Can Codon Usage Bias Explain Intron Phase Distributions and Exon Symmetry?

More introns exist between codons (phase 0) than between the first and the second bases (phase 1) or between the second and the third base (phase 2) within the codon. Many explanations have been suggested for this excess of phase 0. It has, for example, been argued to reflect an ancient utility for introns in separating exons that code for separate protein modules. There may, however, be a simple, alternative explanation. Introns typically require, for correct splicing, particular nucleotides immediately 5 in exons (typically a G) and immediately 3 in the following exon (also often a G). Introns therefore tend to be found between particular nucleotide pairs (e.g., G|G pairs) in the coding sequence. If, owing to bias in usage of different codons, these pairs are especially common at phase 0, then intron phase biases may have a trivial explanation. Here we take codon usage frequencies for a variety of eukaryotes and use these to generate random sequences. We then ask about the phase of putative intron insertion sites. Importantly, in all simulated data sets intron phase distribution is biased in favor of phase 0. In many cases the bias is of the magnitude observed in real data and can be attributed to codon usage bias. It is also known that exons may carry either the same phase (symmetric) or different phases (asymmetric) at the opposite ends. We simulated a distribution of different types of exons using frequencies of introns observed in real genes assuming random combination of intron phases at the opposite sides of exons. Surprisingly the simulated pattern was quite similar to that observed. In the simulants we typically observe a prevalence of symmetric exons carrying phase 0 at both ends, which is common for eukaryotic genes. However, at least in some species, the extent of the bias in favor of symmetric (0,0) exons is not as great in simulants as in real genes. These results emphasize the need to construct a biologically relevant null model of successful intron insertion.Reviewing Editor: Dr. Manyuan Long     

Synonymous Codon Usage Bias and Overexpression of a Synthetic Gene Encoding Interferon α2b in Yeast

To achieve higher level expression of Interferon α2b(IFN-α2b)in methylotrophic yeast(Pichia pastoris),a cDNA fragment coding for the mature IFN-α2b was designed and synthesized based on the synonymous codon bias of P.pastoris and optimized G C content.The synthetic IFN-α2b was inserted into the secreted expression vector pPICZαA,and then integrated into P.pastoris GS115 genome by electroporation.Multi-copy integrants in the Mut recombinant P.pastoris strain were screened by high concentrations of Zeocin.120 hours culturing allowed expression of the IFN-α2b transformant up to 810 mg/L as detected by SDS-PAGE and quantitative methods.In addition,Western blot analysis showed that the recombinant proteins had immunogenicity.The significant antiviral activity of the recombinant IFN-α2b protein was verified by WISH/VSV system,which was 3.3×105 IU/mL.     

Correlation Between Shine–Dalgarno Sequence Conservation and Codon Usage of Bacterial Genes

In this study, we analyzed the correlation between codon usage bias and Shine–Dalgarno (SD) sequence conservation, using complete genome sequences of nine prokaryotes. For codon usage bias, we adopted the codon adaptation index (CAI), which is based on the codon usage preference of genes encoding ribosomal proteins, elongation factors, heat shock proteins, outer membrane proteins, and RNA polymerase subunit proteins. To compute SD sequence conservation, we used SD motif sequences predicted by Tompa and systematically aligned them with 5′UTR sequences. We found that there exists a clear correlation between the CAI values and SD sequence conservation in the genomes of Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Archaeoglobus fulgidus, Methanobacterium thermoautotrophicum, and Methanococcus jannaschii, and no relationship is found in M. genitalium, M. pneumoniae, and Synechocystis. That is, genes with higher CAI values tend to have more conserved SD sequences than do genes with lower CAI values in these organisms. Some organisms, such as M. thermoautotrophicum, do not clearly show the correlation. The biological significance of these results is discussed in the context of the translation initiation process and translation efficiency. Received: 22 June 2000 / Accepted: 18 October 2000     

