蛋白位點分析Ds/Ds1轉位子之顯子化增加玉米蛋白體多樣化

Ds/Ds1 Exonization in Maize Offer New Profiles of Protein Isoforms to Enrich Proteome Complexity by PROSITE Analysis

10.30061/CEB.202312_19.0004

張云甄(Yun-Chen Chang)；劉力瑜(Li-yu Daisy Liu)；常玉強(Yuh-Chyang Charng)

Ds轉位子 ； 選擇性剪接 ； 顯子化 ； 蛋白活性位點 ； Ds transposon ； Alternative splicing ； Exonization ； Protein functional profile

作物、環境與生物資訊

19卷（2023 / 12 / 31）

46 - 58

繁體中文;英文

當基因之顯、隱子剪接點錯亂而產生新轉錄體，稱選擇性剪接（alternative splicing）；轉位子顯子化（exonization）指當轉位子插入基因隱子時，因轉位子序列提供新剪接點，造成新轉錄產物增加部分轉位子及部分隱子之遺傳訊息。玉米之Ac/Ds是最早發現的轉位子，Ds及Ds1同屬Ac轉位子家族，顯子化提供之剪接位點卻大不同，Ds提供5個donor，Ds1同時提供3個donor及2個acceptor（共11種組合），兩者僅重疊1個剪接位。先前模擬Ds/Ds1插入玉米基因隱子之研究顯示，顯子化事件利用兩者提供之剪接位點，將插入位點上下游隱子序列導入轉錄產物中，提高轉錄體豐富度及其蛋白質異構物多樣性。為進一步探討顯子化產生之衍生蛋白異構物序列對多樣性的貢獻，是否超越一般之選擇性剪接，本試驗將先前模擬Ds及Ds1插入玉米全基因組隱子之顯子化衍生蛋白胺基酸序列比對PROSITE資料庫之蛋白質活性位點，並細分衍生蛋白為內部異構物及C端異構物兩類（前者局部微變、後者C端劇變）。將顯子化衍生蛋白與原蛋白相比，當轉位子遺傳序列貢獻專一（原蛋白沒有）活性位點，定義為（Ds/Ds1）依賴型，其他則為獨立型活性位點（一般選擇性剪接），分析玉米顯子化蛋白體之資料，發現獨立型位點之總數超過依賴型，但深入探討活性位點組成種類，依賴型位點種類超過獨立型，即依賴型位點之多樣性更豐富。本研究結果顯示Ds/Ds1顯子化後提供之遺傳序列雖僅14至92鹼基對，但因donor/acceptor各種組合再併入玉米序列而提供許多原基因所缺之活性位點，增加演化篩選優勢。

Alternative splicing (AS) is a process that a gene's one or more exon(s) can be excluded from a pre-mRNA resulting in multiple mRNA isoforms. Exonization means that when a transposed element (TE) is inserted into a gene's intron, the TE sequence can provide new splice sites to replace its original exon splice site during transcription, so that subsequent transcripts will contain both the original exon sequence and genetic information from TEs and introns. Since TE, e.g. Ac/Ds family, sequences can provide little genetic information, it is necessary to determine whether exonization events can provide more diverse functional protein isoforms, rather than regular AS. Previously, we simulated the exonization of Ds/Ds1 in maize genome and analyzed maize transcriptome richness. Here, we analyze how the exonized sequence diversity contributes protein functional complexity. First, the functional profiles of all simulated exonized isoforms and the references were scanned according to PROSITE database. Compared with the reference proteins, protein variants were classified to be interior or C-terminal. An interior variant is expected modified locally while C-terminal severe. All newly added functional profiles provide the exonized variants for selective advantages. Subsequently, the new functional profiles were determined as Ds/Ds1 dependent or in-dependent, according to whether the genetic sequences of Ds/Ds1 contribute to build the functional profile. We found that the total number of Ds/Ds1 in-dependent profiles, which can be built by regular AS, is more than dependent profiles, while dependent profiles provide more profiles' composition items (termed as "unique profile"). These results indicate that although offer provide little genetic information (14 to 92 bp) for exonization, but the resulting protein variants contains more profiles' diversity than regular AS for selective advantages.