Molecular Replicator Dynamics

Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with replication processes is therefore an indispensible prerequisite for any understanding of evolution at the molecular level. Networks of interacting self-replicating species can give rise to a wealth of different dynamical phenomena, from competitive exclusion to permanent coexistence, from global stability to multi-stability and chaotic dynamics. Nevertheless, there are some general principles that govern their overall behavior. We focus on the question to what extent the dynamics of replication can explain the accumulation of genetic information that eventually leads to the emergence of the first cell and hence the origin of life as we know it. A large class of ligation-based replication systems, which includes the experimentally available model systems for template directed self-replication, is of particular interest because its dynamics bridges the gap between the survival of a single fittest species to the global coexistence of everthing. In this intermediate regime the selection is weak enough to allow the coexistence of genetically unrelated replicators and strong enough to limit the accumulation of disfunctional mutants

Replicator Dynamics in Protocells

Replicator equations have been studied for three decades as a generic dynamical system modelling replication processes. Here we show how they arise naturally in models of self-replicating polymers and discuss some of their basic properties. We then concentrate on a minimal dynamic model of a protocell by coupling replicating polymers with a growing membrane

Xylose reductase from Pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Xylose reductase (XR) and xylitol dehydrogenase (XDH) from <it>Pichia stipitis </it>are the two enzymes most commonly used in recombinant <it>Saccharomyces cerevisiae </it>strains engineered for xylose utilization. The availability of NAD⁺for XDH is limited during anaerobic xylose fermentation because of the preference of XR for NADPH. This in turn results in xylitol formation and reduced ethanol yield. The coenzyme preference of <it>P. stipitis </it>XR was changed by site-directed mutagenesis with the aim to engineer it towards NADH-preference.</p> <p>Results</p> <p>XR variants were evaluated in <it>S. cerevisiae </it>strains with the following genetic modifications: overexpressed native <it>P. stipitis </it>XDH, overexpressed xylulokinase, overexpressed non-oxidative pentose phosphate pathway and deleted GRE3 gene encoding an NADPH dependent aldose reductase. All overexpressed genes were chromosomally integrated to ensure stable expression. Crude extracts of four different strains overexpressing genes encoding native <it>P. stipitis </it>XR, K270M and K270R mutants, as well as <it>Candida parapsilosis </it>XR, were enzymatically characterized. The physiological effects of the mutations were investigated in anaerobic xylose fermentation. The strain overexpressing <it>P. stipitis </it>XR with the K270R mutation gave an ethanol yield of 0.39 g (g consumed sugars)^-1, a xylitol yield of 0.05 g (g consumed xylose)^-1and a xylose consumption rate of 0.28 g (g biomass)^-1h^-1in continuous fermentation at a dilution rate of 0.12 h^-1, with 10 g l^-1glucose and 10 g l^-1xylose as carbon sources.</p> <p>Conclusion</p> <p>The cofactor preference of <it>P. stipitis </it>XR was altered by site-directed mutagenesis. When the K270R XR was combined with a metabolic engineering strategy that ensures high xylose utilization capabilities, a recombinant <it>S. cerevisiae </it>strain was created that provides a unique combination of high xylose consumption rate, high ethanol yield and low xylitol yield during ethanolic xylose fermentation.</p

Comparing the xylose reductase/xylitol dehydrogenase and xylose isomerase pathways in arabinose and xylose fermenting Saccharomyces cerevisiae strains

