Codon Usage

A similarity statistic for codon usage was developed and used to compare novel gene sequences found in clinical isolates of Haemophilus influenzae with a reference set of 80 prokaryotic, eukaryotic and viral genomes. These analyses were performed to obtain an indication as to whether individual genes were Haemophilus-like in nature, or if they probably had more recently entered the H.influenzae gene pool via horizontal gene transfer from other species. The average and SD values were calculated for the similarity statistics from a study of the set of all genes in the H.influenzae Rd reference genome that encoded proteins of 100 amino acids or longer. Approximately 80% of Rd genes gave a statistic indicating that they were most like other Rd genes. Genes displaying codon usage statistics .1 SD above this range were either considered part of the highly expressed group of H.influenzae genes, or were considered of foreign origin. An alternative determinant for identifying genes of foreign origin was when the similarity statistics produced a value that was much closer to a non-H.influenzae reference organism than to any of the Haemophilus species contained in the reference set. Approximately 65% of the novel sequences identified in the H.influenzae clinical isolates displayed codon usages most similar to Haemophilus sp. The remaining novel sequences produced similarity statistics closer to one of the other reference genomes thereby suggesting that these sequences may have entered the H.influenzae gene pool more recently via horizontal transfer.

Motivation: At the core of most protein gene-finding algorithms are the coding measures used to make a decision on coding/non-coding. Of the protein coding measures, the Fourier measure is one of the most important. However, due to the limited length of the windows usually used, the accuracy of the measure is not satisfactory. This paper is devoted to improving the accuracy by lengthening the sequence to amplify the periodicity of 3 in the coding regions. Results: A new algorithm is presented called the lengthenshuffle Fourier transform algorithm. For the same window length, the percentage accuracy of the new algorithm is 6-7% higher than that of the ordinary Fourier transform algorithm. The resulting percentage accuracy (average of specificity and sensitivity) of the new measure is 84.9% for the window length 162 bp.

The identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20 000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the ‘yeast‐specific’ genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated ‘Génolevures’.

The identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20 000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the ‘yeast‐specific’ genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated ‘Génolevures’.

The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. For example, in each group, use of amino acids encoded by GC-rich codons increased by approximately 1% for each 10% increase in genomic GC content, while the use of amino acids encoded by ATrich codons decreased by a similar amount. This consistency within every phylum and class studied led us to conclude that GC content appears to be the primary determinant of the codon and amino acid usage patterns observed in bacterial genomes. These results also indicate that selection for translational efficiency of highly expressed genes is constrained by the genomic parameters associated with the GC content of the host genome.

In Caulobacter crescentus, mutations have been isolated in more than 30 fiagellar genes (#a, flb, and flg) which are required in the cell cycle event of flagellum biogenesis. ThefiaF andflaG mut and two newly identified mutations, flbT andflbA (P. V. Schoenlein and B. Ely, J. Bacteriol. 171:000400, 1989), have been localized to theflaiG region. In this study, the genetic and physical organization of this region was analyzed, using the cloned 4.0-kilobase flaFG region in the recombinant plasmid pPLG727. Plamd pPLG727 complemented flaF, flaG, flbA, and flbT mutations. Further complementation studies with pPLG727 deriva- tives indicated that flaF and flbT are unique but overlapping transcription units, whereas flbA and JfG constitute a single transcription unit. To determine the directon of transcription of the putative flbA-flaG operon, the promoterless chloramphenicol transacetylase gene was inserted into various positions in the flbA-flaG region, and merodiploid strains containing these transcriptional fusions were assayed for gene function and expression of chloramphenicol resistance. These studies showed that transcription proceeds from flbA to flaG. To confirm the complementation analysis, Southern analyses were performed on chromosomal DNAs isolated from strains containing insertion and deletion mutations. Taken together, these studies defined the relative gene order at one end of the flaYG flagellar gene cluster as flgL-flaF-flbT-fibA-fliaG. The genus Caulobacter is an elegant developmental sys- tem in which to study fundamental genetic and biochemical processes involved in nonterminal cellular differentiation. During the Caulobacter crescentus cell cycle, the synthesis, assembly, and eventual loss of the single polar flagellum,

