The effect of expression levels on codon usage in Plasmodium falciparum

Amino acid usage and protein expression levels in the flatworm Schistosoma mansoni

Schistosoma mansoni is a parasitic flatworm that causes a human disease called schistosomiasis, or bilharzia. At the genomic level, S. mansoni is AT-rich, but has some compositional heterogeneity. Indeed, some regions of its genome are GC-rich, mainly in the regions located near the extreme ends of the chromosomes. Recently, we showed that, despite the strong bias towards A/T ending codons, highly expressed genes tend to use GC-rich codons. Here, we address the following question: are highly expressed sequences biased in their amino acid frequencies? Our analyses show that these sequences in S. mansoni, as in species ranging from bacteria to human, are strongly biased in nucleotide composition. Highly expressed genes tend to use GC-rich codons (in the first and second codon positions), which code the energetically cheapest amino acids. Therefore, we conclude that amino acid usage, at least in highly expressed genes, is strongly shaped by natural selection to avoid energetically expensive residues. Whether this is an adaptation to the parasitic way of life of S. mansoni, is unclear since the same pattern occurs in free-living species.

Codon usage in the flatworm Schistosoma mansoni is shaped by the mutational bias towards A+T and translational selection, which increases GC-ending codons in highly expressed genes

Schistosoma mansoni is a trematode flatworm that parasitizes humans and produces a disease called bilharzia. At the genomic level, it is characterized by a low genomic GC content and an "isochore-like" structure, where GC-richest regions, mainly placed at the extremes of the chromosomes, are interspersed with low GC-regions. Furthermore, the GC-richest regions are at the same time the gene-richest, and where the most heavily expressed genes are placed. Taking these features into account, we decided to reanalyze the codon usage of this flatworm. Our results show that a) when all genes are considered together, the strong mutational bias towards A + T leads to a predominance of A/T-ending codons, b) a multivariate analysis discriminates between highly and lowly expressed genes, c) the sequences expressed at highest levels display a significant increase in G/C-ending codons, d) when comparing the molecular distances with a closely related species the synonymous distance in highly expressed genes is significantly lower than in lowly expressed sequences. Therefore, we conclude that despite previous results, which were performed with a small sample of genes, codon usage in S. mansoni is the result of two forces that operate in opposite directions: while mutational bias leads to a predominance of A/T codons, translational selection, working at the level of speed, increment G/C ending triplets.

Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.

Analysis of synonymous codon usage of transcriptome database in Rheum palmatum

Background

Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome.

Methods

In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS.

Results

The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.

Protection induced by malaria virus-like particles containing codon-optimized AMA-1 of Plasmodium berghei

Background

Despite the extensive endeavours, developing an effective malaria vaccine remains as a great challenge. Apical membrane antigen 1 (AMA-1) located on the merozoite surface of parasites belonging to the genus Plasmodium is involved in red blood cell invasion.

Methods

Influenza virus-like particle (VLP) vaccines containing codon-optimized or native (non-codon optimized) AMA-1 from Plasmodium berghei were generated. VLP-induced protective immunity was evaluated in a mouse model.

Results

Mice immunized with VLP vaccine containing the codon-optimized AMA-1 elicited higher levels of P. berghei-specific IgG and IgG2a antibody responses compared to VLPs containing non-codon optimized AMA-1 before and after challenge infection. Codon-optimized AMA-1 VLP vaccination induced higher levels of CD4⁺ T cells, CD8⁺ T cells, B cells, and germinal centre cell responses compared to non-codon optimized AMA-1 VLPs. Importantly, the codon-optimized AMA-1 VLP vaccination showed lower body weight loss, longer survival and a significant decrease in parasitaemia compared to non-codon optimized VLP vaccination.

Conclusion

Overall, VLP vaccine expressing codon-optimized AMA-1 induced better protective efficacy than VLPs expressing the non-codon optimized AMA-1. Current findings highlight the importance of codon-optimization for vaccine use and its potential involvement in future malaria vaccine design strategies.

