The time is now: Achieving FH paediatric screening across Europe - The Prague Declaration.

Familial hypercholesterolaemia (FH) is the most common inherited metabolic disorder characterized by high cholesterol and if left untreated leads to premature cardiovascular disease, such as heart attacks. Treatment that begins early in life, particularly in childhood, is highly efficacious in preventing cardiovascular disease and cost-effective, thus early detection of FH is crucial. However, in Europe, less than 10% of people living with FH are diagnosed and even less receive life-saving treatment. The Prague Declaration is a call to action for national and European Union policymakers and decision-makers and a result of the Czech EU Presidency meeting on FH Paediatric Screening (early detection of inherited high cholesterol) at the Czech Senate in Prague on 6th September 2022. It builds on a considerable body of evidence which was discussed at the Technical Meeting under the auspices of the Slovenian EU Presidency in October 2021. The Prague meeting addressed the outstanding barriers to the systematic implementation of FH paediatric screening across Europe. In this article, we present the key points from the Prague meeting and concrete actions needed to move forward.

Effects of temperature and salinity on bioconcentration and toxicokinetics of permethrin in pyrethroid-resistant Hyalella azteca.

Recent studies demonstrated pyrethroid resistance associated with voltage-gated sodium channel mutations in populations of the epibenthic amphipod, Hyalella azteca. Resistant populations were able to tolerate and bioconcentrate pyrethroids at concentrations significantly higher than toxic levels for non-resistant populations. In conjunction with elevated bioconcentration potential, environmental alteration particularly as a result of global climate change is anticipated to significantly alter abiotic parameters including temperature and salinity. These changes are expected to influence uptake and biotransformation of contaminants. Thus, the aims of the current study were a) to examine the bioconcentration potential of permethrin in two pyrethroid-resistant clades of H. azteca and b) assess the influence of temperature and salinity changes on toxicokinetic parameters. Two pyrethroid-resistant clades of H. azteca were exposed to 14C-permethrin at three salinities (0.2, 1.0 and 6.0 practical salinity units (PSU)) and temperatures (18, 23 and 28 °C). Tests were conducted for up to 36 h and uptake, elimination and biotransformation rates were calculated. Both populations demonstrated bioconcentration factors (BCFs) between five and seven times greater than published data for non-resistant H. azteca, with significant differences between clades. Calculated BCF values were comparable to field populations of resistant H. azteca, emphasizing the potential for elevated pyrethroid bioconcentration in the natural environment and increased exposure for predators consuming pyrethroid-resistant aquatic invertebrates. Alterations to temperature and salinity had no statistically significant effect on uptake or parent compound half-life in either population, though biotransformation was elevated at higher temperatures in both populations. Salinity had a variable effect between the two populations, with lower BCF values at 1.0 PSU in clade D H. azteca and greater BCFs at 6.0 PSU in clade C H. azteca. This is the first study to demonstrate the potential for future climate scenarios to influence toxicokinetics in pyrethroid-resistant aquatic organisms.

Microbe Profile: Thermococcus kodakarensis: the model hyperthermophilic archaeon.

Thermococcus kodakarensis is a hyperthermophilic Euryarchaeon that grows well under laboratory conditions and, being naturally competent for genetic transformation, it has become a widely studied experimental model species. With the genome sequence available since 2004, combining genetic, enzymological and structural biochemical approaches has revealed previously unknown and unanticipated features of archaeal molecular biology and metabolism. T. kodakarensis DNA polymerase is already commercialized and with the details of metabolism and hydrogenase available, generating H2 from biopolymers solubilized at high temperatures, most notably chitin, now seems a very attractive possibility as a renewable energy bioprocess.

An Examination of Exposure Routes of Fluvalinate to Larval and Adult Honey Bees (Apis mellifera).

Fluvalinate has been extensively used in the United States to combat honey bee colony loss due to Varroa destructor mites. Our objectives were to investigate the extent of fluvalinate contamination in commercially available wax and to define exposure pathways to larval and adult honey bees. All the commercial wax tested contained elevated fluvalinate concentrations, indicating a need for regulation of the sources of wax being rendered for resale. Based on the negative logarithm of the partition coefficient between wax and pollen (-0.54), it is evident that fluvalinate has the potential to actively transfer from the contaminated wax into hive matrices. This was confirmed by adding fluvalinate-dosed wax, fluvalinate-impregnated strips, or a combination of the 2 to hives. Larvae and adult bees were checked for fluvalinate exposure using gas chromatography-mass spectrometry analysis. Larvae had detectable concentrations of fluvalinate in all treatments. Bioaccumulation in adult bees was significantly affected by the interaction between treatment type and application time. In other words, residues from hives that only had fluvalinate-dosed wax were comparable to residues in hives that were actively being treated, suggesting that transfer of fluvalinate from wax into adult bees was an important exposure route. In conclusion, exposure of fluvalinate from contaminated wax and treatment strips to honey bees needs to be considered when the risk for colony loss in hives is being evaluated. Environ Toxicol Chem 2019;38:1356-1363. © 2019 SETAC.

