Archaeology and evolution of transfer RNA genes in the Escherichia coli genome

Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25

The complement of tRNA genes within a genome is typically considered to be a (relatively) stable characteristic of an organism. Here, we demonstrate that bacterial tRNA gene set composition can be more flexible than previously appreciated, particularly regarding tRNA gene copy number. We report the high-rate occurrence of spontaneous, large-scale, tandem duplication events in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The identified duplications are up to ∼1 Mb in size (∼15% of the wildtype genome) and are predicted to change the copy number of up to 917 genes, including several tRNA genes. The observed duplications are inherently unstable: they occur, and are subsequently lost, at extremely high rates. We propose that this unusually plastic type of mutation provides a mechanism by which tRNA gene set diversity can be rapidly generated, while simultaneously preserving the underlying tRNA gene set in the absence of continued selection. That is, if a tRNA set variant provides no fitness advantage, then high-rate segregation of the duplication ensures the maintenance of the original tRNA gene set. However, if a tRNA gene set variant is beneficial, the underlying duplication fragment(s) may persist for longer and provide raw material for further, more stable, evolutionary change.

On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes

Automated genome annotation is essential for extracting biological information from sequence data. The identification and annotation of tRNA genes is frequently performed by the software package tRNAscan-SE, the output of which is listed for selected genomes in the Genomic tRNA database (GtRNAdb). Here, we highlight a pervasive error in prokaryotic tRNA gene sets on GtRNAdb: the mis-categorization of partial, non-canonical tRNA genes as standard, canonical tRNA genes. Firstly, we demonstrate the issue using the tRNA gene sets of 20 organisms from the archaeal taxon Thermococcaceae. According to GtRNAdb, these organisms collectively deviate from the expected set of tRNA genes in 15 instances, including the listing of eleven putative canonical tRNA genes. However, after detailed manual annotation, only one of these eleven remains; the others are either partial, non-canonical tRNA genes resulting from the integration of genetic elements or CRISPR-Cas activity (seven instances), or attributable to ambiguities in input sequences (three instances). Secondly, we show that similar examples of the mis-categorization of predicted tRNA sequences occur throughout the prokaryotic sections of GtRNAdb. While both canonical and non-canonical prokaryotic tRNA gene sequences identified by tRNAscan-SE are biologically interesting, the challenge of reliably distinguishing between them remains. We recommend employing a combination of (i) screening input sequences for the genetic elements typically associated with non-canonical tRNA genes, and ambiguities, (ii) activating the tRNAscan-SE automated pseudogene detection function, and (iii) scrutinizing predicted tRNA genes with low isotype scores. These measures greatly reduce manual annotation efforts, and lead to improved prokaryotic tRNA gene set predictions.

Microevolution of CG23-I Hypervirulent Klebsiella pneumoniae during Recurrent Infections in a Single Patient

CG23-I lineage constitutes the majority of hypervirulent Klebsiella pneumoniae. A diabetic patient suffered six episodes of infections caused by CG23-I K. pneumoniae. A total of nine isolates were collected in 2020. We performed whole-genome sequencing to elucidate the within-patient evolution of CG23-I K. pneumoniae. The maximum pairwise difference among the nine longitudinally collected isolates was five single nucleotide polymorphisms. One of the mutations was at the Asp87 position of GyrA. Four indels were identified, including an initiator tRNAfMet duplication, a tRNAArg deletion, a 7-bp insertion, and a 22-bp deletion. All 9 isolates had the genomic features of CG23-I K. pneumoniae, a chromosome-borne ICEKp10, and a large virulence plasmid. The carriage of a complete set of genes for the biosynthesis of colibactin by ICEKp10 gave the nine isolates an ability to cause DNA damage to RAW264.7 cells. Compared with the initial isolate, the last isolate with an additional copy of initiator tRNAfMet grew faster in a nutrient-limiting condition and exhibited enhanced virulence in BALB/c mice. Collectively, we characterized the within-patient microevolution of CG23-I K. pneumoniae through an in-depth comparison of genome sequences. Using the in vitro experiments and mouse models, we also demonstrated that these genomic alterations endowed the isolates with advantages to pass through in vivo selection. IMPORTANCE CG23-I is a significant lineage of hypervirulent Klebsiella pneumoniae. This study characterizes the within-patient microevolution of CG23-I K. pneumoniae. Selective pressures from continuous use of antibiotics favored point mutations contributing to bacterial resistance to antibiotics. The duplication of an initiator tRNAfMet gene helped CG23-I K. pneumoniae proliferate to reach a maximal population size during infections. For longer persistence inside a human host, the large virulence plasmid evolved with more flexible control of replication through duplication of the iteron-1 region. With the genomic alterations, the last isolate had a growth advantage over the initial isolate and exhibited enhanced virulence in BALB/c mice. This study gives us a deeper understanding of the genome evolution during the within-patient pathoadaptation of CG23-I K. pneumoniae.

BOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium

We present BOPAL 2.0, an improved version of the BOPAL algorithm for the evolutionary history inference of tRNA and rRNA genes in bacterial genomes. Our approach can infer complete evolutionary scenarios and ancestral gene orders on a phylogeny and considers a wide range of events such as duplications, deletions, substitutions, inversions and transpositions. It is based on the fact that tRNA and rRNA genes are often organized in operons/clusters in bacteria, and this information is used to help identify orthologous genes for each genome comparison. BOPAL 2.0 introduces new features, such as a triple-wise alignment step, context-aware singleton matching and a second pass of the algorithm. Evaluation on simulated datasets shows that BOPAL 2.0 outperforms the original BOPAL in terms of the accuracy of inferred events and ancestral genomes. We also present a study of the tRNA/rRNA gene evolution in the Clostridium genus, in which the organization of these genes is very divergent. Our results indicate that tRNA and rRNA genes in Clostridium have evolved through numerous duplications, losses, transpositions and substitutions, but very few inversions were inferred.

Social Networking of Quasi-Species Consortia drive Virolution via Persistence

The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.

The birth of a bacterial tRNA gene by large-scale, tandem duplication events

Organisms differ in the types and numbers of tRNA genes that they carry. While the evolutionary mechanisms behind tRNA gene set evolution have been investigated theoretically and computationally, direct observations of tRNA gene set evolution remain rare. Here, we report the evolution of a tRNA gene set in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The growth defect caused by deleting the single-copy tRNA gene, serCGA, is rapidly compensated by large-scale (45–290 kb) duplications in the chromosome. Each duplication encompasses a second, compensatory tRNA gene (serTGA) and is associated with a rise in tRNA-Ser(UGA) in the mature tRNA pool. We postulate that tRNA-Ser(CGA) elimination increases the translational demand for tRNA-Ser(UGA), a pressure relieved by increasing serTGA copy number. This work demonstrates that tRNA gene sets can evolve through duplication of existing tRNA genes, a phenomenon that may contribute to the presence of multiple, identical tRNA gene copies within genomes.

Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis

BACKGROUND

Trichomonas vaginalis, the causative agent of a prevalent urogenital infection in humans, is an evolutionarily divergent protozoan. Protein-coding genes in T. vaginalis are largely controlled by two core promoter elements, producing mRNAs with short 5' UTRs. The specific mechanisms adopted by T. vaginalis to fine-tune the translation efficiency (TE) of mRNAs remain largely unknown.

RESULTS

Using both computational and experimental approaches, this study investigated two key factors influencing TE in T. vaginalis: codon usage and mRNA secondary structure. Statistical dependence between TE and codon adaptation index (CAI) highlighted the impact of codon usage on mRNA translation in T. vaginalis. A genome-wide interrogation revealed that low structural complexity at the 5' end of mRNA followed closely by a highly structured downstream region correlates with TE variation in this organism. To validate these findings, a synthetic library of 15 synonymous iLOV genes was created, representing five mRNA folding profiles and three codon usage profiles. Fluorescence signals produced by the expression of these synonymous iLOV genes in T. vaginalis were consistent with and validated our in silico predictions.

CONCLUSIONS

This study demonstrates the role of codon usage bias and mRNA secondary structure in TE of T. vaginalis mRNAs, contributing to a better understanding of the factors that influence, and possibly regulate, gene expression in this human pathogen.

Operon-based approach for the inference of rRNA and tRNA evolutionary histories in bacteria

Background

In bacterial genomes, rRNA and tRNA genes are often organized into operons, i.e. segments of closely located genes that share a single promoter and are transcribed as a single unit. Analyzing how these genes and operons evolve can help us understand what are the most common evolutionary events affecting them and give us a better picture of ancestral codon usage and protein synthesis.

Results

We introduce BOPAL, a new approach for the inference of evolutionary histories of rRNA and tRNA genes in bacteria, which is based on the identification of orthologous operons. Since operons can move around in the genome but are rarely transformed (e.g. rarely broken into different parts), this approach allows for a better inference of orthologous genes in genomes that have been affected by many rearrangements, which in turn helps with the inference of more realistic evolutionary scenarios and ancestors.

Conclusions

From our comparisons of BOPAL with other gene order alignment programs using simulated data, we have found that BOPAL infers evolutionary events and ancestral gene orders more accurately than other methods based on alignments. An analysis of 12 Bacillus genomes also showed that BOPAL performs just as well as other programs at building ancestral histories in a minimal amount of events.

tRNA Genes Affect Chromosome Structure and Function via Local Effects

The genome is packaged and organized in an ordered, nonrandom manner, and specific chromatin segments contact nuclear substructures to mediate this organization. tRNA genes (tDNAs) are binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome. In this study, we investigate the roles of tDNAs in genomic organization and chromosome function by editing a chromosome so that it lacked any tDNAs. Surprisingly our analyses of this tDNA-less chromosome show that loss of tDNAs does not grossly affect chromatin architecture or chromosome tethering and mobility. However, loss of tDNAs affects local nucleosome positioning and the binding of SMC proteins at these loci. The absence of tDNAs also leads to changes in centromere clustering and a reduction in the frequency of long-range HML-HMR heterochromatin clustering with concomitant effects on gene silencing. We propose that the tDNAs primarily affect local chromatin structure, which results in effects on long-range chromosome architecture.

Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites

The major codon preference model suggests that codons read by tRNAs in high concentrations are preferentially utilized in highly expressed genes. However, the identity of the optimal codons differs between species although the forces driving such changes are poorly understood. We suggest that these questions can be tackled by placing codon usage studies in a phylogenetic framework and that bacterial genomes with extreme nucleotide composition biases provide informative model systems. Switches in the background substitution biases from GC to AT have occurred in Gardnerella vaginalis (GC = 32%), and from AT to GC in Lactobacillus delbrueckii (GC = 62%) and Lactobacillus fermentum (GC = 63%). We show that despite the large effects on codon usage patterns by these switches, all three species evolve under selection on synonymous sites. In G. vaginalis, the dramatic codon frequency changes coincide with shifts of optimal codons. In contrast, the optimal codons have not shifted in the two Lactobacillus genomes despite an increased fraction of GC-ending codons. We suggest that all three species are in different phases of an on-going shift of optimal codons, and attribute the difference to a stronger background substitution bias and/or longer time since the switch in G. vaginalis. We show that comparative and correlative methods for optimal codon identification yield conflicting results for genomes in flux and discuss possible reasons for the mispredictions. We conclude that switches in the direction of the background substitution biases can drive major shifts in codon preference patterns even under sustained selection on synonymous codon sites.

Novel Genomic and Evolutionary Perspective of Cyanobacterial tRNAs

Transfer RNA (tRNA) plays a central role in protein synthesis and acts as an adaptor molecule between an mRNA and an amino acid. A tRNA has an L-shaped clover leaf-like structure and contains an acceptor arm, D-arm, D-loop, anti-codon arm, anti-codon loop, variable loop, Ψ-arm and Ψ-loop. All of these arms and loops are important in protein translation. Here, we aimed to delineate the genomic architecture of these arms and loops in cyanobacterial tRNA. Studies from tRNA sequences from 61 cyanobacterial species showed that, except for few tRNAs (tRNA^Asn, tRNA^Leu, tRNA^Gln, and tRNA^Met), all contained a G nucleotide at the 1st position in the acceptor arm. tRNA^Leu and tRNA^Met did not contain any conserved nucleotides at the 1st position whereas tRNA^Asn and tRNA^Gln contained a conserved U¹ nucleotide. In several tRNA families, the variable region also contained conserved nucleotides. Except for tRNA^Met and tRNA^Glu, all other tRNAs contained a conserved A nucleotide at the 1st position in the D-loop. The Ψ-loop contained a conserved U¹-U²-C³-x-A⁵-x-U⁷ sequence, except for tRNA^Gly, tRNA^Ala, tRNA^Val, tRNA^Phe, tRNA^Thr, and tRNA^Gln in which the U⁷ nucleotide was not conserved. However, in tRNA^Asp, the U⁷ nucleotide was substituted with a C⁷ nucleotide. Additionally, tRNA^Arg, tRNA^Gly, and tRNA^Lys of cyanobacteria contained a group I intron within the anti-codon loop region. Maximum composite likelihood study on the transition/transversion of cyanobacterial tRNA revealed that the rate of transition was higher than the rate of transversion. An evolutionary tree was constructed to understand the evolution of cyanobacterial tRNA and analyses revealed that cyanobacterial tRNA may have evolved polyphyletically with high rate of gene loss.

A Comprehensive tRNA Genomic Survey Unravels the Evolutionary History of tRNA Arrays in Prokaryotes

Considering the importance of tRNAs in the translation machinery, scant attention has been paid to tRNA array units defined as genomic regions containing at least 20 tRNA genes with a minimal tRNA gene density of two tRNA genes per kilobase. Our analysis of Acidithiobacillus ferrivorans CF27 and Acidithiobacillus ferrooxidans ATCC 23270(T) genomes showed that both display a tRNA array unit with syntenic conservation which mainly contributed to the tRNA gene redundancy in these two organisms. Our investigations into the occurrence and distribution of tRNA array units revealed that 1) this tRNA organization is limited to few phyla and mainly found in Gram-positive bacteria; and 2) the presence of tRNA arrays favors the redundancy of tRNA genes, in particular those encoding the core tRNA isoacceptors. Finally, comparative array organization revealed that tRNA arrays were acquired through horizontal gene transfer (from Firmicutes or unknown donor), before being subjected to tRNA rearrangements, deletions, and duplications. In Bacilli, the most parsimonious evolutionary history involved two common ancestors and the acquisition of their arrays arose late in evolution, in the genera branches. Functional roles of the array units in organism lifestyle, selective genetic advantage and translation efficiency, as well as the evolutionary advantages of organisms harboring them were proposed. Our study offers new insight into the structural organization and evolution of tRNA arrays in prokaryotic organisms.

