Bacterial DNA Uptake Sequences Can Accumulate by Molecular Drive Alone

Uptake signal sequences are DNA motifs that promote DNA uptake by competent bacteria in the family Pasteurellaceae and the genus Neisseria. The genomes of these bacteria contain many copies of their canonical uptake sequence (often >100-fold overrepresentation), so the bias of the uptake machinery causes cells to prefer DNA derived from close relatives over DNA from other sources. However, the molecular and evolutionary forces responsible for the abundance of uptake sequences in these genomes are not well understood, and their presence is not easily explained by any of the current models of the evolution of competence. Here we describe use of a computer simulation model to thoroughly evaluate the simplest explanation for uptake sequences, that they accumulate in genomes by a form of molecular drive generated by biased DNA uptake and evolutionarily neutral (i.e., unselected) recombination. In parallel we used an unbiased search algorithm to characterize genomic uptake sequences and DNA uptake assays to refine the Haemophilus influenzae uptake specificity. These analyses showed that biased uptake and neutral recombination are sufficient to drive uptake sequences to high densities, with the spacings, stabilities, and strong consensuses typical of uptake sequences in real genomes. This result greatly simplifies testing of hypotheses about the benefits of DNA uptake, because it explains how genomes could have passively accumulated sequences matching the bias of their uptake machineries.MANY bacteria are able to take up DNA fragments from their environment, a genetically specified trait called natural competence (Chen and Dubnau 2004; Johnsborg et al. 2007; Maughan et al. 2008). Many other species have homologs of competence genes, suggesting that although they are not competent under laboratory conditions, they may be competent under natural conditions (Claverys and Martin 2003; Kovacs et al. 2009). Such a widespread trait must be beneficial but the evolutionary function of DNA uptake remains controversial. Cells can use the nucleotides released by degradation of both incoming DNA and any strands displaced by its recombination, thus reducing demands on their nucleotide salvage and biosynthesis pathways (Redfield 1993; Palchevskiy and Finkel 2009). Cells may also benefit if recombination of the incoming DNA provides templates for DNA repair or introduces beneficial mutations, but may suffer if recombination introduces damage or harmful mutations (Redfield 1988; Michod et al. 2008).Although most bacteria that have been tested show no obvious preferences for specific DNA sources or sequences, bacteria in the family Pasteurellaceae and the genus Neisseria strongly prefer DNA fragments from close relatives. Two factors are responsible: First, the DNA uptake machineries of these bacteria are strongly biased toward certain short DNA sequence motifs. Second, the genomes of these bacteria contain hundreds of occurrences of the preferred sequences. The Pasteurellacean motif is called the uptake signal sequence (USS); its Neisseria counterpart is called the DNA uptake sequence (DUS). All Neisseria genomes contain the same consensus DUS [core GCCGTCTGAA (Treangen et al. 2008)], but divergence in the Pasteurellaceae has produced two subclades, one of species sharing the canonical Haemophilus influenzae 9-bp USS (Hin-USS core AAGTGCGGT) and the other of species with a variant USS that differs at three core positions (Apl-USS core: ACAAGCGGT) and has a longer flanking consensus (Redfield et al. 2006). Uptake sequence biases are strong but not absolute; for example, replacing the Hin-USS with the Apl-USS reduces H. influenzae DNA uptake only 10-fold (Redfield et al. 2006) and DNA from Escherichia coli is taken up in the absence of competing H. influenzae DNA (Goodgal and Mitchell 1984).Most studies of the distribution and consensus of uptake sequences in genomes have examined only those occurrences that perfectly match the above core DUS and USS sequences. Here we call these perfect matches “core-consensus” (cc) uptake sequences. These cc-uptake sequences occupy ∼1% of their genomes; they are equally frequent in the plus and minus orientations of the genome sequence but are underrepresented in coding sequences, with the noncoding 14% and 20% of their respective genomes containing 35% of cc-USSs and 65% of cc-DUSs (Smith et al. 1995). Although many of these intergenic cc-DUSs and cc-USSs occur in inverted-repeat pairs that function as terminators (Kingsford et al. 2007), most uptake sequences are too far apart or in genes or other locations where termination does not occur. Within coding regions uptake sequences occur more often in weakly conserved genes, in weakly conserved parts of genes, and in reading frames that encode common tripeptides (Findlay and Redfield 2009), all of which are consistent with selection acting mainly to eliminate mutations that improve uptake from genome regions constrained by coding or other functions.Analyses that focus on cc-uptake sequences effectively treat uptake sequences as replicative elements (Smith et al. 1995; Redfield et al. 2006; Ambur et al. 2007; Treangen et al. 2008). However, USS and DUS are known to originate in situ by normal mutational processes, mainly point mutations, and to spread between genomes mainly by homologous recombination (Redfield et al. 2006; Treangen et al. 2008). As they are not replicating elements, why are they up to 1000-fold more common in their genomes than expected for unselected sequences (e.g., H. influenzae, 1471 cc-USS vs. 8 expected by chance; N. gonorrheae, 1892 cc-DUS vs. 2 expected by chance)?The explanation for this abundance must lie with the specificity of the DNA uptake system, because the strong correspondence between the uptake bias and the uptake sequences in the genome is far too improbable to be a coincidence. However, uptake specificity is not easily accommodated by either of the hypothesized functions of DNA uptake. If bacteria take up DNA to get benefits from homologous genetic recombination, the combination of uptake bias and uptake sequences might serve as a mate-choice adaptation that maximizes these benefits by excluding foreign DNAs (Treangen et al. 2008). Although this explanation is appealing, it requires simultaneous evolution of bias in the uptake machinery and of genomic sequences matching this bias. Another problem is that the genomic sequences can be “selected” only after the cell carrying them is dead. On the other hand, if bacteria instead take up DNA as a source of nutrients, all DNAs should be equally useful, so uptake bias and uptake sequences would likely reduce rather than increase this benefit. Although the sequence bias could be explained as a consequence of mechanistic constraints on DNA uptake, this would not account for the high density of the preferred sequences in the genome.However, both hypotheses may be simplified by a process called molecular drive, under which uptake sequences would gradually accumulate over evolutionary time as a direct consequence of biased uptake and recombination (Danner et al. 1980; Bakkali et al. 2004; Bakkali 2007), without any need for natural selection. This drive is proposed to work as follows: First, random mutation continuously creates variation in DNA sequences that affects their probability of uptake, and random cell death allows DNA fragments containing preferred variants to be taken up by other cells. Second, repeated recombination of such preferred DNA sequences with their chromosomal homologs gradually increases their abundance in the genomes of competent cells'' descendants. Thus mutations that create matches to the bias of the uptake machinery are horizontally transmitted to other members of the same species more often than other mutations. Because some recombination may be inevitable even if DNA''s main benefit is nutritional, molecular drive could account for uptake sequence accumulation under both hypotheses, leaving only the biased uptake process to be explained by natural selection for either genetic variation or nutrients.Although drive is plausible, its ability to account for the observed properties of genomic uptake sequences has never been evaluated. To do this, we developed a realistic computer simulation model that includes only the processes thought to generate molecular drive. Below we first use this model to identify the conditions that determine whether uptake sequences will accumulate and then compare the properties of these simulated uptake sequences to those of the uptake sequences in the N. meningitidis and H. influenzae genomes. In parallel we use unbiased motif searches to better characterize genomic uptake sequences and DNA uptake assays to refine the H. influenzae uptake specificity.     

