TGA Codon Research Articles

Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

We present a comprehensive analysis of stop codon usage in bacteria by analyzing over eight million coding sequences of 4684 bacterial sequences. Using a newly developed program called "stop codon counter," the frequencies of the three classical stop codons TAA, TAG, and TGA were analyzed, and a publicly available stop codon database was built. Our analysis shows that with increasing genomic GC content the frequency of the TAA codon decreases and that of the TGA codon increases in a reciprocal manner. Interestingly, the release factor 1-specific codon TAG maintains a more or less uniform frequency (∼20%) irrespective of the GC content. The low abundance of TAG is also valid with respect to expression level of the genes ending with different stop codons. In contrast, the highly expressed genes predominantly end with TAA, ensuring termination with either of the two release factors. Using three model bacteria with different stop codon usage (Escherichia coli, Mycobacterium smegmatis, and Bacillus subtilis), we show that the frequency of TAG and TGA codons correlates well with the relative steady state amount of mRNA and protein for release factors RF1 and RF2 during exponential growth. Furthermore, using available microarray data for gene expression, we show that in both fast growing and contrasting biofilm formation conditions, the relative level of RF1 is nicely correlated with the expression level of the genes ending with TAG.

Novel Point Mutation of the α2-Globin Gene (HBA2) and a Rare 2.4 kb Deletion of the α1-Globin Gene (HBA1), Identified in Two Chinese Patients with Hb H Disease

Two Chinese patients with mild and moderate Hb H disease were investigated for rare mutations on the α-globin genes (HBA1, HBA2) in addition to the – –SEA deletion. One patient was a 41-year old man with mild anemia (Hb 11.3 g/dL). Multiplex ligation-dependent probe amplification (MLPA) revealed a rare 2392 bp deletion involving the entire HBA1 gene. Mapping by gap-polymerase chain reaction (gap-PCR) defined the exact breakpoints of this deletion (HBA1: g36859_39252del2392) and confirmed its identity with a recently reported HBA1 deletion found in a Southern Chinese. The other patient was a 53-year old man with moderate anemia (Hb 9.5 g/dL). Automated direct nucleotide (nt) sequencing identified a novel single nt deletion at codon 40 (HBA2: c.123delG). This leads to a frameshift that modifies the C-terminal sequence to (40)Lys-Pro-Thr-Ser-Arg-Thr-Ser-Thr(47)COOH and the introduction of a stop codon TGA 23 nts downstream. These two cases demonstrate the power of MLPA and direct nt sequencing to detect and characterize rare and novel mutations. They also highlight the differential effect of HBA1 and HBA2 gene mutations on an α-thalassemia (α-thal) phenotype due to their different transcriptional activity.

Analysis of the Secretome and Identification of Novel Constituents from Culture Filtrate of Bacillus Calmette-Guérin Using High-resolution Mass Spectrometry

Tuberculosis (TB) is an infectious bacterial disease that causes morbidity and mortality, especially in developing countries. Although its efficacy against TB has displayed a high degree of variability (0%-80%) in different trials, Mycobacterium bovis bacillus Calmette-Guérin (BCG) has been recognized as an important weapon for preventing TB worldwide for over 80 years. Because secreted proteins often play vital roles in the interaction between bacteria and host cells, the secretome of mycobacteria is considered to be an attractive reservoir of potential candidate antigens for the development of novel vaccines and diagnostic reagents. In this study, we performed a proteomic analysis of BCG culture filtrate proteins using SDS-PAGE and high-resolution Fourier transform mass spectrometry. In total, 239 proteins (1555 unique peptides) were identified, including 185 secreted proteins or lipoproteins. Furthermore, 17 novel protein products not annotated in the BCG database were detected and validated by means of RT-PCR at the transcriptional level. Additionally, the translational start sites of 52 proteins were confirmed, and 22 proteins were validated through extension of the translational start sites based on N-terminus-derived peptides. There are 103 secreted proteins that have not been reported in previous studies on BCG [corrected] secretome and are unique to our study. The physicochemical characteristics of the secreted proteins were determined. Major components from the culture supernatant, including low-molecular-weight antigens, lipoproteins, Pro-Glu and Pro-Pro-Glu family proteins, and Mce family proteins, are discussed; some components represent potential predominant antigens in the humoral and cellular immune responses.

