Martínez-Montiel Nancy, Morales-Lara Laura, Hernández-Pérez Julio M, Martínez-Contreras Rebeca D
Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México.
Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, México.
PLoS One. 2016 Feb 10;11(2):e0148191. doi: 10.1371/journal.pone.0148191. eCollection 2016.
The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability, physicochemical properties and spatial organization in comparison to the NMD factor depicted for Homo sapiens. These observations strongly support the notion that human and fungal UPF1 could perform equivalent biological activities.
调控基因表达准确性的分子机制仍未完全明晰。在这些机制中，无义介导的mRNA降解（NMD）是一种质量控制过程，可检测转录后异常的转录本并使其降解。UPF1蛋白是NMD的核心，针对该因子（主要针对智人和酿酒酵母）报道的若干结构和功能特征表明了这一点。此过程在真核生物中高度保守，但在不同物种中可观察到功能多样性。玉米黑粉菌是一种担子菌，也是最知名的黑粉菌，已成为研究分子和细胞真核机制的模型。在本研究中，我们进行了计算机分析，以研究玉米黑粉菌中假定的UPF1同源物的结构和生化特性。在担子菌的注释基因组中识别出了UPF1的假定同源物，其在蛋白质水平上与其人类对应物具有66%的同一性。还发现了UPF1同源物的已知结构和功能结构域。基于UPF1可用的晶体结构，我们构建了umUPF1的不同三维模型，以分析该因子的二级和三级结构特征。利用这些模型，我们研究了umUPF1的空间排列及其与UPF2相互作用的能力。此外，我们确定了介导umUPF1与UPF2、ATP、RNA以及与UPF1自身相互作用的关键氨基酸。在计算机上对这些氨基酸进行突变显示对天然结构有重要影响。最后，我们对来自智人和玉米黑粉菌的UPF1蛋白进行了分子动力学模拟，所得结果表明这两种生物体中的蛋白质具有相似的行为和物理化学性质。总体而言，我们的结果表明，与智人所描述的NMD因子相比，在玉米黑粉菌中鉴定出의假定UPF1显示出非常相似的序列、结构组织、机械稳定性、物理化学性质和空间组织。这些观察结果有力地支持了人类和真菌UPF1可能具有等效生物学活性的观点。