The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli

Background

The introduction of foreign DNA by Lateral Gene Transfer (LGT) can quickly and drastically alter genome composition. Problems can arise if the genes introduced by LGT use codons that are not suited to the host’s translational machinery. Here we investigate compensatory adaptation of E. coli in response to the introduction of large volumes of codons that are rarely used by the host genome.

Results

We analyze genome sequences from the E. coli/Shigella complex, and find that certain tRNA genes are present in multiple copies in two pathogenic Shigella and O157:H7 subgroups of E. coli. Furthermore, we show that the codons that correspond to these multi-copy number tRNA genes are enriched in the high copy number Selfish Genetic Elements (SGE’s) in Shigella and laterally introduced genes in O157:H7. We analyze the duplicate copies and find evidence for the selective retention of tRNA genes introduced by LGT in response to the changed codon content of the genome.

Conclusion

These data support a model where the relatively rapid influx of LGT genes and SGE’s introduces a large number of genes maladapted to the host’s translational machinery. Under these conditions, it becomes advantageous for the host to retain tRNA genes that are required for the incorporation of amino acids at these codons. Subsequently, the increased number of copies of these specific tRNA genes adjusts the cellular tRNA pool to the demands set by global shifts in codon usage.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0441-y) contains supplementary material, which is available to authorized users.

The link between independent acquisition of intracellular gamma-endosymbionts and concerted evolution in Tremblaya princeps

Many insect species establish mutualistic symbiosis with intracellular bacteria that complement their unbalanced diets. The betaproteobacterium "Candidatus Tremblaya" maintains an ancient symbiosis with mealybugs (Hemiptera: Pseudococcidae), which are classified in subfamilies Phenacoccinae and Pseudococcinae. Most Phenacoccinae mealybugs have "Candidatus Tremblaya phenacola" as their unique endosymbiont, while most Pseudococcinae mealybugs show a nested symbiosis (a bacterial symbiont placed inside another one) where every "Candidatus Tremblaya princeps" cell harbors several cells of a gammaproteobacterium. Genomic characterization of the endosymbiotic consortium from Planococcus citri, composed by "Ca. Tremblaya princeps" and "Candidatus Moranella endobia," unveiled several atypical features of the former's genome, including the concerted evolution of paralogous loci. Its comparison with the genome of "Ca. Tremblaya phenacola" PAVE, single endosymbiont of Phenacoccus avenae, suggests that the atypical reductive evolution of "Ca. Tremblaya princeps" could be linked to the acquisition of "Ca. Moranella endobia," which possess an almost complete set of genes encoding proteins involved in homologous recombination. In order to test this hypothesis, we performed comparative genomics between "Ca. Tremblaya phenacola" and "Ca. Tremblaya princeps" and searched for the co-occurrence of concerted evolution and homologous recombination genes in endosymbiotic consortia from four unexplored mealybug species, Dysmicoccus boninsis, Planococcus ficus, Pseudococcus longispinus, and Pseudococcus viburni. Our results support a link between concerted evolution and nested endosymbiosis.

The duplication-loss small phylogeny problem: from cherries to trees

The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest since it can help to reveal the genomic basis of phenotypes. The sequencing of whole genomes faciliates the study of gene families that vary in size through duplication and loss events, like transfer RNA. However, a high sequence similarity often does not allow one to distinguish between orthologs and paralogs. Previous methods have addressed this difficulty by taking into account flanking regions of members of a family independently. We go one step further by inferring the order of genes of (a set of) families for ancestral genomes by considering the order of these genes on sequenced genomes. We present a novel branch-and-cut algorithm to solve the two species small phylogeny problem in the evolutionary model of duplications and losses. On average, our implementation, DupLoCut, improves the running time of a recently proposed method in the experiments on six Vibrionaceae lineages by a factor of ∼200. Besides the mere improvement in running time, the efficiency of our approach allows us to extend our model from cherries of a species tree, that is, subtrees with two leaves, to the median of three species setting. Being able to determine the median of three species is of key importance to one of the most common approaches to ancestral reconstruction, and our experiments show that its repeated computation considerably reduces the number of duplications and losses along the tree both on simulated instances comprising 128 leaves and a set of Bacillus genomes. Furthermore, in our simulations we show that a reduction in cost goes hand in hand with an improvement of the predicted ancestral genomes. Finally, we prove that the small phylogeny problem in the duplication-loss model is NP-complete already for two species.

tRNA genes rapidly change in evolution to meet novel translational demands

Changes in expression patterns may occur when organisms are presented with new environmental challenges, for example following migration or genetic changes. To elucidate the mechanisms by which the translational machinery adapts to such changes, we perturbed the tRNA pool of Saccharomyces cerevisiae by tRNA gene deletion. We then evolved the deletion strain and observed that the genetic adaptation was recurrently based on a strategic mutation that changed the anticodon of other tRNA genes to match that of the deleted one. Strikingly, a systematic search in hundreds of genomes revealed that anticodon mutations occur throughout the tree of life. We further show that the evolution of the tRNA pool also depends on the need to properly couple translation to protein folding. Together, our observations shed light on the evolution of the tRNA pool, demonstrating that mutation in the anticodons of tRNA genes is a common adaptive mechanism when meeting new translational demands.