Some new characteristics of large genomes

This paper reports the results of calculations for some new characteristics of large genomes. Twelve genomes with a total of 203942 genes have been analyzed. The study is based on theoretical research on gene blocking published in 2010 in this journal. The calculations have shown that for all genomes the blocking is not random and not extreme. For the human genome its average value is less than a third of the maximum theoretical value and by a factor of 2.5 larger than its theoretical minimal value. It is shown that plus and minus in the DNA chain are blocked practically in the same way for all studied genomes. The participation of termination codons in blockings was found to be not equally probable. For almost all considered genomes the TGA codon was used more than 50% compared to TAA and TAG. The fact that as of September 2011 more than 1200 large genomes are being decoded in the world adds relevance to this work.

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

The composition of the human microbiota is recognized as an important factor in human health and disease. Many of our cohabitating microbes belong to phylum-level divisions for which there are no cultivated representatives and are only represented by small subunit rRNA sequences. For one such taxon (SR1), which includes bacteria with elevated abundance in periodontitis, we provide a single-cell genome sequence from a healthy oral sample. SR1 bacteria use a unique genetic code. In-frame TGA (opal) codons are found in most genes (85%), often at loci normally encoding conserved glycine residues. UGA appears not to function as a stop codon and is in equilibrium with the canonical GGN glycine codons, displaying strain-specific variation across the human population. SR1 encodes a divergent tRNA(Gly)UCA with an opal-decoding anticodon. SR1 glycyl-tRNA synthetase acylates tRNA(Gly)UCA with glycine in vitro with similar activity compared with normal tRNA(Gly)UCC. Coexpression of SR1 glycyl-tRNA synthetase and tRNA(Gly)UCA in Escherichia coli yields significant β-galactosidase activity in vivo from a lacZ gene containing an in-frame TGA codon. Comparative genomic analysis with Human Microbiome Project data revealed that the human body harbors a striking diversity of SR1 bacteria. This is a surprising finding because SR1 is most closely related to bacteria that live in anoxic and thermal environments. Some of these bacteria share common genetic and metabolic features with SR1, including UGA to glycine reassignment and an archaeal-type ribulose-1,5-bisphosphate carboxylase (RubisCO) involved in AMP recycling. UGA codon reassignment renders SR1 genes untranslatable by other bacteria, which impacts horizontal gene transfer within the human microbiota.

Bacterial phylogenetic tree construction based on genomic translation stop signals

BackgroundThe efficiencies of the stop codons TAA, TAG, and TGA in protein synthesis termination are not the same. These variations could allow many genes to be regulated. There are many similar nucleotide trimers found on the second and third reading-frames of a gene. They are called premature stop codons (PSC). Like stop codons, the PSC in bacterial genomes are also highly bias in terms of their quantities and qualities on the genes. Phylogenetically related species often share a similar PSC profile. We want to know whether the selective forces that influence the stop codons and the PSC usage biases in a genome are related. We also wish to know how strong these trimers in a genome are related to the natural history of the bacterium. Knowing these relations may provide better knowledge in the phylogeny of bacteriaResultsA 16SrRNA-alignment tree of 19 well-studied α-, β- and γ-Proteobacteria Type species is used as standard reference for bacterial phylogeny. The genomes of sixty-one bacteria, belonging to the α-, β- and γ-Proteobacteria subphyla, are used for this study. The stop codons and PSC are collectively termed “Translation Stop Signals” (TSS). A gene is represented by nine scalars corresponding to the numbers of counts of TAA, TAG, and TGA on each of the three reading-frames of that gene. “Translation Stop Signals Ratio” (TSSR) is the ratio between the TSS counts. Four types of TSSR are investigated. The TSSR-1, TSSR-2 and TSSR-3 are each a 3-scalar series corresponding respectively to the average ratio of TAA: TAG: TGA on the first, second, and third reading-frames of all genes in a genome. The Genomic-TSSR is a 9-scalar series representing the ratio of distribution of all TSS on the three reading-frames of all genes in a genome. Results show that bacteria grouped by their similarities based on TSSR-1, TSSR-2, or TSSR-3 values could only partially resolve the phylogeny of the species. However, grouping bacteria based on thier Genomic-TSSR values resulted in clusters of bacteria identical to those bacterial clusters of the reference tree. Unlike the 16SrRNA method, the Genomic-TSSR tree is also able to separate closely related species/strains at high resolution. Species and strains separated by the Genomic-TSSR grouping method are often in good agreement with those classified by other taxonomic methods. Correspondence analysis of individual genes shows that most genes in a bacterial genome share a similar TSSR value. However, within a chromosome, the Genic-TSSR values of genes near the replication origin region (Ori) are more similar to each other than those genes near the terminus region (Ter).ConclusionThe translation stop signals on the three reading-frames of the genes on a bacterial genome are interrelated, possibly due to frequent off-frame recombination facilitated by translational-associated recombination (TSR). However, TSR may not occur randomly in a bacterial chromosome. Genes near the Ori region are often highly expressed and a bacterium always maintains multiple copies of Ori. Frequent collisions between DNA- polymerase and RNA-polymerase would create many DNA strand-breaks on the genes; whereas DNA strand-break induced homologues-recombination is more likely to take place between genes with similar sequence. Thus, localized recombination could explain why the TSSR of genes near the Ori region are more similar to each other. The quantity and quality of these TSS in a genome strongly reflect the natural history of a bacterium. We propose that the Genomic- TSSR can be used as a subjective biomarker to represent the phyletic status of a bacterium.