Impact of Xenogeneic Silencing on Phage–Host Interactions

Phages, viruses that prey on bacteria, are the most abundant and diverse inhabitants of the Earth. Temperate bacteriophages can integrate into the host genome and, as so-called prophages, maintain a long-term association with their host. The close relationship between host and virus has significantly shaped microbial evolution and phage elements may benefit their host by providing new functions. Nevertheless, the strong activity of phage promoters and potentially toxic gene products may impose a severe fitness burden and must be tightly controlled. In this context, xenogeneic silencing (XS) proteins, which can recognize foreign DNA elements, play an important role in the acquisition of novel genetic information and facilitate the evolution of regulatory networks. Currently known XS proteins fall into four classes (H-NS, MvaT, Rok and Lsr2) and have been shown to follow a similar mode of action by binding to AT-rich DNA and forming an oligomeric nucleoprotein complex that silences gene expression. In this review, we focus on the role of XS proteins in phage–host interactions by highlighting the important function of XS proteins in maintaining the lysogenic state and by providing examples of how phages fight back by encoding inhibitory proteins that disrupt XS functions in the host. Sequence analysis of available phage genomes revealed the presence of genes encoding Lsr2-type proteins in the genomes of phages infecting Actinobacteria. These data provide an interesting perspective for future studies to elucidate the impact of phage-encoded XS homologs on the phage life cycle and phage–host interactions.     

Arrangement of the Template 3′ of the A-Site Codon on the Human 80S Ribosome

The arrangement of the template sequence 3′ of the A-site codon on the 80S ribosome was studied using mRNA analogs containing Phe codon UUU at the 5′ end and a photoreactive perfluoroarylazido group linked to C5 of U or N7 of G. The analogs were positioned on the ribosome with the use of tRNA^Phe, which directed the UUU codon to the P site, bringing a modified nucleotide to position +9 or +12 relative to the first nucleotide of the P-site codon. Upon mild UV irradiation of ribosome complexes, the analogs of both types crosslinked to the 18S rRNA and proteins of the 40S subunit. Comparisons were made with the crosslinking patterns of complexes in which an mRNA analog contained a modified nucleotide in position +7 (the crosslinking to 18S rRNA in such complexes has been studied previously). The efficiency of crosslinking to ribosomal components depended on the nature of the modified nucleotide of an mRNA analog and its position on the ribosome. The extent of crosslinking to the 18S rRNA drastically decreased as the modified nucleotide was transferred from position +7 to position +12. The 18S rRNA nucleotides involved in crosslinking were identified. A modified nucleotide in position +9 crosslinked to the invariant dinucleotide A1824/A1825 and variable A1823 in the 3′ minidomain of the 18S rRNA and to S15. The same ribosomal components have earlier been shown to crosslink to modified nucleotides in positions +4 to +7. In addition, all mRNA analogs crosslinked to invariant C1698 in the 3′ minidomain and to conserved region 605–620, which closes helix 18 in the 5′ domain.     

Membrane Domains Based on Ankyrin and Spectrin Associated with Cell–Cell Interactions