Compositional properties and codon usage pattern of mitochondrial ATP gene in different classes of Arthropoda

Codon usage bias (CUB) is defined as the usage of synonymous codons unequally for an amino acid in a gene transcript. It is influenced by both mutation pressure and natural selection and is a species-specific property. In our current study, we used bioinformatic methods to investigate the coding sequences of mitochondrial adenosine triphosphate gene (MT-ATP) in different classes of arthropoda to know the codon usage pattern of the gene as no work was described earlier. The analysis of compositional properties suggested that the gene is AT rich. The effective number of codons revealed the CUB of both ATP6 and ATP8 gene was moderate. Heat map showed that the codons ending with AT were negatively associated with GC3 while the codons ending with GC were positively associated with GC3 in all the classes of arthropoda. Correspondence study revealed that the pattern of codon usage of ATP6 and ATP8 genes differed across classes. Neutrality plot suggested the codon usage bias of these two genes in phylum arthropoda was influenced by both mutation pressure and natural selection.

Forces acting on codon bias in malaria parasites

Malaria parasite genomes have a range of codon biases, with Plasmodium falciparum one of the most AT-biased genomes known. We examined the make up of synonymous coding sites and stop codons in the core genomes of representative malaria parasites, showing first that local DNA context influences codon bias similarly across P. falciparum, P. vivax and P. berghei, with suppression of CpG dinucleotides and enhancement of CpC dinucleotides, both within and aross codons. Intense asexual phase gene expression in P. falciparum and P. berghei is associated with increased A3:G3 bias but reduced T3:C3 bias at 2-fold sites, consistent with adaptation of codons to tRNA pools and avoidance of wobble tRNA interactions that potentially slow down translation. In highly expressed genes, the A3:G3 ratio can exceed 30-fold while the T3:C3 ratio can be less than 1, according to the encoded amino acid and subsequent base. Lysine codons (AAA/G) show distinctive behaviour with substantially reduced A3:G3 bias in highly expressed genes, perhaps because of selection against frameshifting when the AAA codon is followed by another adenine. Intense expression is also associated with a strong bias towards TAA stop codons (found in 94% and 89% of highly expressed P. falciparum and P. berghei genes respectively) and a proportional rise in the TAAA stop ‘tetranucleotide’. The presence of these expression-linked effects in the relatively AT-rich malaria parasite species adds weight to the suggestion that AT-richness in the Plasmodium genus might be a fitness adaptation. Potential explanations for the relative lack of codon bias in P. vivax include the distinct features of its lifecycle and its effective population size over evolutionary time.

New insights into the factors affecting synonymous codon usage in human infecting Plasmodium species

Codon usage bias is due to the non-random usage of synonymous codons for coding amino acids. The synonymous sites are under weak selection, and codon usage bias is maintained by the equilibrium in mutational bias, genetic drift and selection pressure. The differential codon usage choices are also relevant to human infecting Plasmodium species. Recently, P. knowlesi switches its natural host, long-tailed macaques, and starts infecting humans. This review focuses on the comparative analysis of codon usage choices among human infecting P. falciparum and P. vivax along with P. knowlesi species taking their coding sequence data. The variation in GC content, amino acid frequencies, effective number of codons and other factors plays a crucial role in determining synonymous codon choices. Within species codon choices are more similar for P. vivax and P. knowlesi in comparison with P. falciparum species. This study suggests that synonymous codon choice modulates the gene expression level, mRNA stability, ribosome speed, protein folding, translation efficiency and its accuracy in Plasmodium species, and provides a valuable information regarding the codon usage pattern to facilitate gene cloning as well as expression and transfection studies for malaria causing species.