Bioinformatic prediction of selenoprotein genes in the dolphin genome

Selenium (Se), an essential trace element in vivo, is present mainly as selenocystein (Sec) in various selenoproteins. The Sec residue is translated from an in-frame TGA codon, which traditionally functions as a stop codon. Prediction of selenoprotein genes is difficult due to the lack of an effective method for distinguishing the dual function of the TGA codon in the open reading frame of a selenoprotein gene. In this article a eukaryotic bioinformatic prediction system that we have developed was used to predict selenoprotein genes from the genome of the common bottlenose dolphin, Tursiops truncatus. Sixteen selenoprotein genes were predicted, including selenoprotein P and glutathione peroxidase. In particular, a type II iodothyronine deiodinase was found to have two Sec residues, while the type I iodothyronine deiodinase gene has two alternative splice forms. These results provide important information for the investigation of the relationship between a variety of selenoproteins and the evolution of the marine-living dolphin.

Expression patterns of type II and III iodothyronine deiodinase genes in the liver of the goldlined spinefoot, Siganus guttatus

Iodothyronine deiodinases play an important role in thyroid hormone regulation in vertebrates. The aim of this study was to clone type II (SgD2) and type III (SgD3) iodothyronine deiodinase cDNA from the goldlined spinefoot (Siganus guttatus) using 3′- and 5′-rapid amplification of cDNA ends and then to assess their expression patterns in the liver under several experimental conditions by using quantitative real-time PCR. SgD2 (1013 bp) and SgD3 (1492 bp) contained open reading frames of 810 and 804 bp and encoded 270 and 269 amino acids, respectively. They were characterized by an in-frame TGA codon that was considered to be selenocysteine. An abundance of SgD2 and SgD3 mRNA was expressed in several tissues, with an increase at 1200 hours and a decrease at 2400 hours. Food deprivation suppressed the expression of SgD2, but not SgD3. Higher SgD2 and SgD3 mRNA levels in the liver were found in fish reared at 25°C than in those reared at 20 and 30°C. These results suggest that exogenous factors influence the mRNA levels of iodothyronine deiodinase genes in the liver and that transcription of the genes in certain tissues is partially regulated in a circadian manner.