At a specific time in the Caulobacter crescentus cell cycle, a single flagellar ifiament and multiple receptor sites for the swarmer-specific phage +Cbk are assembled at one pole of the predivisional cell. One cluster of genes required for this morphogenesis, theflaYG region, includes theflgJKL genes, which encode structural proteins of the flageliar filament. These flageilin genes are flanked by genes required for filament assembly, theflaYE genes at one end and theflaF-flbT-flbA-flaG genes at the other. In this study, we characterized mutants carrying large chromosomal deletions within this region. Several of these strains are +CbK resistant and produce a novel 22-kDa flagellin that is not assembled into flagella. Merodiploid strains containing either the entireJfaFG region or individual Jfi transcription units from this region were constructed. These strains were used to correlate the presence or absence of specific gene products to changes in flagellin synthesis, filament assembly, or phage sensitivity. As a result of these studies, we were able to conclude that (i) the production of the 22-kDa flageilin results from the absence of the flbA and faG gene products, which appear to be components of a flageilin-processing pathway common to the 25-, 27-, and 29-kDa flageilins; (ii) lbT negatively modulates the synthesis of the 27and 25-kDa flagellins from two genetically unlinked gene clusters; (iii) flgL is the only flagellin gene able to encode the 27-kDa flagellin, and this flagellin appears to be required for the efficient assembly of the 25-kDa flagellins; (iv)flaF is required for filament assembly; and (v) +CbK resistance results from the deletion of at least two genes in theflaFG region. The life cycle of Caulobacter crescentus provides a model system for the analysis of programmed developmental events. During each DNA replication cycle, a predivisional cell divides asymmetrically to produce two cell types with distinct morphologies, a motile swarmer cell and a sessile stalked cell. Prior to cell division, flagellum biogenesis is initiated in the predivisional cell. At least 40 genes are required for the synthesis and assembly of a functional polar flagellar organelle (6). This complex organelle consists of a basal complex and a hook and rod structure, onto which flagellin proteins are assembled into a filament. A 29-kDa flagellin is initially assembled at the hook-proximal portion of the filament (3), after which the 27-and the 25-kDa proteins are successively assembled . The 25-kDa flagellin constitutes the distal two-thirds of the filament. The basal complex itself is embedded in the cell envelope by a series of protein rings. Six flagellin genes (fig) constitute a multigene family localized to two genetically unlinked loci, a and 13 (Fig. ) (11). The flgJ (29-kDa flagellin), flgK (25-kDa flagellin), and flgL (27-kDa flagellin) genes comprise the a cluster of flagellin genes and are located within the flaYG gene cluster. This gene cluster also contains the flaY, flaE, flaF, flbT, and flbA-flaG transcription units. Previous genetic and physical studies (28, 29) and sequence analysis defined the gene order in this region as flaY-flaE-flgJ-flgK-flgL-flaF-flbT-flbA-flaG (Fig. ). A second set of flagellin genes, the beta cluster, is

In Caulobacter crescentus, mutations have been isolated in more than 30 fiagellar genes (#a, flb, and flg) which are required in the cell cycle event of flagellum biogenesis. ThefiaF andflaG mut and two newly identified mutations, flbT andflbA (P. V. Schoenlein and B. Ely, J. Bacteriol. 171:000400, 1989), have been localized to theflaiG region. In this study, the genetic and physical organization of this region was analyzed, using the cloned 4.0-kilobase flaFG region in the recombinant plasmid pPLG727. Plamd pPLG727 complemented flaF, flaG, flbA, and flbT mutations. Further complementation studies with pPLG727 deriva- tives indicated that flaF and flbT are unique but overlapping transcription units, whereas flbA and JfG constitute a single transcription unit. To determine the directon of transcription of the putative flbA-flaG operon, the promoterless chloramphenicol transacetylase gene was inserted into various positions in the flbA-flaG region, and merodiploid strains containing these transcriptional fusions were assayed for gene function and expression of chloramphenicol resistance. These studies showed that transcription proceeds from flbA to flaG. To confirm the complementation analysis, Southern analyses were performed on chromosomal DNAs isolated from strains containing insertion and deletion mutations. Taken together, these studies defined the relative gene order at one end of the flaYG flagellar gene cluster as flgL-flaF-flbT-fibA-fliaG. The genus Caulobacter is an elegant developmental sys- tem in which to study fundamental genetic and biochemical processes involved in nonterminal cellular differentiation. During the Caulobacter crescentus cell cycle, the synthesis, assembly, and eventual loss of the single polar flagellum,