Factors influencing codon usage of mitochondrial ND1 gene in pisces, aves and mammals

Animal mitochondrial genome harbours 13 protein coding genes which regulate the process of respiration. The mitochondrial NADH dehydrogenase 1 (MT-ND1) gene, one of the 13 protein-coding genes, encodes the NADH dehydrogenase 1 enzyme of the respiratory chain. Analysis of codon usage bias (CUB) acquires importance for better understanding of the molecular biology, new gene discovery, design of transgenes and gene evolution. The MT-ND1 gene seems to be a good candidate for analyzing codon usage pattern, since no work has yet been reported. Moreover, it is still not clear which factors significantly influence the codon usage pattern. In the present study, comparative analysis of codon usage pattern, expression level and influencing factors for MT-ND1 gene from 100 different species each of pisces, aves and mammals were used for CUB analysis. Our result suggests that the gene is AT rich in pisces, aves and mammals and most of the nucleotides significantly differ among them as revealed from t-test. CUB was not remarkable as reflected by high value of effective number of codons and it also significantly differs among pisces, aves and mammals. Although we found that CUB is mainly influenced by natural selection and mutation pressure for MT-ND1 gene as suggested by correlation and correspondence analysis but neutrality plot further revealed that natural selection played a major role and mutation pressure played a minor role in codon usage pattern. Additionally, t-test analysis showed that the MT-ND1 gene has a wide significant discrepancy in codon choices in pisces, aves and mammals. This study has contributed to boost our understanding about the mechanism of distribution of the codons and the factors that may influence the evolution of the MT-ND1 gene.

Frequent GU wobble pairings reduce translation efficiency in Plasmodium falciparum

Plasmodium falciparum genome has 81% A+T content. This nucleotide bias leads to extreme codon usage bias and culminates in frequent insertion of asparagine homorepeats in the proteome. Using recodonized GFP sequences, we show that codons decoded via G:U wobble pairing are suboptimal codons that are negatively associated to protein translation efficiency. Despite this, one third of all codons in the genome are GU wobble codons, suggesting that codon usage in P. falciparum has not been driven to maximize translation efficiency, but may have evolved as translational regulatory mechanism. Particularly, asparagine homorepeats are generally encoded by locally clustered GU wobble AAT codons, we demonstrated that this GU wobble-rich codon context is the determining factor that causes reduction of protein level. Moreover, insertion of clustered AAT codons also causes destabilization of the transcripts. Interestingly, more frequent asparagine homorepeats insertion is seen in single-exon genes, suggesting transcripts of these genes may have been programmed for rapid mRNA decay to compensate for the inefficiency of mRNA surveillance regulation on intronless genes. To our knowledge, this is the first study that addresses P. falciparum codon usage in vitro and provides new insights on translational regulation and genome evolution of this parasite.

Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) and its relation to evolution

BACKGROUND

Analysis of codon usage bias is an extremely versatile method using in furthering understanding of the genetic and evolutionary paths of species. Codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus (NPV) has remained largely unexplored at present. Hence, the codon usage bias of NPV envelope glycoprotein was analyzed here to reveal the genetic and evolutionary relationships between different viral species in baculovirus genus.

RESULTS

A total of 9236 codons from 18 different species of NPV of the baculovirus genera were used to perform this analysis. Glycoprotein of NPV exhibits weaker codon usage bias. Neutrality plot analysis and correlation analysis of effective number of codons (ENC) values indicate that natural selection is the main factor influencing codon usage bias, and that the impact of mutation pressure is relatively smaller. Another cluster analysis shows that the kinship or evolutionary relationships of these viral species can be divided into two broad categories despite all of these 18 species are from the same baculovirus genus.

CONCLUSIONS

There are many elements that can affect codon bias, such as the composition of amino acids, mutation pressure, natural selection, gene expression level, and etc. In the meantime, cluster analysis also illustrates that codon usage bias of virus envelope glycoprotein can serve as an effective means of evolutionary classification in baculovirus genus.

