as recently proposed for a bacterial homolog.

scholarly journals Species-specific recognition of Sulfolobales mediated by UV-inducible pili and S-layer glycosylation patterns

2019 ◽  
Author(s):  
Marleen van Wolferen ◽  
Asif Shajahan ◽  
Kristina Heinrich ◽  
Susanne Brenzinger ◽  
Ian M. Black ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Genome Stability ◽  
Binding Pocket ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Type Iv ◽  
Self Recognition ◽  
The One ◽  
Species Specific ◽  
First Time

AbstractThe UV-inducible pili system of Sulfolobales (Ups) mediates the formation of species-specific cellular aggregates. Within these aggregates, cells exchange DNA in order to repair DNA double strand breaks via homologous recombination. Substitution of theS. acidocaldariuspilin subunits UpsA and UpsB with their homologs fromSulfolobus tokodaiishowed that these subunits facilitate species-specific aggregation. A region of low conservation within the UpsA homologs is primarily important for this specificity. Aggregation assays in the presence of different sugars showed the importance ofN-glycosylation in the recognition process. In addition, theN-glycan decorating the S-layer ofS. tokodaiiis different from the one ofS. acidocaldarius. Therefore, eachSulfolobusspecies seems to have developed a unique UpsA binding pocket and uniqueN-glycan composition to ensure aggregation and consequently also DNA exchange with cells from only the same species, which is essential for DNA repair by homologous recombination.ImportanceType IV pili can be found on the cell surface of many archaea and bacteria where they play important roles in different processes. The Ups-pili from the crenarchaeal Sulfolobales species are essential in establishing species-specific mating partners, ensuring genome stability. With this work, we show that differentSulfolobusspecies have species-specific regions in their Ups-pilin subunits, which allow them to interact only with cells from the same species. Additionally, differentSulfolobusspecies all have unique S-layerN-glycosylation patterns. We propose that the unique features of each species allow the recognition of specific mating partners. This knowledge for the first time gives insights into the molecular basis of archaeal self-recognition.

scholarly journals TACI deficiency impairs sustained Blimp-1 expression in B cells decreasing long-lived plasma cells in the bone marrow

Blood ◽  
2011 ◽  
Vol 118 (22) ◽  
pp. 5832-5839 ◽  
Author(s):  
Shoichiro Tsuji ◽  
Catarina Cortesão ◽  
Richard J. Bram ◽  
Jeffrey L. Platt ◽  
Marilia Cascalho
Keyword(s):  
Immune Deficiency ◽  
B Cells ◽  
Plasma Cells ◽  
Common Variable Immune Deficiency ◽  
Dna Double Strand Breaks ◽  
Protein Antigens ◽  
Strand Breaks ◽  
First Time ◽  
Common Variable ◽  
Antibody Secreting Cells

Abstract Deficiencies in transmembrane activator and CAML interactor (TACI) result in common variable immune deficiency, a syndrome marked by recurrent infections with encapsulated microorganisms, impaired production of antibodies, and lymphoproliferation. How TACI promotes antibody production and inhibits lymphoproliferation is not understood. To answer this question, we studied the generation of immunity to protein antigens in both TACI-deficient and TACI-proficient mice. We show that TACI promotes sustained Blimp-1 expression by B cells responding to antigen, which in turn limits B-cell clonal expansion and facilitates differentiation of long-lived antibody-secreting cells. Short-term IgG secretion occurs independently of TACI as DNA double-strand breaks associated with isotype class switching induce Blimp-1 transiently, independently of TACI. Our results showing that TACI induces and maintains Blimp-1 provide, for the first time, a unified molecular and cellular mechanism explaining the primary features of common variable immune deficiency, exquisite vulnerability to infection with encapsulated organisms, lymphoproliferation, and hypogammaglobulinemia.

scholarly journals γ-H2AX is present at mouse meiotic kinetochores

2020 ◽  
Author(s):  
Andrea Guajardo ◽  
Alberto Viera ◽  
María Teresa Parra ◽  
Manuel M. Valdivia ◽  
Julio S. Rufas ◽  
...  
Keyword(s):  
Meiotic Recombination ◽  
Meiotic Prophase ◽  
Male Mouse ◽  
Sex Chromosome ◽  
Double Strand Breaks ◽  
Chromosome Inactivation ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Meiotic Sex Chromosome Inactivation ◽  
First Time

AbstractThe histone variant H2AX phosphorylated on serine 139, named γ-H2AX, is a canonical DNA double-strand breaks marker. During mammalian meiotic prophase I, γ-H2AX participates in meiotic recombination, meiotic sex chromosome inactivation and meiotic silencing of unsynapsed chromatin. In this study, we have analyzed the distribution of γ-H2AX during male mouse meiosis by immunofluorescence on spread and squashed spermatocytes. We have found that γ-H2AX locates at the inner kinetochore plate of meiotic kinetochores in both meiotic divisions. Therefore our results, for the first time, uncover a novel role for γ-H2AX at mammalian meiotic kinetochores.

scholarly journals Evolutionary and Comparative analysis of bacterial Non-Homologous End Joining Repair