At a specific time in the Caulobacter crescentus cell cycle, a single flagellar ifiament and multiple receptor sites for the swarmer-specific phage +Cbk are assembled at one pole of the predivisional cell. One cluster of genes required for this morphogenesis, theflaYG region, includes theflgJKL genes, which encode structural proteins of the flageliar filament. These flageilin genes are flanked by genes required for filament assembly, theflaYE genes at one end and theflaF-flbT-flbA-flaG genes at the other. In this study, we characterized mutants carrying large chromosomal deletions within this region. Several of these strains are +CbK resistant and produce a novel 22-kDa flagellin that is not assembled into flagella. Merodiploid strains containing either the entireJfaFG region or individual Jfi transcription units from this region were constructed. These strains were used to correlate the presence or absence of specific gene products to changes in flagellin synthesis, filament assembly, or phage sensitivity. As a result of these studies, we were able to conclude that (i) the production of the 22-kDa flageilin results from the absence of the flbA and faG gene products, which appear to be components of a flageilin-processing pathway common to the 25-, 27-, and 29-kDa flageilins; (ii) lbT negatively modulates the synthesis of the 27and 25-kDa flagellins from two genetically unlinked gene clusters; (iii) flgL is the only flagellin gene able to encode the 27-kDa flagellin, and this flagellin appears to be required for the efficient assembly of the 25-kDa flagellins; (iv)flaF is required for filament assembly; and (v) +CbK resistance results from the deletion of at least two genes in theflaFG region. The life cycle of Caulobacter crescentus provides a model system for the analysis of programmed developmental events. During each DNA replication cycle, a predivisional cell divides asymmetrically to produce two cell types with distinct morphologies, a motile swarmer cell and a sessile stalked cell. Prior to cell division, flagellum biogenesis is initiated in the predivisional cell. At least 40 genes are required for the synthesis and assembly of a functional polar flagellar organelle (6). This complex organelle consists of a basal complex and a hook and rod structure, onto which flagellin proteins are assembled into a filament. A 29-kDa flagellin is initially assembled at the hook-proximal portion of the filament (3), after which the 27-and the 25-kDa proteins are successively assembled . The 25-kDa flagellin constitutes the distal two-thirds of the filament. The basal complex itself is embedded in the cell envelope by a series of protein rings. Six flagellin genes (fig) constitute a multigene family localized to two genetically unlinked loci, a and 13 (Fig. ) (11). The flgJ (29-kDa flagellin), flgK (25-kDa flagellin), and flgL (27-kDa flagellin) genes comprise the a cluster of flagellin genes and are located within the flaYG gene cluster. This gene cluster also contains the flaY, flaE, flaF, flbT, and flbA-flaG transcription units. Previous genetic and physical studies (28, 29) and sequence analysis defined the gene order in this region as flaY-flaE-flgJ-flgK-flgL-flaF-flbT-flbA-flaG (Fig. ). A second set of flagellin genes, the beta cluster, is

At a specific time in the Caulobacter crescentus cell cycle, a single flagellar filament and multiple receptor sites for the swarmer-specific phage phi Cbk are assembled at one pole of the predivisional cell. One cluster of genes required for this morphogenesis, the flaYG region, includes the flgJKL genes, which encode structural proteins of the flagellar filament. These flagellin genes are flanked by genes required for filament assembly, the flaYE genes at one end and the flaF-flbT-flbA-flaG genes at the other. In this study, we characterized mutants carrying large chromosomal deletions within this region. Several of these strains are phi CbK resistant and produce a novel 22-kDa flagellin that is not assembled into flagella. Merodiploid strains containing either the entire flaFG region or individual fla transcription units from this region were constructed. These strains were used to correlate the presence or absence of specific gene products to changes in flagellin synthesis, fila...