Nodes of Ranvier and axon initial segments of myelinated nerves, sites of cell–cell contact in early embryos and epithelial cells, and neuromuscular junctions of skeletal muscle all perform physiological functions that depend on clustering of functionally related but structurally diverse ion transporters and cell adhesion molecules within microdomains of the plasma membrane. These specialized cell surface domains appeared at different times in metazoan evolution, involve a variety of cell types, and are populated by distinct membrane-spanning proteins. Nevertheless, recent work has shown that these domains all share on their cytoplasmic surfaces a membrane skeleton comprised of members of the ankyrin and spectrin families. This review will summarize basic features of ankyrins and spectrins, and will discuss emerging evidence that these proteins are key players in a conserved mechanism responsible for assembly and maintenance of physiologically important domains on the surfaces of diverse cells.Spectrins are flexible rods 0.2 microns in length with actin-binding sites at each end (Shotton et al. 1979; Bennett et al. 1982) (Fig. 1A). Spectrins are assembled from α and β subunits, each comprised primarily of multiple copies of a 106-amino acid repeat (Speicher and Marchesi 1984). In addition to the canonical 106-residue repeat, β spectrins also have a carboxy-terminal pleckstrin homology domain (Zhang et al. 1995; Macias et al. 1994) and tandem amino-terminal calponin homology domains (Bañuelos et al. 1998), whereas α spectrins contain an Src homology domain 3 (SH3) site (Musacchio et al. 1992), a calmodulin-binding site (Simonovic et al. 2006), and EF hands (Travé et al. 1995) (Fig. 1A). Spectrin α and β subunits are assembled antiparallel and side-to-side into heterodimers, which in turn are associated head-to-head to form tetramers (Clarke 1971; Shotton et al. 1979; Davis and Bennett 1983) (Fig. 1A). In human erythrocytes, in which spectrin was first characterized (Marchesi and Steers 1968; Clarke 1971), actin oligomers containing 10–14 monomers are each linked to five to six spectrin tetramers by accessory proteins to form a geodesic domelike structure that has been resolved by electron microscopy (Byers and Branton 1985). The principal proteins at the spectrin–actin junction are protein 4.1, adducin, tropomyosin, tropomodulin, and dematin (Bennett and Baines 2001) (Open in a separate windowFigure 1.Domain structure and variants of spectrin and ankyrin proteins. (A) Molecular domains of spectrins: Two α spectrins and five β spectrins are shown. Spectrins are comprised of modular units called spectrin repeats (yellow). Other domains such as the ankyrin binding domain (purple), Src-homology domain 3 (SH3, blue), EF-hand domain (red), and calmodulin-binding domain (green) promote interactions with binding targets important for spectrin function. The pleckstrin homology domain (black) promotes association with the plasma membrane and the actin binding domain (grey) tethers the spectrin-based membrane skeleton to the underlying actin cytoskeleton. (B) The spectrin tetramer, the fundamental unit of the spectrin-based membrane skeleton. The spectrin repeat domains of α and β spectrin associate end-to-end to form heterodimers. Heterodimers associate laterally in an antiparallel fashion to form tetramers. The tetramers can then associate end-to-end to form extended macromolecules that link into a geodesic dome shape directly underneath the plasma membrane. (C) Molecular domains present in canonical ankyrins. The membrane binding domain of ankyrin isoforms (orange) is comprised of 24 ANK repeats. The spectrin binding domain (green-blue) allows ankyrins to coordinate integral membrane proteins to the membrane skeleton. The death domain (pink) is the most highly conserved domain. The regulatory domain (brown) is the most variable region of ankyrins. The regulatory domain interacts intramolecularly with the membrane binding domain to modulate ankyrin’s affinity for other binding partners. All ankyrins and spectrins are subject to alternative splicing, which further increases their functional diversity.

Table 1.

Binding partners of spectrin and ankyrins

Efficiency of the miRNA–mRNA Interaction Prediction Programs

miRNAs play a key role in regulation of gene expression. Nowadays it is known more than 2500 human miRNAs, while a majority of miRNA–mRNA interactions remains unidentified. The recent development of a high-throughput CLASH (crosslinking, ligation and sequencing of hybrids) technique for discerning miRNA–mRNA interactions allowed an experimental analysis of the human miRNA–mRNA interactome. Therefore, it allowed us, for the first time, make an experimental analysis of the human miRNA–mRNA interactome as a whole and an evaluation of the quality of most commonly used miRNA prediction tools (TargetScan, PicTar, PITA, RNA22 and miRanda). To estimate efficiency of the miRNA–mRNA prediction tools, we used next parameters: sensitivity, positive predicted value, predictions in different mRNA regions (3' UTR, CDS, 5' UTR), predictions for different types of interactions (5 classes), predictions of “canonical” and “nocanonical” interactions, similarity with the random generated data. The analysis revealed low efficiency of all prediction programs in comparison with the CLASH data in terms of the all examined parameters.     

