The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression

"Codon optimization" is a general approach to improving heterologous expression where genes are moved from their native genomes into alternatives that exhibit different patterns of codon usage. However, despite reports of successful manipulations and the existence of stand-alone codon optimization software packages or commercial services that offer to redesign genes, the scientific community lacks any systematic understanding of what exactly it means to optimize codon usage. Thus we present a bona fide web application, the "Synthetic Gene Designer," which contrasts with existing software by providing a centralized, free, and transparent platform for the broader scientific community to develop knowledge about synthetic gene design. Consistent with this goal, our software is associated with a moderated e-forum that promotes discussion of synthetic gene design and offers technical support. In addition, the Synthetic Gene Designer presents enhanced functionality over existing software options: for example, it enables users to work with non-standard genetic codes, with user-defined patterns of codon usage and an expanded range of methods for codon optimization. The Synthetic Gene Designer, together with on-line tutorials and the forum, is available at .     

Codon bias of the gene for chloroplast glycerol-3-phosphate acyltransferase in Camellia sinensis (L.) O. Kuntze

The analysis on codon usage bias of GPAT gene of Camellia sinensis (L.) O. Kuntze may provide a basis for understanding the evolution relationship of C. sinensis and for selecting appropriate host expression systems to improve the expression of target genes. In the present study, the coding sequence of CsGPAT was analyzed with CodonW, CHIPS and CUSP programs, and compared with the genome of C. sinensis and GPAT genes of other 9 plant species. Our results showed that the cluster tree based on CDs could reveal the evolutional relations among the 10 plant species, whereas the cluster tree based on relative synonymous codon usage (RSCU) could not. There were 31 codons showing distinct usage differences between CsGPAT and genome of Escherichia coli, 21 between CsGPAT and yeast, but 13 between CsGPAT and Arabidopsis thaliana. But there were slightly fewer differences in codon usage between CsGPAT and A. thaliana. Therefore, the A. thaliana expression system may be more suitable for the expression of CsGPAT. These results may improve our understanding of the codon usage bias and functional studies of CsGPAT.     

Over expression and purification of recombinant human myocilin

Human myocilin is a 55 kDa protein that is implicated in primary open angle glaucoma (POAG). Understanding the structure and folding of the native protein and the mutants that increase aggregation could lead to possible prevention of the condition. We report here the over expression and purification of the human myocilin in E. coli. The initial expression of recombinant myocilin in E. coli was found to be low. The problem of low yield was found to be due to multiple causes and was overcome using a suitable combination of vectors, tags, host background and expression protocols. The overexpressed human myocilin was purified by affinity column chromatography to yield about 8 mg of protein from 1 l of culture. The protein purity and folding were confirmed using electrophoresis, immunoblotting and fluorescence spectroscopy. Further biophysical characterization and crystallization trials using the recombinant human myocilin will pave the way for better understanding of the structure–aggregation relationship that is involved in causing POAG.     

Optimization protein productivity of human interleukin-2 through codon usage,gene copy number and intracellular tRNA concentration in CHO cells

Transfer RNA (tRNA) abundance is one of the critical factors for the enhancement of protein productivity in prokaryotic and eukaryotic hosts. Gene copy number of tRNA and tRNA codon usage bias are generally used to match tRNA abundance of protein-expressing hosts and to optimize the codons of recombinant proteins. Because sufficient concentration of intracellular tRNA and optimized codons of recombinant proteins enhanced translation efficiency, we hypothesized that sufficient supplement of host’s tRNA improved protein productivity in mammalian cells. First, the small tRNA sequencing results of CHO-K1 cells showed moderate positive correlation with gene copy number and codon usage bias. Modification of human interleukin-2 (IL-2) through codons with high gene copy number and high codon usage bias (IL-2 HH, modified on Leu, Thr, Glu) significantly increased protein productivity in CHO-K1 cells. In contrast, modification through codons with relatively high gene copy number and low codon usage bias (IL-2 HL, modified on Ala, Thr, Val), or relatively low gene copy number and low codon usage bias (IL-2 LH, modified on Ala, Thr, Val) did not increase IL-2 productivity significantly. Furthermore, supplement of the alanine tRNA or threonine tRNA increased IL-2 productivity of IL-2 HL. In summary, we revealed a potential strategy to enhance productivity of recombinant proteins, which may be applied in production of protein drug or design of DNA vaccine.     

