Morris R C, Brown K G, Elliott M S
Department of Biochemistry and Chemistry, Old Dominion University, Norfolk, VA 23529, USA.
J Biomol Struct Dyn. 1999 Feb;16(4):757-74. doi: 10.1080/07391102.1999.10508291.
Computational modeling was performed to determine the potential function of the queuosine modification of tRNA found in wobble position 34 of tRNAasp, tRNAasn, tRNAhis, and tRNAtyr. Using the crystal structure of tRNAasp and a tRNA-tRNA-mRNA complex model, we show that the queuosine modification serves as a structurally restrictive base for tRNA anticodon loop flexibility. An extended intraresidue and intramolecular hydrogen bonding network is established by queuosine. The quaternary amine of the 7-aminomethyl side chain hydrogen bonds with the base's carbonyl oxygen. This positions the dihydroxycyclopentenediol ring of queuosine in proper orientation for hydrogen bonding with the backbone of the neighboring uridine 33 residue. The interresidue association stabilizes the formation of a cross-loop hydrogen bond between the uridine 33 base and the phosphoribosyl backbone of the cytosine at position 36. Additional interactions between RNAs in the translation complex were studied with regard to potential codon context and codon bias effects. Neither steric nor electrostatic interaction occurs between aminoacyl- and peptidyl-site tRNA anticodon loops that are modified with queuosine. However, there is a difference in the strength of anticodon/codon associations (codon bias) based on the presence or lack of queuosine in the wobble position of the tRNA. Unmodified (guanosine-containing) tRNAasp forms a very stable association with cytosine (GAC), but is much less stable in complex with a uridine-containing codon (GAU). Queuosine-modified tRNAasp exhibits no bias for either of cognate codons GAC or GAU and demonstrates a lower binding energy similar to the wobble pairing of guanosine-containing tRNA with a GAU codon. This is proposed to be due to the inflexibility of the queuosine-modified anticodon loop to accommodate proper positioning for optimal Watson-Crick type associations. A preliminary survey of codon usage patterns in oncodevelopmental versus housekeeping gene transcripts suggests a significant difference in bias for the queuosine-associated codons. Therefore, the queuosine modification may have the potential to influence cellular growth and differentiation by codon bias-based regulation of protein synthesis for discrete mRNA transcripts.
进行了计算建模，以确定在天冬氨酸tRNA、天冬酰胺tRNA、组氨酸tRNA和酪氨酸tRNA的第34位摆动位置发现的tRNA的queuosine修饰的潜在功能。利用天冬氨酸tRNA的晶体结构和tRNA - tRNA - mRNA复合物模型，我们表明queuosine修饰作为tRNA反密码子环灵活性的结构限制碱基。queuosine建立了一个扩展的残基内和分子内氢键网络。7 - 氨甲基侧链的季胺与碱基的羰基氧形成氢键。这使queuosine的二羟基环戊二烯醇环处于适当的方向，以便与相邻尿苷33残基的主链形成氢键。残基间的缔合稳定了尿苷33碱基与第36位胞嘧啶的磷酸核糖主链之间的交叉环氢键的形成。关于潜在的密码子上下文和密码子偏好效应，研究了翻译复合物中RNA之间的其他相互作用。用queuosine修饰的氨酰基和肽基位点tRNA反密码子环之间既没有空间相互作用也没有静电相互作用。然而，基于tRNA摆动位置上queuosine的存在或缺失，反密码子/密码子缔合的强度（密码子偏好）存在差异。未修饰的（含鸟苷的）天冬氨酸tRNA与胞嘧啶（GAC）形成非常稳定的缔合，但与含尿苷的密码子（GAU）形成复合物时稳定性要低得多。用queuosine修饰的天冬氨酸tRNA对同源密码子GAC或GAU均无偏好，并表现出较低的结合能，类似于含鸟苷的tRNA与GAU密码子的摆动配对。这被认为是由于用queuosine修饰的反密码子环缺乏灵活性，无法为最佳的沃森-克里克型缔合提供适当的定位。对肿瘤发生相关基因与管家基因转录本中密码子使用模式的初步调查表明，queuosine相关密码子的偏好存在显著差异。因此，queuosine修饰可能具有通过基于密码子偏好的离散mRNA转录本蛋白质合成调控来影响细胞生长和分化的潜力。
