基因總覽
TFEB 是蛋白質編碼基因,產物為 transcription factor EB,屬於 MiT/TFE 家族。這種轉錄因子具有 bHLH 結構域,可透過與自身或家族成員形成二聚體來結合 DNA;其蛋白質序列另含 leucine-zipper 區域及轉錄活化區。TFEB 的主要角色是調節多類細胞反應相關基因的表現,參與溶酶體與自噬等過程,也與脂質分解、能量代謝及免疫反應有關。其活性會隨營養狀態及細胞壓力而改變,使細胞能調整相關基因的轉錄。
基因異名與舊稱
異名取自 HGNC,可能包含歷史名稱;蛋白質名稱以 UniProt 註解為準。
染色體位置與基因結構
查看實際轉錄本與 exon 註解
| Transcript | Genomic coordinates | Exons |
|---|---|---|
| ENST00000373033 ★ | 41,683,978–41,735,608 | 9 |
| ENST00000406563 | 41,683,978–41,691,213 | 7 |
| ENST00000343317 | 41,683,978–41,691,476 | 8 |
| ENST00000419574 | 41,683,978–41,705,940 | 9 |
| ENST00000445214 | 41,683,978–41,705,940 | 10 |
| ENST00000416140 | 41,683,978–41,723,726 | 9 |
| ENST00000419396 | 41,683,978–41,733,690 | 10 |
| ENST00000678831 | 41,683,978–41,733,828 | 9 |
| ENST00000424495 | 41,683,978–41,734,179 | 9 |
| ENST00000420312 | 41,683,978–41,734,194 | 9 |
| ENST00000403298 | 41,683,978–41,734,401 | 9 |
| ENST00000230323 | 41,683,978–41,735,060 | 10 |
顯示 12/42 個蛋白質編碼轉錄本;canonical 優先。
帶型與著絲點依 Ensembl 座標繪製;核染色體長度以 GRCh38 第 1 號染色體為共同尺度。黃色標記表示本基因位置,細小區間加粗以利辨識;實際基因長度與 exon 見下方資料。
分子功能與生物學過程
TFEB 是溶酶體生成、自噬、溶酶體胞吐、脂質分解、能量代謝及免疫反應的重要轉錄調節因子。它辨識 E-box DNA 序列(5'-CANNTG-3'),有效結合 DNA 需要與自身或其他 MiT/TFE 家族成員(如 TFE3、MITF)形成二聚體。TFEB 也能辨識溶酶體基因調控區中的 CLEAR-box 序列(5'-GTCACGTGAC-3'),促進這些基因的表現,因而在溶酶體相關基因轉錄中居於核心位置。
TFEB 的轉錄活性會依細胞營養與溶酶體狀態調整。在營養充足時,MTOR 磷酸化 TFEB,使其滯留於細胞質並失去活性;飢餓或溶酶體壓力則會抑制 MTOR,促使 TFEB 去磷酸化並進入細胞核,啟動轉錄。這種調節把營養狀態與溶酶體及自噬基因的表現連結起來。TFEB 也可促進自噬相關基因表現;在營養缺乏時,與 ACSS2 協同促進溶酶體生成及自噬相關基因的表現。
營養缺乏時,TFEB 透過促進 PIP4P1 表現調節溶酶體定位。感染 S. aureus、S. typhimurium 或 S. enterica 時,itaconate 的生成會導致 TFEB 烷基化,使其進入細胞核並產生轉錄活性;此反應可活化 TFEB 依賴的溶酶體生成,促進抗菌先天免疫反應中的細菌清除。
TFEB 亦參與免疫與發育相關的轉錄調節。它與 TFE3 協同活化 T 細胞中的 CD40L 表現,與活化 CD4(+) T 細胞的 T 細胞依賴性抗體反應及胸腺依賴性體液免疫有關;它也辨識重鏈免疫球蛋白增強子中的 gamma-E3 box。另有資料指出,TFEB 參與胎盤正常血管化所需的訊號傳遞過程。
Promoter 與基因調控
>TFEB ENST00000373033 GRCh38 chr6:41735508-41736608 strand=-1 5′→3′ 相對 TSS:-1000 到 +100 bp;1101 bp 依轉錄本 TSS 擷取的基因組序列;TSS = 0,兩端包含,未驗證為 promoter GCTTGGGATGGGCTCTGTAACCCTCAGAGCTTAAAGTTCATACTTTTCCCCTGGAAAGGGAAGACAGTGG TAGCGCCATCATGGGTGGGTGGGTGGCGGGCCGGGGGAGAGTGTTCCTACTTGAGTCACAGAGAAATCGA GCCTATTTGCTGGAACCAACTCAGCAAGGGATCTTGTCCCTTTGGACTTCATCCCTGTCCTCCTCAGGAG CCTCTTAGCAAAAGATCCAGAAACCAGGAGCAACATTGTATGTGGGGAAGGAGGAGAGAGAGGAAGAAAA GGAGGAGGGGAAGGAGAAGAAAAGCAGGGGAGGGGCTGGGGGAGGAGACAGGGAAAAAGGGGCGGGGAAG AGGAGAAAGTAGAGAATGATGCCTCCGCACCCTGTGAACTTCCAACAAGGGAAGGTGACATGAAAGGAGC TCAGACAATTTCTGTCCAGCAACATGACAGCAAGCTCAGGCTGGTGAGTGGGGCGTGAATGTAGAACCCA TAATGGGGGCAGGCTGCCTTCTACTGTCATATTTTACCCTGTACTTCGCCAGGCTCACCCTGGCCTTGCC CCTTATGATCGGGGCAGGGATAAAAGTGCAAGATCCAGGTCCTGCACCCTACTCCTGAAGAGAAGCTGGA ATTTGCCACAGGTGGAGTTTCTATGGCAACAGCACACCATCTGGGACCCTCTCTTTCTTAGACTGCCGAA