2019 ◽  
Author(s):  
Mohak Sharda ◽  
Anjana Badrinarayanan ◽  
Aswin Sai Narain Seshasayee
Keyword(s):  
Growth Rates ◽  
Genome Stability ◽  
Ancestral Reconstruction ◽  
Dna Double Strand Breaks ◽  
End Joining ◽  
Strand Breaks ◽  
Domains Of Life ◽  
History Of ◽  
Non Homologous End Joining ◽  
Two Kingdoms

AbstractDNA double-strand breaks (DSBs) are a threat to genome stability. In all domains of life, DSBs are faithfully fixed via homologous recombination. Recombination requires the presence of an uncut copy of duplex DNA that is used as a template for repair. Alternatively, in the absence of a template, cells utilize error-prone Non-homologous end joining (NHEJ). Although ubiquitously found in eukaryotes, NHEJ is not universally present in bacteria. It is unclear as to why many prokaryotes lack this pathway. To understand what could have led to the current distribution of bacterial NHEJ, we carried out comparative genomics and phylogenetic analysis across ~6000 genomes. Our results show that this pathway is sporadically distributed across the phylogeny. Ancestral reconstruction further suggests that NHEJ was absent in the eubacterial ancestor, and can be acquired via specific routes. Integrating NHEJ occurrence data for archaea, we also find evidence for extensive horizontal exchange of NHEJ genes between the two kingdoms as well as across bacterial clades. The pattern of occurrence in bacteria is consistent with correlated evolution of NHEJ with key genome characteristics of genome size and growth rates; NHEJ presence is associated with large genome sizes and/or slow growth rates, with the former being the dominant correlate. Given the central role these traits play in determining the ability to carry out recombination, it is possible that the evolutionary history of bacterial NHEJ may have been shaped by requirement for efficient DSB repair.

scholarly journals RexAB is essential for the mutagenic repair ofStaphylococcus aureusDNA damage caused by co-trimoxazole

2019 ◽  
Author(s):  
Rebecca S. Clarke ◽  
Maya S. Bruderer ◽  
Kam Pou Ha ◽  
Andrew M. Edwards
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Sos Response ◽  
Dna Double Strand Breaks ◽  
Bacterial Dna ◽  
Strand Breaks ◽  
Therapeutic Value ◽  
Resistant Strains ◽  
Emergence Of Resistance

AbstractCo-trimoxazole (SXT) is a combination therapeutic that consists of sulfamethoxazole and trimethoprim that is increasingly used to treat skin and soft-tissue infections caused by methicillin-resistantStaphylococcus aureus(MRSA). However, the use of SXT is limited to the treatment of low-burden, superficialS. aureusinfections and its therapeutic value is compromised by the frequent emergence of resistance. As a first step towards the identification of approaches to enhance the efficacy of SXT, we examined the role of bacterial DNA repair in antibiotic susceptibility and mutagenesis. This revealed that SXT caused DNA damage inS. aureusvia both thymidine limitation and the generation of reactive oxygen species. Then, using mutants defective for DNA repair, it was found that repair of this damage required the RexAB nuclease/helicase complex, indicating that SXT causes DNA double-strand breaks. Furthermore, RexAB-mediated DNA repair led to induction of the SOS response, which resulted in an increased mutation rate and may explain the frequent emergence of resistant strains during SXT therapy. In summary, this work determined that SXT causes DNA damage inS. aureusvia both thymidine limitation and oxidative stress, which is repaired by the RexAB complex, leading to induction of the mutagenic SOS response. Small molecule inhibitors of RexAB could therefore have therapeutic value by increasing the efficacy of SXT and decreasing the emergence of drug-resistance during treatment of infections caused byS. aureus.

scholarly journals qDSB-Seq: quantitative DNA double-strand break sequencing

2017 ◽  
Author(s):  
Yingjie Zhu ◽  
Anna Biernacka ◽  
Benjamin Pardo ◽  
Norbert Dojer ◽  
Romain Forey ◽  
...  
Keyword(s):  
Replication Fork ◽  
Strand Break ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Site Specific ◽  
Strand Breaks ◽  
Dna Double Strand Break ◽  
Physiological Relevance ◽  
A Site ◽  
First Time

AbstractSequencing-based methods for mapping DNA double-strand breaks (DSBs) allow measurement only of relative frequencies of DSBs between loci, which limits our understanding of the physiological relevance of detected DSBs. We propose quantitative DSB sequencing (qDSB-Seq), a method providing both DSB frequencies per cell and their precise genomic coordinates. We induced spike-in DSBs by a site-specific endonuclease and used them to quantify labeled DSBs (e.g. using i-BLESS). Utilizing qDSB-Seq, we determined numbers of DSBs induced by a radiomimetic drug and various forms of replication stress, and revealed several orders of magnitude differences in DSB frequencies. We also measured for the first time Top1-dependent absolute DSB frequencies at replication fork barriers. qDSB-Seq is compatible with various DSB labeling methods in different organisms and allows accurate comparisons of absolute DSB frequencies across samples.

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