An assessment of pesticide exposures and land use of honey bees in Virginia.

Large-scale honey bee colony loss threatens pollination services throughout the United States. An increase in anthropogenic pressure may influence the exposure of hives to household and agricultural pesticides. The objective of this survey was to provide an assessment of the risk of exposure to commonly used pesticides to honey bee colonies in Virginia in relation to land use. Adult honey bee, pollen, and wax samples from colonies throughout Virginia were evaluated for pyrethroid, organophosphate, organochlorine, and triazine pesticides using gas chromatography-mass spectrometry analysis. Of the 11 pesticides analyzed, nine were detected in one or more hive matrices. The probability of detecting a pesticide in pollen was less in forests than in pasture, agriculture, or urban landscapes. Coumaphos and fluvalinate were significantly more likely to be detected across all matrices with concentrations in wax as high as 15500 and 6970 ng/g (dry weight), respectively, indicating the need for further research on the potential effects of miticide accumulation in wax to larval and adult bees.

Metabolism of cyanogenic glycosides: A review.

Potential toxicity of cyanogenic glycosides arises from enzymatic degradation to produce hydrogen cyanide. Information on the metabolism of cyanogenic glycosides is available from in vitro, animal and human studies. In the absence of ß-glucosidase enzymes from the source plant material, two processes appear to contribute to the production of cyanide from cyanogenic glycosides; the proportion of the glycoside dose that reaches the large intestine, where most of the bacterial hydrolysis occurs, and the rate of hydrolysis of cyanogenic glycosides to cyanohydrin and cyanide. Some cyanogenic glycosides, such as prunasin, are actively absorbed in the jejunum by utilising the epithelial sodium-dependent monosaccharide transporter (SGLT1). The rate of cyanide production from cyanogenic glycosides due to bacterial ß-glycosidase activity depends on; the sugar moiety in the molecule and the stability of the intermediate cyanohydrin following hydrolysis by bacterial ß-glucosidase. Cyanogenic glycosides with a gentiobiose sugar, amygdalin, linustatin, and neolinustatin, undergo a two stage hydrolysis, with gentiobiose initially being hydrolysed to glucose to form prunasin, linamarin and lotaustralin, respectively. While the overall impact of these metabolic factors is difficult to predict, the toxicity of cyanogenic glycosides will be less than the toxicity suggested by their theoretical hydrocyanic acid equivalents.

Poisoning due to tutin in honey-a report of an outbreak in New Zealand.

AIM: In autumn 2008, an outbreak of toxic honey poisoning was identified. The outbreak was not recognised initially until three cases from one family group presented to hospital, with a common factor of recent consumption of locally produced honey. The aim of this study was to investigate potential cases of this honey poisoning and determine which toxin was involved. METHOD: The incident was investigated retrospectively by Waikato District Health Board's Population Health unit and the New Zealand Food Safety Authority (NZFSA). Identified patients were followed up by questionnaire to gather case information. HortResearch (now Plant and Food Research) tested honey samples for toxins. RESULTS: The causative agent was identified as tutin, which comes from the New Zealand native plant tutu (Coriaria arborea) which has long been known as a potential source of contamination of honey produced in the warmer parts of New Zealand. Retrospective case investigation identified a total of 22 possible or probable cases, based on a clinical case definition. The spectrum of toxic effects reported were broadly similar to those previously described for tutin, derived either directly from the plant itself or indirectly from honey. There were 13 samples of honey, linked to symptomatic individuals, which were available for testing. Of these, 10 were positive for tutin and its hydroxy metabolite hyenanchin (hydroxytutin) and one was positive for hyenanchin alone. CONCLUSION: Toxic honey production is a significant risk in parts of New Zealand. Beekeepers and health professionals need to be informed of this risk and know how best to manage it. Due to this poisoning incident, public and professional awareness of honey poisoning has been substantially enhanced. This incident led to development of new food safety standards for New Zealand honey.