Expression levels and codon usage patterns in nuclear genes of the filarial nematode Wucheraria bancrofti and the blood fluke Schistosoma haematobium

Synonymous codons are used with different frequencies, a phenomenon known as codon bias, which exists in many genomes and is mainly resolute by mutation and selection. To elucidate the genetic characteristics and evolutionary relationship of Wucheraria bancrofti and Schistosoma haematobium we examined the pattern of synonymous codon usage in nuclear genes of both the species. The mean overall GC contents of W. bancrofti and S. haematobium were 43.41 and 36.37%, respectively, which suggests that genes in both the species were AT rich. The value of the High Effective Number of Codons in both species suggests that codon usage bias was weak. Both species had a wide range of P3 distribution in the neutrality plot, with a significant correlation between P12 and P3. The codons were closer to the axes in correspondence analysis, suggesting that mutation pressure influenced the codon usage pattern in these species. We have identified the more frequently used codons in these species, most codons ending with an A or T. The nucleotides A/T and C/G were not proportionally used at the third position of codons, which reveals that natural selection might influence the codon usage patterns. The regression equation of P12 on P3 suggests that natural selection might have played a major role, while mutational pressure played a minor role in codon usage pattern in both species. These results form the basis of exploring the evolutionary mechanisms and the heterologous expression of medically important proteins of W. bancrofti and S. haematobium.

Genome Sequence and Analysis of Peptoclostridium difficile Strain ZJCDC-S82

Peptoclostridium difficile (Clostridium difficile) is the major pathogen associated with infectious diarrhea in humans. Concomitant with the increased incidence of C. difficile infection worldwide, there is an increasing concern regarding this infection type. This study reports a draft assembly and detailed sequence analysis of C. difficile strain ZJCDC-S82. The de novo assembled genome was 4.19 Mb in size, which includes 4,013 protein-coding genes, 41 rRNA genes, and 84 tRNA genes. Along with the nuclear genome, we also assembled sequencing information for a single plasmid consisting of 11,930 nucleotides. Comparative genomic analysis of C. difficile ZJCDC-S82 and two other previously published strains, such as M120 and CD630, showed extensive similarity. Phylogenetic analysis revealed that genetic diversity among C. difficile strains was not influenced by geographic location. Evolutionary analysis suggested that four genes encoding surface proteins exhibited positive selection in C. difficile ZJCDC-S82. Codon usage analysis indicated that C. difficile ZJCDC-S82 had high codon usage bias toward A/U-ended codons. Furthermore, codon usage patterns in C. difficile ZJCDC-S82 were predominantly affected by mutation pressure. Our results provide detailed information pertaining to the C. difficile genome associated with a strain from mainland China. This analysis will facilitate the understanding of genomic diversity and evolution of C. difficile strains in this region.

Codon bias and gene expression of mitochondrial ND2 gene in chordates

Background: Mitochondrial ND gene, which encodes NADH dehydrogenase, is the first enzyme of the mitochondrial electron transport chain. Leigh syndrome, a neurodegenerative disease caused by mutation in the ND2 gene (T4681C), is associated with bilateral symmetric lesions in basal ganglia and subcortical brain regions. Therefore, it is of interest to analyze mitochondrial DNA to glean information for evolutionary relationship. This study highlights on the analysis of compositional dynamics and selection pressure in shaping the codon usage patterns in the coding sequence of MT-ND2 gene across pisces, aves and mammals by using bioinformatics tools like effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU) etc. Results: We observed a low codon usage bias as reflected by high ENC values in MT-ND2 gene among pisces, aves and mammals. The most frequently used codons were ending with A/C at the 3^rd position of codon and the gene was AT rich in all the three classes. The codons TCA, CTA, CGA and TGA were over represented in all three classes. The F1 correspondence showed significant positive correlation with G, T3 and CAI while the F2 axis showed significant negative correlation with A and T but significant positive correlation with G, C, G3, C3, ENC, GC, GC1, GC2 and GC3. Conclusions: The codon usage bias in MTND2 gene is not associated with expression level. Mutation pressure and natural selection affect the codon usage pattern in MT-ND 2 gene.

Non-uniqueness of factors constraint on the codon usage in Bombyx mori

Background

The analysis of codon usage is a good way to understand the genetic and evolutionary characteristics of an organism. However, there are only a few reports related with the codon usage of the domesticated silkworm, Bombyx mori (B. mori). Hence, the codon usage of B. mori was analyzed here to reveal the constraint factors and it could be helpful to improve the bioreactor based on B. mori.

