Flap Endonuclease Disengages Dna2 Helicase/Nuclease from Okazaki Fragment Flaps

Okazaki fragments contain an initiator RNA/DNA primer that must be removed before the fragments are joined. In eukaryotes, the primer region is raised into a flap by the strand displacement activity of DNA polymerase {delta}. The Dna2 helicase/nuclease and then flap endonuclease 1 (FEN1) are proposed to act sequentially in flap removal. Dna2 and FEN1 both employ a tracking mechanism to enter the flap 5' end and move toward the base for cleavage. In the current model, Dna2 must enter first, but FEN1 makes the final cut at the flap base, raising the issue of how FEN1 passes the Dna2. To address this, nuclease-inactive Dna2 was incubated with a DNA flap substrate and found to bind with high affinity. FEN1 was then added, and surprisingly, there was little inhibition of FEN1 cleavage activity. FEN1 was later shown, by gel shift analysis, to remove the wild type Dna2 from the flap. RNA can be cleaved by FEN1 but not by Dna2. Pre-bound wild type Dna2 was shown to bind an RNA flap but not inhibit subsequent FEN1 cleavage. These results indicate that there is a novel interaction between the two proteins in which FEN1 disengages the Dna2 tracking mechanism. This interaction is consistent with the idea that the two proteins have evolved a special ability to cooperate in Okazaki fragment processing

Dynamic removal of replication protein A by Dna2 facilitates primer cleavage during Okazaki fragment processing in Saccharomyces cerevisiae

Eukaryotic Okazaki fragments are initiated by an RNA/DNA primer, which is removed before the fragments are joined. Polymerase d displaces the primer into a flap for processing. Dna2 nuclease/helicase and flap endonuclease 1 (FEN1) are proposed to cleave the flap. The single-stranded DNA binding protein, replication protein A (RPA), governs cleavage activity. Flap-bound RPA inhibits FEN1. This necessitates cleavage by Dna2, which is stimulated by RPA. FEN1 then cuts the remaining RPA-free flap to create a nick for ligation. Cleavage by Dna2 requires that it enter the 5'-end and track down the flap. Since Dna2 cleaves the RPA-bound flap, we investigated the mechanism by which Dna2 accesses the protein-coated flap for cleavage. Using a nuclease-defective Dna2 mutant, we showed that just binding of Dna2 dissociates the flap-bound RPA. Facile dissociation is specific to substrates with a genuine flap, and will not occur with an RPA-coated single strand. We also compared the cleavage patterns of Dna2 with and without RPA to better define RPA stimulation of Dna2. Stimulation derived from removal of DNA folding in the flap. Apparently, coordinated with its dissociation, RPA relinquishes the flap to Dna2 for tracking in a way that does not allow flap structure to reform. We also found that RPA strand melting activity promotes excessive flap elongation, but it is suppressed by Dna2-promoted RPA dissociation. Overall, results indicate that Dna2 and RPA coordinate their functions for efficient flap cleavage and preparation for FEN1

Pif1 Helicase Lengthens Some Okazaki Fragment Flaps Necessitating Dna2 Nuclease/Helicase Action in the Two-nuclease Processing Pathway

We have developed a system to reconstitute all of the proposed steps of Okazaki fragment processing using purified yeast proteins and model substrates. DNA polymerase δ was shown to extend an upstream fragment to displace a downstream fragment into a flap. In most cases, the flap was removed by flap endonuclease 1 (FEN1), in a reaction required to remove initiator RNA in vivo. The nick left after flap removal could be sealed by DNA ligase I to complete fragment joining. An alternative pathway involving FEN1 and the nuclease/helicase Dna2 has been proposed for flaps that become long enough to bind replication protein A (RPA). RPA binding can inhibit FEN1, but Dna2 can shorten RPA-bound flaps so that RPA dissociates. Recent reconstitution results indicated that Pif1 helicase, a known component of fragment processing, accelerated flap displacement, allowing the inhibitory action of RPA. In results presented here, Pif1 promoted DNA polymerase δ to displace strands that achieve a length to bind RPA, but also to be Dna2 substrates. Significantly, RPA binding to long flaps inhibited the formation of the final ligation products in the reconstituted system without Dna2. However, Dna2 reversed that inhibition to restore efficient ligation. These results suggest that the two-nuclease pathway is employed in cells to process long flap intermediates promoted by Pif1

Association between neighbourhood fast-food and full-service restaurant density and BMI: A cross-sectional study of Canadian adults