Synchrony, Weather, and Cycles in Southern Pine Beetle (Coleoptera: Curculionidae).

Spatial synchrony and cycles are common features of forest insect pests, but are often studied as separate phenomenon. Using time series of timber damage caused by Dendroctonus frontalis Zimmermann (Coleoptera: Curculionidae) (southern pine beetle) in 10 states within the southern United States, this study examines synchrony in D. frontalis abundance, the synchronizing effects of temperature extremes, and the evidence for shared cycles among state populations. Cross-correlation and cluster analyses are used to quantify synchrony across a range of geographic distances and to identify groups of states with synchronous dynamics. Similar techniques are used to quantify spatial synchrony in temperature extremes and to examine their relationship to D. frontalis fluctuations. Cross-wavelet analysis is then used to examine pairs of time series for shared cycles. These analyses suggest there is substantial synchrony among states in D. frontalis fluctuations, and there are regional groups of states with similar dynamics. Synchrony in D. frontalis fluctuations also appears related to spatial synchrony in summer and winter temperature extremes. The cross-wavelet results suggest that D. frontalis dynamics may differ among regions and are not stationary. Significant oscillations were present in some states over certain time intervals, suggesting an endogenous feedback mechanism. Management of D. frontalis outbreaks could potentially benefit from a multistate regional approach because populations are synchronous on this level. Extreme summer temperatures are likely to become the most important synchronizing agent due to climate change.

Genome Replication in Thermococcus kodakarensis Independent of Cdc6 and an Origin of Replication.

The initiation of DNA replication is typically tightly regulated by proteins that form initiation complexes at specific sequences known as replication origins. In Archaea and Eukaryotes, Cdc6, a near-universally conserved protein binds and facilitates the origin-dependent assembly of the replicative apparatus. TK1901 encodes Cdc6 in Thermococcus kodakarensis but, as we report here, TK1901 and the presumed origin of replication can be deleted from the genome of this hyperthermophilic Archaeon without any detectable effects on growth, genetic competence or the ability to support autonomous plasmid replication. All regions of the genome were equally represented in the sequences generated by whole genome sequencing of DNA isolated from T. kodakarensis strains with or without TK1901, inconsistent with DNA initiation occurring at one or few origins, and instead suggestive of replication initiating at many sites distributed throughout the genome. We were unable to generate strains lacking the recombination factors, RadA or RadB, consistent with T. kodakarensis cells, that are oligoploid (7-19 genomes per cell), employing a recombination-based mechanism of DNA replication. Deletion of the previously presumed origin region reduced the long-term viability of cultures supporting the possibility that retaining an origin-based mechanism of DNA initiation provides a survival mechanism for stationary phase cells with only one genome.

Structure of histone-based chromatin in Archaea.

Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, illuminating the origin of the nucleosome.

The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis.

Many aspects of and factors required for DNA replication are conserved across all three domains of life, but there are some significant differences surrounding lagging-strand synthesis. In Archaea, a 5'-to-3' exonuclease, related to both bacterial RecJ and eukaryotic Cdc45, that associates with the replisome specifically through interactions with GINS was identified and designated GAN (for GINS-associated nuclease). Despite the presence of a well-characterized flap endonuclease (Fen1), it was hypothesized that GAN might participate in primer removal during Okazaki fragment maturation, and as a Cdc45 homologue, GAN might also be a structural component of an archaeal CMG (Cdc45, MCM, and GINS) replication complex. We demonstrate here that, individually, either Fen1 or GAN can be deleted, with no discernible effects on viability and growth. However, deletion of both Fen1 and GAN was not possible, consistent with both enzymes catalyzing the same step in primer removal from Okazaki fragments in vivo RNase HII has also been proposed to participate in primer processing during Okazaki fragment maturation. Strains with both Fen1 and RNase HII deleted grew well. GAN activity is therefore sufficient for viability in the absence of both RNase HII and Fen1, but it was not possible to construct a strain with both RNase HII and GAN deleted. Fen1 alone is therefore insufficient for viability in the absence of both RNase HII and GAN. The ability to delete GAN demonstrates that GAN is not required for the activation or stability of the archaeal MCM replicative helicase.IMPORTANCE The mechanisms used to remove primer sequences from Okazaki fragments during lagging-strand DNA replication differ in the biological domains. Bacteria use the exonuclease activity of DNA polymerase I, whereas eukaryotes and archaea encode a flap endonuclease (Fen1) that cleaves displaced primer sequences. RNase HII and the GINS-associated exonuclease GAN have also been hypothesized to assist in primer removal in Archaea Here we demonstrate that in Thermococcus kodakarensis, either Fen1 or GAN activity is sufficient for viability. Furthermore, GAN can support growth in the absence of both Fen1 and RNase HII, but Fen1 and RNase HII are required for viability in the absence of GAN.