Results

A total of 1,097 annotated mRNA sequences from B. mori were analyzed, revealing there is only a weak codon bias. It also shows that the gene expression level is related to the GC content, and the amino acids with higher general average hydropathicity (GRAVY) and aromaticity (Aromo). And the genes on the primary axis are strongly positively correlated with the GC content, and GC3s. Meanwhile, the effective number of codons (ENc) is strongly correlated with codon adaptation index (CAI), gene length, and Aromo values. However, the ENc values are correlated with the second axis, which indicates that the codon usage in B. mori is affected by not only mutation pressure and natural selection, but also nucleotide composition and the gene expression level. It is also associated with Aromo values, and gene length. Additionally, B. mori has a greater relative discrepancy in codon preferences with Drosophila melanogaster (D. melanogaster) or Saccharomyces cerevisiae (S. cerevisiae) than with Arabidopsis thaliana (A. thaliana), Escherichia coli (E. coli), or Caenorhabditis elegans (C. elegans).

Conclusions

The codon usage bias in B. mori is relatively weak, and many influence factors are found here, such as nucleotide composition, mutation pressure, natural selection, and expression level. Additionally, it is also associated with Aromo values, and gene length. Among them, natural selection might play a major role. Moreover, the “optimal codons” of B. mori are all encoded by G and C, which provides useful information for enhancing the gene expression in B. mori through codon optimization.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1596-z) contains supplementary material, which is available to authorized users.

The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional constraints on proteins.

In vitro resistance selections for Plasmodium falciparum dihydroorotate dehydrogenase inhibitors give mutants with multiple point mutations in the drug-binding site and altered growth

Malaria is a preventable and treatable disease; yet half of the world's population lives at risk of infection, and an estimated 660,000 people die of malaria-related causes every year. Rising drug resistance threatens to make malaria untreatable, necessitating both the discovery of new antimalarial agents and the development of strategies to identify and suppress the emergence and spread of drug resistance. We focused on in-development dihydroorotate dehydrogenase (DHODH) inhibitors. Characterizing resistance pathways for antimalarial agents not yet in clinical use will increase our understanding of the potential for resistance. We identified resistance mechanisms of Plasmodium falciparum (Pf) DHODH inhibitors via in vitro resistance selections. We found 11 point mutations in the PfDHODH target. Target gene amplification and unknown mechanisms also contributed to resistance, albeit to a lesser extent. These mutant parasites were often hypersensitive to other PfDHODH inhibitors, which immediately suggested a novel combination therapy approach to preventing resistance. Indeed, a combination of wild-type and mutant-type selective inhibitors led to resistance far less often than either drug alone. The effects of point mutations in PfDHODH were corroborated with purified recombinant wild-type and mutant-type PfDHODH proteins, which showed the same trends in drug response as the cognate cell lines. Comparative growth assays demonstrated that two mutant parasites grew less robustly than their wild-type parent, and the purified protein of those mutants showed a decrease in catalytic efficiency, thereby suggesting a reason for the diminished growth rate. Co-crystallography of PfDHODH with three inhibitors suggested that hydrophobic interactions are important for drug binding and selectivity.

Metabolic and translational efficiency in microbial organisms

Metabolic efficiency, as a selective force shaping proteomes, has been shown to exist in Escherichia coli and Bacillus subtilis and in a small number of organisms with photoautotrophic and thermophilic lifestyles. Earlier attempts at larger-scale analyses have utilized proxies (such as molecular weight) for biosynthetic cost, and did not consider lifestyle or auxotrophy. This study extends the analysis to all currently sequenced microbial organisms that are amenable to these analyses while utilizing lifestyle specific amino acid biosynthesis pathways (where possible) to determine protein production costs and compensating for auxotrophy. The tendency for highly expressed proteins (with adherence to codon usage bias as a proxy for expressivity) to utilize less biosynthetically expensive amino acids is taken as evidence of cost selection. A comprehensive analysis of sequenced genomes to identify those that exhibit strong translational efficiency bias (389 out of 1,700 sequenced organisms) is also presented.