OBJECTIVE: Frequent fast-food consumption is a well-known risk factor for obesity. This study sought to determine whether the availability of fast-food restaurants has an influence on body mass index (BMI). METHODS: BMI and individual-level confounding variables were obtained from the 2007-08 Canadian Community Health Survey. Neighbourhood socio-demographic variables were acquired from the 2006 Canadian Census. The geographic locations of all restaurants in Canada were assembled from a validated business registry database. The density of fast-food, full-service and non-chain restaurants per 10,000 individuals was calculated for respondents’ forward sortation area. Multivariable regression analyses were conducted to analyze the association between restaurant density and BMI. RESULTS: Fast-food, full-service and non-chain restaurant density variables were statistically significantly associated with BMI. Fast-food density had a positive association whereas full-service and non-chain restaurant density had a negative association with BMI (additional 10 fast-food restaurants per capita corresponded to a weight increase of 1 kilogram; p\u3c0.001). These associations were primarily found in Canada’s major urban jurisdictions. CONCLUSIONS: This research was the first to investigate the influence of fast-food and full-service restaurant density on BMI using individual-level data from a nationally representative Canadian survey. The finding of a positive association between fast-food restaurant density and BMI suggests that interventions aiming to restrict the availability of fast-food restaurants in local neighbourhoods may be a useful obesity prevention strategy

Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1

In eukaryotic Okazaki fragment processing, the RNA primer is displaced into a single-stranded flap prior to removal. Evidence suggests that some flaps become long before they are cleaved, and that this cleavage involves the sequential action of two nucleases. Strand displacement characteristics of the polymerase show that a short gap precedes the flap during synthesis. Using biochemical techniques, binding and cleavage assays presented here indicate that when the flap is ∼30 nt long the nuclease Dna2 can bind with high affinity to the flap and downstream double strand and begin cleavage. When the polymerase idles or dissociates the Dna2 can reorient for additional contacts with the upstream primer region, allowing the nuclease to remain stably bound as the flap is further shortened. The DNA can then equilibrate to a double flap that can bind Dna2 and flap endonuclease (FEN1) simultaneously. When Dna2 shortens the flap even more, FEN1 can displace the Dna2 and cleave at the flap base to make a nick for ligation

Species differences in egocentric navigation : the effect of burrowing ecology on a spatial cognitive trait in mice

This study was funded by start-up funds from Oklahoma State University to P.C.Efficient navigation is a critical component of fitness for most animals. While most species use a combination of allocentric (external) and egocentric (internal) cues to navigate through their environment, subterranean environments present a unique challenge in that visually mediated allocentric cues are unavailable. The relationship between egocentric spatial cognition and species differences in ecology is surprisingly understudied. We used a maze-learning task to test for differences in egocentric navigation between two closely related species of mice, the eastern house mouse, Mus musculus musculus, and the mound-building mouse, Mus spicilegus. The two species are sympatric in Eastern Europe and overlap in summer habitat use but differ dramatically in winter space use: whereas house mice occupy anthropogenic structures, mound-building mice survive the winter underground in intricate burrow systems. Given species differences in burrowing ecology, we predicted that M. spicilegus would learn the maze significantly faster than M. m. musculus when tested in complete darkness, a condition that eliminated allocentric spatial information and served as a proxy for the subterranean environment. We found strong support for this prediction. In contrast, the two species performed equally well when different mice were tested in the same maze with lights on. This context-specific species difference in spatial cognition suggests that enhanced egocentric navigation in M. spicilegus is an adaptation to the burrow systems on which the overwinter survival of young mound-building mice depends. The results of this study highlight the importance of ecological adaptations to the evolution of cognitive traits.PostprintPeer reviewe

If You Make it Free, Will They Come? Using a Physical Activity Accessibility Model to Understand the Use of a Free Children’s Recreation Pass

Background: Children’s sedentary lifestyles and low physical activity levels may be countered using population-level interventions. This study examines factors influencing the use of a free community-wide physical activity access pass for grade 5 students (G5AP). Methods: A natural experiment with longitudinal data collection. A sample of 881 children completed the 9-month follow-up survey self-reporting where they used the G5AP. Two analyses were conducted: Getis-Ord GI* geographic cluster analysis of the spatial distribution of users, and logistic regression examining the relationship between use and accessibility (informational, economic, and geographic) and mobility options, while accounting for intrapersonal and interpersonal factors. Results: Overall, 44.9% of children used the G5AP with clusters of high use in urban areas and low use in the suburbs. Other factors significantly related to G5AP included gender (girls), informational accessibility (active recruitment), economic accessibility (median household income), geographic accessibility (facilities within 1.6 km of home), and mobility options (access to Boys & Girls Club bus). Conclusions: This study found that a diverse population of children used the G5AP. To continue being successful, community-based physical activity interventions need to ensure that the intervention increases geographic, economic, and informational accessibility and provides mobility options that are available to the target population