The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. For example, in each group, use of amino acids encoded by GC-rich codons increased by approximately 1% for each 10% increase in genomic GC content, while the use of amino acids encoded by AT-rich codons decreased by a similar amount. This consistency within every phylum and class studied led us to conclude that GC content appears to be the primary determinant...

In Caulobacter crescentus, mutations have been isolated in more than 30 flagellar genes (fla, flb, and flg) which are required in the cell cycle event of flagellum biogenesis. The flaF and flaG mutations and two newly identified mutations, flbT and flbA (P.V. Schoenlein and B. Ely, J. Bacteriol. 171:000-000, 1989), have been localized to the flaFG region. In this study, the genetic and physical organization of this region was analyzed, using the cloned 4.0-kilobase flaFG region in the recombinant plasmid pPLG727. Plasmid pPLG727 complemented flaF, flaG, flbA, and flbT mutations. Further complementation studies with pPLG727 derivatives indicated that flaF and flbT are unique but overlapping transcription units, whereas flbA and flaG constitute a single transcription unit. To determine the direction of transcription of the putative flbA-flaG operon, the promoterless chloramphenicol transacetylase gene was inserted into various positions in the flbA-flaG region, and merodiploid strains...

The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. For example, in each group, use of amino acids encoded by GC-rich codons increased by approximately 1% for each 10% increase in genomic GC content, while the use of amino acids encoded by ATrich codons decreased by a similar amount. This consistency within every phylum and class studied led us to conclude that GC content appears to be the primary determinant of the codon and amino acid usage patterns observed in bacterial genomes. These results also indicate that selection for translational efficiency of highly expressed genes is constrained by the genomic parameters associated with the GC content of the host genome.

Background: Codon usage bias is a widespread phenomenon in many organisms, including higher plants and plays an important role in regulating gene expression efficiency and accuracy. As an important forage species with high nutritional value, Medicago sativa (alfalfa) has been extensively utilized not only in traditional breeding but also in molecular genetic improvement. Understanding the characteristics of codon preference in its organelle genomes can provide valuable guidance for optimizing gene design and enhancing the expression of exogenous genes in alfalfa or related species. Methods: A total of 30 mitochondrial and 51 chloroplast high-quality coding sequences were obtained from the NCBI database. Codon usage patterns and preferences were analyzed using CodonW, R, MEGA and Excel. Result: The effective number of codons (ENC) in mitochondria ranged from 44.73 to 61.0, with an average GC content of 0.42 and GC content at the third codon position (GC3s) of 0.37. In chloroplasts, the ENC ranged from 38.90 to 57.76, with an average GC content of 0.37 and GC3s of 0.27. Analyses using ENC-plot, neutrality plot and PR2 bias analysis suggested that codon usage bias in Medicago sativa is influenced by both natural selection and mutation pressure. Twelve optimal codons were identified in mitochondria (mostly ending in 'A' and 'U') and fourteen in chloroplasts, also showing a preference for 'A/U'-ending codons.

Highly expressed genes in bacteria often have a stronger codon bias than genes expressed at lower levels, due to translational selection. In this study, a comparative analysis of predicted highly expressed (PHX) genes in the Streptomyces coelicolor and Streptomyces avermitilis genomes was performed using the codon adaptation index (CAI) as a numerical estimator of gene expression level. Although it has been suggested that there is little heterogeneity in codon usage in G+C-rich bacteria, considerable heterogeneity was found among genes in these two G+C-rich Streptomyces genomes. Using ribosomal protein genes as references, ~10 % of the genes were predicted to be PHX genes using a CAI cutoff value of greater than 0?78 and 0?75 in S. coelicolor and S. avermitilis, respectively. The PHX genes showed good agreement with the experimental data on expression levels obtained from proteomic analysis by previous workers. Among 724 and 730 PHX genes identified from S. coelicolor and S. avermitilis, 368 are orthologue genes present in both genomes, which were mostly 'housekeeping' genes involved in cell growth. In addition, 61 orthologous gene pairs with unknown functions were identified as PHX. Only one polyketide synthase gene from each Streptomyces genome was predicted as PHX. Nevertheless, several key genes responsible for producing precursors for secondary metabolites, such as crotonyl-CoA reductase and propionyl-CoA carboxylase, and genes necessary for initiation of secondary metabolism, such as adenosylmethionine synthetase, were among the PHX genes in the two Streptomyces species. The PHX genes exclusive to each genome, and what they imply regarding cellular metabolism, are also discussed.