Some effects of prolonged polarization on membrane currents in bullfrog atrial muscle

Summary Bullfrog atrial trabecula were voltage-clamped using a double-sucrose-gap method. Step depolarization produced a slowly changing outward current which was studied by analyzing the current tail produced by repolarization. The initial phase of the current tail (time constant 0.1 to 0.7 sec at –60 mV) had a reversal potential which depended upon the duration and magnitude of the preceding depolarization. Calculations based on trabecular geometry and the behavior of the currents in high external potassium suggest that part of the current tail reflects a restoration to a lower steadystate concentration of external potassium which had accumulated in narrow clefts between cells during the preceding depolarization. Step hyperpolarization produced a declining inward current (time constant 0.3 sec at –100 mV) which can be explained on the basis of a depletion of potassium from these intercellular clefts (about 0.5% of the trabecular volume).     

The effects of a glycogen loading regimen on acid-base status and blood lactate concentration before and after a fixed period of high intensity exercise in man

Six healthy male subjects exercised after an overnight fast for a fixed 3 min period at a workload equivalent to 100% of their maximal oxygen uptake ( ) on 3 separate occasions. The first test took place after subjects had consumed a mixed diet (43±3% carbohydrate (CHO), 41±5% fat and 16±3% protein) for 3 days, and was followed 2 h later by prolonged cycling to exhaustion at 77±3% to deplete muscle glycogen stores. Following this, subjects consumed a low CHO diet (4±1% CHO, 63±5% fat and 33±6% protein) for the remainder of the day and for the subsequent 2 days; on the morning of the next day a second high intensity test took place. Finally subjects followed a 3 day high CHO diet (73±7% CHO, 17±6% fat and 10±1% protein) before their last test. Acid-base status and selected metabolites were measured on arterialised-venous blood at rest prior to exercise and at intervals for 15 min following exercise. Prior to exercise, plasma pH and blood lactate concentration were higher (p<0.05) after the high CHO diet when compared with the low CHO diet. Pre-exercise plasma bicarbonate, blood PCO₂ and blood base excess were all higher after the high (p<0.001,p<0.01,p<0.01 respectively) and normal (p<0.05,p<0.05,p<0.05 respectively) CHO diets when compared with the low CHO diet. During the post-exercise period there were no differences in plasma pH or blood base excess between the three experimental situations; plasma bicarbonate was higher (p<0.05) at 2 min post-exercise after the high CHO diet when compared with the low CHO diet; blood PCO₂ was higher throughout the post-exercise period after the high CHO diet when compared with the low CHO diet and at 2 min post-exercise was higher after the normal CHO diet than after the low CHO diet (p<0.5). The post-exercise blood lactate concentration after the high CHO diet was at all times higher than the corresponding values recorded after the normal CHO diet and until 15 min post-exercise was significantly higher than the values recorded after the low CHO diet. The present experiment further substantiates the view that a pattern of dietary and exercise manipulation can significantly influence the acid-base status of the blood and by doing so may influence high intensity exercise performance.     

Neutron RBEs for mouse skin at low doses per fraction

The effect of low doses of 240 kVp X rays or of 3 MeV neutrons has been investigated using skin reactions on mouse feet as the biological system. Eight or nine repeated small doses of radiation were used, followed by graded "top-up" doses to bring the reactions into a detectable range. By comparing dose-response curves, the RBE has been determined for neutron doses per fraction ranging from 0.25-1.0 Gy. The data are consistent with a limiting RBE of between 7 and 10 at very low doses. A review of other published RBE values for low doses per fraction shows a wide range of RBEs . Very few studies show a plateau value for the RBE. These findings are more consistent with dose-response data that fit a linear-quadratic model than with a multitarget single-hit model.