Alternative mRNA Editing in Trypanosomes Is Extensive and May Contribute to Mitochondrial Protein Diversity

The editing of trypanosome mitochondrial mRNAs produces transcripts necessary for mitochondrial functions including electron transport and oxidative phosphorylation. Precursor-mRNAs are often extensively edited by specific uridine insertion or deletion that is directed by small guide RNAs (gRNAs). Recently, it has been shown that cytochrome c oxidase subunit III (COXIII) mRNAs can be alternatively edited to encode a novel mitochondrial membrane protein composed of a unique hydrophilic N-terminal sequence of unknown function and the C-terminal hydrophobic segment of COXIII. To extend the analysis of alternative editing in Trypanosoma brucei we have constructed libraries with over 1100 full-length mitochondrial cDNAs and the sequences of over 1200 gRNA genes. Using this data, we show that alternative editing of COXIII, ATPase subunit 6 (A6), and NADH dehydrogenase subunits 7, 8 and 9 (ND7, 8, 9) mRNAs can produce novel open reading frames (ORFs). Several gRNAs potentially responsible for the alternative editing of these mRNAs were also identified. These findings show that alternative editing of mitochondrial mRNAs is common in T. brucei and expands the diversity of mitochondrial proteins in these organisms

The Pathway to Detangle a Scrambled Gene

Programmed DNA elimination and reorganization frequently occur during cellular differentiation. Development of the somatic macronucleus in some ciliates presents an extreme case, involving excision of internal eliminated sequences (IESs) that interrupt coding DNA segments (macronuclear destined sequences, MDSs), as well as removal of transposon-like elements and extensive genome fragmentation, leading to 98% genome reduction in Stylonychia lemnae. Approximately 20-30% of the genes are estimated to be scrambled in the germline micronucleus, with coding segment order permuted and present in either orientation on micronuclear chromosomes. Massive genome rearrangements are therefore critical for development.To understand the process of DNA deletion and reorganization during macronuclear development, we examined the population of DNA molecules during assembly of different scrambled genes in two related organisms in a developmental time-course by PCR. The data suggest that removal of conventional IESs usually occurs first, accompanied by a surprising level of error at this step. The complex events of inversion and translocation seem to occur after repair and excision of all conventional IESs and via multiple pathways.This study reveals a temporal order of DNA rearrangements during the processing of a scrambled gene, with simpler events usually preceding more complex ones. The surprising observation of a hidden layer of errors, absent from the mature macronucleus but present during development, also underscores the need for repair or screening of incorrectly-assembled DNA molecules

The Evolution of Enzyme Specificity in the Metabolic Replicator Model of Prebiotic Evolution

The chemical machinery of life must have been catalytic from the outset. Models of the chemical origins have attempted to explain the ecological mechanisms maintaining a minimum necessary diversity of prebiotic replicator enzymes, but little attention has been paid so far to the evolutionary initiation of that diversity. We propose a possible first step in this direction: based on our previous model of a surface-bound metabolic replicator system we try to explain how the adaptive specialization of enzymatic replicator populations might have led to more diverse and more efficient communities of cooperating replicators with two different enzyme activities. The key assumptions of the model are that mutations in the replicator population can lead towards a) both of the two different enzyme specificities in separate replicators: efficient “specialists” or b) a “generalist” replicator type with both enzyme specificities working at less efficiency, or c) a fast-replicating, non-enzymatic “parasite”. We show that under realistic trade-off constraints on the phenotypic effects of these mutations the evolved replicator community will be usually composed of both types of specialists and of a limited abundance of parasites, provided that the replicators can slowly migrate on the mineral surface. It is only at very weak trade-offs that generalists take over in a phase-transition-like manner. The parasites do not seriously harm the system but can freely mutate, therefore they can be considered as pre-adaptations to later, useful functions that the metabolic system can adopt to increase its own fitness

A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes.

BackgroundCorrelations between genome composition (in terms of GC content) and usage of particular codons and amino acids have been widely reported, but poorly explained. We show here that a simple model of processes acting at the nucleotide level explains codon usage across a large sample of species (311 bacteria, 28 archaea and 257 eukaryotes). The model quantitatively predicts responses (slope and intercept of the regression line on genome GC content) of individual codons and amino acids to genome composition.ResultsCodons respond to genome composition on the basis of their GC content relative to their synonyms (explaining 71-87% of the variance in response among the different codons, depending on measure). Amino-acid responses are determined by the mean GC content of their codons (explaining 71-79% of the variance). Similar trends hold for genes within a genome. Position-dependent selection for error minimization explains why individual bases respond differently to directional mutation pressure.ConclusionsOur model suggests that GC content drives codon usage (rather than the converse). It unifies a large body of empirical evidence concerning relationships between GC content and amino-acid or codon usage in disparate systems. The relationship between GC content and codon and amino-acid usage is ahistorical; it is replicated independently in the three domains of living organisms, reinforcing the idea that genes and genomes at mutation/selection equilibrium reproduce a unique relationship between nucleic acid and protein composition. Thus, the model may be useful in predicting amino-acid or nucleotide sequences in poorly characterized taxa

Universal Molecular Computation in Ciliates

How do cells and nature "compute"? They read and "rewrite" DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman's elegant solution to a seven-city Directed Hamiltonian Path problem using DNA [1] launched the new field of DNA computing, which in a few years has grown to international scope. However, unknown to this field, ciliated protozoans of genus Oxytricha and Stylonychia had solved a potentially harder problem using DNA several million years earlier. The solution to this "problem", which occurs during the process of gene unscrambling, represents one of nature's ingenious solutions to the problem of the creation of genes. Here we develop a model for the guided homologous recombinations that take place during gene rearrangement and prove that such a model has the computational power of a Turing machine, the accepted formal model of computation. This indicates that, in principle, these unicellular organisms may have the capacity to perform at ..

Journeys in Non-Classical Computation I: A Grand Challenge for computing research

A gateway event is a change to a system that leads to the possibility of huge increases in kinds and levels of complexity. It opens up a whole new kind of phase space to the systemÕs dynamics. Gateway events during evolution of life on earth include the appearance of eukaryotes (organisms with a cell nucleus), an oxygen atmosphere, multi-cellular organisms and grass. Gateway events during the development of mathematics include each invention of a new class of numbers (negative, irrational, imaginary, ...), and dropping Euclid's parallel postulate. A gateway event produces a profound and fundamental change to the system: Once through the gateway, life is never the same again. We are currently poised on the threshold of a significant gateway event in computation: That of breaking free from many of our current Òclassical computationalÓ assumptions. Our Grand Challenge for computer science is to journey through the gateway event obtained by breaking our current classical computational assumptions, and thereby develop a mature science of Non-Classical Computatio

Are the Gödel incompleteness theorems limitative results for the neurosciences?

There are many kinds of limitative results in the sciences, some of which are philosophical. I am interested in examining one kind of limitative result in the neurosciences that is mathematical—a result secured by the Gödel incompleteness theorems. I will view the incompleteness theorems as independence results, develop a connection with independence results in set theory, and then argue that work in the neurosciences (as well as in molecular, systems and synthetic biology) may well avoid these mathematical limitative results. In showing this, I argue that demonstrating that one cannot avoid them is a computational task that is beyond the computational capacities of finitary minds. Along the way, I reformulate three philosophical claims about the nature of consciousness in terms of the Gödel incompleteness theorems and argue that these precise reformulations of the claims can be disarmed