Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational proper...Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.展开更多
To investigate how synonymous codons have been adapted to the formation of ribonucleic acid(RNA)G-quadruplex(rG4)structure,a computational searching algorithm G4Hunter was applied to detect rG4 structures in protein-c...To investigate how synonymous codons have been adapted to the formation of ribonucleic acid(RNA)G-quadruplex(rG4)structure,a computational searching algorithm G4Hunter was applied to detect rG4 structures in protein-coding sequences of mRNAs in five eukaryotic species.The native sequences forming rG4s were then compared with randomized sequences to evaluate selection on synonymous codons.Factors that may influence the formation of rG4 were also investigated,and the selection pressures of rG4 in different gene regions were compared to explore its potential roles in gene regulation.The results show universal selective pressure acts on synonymous codons in rG4 regions to facilitate rG4 formation in five eukaryotic organisms.While G-rich codon combinations are preferred in the rG4 structural region,C-rich codon combinations are selectively unfavorable for rG4 formation.Gene's codon usage bias,nucleotide composition,and evolutionary rate can account for the selective variations on synonymous codons among rG4 structures within a species.Moreover,rG4 structures in the translational initiation region showed significantly higher selective pressures than those in the translational elongation region.展开更多
This is an attempt to explain mRNA-dependent non-stationary semantic values of codons (triplets) and nucleotides (letters) in codon composition during protein biosynthesis. This explanation is realized by comparing th...This is an attempt to explain mRNA-dependent non-stationary semantic values of codons (triplets) and nucleotides (letters) in codon composition during protein biosynthesis. This explanation is realized by comparing the different protein codes of various biosystem taxa, and, comparing mitochondrial code with the standard code. An initial mRNA transcriptional virtuality (Virtual-Reality) is transformed into material reality at the level of translation of virtual triplets into real (material) amino acids or into a real stop command of protein biosynthesis. The transformation of virtuality into reality occurs de facto when the linguistic sign1 functions of the codon syhoms are realized in the 3’ nucleotide (wobbling nucleotide according to F. Crick) in the process of protein biosynthesis. This corresponds to the theoretical works of the authors of this article. Despite the illusory appearance of semantic arbitrariness during the operation of ribosomes in the mode of codon semantic non-stationarity, this phenomenon probably provides biosystems with an unusually high level of adaptability to changes in the external environment as well as to internal (mental) dynamics of neuron’s genome in the cerebral cortex. The genome’s non-stationarity properties at the nucleotide, codon, gene and mental levels have fractal structure and corresponding dimensions. The highest form of such fractality (with maximum dimension) is probably realized in the genomic continuum of neurons in the human cerebral cortex through this semantic Virtual-to-Real (VR) codon transcoding with the biosynthesis of short-living semantic proteins, as the equivalents of material thinking-consciousness. In fact, this is the language of the brain’s genome, that is, our own language. In this case, the same thing happens in natural, primarily mental (non-verbal) languages. Their materialization is recorded in vocables (sounding words) and in writing. Such writing is the amino acid sequence in the semantic proteins of the human cerebral cortex. Rapidly decaying, such proteins can leave a long-lasting “so-called” Schrödinger wave holographic memory in the cerebral cortex. The presented below study is purely theoretical and based on a logical approach. The topic of the study is very complex and is subject to further development.展开更多
Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method num...Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (austin model 1) methods. As distinct from previous calculations, for nucleotides the interaction with neighbours is taken into account up to gradient of convergence equaling 1. The dependencies of these variables from the place in the codon and the de- terminative degree were obtained. The difference of these variables for codons and anticodons is shown.展开更多
Codon nonsense mutations include amber, ochre, or opal mutations according to termination codon consisting of three types (TAG, TAA and TGA). Codon nonsense mutations are also divided into natural and artificial mutat...Codon nonsense mutations include amber, ochre, or opal mutations according to termination codon consisting of three types (TAG, TAA and TGA). Codon nonsense mutations are also divided into natural and artificial mutations. We discussed the interaction of codon nonsense mutations and suppressor tRNAs in vitro and in vivo. Nonsense suppressions do not only happen in prokaryotes but also in eukaryotes. Meanwhile, the misreading of termination codon and in-corporation of nonnatural amino acids into proteins are also introduced.展开更多
