table_1_Evidence for Shaping of Light Chain Repertoire by Structural Selection.docx

The naïve immunoglobulin (IG) repertoire in the blood differs from the direct output of the rearrangement process. These differences stem from selection that affects the germline gene usage and the junctional nucleotides. A major complication obscuring the details of the selection mechanism in the heavy chain is the failure to properly identify the D germline and determine the nucleotide addition and deletion in the junction region. The selection affecting junctional diversity can, however, be studied in the light chain that has no D gene. We use probabilistic and deterministic models to infer and disentangle generation and selection of the light chain, using large samples of light chains sequenced from healthy donors and transgenic mice. We have previously used similar models for the beta chain of T-cell receptors and the heavy chain of IGs. Selection is observed mainly in the CDR3. The CDR3 length and mass distributions are narrower after selection than before, indicating stabilizing selection for mid-range values. Within the CDR3, proline and cysteine undergo negative selection, while glycine undergoes positive selection. The results presented here suggest structural selection maintaining the size of the CDR3 within a limited range, and preventing turns in the CDR3 region.血液中的初始免疫球蛋白（Immunoglobulin, IG）组库与重排过程的直接产物存在差异。这类差异源于影响种系基因使用模式与连接区核苷酸组成的选择作用。阻碍解析免疫球蛋白重链选择机制细节的主要难题在于，无法准确识别D种系基因，以及无法确定连接区的核苷酸添加与缺失情况。不过，对于不含D基因的免疫球蛋白轻链而言，我们可以开展影响连接区多样性的选择作用研究。本研究采用概率模型与确定性模型，基于健康供体与转基因小鼠的大规模免疫球蛋白轻链测序样本，对轻链的生成与选择过程进行推断与拆解。此前我们曾将类似模型应用于T细胞受体β链与免疫球蛋白重链的相关研究。研究发现，选择作用主要发生在互补决定区3（Complementarity Determining Region 3, CDR3）。经选择作用后，CDR3的长度与质量分布相较于选择前更为狭窄，这表明存在针对中等长度范围的稳定选择。在CDR3区域内，脯氨酸与半胱氨酸受到负选择，而甘氨酸则受到正选择。本研究结果提示，存在结构性选择作用，将CDR3的大小维持在有限范围内，并阻止CDR3区域出现蛋白质转角结构。