The modest correlation between mRNA expression and protein abundance in large-scale data sets is explained in part by experimental challenges, such as technological limitations, and in part by fundamental biological factors in the transcription and translation processes. Among various factors affecting the mRNA-protein correlation, the roles of biological factors related to translation are poorly understood. In this study, using experimental mRNA expression and protein abundance data collected from Desulfovibrio vulgaris by DNA microarray and liquid chromatography coupled with tandem mass spectrometry (LC-MS/ MS) proteomic analysis, we quantitatively examined the effects of several translational-efficiency-related sequence features on mRNA-protein correlation. Three classes of sequence features were investigated according to different translational stages: (i) initiation, Shine-Dalgarno sequences, start codon identity, and start codon context; (ii) elongation, codon usage and amino acid usage; and (iii) termination, stop codon identity and stop codon context. Surprisingly, although it is widely accepted that translation initiation is the rate-limiting step for translation, our results showed that the mRNA-protein correlation was affected the most by the features at elongation stages, i.e., codon usage and amino acid composition (5.3-15.7% and 5.8-11.9% of the total variation of mRNA-protein correlation, respectively), followed by stop codon context and the Shine-Dalgarno sequence (3.7-5.1% and 1.9-3.8%, respectively). Taken together, all sequence features contributed to 15.2-26.2% of the total variation of mRNA-protein correlation. This study provides the first comprehensive quantitative analysis of the mRNA-protein correlation in bacterial D. vulgaris and adds new insights into the relative importance of various sequence features in prokaryotic protein translation.

Codon optimization' is a general approach that seeks to improve heterologous expression when a gene is moved into a foreign genome that exhibits different codon usage from its native genome. However, it is still unclear exactly what it means to optimize codons for protein expression: diverse interpretations exist, and exploratory research continues. Thus, to facilitate flexible redesign of genes for heterologous expression, we have developed a bona fide web application: the "Synthetic Gene Designer". Compared with existing codon optimization software, the Synthetic Gene Designer provides greater flexibility in several key features of codon optimization strategy. The software, together with online tutorials and help, is available at .

Codon optimization' is a general approach that seeks to improve heterologous expression when a gene is moved into a foreign genome that exhibits different codon usage from its native genome. However, it is still unclear exactly what it means to optimize codons for protein expression: diverse interpretations exist, and exploratory research continues. Thus, to facilitate flexible redesign of genes for heterologous expression, we have developed a bona fide web application: the "Synthetic Gene Designer". Compared with existing codon optimization software, the Synthetic Gene Designer provides greater flexibility in several key features of codon optimization strategy. The software, together with online tutorials and help, is available at .

This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as HsfA that have a domain of transcriptional activation for tolerance to heat and other abiotic stresses. The values of the codon adaptation index (CAI) ranged from 0.80 in Seq19 to 0.65 in Seq10, based on the mRNA of heat shock proteins for tomatoes. Asparagine (AAT, AAC), aspartic acid (GAT, GAC), phenylalanine (TTT, TTC), and tyrosine (TAT, TAC) have relative synonymous codon usage (RSCU) values bigger than 0.5. In modified relative codon bias (MRCBS), the high gene expressions of the amino acids under heat stress were histidine, tryptophan, asparagine, aspartic acid, lysine, phenylalanine, isoleucine, cysteine, and threonine. RSCU values that were less than 0.5 were considered rare codons that affected the rate of translation, and thus selection could be effective by reducing the frequency of expressed genes under heat stress. The normal distribution of RSCU shows about 68% of the values drawn from the standard normal distribution were within 0.22 and -0.22 standard deviations that tend to cluster around the mean. The most critical component based on principal component analysis (PCA) was the RSCU. These findings would help plant breeders in the development of growth habits for tomatoes during breeding programs.