DOI:http://dx.doi.org/10.7554/eLife.01339.001

Genes contain the blueprints for the proteins that are essential for countless biological functions and processes, and the path that leads from a particular gene to the corresponding protein is long and complex. The genetic information stored in the DNA must first be transcribed to produce a messenger RNA molecule, which then has to be translated to produce a string of amino acids that fold to form a protein. The translation step is performed by a molecular machine called the ribosome, with transfer RNA molecules bringing the amino acids that are needed to make the protein.

The information in messenger RNA is stored as a series of letters, with groups of three letters called codons representing the different amino acids. Since there are four letters—A, C, G and U—it is possible to form 64 different codons. And since there are only 20 amino acids, two or more different codons can specify the same amino acid (for example, AGU and AGC both specify serine), and two or more different transfer RNA molecules can take this amino acid to the ribosome. Moreover, some codons are found more often than others in the messenger RNA molecules, so the genes that encode the related transfer RNA molecules are more common than the genes for other transfer RNA molecules.

Environmental pressures mean that organisms must adapt to survive, with some genes and proteins increasing in importance, and others becoming less important. Clearly the relative numbers of the different transfer RNA molecules will also need to change to reflect these evolutionary changes, but the details of how this happens were not understood.

Now Yona et al. have explored this issue by studying yeast cells that lack a gene for one of the less common transfer RNA molecules (corresponding to the codon AGG, which specifies the amino acid arginine). At first this mutation resulted in slower growth of the yeast cells, but after being allowed to evolve over 200 generations, the rate of growth matched that of a normal strain with all transfer RNA genes. Yona et al. found that the gene for a more common transfer RNA molecule, corresponding to the codon AGA, which also specifies arginine, had mutated to AGG. As a result, the mutated yeast was eventually able to produce proteins as quickly as wild type yeast. Moreover, further experiments showed that the levels of some transfer RNAs are kept deliberately low in order to slow down the production of proteins so as to ensure that the proteins assume their correct structure.

But does the way these cells evolved in the lab resemble what happened in nature? To address this question Yona et al. examined a database of transfer RNA sequences from more than 500 species, and found evidence for the same codon-based switching mechanism in many species across the tree of life.

DOI:http://dx.doi.org/10.7554/eLife.01339.002

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

Messenger RNA is a key component of an intricate regulatory network of its own. It accommodates numerous nucleotide signals that overlap protein coding sequences and are responsible for multiple levels of regulation and generation of biological complexity. A wealth of structural and regulatory information, which mRNA carries in addition to the encoded amino acid sequence, raises the question of how these signals and overlapping codes are delineated along non-synonymous and synonymous positions in protein coding regions, especially in eukaryotes. Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides. The RNA level selection is acting on synonymous sites in both prokaryotes and eukaryotes and is more common than previously thought. Selection pressure on the coding gene regions follows three-nucleotide periodic pattern of nucleotide base-pairing in mRNA, which is imposed by the genetic code. Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles. Recent experimental evidence and analysis of mRNA structure and interspecies conservation suggest that there is an evolutionary tradeoff between selective pressure acting at the RNA and protein levels. Here we provide a comprehensive overview of the studies that define the role of silent positions in regulating RNA structure and processing that exert downstream effects on proteins and their functions.

Evolution of optimal codon choices in the family Enterobacteriaceae

The Enterobacteriaceae are a large family of Proteobacteria that include many well-known prokaryotic genera, such as Escherichia, Yersinia and Salmonella. The main ideas of synonymous codon usage (CU) evolution and translational selection have been deeply influenced by studies with these bacterial groups. In this work we report the analysis of the CU pattern of completely sequenced bacterial genomes that belong to the Enterobacteriaceae. The effect of selection in translation acting at the levels of speed and accuracy, and phylogenetic trends within this group are described. Preferred (optimal) codons were identified. The evolutionary dynamics of these codons were studied and following a Bayesian approach these preferences were traced back to the common ancestor of the family. We found that there is some level of variation in selection among the analysed micro-organisms that is probably associated with lineage-specific trends. The codon bias was largely conserved across the evolutionary time of the family in highly expressed genes and protein conserved regions, suggesting a major role of negative selection. In this sense, the results support the idea that the extant CU bias is finely tuned over the ancestral well-conserved pool of tRNAs.