A Generalized Michaelis–Menten Equation in Protein Synthesis: Effects of Mis-Charged Cognate tRNA and Mis-Reading of Codon

The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. We develop a stochastic kinetic model that captures the possibilities of mis-reading of mRNA codon and prior mis-charging of a tRNA. By a combination of analytical and numerical methods, we obtain the distribution of the times taken for incorporation of the successive amino acids in the growing protein in this mathematical model. The corresponding exact analytical expression for the average rate of elongation of a nascent protein is a ‘biologically motivated’ generalization of the Michaelis–Menten formula for the average rate of enzymatic reactions. This generalized Michaelis–Menten-like formula (and the exact analytical expressions for a few other quantities) that we report here display the interplay of four different branched pathways corresponding to selection of four different types of tRNA.     

Setting Fish Quotas Based on Holistic Ecosystem Modelling Including Environmental Factors and Foodweb Interactions – A New Approach

We present a new approach to set fish quotas from holistic aquatic foodweb modelling (the LakeWeb-approach). This modelling includes changes in environmental conditions (nutrients, salinity, temperature, oxygen), process-based mass-balance calculations of nutrient concentrations from inflow, internal processes and outflow, calculations of how changes in nutrient concentrations affect primary production, how such changes influence secondary production and how this influence fish production and biomass. This approach gives dynamic, quantitative responses to alterations in driving variables and abiotic/biotic feedbacks. We have applied this approach for preliminary simulations of the cod biomass in the Baltic. We also show that this approach adds a new dimension in setting fish quotas, which in the future could complement, rather than compete with, the more established methods used today based on fish catch statistics and models based on other presuppositions. Our preliminary results indicate that under present environmental conditions (2003), the cod is likely to be extinct if the annual catch is between 95 and 100 kt. The present fish quota is 75 kt/yr in the Baltic, but the overfishing may be 35 kt/yr. We discuss cause–effect relationships regulating fish production, key factors influencing thresholds and points of no return connected to overfishing and changes in environmental conditions, factors regulating recovery and methods for setting optimal fish quotas using this modelling approach.     

Importance of Metal–Adsorbate Interactions for the Surface-enhanced Raman Scattering of Molecules Adsorbed on Plasmonic Nanoparticles

The interaction between adsorbates of different nature and plasmonic nanoparticles is reviewed here on the basis of the work done in our laboratory in the past few years. The paper is structured for analyzing the interaction of adsorbates with metal nanoparticles as function of the interacting atom (O, N, or S) and the adsorbate conformation. In the study of the adsorption of molecular species on metals, it is necessary to take into account that different interaction mechanisms are possible, leading to the existence of different molecular forms (isomers or conformers). These forms can be evidenced by changing the excitation wavelength, due to a resonant selection of these wavelengths. Charge-transfer complexes and electrostatic interactions are the usual driving forces involved in the interaction of adsorbates on metal surfaces when these metallic systems are used in wet conditions. The understanding of the metal–adsorbate interaction is crucial in the surface functionalization of metal surfaces, which has a growing importance in the development of sensing systems or optoelectronic devices. In relation to this, special attention is paid in this work to the study of the adsorption of calixarene host molecules on plasmonic nanoparticles.     

The Use of the Rare TTA Codon in Streptomyces Genes: Significance of the Codon Context?