Mycoplasma gallisepticum and Mycoplasma synoviae express a cysteine protease CysP, which can cleave chicken IgG into Fab and Fc

Major poultry pathogens M. gallisepticum and M. synoviae share a gene encoding a putative cysteine protease CysP similar to papain cysteine protease (C1A subfamily). Comparison of the cysP gene sequences of 18 M. synoviae and 10 M. gallisepticum strains sequenced in this study showed polymorphisms, including deletions. Seven M. synoviae strains, including the type strain WVU 1853, had a 39 bp deletion in the 3' end of the cysP gene. In the same cysP region, all M. gallisepticum strains showed a deletion of 66 bp. Immunoblot analysis with specific antibodies demonstrated that M. synoviae strains expressed CysP, which was approximately 65 kDa. Both M. synoviae and M. gallisepticum were able to digest chicken IgG (cIgG). Incubation of cIgG (∼170 kDa) with M. synoviae or M. gallisepticum cells (∼15 h at 37 °C) resulted in a papain-like cleavage pattern of cIgG and fragments corresponding to the antigen-binding fragment of IgG (Fab, ∼45 kDa) and the crystallizable region fragment (Fc) of the IgG heavy chain (dimer of ∼60 kDa). Iodoacetamide (50 mM) prevented cleavage of cIgG by both Mycoplasma species. Following site-directed mutagenesis (eight TGA codons were changed to TGG) the cysP gene of M. synoviae ULB 925 was expressed as a His-tagged protein in a cell-free system. Purified recombinant CysP (rCysP; ∼67 kDa, pI∼8) cleaved cIgG into Fab and Fc fragments. This indicates that CysP is responsible for the cIgG cleavage caused by M. synoviae and, probably, by M. gallisepticum. This is the first evidence to our knowledge that mycoplasmas have enzymes that can cleave the host IgG and indicates a novel strategy used by M. gallisepticum and M. synoviae for prolonged survival despite the antibody response of their host.

An adhesion molecule-based colloidal gold immunochromatography assay strip for rapidly and specifically detecting chicken antibodies against Mycoplasma gallisepticum

The fragment of the VlhA1.2 gene was cloned from a Mycoplasma gallisepticum (MG) DNA library by serial PCRs after the same-sense mutagenesis of three TGA codons encoding tryptophan (Trp). Following transforming the generated plasmid of pKG-VlhA1.2, the recombinant VlhA1.2-GST fusion protein of 92 kDa was induced and recognized by anti-MG sera. After GST-affinity chromatographic purification, the VlhA-based colloidal gold immunochromatography assay (GICA) strips were generated. The GICA strips specifically detected anti-MG antibodies, but not antibodies against Mycoplasma synoviae and other positive sera against non-MG pathogens tested. The GICA strips were 128-fold more sensitive to detect anti-MG antibodies, as compared with traditional serological methods and were stored at 4 °C for 15 months without loss of their sensitivity and specificity. Analysis of sample revealed that, the GICA strips were highly sensitive, specific and stable for the on-site surveillance of MG infections by unskilled users.

Preparation of two types p53 recombinant adenovirus and quantitative exogenous expression of green fluorescence protein by flow cytometry

背景与目的p53作为转录因子，在细胞应激时呈活化型，可调控细胞周期和程序性死亡抑制肿瘤生长，通常通过各种机制可使p53呈现非活化状态，其中包括p53 C-末端负调控序列的作用。本研究旨在制备携带全长和缺失这些负调控序列p53的两种重组腺病毒，并采用流式细胞仪散点图（flow cytometry scater plot, FCM）检测人肺癌细胞外源绿荧光蛋白（green fluorescence protein, GFP）表达。方法利用pAdEasy-Track载体系统，构建两种p53重组质粒并在细菌中产生重组体，转染L293细胞产生三种重组腺病毒，测序证明。三种不同浓度病毒分别感染人肺癌801D细胞，FCM scater plot检测其GFP表达。结果测序证明重组腺病毒：Ad-p53(del)缺失p53 C-末端终止密码子前111个碱基和非编码区，Ad-p53(wtp)无p53碱基缺失。Ad-(empty carrier)无p53。FCM scater plot显示三种病毒感染801D细胞表达GFP百分率接近并随病毒浓度递增。801D包含了不同荧光强度比率的细胞。结论构建和制备了去C-末端p53和全长p53的两种重组腺病毒：Ad-p53(del)、Ad-p53(wtp)及空载体Ad-(empty carrier)。流式细胞仪散点图证明该病毒试验系统可靠，可定量外源GFP表达为病毒感染细胞选择浓度提供准确方法。