The adaptation of temperate bacteriophages to their host genomes

Rapid turnover of mobile elements drives the plasticity of bacterial genomes. Integrated bacteriophages (prophages) encode host-adaptive traits and represent a sizable fraction of bacterial chromosomes. We hypothesized that natural selection shapes prophage integration patterns relative to the host genome organization. We tested this idea by detecting and studying 500 prophages of 69 strains of Escherichia and Salmonella. Phage integrases often target not only conserved genes but also intergenic positions, suggesting purifying selection for integration sites. Furthermore, most integration hotspots are conserved between the two host genera. Integration sites seem also selected at the large chromosomal scale, as they are nonrandomly organized in terms of the origin-terminus axis and the macrodomain structure. The genes of lambdoid prophages are systematically co-oriented with the bacterial replication fork and display the host high frequency of polarized FtsK-orienting polar sequences motifs required for chromosome segregation. matS motifs are strongly avoided by prophages suggesting counter selection of motifs disrupting macrodomains. These results show how natural selection for seamless integration of prophages in the chromosome shapes the evolution of the bacterium and the phage. First, integration sites are highly conserved for many millions of years favoring lysogeny over the lytic cycle for temperate phages. Second, the global distribution of prophages is intimately associated with the chromosome structure and the patterns of gene expression. Third, the phage endures selection for DNA motifs that pertain exclusively to the biology of the prophage in the bacterial chromosome. Understanding prophage genetic adaptation sheds new lights on the coexistence of horizontal transfer and organized bacterial genomes.

A role for tRNA modifications in genome structure and codon usage

Transfer RNA (tRNA) gene content is a differentiating feature of genomes that contributes to the efficiency of the translational apparatus, but the principles shaping tRNA gene copy number and codon composition are poorly understood. Here, we report that the emergence of two specific tRNA modifications shaped the structure and composition of all extant genomes. Through the analysis of more than 500 genomes, we identify two kingdom-specific tRNA modifications as major contributors that separated archaeal, bacterial, and eukaryal genomes in terms of their tRNA gene composition. We show that, contrary to prior observations, genomic codon usage and tRNA gene frequencies correlate in all kingdoms if these two modifications are taken into account and that presence or absence of these modifications explains patterns of gene expression observed in previous studies. Finally, we experimentally demonstrate that human gene expression levels correlate well with genomic codon composition if these identified modifications are considered.

Human tRNA genes function as chromatin insulators

Insulators help separate active chromatin domains from silenced ones. In yeast, gene promoters act as insulators to block the spread of Sir and HP1 mediated silencing while in metazoans most insulators are multipartite autonomous entities. tDNAs are repetitive sequences dispersed throughout the human genome and we now show that some of these tDNAs can function as insulators in human cells. Using computational methods, we identified putative human tDNA insulators. Using silencer blocking, transgene protection and repressor blocking assays we show that some of these tDNA-containing fragments can function as barrier insulators in human cells. We find that these elements also have the ability to block enhancers from activating RNA pol II transcribed promoters. Characterization of a putative tDNA insulator in human cells reveals that the site possesses chromatin signatures similar to those observed at other better-characterized eukaryotic insulators. Enhanced 4C analysis demonstrates that the tDNA insulator makes long-range chromatin contacts with other tDNAs and ETC sites but not with intervening or flanking RNA pol II transcribed genes.

Quantification of codon selection for comparative bacterial genomics

Background

Statistics measuring codon selection seek to compare genes by their sensitivity to selection for translational efficiency, but existing statistics lack a model for testing the significance of differences between genes. Here, we introduce a new statistic for measuring codon selection, the Adaptive Codon Enrichment (ACE).

Results

This statistic represents codon usage bias in terms of a probabilistic distribution, quantifying the extent that preferred codons are over-represented in the gene of interest relative to the mean and variance that would result from stochastic sampling of codons. Expected codon frequencies are derived from the observed codon usage frequencies of a broad set of genes, such that they are likely to reflect nonselective, genome wide influences on codon usage (e.g. mutational biases). The relative adaptiveness of synonymous codons is deduced from the frequency of codon usage in a pre-selected set of genes relative to the expected frequency. The ACE can predict both transcript abundance during rapid growth and the rate of synonymous substitutions, with accuracy comparable to or greater than existing metrics. We further examine how the composition of reference gene sets affects the accuracy of the statistic, and suggest methods for selecting appropriate reference sets for any genome, including bacteriophages. Finally, we demonstrate that the ACE may naturally be extended to quantify the genome-wide influence of codon selection in a manner that is sensitive to a large fraction of codons in the genome. This reveals substantial variation among genomes, correlated with the tRNA gene number, even among groups of bacteria where previously proposed whole-genome measures show little variation.

Conclusions

The statistical framework of the ACE allows rigorous comparison of the level of codon selection acting on genes, both within a genome and between genomes.

