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Is there a close relationship between synonymous codon bias and codon-anticodon binding strength in human genes?

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Chinese Science Bulletin 2001年第12期46卷 1015-1019页

作者： Xiufan Shi Jingfei Huang Chongrong Liang Shuqun Liu Jun Xie Ciquan Liu Chinese Acad Sci Kunming Inst Zool Cellular & Mol Evolutionary Lab Kunming 650223 Peoples R China

synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon binding strength has been estimated by the stacking energies of codon-anticodon bases in Watson-Crick pairs. The data show common features in synonymous codon bias for all codon families in human genes: all C-ending codons, which possess the strongest codon-anticodon binding energies, are the most favored codons in almost all codon families, and those codons with medium codon-anticodon binding energies are avoided. Data analysis suggests that besides isochore and genome signature, codon-anticodon binding strength may be closely related to synonymous codon choice in human genes. The join-effect of these factors on human genes results in the common features in codon bias.

关键词： codon bias synonymous codons human genes.

A synonymous Polymorphism of APCDD1 Affects Translation Efficacy and is Associated with Androgenic Alopecia

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Journal of Life Sciences 2014年第2期8卷 106-114页

作者： Nikoletta Nagy Katalin Farkas Agnes Kinyo Barbara Fazekas Kornelia Szabo Edit Kollar Balazs Sztano Angela Meszes Dora Beke Lajos Kemeny Laszlo Royo Marta Szell Department of Medical Genetics University of Szeged Szeged 6720 Hungary Department of Dermatology andAllergology University ofSzeged Szeged 6720 Hungary Dermatological Research Group Hungarian Academy of Sciences Szeged 6720 Hungary Department of Rhino-Laryngology and Head-Neck Surgery University ofSzeged Szeged 6720 Hungary

The APCDDI （adenomatosis polyposis coli down-regulated 1） gene is an inhibitor of the Wnt signaling pathway, and a rare mutation of this gene has been associated with hereditary hypotrichosis simplex. In this study, the authors aimed to investigate whether common APCDD1 gene polymorphisms contribute to the development of androgenic alopecia. Patients （n = 210） with androgenic alopecia and 98 controls were investigated. SNPs （Single nucleotide polymorphisms） in the coding region of the gene were sequenced. A significant difference in genotype distribution was found for the c. 1781C/T, p.L476L SNP （rs3185480） of the APCDD1 gene. This SNP is located in exon 5 and is associated with a 3.5- and a 2.8-fold increase in risk for the development of androgenic alopecia for homozygote （CI 0.933-13.125; nominal regression P = 0.063） and heterozygote （CI 1.086-7.217; nominal regression P = 0.033） carriers, respectively. These data suggest that the rs3185480 polymorphism contributes to the development of androgenic alopecia. Protein expression experiments revealed that the polymorphism is associated with reduced APCDDI protein abundance. This reduction is likely due to altered codon usage for leucine from a preferred codon （CTC） to a rare codon （CTT）, which might influence translation efficiency and, thus, APCDDI protein level.

关键词： Adenomatosis polyposis coli down-regulated 1 gene hereditary hypotrichosis simplex androgenic alopecia,polymorphism synonymous translation efficacy preferable codon.

Surveillance of chikungunya virus in Andhra Pradesh,Southern India

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Asian Pacific Journal of Tropical Medicine 2010年第11期3卷 860-865页

作者： CVM Naresh Kumar P Sangamithra M Rajasekhar DVR Saigopal Department of Virology College of SciencesSri Venkateswara UniversityTirupati-517502Andhra PradeshIndia Medical Officer Mobile Medical UnitDistrict Medical Health OfficeKadapa-516001Andhra PradeshIndia