Enhancement of copper content and specific activity of CotA laccase from Bacillus licheniformis by coexpression with CopZ copper chaperone in E. coli

Copper depletion of bacterial laccases obtained by heterologous expression in Escherichia coli is a common problem in production of these versatile biocatalysts. We demonstrate that coexpression of small soluble copper chaperones can mitigate this problem. The laccase CotA and the copper chaperone CopZ both from Bacillus licheniformis were used as model system. The use of the E. coli BL21(DE3) strain expressing CopZ and CotA simultaneously from two plasmids resulted in an 20% increase in copper occupancy and in 26% higher specific activity. We conclude that not only intracellular copper ion concentration, but also presence of an appropriate copper chaperone influences copper ion insertion into CotA laccase. Moreover, E. coli BL21(DE3) seems to lack such a copper chaperone which can be partially complemented by heterologous expression thereof. The presented system is simple and can routinely be used for improved heterologous production of bacterial laccase in E. coli.     

用图论方法研究核酸序列的密码子使用与基因表达水平的关系

研究了Escherichiacoli（115个基因）和SacharomycesYeast（97个基因）核酸序列的密码子使用频率与基因表达水平的关系．将同义密码子按使用频率统计值分成三种特性的密码子：最适密码子（H）、非最适密码子（L）和稀有密码子（R）,对每一基因序列的编码区,算出它们各自出现的概率P（H）,P（L）和P（R）．以P（H）和P（R）为指标,用图论法聚类,发现每种生物的高低表达基因明显分开,基因表达水平被分为四级：甚高表达基因（VH）、高表达基因（H）、较低表达基因（LM）和低表达基因（LL）．每类基因的表达水平与实验结果保持了很好的相关性,与E．coli和Yeast的现有资料相比,符合很好．     

The methylotrophic yeast Pichia pastoris as a host for the expression and production of thermostable xylanase from the bacterium Rhodothermus marinus

A thermostable glycoside hydrolase family-10 xylanase originating from Rhodothermus marinus was cloned and expressed in the methylotrophic yeast Pichia pastoris (SMD1168H). The DNA sequence from Rmxyn10A encoding the xylanase catalytic module was PCR-amplified and cloned in frame with the Saccharomyces cerevisiae alpha-factor secretion signal under the control of the alcohol oxidase (AOX1) promotor. Optimisation of enzyme production in batch fermentors, with methanol as a sole carbon source, enabled secretion yields up to 3gl(-1) xylanase with a maximum activity of 3130Ul(-1) to be achieved. N-terminal sequence analysis of the heterologous xylanase indicated that the secretion signal was correctly processed in P. pastoris and the molecular weight of 37kDa was in agreement with the theoretically calculated molecular mass. Introduction of a heat-pretreatment step was however necessary in order to fold the heterologous xylanase to an active state, and at the conditions used this step yielded a 200-fold increase in xylanase activity. Thermostability of the produced xylanase was monitored by differential-scanning calorimetry, and the transition temperature (T(m)) was 78 degrees C. R. marinus xylanase is the first reported thermostable gram-negative bacterial xylanase efficiently secreted by P. pastoris.     

Toxicity of a heterologous leucyl-tRNA (anticodon CAG) in the pathogen Candida albicans: in vivo evidence for non-standard decoding of CUG codons

Plasmids containing derivatives of the Saccharomyces cerevisiae leucyl-tRNA (tRNA3₃^Leu) gene that vary in anticodon sequence were constructed and transformed into the pathogen Candida albicans and S. cerevisiae. C. albicans could readily be transformed with plasmids encoding leucyl-tRNA genes with the anticodons CAA and UAA (recognizing the codons UUG and UUA) and expression of the heterologous tRNA^Leu could be demonstrated by Northern RNA blotting. In contrast, no transformants were obtained if the anticodons were UAG (codons recognized CUN, UUR) and CAG (codon CUG), indicating that the insertion of leucine at CUG codons is toxic for C. albicans. All tRNA^Leu-encoding plasmids transformed S. cerevisiae with equally high efficiencies. These results provide in vivo evidence that non-standard decoding of CUG codons is essential for the viability of C. albicans.     