In silico identification of the sea squirt selenoproteome

BackgroundComputational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF) of eukaryotic selenoprotein gene, because the TGA codon for a selenocysteine (Sec) residue in the active centre of selenoprotein is traditionally a terminal signal of protein translation. Although the identification of selenoproteins from genomes through bioinformatics methods has been conducted in bacteria, unicellular eukaryotes, insects and several vertebrates, only a few results have been reported on the ancient chordate selenoproteins.ResultsA gene assembly algorithm SelGenAmic has been constructed and presented in this study for identifying selenoprotein genes from eukaryotic genomes. A method based on this algorithm was developed to build an optimal TGA-containing-ORF for each TGA in a genome, followed by protein similarity analysis through conserved sequence alignments to screen out selenoprotein genes form these ORFs. This method improved the sensitivity of detecting selenoproteins from a genome due to the design that all TGAs in the genome were investigated for its possibility of decoding as a Sec residue. Using this method, eighteen selenoprotein genes were identified from the genome of Ciona intestinalis, leading to its member of selenoproteome up to 19. Among them a selenoprotein W gene was found to have two SECIS elements in the 3'-untranslated region. Additionally, the disulfide bond formation protein A (DsbA) was firstly identified as a selenoprotein in the ancient chordates of Ciona intestinalis, Ciona savignyi and Branchiostoma floridae, while selenoprotein DsbAs had only been found in bacteria and green algae before.ConclusionThe method based on SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes. Application of this method to Ciona intestinalis proves its successes in finding Sec-decoding TGA from large-scale eukaryotic genome sequences, which fills the gap in our knowledge on the ancient chordate selenoproteins.

Spiralin-like protein SLP31 from Spiroplasma eriocheiris as a potential antigen for immunodiagnostics of tremor disease in Chinese mitten crab Eriocheir sinensis

Spiroplasma eriocheiris caused massive mortality of Chinese mitten crab Eriocheir sinensis but little is known about the molecular characteristics of this microorganism. We described here the identification of a spiralin-like protein (SLP31) from S. eriocheiris and expression in Escherichia coli. Analysis of the nucleotide sequence revealed that the clone has an open reading frame of 837 bp encoding a protein of 279 amino acids. Theoretical isoelectric point and molar mass for SLP31 are 7.72 and 31 kDa, respectively. The similarity of SLP31 deduced amino acid sequence shared with the spiralin from other species indicated that the gene may be a member of spiralin family. The TGA codon in Spiroplasma serves not as a stop signal but as a code for the amino acid tryptophan. After cloning the SLP31, the gene was site-mutated from TGA to TGG and transcribed in E. coli to full expression of SLP31. The purified recombinant protein was used to determine the immune reactivity by Western blotting which suggests that SLP31 could be a good antigen for immunodiagnostic of tremor disease in E. sinensis.

Abstract B9: Germline conservation of hypermutable codons in gatekeeper tumor suppressor genes implicates pro-carcinogenic CpG sites in vivo as anti-teratogenic ‘shock absorbers’ in utero

Abstract Purpose: Methylated CpG sites are readily mutated, yet are strongly conserved in tumor suppressor genes. Uniquely, the arginine-encoding CGA codon may undergo methylation-dependent point mutation to a stop codon (TGA), whereas the arginine-encoding AGA codon is stable. To clarify the relationship between germline codon mutability and somatic carcinogenesis, we compared patterns of codon usage in tumor suppressor gene subsets known to differ in function and evolutionary stability. Procedures: Human tumor suppressor genes were classified as either pro-apoptotic (gatekeepers; high-essentiality, low Ka/Ks) or repair-type (caretakers; low-essentiality, high Ka/Ks). Reference normal and tumor gene sequence databases were analysed in terms of nucleotide composition (GC%), intragenic CpG sites, and CGA/AGA codon patterns. Phylogenetic analyses of relevant codon frequencies across 24 species from the UCSC database were performed as a control. Results: Species-specific stop codon frequency varies with genomic GC content in a methylation-regulated manner, whereas CGA frequency is GC-independent. Whole-genome frequencies of CGA and TGA codons are positively correlated (p = 0.013). CGA mutation in tumors is asymmetric (TGA >> CAA; p < 0.001), with such mutations 3-fold more likely to be nonsense-type in gatekeepers than in caretakers. Non-random CGA clustering is demonstrable in canonical gatekeepers such as NF1, Rb and TP53 (p < 0.02). Conclusion: Human pro-apoptotic suppressor genes are selectively enriched for the presence of nonsense-prone CpG-containing codons involved in somatic adult-onset tumor progression. We propose that this germline vulnerability is conserved as part of a methylation-dependent embryonic response to environmental teratogens which otherwise cause excessive apoptosis, somatic malformations, and reduced fitness. Citation Information: Clin Cancer Res 2010;16(7 Suppl):B9

