Codon usage patterns in chromosomal and retrotransposon genes of the mosquito Anopheles gambiae

Codon usage was compiled for fourteen chromosomal genes and four retrotransposons from the mosquito Anopheles gambiae. Variation exists among chromosomal genes in the degree of bias. The genes showing the highest bias are probably most highly expressed. In these genes, the base composition at the third codon position is much richer in G + C than is the overall coding sequence. Thus, codon usage is biased toward G- or C-ending codons. Codon usage in each retrotransposon is quite different, not only from chromosomal genes but also from the other retrotransposons. Codon usage comparisons among homologous genes from An. gambiae and two other Dipterans, the yellow fever mosquito Aedes aegypti and the fruitfly Drosophila melanogaster, show that while there are similarities, particularly between An. gambiae and D. melanogaster in the preference for G-and C-ending codons, each species has evolved a distinct pattern of codon usage.     

人促红细胞生成素在大肠杆菌中融合高表达：稀有密码子对外源蛋白翻译速率的影响

本实验分别用两种融合表达载体（ｐＧＥＸ－２Ｔ及ｐＤＳ－６Ｈ）在大肠杆菌ＸＬ１－Ｂｌｕｅ中表达人促红细胞生成素（ｈ－ＥＰＯ）。结果发现，虽然ｈ－ＥＰＯ基因中大肠杆菌使用频率为０％或１％的密码子占密码子总量的１４．３％，但实验中却取得了较高的蛋白表达量。ｐＧＥＸ－２Ｔ和ｐＤＳ－６Ｈ中表达的融合蛋白（分子量：４４４００和２３８００）分别占细菌总蛋白的２９．７％和１７．５％。从而提示，一个基因中的密码子使用频率与翻译延长速率之间可能不是一种简单的对应关系。表达载体ｐＧＥＸ－２Ｔ中５＇融合基因长度达１３００ｂｐ，而ｐＤＳ－６Ｈ中仅为３６ｂｐ，而ｐＤＳ－６Ｈ但两者表达水平却无显著差异，因此作为翻译起始限制因素的翻译起始区的ＡＴＧ下游顺序仅需长约３６个核苷酸。     

Hemoglobin constant spring defined by specific oligonucleotide hybridization and hemoglobin D Punjab (beta 121----Gln) in a Batak Indonesian family

A Batak Indonesian from North Sumatra with hemoglobin (Hb) D Punjab (alpha 2 beta 2 121----Gln) and hemoglobin Constant Spring (Hb CoSp) is described. The 24-year-old man did not have clinical symptoms, and his hematological indices were normal. However, he had a persistent slight elevation of fetal hemoglobin level. His mother and his brother were heterozygous for Hb D Punjab; his father had Hb CoSp trait. A sister did not have any abnormal hemoglobin. To show the exact molecular defect leading to the synthesis of Hb CoSp in this family, genomic DNA from the father was analyzed by hybridization with synthetic oligonucleotides. Genomic DNA was digested with Sst I and Hind III producing a 1.05-kb fragment from the 3' end segment of the alpha 2-globin gene, including the termination codon. Two nonadecamers were synthesized to serve as probes: one, entirely homologous to the normal 3' end of alpha 2A-globin gene sequence, including the termination codon TAA, the other different from it by a replacement of the T in the termination codon TAA with C, changing it to CAA, the codon for the amino acid glutamine. DNA from normal controls gave a positive signal with the normal alpha 2TAA oligonucleotide probe but negative with the alpha 2 CAA probe. The father of propositus who had Hb CoSp trait gave a positive signal with the normal alpha 2TAA oligonucleotide probe as well as with the alpha 2CAA oligonucleotide probe, showing him to be heterozygous for the alpha 2CAA-globin gene. This result shows that the Hb CoSp in the Batak family is indeed due to a replacement of T by C in the TAA termination codon of the alpha 2-globin gene changing it to CAA the condon for glutamine. This explains the resulting readthrough of the untranslated sequence of the mRNA.     

黄背草与2种菅属植物叶绿体基因组特征比较及系统发育分析

目的 以黄背草Themeda japonica为试验材料,比较分析其与阿拉伯黄背草T. triandra、中华菅T. quadrivalvis2种同属植物的叶绿体基因组特征及其与近缘物种的系统发育关系。方法 采用Illumina HiSeq高通量测序平台首次对黄背草叶绿体基因组进行测序,使用SPAdes和CpGAVAS2分别对其进行组装和注释,并用Codon W、DnaSP和MISA等对其与2种同属植物进行一系列比较基因组分析,利用最大似然法（maximum likelihood,ML）构建系统进化树。结果 3个叶绿体基因组全长为138 735～138 961 bp,具有典型的四分体结构,共注释出129个基因;黄背草与其同属的2个物种相比,反向重复区（inverted repeats,IR）收缩了2132 bp,大单拷贝区（large single copy region,LSC）扩张了约4000 bp,而小单拷贝区（small single copy region,SSC）变化不大。密码子偏好性分析显示,3个叶绿体基因组相对丰度最大和最小的密码子都相同,同义密码子相对使用丰度略有不同...     