The evolution of tRNA genes in Drosophila

The structure and function of transfer RNA (tRNA) genes have been extensively studied for several decades, yet the general mechanisms controlling tRNA gene family evolution remain unclear, primarily because previous phylogenetics-based methods fail to distinguish between paralogs and orthologs that are highly similar in sequence. We have developed a system for identifying orthologs of tRNAs using flanking sequences to identify regions of conserved synteny and used it to annotate sets of orthologous tRNA genes across the 12 sequenced species of Drosophila. These data have allowed us to place the gains and losses of individual tRNA genes on each branch of the Drosophila tree and estimate rates of tRNA gene turnover. Our results show extensive rearrangement of the Drosophila tRNA gene complement over the last 60 My. We estimate a combined average rate of 2.18 ± 0.10 tRNA gene gains and losses per million years across the Drosophila lineage. We have identified 192 tRNAs that are ancestral to the genus, of which 157 are “core” tRNAs conserved in at least 11 of 12 extant species. We provide evidence that the core set of tRNA genes encode a nearly complete set of anticodons and have different properties from other “peripheral” tRNA genes, such as preferential location outside large tRNA clusters and higher sequence conservation. We also demonstrate that tRNA isoacceptor and alloacceptor changes by anticodon shifts have occurred several times in Drosophila, annotating 16 such events in functional tRNAs during the evolution of the genus.

Genomic organization of eukaryotic tRNAs

BACKGROUND

Surprisingly little is known about the organization and distribution of tRNA genes and tRNA-related sequences on a genome-wide scale. While tRNA gene complements are usually reported in passing as part of genome annotation efforts, and peculiar features such as the tandem arrangements of tRNA gene in Entamoeba histolytica have been described in some detail, systematic comparative studies are rare and mostly restricted to bacteria. We therefore set out to survey the genomic arrangement of tRNA genes and pseudogenes in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities.

RESULTS

In line with previous reports, we find that tRNA complements evolve rapidly and tRNA gene and pseudogene locations are subject to rapid turnover. At phylum level, the distributions of the number of tRNA genes and pseudogenes numbers are very broad, with standard deviations on the order of the mean. Even among closely related species we observe dramatic changes in local organization. For instance, 65% and 87% of the tRNA genes and pseudogenes are located in genomic clusters in zebrafish and stickleback, resp., while such arrangements are relatively rare in the other three sequenced teleost fish genomes. Among basal metazoa, Trichoplax adherens has hardly any duplicated tRNA gene, while the sea anemone Nematostella vectensis boasts more than 17000 tRNA genes and pseudogenes. Dramatic variations are observed even within the eutherian mammals. Higher primates, for instance, have 616 +/- 120 tRNA genes and pseudogenes of which 17% to 36% are arranged in clusters, while the genome of the bushbaby Otolemur garnetti has 45225 tRNA genes and pseudogenes of which only 5.6% appear in clusters. In contrast, the distribution is surprisingly uniform across plant genomes. Consistent with this variability, syntenic conservation of tRNA genes and pseudogenes is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. Despite this large variation in abundance in Eukarya we observe a significant correlation between the number of tRNA genes, tRNA pseudogenes, and genome size.

CONCLUSIONS

The genomic organization of tRNA genes and pseudogenes shows complex lineage-specific patterns characterized by an extensive variability that is in striking contrast to the extreme levels of sequence-conservation of the tRNAs themselves. The comprehensive analysis of the genomic organization of tRNA genes and pseudogenes in Eukarya provides a basis for further studies into the interplay of tRNA gene arrangements and genome organization in general.

On finding poorly translated codons based on their usage frequency

Long stretches of “rare” codons are known to severely inhibit the efficiency of translation. Understanding the distribution of such rare codons is of critical importance in improving the efficiency of heterologous gene expression systems. Accurate estimates of codon usage take the abundance of each protein into consideration. In this paper, we analyze the correlation between approximate measures of codon usage and the availability of tRNA at various growth rates in E coli. We show that the computationally derived estimates of tRNA isoacceptor concentration enable the finding of poorly translated codons.

Transcription independent insulation at TFIIIC-dependent insulators

Chromatin insulators separate active from repressed chromatin domains. In yeast the RNA pol III transcription machinery bound to tRNA genes function with histone acetylases and chromatin remodelers to restrict the spread of heterochromatin. Our results collectively demonstrate that binding of TFIIIC is necessary for insulation but binding of TFIIIB along with TFIIIC likely improves the probability of complex formation at an insulator. Insulation by this transcription factor occurs in the absence of RNA polymerase III or polymerase II but requires specific histone acetylases and chromatin remodelers. This analysis identifies a minimal set of factors required for insulation.