Acute Toxicities of the Saxitoxin Congeners Gonyautoxin 5, Gonyautoxin 6, Decarbamoyl Gonyautoxin 2&3, Decarbamoyl Neosaxitoxin, C-1&2 and C-3&4 to Mice by Various Routes of Administration.

Paralytic shellfish poisoning results from consumption of seafood naturally contaminated by saxitoxin and its congeners, the paralytic shellfish toxins (PSTs). The levels of such toxins are regulated internationally, and maximum permitted concentrations in seafood have been established in many countries. A mouse bioassay is an approved method for estimating the levels of PSTs in seafood, but this is now being superseded in many countries by instrumental methods of analysis. Such analyses provide data on the levels of many PSTs in seafood, but for risk assessment, knowledge of the relative toxicities of the congeners is required. These are expressed as "Toxicity Equivalence Factors" (TEFs). At present, TEFs are largely based on relative specific activities following intraperitoneal injection in a mouse bioassay rather than on acute toxicity determinations. A more relevant parameter for comparison would be median lethal doses via oral administration, since this is the route through which humans are exposed to PSTs. In the present study, the median lethal doses of gonyautoxin 5, gonyautoxin 6, decarbamoyl neosaxitoxin and of equilibrium mixtures of decarbamoyl gonyautoxins 2&3, C1&2 and C3&4 by oral administration to mice have been determined and compared with toxicities via intraperitoneal injection. The results indicate that the TEFs of several of these substances require revision in order to more accurately reflect the risk these toxins present to human health.

Variable prey development time suppresses predator-prey cycles and enhances stability.

Although theoretical models have demonstrated that predator-prey population dynamics can depend critically on age (stage) structure and the duration and variability in development times of different life stages, experimental support for this theory is non-existent. We conducted an experiment with a host-parasitoid system to test the prediction that increased variability in the development time of the vulnerable host stage can promote interaction stability. Host-parasitoid microcosms were subjected to two treatments: Normal and High variance in the duration of the vulnerable host stage. In control and Normal-variance microcosms, hosts and parasitoids exhibited distinct population cycles. In contrast, insect abundances were 18-24% less variable in High- than Normal-variance microcosms. More significantly, periodicity in host-parasitoid population dynamics disappeared in the High-variance microcosms. Simulation models confirmed that stability in High-variance microcosms was sufficient to prevent extinction. We conclude that developmental variability is critical to predator-prey population dynamics and could be exploited in pest-management programs.

Patch-Burn Grazing Effects on the Ecological Integrity of Tallgrass Prairie Streams.

Conversion to agriculture, habitat fragmentation, and the loss of native grazers have made tallgrass prairie one of the most endangered ecosystems. One management option for the remaining prairie parcels, patch-burn grazing (PBG), applies a controlled burn to a portion of the prairie to attract cattle, creating a mosaic of more- and less-grazed patches. Although beneficial to cattle and grassland birds, the potential impacts of PBG on streams have not been studied, and a holistic approach is needed to ensure against adverse effects. We used a Before-After-Control-Impact design to assess potential impacts of PBG with and without riparian protection on tallgrass prairie headwater streams. We sampled stream macroinvertebrates and benthic organic matter 2 yr before and 2 yr during PBG treatments on two grazed watersheds with riparian fencing (fenced), two unfenced grazed watersheds (unfenced), and two ungrazed (control) watersheds. Very fine benthic organic matter increased significantly (51%) in unfenced streams compared with controls ( < 0.007), and fine particulate organic matter (<1 mm and >250 µm) increased 3-fold in the unfenced streams compared with controls ( = 0.008). The contribution of fine inorganic sediments to total substrata increased 28% in unfenced streams during PBG, which was significantly different from controls ( = 0.03). Additionally, the abundance of Ephemeroptera, Plecoptera, and Trichoptera taxa decreased from 7635 to 687 individuals m in unfenced streams, which was significantly lower than in control streams ( = 0.008). Our results indicate that PBG adversely influences prairie streams through sediment inputs and reductions in sensitive invertebrate taxa, but riparian fencing can alleviate these impacts.