<p>Abstract</p> <p>Background</p> <p>Ethanolic fermentation of lignocellulosic biomass is a sustainable option for the production of bioethanol. This process would greatly benefit from recombinant <it>Saccharomyces cerevisiae </it>strains also able to ferment, besides the hexose sugar fraction, the pentose sugars, arabinose and xylose. Different pathways can be introduced in <it>S. cerevisiae </it>to provide arabinose and xylose utilisation. In this study, the bacterial arabinose isomerase pathway was combined with two different xylose utilisation pathways: the xylose reductase/xylitol dehydrogenase and xylose isomerase pathways, respectively, in genetically identical strains. The strains were compared with respect to aerobic growth in arabinose and xylose batch culture and in anaerobic batch fermentation of a mixture of glucose, arabinose and xylose.</p> <p>Results</p> <p>The specific aerobic arabinose growth rate was identical, 0.03 h^-1, for the xylose reductase/xylitol dehydrogenase and xylose isomerase strain. The xylose reductase/xylitol dehydrogenase strain displayed higher aerobic growth rate on xylose, 0.14 h^-1, and higher specific xylose consumption rate in anaerobic batch fermentation, 0.09 g (g cells)^-1h^-1than the xylose isomerase strain, which only reached 0.03 h^-1and 0.02 g (g cells)^-1h^-1, respectively. Whereas the xylose reductase/xylitol dehydrogenase strain produced higher ethanol yield on total sugars, 0.23 g g^-1compared with 0.18 g g^-1for the xylose isomerase strain, the xylose isomerase strain achieved higher ethanol yield on consumed sugars, 0.41 g g^-1compared with 0.32 g g^-1for the xylose reductase/xylitol dehydrogenase strain. Anaerobic fermentation of a mixture of glucose, arabinose and xylose resulted in higher final ethanol concentration, 14.7 g l^-1for the xylose reductase/xylitol dehydrogenase strain compared with 11.8 g l^-1for the xylose isomerase strain, and in higher specific ethanol productivity, 0.024 g (g cells)^-1h^-1compared with 0.01 g (g cells)^-1h^-1for the xylose reductase/xylitol dehydrogenase strain and the xylose isomerase strain, respectively.</p> <p>Conclusion</p> <p>The combination of the xylose reductase/xylitol dehydrogenase pathway and the bacterial arabinose isomerase pathway resulted in both higher pentose sugar uptake and higher overall ethanol production than the combination of the xylose isomerase pathway and the bacterial arabinose isomerase pathway. Moreover, the flux through the bacterial arabinose pathway did not increase when combined with the xylose isomerase pathway. This suggests that the low activity of the bacterial arabinose pathway cannot be ascribed to arabitol formation via the xylose reductase enzyme.</p

U7 snRNAs

U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase II. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database

Evolution of the vertebrate Y RNA cluster

Relatively little is known about the evolutionary histories of most classes of non-protein coding RNAs. Here we consider Y RNAs, a relatively rarely studied group of related pol-III transcripts. A single cluster of functional genes is preserved throughout tetrapod evolution, which however exhibits clade-specific tandem duplications, gene-losses, and rearrangements

PGM2 overexpression improves anaerobic galactose fermentation in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>In <it>Saccharomyces cerevisiae </it>galactose is initially metabolized through the Leloir pathway after which glucose 6-phosphate enters glycolysis. Galactose is controlled both by glucose repression and by galactose induction. The gene <it>PGM2 </it>encodes the last enzyme of the Leloir pathway, phosphoglucomutase 2 (Pgm2p), which catalyses the reversible conversion of glucose 1-phosphate to glucose 6-phosphate. Overexpression of <it>PGM2 </it>has previously been shown to enhance aerobic growth of <it>S. cerevisiae </it>in galactose medium.</p> <p>Results</p> <p>In the present study we show that overexpression of <it>PGM2 </it>under control of the <it>HXT7'</it>promoter from an integrative plasmid increased the PGM activity 5 to 6 times, which significantly reduced the lag phase of glucose-pregrown cells in an anaerobic galactose culture. <it>PGM2 </it>overexpression also increased the anaerobic specific growth rate whereas ethanol production was less influenced. When <it>PGM2 </it>was overexpressed from a multicopy plasmid instead, the PGM activity increased almost 32 times. However, this increase of PGM activity did not further improve aerobic galactose fermentation as compared to the strain carrying <it>PGM2 </it>on the integrative plasmid.</p> <p>Conclusion</p> <p><it>PGM2 </it>overexpression in <it>S. cerevisiae </it>from an integrative plasmid is sufficient to reduce the lag phase and to enhance the growth rate in anaerobic galactose fermentation, which results in an overall decrease in fermentation duration. This observation is of particular importance for the future development of stable industrial strains with enhanced PGM activity.</p