Sweet potatoes are significant cash crops,however,their yield and quality are greatly compromised by viral diseases.In this study,the complete genomic sequences of two Sweet Potato Virus 2(SPV2)isolates from infected ...Sweet potatoes are significant cash crops,however,their yield and quality are greatly compromised by viral diseases.In this study,the complete genomic sequences of two Sweet Potato Virus 2(SPV2)isolates from infected sweet potato leaves in the Shandong(designated as SPV2-SDYT,GenBank No.PQ855660.1)and Jiangsu(designated as SPV2-JSXZ,GenBank No.PQ855661.1)provinces in China were obtained using 5′RACE and RT-PCR amplification.Consistency,phylogeny,codon usage bias,recombination,and selection pressure analyses were conducted using the SPV2-SDYT and SPV2-JSXZ genome sequences.The complete genome sequences of SPV2-SDYT and SPV2-JSXZ were 10561 nucleotides(nt)in length,with respective nucleotide and amino acid identities of 99.25%and 99.12%,respectively.Both isolates were closely related to the SPV2 isolate from China(SPV2-LN).In both SPV2-SDYT and SPV2-JSXZ,the identity of the P1 protein was the highest,whereas that of the P3 protein was the lowest.There were 26 codons with relatively synonymous codon usage(RSCU)values greater than 1 in SPV2-SDYT and 27 codons with RSCU values greater than 1 in SPV2-JSXZ.High-frequency codons in their genomes were predominantly found to end with A/U.Recombination analysis revealed no major recombination sites in either SPV2-SDYT or SPV2-JSXZ.Further selection pressure analysis showed that the non-synonymous substitution rate/synonymous substitution rate(dN/dS)value of all 10 SPV2 proteins was less than 1.This is the first report on the evolutionary relationships of the 17 known SPV2 isolates.Our findings lay the molecular groundwork for preventing and controlling SPV2 infection in root-tuber crops.These findings also contribute to our understanding of the spread and evolution of SPV2,its pathogenic mechanisms,and the development of antiviral strategies against it.展开更多
We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 19...We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 1997 to 2007, except viruses from 2000. The haemagglutinin sequences of viruses from southeast Asia, Hong Kong and China's Mainland were the most polymorphic and had similar nonsyn-onymous profiles. Some sites were positively selected in viruses from most regions and a few of these sites displayed different amino acid patterns. Selection appeared to produce different outcomes in vi-ruses from Europe, Africa and Russia and from different host types. One position was found to be positively selected for human isolates only. Although the functions of some positively selected posi-tions are unknown, our analysis provided evidence of different temporal, spatial and host adaptations for H5N1 avian influenza viruses.展开更多
Tgf2 transposase(Tgf2-TPase),a hAT transposase from goldfish,plays an important role in fish transgenic applications.Previously,the production of the recombinant Tgf2-TPase protein required rigorous fermentation at lo...Tgf2 transposase(Tgf2-TPase),a hAT transposase from goldfish,plays an important role in fish transgenic applications.Previously,the production of the recombinant Tgf2-TPase protein required rigorous fermentation at low temperatures(22℃)and early log phase induction(OD600=0.3–0.4)in Rosetta 1(DE3)Escherichia coli lines.In order to better express the Tgf2-TPase and detect its enzyme activity,83 rare codons in Tgf2-TPase were optimized and designated Tgf2-TPase^(83).The expression results showed that the soluble recombinant Tgf2-TPase83 was highly expressed at 30℃ and was inducible at an OD600 of 0.5–0.6 in the same prokaryotic expression system.After purification by affinity chromatography,Tgf2-TPase83 with codon optimization had higher enzyme activity than the Tgf2-TPase control.Comparison of different preservation methods(freezedrying at−80℃,storage in 20%-glycerol,8%-sucrose,4%-mannitol),revealed storage of Tgf2-TPase^(83) in glycerol helped to preserve its DNase digestion activity.Furthermore,size exclusion chromatography suggested that the purified Tgf2-TPase^(83) could recognize and bind to DNA probes containing a terminal inverted repeat(TIR)and a subterminal repeat(STR)sequence of the Tgf2 transposon.Overall,the results showed that optimizing the 83 codons of Tgf2 transposase can simplify the fermentation process and improve the enzyme activity.We propose that the production of the Tgf2-Tpase83 protein in a soluble and active form could provide an alternative tool for genetic modification of fish.展开更多
Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals ...Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.展开更多
Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different specie...Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.展开更多
Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstl...Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ＇optimal codons＇ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.展开更多
文摘Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.