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift

The genetic code is redundant with most amino acids using multiple codons. In many organisms, codon usage is biased toward particular codons. Understanding the adaptive and nonadaptive forces driving the evolution of codon usage bias (CUB) has been an area of intense focus and debate in the fields of molecular and evolutionary biology. However, their relative importance in shaping genomic patterns of CUB remains unsolved. Using a nested model of protein translation and population genetics, we show that observed gene level variation of CUB in Saccharomyces cerevisiae can be explained almost entirely by selection for efficient ribosomal usage, genetic drift, and biased mutation. The correlation between observed codon counts within individual genes and our model predictions is 0.96. Although a variety of factors shape patterns of CUB at the level of individual sites within genes, our results suggest that selection for efficient ribosome usage is a central force in shaping codon usage at the genomic scale. In addition, our model allows direct estimation of codon-specific mutation rates and elongation times and can be readily applied to any organism with high-throughput expression datasets. More generally, we have developed a natural framework for integrating models of molecular processes to population genetics models to quantitatively estimate parameters underlying fundamental biological processes, such a protein translation.

Selected codon usage bias in members of the class Mollicutes

Mollicutes are parasitic microorganisms mainly characterized by small cell sizes, reduced genomes and great A and T mutational bias. We analyzed the codon usage patterns of the completely sequenced genomes of bacteria that belong to this class. We found that for many organisms not only mutational bias but also selection has a major effect on codon usage. Through a comparative perspective and based on three widely used criteria we were able to classify Mollicutes according to the effect of selection on codon usage. We found conserved optimal codons in many species and study the tRNA gene pool in each genome. Previous results are reinforced by the fact that, when selection is operative, the putative optimal codons found match the respective cognate tRNA. Finally, we trace selection effect backwards to the common ancestor of the class and estimate the phylogenetic inertia associated with this character. We discuss the possible scenarios that explain the observed evolutionary patterns.

Sequences conserved by selection across mouse and human malaria species

Background

Little is known, either experimentally or computationally, about the genomic sequence features that regulate malaria genes. A sequence conservation analysis of the malaria species P. falciparum, P. berghei, P. yoelii, and P. chabaudi could significantly advance knowledge of malaria gene regulation.

Results

We computationally identify intergenic sequences conserved beyond neutral expectations, using a conservation algorithm that accounts for the strong compositional biases in malaria genomes. We first quantify the composition-specific divergence at silent positions in coding sequence. Using this as a background, we examine gene 5' regions, identifying 610 blocks conserved far beyond neutral expectations across the three mouse malariae, and 81 blocks conserved as strongly across all four species (p < 10^-6). Detailed analysis of these blocks indicates that only a minor fraction are likely to be previously unknown coding sequences. Analogous noncoding conserved blocks have been shown to regulate adjacent genes in other phylogenies, making the predicted blocks excellent candidates for novel regulatory functions. We also find three potential transcription factor binding motifs which exhibit strong conservation and overrepresentation among the rodent malariae.

Conclusion

A broader finding of our analysis is that less malaria intergenic sequence has been conserved by selection than in yeast or vertebrate genomes. This supports the hypothesis that transcriptional regulation is simpler in malaria than other eukaryotic species. We have built a public database containing all sequence alignments and functional predictions, and we expect this to be a valuable resource to the malaria research community.

Selection on synthesis cost affects interprotein amino acid usage in all three domains of life

Most investigations of the forces shaping protein evolution have focused on protein function. However, cells are typically 50%-75% protein by dry weight, with protein expression levels distributed over five orders of magnitude. Cells may, therefore, be under considerable selection pressure to incorporate amino acids that are cheap to synthesize into proteins that are highly expressed. Such selection pressure has been demonstrated to alter amino acid usage in a few organisms, but whether "cost selection" is a general phenomenon remains unknown. One reason for this is that reliable protein expression level data is not available for most organisms. Accordingly, I have developed a new method for detecting cost selection. This method depends solely on interprotein gradients in amino acid usage. Applying it to an analysis of 43 whole genomes from all three domains of life, I show that selection on the synthesis cost of amino acids is a pervasive force in shaping the composition of proteins. Moreover, some amino acids have different price tags for different organisms--the cost of amino acids is changed for organisms living in hydrothermal vents compared with those living at the sea surface or for organisms that have difficulty acquiring elements such as nitrogen compared with those that do not--so I also investigated whether differences between organisms in amino acid usage might reflect differences in synthesis or acquisition costs. The results suggest that organisms evolve to alter amino acid usage in response to environmental conditions.