Effects of dietary protein and fiber at breakfast on appetite, ad libitum energy intake at lunch, and neural responses to visual food stimuli in overweight adults

Increasing either protein or fiber at mealtimes has relatively modest effects on ingestive behavior. Whether protein and fiber have additive or interactive effects on ingestive behavior is not known. Fifteen overweight adults (5 female, 10 male; BMI: 27.1 ± 0.2 kg/m²; aged 26 ± 1 year) consumed four breakfast meals in a randomized crossover manner (normal protein (12 g) + normal fiber (2 g), normal protein (12 g) + high fiber (8 g), high protein (25 g) + normal fiber (2 g), high protein (25 g) + high fiber (8 g)). The amount of protein and fiber consumed at breakfast did not influence postprandial appetite or ad libitum energy intake at lunch. In the fasting-state, visual food stimuli elicited significant responses in the bilateral insula and amygdala and left orbitofrontal cortex. Contrary to our hypotheses, postprandial right insula responses were lower after consuming normal protein vs. high protein breakfasts. Postprandial responses in other a priori brain regions were not significantly influenced by protein or fiber intake at breakfast. In conclusion, these data do not support increasing dietary protein and fiber at breakfast as effective strategies for modulating neural reward processing and acute ingestive behavior in overweight adults.R01 MH102224 - NIMH NIH HHS; UL1 TR001108 - NCATS NIH HHS; UL1TR001108 - NCATS NIH HH

An Alternative Pathway for Okazaki Fragment Processing - Resolution of Fold-Back Flaps by Pif1 Helicase

Two pathways have been proposed for eukaryotic Okazaki fragment RNA primer removal. Results presented here provide evidence for an alternative pathway. Primer extension by DNA polymerase δ (pol δ) displaces the downstream fragment into an RNA-initiated flap. Most flaps are cleaved by flap endonuclease 1 (FEN1) while short, and the remaining nicks joined in the first pathway. A small fraction escapes immediate FEN1 cleavage and is further lengthened by Pif1 helicase. Long flaps are bound by replication protein A (RPA), which inhibits FEN1. In the second pathway, Dna2 nuclease cleaves an RPA-bound flap and displaces RPA, leaving a short flap for FEN1. Pif1 flap lengthening creates a requirement for Dna2. This relationship should not have evolved unless Pif1 had an important role in fragment processing. In this study, biochemical reconstitution experiments were used to gain insight into this role. Pif1 did not promote synthesis through GC-rich sequences, which impede strand displacement. Pif1 was also unable to open fold-back flaps that are immune to cleavage by either FEN1 or Dna2 and cannot be bound by RPA. However, Pif1 working with pol δ readily unwound a full-length Okazaki fragment initiated by a fold-back flap. Additionally, a fold-back in the template slowed pol δ synthesis, so that the fragment could be removed before ligation to the lagging strand. These results suggest an alternative pathway in which Pif1 removes Okazaki fragments initiated by fold-back flaps in vivo

Socioeconomic status and adverse birth outcomes: a population-based Canadian sample

This study assessed the strength of the association between socioeconomic status (SES) and low birth weight (LBW) and preterm birth (PTB) in Southwestern Ontario. Utilizing perinatal and neonatal databases at the London Health Science Centre, maternal postal codes were entered into a Geographic Information System to determine home neighbourhoods. Neighbourhoods were defined by dissemination areas (DAs). Median household income for each DA was extracted from the latest Canadian Census and linked to each mother. All singleton infants born between February 2009 and February 2014 were included. Of 26,654 live singleton births, 6.4% were LBW and 9.7% were PTB. Top risk factors for LBW were: maternal amphetamine use, chronic hypertension and maternal marijuana use (OR respectively: 17.51, 3.18, 2.72); previously diagnosed diabetes, maternal narcotic use and insulin-controlled gestational diabetes predicted PTB (OR respectively: 17.95, 2.69, 2.42). Overall, SES had little impact on adverse birth outcomes, although low maternal education increased the likelihood of a LBW neonate (OR: 1.01)