基金The National Key Research and Development Program of China(No.2018YFC1314900,2018YFC1314902)the National Natural Science Foundation of China(No.61571109)the Fundamental Research Funds for the Central Universities(No.2242017K3DN04).
文摘To investigate how synonymous codons have been adapted to the formation of ribonucleic acid(RNA)G-quadruplex(rG4)structure,a computational searching algorithm G4Hunter was applied to detect rG4 structures in protein-coding sequences of mRNAs in five eukaryotic species.The native sequences forming rG4s were then compared with randomized sequences to evaluate selection on synonymous codons.Factors that may influence the formation of rG4 were also investigated,and the selection pressures of rG4 in different gene regions were compared to explore its potential roles in gene regulation.The results show universal selective pressure acts on synonymous codons in rG4 regions to facilitate rG4 formation in five eukaryotic organisms.While G-rich codon combinations are preferred in the rG4 structural region,C-rich codon combinations are selectively unfavorable for rG4 formation.Gene's codon usage bias,nucleotide composition,and evolutionary rate can account for the selective variations on synonymous codons among rG4 structures within a species.Moreover,rG4 structures in the translational initiation region showed significantly higher selective pressures than those in the translational elongation region.
文摘This is an attempt to explain mRNA-dependent non-stationary semantic values of codons (triplets) and nucleotides (letters) in codon composition during protein biosynthesis. This explanation is realized by comparing the different protein codes of various biosystem taxa, and, comparing mitochondrial code with the standard code. An initial mRNA transcriptional virtuality (Virtual-Reality) is transformed into material reality at the level of translation of virtual triplets into real (material) amino acids or into a real stop command of protein biosynthesis. The transformation of virtuality into reality occurs de facto when the linguistic sign1 functions of the codon syhoms are realized in the 3’ nucleotide (wobbling nucleotide according to F. Crick) in the process of protein biosynthesis. This corresponds to the theoretical works of the authors of this article. Despite the illusory appearance of semantic arbitrariness during the operation of ribosomes in the mode of codon semantic non-stationarity, this phenomenon probably provides biosystems with an unusually high level of adaptability to changes in the external environment as well as to internal (mental) dynamics of neuron’s genome in the cerebral cortex. The genome’s non-stationarity properties at the nucleotide, codon, gene and mental levels have fractal structure and corresponding dimensions. The highest form of such fractality (with maximum dimension) is probably realized in the genomic continuum of neurons in the human cerebral cortex through this semantic Virtual-to-Real (VR) codon transcoding with the biosynthesis of short-living semantic proteins, as the equivalents of material thinking-consciousness. In fact, this is the language of the brain’s genome, that is, our own language. In this case, the same thing happens in natural, primarily mental (non-verbal) languages. Their materialization is recorded in vocables (sounding words) and in writing. Such writing is the amino acid sequence in the semantic proteins of the human cerebral cortex. Rapidly decaying, such proteins can leave a long-lasting “so-called” Schrödinger wave holographic memory in the cerebral cortex. The presented below study is purely theoretical and based on a logical approach. The topic of the study is very complex and is subject to further development.
文摘Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (austin model 1) methods. As distinct from previous calculations, for nucleotides the interaction with neighbours is taken into account up to gradient of convergence equaling 1. The dependencies of these variables from the place in the codon and the de- terminative degree were obtained. The difference of these variables for codons and anticodons is shown.
文摘Codon nonsense mutations include amber, ochre, or opal mutations according to termination codon consisting of three types (TAG, TAA and TGA). Codon nonsense mutations are also divided into natural and artificial mutations. We discussed the interaction of codon nonsense mutations and suppressor tRNAs in vitro and in vivo. Nonsense suppressions do not only happen in prokaryotes but also in eukaryotes. Meanwhile, the misreading of termination codon and in-corporation of nonnatural amino acids into proteins are also introduced.
基金Funding Statement:This work was funded by the National Natural Science Foundation of China(32100132)Shandong Province Natural Sciences Foundation of China(ZR2021QC008)+1 种基金Youth Innovation Team Program'in College of Shandong Province of China(2022KJ119)supported by Young Talent of Lifting Engineering for Science and Technology in Shandong,China(SDAST2024QT085).