Analysis of p53 codon 72 polymorphism and its association with human papillomavirus 16 and 18 E6 in Chinese cervical lesions

The aim of this study was to analysis the relationship between p53 codon 72 polymorphism with human papillomavirus (HPV) 16 and 18 E6 in Chinese cervical cancer. A total of 81 cervical squamous cancer (specimens of G1, G2, and G3 are 13, 24, and 44, respectively; and of stage IB, IIA, IIB, and IIIA are 15, 37, 24, and 5, respectively), 18 cervical adenocarcinoma, 88 cervical intraepithelial neoplasm (CIN) (specimens of CIN II and III are 30 and 58), and 60 normal cervical specimens were included in this study. Polymerase chain reaction was used to examine p53 genotypes and HPV 16 and 18 E6. The frequencies of p53 Arg homozygosity in cervical squamous cancer, cervical adenocarcinoma, and CIN (II-III) were 58.02%, 55.55%, and 59.09%, respectively, that was much higher than that of p53 Arg/Pro heterozygosity (30.86%, 27.78%, and 21.59%) and of p53 Pro homozygosity (11.12%, 16.67%, and 19.32%) in each groups and higher than the frequency of p53 Arg homozygosity in normal samples (23.33%). There is no statistic difference in the normal samples for the frequency of p53 Arg homozygosity, p53 Arg/Pro heterozygosity, and p53 Pro homozygosity (23.33%, 40.00%, and 36.67%, respectively). The frequency of p53 Arg homozygosity in high risk (HR)-HPV E6-positive cervical squamous cancer samples (64.06%) is much higher than that in (HR)-HPV E6-negative cervical squamous cancer samples (35.29%) and in HR-HPV E6-positive normal samples (33.33%). No difference of p53 codon 72 polymorphism was found according to FIGO staging and grades. In conclusion, based on the findings of this study, it is suggested that p53 Arg homozygosity could act as a potential risk factor for the tumorigenesis of the cervix. p53 codon 72 polymorphism has no relation with the FIGO staging and grades of cervical cancer. p53 Arg homozygosity and HR-HPV E6 positive simultaneously can predict the fate of cervical lesions.     

A Clinical Update of the Hb Siirt [β27(B9)Ala→Gly; HBB: c.83C>G] Hemoglobin Variant

We report a clinical update of the hemoglobin (Hb) variant [β27(B9)Ala→Gly; HBB: c.83C>G], named Hb Siirt, that was previously described as a silent variant in a 23-year-old Kurdish female. The patient was also a carrier of the codon 5 (–CT) (HBB: c.17_18delCT) frameshift mutation and of the ααα ^{anti 3.7} triplication. Her initial moderate β-thalassemia intermedia (β-TI) phenotype worsened with time, causing the patient to become a transfusion-dependent subject at the age of ～40 years. Subsequent molecular characterization of both parents revealed that the Hb Siirt variant was inherited by the mother, while the other two globin alterations (HBB: c.17_18delCT and ααα^{anti 3.7} triplication) were genetically transmitted by the father. The latter remained a carrier of a mild β-TI phenotype throughout his life, at least until the age of 65 years. We hypothesize that the worsened clinical conditions in the daughter were due to the additional, maternally inherited Hb Siirt variant. However, protein 3D conformational analysis did not seem to reveal substantial overall structural changes. Among the other three described variants [Hb Volga (HBB: c.83C>A), Hb Knossos (HBB: c.82?G>T), Hb Grange-Blanche (HBB: c.83C>T] that are due to nucleotide substitutions at codon 27 of the β-globin gene; only Hb Knossos causes a β⁺-thalassemia (β⁺-thal) phenotype.     

The hunt for a yet unknown: Common molecular signature in some genetically monomorphic enterobacteria

Mark Achtman introduced the term “genetically monomorphic bacteria” (GM bacteria) for some human and plant pathogens. They displayed a great uniformity in terms of their “genetic” properties. This “uniformity” poses a challenge to microbiologists. To address these problems, we used CodonW and IslandViewer 3 as analytical tools and took Escherichia coli, Salmonella, and Shigella strains as a model organisms. We hypothesized that GM bacterium contains a common molecular signature among them. We have found a significant correlation regarding the number of protein-coding genes, predicted highly expressed genes, and the highest length of gene in this regard. On the other hand, the correspondence analysis of pathogenicity-related genes identified by IslandViewer 3 displayed a somewhat unique pattern in GM bacteria. The probable pathogenic genes are clustered into two separate groups, which is a hallmark of some pattern. Similar genes of non-monomorphic pathogenic strain clustered almost similarly, but the clusters are joined together, they are not completely separated. These features, in our considered view, may be considered as codon usages signatures of these bacteria, and E. coli in particular.     

Searching for the initiating site of the major capsid protein to generate virus-like particles for a novel laboratory mouse papillomavirus

Correctly folded virus-like particles (VLPs) of papillomavirus (PV) display conformationally dependent epitopes that are type specific, maintained on authentic virions, and induce neutralizing antibodies. Alignment of the L1 amino acid (aa) sequences of 84 PVs revealed that the lengths of their N-termini are diverse and that multiple, possible initiation methionine (met) codons exist. The L1 gene of MusPV (MmuPV1), that naturally infects immunodeficient laboratory mouse strain (NMRI-Foxn1^nu/Foxn1^nu), has four met codons at the 1st, 2nd, 28th, and 30th aas from its N-terminus. Of these, the 3rd and 4th mets, that are at the 28th and 30th aa position from the N-termius, respectively, are located at the position where most PVs have their first met. These two mets, located at the 9th and 11th from the YLPP conserved aas of most PVs, should be considered as consensus initiation codons of PV L1s. Three L1 proteins of MusPV, starting from the 2nd, 3rd, and 4th mets, were expressed using a baculovirus expression system and characterized for their ability to self-assemble into VLPs. While MusPV L1 proteins starting from the 2nd met expressed an L1 protein that did not fold into VLPs, the L1s starting from the 3rd and 4th mets generated correct VLPs in abundant quantities. We now conclude that the highest quantity and best quality VLPs are made from the consensus L1 met of MusPV.