Objective:The study involved survey and screening of areas suspected of chikungunya virus (CHIKV) infection,characterizing the causative agent and identifying the circulating CHIKV ***:Acute phase samples were screened by the use of RTPCR using primer set DVRChk-F/DVRChk-R whereas convalescent samples were tested by CHIKV IgM strips. Results:Two hundred and seventy five acute phase samples were screened by *** which 149(54.18%) showed positivity for *** on 192 convalescent phase samples were tested for CHIKV specific antibodies in which 125(65.10%) samples were found to be *** CHIKV strains were selected and subjected to cloning followed by nucleotide sequencing and were submitted to the Genbank DMA database with the Accession numbers(GQ119362,GQ119363, GQl 19364,and FJ225403).The Sequence analysis of "CHIK-Kadapa" strain(GQ119362) with other CHIKV isolates suggested that the present CHIKV strain has(99.23±0.52)%and 100%identity with Central East South African isolates(CESA) at nucleotide and amino acid levels *** unique non synonymous mutations S168L and D183V were depicted in El gene of the selected strains of the present ***:The 14 months survey revealed the circulation of CHIKV in 2008-2009 in Andhra Pradesh and the causative agent is identified to be of Central East South African(CESA) *** importance of the non synonymous mutations(S168L and D183V) and their role in the mobility and strength of the El-El and E1-E2 interactions needs further *** study also urges the need for intensifying the epidemiological and entomological surveillance to combat any such CHIKV outbreak in the near future.

关键词： Chikungunya virus E1 gene RT-PCR Non synonymous mutations Screening

Exploring the structural and functional effect of pRB by significant nsSNP in the coding region of RB1 gene causing retinoblastoma

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Science China(Life Sciences) 2010年第2期53卷 234-240页

作者： Rajasekaran R Rao Sethumadhavan Bioinformatics Division School of BiotechnologyChemical and Biomedical EngineeringVellore Institute of Technology

In this study,we identified the most deleterious nsSNP in RB1 gene through structural and functional properties of its protein (pRB) and investigated its binding affinity with *** of 956 SNPs,we investigated 12 nsSNPs in coding region in which three of them (SNPids rs3092895,rs3092903 and rs3092905) are commonly found to be damaged by I-Mutant 2.0,SIFT and PolyPhen *** this effort,we modeled the mutant pRB proteins based on these deleterious *** a comparison of total energy,stabilizing residues and RMSD of these three mutant proteins with native pRB protein,we identified that the major mutation is from Glutamic acid to Glycine at the residue position of 746 of ***,we compared the binding efficiency of both native and mutant pRB (E746G) with *** found that mutant pRB has less binding affinity with E2F-2 as compared to native *** is due to sixteen hydrogen bonding and two salt bridges that exist between native type and E2F-2,whereas mutant type makes only thirteen hydrogen bonds and one salt bridge with *** on our investigation,we propose that the SNP with an id rs3092905 could be the most deleterious nsSNP in RB1 gene causing retinoblastoma.

关键词： retinoblastoma non synonymous SNP RB1 gene pRB E2F-2

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纳西东巴文同义换读研究

Covariation of mutation pairs expressed in HIV-1 protease and reverse transcriptase genes subjected to varying treatments

语言文字学 2018年第11期 55-64页

作者：喻遂生

[原刊主持人语] “东巴”是我国纳西族对民间原始宗教祭司的称呼，这种原始宗教及所用的经书、文字因此被称为“东巴教”“东巴经”和“东巴文”。东巴经是纳西族古代文化的主要载体，其内容涉及纳西族古代社会的语言、文字、历史、地... 详细信息