GGACAGCAGGCTGCAGGTTCCTTTTAGGGGGTCGGACAGGCTACAGAATGTATCTTAGTGAGCCCTGGTT TGGGACTTTACTGAGAGGAGAAAGAAAACTTGCAAAGAGGTAGAAGTGGATCAGAGGTTCCAAGTCAAGA GCCTCTTTCCCTGTAAGCCTTAGTCCGCTGAGCGGGACTACAAATCCCGGCGTGCCTAGCGGGACTGCAG CGAGAACTACGCTTCCCAGTGGGCGCCGAGGCAGAGCGGCTGGGAGGCGGGGCGGGTGCTGCCCTCTGCC GGGCGCGGAGGGAAGTGTGCGTGGAGTGACAGCCGGAGCCCGGGCGCCGGGCGCGGGGCTCGGTGACAGC GGAGGCGGCGGCCCGGGCGGGACGCAGGGAGCGGCCGCGGCGCCGACGGCG
EPDnew 實驗支持 promoter/TSS · 6 筆
| EPDnew ID | TSS(1-based) | 股向 | 來源顯示區間 |
|---|---|---|---|
| TFEB_4 ↗ | 6:41,723,563 | 負股 | 41,723,553–41,723,612 |
| TFEB_2 ↗ | 6:41,733,853 | 負股 | 41,733,843–41,733,902 |
| TFEB_5 ↗ | 6:41,734,169 | 負股 | 41,734,159–41,734,218 |
| TFEB_6 ↗ | 6:41,735,021 | 負股 | 41,735,011–41,735,070 |
| TFEB_1 ↗ | 6:41,735,608 | 負股 | 41,735,598–41,735,657 |
| TFEB_3 ↗ | 6:41,736,248 | 負股 | 41,736,238–41,736,297 |
EPDnew human v006 · UCSC hg38,GRCh38/hg38,透過 UCSC 取得。TSS 具有 CAGE/RAMPAGE 等實驗資料支持;任意擷取的上下游區間仍需另行判讀調控功能,不能視為整段皆經功能驗證。
EPD 封存狀態 ↗ · UCSC 資料說明 ↗ · EPD team, SIB Swiss Institute of Bioinformatics; UCSC Genome Browser · CC BY 4.0
查看已取得的調控/motif 註解
ENSR6_8385FN · enhancer · 41730558–41730801 · regulatory
ENSR6_C65RT · enhancer · 41732538–41733679 · regulatory
ENSR6_C65RZ · promoter · 41733680–41734891 · regulatory
ENSR6_9LK97 · promoter · 41735050–41735550 · regulatory
ENSR6_9LK9C · promoter · 41735598–41736098 · regulatory
ENSR6_5CS3BJ · CTCF_binding_site · 41735623–41735644 · regulatory
ENSR6_5CS3DN · CTCF_binding_site · 41736088–41736109 · regulatory
ENSR6_9LK9H · promoter · 41736249–41736537 · regulatory
· motif · 41730713–41730726 · motif
· motif · 41730713–41730726 · motif
· motif · 41730830–41730843 · motif
· motif · 41731092–41731100 · motif
· motif · 41731195–41731217 · motif
· motif · 41731195–41731217 · motif
· motif · 41731494–41731507 · motif
· motif · 41731549–41731560 · motif
· motif · 41731582–41731602 · motif
· motif · 41731700–41731711 · motif
· motif · 41732031–41732042 · motif
· motif · 41732494–41732505 · motif
· motif · 41732494–41732505 · motif
· motif · 41732804–41732817 · motif
· motif · 41732930–41732943 · motif
· motif · 41732930–41732943 · motif
· motif · 41733030–41733040 · motif
· motif · 41733033–41733042 · motif
· motif · 41733037–41733052 · motif
· motif · 41733491–41733504 · motif
· motif · 41733491–41733504 · motif
· motif · 41733635–41733647 · motif
· motif · 41733637–41733644 · motif
· motif · 41733693–41733705 · motif
· motif · 41733956–41733971 · motif
· motif · 41733963–41733985 · motif
· motif · 41733963–41733985 · motif
· motif · 41734010–41734023 · motif
· motif · 41734202–41734213 · motif
· motif · 41734384–41734400 · motif