文摘Sweet potatoes are significant cash crops,however,their yield and quality are greatly compromised by viral diseases.In this study,the complete genomic sequences of two Sweet Potato Virus 2(SPV2)isolates from infected sweet potato leaves in the Shandong(designated as SPV2-SDYT,GenBank No.PQ855660.1)and Jiangsu(designated as SPV2-JSXZ,GenBank No.PQ855661.1)provinces in China were obtained using 5′RACE and RT-PCR amplification.Consistency,phylogeny,codon usage bias,recombination,and selection pressure analyses were conducted using the SPV2-SDYT and SPV2-JSXZ genome sequences.The complete genome sequences of SPV2-SDYT and SPV2-JSXZ were 10561 nucleotides(nt)in length,with respective nucleotide and amino acid identities of 99.25%and 99.12%,respectively.Both isolates were closely related to the SPV2 isolate from China(SPV2-LN).In both SPV2-SDYT and SPV2-JSXZ,the identity of the P1 protein was the highest,whereas that of the P3 protein was the lowest.There were 26 codons with relatively synonymous codon usage(RSCU)values greater than 1 in SPV2-SDYT and 27 codons with RSCU values greater than 1 in SPV2-JSXZ.High-frequency codons in their genomes were predominantly found to end with A/U.Recombination analysis revealed no major recombination sites in either SPV2-SDYT or SPV2-JSXZ.Further selection pressure analysis showed that the non-synonymous substitution rate/synonymous substitution rate(dN/dS)value of all 10 SPV2 proteins was less than 1.This is the first report on the evolutionary relationships of the 17 known SPV2 isolates.Our findings lay the molecular groundwork for preventing and controlling SPV2 infection in root-tuber crops.These findings also contribute to our understanding of the spread and evolution of SPV2,its pathogenic mechanisms,and the development of antiviral strategies against it.
文摘We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 1997 to 2007, except viruses from 2000. The haemagglutinin sequences of viruses from southeast Asia, Hong Kong and China's Mainland were the most polymorphic and had similar nonsyn-onymous profiles. Some sites were positively selected in viruses from most regions and a few of these sites displayed different amino acid patterns. Selection appeared to produce different outcomes in vi-ruses from Europe, Africa and Russia and from different host types. One position was found to be positively selected for human isolates only. Although the functions of some positively selected posi-tions are unknown, our analysis provided evidence of different temporal, spatial and host adaptations for H5N1 avian influenza viruses.
基金This work was supported by the National Science Foundation of China(31572220,31272633,31201760)the National High Technology Research and Development Program of China(863 Program)(2011AA100403)the Shanghai University Knowledge Service Platform(ZF1206).
文摘Tgf2 transposase(Tgf2-TPase),a hAT transposase from goldfish,plays an important role in fish transgenic applications.Previously,the production of the recombinant Tgf2-TPase protein required rigorous fermentation at low temperatures(22℃)and early log phase induction(OD600=0.3–0.4)in Rosetta 1(DE3)Escherichia coli lines.In order to better express the Tgf2-TPase and detect its enzyme activity,83 rare codons in Tgf2-TPase were optimized and designated Tgf2-TPase^(83).The expression results showed that the soluble recombinant Tgf2-TPase83 was highly expressed at 30℃ and was inducible at an OD600 of 0.5–0.6 in the same prokaryotic expression system.After purification by affinity chromatography,Tgf2-TPase83 with codon optimization had higher enzyme activity than the Tgf2-TPase control.Comparison of different preservation methods(freezedrying at−80℃,storage in 20%-glycerol,8%-sucrose,4%-mannitol),revealed storage of Tgf2-TPase^(83) in glycerol helped to preserve its DNase digestion activity.Furthermore,size exclusion chromatography suggested that the purified Tgf2-TPase^(83) could recognize and bind to DNA probes containing a terminal inverted repeat(TIR)and a subterminal repeat(STR)sequence of the Tgf2 transposon.Overall,the results showed that optimizing the 83 codons of Tgf2 transposase can simplify the fermentation process and improve the enzyme activity.We propose that the production of the Tgf2-Tpase83 protein in a soluble and active form could provide an alternative tool for genetic modification of fish.
基金funded by the grant National Key R&D Program of China(2017ZX10103011-004 and 2018YFC1603804)the Science and Technology Program of Guangdong Province(2018B020207013 and 2019B030316013).
文摘Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.
基金This work was supported by the National Major Basic Research and Development Program(No.TG1999016004)Jiangsu Provincial Natural Science Foundation(No.BK2003213).
文摘Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.
文摘Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ＇optimal codons＇ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.