Streptomycetes, Gram-positive bacteria with huge and GC-rich genomes provide an ample example of codon usage bias taken to the extreme. Particularly, in all sequenced to date streptomycete genomes leucyl codon TTA is the rarest one. It is present (usually once or twice) in 70–200 out of 7000–8000 coding sequences that make up a typical streptomycete genome. tRNA^Leu_UAA of streptomycetes, encoded by the bldA gene, has been shown to be present in mature form only after the onset of morphological differentiation and activation of secondary metabolism. Consequently, during the early stages of cell growth, the translation of genes carrying the TTA codon can be interrupted due to the absence of tRNA^Leu_UAA. Several reports show that mutations of TTA to synonymous codons in certain genes indeed relieve their expression from bldA dependence. However, the deletion of bldA does not always arrest the expression of TTA-containing genes. The nucleotides T/C downstream of TTA were suggested, in 2002, to favor TTA mistranslation. We tested this hypothesis using sizable datasets derived from individual Streptomyces genome and a subset of TTA+ genes for secondary metabolism known for their active expression. Our results revealed nucleotide biases downstream of NNA codons family, such as the preference for C and the avoidance of A. Yet, none of the observed biases was sufficient to claim a special case for TTA codon. Hence, the issue of codon context and TTA codon mistranslation in Streptomyces deserves further elaboration.Electronic supplementary materialThe online version of this article (10.1007/s12088-020-00902-6) contains supplementary material, which is available to authorized users.     

Effect of the Bacterial Hemoglobin vhbGene on the Efficiency of Intergeneric Conjugation Escherichia coli–Streptomyces and Biosynthesis of Antibiotics in Streptomyces

The bacterial hemoglobin vhbgene was cloned from sliding bacterium Vitreoscillasp. as an element of the system ensuring survival of this microorganism in an environment that contains insufficient amount of oxygen. The vhbgene was transferred fromEscherichia colito some Streptomycesstrains, producers of antibiotics, by the method of intergeneric conjugation using conjugative–integrative plasmid vectors pIH1 and pCH2. The stability of plasmid DNA inheritance was analyzed in the genomes of exconjugants. A positive effect of the vhbgene on processes of conjugation and antibiotic production in a number of examined strains was shown.     

Host–Parasite Interactions and the Evolution of Gene Expression

Interactions between hosts and parasites provide an ongoing source of selection that promotes the evolution of a variety of features in the interacting species. Here, we use a genetically explicit mathematical model to explore how patterns of gene expression evolve at genetic loci responsible for host resistance and parasite infection. Our results reveal the striking yet intuitive conclusion that gene expression should evolve along very different trajectories in the two interacting species. Specifically, host resistance loci should frequently evolve to co-express alleles, whereas parasite infection loci should evolve to express only a single allele. This result arises because hosts that co-express resistance alleles are able to recognize and clear a greater diversity of parasite genotypes. By the same token, parasites that co-express antigen or elicitor alleles are more likely to be recognized and cleared by the host, and this favours the expression of only a single allele. Our model provides testable predictions that can help interpret accumulating data on expression levels for genes relevant to host−parasite interactions.     

A Statistical Method of Identifying Interactions in Neuron–Glia Systems Based on Functional Multicell Ca2+ Imaging

Crosstalk between neurons and glia may constitute a significant part of information processing in the brain. We present a novel method of statistically identifying interactions in a neuron–glia network. We attempted to identify neuron–glia interactions from neuronal and glial activities via maximum-a-posteriori (MAP)-based parameter estimation by developing a generalized linear model (GLM) of a neuron–glia network. The interactions in our interest included functional connectivity and response functions. We evaluated the cross-validated likelihood of GLMs that resulted from the addition or removal of connections to confirm the existence of specific neuron-to-glia or glia-to-neuron connections. We only accepted addition or removal when the modification improved the cross-validated likelihood. We applied the method to a high-throughput, multicellular in vitro Ca2+ imaging dataset obtained from the CA3 region of a rat hippocampus, and then evaluated the reliability of connectivity estimates using a statistical test based on a surrogate method. Our findings based on the estimated connectivity were in good agreement with currently available physiological knowledge, suggesting our method can elucidate undiscovered functions of neuron–glia systems.     