[原刊主持人语] “东巴”是我国纳西族对民间原始宗教祭司的称呼，这种原始宗教及所用的经书、文字因此被称为“东巴教”“东巴经”和“东巴文”。东巴经是纳西族古代文化的主要载体，其内容涉及纳西族古代社会的语言、文字、历史、地理、宗教、哲学、民族、民俗、文学、艺术、天文、历法、农业、畜牧、医药等领域，是纳西族古代文化的百科全书，也是中华民族历史文化的瑰宝。现在，对纳西东巴文化的研究，已成为一门国际性的显学，成果十分丰富。但相对于历史、文化、文学、文献、文字等方面的研究，对东巴经所记录的语言的研究还十分薄弱。与现代纳西语相比，东巴经语言保留了很多古音古语古义和古代文化，用现代纳西语和现代人的体验已很难解释。东巴文形态比较原始，文字制度还不够完善，字词关系比较复杂，文字异读现象比较普遍。其中古今异读、方言异读、借词异读、构词异读学界研究较多，而经书中字写作A，实际上读作与A意义相同或相近的B的同义换读还很少有人研究。与其他文字相比，东巴文的同义换读更丰富多彩，更灵活多变，更有学术研究价值。喻遂生《纳西东巴文同义换读研究》对东巴文同义换读的类别、使用、性质和学术价值进行了初步的探讨，这对于认识东巴经文字和语言的关系、正确解读经书、探索换读所蕴含的民族文化信息有重要的意义，对于其他民族古文字和普通文字学理论研究也有参考价值。 “同义换读”，是指在文献中字写作A，而实际上读作与A意义相同或相近的B的语言文字现象。所谓“意义相近”，应作比较宽泛的理解，有的词平时意义未必相近，但在一定的语境中也可以互换，也属于同义换读。早在20世纪40年代初，沈兼士先生就指出，《说文》中的重文，前人多认为是“音义悉同形体变异”的异体，实际上有一些是“义通换读”（沈文又称“义通换用”“义同换读”）。如《说文·糸部》：“续，连也。从糸，卖声。赓，古文续，从庚贝。”“续”和“赓”读音不同，表示的词也不同，但都有连续义，《说文》就将“赓”看作“续”的古文了。①东巴文的同义换读比汉古文字数量更多，情况更复杂，也更丰富多彩，但这个问题还没有引起学界的重视和深入研究。东巴文同义换读研究，对于认识东巴经文字和语言的关系、正确解读经书、探索换读所蕴含的民族文化信息有重要的意义，对于其他民族古文字和普通文字学理论研究也有重要参考价值。本文拟对东巴文同义换读的类别、使用、性质、学术价值等作一初步的研究，希望能引起学界对此问题的关注。

关键词： Dong-ba scripts synonymous replacement

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Journal of Biomedical Science and Engineering 2010年第3期3卷 291-299页

作者： David King Roger Cherry Wei Hu 不详

A previous study, focused on the correlation of muta-tion pairs of synonymous (S) and asynonymous (A) mutations, distinguished only between the treated and untreated data of protease and reverse tran-scriptase (RT) of HIV-1 subtype B. It is well known that single mutation patterns in HIV-1 are treat-ment-specific. It logically follows that covariation between mutations will also be treatment specific. Thus, our motivation is to give a more in depth study of the covariation between mutation pairs, analyzing not only treated and untreated, but what specific treatments were used, and how they affected the co-variation between the mutations differently. We in-tended to further deepen this study by analyzing the covariation of mutations in protease and RT in dif-ferent subtypes of HIV-1. We found that virus sam-ples subjected to antiretroviral Protease- and RT- inhibitors do show different patterns of mutation covariation in B-subtype protease and RT of HIV-1, while maintaining the same overall trend. covariation will tend to be higher and more distinct from and covariation after treatment. The same trend continues in protease and RT re-gardless of subtype. We also found the highly cova-ried codon positions, position pairs, and position- covariation clusters in protease, affected by different treatments. Most of them are well known major drug-resistance sites for these treatments.

关键词： HIV Covariation synonymous Mutation Asynonymous Mutation Protease Reverse Transcriptase Drug Resistance

Analysis of Codon Usage Pattern of Banana Basic Secretory Protease Gene

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Plant Diseases and Pests 2019年第1期10卷 1-4,9页

作者： Mensah Raphael Anue Sun Xueli Cheng Chunzhen Lai Zhongxiong College of Horticulture/Institute of Horticultural Biotechnology Fujian Agriculture and Forestry University

[Objective] The objective of this study was to understand the codon usage bias pattern of banana pathogenesis-related 17 gene, Basic Secretory Protease gene(MaBSP). [Method] Relative codon usage patterns of MaBSP were calculated using the software CodonW version 1.4.2. and the web-based tool(http://***/codon/).[Result] Our findings showed that C-ended and G-ended codons were the most preferential except the TER codon UGA which was coded for by just one codon. The ENc value, relationship between AT bias and GC bias, Random synonymous codon usage(RSCU) and CAI all showed that codon bias usage existed in MaBSP gene.[Conclusion] The codon usage patterns of MaBSP gene is principally influenced by natural selection in the third position. However, other multiple factors also influence this pattern.

关键词： Codon usage Codon bias Natural selection Mutation bias Random synonymous codon usage Pathogenesis-related(PR)gene