Genetic and biochemical identification of a novel single-stranded DNA-binding complex in Haloferax volcanii

Single-stranded DNA (ssDNA)-binding proteins play an essential role in DNA replication and repair. They use oligonucleotide/oligosaccharide-binding (OB)-folds, a five-stranded β-sheet coiled into a closed barrel, to bind to ssDNA thereby protecting and stabilizing the DNA. In eukaryotes the ssDNA-binding protein (SSB) is known as replication protein A (RPA) and consists of three distinct subunits that function as a heterotrimer. The bacterial homolog is termed SSB and functions as a homotetramer. In the archaeon Haloferax volcanii there are three genes encoding homologs of RPA. Two of the rpa genes (rpa1 and rpa3) exist in operons with a novel gene specific to Euryarchaeota; this gene encodes a protein that we have termed RPA-associated protein (rpap). The rpap genes encode proteins belonging to COG3390 group and feature OB-folds, suggesting that they might cooperate with RPA in binding to ssDNA. Our genetic analysis showed that rpa1 and rpa3 deletion mutants have differing phenotypes; only Δrpa3 strains are hypersensitive to DNA damaging agents. Deletion of the rpa3-associated gene rpap3 led to similar levels of DNA damage sensitivity, as did deletion of the rpa3 operon, suggesting that RPA3 and RPAP3 function in the same pathway. Protein pull-downs involving recombinant hexahistidine-tagged RPAs showed that RPA3 co-purifies with RPAP3, and RPA1 co-purifies with RPAP1. This indicates that the RPAs interact only with their respective associated proteins; this was corroborated by the inability to construct rpa1 rpap3 and rpa3 rpap1 double mutants. This is the first report investigating the individual function of the archaeal COG3390 RPA-associated proteins (RPAPs). We have shown genetically and biochemically that the RPAPs interact with their respective RPAs, and have uncovered a novel single-stranded DNA-binding complex that is unique to Euryarchaeota

Genetic and Biochemical Identification of a Novel Single-Stranded DNA-Binding Complex in Haloferax volcanii

Single-stranded DNA (ssDNA)-binding proteins play an essential role in DNA replication and repair. They use oligonucleotide/oligosaccharide-binding (OB)-folds, a five-stranded β-sheet coiled into a closed barrel, to bind to ssDNA thereby protecting and stabilizing the DNA. In eukaryotes the ssDNA-binding protein (SSB) is known as replication protein A (RPA) and consists of three distinct subunits that function as a heterotrimer. The bacterial homolog is termed SSB and functions as a homotetramer. In the archaeon Haloferax volcanii there are three genes encoding homologs of RPA. Two of the rpa genes (rpa1 and rpa3) exist in operons with a novel gene specific to Euryarchaeota; this gene encodes a protein that we have termed RPA-associated protein (rpap). The rpap genes encode proteins belonging to COG3390 group and feature OB-folds, suggesting that they might cooperate with RPA in binding to ssDNA. Our genetic analysis showed that rpa1 and rpa3 deletion mutants have differing phenotypes; only Δrpa3 strains are hypersensitive to DNA damaging agents. Deletion of the rpa3-associated gene rpap3 led to similar levels of DNA damage sensitivity, as did deletion of the rpa3 operon, suggesting that RPA3 and RPAP3 function in the same pathway. Protein pull-downs involving recombinant hexahistidine-tagged RPAs showed that RPA3 co-purifies with RPAP3, and RPA1 co-purifies with RPAP1. This indicates that the RPAs interact only with their respective associated proteins; this was corroborated by the inability to construct rpa1 rpap3 and rpa3 rpap1 double mutants. This is the first report investigating the individual function of the archaeal COG3390 RPA-associated proteins (RPAPs). We have shown genetically and biochemically that the RPAPs interact with their respective RPAs, and have uncovered a novel single-stranded DNA-binding complex that is unique to Euryarchaeota

DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii

In prokaryotes the genome is organized in a dynamic structure called the nucleoid, which is embedded in the cytoplasm. We show here that in the archaeon Haloferax volcanii, compaction and reorganization of the nucleoid is induced by stresses that damage the genome or interfere with its replication. The fraction of cells exhibiting nucleoid compaction was proportional to the dose of the DNA damaging agent, and results obtained in cells defective for nucleotide excision repair suggest that breakage of DNA strands triggers reorganization of the nucleoid. We observed that compaction depends on the Mre11-Rad50 complex, suggesting a link to DNA double-strand break repair. However, compaction was observed in a radA mutant, indicating that the role of Mre11-Rad50 in nucleoid reorganisation is independent of homologous recombination. We therefore propose that nucleoid compaction is part of a DNA damage response that accelerates cell recovery by helping DNA repair proteins to locate their targets, and facilitating the search for intact DNA sequences during homologous recombination

Diversity of DNA replication in the archaea

DNA replication is arguably the most fundamental biological process. On account of their shared evolutionary ancestry, the replication machinery found in archaea is similar to that found in eukaryotes. DNA replication is initiated at origins and is highly conserved in eukaryotes, but our limited understanding of archaea has uncovered a wide diversity of replication initiation mechanisms. Archaeal origins are sequence‐based, as in bacteria, but are bound by initiator proteins that share homology with the eukaryotic origin recognition complex subunit Orc1 and helicase loader Cdc6). Unlike bacteria, archaea may have multiple origins per chromosome and multiple Orc1/Cdc6 initiator proteins. There is no consensus on how these archaeal origins are recognised— some are bound by a single Orc1/Cdc6 protein while others require a multi‐ Orc1/Cdc6 complex. Many archaeal genomes consist of multiple parts—the main chromosome plus several megaplasmids—and in polyploid species these parts are present in multiple copies. This poses a challenge to the regulation of DNA replication. However, one archaeal species (Haloferax volcanii) can survive without replication origins; instead, it uses homologous recombination as an alternative mechanism of initiation. This diversity in DNA replication initiation is all the more remarkable for having been discovered in only three groups of archaea where in vivo studies are possible

DNA repair in the archaea: an emerging picture

There has long been a fascination in the DNA Repair pathways of archaea, for two main reasons. Firstly, many archaea inhabit extreme environments where the rate of physical damage to DNA is accelerated. These archaea might reasonably be expected to have particularly robust or novel DNA repair pathways to cope with this. Secondly, the archaea have long been understood to be a lineage distinct from the bacteria, and to share a close relationship with the eukarya, particularly in their information processing systems. Recent discoveries suggest the eukarya arose from within the archaeal domain, and in particular from lineages related to the TACK superphylum and Lokiarchaea. Thus, archaeal DNA repair proteins and pathways can represent a useful model system. This review focuses on recent advances in our understanding of archaeal DNA repair processes including Base Excision Repair (BER), Nucleotide Excision Repair (NER), Mismatch Repair (MMR) and Double Strand Break Repair (DSBR). These advances are discussed in the context of the emerging picture of the evolution and relationship of the three domains of life

Negative Reactant Ion Formation in High Kinetic Energy Ion Mobility Spectrometry (HiKE-IMS)

Due to the operation at background pressures between 10-40 mbar and high reduced electric field strengths of up to 120 Td, the ion–molecule reactions in High Kinetic Energy Ion Mobility Spectrometers (HiKE-IMS) differ from those in classical ambient pressure IMS. In the positive ion polarity mode, the reactant ions H+(H2O)n, O2+(H2O)n, and NO+(H2O)n are observed in the HiKE-IMS. The relative abundances of these reactant ion species significantly depend on the reduced electric field strength in the reaction region, the operating pressure, and the water concentration in the reaction region. In this work, the formation of negative reactant ions in HiKE-IMS is investigated in detail. On the basis of kinetic and thermodynamic data from the literature, the processes resulting in the formation of negative reactant ions are kinetically modeled. To verify the model, we present measurements of the negative reactant ion population in the HiKE-IMS and its dependence on the reduced electric field strength as well as the water and carbon dioxide concentrations in the reaction region. The ion species underlying individual peaks in the ion mobility spectrum are identified by coupling the HiKE-IMS to a time-of-flight mass spectrometer (TOF-MS) using a simple gated interface that enables the transfer of selected peaks of the ion mobility spectrum into the TOF-MS. Both the theoretical model as well as the experimental data suggest the predominant generation of the oxygen-based ions O–, OH–, O2–, and O3– in purified air containing 70 ppmv of water and 30 ppmv of carbon dioxide. Additionally, small amounts of NO2– and CO3– are observed. Their relative abundances highly depend on the reduced electric field strength as well as the water and carbon dioxide concentration. An increase of the water concentration in the reaction region results in the generation of OH– ions, whereas increasing the carbon dioxide concentration favors the generation of CO3– ions, as expected