· motif · 41734662–41734675 · motif
· motif · 41734662–41734675 · motif
· motif · 41734667–41734679 · motif
· motif · 41734701–41734714 · motif
· motif · 41734798–41734811 · motif
· motif · 41734844–41734857 · motif
· motif · 41734876–41734889 · motif
· motif · 41734886–41734895 · motif
· motif · 41734948–41734961 · motif
· motif · 41735093–41735106 · motif
· motif · 41735175–41735188 · motif
· motif · 41735194–41735207 · motif
· motif · 41735254–41735263 · motif
· motif · 41735359–41735366 · motif
· motif · 41735625–41735641 · motif
· motif · 41736090–41736106 · motif
蛋白質結構域與序列
參考蛋白質長度:476 aa
transcription factor EB 長 476 個胺基酸,屬於 MiT/TFE 家族。其 bHLH 結構域位於胺基酸 235–288,另有 leucine-zipper 區域及強轉錄活化區。蛋白質 N 端 1–167 位為與 ACSS2 互作的區域;序列亦註記有核輸出訊號與核定位訊號。多段區域被註記為無序區。
蛋白質三維結構
細胞內定位
TFEB 主要位於細胞質,並可在細胞質、細胞核與溶酶體膜之間轉換。 營養充足時,它經 RagC 或 RagD 招募至溶酶體膜並受 MTOR 磷酸化,這會促進其與 14-3-3 蛋白(如 YWHAZ)互作,限制核轉位;營養缺乏、mTORC1 抑制或溶酶體受損時,去磷酸化則伴隨核轉位。 溶酶體儲積異常及活的 S. enterica 感染巨噬細胞也與核轉位相關;Coxsackievirus B3 感染後,全長 TFEB 與病毒蛋白酶 3C 切割產物均會由細胞質轉入細胞核。
深綠色圓點:來源記載的蛋白質定位;數量不表示含量。
動物細胞結構示意;器官大小與數量不按比例。點選細胞構造可查看定位註解。
交互作用與訊號網絡
拖曳節點後放開可帶動位置變化;點選夥伴查看證據。位置與連線長度不代表結合強度,圖中未推定夥伴彼此之間的關係。
更多交互作用夥伴 · 已取得 3 個夥伴
- MITFO75030 · UniProt INTERACTION · 3 experiments
- SUMO1P63165 · UniProt INTERACTION · 2 experiments
- YWHAEP62258 · UniProt INTERACTION · 5 experiments
TFEB 可形成同源二聚體,也可與 TFE3 或 MITF 形成異源二聚體。營養充足且受 MTOR 磷酸化時,TFEB 與 YWHAZ 的互作有助於使其留在細胞質;它也與 Rag 小 GTPase 互作,促進營養充足時被招募至溶酶體膜。IRGM 促進 TFEB 與 PPP3CB 的關聯及去磷酸化;TFEB 另與 ACSS2 互作。這些資料所述關係包括直接互作及促進定位或去磷酸化的功能關聯。
疾病與遺傳關聯
Contextual Functional Evidence Matrix
矩陣以「功能主張」為列,以細胞情境、干預條件、量測結果與證據來源為欄,方便比較同一功能在不同條件下的支持情形。只有含情境與實驗資訊的紀錄會列入矩陣;一般功能註解另列於下方。
功能註解總覽 · 4 筆
| 功能面向 | 功能敘述 | 證據類型 | 可查核來源 |
|---|---|---|---|
| 功能 | TFEB 是調節溶酶體生成、自噬、溶酶體胞吐、脂質分解、能量代謝及免疫反應的轉錄因子。它辨識 E-box 與 CLEAR-box 序列,需與自身或 MiT/TFE 家族成員二聚才能有效結合 DNA。營養充足時,MTOR 磷酸化使 TFEB 滯留細胞質;飢餓或溶酶體壓力則促進去磷酸化與核轉位。TFEB 亦參與溶酶體定位、自噬、特定免疫反應、胎盤血管化,以及細菌感染相關的溶酶體生成與清除。 | 含實驗來源 | 證據與來源Transcription factor that acts as a master regulator of lysosomal biogenesis, autophagy, lysosomal exocytosis, lipid catabolism, energy metabolism and immune response. Specifically recognizes and binds E-box sequences (5'-CANNTG-3'); efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFE3 or MITF. Involved in the cellular response to amino acid availability by acting downstream of MTOR: in the presence of nutrients, TFEB phosphorylation by MTOR promotes its cytosolic retention and subsequent inactivation. Upon starvation or lysosomal stress, inhibition of MTOR induces TFEB dephosphorylation, resulting in nuclear localization and transcription factor activity. Specifically recognizes and binds the CLEAR-box sequence (5'-GTCACGTGAC-3') present in the regulatory region of many lysosomal genes, leading to activate their expression, thereby playing a central role in expression of lysosomal genes. Regulates lysosomal positioning in response to nutrient deprivation by promoting the expression of PIP4P1. Acts as a positive regulator of autophagy by promoting expression of genes involved in autophagy. In association with TFE3, activates the expression of CD40L in T-cells, thereby playing a role in T-cell-dependent antibody responses in activated CD4(+) T-cells and thymus-dependent humoral immunity (By similarity). Specifically recognizes the gamma-E3 box, a subset of E-boxes, present in the heavy-chain immunoglobulin enhancer. Plays a role in the signal transduction processes required for normal vascularization of the placenta (By similarity). Involved in the immune response to infection by the bacteria S.aureus, S.typhimurium or S.enterica: infection promotes itaconate production, leading to alkylation, resulting in nuclear localization and transcription factor activity. Itaconate-mediated alkylation activates TFEB-dependent lysosomal biogenesis, facilitating the bacteria clearance during the antibacterial innate immune response. In association with ACSS2, promotes the expression of genes involved in lysosome biogenesis and both autophagy upon glucose deprivation PMID 1748288 ↗ · PMID 19556463 ↗ · PMID 2115126 ↗ · PMID 21617040 ↗ · PMID 22343943 ↗ · PMID 22576015 ↗ · PMID 22692423 ↗ · PMID 23434374 ↗ · PMID 25720963 ↗ · PMID 27278822 ↗ · PMID 28552616 ↗ · PMID 29146937 ↗ · PMID 30120233 ↗ · PMID 31672913 ↗ · PMID 32612235 ↗ · PMID 32753672 ↗ · PMID 35662396 ↗ · PMID 36697823 ↗ · PMID 36749723 ↗ · PMID 37079666 ↗ |
| 交互作用 | TFEB 可形成同源二聚體,亦可與 TFE3 或 MITF 形成異源二聚體。MTOR 磷酸化後,TFEB 與 YWHAZ 互作並促進其留在細胞質;TFEB 與 IRGM 互作,促進其與 PPP3CB 關聯及去磷酸化。TFEB 也與 Rag 小 GTPase 互作,營養充足時有助於招募至溶酶體膜,並與 ACSS2 互作。 | 含實驗來源 | 證據與來源Homodimer and heterodimer; with TFE3 or MITF. Interacts (when phosphorylated by MTOR) with YWHAZ; promoting retention in the cytosol. Interacts with IRGM; promoting association between TFEB and PPP3CB and dephosphorylation. Interacts with small GTPases Rag (RagA/RRAGA, RagB/RRAGB, RagC/RRAGC and/or RagD/RRAGD); promoting its recruitment to lysosomal membrane in the presence of nutrients. Interacts with ACSS2 PMID 15507434 ↗ · PMID 1748288 ↗ · PMID 23401004 ↗ · PMID 28552616 ↗ · PMID 32753672 ↗ · PMID 34071043 ↗ · PMID 35662396 ↗ · PMID 37057673 ↗ |