Human pharmacokinetic study of tutin in honey; a plant-derived neurotoxin.

Over the last 150 years a number of people in New Zealand have been incapacitated, hospitalised, or died from eating honey contaminated with tutin, a plant-derived neurotoxin. A feature of the most recent poisoning incident in 2008 was the large variability in the onset time of clinical signs and symptoms of toxicity (0.5-17 h). To investigate the basis of this variability a pharmacokinetic study was undertaken in which 6 healthy males received a single oral dose of tutin-containing honey giving a tutin dose of 1.8 µg/kg body weight. The serum concentration-time curve for all volunteers exhibited two discrete peaks with the second and higher level occurring at approximately 15 h post-dose. Two subjects reported mild, transient headache at a time post-dose corresponding to maximum tutin concentrations. There were no other signs or symptoms typical of tutin intoxication such as nausea, vomiting, dizziness or seizures. Pharmacokinetic analysis using a two-site absorption model resulted in a good fit to the observed concentration data. A novel analytical method subsequently revealed the presence of glycoside conjugates of tutin in addition to unconjugated tutin in honey. These pharmacokinetic data will be important to better define a safe maximum tutin concentration in honey.

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis.

BACKGROUND: Prokaryotes have relatively small genomes, densely-packed with protein-encoding sequences. RNA sequencing has, however, revealed surprisingly complex transcriptomes and here we report the transcripts present in the model hyperthermophilic Archaeon, Thermococcus kodakarensis, under different physiological conditions. RESULTS: Sequencing cDNA libraries, generated from RNA isolated from cells under different growth and metabolic conditions has identified >2,700 sites of transcription initiation, established a genome-wide map of transcripts, and consensus sequences for transcription initiation and post-transcription regulatory elements. The primary transcription start sites (TSS) upstream of 1,254 annotated genes, plus 644 primary TSS and their promoters within genes, are identified. Most mRNAs have a 5'-untranslated region (5'-UTR) 10 to 50 nt long (median = 16 nt), but ~20% have 5'-UTRs from 50 to 300 nt long and ~14% are leaderless. Approximately 50% of mRNAs contain a consensus ribosome binding sequence. The results identify TSS for 1,018 antisense transcripts, most with sequences complementary to either the 5'- or 3'-region of a sense mRNA, and confirm the presence of transcripts from all three CRISPR loci, the RNase P and 7S RNAs, all tRNAs and rRNAs and 69 predicted snoRNAs. Two putative riboswitch RNAs were present in growing but not in stationary phase cells. The procedure used is designed to identify TSS but, assuming that the number of cDNA reads correlates with transcript abundance, the results also provide a semi-quantitative documentation of the differences in T. kodakarensis genome expression under different growth conditions and confirm previous observations of substrate-dependent specific gene expression. Many previously unanticipated small RNAs have been identified, some with relative low GC contents (≤ 50%) and sequences that do not fold readily into base-paired secondary structures, contrary to the classical expectations for non-coding RNAs in a hyperthermophile. CONCLUSION: The results identify >2,700 TSS, including almost all of the primary sites of transcription initiation upstream of annotated genes, plus many secondary sites, sites within genes and sites resulting in antisense transcripts. The T. kodakarensis genome is small (~2.1 Mbp) and tightly packed with protein-encoding genes, but the transcriptomes established also contain many non-coding RNAs and predict extensive RNA-based regulation in this model Archaeon.

Risk assessment of shellfish toxins.

Complex secondary metabolites, some of which are highly toxic to mammals, are produced by many marine organisms. Some of these organisms are important food sources for marine animals and, when ingested, the toxins that they produce may be absorbed and stored in the tissues of the predators, which then become toxic to animals higher up the food chain. This is a particular problem with shellfish, and many cases of poisoning are reported in shellfish consumers each year. At present, there is no practicable means of preventing uptake of the toxins by shellfish or of removing them after harvesting. Assessment of the risk posed by such toxins is therefore required in order to determine levels that are unlikely to cause adverse effects in humans and to permit the establishment of regulatory limits in shellfish for human consumption. In the present review, the basic principles of risk assessment are described, and the progress made toward robust risk assessment of seafood toxins is discussed. While good progress has been made, it is clear that further toxicological studies are required before this goal is fully achieved.

Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs.