Field-Dependent Reduced Ion Mobilities of Positive and Negative Ions in Air and Nitrogen in High Kinetic Energy Ion Mobility Spectrometry (HiKE-IMS)

In High Kinetic Energy Ion Mobility Spectrometry (HiKE-IMS), ions are formed in a reaction region and separated in a drift region, which is similar to classical drift tube ion mobility spectrometers (IMS) operated at ambient pressure. However, in contrast to the latter, the HiKE-IMS is operated at a decreased background pressure of 10–40 mbar and achieves high reduced electric field strengths of up to 120 Td in both the reaction and the drift region. Thus, the HiKE-IMS allows insights into the chemical kinetics of ion-bound water cluster systems at effective ion temperatures exceeding 1000 K, although it is operated at the low absolute temperature of 45 °C. In this work, a HiKE-IMS with a high resolving power of RP = 140 is used to study the dependence of reduced ion mobilities on the drift gas humidity and the effective ion temperature for the positive reactant ions H3O+(H2O)n, O2+(H2O)n, NO+(H2O)n, NO2+(H2O)n, and NH4+(H2O)n, as well as the negative reactant ions O2–(H2O)n, O3–(H2O)n, CO3–(H2O)n, HCO3–(H2O)n, and NO2–(H2O)n. By varying the reduced electric field strength in the drift region, cluster transitions are observed in the ion mobility spectra. This is demonstrated for the cluster systems H3O+(H2O)n and NO+(H2O)n

High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon

CRISPR-Cas systems allow bacteria and archaea to acquire sequence-specific immunity against selfish genetic elements such as viruses and plasmids, by specific degradation of invader DNA or RNA. However, this involves the risk of autoimmunity if immune memory against host DNA is mistakenly acquired. Such autoimmunity has been shown to be highly toxic in several bacteria and is believed to be one of the major costs of maintaining these defense systems. Here we generated an experimental system in which a non-essential gene, required for pigment production and the reddish colony color, is targeted by the CRISPR-Cas I-B system of the halophilic archaeon Haloferax volcanii. We show that under native conditions, where both the self-targeting and native crRNAs are expressed, self-targeting by CRISPR-Cas causes no reduction in transformation efficiency of the plasmid encoding the self-targeting crRNA. Furthermore, under such conditions, no effect on organismal growth rate or loss of the reddish colony phenotype due to mutations in the targeted region could be observed. In contrast, in cells deleted for the pre-crRNA processing gene cas6, where only the self-targeting crRNA exists as mature crRNA, self-targeting leads to moderate toxicity and the emergence of deletion mutants. Sequencing of the deletions caused by CRISPR-Cas self targeting indicated DNA repair via microhomology-mediated end joining

Positive Reactant Ion Formation in High Kinetic Energy Ion Mobility Spectrometry (HiKE-IMS)

In contrast to classical Ion Mobility Spectrometers (IMS) operating at ambient pressure, the High Kinetic Energy Ion Mobility Spectrometer (HiKE-IMS) is operated at reduced pressures of between 10 and 40 mbar and higher reduced electric field strengths of up to 120 Td. Thus, the ion–molecule reactions occurring in the HiKE-IMS can significantly differ from those in classical ambient pressure IMS. In order to predict the ionization pathways of specific analyte molecules, profound knowledge of the reactant ion species generated in HiKE-IMS and their dependence on the ionization conditions is essential. In this work, the formation of positive reactant ions in HiKE-IMS is investigated in detail. On the basis of kinetic and thermodynamic data from the literature, the ion–molecule reactions are kinetically modeled. To verify the model, we present measurements of the reactant ion population and its dependence on the reduced electric field strength, the operating pressure, and the water concentration in the sample gas. All of these parameters significantly affect the reactant ion population formed in HiKE-IMS