through interactions with the cell membrane. ᭧ 2002 Gp110 of Epstein-Barr virus (EBV) is a glycoprotein Elsevier Science (USA) that functions exclusively during the assembly of EBV Key Words: EBV; gp110; tandem AGA; circular dichronucleocapsid and the release of infectious EBV. Its Cism; micelle. terminal tail domain (gp110 CTD) is essential for gp110's function and may provide signals that are responsible for the assembly and release of EBV. In the Epstein-Barr virus (EBV) 2 is classified among the ␥present study, to get large amounts of gp110 CTD for herpesviruses and establishes latent infection in hustructural analysis, the effects of vector system, codon man B lymphocytes (1). Glycoprotein 110 (gp110), one usage, and host strain on expression levels of gp110 of the nine glycoproteins encoded by EBV (2-8), has CTD in Escherichia coli have been investigated. The been known to be essential for virus assembly in vivo coding region of gp110 CTD (11 kDa) was subcloned . Gp110 is a homologue of gB, which is the most into the expression vectors pSE 280, pET-15b, pET-29a, highly conserved glycoprotein among herpesviruses, pMAL-c2x, and pGEX-4T-1. Except the pMAL-c2x conwith the herpes simplex virus (HSV) gB being the protostruct, all the others failed to express detectable type (11). While gp110 has considerable amino acid and amounts of recombinant gp110 CTD. Substituting a predicted secondary structure homology to gB (12), tandem rare AGA (Arg) codon with a synonymous CGC gp110 localizes predominantly to the inner and outer (Arg) codon facilitated expression of the recombinant membranes of the nucleus in infected cells, unlike gB, protein, while a protease-deficient host E. coli strain which is mainly found in the plasma membrane (13helped in the accumulation of a soluble form of gp110 16), indicating that the biological role of gp110 is funda-CTD fusion. The secondary structures of the obtained mentally different from that of gB (10, 17). Consistent recombinant gp110 CTD purified from soluble extracts with such observations, antibodies directed against and inclusion bodies were compared using circular gp110 fail to neutralize EBV infectivity (15). dichroism analysis. In aqueous solutions, both samples Gp110 has a primary sequence of 857 amino acids equally adopt a mixed ␣ -helix and ␤ -sheet conformawith nine potential sites for N-linked glycosylation, tion as well as a partly unordered structure. Notably, three potential membrane-spanning domains that conin the membrane-mimicking environments the helical sist of 70 amino acids, and an unusual C-terminal dopropensity of gp110 CTD increased up to the previously main characterized by a long stretch of basic amino predicted level based on its sequence, suggesting that acids (12,13). The C-terminal tail domain of gp110 gp110 CTD may fold into a more stable conformation

We have used the Monte Carlo method for simulating the evolution of protein coding sequences from the Borrelia burgdorferi genome under the directional mutational pressure, described by the nucleotide substitution matrix experimentally found for this genome. Since the mutational pressure is asymmetric -different for each of the two DNA strands, and the coding sequences are also asymmetric, the mutagenic effect depends on the topology of the coding sequence on the chromosome. While the direct effect of the directional mutational pressure on the codon usage is predictable, the effect on the amino-acid composition depends on the degeneracy of the genetic code, initial composition of the protein sequence and codon usage. Assuming additional degeneracy of information connected with the structure of amino-acids, we have found that the best strategy for the evolution of some genes in the B. burgdorferi genome is to change the mutational pressure by inversions, which corresponds to changing the substitution matrix to the mirror one. It mimics the behavior of a stock market player who can gain by investing only in two stock sets even if during that time both sets have lost. To whom all correspondence should be sent.

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model.

In microbial corrinoid-dependent methyltransferase systems, adventitious Co(I)-corrinoid oxidation halts catalysis and necessitates repair by ATP-dependent reductive activases. RamA, an activase with a C-terminal ferredoxin domain with two [4Fe-4S] clusters from methanogenic archaea has been far less studied than the bacterial activases bearing an N-terminal ferredoxin domain with one [2Fe-2S] cluster. These differences suggest RamA might prove to have other distinctive characteristics. Here, we examine RamA kinetics and the stoichiometry of the corrinoid protein:RamA complex. Like bacterial activases, K+ stimulates RamA. Potassium stimulation had been questioned due to differences in the primary structure of bacterial and methanogen activases. Unlike one bacterial activase, ATP is not inhibitory allowing the first determination of apparent kinetic parameters for any corrinoid activase. Unlike bacterial activases, a single RamA monomer complexes a single corrinoid protein monomer. A...