GO4genome: a prokaryotic phylogeny based on genome organization

Determining the phylogeny of closely related prokaryotes may fail in an analysis of rRNA or a small set of sequences. Whole-genome phylogeny utilizes the maximally available sample space. For a precise determination of genome similarity, two aspects have to be considered when developing an algorithm of whole-genome phylogeny: (1) gene order conservation is a more precise signal than gene content; and (2) when using sequence similarity, failures in identifying orthologues or the in situ replacement of genes via horizontal gene transfer may give misleading results. GO4genome is a new paradigm, which is based on a detailed analysis of gene function and the location of the respective genes. For characterization of genes, the algorithm uses gene ontology enabling a comparison of function independent of evolutionary relationship. After the identification of locally optimal series of gene functions, their length distribution is utilized to compute a phylogenetic distance. The outcome is a classification of genomes based on metabolic capabilities and their organization. Thus, the impact of effects on genome organization that are not covered by methods of molecular phylogeny can be studied. Genomes of strains belonging to Escherichia coli, Shigella, Streptococcus, Methanosarcina, and Yersinia were analyzed. Differences from the findings of classical methods are discussed.

Analysis of the complement and molecular evolution of tRNA genes in cow

Background

Detailed information regarding the number and organization of transfer RNA (tRNA) genes at the genome level is becoming readily available with the increase of DNA sequencing of whole genomes. However the identification of functional tRNA genes is challenging for species that have large numbers of repetitive elements containing tRNA derived sequences, such as Bos taurus. Reliable identification and annotation of entire sets of tRNA genes allows the evolution of tRNA genes to be understood on a genomic scale.

Results

In this study, we explored the B. taurus genome using bioinformatics and comparative genomics approaches to catalogue and analyze cow tRNA genes. The initial analysis of the cow genome using tRNAscan-SE identified 31,868 putative tRNA genes and 189,183 pseudogenes, where 28,830 of the 31,868 predicted tRNA genes were classified as repetitive elements by the RepeatMasker program. We then used comparative genomics to further discriminate between functional tRNA genes and tRNA-derived sequences for the remaining set of 3,038 putative tRNA genes. For our analysis, we used the human, chimpanzee, mouse, rat, horse, dog, chicken and fugu genomes to predict that the number of active tRNA genes in cow lies in the vicinity of 439. Of this set, 150 tRNA genes were 100% identical in their sequences across all nine vertebrate genomes studied. Using clustering analyses, we identified a new tRNA-Gly^CCC subfamily present in all analyzed mammalian genomes. We suggest that this subfamily originated from an ancestral tRNA-Gly^GCC gene via a point mutation prior to the radiation of the mammalian lineages. Lastly, in a separate analysis we created phylogenetic profiles for each putative cow tRNA gene using a representative set of genomes to gain an overview of common evolutionary histories of tRNA genes.

Conclusion

The use of a combination of bioinformatics and comparative genomics approaches has allowed the confident identification of a set of cow tRNA genes that will facilitate further studies in understanding the molecular evolution of cow tRNA genes.

Regulation dynamics of WGD genes during yeast metabolic oscillation

Saccharomyces cerevisiae and its close relatives are characterized by their propensity to ferment even in the presence of oxygen. It was hypothesized that whole-genome duplication (WGD) led to the development of this efficient fermentative lifestyle (WGD-fermentation hypothesis, Piskur 2001. In this study, we found that a significantly higher proportion of WGD genes than non-WGD genes are dynamically regulated during metabolic oscillation in response to oxygen change. The same data set also shows that the WGD genes, as compared with the smaller scale duplicate genes, are enriched with pairs where both copies have cyclic expression during the metabolic oscillation (either with the same or different phases). These results provide new evidences for the WGD-fermentation hypothesis and new insights into the relationship between the genome duplication and the evolution of new lifestyles in eukaryotic organisms.

Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia

Can dosage compensation completely explain gene retention after whole-genome duplication?

The high retention of duplicate genes in the genome of Paramecium tetraurelia has led to the hypothesis that most of the retained genes have persisted because of constraints due to gene dosage. This and other possible mechanisms are discussed in the light of expectations from population genetics and systems biology.

Diversity of tRNA genes in eukaryotes

We compare the diversity of chromosomal-encoded transfer RNA (tRNA) genes from 11 eukaryotes as identified by tRNAScan-SE of their respective genomes. They include the budding and fission yeast, worm, fruit fly, fugu, chicken, dog, rat, mouse, chimp and human. The number of tRNA genes are between 170 and 570 and the number of tRNA isoacceptors range from 41 to 55. Unexpectedly, the number of tRNA genes having the same anticodon but different sequences elsewhere in the tRNA body (defined here as tRNA isodecoder genes) varies significantly (10-246). tRNA isodecoder genes allow up to 274 different tRNA species to be produced from 446 genes in humans, but only up to 51 from 275 genes in the budding yeast. The fraction of tRNA isodecoder genes among all tRNA genes increases across the phylogenetic spectrum. A large number of sequence differences in human tRNA isodecoder genes occurs in the internal promoter regions for RNA polymerase III. We also describe a systematic, ligation-based method to detect and quantify tRNA isodecoder molecules in human samples, and show differential expression of three tRNA isodecoders in six human tissues. The large number of tRNA isodecoder genes in eukaryotes suggests that tRNA function may be more diverse than previously appreciated.