Insights into eukaryotic evolution from transmembrane domain lengths

Biological membranes, comprised of proteins anchored by their trans-membrane domains (TMDs) creating a semi-permeable phase with lipid constituents, serve as ‘checkposts’ for not only intracellular trafficking in eukaryotic cells but also for material transactions of all living cells with external environments. Hydropathy (or hydrophobicity) plots of ‘bitopic’ proteins (i.e. having single alpha-helical TMDs) are routinely utilized in biochemistry texts for predicting their TMDs. The number of amino acids (i.e. TMD length) embedded as alpha-helices may serve as indicators of thickness of biological membranes in which they reside under assumptions that are universally applied for fixing window sizes for identifying TMDs using hydropathy plots. In this work we explore variations in thickness of different eukaryotic biological membranes (reflected by TMD lengths of their resident proteins) over evolutionary time scales. Rigorous <i>in silico</i> analyses of over 23,000 non-redundant membrane proteins residing in different subcellular locations from over 200 genomes of fungi, plants, non-mammalian vertebrates and mammals, reveal that differences in plasma membrane and organellar TMD lengths have decreased over time (scales) of eukaryotic cellular evolution. While earlier work has indicated decreasing differences in TMD lengths with increasing ‘perceived’ organismal complexity, this work is the first report on TMD length variations as a function of evolutionary time of eukaryotic cellular systems. We report that differences in TMD lengths of bitopic proteins residing in plasma membranes and other intra-cellular locations have decreased with evolutionary time, suggesting better/more avenues of intracellular trafficking in the emergence of eukaryotic organisms.

生物膜由通过跨膜结构域（trans-membrane domains, TMDs）锚定的蛋白质与脂质组分共同构成半渗透相，其不仅作为真核细胞内物质运输的“检查节点”，同时也是所有活细胞与外界环境进行物质交换的关键界面。针对单跨膜蛋白（bitopic proteins，即仅含单个α螺旋跨膜结构域的蛋白质）的亲水性（hydropathy，或称疏水性hydrophobicity）图谱，是生物化学教材中常规用于预测其跨膜结构域的经典分析工具。以α螺旋形式嵌入膜内的氨基酸残基数量（即跨膜结构域长度）可作为其所在生物膜厚度的指示参数，这一假设亦是利用亲水性图谱识别跨膜结构域时通用的窗口尺寸设定依据。本研究探究了不同真核生物膜的厚度随进化时间尺度的变化规律，其厚度可通过驻留蛋白的跨膜结构域长度间接反映。本研究从真菌、植物、非哺乳类脊椎动物和哺乳动物共200余个基因组中，选取了分布于不同亚细胞位置的23000余种非冗余膜蛋白，开展了严谨的计算机模拟（in silico）分析。结果显示：在真核细胞进化的时间尺度上，质膜与细胞器膜的跨膜结构域长度差异逐渐缩小。尽管已有研究表明，随着“感知到的”生物体复杂度提升，跨膜结构域长度的差异会逐渐缩小，但本研究首次针对真核细胞系统中跨膜结构域长度变化随进化时间的演化规律展开了系统报道。本研究发现，驻留于质膜与其他细胞内区域的单跨膜蛋白的跨膜结构域长度差异随进化时间逐渐缩小，这表明真核生物演化过程中细胞内运输的通路更为完善与多样。