de Oliveira Tulio, Engelbrecht Susan, Janse van Rensburg Estrelita, Gordon Michelle, Bishop Karen, zur Megede Jan, Barnett Susan W, Cassol Sharon
HIV-1 Molecular Virology and Bioinformatics Unit, Africa Centre for Health and Population Studies, and the Nelson R. Mandela School of Medicine, University of Natal, Durban, South Africa.
J Virol. 2003 Sep;77(17):9422-30. doi: 10.1128/jvi.77.17.9422-9430.2003.
Naturally occurring polymorphisms in the protease of human immunodeficiency virus type 1 (HIV-1) subtype C would be expected to lead to adaptive (compensatory) changes in protease cleavage sites. To test this hypothesis, we examined the prevalences and patterns of cleavage site polymorphisms in the Gag, Gag-Pol, and Nef cleavage sites of C compared to those in non-C subtypes. Codon-based maximum-likelihood methods were used to assess the natural selection and evolutionary history of individual cleavage sites. Seven cleavage sites (p17/p24, p24/p2, NC/p1, NC/TFP, PR/RT, RT/p66, and p66/IN) were well conserved over time and in all HIV-1 subtypes. One site (p1/p6(gag)) exhibited moderate variation, and four sites (p2/NC, TFP/p6(pol), p6(pol)/PR, and Nef) were highly variable, both within and between subtypes. Three of the variable sites are known to be major determinants of polyprotein processing and virion production. P2/NC controls the rate and order of cleavage, p6(gag) is an important phosphoprotein required for virion release, and TFP/p6(pol), a novel cleavage site in the transframe domain, influences the specificity of Gag-Pol processing and the activation of protease. Overall, 58.3% of the 12 HIV-1 cleavage sites were significantly more diverse in C than in B viruses. When analyzed as a single concatenated fragment of 360 bp, 96.0% of group M cleavage site sequences fell into subtype-specific phylogenetic clusters, suggesting that they coevolved with the virus. Natural variation at C cleavage sites may play an important role, not only in regulation of the viral cycle but also in disease progression and response to therapy.
预计人类免疫缺陷病毒1型（HIV-1）C亚型蛋白酶中自然存在的多态性会导致蛋白酶切割位点出现适应性（补偿性）变化。为了验证这一假设，我们研究了C亚型与非C亚型在Gag、Gag-Pol和Nef切割位点上切割位点多态性的流行情况和模式。基于密码子的最大似然法用于评估各个切割位点的自然选择和进化历史。七个切割位点（p17/p24、p24/p2、NC/p1、NC/TFP、PR/RT、RT/p66和p66/IN）在所有HIV-1亚型中随时间推移都高度保守。一个位点（p1/p6(gag)）表现出中等程度的变异，四个位点（p2/NC、TFP/p6(pol)、p6(pol)/PR和Nef）在亚型内部和亚型之间都具有高度变异性。其中三个可变位点已知是多蛋白加工和病毒体产生的主要决定因素。P2/NC控制切割的速率和顺序，p6(gag)是病毒体释放所需的一种重要磷蛋白，而TFP/p6(pol)是反式阅读框结构域中的一个新切割位点，影响Gag-Pol加工的特异性和蛋白酶的激活。总体而言，12个HIV-1切割位点中有58.3%在C亚型中比在B亚型病毒中具有显著更高的多样性。当作为一个360 bp的单一串联片段进行分析时，96.0%的M组切割位点序列落入亚型特异性系统发育簇中，这表明它们与病毒共同进化。C亚型切割位点的自然变异可能不仅在病毒周期调节中发挥重要作用，还在疾病进展和治疗反应中起重要作用。