Cloning, characterization, and expression analysis of goat (Capra hircus) phospholipid hydroperoxide glutathione peroxidase (PHGPx)

Phospholipid hydroperoxide glutathione peroxidase (PHGPx), as a ubiquitous antioxidant enzyme in the glutathione peroxidases (GPx) family, plays multiple roles in organisms. However, there is very little information on PHGPx in goats (Capra hircus). In this study, a full-length cDNA was cloned and characterized from Taihang black goat testes. The 844 bp cDNA contains an open reading frame (ORF) of 597 bp. The goat PHGPx nucleotide sequence contains a selenocysteine (sec) codon TGA(244-246), two potential start codons ATG(20-22) and ATG(108-110), a polyadenylation signal AATAAA(813-818) and selenocysteine insertion sequence (SECIS) motif AUGA(688-691), UGA(729-731) and AAA(703-705). As a selenoprotein, the active-site motifs and GPx family signature motifs LAFPCNQF(101-108) and WNFEK(165-170) were also found. The order of PHGPx mRNA expression levels was: testes >> heart > brain > epididymis > kidney > liver > lung > spleen > muscle. Real-time PCR and immunohistochemistry results revealed similar expression differences in different age testes, with high expression levels during adolescence. Immunofluorescence results suggested that PHGPx mainly expressed in Leydig cells and spermatids in mature goat testes.

Molecular Cloning, Characterization, and Expression Analysis of Chicken Δ-6 Desaturase

Long-chain polyunsaturated fatty acids (LC-PUFA) promote the development of brain and vision of the fetus, relieve inflammation, inhibit oral dysplasia of rumor cell, decrease the incidence of cardiovascular disease and regulate arrhythmia. Δ-6 desaturase is the rate-limited enzyme in the desaturation process. This study reports the cloning, characterization and tissue expression of a Δ-6 desaturase gene in the chicken. PCR primers were designed based on the predicted sequence of chicken Δ-6 desaturase (accession number: XM421053) and used to isolate a cDNA fragment of 1,323 bp from chicken liver. Based on the 1,323 bp fragment an EST (BI390105) was obtained by BLAST. The EST and 5'end of the 1,323 bp fragment were partially overlapped. Gene specific primers derived from the EST were used for amplification of the 5'end. Another gene-specific primer derived from the 1,323 bp fragment was used for amplification of the 3'end by 3'RACE. Then the three overlapping cDNA sequences obtained were assembled with DNAMAN software and a full-length Δ-6 desaturase of 2,153 bp was obtained. The full-length cDNA contained an ORF of 1,335 bp with a 5'untranslated region of 147 nucleotides followed by an ATG initiation codon. Stop codon TGA was at position 1,481-1,483 bp. The deduced amino acids shared an homology above 77% with bovine, mice, orangutan, rat and human. The protein sequence had three histidine-rich regions HDFGH (HisI region), HFQHH (HisII region) and HH (HisIII region), a cytochrome b 5 -like domain containing a heme-binding motif and two transmembrane domains. Sequence analysis of the chicken genomic DNA revealed that the coding sequence of chicken Δ-6 desaturase included 12 exons and 11 introns. Semi-quantitative RT-PCR showed that the Δ-6 desaturase expression levels were in turn liver, spleen, pancreas, lung, breast muscle, heart, and abdominal fat. The expression of Δ-6 desaturase in liver was significantly higher than that in breast muscle (p<0.01). The expression of Δ-6 desaturase in lung was significantly higher than that in abdominal fat (p<0.01). This is the first clone of chicken Δ - 6 desaturase.