BACKGROUND: Histone wrapping of DNA into nucleosomes almost certainly evolved in the Archaea, and predates Eukaryotes. In Eukaryotes, nucleosome positioning plays a central role in regulating gene expression and is directed by primary sequence motifs that together form a nucleosome positioning code. The experiments reported were undertaken to determine if archaeal histone assembly conforms to the nucleosome positioning code. RESULTS: Eukaryotic nucleosome positioning is favored and directed by phased helical repeats of AA/TT/AT/TA and CC/GG/CG/GC dinucleotides, and disfavored by longer AT-rich oligonucleotides. Deep sequencing of genomic DNA protected from micrococcal nuclease digestion by assembly into archaeal nucleosomes has established that archaeal nucleosome assembly is also directed and positioned by these sequence motifs, both in vivo in Methanothermobacter thermautotrophicus and Thermococcus kodakarensis and in vitro in reaction mixtures containing only one purified archaeal histone and genomic DNA. Archaeal nucleosomes assembled at the same locations in vivo and in vitro, with much reduced assembly immediately upstream of open reading frames and throughout the ribosomal rDNA operons. Providing further support for a common positioning code, archaeal histones assembled into nucleosomes on eukaryotic DNA and eukaryotic histones into nucleosomes on archaeal DNA at the same locations. T. kodakarensis has two histones, designated HTkA and HTkB, and strains with either but not both histones deleted grow normally but do exhibit transcriptome differences. Comparisons of the archaeal nucleosome profiles in the intergenic regions immediately upstream of genes that exhibited increased or decreased transcription in the absence of HTkA or HTkB revealed substantial differences but no consistent pattern of changes that would correlate directly with archaeal nucleosome positioning inhibiting or stimulating transcription. CONCLUSIONS: The results obtained establish that an archaeal histone and a genome sequence together are sufficient to determine where archaeal nucleosomes preferentially assemble and where they avoid assembly. We confirm that the same nucleosome positioning code operates in Archaea as in Eukaryotes and presumably therefore evolved with the histone-fold mechanism of DNA binding and compaction early in the archaeal lineage, before the divergence of Eukaryotes.

Thermococcus kodakarensis has two functional PCNA homologs but only one is required for viability.

Proliferating cell nuclear antigen (PCNA) monomers assemble to form a ring-shaped clamp complex that encircles duplex DNA. PCNA binding to other proteins tethers them to the DNA providing contacts and interactions for many other enzymes essential for DNA metabolic processes. Most eukarya and euryarchaea have only one PCNA homolog but Thermococcus kodakarensis uniquely has two, designated PCNA1 and PCNA2, encoded by TK0535 and TK0582, respectively. Here, we establish that both PCNA1 and PCNA2 form homotrimers that stimulate DNA synthesis by archaeal DNA polymerases B and D and ATP hydrolysis by the replication factor C complex. In exponentially growing cells, PCNA1 is abundant and present at an ~100-fold higher concentration than PCNA2 monomers. Deletion of TK0582 (PCNA2) had no detectable effects on viability or growth whereas repeated attempts to construct a T. kodakarensis strain with TK0535 (PCNA1) deleted were unsuccessful. The implications of these observations for PCNA1 function and the origin of the two PCNA-encoding genes in T. kodakarensis are discussed.

Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis.

Three evolutionarily distinct families of replicative DNA polymerases, designated polymerase B (Pol B), Pol C, and Pol D, have been identified. Members of the Pol B family are present in all three domains of life, whereas Pol C exists only in Bacteria and Pol D exists only in Archaea. Pol B enzymes replicate eukaryotic chromosomal DNA, and as members of the Pol B family are present in all Archaea, it has been assumed that Pol B enzymes also replicate archaeal genomes. Here we report the construction of Thermococcus kodakarensis strains with mutations that delete or inactivate key functions of Pol B. T. kodakarensis strains lacking Pol B had no detectable loss in viability and no growth defects or changes in spontaneous mutation frequency but had increased sensitivity to UV irradiation. In contrast, we were unable to introduce mutations that inactivated either of the genes encoding the two subunits of Pol D. The results reported establish that Pol D is sufficient for viability and genome replication in T. kodakarensis and argue that Pol D rather than Pol B is likely the replicative DNA polymerase in this archaeon. The majority of Archaea contain Pol D, and, as discussed, if Pol D is the predominant replicative polymerase in Archaea, this profoundly impacts hypotheses for the origin(s), evolution, and distribution of the different DNA replication enzymes and systems now employed in the three domains of life.