Arabinose and xylose fermentation by recombinant Saccharomyces cerevisiae expressing a fungal pentose utilization pathway

<p>Abstract</p> <p>Background</p> <p>Sustainable and economically viable manufacturing of bioethanol from lignocellulose raw material is dependent on the availability of a robust ethanol producing microorganism, able to ferment all sugars present in the feedstock, including the pentose sugars L-arabinose and D-xylose. <it>Saccharomyces cerevisiae </it>is a robust ethanol producer, but needs to be engineered to achieve pentose sugar fermentation.</p> <p>Results</p> <p>A new recombinant <it>S. cerevisiae </it>strain expressing an improved fungal pathway for the utilization of L-arabinose and D-xylose was constructed and characterized. The new strain grew aerobically on L-arabinose and D-xylose as sole carbon sources. The activities of the enzymes constituting the pentose utilization pathway(s) and product formation during anaerobic mixed sugar fermentation were characterized.</p> <p>Conclusion</p> <p>Pentose fermenting recombinant <it>S. cerevisiae </it>strains were obtained by the expression of a pentose utilization pathway of entirely fungal origin. During anaerobic fermentation the strain produced biomass and ethanol. L-arabitol yield was 0.48 g per gram of consumed pentose sugar, which is considerably less than previously reported for D-xylose reductase expressing strains co-fermenting L-arabinose and D-xylose, and the xylitol yield was 0.07 g per gram of consumed pentose sugar.</p

Saddles and Barrier in Landscapes of Generalized Search Operators

Barrier trees are a convenient way of representing the structure of complex combinatorial landscapes over graphs. Here we generalize the concept of barrier trees to landscapes defined over general multi-parent search operators based on a suitable notion of topological connectedness that depends explicitly on the search operator. We show that in the case of recombination spaces, path-connectedness coincides with connectedness as defined by the mutation operator alone. In contrast, topological connectedness is more general and depends on the details of the recombination operators as well. Barrier trees can be meaningfully defined for both concepts of connectedness

Comparison of the xylose reductase-xylitol dehydrogenase and the xylose isomerase pathways for xylose fermentation by recombinant Saccharomyces cerevisiae

BACKGROUND: Two heterologous pathways have been used to construct recombinant xylose-fermenting Saccharomyces cerevisiae strains: i) the xylose reductase (XR) and xylitol dehydrogenase (XDH) pathway and ii) the xylose isomerase (XI) pathway. In the present study, the Pichia stipitis XR-XDH pathway and the Piromyces XI pathway were compared in an isogenic strain background, using a laboratory host strain with genetic modifications known to improve xylose fermentation (overexpressed xylulokinase, overexpressed non-oxidative pentose phosphate pathway and deletion of the aldose reductase gene GRE3). The two isogenic strains and the industrial xylose-fermenting strain TMB 3400 were studied regarding their xylose fermentation capacity in defined mineral medium and in undetoxified lignocellulosic hydrolysate. RESULTS: In defined mineral medium, the xylose consumption rate, the specific ethanol productivity, and the final ethanol concentration were significantly higher in the XR- and XDH-carrying strain, whereas the highest ethanol yield was achieved with the strain carrying XI. While the laboratory strains only fermented a minor fraction of glucose in the undetoxified lignocellulose hydrolysate, the industrial strain TMB 3400 fermented nearly all the sugar available. Xylitol was formed by the XR-XDH-carrying strains only in mineral medium, whereas in lignocellulose hydrolysate no xylitol formation was detected. CONCLUSION: Despite by-product formation, the XR-XDH xylose utilization pathway resulted in faster ethanol production than using the best presently reported XI pathway in the strain background investigated. The need for robust industrial yeast strains for fermentation of undetoxified spruce hydrolysates was also confirmed