Analysis of Nanoarchaeum equitans genome and proteome composition: indications for hyperthermophilic and parasitic adaptation

Background

Nanoarchaeum equitans, the only known hyperthermophilic archaeon exhibiting parasitic life style, has raised some new questions about the evolution of the Archaea and provided a model of choice to study the genome landmarks correlated with thermo-parasitic adaptation. In this context, we have analyzed the genome and proteome composition of N. equitans and compared the same with those of other mesophiles, hyperthermophiles and obligatory host-associated organisms.

Results

Analysis of nucleotide, codon and amino acid usage patterns in N. equitans indicates the presence of distinct selective constraints, probably due to its adaptation to a thermo-parasitic life-style. Among the conspicuous characteristics featuring its hyperthermophilic adaptation are overrepresentation of purine bases in protein coding sequences, higher GC-content in tRNA/rRNA sequences, distinct synonymous codon usage, enhanced usage of aromatic and positively charged residues, and decreased frequencies of polar uncharged residues, as compared to those in mesophilic organisms. Positively charged amino acid residues are relatively abundant in the encoded gene-products of N. equitans and other hyperthermophiles, which is reflected in their isoelectric point distribution. Pairwise comparison of 105 orthologous protein sequences shows a strong bias towards replacement of uncharged polar residues of mesophilic proteins by Lys/Arg, Tyr and some hydrophobic residues in their Nanoarchaeal orthologs. The traits potentially attributable to the symbiotic/parasitic life-style of the organism include the presence of apparently weak translational selection in synonymous codon usage and a marked heterogeneity in membrane-associated proteins, which may be important for N. equitans to interact with the host and hence, may help the organism to adapt to the strictly host-associated life style. Despite being strictly host-dependent, N. equitans follows cost minimization hypothesis.

Conclusion

The present study reveals that the genome and proteome composition of N. equitans are marked with the signatures of dual adaptation – one to high temperature and the other to obligatory parasitism. While the analysis of nucleotide/amino acid preferences in N. equitans offers an insight into the molecular strategies taken by the archaeon for thermo-parasitic adaptation, the comparative study of the compositional characteristics of mesophiles, hyperthermophiles and obligatory host-associated organisms demonstrates the generality of such strategies in the microbial world.

Comparative rates of evolution in endosymbiotic nuclear genomes

BACKGROUND

The nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. They also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they are encoded.

RESULTS

Here, we test whether the phylogenetically distinct nucleomorph genomes of the cryptomonad, Guillardia theta, and the chlorarachniophyte, Bigelowiella natans, have experienced similar evolutionary pressures during their transformation to reduced organelles. We compared the evolutionary rates of genes from nuclear, nucleomorph, and plastid genomes, all of which encode proteins that function in the same cellular compartment, the plastid, and are thus subject to similar selection pressures. Furthermore, we investigated the divergence of nucleomorphs within cryptomonads by comparing G. theta and Rhodomonas salina.

CONCLUSION

Chlorarachniophyte nucleomorph genes have accumulated errors at a faster rate than other genomes within the same cell, regardless of the compartment where the gene product functions. In contrast, most nucleomorph genes in cryptomonads have evolved faster than genes in other genomes on average, but genes for plastid-targeted proteins are not overly divergent, and it appears that cryptomonad nucleomorphs are not presently evolving rapidly and have therefore stabilized. Overall, these analyses suggest that the forces at work in the two lineages are different, despite the similarities between the structures of their genomes.

