A study on the correlation of nucleotide skews and the positioning of the origin of replication: different modes of replication in bacterial species

Deviations from Chargaff's 2nd parity rule, according to which A∼T and G∼C in single stranded DNA, have been associated with replication as well as with transcription in prokaryotes. Based on observations regarding mainly the transcription-replication co-linearity in a large number of prokaryotic species, we formulate the hypothesis that the replication procedure may follow different modes between genomes throughout which the skews clearly follow different patterns. We draw the conclusion that multiple functional sites of origin of replication may exist in the genomes of most archaea and in some exceptional cases of eubacteria, while in the majority of eubacteria, replication occurs through a single fixed origin

Validation of Bacterial Replication Termination Models Using Simulation of Genomic Mutations

In bacterial circular chromosomes and most plasmids, the replication is known to be terminated when either of the following occurs: the forks progressing in opposite directions meet at the distal end of the chromosome or the replication forks become trapped by Tus proteins bound to Ter sites. Most bacterial genomes have various polarities in their genomic structures. The most notable feature is polar genomic compositional asymmetry of the bases G and C in the leading and lagging strands, called GC skew. This asymmetry is caused by replication-associated mutation bias, and this “footprint" of the replication machinery suggests that, in contrast to the two known mechanisms, replication termination occurs near the chromosome dimer resolution site dif. To understand this difference between the known replication machinery and genomic compositional bias, we undertook a simulation study of genomic mutations, and we report here how different replication termination models contribute to the generation of replication-related genomic compositional asymmetry. Contrary to naive expectations, our results show that a single finite termination site at dif or at the GC skew shift point is not sufficient to reconstruct the genomic compositional bias as observed in published sequences. The results also show that the known replication mechanisms are sufficient to explain the position of the GC skew shift point

Codon usage optimization in the prokaryotic tree of life: how synonymous codons are differentially selected in sequence domains with different expression levels and degrees of conservation

Prokaryote genomes exhibit a wide range of GC contents and codon usages, both resulting from an interaction between mutational bias and natural selection. In order to investigate the basis underlying specific codon changes, we performed a comprehensive analysis of 29 different prokaryote families. The analysis of core gene sets with increasing ancestries in each family lineage revealed that the codon usages became progressively more adapted to the tRNA pools. While, as previously reported, highly expressed genes presented the most optimized codon usage, the singletons contained the less selectively favored codons. The results showed that usually codons with the highest translational adaptation were preferentially enriched. In agreement with previous reports, a C bias in 2- to 3-fold pyrimidine-ending codons, and a U bias in 4-fold codons occurred in all families, irrespective of the global genomic GC content. Furthermore, the U biases suggested that U3-mRNA–U34-tRNA interactions were responsible for a prominent codon optimization in both the most ancestral core and the highly expressed genes. A comparative analysis of sequences that encode conserved (cr) or variable (vr) translated products, with each one being under high (HEP) and low (LEP) expression levels, demonstrated that the efficiency was more relevant (by a factor of 2) than accuracy to modeling codon usage. Finally, analysis of the third position of codons (GC3) revealed that in genomes with global GC contents higher than 35 to 40%, selection favored a GC3 increase, whereas in genomes with very low GC contents, a decrease in GC3 occurred. A comprehensive final model is presented in which all patterns of codon usage variations are condensed in four distinct behavioral groups. IMPORTANCE The prokaryotic genomes—the current heritage of the most ancient life forms on earth—are comprised of diverse gene sets, all characterized by varied origins, ancestries, and spatial-temporal expression patterns. Such genetic diversity has for a long time raised the question of how cells shape their coding strategies to optimize protein demands (i.e., product abundance) and accuracy (i.e., translation fidelity) through the use of the same genetic code in genomes with GC contents that range from less than 20 to more than 80%. Here, we present evidence on how codon usage is adjusted in the prokaryotic tree of life and on how specific biases have operated to improve translation. Through the use of proteome data, we characterized conserved and variable sequence domains in genes of either high or low expression level and quantitated the relative weight of efficiency and accuracy—as well as their interaction—in shaping codon usage in prokaryotes.Fil: López, José Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Lozano, Mauricio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Fabre, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Lagares, Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentin

Translational Selection Is Ubiquitous in Prokaryotes

Codon usage bias in prokaryotic genomes is largely a consequence of background substitution patterns in DNA, but highly expressed genes may show a preference towards codons that enable more efficient and/or accurate translation. We introduce a novel approach based on supervised machine learning that detects effects of translational selection on genes, while controlling for local variation in nucleotide substitution patterns represented as sequence composition of intergenic DNA. A cornerstone of our method is a Random Forest classifier that outperformed previous distance measure-based approaches, such as the codon adaptation index, in the task of discerning the (highly expressed) ribosomal protein genes by their codon frequencies. Unlike previous reports, we show evidence that translational selection in prokaryotes is practically universal: in 460 of 461 examined microbial genomes, we find that a subset of genes shows a higher codon usage similarity to the ribosomal proteins than would be expected from the local sequence composition. These genes constitute a substantial part of the genome—between 5% and 33%, depending on genome size—while also exhibiting higher experimentally measured mRNA abundances and tending toward codons that match tRNA anticodons by canonical base pairing. Certain gene functional categories are generally enriched with, or depleted of codon-optimized genes, the trends of enrichment/depletion being conserved between Archaea and Bacteria. Prominent exceptions from these trends might indicate genes with alternative physiological roles; we speculate on specific examples related to detoxication of oxygen radicals and ammonia and to possible misannotations of asparaginyl–tRNA synthetases. Since the presence of codon optimizations on genes is a valid proxy for expression levels in fully sequenced genomes, we provide an example of an “adaptome” by highlighting gene functions with expression levels elevated specifically in thermophilic Bacteria and Archaea

Doctor of Philosophy

dissertationA diverse array of insect species harbor maternally transmitted mutualistic bacterial endosymbionts that perform a variety of functions within their hosts. Many of these associations are obligate in nature with the insect relying on the bacterial symbiont to provide nutrients that are lacking in the insect's natural diet. These obligate endosymbionts often show a highly reduced genome size and maintain only a small fraction of the gene inventory of free-living bacteria. Some of the smallest known bacterial genomes are from obligate endosymbionts that have been associated with their insect hosts for long periods of time. In addition to their small size, the genomes of ancient obligate symbionts also show an increased rate of DNA and polypeptide sequence evolution as well as a nucleotide composition bias that results in an increased ratio of adenine and thymine residues. Despite extensive study of these ancient endosymbionts, little is known about their origins. To address this issue and to better understand the forces shaping genomes in the early stages of an endosymbiotic association, this work focuses on two bacteria: strain HS, a recently characterized free-living bacterium that likely served as a progenitor to the Sodalis-allied clade of bacterial endosymbionts, and the Sitophilus oryzae primary endosymbiont (SOPE), a very recent established maternally transmitted obligate endosymbiont of the rice weevil. The complete genome sequencing of these two bacteria along with comparative genomic analyses revealed that SOPE has undergone a very rapid degeneration of its genome, losing nearly half of its coding capacity, a massive expansion of insertion sequence (IS) elements and numerous intragenomic rearrangements facilitated by the IS elements. Surprisingly, these changes have happened very recently since strain HS and SOPE shared a common ancestor approximately 28,000 years ago

Selective Forces That Shape the VLS Antigenic Variation System in Borrelia Burgdorferi

Evolutionary success of microbial pathogens requires survival within hosts, despite the rapidly changing and lethal immune response. Pathogens such as the Lyme disease bacteria Borrelia burgdorferi have evolved antigenic variation systems that are necessary for survival within the adverse immune environment. Although antigenic variation systems are essential to both microbial pathogenesis and microbial evolution, it is largely unclear what selective forces have influenced the evolution of antigenic variation systems. In this thesis, we investigate evolution of the vls antigenic variation system in B. burgdorferi by asking two major questions: First, what traits relevant to the vls antigenic variation system have natural selection acted on? Second, how did the selective forces shape the genetic sequences of the vls antigenic variation systems? We characterize sources of natural selection using mathematical modeling, computational simulation and mutagenesis experiments. Our findings show that natural selection has promoted diversity among VlsE variants on both sequence and structure by organizing the variable sites in the vls unexpressed cassettes. We also show that the level of diversity among the VlsE variants may strongly influence the within-host dynamics of Bb, an important fitness component of B. burgdorferi. Finally, our results indicate that diversity among VlsE variants might be constrained by purifying or stabilizing selections on translational efficiency and structural stability of the VlsE variants