DNA has an extraordinary capacity to direct the synthesis of many different proteins through the information encoded in its nucleotide sequences. When a specific gene sequence for a protein is not readily available as a single continuous segment, the cell can still produce the required protein by utilizing fragments from different regions of the DNA. During replication processes, short DNA fragments can be synthesized or copied from various parts of the genome and later joined together to form a functional sequence that resembles the needed gene. Once this reconstructed sequence is established, it can be transcribed into messenger RNA (mRNA), which then guides the ribosomes to assemble the corresponding protein. This ability of DNA to reorganize and utilize dispersed fragments highlights the flexibility and complexity of genetic information management within the cell, enabling the production of diverse proteins essential for life.

In the context of the international project aimed at sequencing the whole genome of Bacillus subtilis we have developed a non-redundant, fully annotated database of sequences from this organism. Starting from the B.subtilis sequences available in the EMBL, GenBank and DDBJ collections we have removed all encountered duplications and then added extra annotations to the sequences (e.g. accession numbers for the genes, locations on the genetic map, codon usage, etc.) We have also added cross-references to the EMBL, MEDLINE, SWISS-PROT and ENZYME data banks. The present system results from merging of the NRSub and SubtiList databases and the sequence contigs used in the two systems are identical. NRSub is distributed as a flatfile in EMBL format (which is supported by most sequence analysis software packages) and as an ACNUC database, while SubtiList is distributed as a relational database under 4th Dimension. It is possible to access the data through two dedicated World Wide Web servers located in France and Japan.

Dengue is becoming the most devastating endemic disease in the last few years all over the world. Four serotypes DENV1, DENV2, DENV3 and DENV4 show strong adaptation against host defence. DENV4 is phylogenetically most divergent serotype and highlights the importance of the study about evolution and genomics of DENV4 genome. Overall, study of codon usage pattern at gene level and the effect of mutational bias, natural selection, translational selection and gene length were estimated. A multivariate statistical analysis showed the conservation of codon usage pattern among phylogenetically closely related DENV4 genomes. For compositional constraint, most of the preferred codons in DENV4 genes contain 'A' and/or 'T' at 3 rd position. Moreover, mutational bias and gene length were also functioning for the variation in codon usage. Pyrimidines ending preferred codons were slightly numerous in highly expressed genes, but codon usage bias was higher in non-structural genes than structural one, which was the evidence for the absence of the effect of translational selection on codon usage variation of DENV4 genome. The study is helpful to understand the evolution of DENV4 genome and gradual change in their pathogenicity.

Codon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes.We assign an evolutionary age to a gene based on the relative positions of its identified homologues in a standard phylogenetic tree. This yields a classification of all genes in a genome to several evolutionary age classes. The present study starts from the observation that each age class of genes has a unique codon usage and proceeds to provide a quantitative analysis of the codon usage in these classes. This observation is made for the genomes of Homo sapiens, ...

Viruses differ markedly in their specificity toward host organisms. Here, we test the level of general sequence adaptation that viruses display toward their hosts. We compiled a representative data set of viruses that infect hosts ranging from bacteria to humans. We consider their respective amino acid and codon usages and compare them among the viruses and their hosts. We show that bacteria infecting viruses are strongly adapted to their specific hosts, but that they differ from other unrelated bacterial hosts. Viruses that infect humans, but not those that infect other mammals or aves, show a strong resemblance to most mammalian and avian hosts, in terms of both amino acid and codon preferences. In groups of viruses that infect humans or other mammals, the highest observed level of adaptation of viral proteins to host codon usages is for those proteins that appear abundantly in the virion. In contrast, proteins that are known to participate in host-specific recognition do not necessarily adapt to their respective hosts. The implication for the potential of viral infectivity is discussed.