Template Location on the Human Ribosome: Environment of the mRNA Nucleotide Adjacent to the A-Site Codon on the 3′-Side

The 18S rRNA nucleotides close to the template nucleotide adjacent to the 80S ribosomal A-site codon on the 3′-end (i.e., the nucleotide in position +7 relative to the first nucleotide of the P-site codon) were identified using the affinity crosslinking approach. For this purpose, the photoreactive mRNA analogues with a perfluorophenylazide group attached through various linkers to the uridine C5, 3′-terminal phosphate or guanosine N7 were used. The position of the mRNA analogues on the ribosome was preset using tRNA^Phe, which recognized the phenylalanine codon directed to the P-site. An analysis of the rRNAs isolated from the irradiated complexes of 80S ribosomes showed that all the analogues are almost equally crosslinked to the 18S rRNA nucleotides we attributed to the A-site codon environment: namely, to nucleotides A1823, A1824, and A1825 of the 3′-minidomain and to the 620–630 fragment of the 18S rRNA 5′-domain. In addition, we identified a new component of the mRNA binding site of human ribosomes, nucleotide C1698, belonging to the 18S rRNA 3′-minidomain, using analogues bearing a perfluorophenylazide group on uridine and guanine residues.__________Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 3, 2005, pp. 295–302.Original Russian Text Copyright © 2005 by Demeshkina, Styazhkina, Bulygin, Repkova, Ven’yaminova, Karpova.     

The Structure of the Gene Pools of the Ethnic Populations of Altai–Sayan Region Based on of Mitochondrial DNA Polymorphism Data

Using the data on mitochondrial DNA (mtDNA) polymorphism, genetic structures of the four Turkic-speaking ethnic groups of Altai–Sayan highlands, Southern Altaians (Altai- Kizhi), Khakassians, Shorians, and Sojots, were described. Mitochondrial gene pools of the populations examined were characterized by different ratios between Mongoloid (M*, C, D, E, G, A, B, and F) and Caucasoid (H, U, T, J, and K) mtDNA lineages. All the populations studied had a strongly pronounced Mongoloid component, the frequency of which was 88.2% in Sojots, 75.9% in Khakassians, 67.4% in Altaians, and 64.3% in Shorians. Maximum frequency of the Caucasoid component (35.7%) was observed in Shorians. Phylogenetic and statistical analyses of the mtDNA group frequency distribution patterns in the gene pools of the ethnic populations of Altai–Sayan highlands and the adjacent territories showed that the populations of the region fell into three groups. The first group included Khakassians, Tuvinians and Altaians, the second group consisted of Sojots, Buryats, and Mongols, while the third group was composed of Uigurs, Kazakhs, and Kyrgyzes. The isolated position of Shorians among the populations examined can be explained by their different anthropological composition and their presumptive relatedness to Finno-Ugric populations of Siberia.     

Effect of Crystallization State on the Gel Properties of Oleogels Based on β-sitosterol

Oleogels based on three different oils (sunflower oil, solid coconut oil and liquid coconut oil) were formulated using β-sitosterol. In general, an observed increase in crystallinity was correlated with an increase in the gel storage modulus and hardness. Addition of lecithin promoted the formation of needle-like crystals of β-sitosterol with a corresponding increase in strain tolerance and oil-trapping capacity for oleogels produced with liquid oils. However, the incorporation of β-sitosterol crystals with or without lecithin into oleogels containing solid coconut oil reduced its strain tolerance by interrupting the formation of continual radiolitic crystal structures. The use of sunflower oil (long chain fatty acids) was more favourable to the packing and growth of gelator crystals and the formation of an elastic gel, in comparison to liquid coconut oil (short chain fatty acids). Overall, the type and physical state of oil influence the formation of oil crystal network, thus affecting its gel properties. These findings allow the better understanding of β-sitosterol-based oleogels, providing opportunity to design for the application as a fat-replacer and lowering solid fat content.