The Role of Context-Dependent Mutations in Generating Compositional and Codon Usage Bias in Grass Chloroplast DNA

Abstract The influence of local base composition on mutations in chloroplast DNA (cpDNA) is studied in detail and the resulting, empirically derived, mutation dynamics are used to analyze both base composition and codon usage bias. A 4 × 4 substitution matrix is generated for each of the 16 possible flanking base combinations (contexts) using 17,253 noncoding sites, 1309 of which are variable, from an alignment of three complete grass chloroplast genome sequences. It is shown that substitution bias at these sites is correlated with flanking base composition and that the A+T content of these flanking sites as well as the number of flanking pyrimidines on the same strand appears to have general influences on substitution properties. The context-dependent equilibrium base frequencies predicted from these matrices are then applied to two analyses. The first examines whether or not context dependency of mutations is sufficient to generate average compositional differences between noncoding cpDNA and silent sites of coding sequences. It is found that these two classes of sites exist, on average, in very different contexts and that the observed mutation dynamics are expected to generate significant differences in overall composition bias that are similar to the differences observed in cpDNA. Context dependency, however, cannot account for all of the observed differences: although silent sites in coding regions appear to be at the equilibrium predicted, noncoding cpDNA has a significantly lower A+T content than expected from its own substitution dynamics, possibly due to the influence of indels. The second study examines the codon usage of low-expression chloroplast genes. When context is accounted for, codon usage is very similar to what is predicted by the substitution dynamics of noncoding cpDNA. However, certain codon groups show significant deviation when followed by a purine in a manner suggesting some form of weak selection other than translation efficiency. Overall, the findings indicate that a full understanding of mutational dynamics is critical to understanding the role selection plays in generating composition bias and sequence structure.     

西藏高原人群铁调素基因hamp密码子偏好性分析

目的:通过对西藏高原人群及平原人群、恒河猴等其他5种物种的密码子使用进行分析,从而得出西藏高原人群铁调素基因(hamp)的密码子偏好性。方法:采用PCR技术获得西藏高原人群铁调素全基因序列,利用在线软件CodonW进行密码子偏好性分析,通过在线软件PredictProtein以及Signal P等软件进行西藏高原人群铁调素基因的结构分析,比较与GenBank数据库中选取的平原人群、恒河猴等其他5种物种的密码子偏好性的差异。结果:西藏高原人群的铁调素基因全长为2681 bp,由3个外显子和2个内含子组成,编码84个氨基酸的铁调素前体肽,包含信号肽、中间肽与成熟肽,其密码子偏好性与平原人群、恒河猴等其他5个物种的密码子偏好性均有不同程度的差异。结论:西藏高原人群铁调素基因hamp密码子偏好性与其他物种的密码子偏好性均有不同程度的差异。     

Codon Bias and Noncoding GC Content Correlate Negatively with Recombination Rate on the Drosophila X Chromosome

The patterns and processes of molecular evolution may differ between the X chromosome and the autosomes in Drosophila melanogaster. This may in part be due to differences in the effective population size between the two chromosome sets and in part to the hemizygosity of the X chromosome in Drosophila males. These and other factors may lead to differences both in the gene complements of the X and the autosomes and in the properties of the genes residing on those chromosomes. Here we show that codon bias and recombination rate are correlated strongly and negatively on the X chromosome, and that this correlation cannot be explained by indirect relationships with other known determinants of codon bias. This is in dramatic contrast to the weak positive correlation found on the autosomes. We explored possible explanations for these patterns, which required a comprehensive analysis of the relationships among multiple genetic properties such as protein length and expression level. This analysis highlights conserved features of coding sequence evolution on the X and the autosomes and illuminates interesting differences between these two chromosome sets.[Reviewing editor: Dr. Richard Kliman]     

巴斯德毕赤酵母表达系统在外源基因表达中的研究进展

巴斯德毕赤酵母是目前应用最广泛的外源蛋白表达系统。分别从的菌株、载体、外源基因整合、表达产物糖基化和外源基因高效表达等方面综述了毕赤酵母表达系统的研究进展。     

Codon usage bias as a function of generation time and life expectancy

It has recently been demonstrated that human natural codon usage bias is optimized towards a higher buffering capacity to mutations (measured as the tendency of single point mutations in a DNA sequence to yield the same or similar amino acids) compared to random sequences. In this work, we investigate this phenomenon further by analyzing the natural DNA of four different species (human, mouse, zebrafish and fruit fly) to determine whether such a tolerance to mutations is correlated with the life span and age of sexual maturation for the corresponding organisms. We also propose a new measure to quantify the buffering capacity of a DNA sequence to mutations that takes into account the observed mutation rates within every genome and the effect of the corresponding mutation.Our results suggest there is a propensity for tolerance to mutations that is positively correlated with the life expectancy of the considered organisms. Moreover, random sequences that are constrained to produce the same protein as the naturally occurring sequences are found to be more buffered than completely random sequences while being less buffered than the natural sequences. These results suggest that optimization toward protective mechanisms tolerant to mutations is correlated with both life expectancy and age to sexual maturity at both the levels of codon usage bias and the bias of the natural sequence of codons itself.