Evolutionary constraints on codon and amino acid usage in two strains of human pathogenic actinobacteria Tropheryma whipplei

The factors governing codon and amino acid usages in the predicted protein-coding sequences of Tropheryma whipplei TW08/27 and Twist genomes have been analyzed. Multivariate analysis identifies the replicational-transcriptional selection coupled with DNA strand-specific asymmetric mutational bias as a major driving force behind the significant interstrand variations in synonymous codon usage patterns in T. whipplei genes, while a residual intrastrand synonymous codon bias is imparted by a selection force operating at the level of translation. The strand-specific mutational pressure has little influence on the amino acid usage, for which the mean hydropathy level and aromaticity are the major sources of variation, both having nearly equal impact. In spite of the intracellular lifestyle, the amino acid usage in highly expressed gene products of T. whipplei follows the cost-minimization hypothesis. The products of the highly expressed genes of these relatively A + T-rich actinobacteria prefer to use the residues encoded by GC-rich codons, probably due to greater conservation of a GC-rich ancestral state in the highly expressed genes, as suggested by the lower values of the rate of nonsynonymous divergences between orthologous sequences of highly expressed genes from the two strains of T. whipplei. Both the genomes under study are characterized by the presence of two distinct groups of membrane-associated genes, products of which exhibit significant differences in primary and potential secondary structures as well as in the propensity of protein disorder.

Proteome composition in Plasmodium falciparum: higher usage of GC-rich nonsynonymous codons in highly expressed genes

The parasite Plasmodium falciparum, responsible for the most deadly form of human malaria, is one of the extremely AT-rich genomes sequenced so far and known to possess many atypical characteristics. Using multivariate statistical approaches, the present study analyzes the amino acid usage pattern in 5038 annotated protein-coding sequences in P. falciparum clone 3D7. The amino acid composition of individual proteins, though dominated by the directional mutational pressure, exhibits wide variation across the proteome. The Asn content, expression level, mean molecular weight, hydropathy, and aromaticity are found to be the major sources of variation in amino acid usage. At all stages of development, frequencies of residues encoded by GC-rich codons such as Gly, Ala, Arg, and Pro increase significantly in the products of the highly expressed genes. Investigation of nucleotide substitution patterns in P. falciparum and other Plasmodium species reveals that the nonsynonymous sites of highly expressed genes are more conserved than those of the lowly expressed ones, though for synonymous sites, the reverse is true. The highly expressed genes are, therefore, expected to be closer to their putative ancestral state in amino acid composition, and a plausible reason for their sequences being GC-rich at nonsynonymous codon positions could be that their ancestral state was less AT-biased. Negative correlation of the expression level of proteins with respective molecular weights supports the notion that P. falciparum, in spite of its intracellular parasitic lifestyle, follows the principle of cost minimization.

Strategies for efficient production of heterologous proteins in Escherichia coli

In recent years, the number of recombinant proteins used for therapeutic applications has increased dramatically. Production of these proteins has a remarkable demand in the market. Escherichia coli offers a means for the rapid and economical production of recombinant proteins. These advantages, coupled with a wealth of biochemical and genetic knowledge, have enabled the production of such economically therapeutic proteins such as insulin and bovine growth hormone. These demands have driven the development of a variety of strategies for achieving high-level expression of protein, particularly involving several aspects such as expression vectors design, gene dosage, promoter strength (transcriptional regulation), mRNA stability, translation initiation and termination (translational regulation), host design considerations, codon usage, and fermentation factors available for manipulating the expression conditions, which are the major challenges is obtaining the high yield of protein at low cost.

On the evolution of codon volatility

Volatility of a codon is defined as the probability that a random point mutation in the codon generates a nonsynonymous change. It has been proposed that higher-than-expected mean codon volatility of a gene indicates that positive selection for nonsynonymous changes has acted on the gene in the recent past. I show that strong frequency-dependent selection (minority advantage) in large populations can increase codon volatility slightly, whereas directional positive selection has no effect on volatility. Factors unrelated to positive selection, such as expression-related or GC-content-related codon usage bias, also affect volatility. These and other considerations suggest that codon volatility has only limited utility for detecting positive selection at the DNA sequence level.