| 細胞定位 | TFEB 主要位於細胞質,也可見於細胞核及溶酶體膜。營養充足時,GDP 結合的 RagC 或 RagD 可將其招募至溶酶體膜,隨後由 MTOR 磷酸化;磷酸化促進與 14-3-3 蛋白(如 YWHAZ)互作,限制核轉位及活性。飢餓、mTORC1 抑制或溶酶體破壞會促進去磷酸化和核轉位;溶酶體儲積異常及活的 S. enterica 感染巨噬細胞也與核轉位相關。營養恢復時 TFEB 可自細胞核輸出,ATP13A2 調節其核轉位。 | 含實驗來源 | 證據與來源Nucleus; Cytoplasm, cytosol; Lysosome membrane; Mainly present in the cytoplasm. When nutrients are present, recruited to the lysosomal membrane via association with GDP-bound RagC/RRAGC (or RagD/RRAGD): it is then phosphorylated by MTOR. Phosphorylation by MTOR prevents nuclear translocation and activity by promoting interaction with 14-3-3 proteins, such as YWHAZ. Under aberrant lysosomal storage conditions, it translocates from the cytoplasm to the nucleus. The translocation to the nucleus is regulated by ATP13A2. Conversely, inhibition of mTORC1, starvation and lysosomal disruption, promotes dephosphorylation and translocation to the nucleus. Exported from the nucleus in response to nutrient availability. In macrophages, translocates into the nucleus upon live S.enterica infection PMID 21617040 ↗ · PMID 22343943 ↗ · PMID 22576015 ↗ · PMID 22692423 ↗ · PMID 23401004 ↗ · PMID 23434374 ↗ · PMID 24081491 ↗ · PMID 25720963 ↗ · PMID 27184844 ↗ · PMID 27278822 ↗ · PMID 28552616 ↗ · PMID 30120233 ↗ · PMID 32612235 ↗ · PMID 32753672 ↗ · PMID 33691586 ↗ · PMID 35662396 ↗ · PMID 36697823 ↗ · PMID 37079666 ↗ |
| 細胞定位 | Coxsackievirus B3 感染後,全長 TFEB 以及由病毒蛋白酶 3C 介導產生的切割產物,會由細胞質轉位至細胞核。 | 含實驗來源 | 證據與來源Nucleus; (Microbial infection) Following Coxsackievirus B3 infection, full length TFEB and viral protease 3C-mediated cleavage product are translocated from the cytoplasm to the nucleus PMID 33691586 ↗ |
核酸與蛋白質序列
GTGGAGTGACAGCCGGAGCCCGGGCGCCGGGCGCGGGGCT40CGGTGACAGCGGAGGCGGCGGCCCGGGCGGGACGCAGGGA80GCGGCCGCGGCGCCGACGGCGGCGGGAAGGGCGGACGGGG120CGGGCCTCCCTGGTGGCACGGGGCCGGAGCAGGCCGGGAG160CAGGTGGCGGGCACAGCTTGCGGGCCAGGCACCCGAACTT200GCGACAAGTTGCCGGAGCCGCGGGGCGCGGGCGGCGGACA240GATTGACCTTCAGAGCGAGGGAGCCAGCGCCGGCAGCCAC280CATGGCGTCACGCATAGGGTTGCGCATGCAGCTCATGCGG320GAGCAGGCGCAGCAGGAGGAGCAGCGGGAGCGCATGCAGC360AACAGGCTGTCATGCATTACATGCAGCAGCAGCAGCAGCA400GCAACAGCAGCAGCTCGGAGGGCCGCCCACCCCGGCCATC440AATACCCCCGTCCACTTCCAGTCGCCACCACCTGTGCCTG480GGGAGGTGTTGAAGGTGCAGTCCTACCTGGAGAATCCCAC520ATCCTACCATCTGCAGCAGTCGCAGCATCAGAAGGTGCGG560GAGTACCTGTCCGAGACCTATGGGAACAAGTTTGCTGCCC600ACATCAGCCCAGCCCAGGGCTCTCCGAAACCCCCACCAGC640CGCCTCCCCAGGGGTGCGAGCTGGACACGTGCTGTCCTCC680TCCGCTGGCAACAGTGCTCCCAATAGCCCCATGGCCATGC720TGCACATTGGCTCCAACCCTGAGAGGGAGTTGGATGATGT760CATTGACAACATTATGCGTCTGGACGATGTCCTTGGCTAC800ATCAATCCTGAAATGCAGATGCCCAACACGCTACCCCTGT840CCAGCAGCCACCTGAATGTGTACAGCAGCGACCCCCAGGT880CACAGCCTCCCTGGTGGGCGTCACCAGCAGCTCCTGCCCT920GCGGACCTGACCCAGAAGCGAGAGCTCACAGATGCTGAGA960cDNA 使用 DNA 字母 T;mRNA 模式改以 U 顯示。轉錄本保留已註解的非編碼區,未另外加入 poly(A) 尾;非編碼 RNA 的參考轉錄本也可能仍需後續加工。數字為所選序列的 1-based 位置。長序列以黃色捲軸瀏覽,可複製或下載完整轉錄本與蛋白質;基因組 DNA 隨捲動取得所需範圍。