Recombinant Surface Proteomics as a Tool to Analyze Humoral Immune Responses in Bovines Infected by Mycoplasma mycoides Subsp. mycoides Small Colony Type

A systematic approach to characterize the surface proteome of Mycoplasma mycoides subspecies mycoides small colony type (M. mycoides SC), the causative agent of contagious bovine pleuropneumonia (CBPP) in cattle, is presented. Humoral immune responses in 242 CBPP-affected cattle and controls were monitored against one-third of the surface proteins of M. mycoides SC in a high throughput magnetic bead-based assay. Initially, 64 surface proteins were selected from the genome sequence of M. mycoides SC and expressed as recombinant proteins in Escherichia coli. Binding of antibodies to each individual protein could then be analyzed simultaneously in minute sample volumes with the Luminex suspension array technology. The assay was optimized on Namibian CBPP-positive sera and Swedish negative controls to allow detection and 20-fold mean signal separation between CBPP-positive and -negative sera. Signals were proven to be protein-specific by inhibition experiments, and results agreed with Western blot experiments. The potential of the assay to monitor IgG, IgM, and IgA responses over time was shown in a proof-of-concept study with 116 sera from eight animals in a CBPP vaccine study. In conclusion, a toolbox with recombinant proteins and a flexible suspension array assay that allows multiplex analysis of humoral immune responses to M. mycoides SC has been created.

Efficient site-directed mutagenesis using an overlap extension-PCR method for expressing Mycoplasma hyopneumoniae genes in Escherichia coli

Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia and results in significant economic losses in swine production worldwide. Vaccination is considered to be the most cost-effective strategy for control and prevention of this disease. However, the development of new recombinant subunit vaccines is often hampered by the unusual codon usage of this bacterium. To express M. hyopneumoniae proteins in heterologous systems such as Escherichia coli, the TGA codons that encode tryptophan in M. hyopneumoniae genes need to be replaced with the TGG codon. In this study we employed a modified overlap extension-PCR method for site-directed mutagenesis of selected TGA codons. Primers carrying the appropriate TGA to TGG mutation were employed in a two-step PCR amplification. The mutated PCR products were subsequently cloned into E. coli expression vectors. Using this method, we obtained 14 M. hyopneumoniae genes with up to three TGA to TGG substitutions per gene. Expression of the 10 mutated genes in E. coli was achieved. The method was rapid, simple and highly efficient in introducing the desired mutations in the A + T rich M. hyopneumoniae genes. In conclusion, this modified overlap extension-PCR method is suitable for large-scale site-directed mutagenesis of M. hyopneumoniae genes for heterologous expression.

Mapping of 5′ and 3′-ends of sunflower mitochondrial nad6 mRNAs reveals a very complex transcription pattern which includes primary transcripts lacking 5′-UTR

Nad6 orf, encoded in the sunflower mitochondrial genome in single copy contains a non-conserved 3′-extension. The transcription of the nad6 locus generates a highly complex pattern. Three main transcripts of 1240, 960 and 870 nt have been characterized by different approaches. The two smaller ones are apparently the most abundant of the steady-state RNA population and are generated as primary transcription products as well as by processing of the 1240 nt transcript. Their 5′-UTRs are absent or very short. Whereas the 3′-ends of the 960 nt transcripts contain a TGA codon the shorter one terminates at positions excluding the stop codon. The fate of transcripts to promote the synthesis of NAD6 sunflower protein seems, thus, to rely on the occurrence of mechanisms yet to be identified.

The structural analysis of protein sequences based on the quasi-amino acids code

Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Genome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system (Σ, +, *) is introduced, where Σ is the set of 64 codons. According to the characteristics of (Σ, +, *), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, ⊕, ⊗) is a field. Furthermore, the operational results display that the codon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of ‘the 64 codon assignments of mRNA to amino acids is probably completely wrong’ proposed by Yang (2006 Progress in Modern Biomedicine 6 3).