Non-Apoptotic Caspase Activity Preferentially Targets a Novel Consensus Sequence Associated With Cytoskeletal Proteins in the Developing Auditory Brainstem.
Non-Apoptotic Caspase Activity Preferentially Targets a Novel Consensus Sequence Associated With Cytoskeletal Proteins in the Developing Auditory Brainstem.
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DOI：
10.3389/fcell.2022.844844
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发表时间：
2022
影响因子：
5.5
通讯作者：
Cramer KS
中科院分区：
文献类型：
--
作者：
Weghorst F;Mirzakhanyan Y;Hernandez KL;Gershon PD;Cramer KS
听觉脑干依赖于精确的电路来促进声源定位。在小鸡中，这种专门的电路的发展需要caspase-3的非凋亡活性，我们以前确定了几百个蛋白水解底物。在这里，我们测试了caspase裂解位点的序列是否在凋亡和非凋亡背景下差异编码蛋白水解偏好。我们在非凋亡鸡听脑干中构建了半胱天冬酶活性的共有序列，包括切割位点N-末端的四个残基：IX（G/R）D↓，其中X表示无显著富集，↓表示切割位点。我们鉴定了在含有在上述共有序列中发现的基序的半胱天冬酶底物中显著富集的GO术语。（G/R）D↓与术语“细胞骨架的结构成分”（SCoC）相关，表明SCoC蛋白可能在非凋亡发育过程中被caspase活性特异性靶向。为了确定该共有序列是否特异于胚胎第10天（E）的非凋亡听性脑干，我们使用了在听性脑干神经元经历凋亡细胞死亡（E13）时收获的脑干的蛋白质质谱。凋亡基序VD显着富集E13切割位点，表明在P2亚位点的基序偏好已转向典型的caspase共识序列。此外，Monte Carlo模拟显示，只有GD基序与凋亡听觉脑干中的SCoC底物相关，表明GD在非凋亡和凋亡背景下编码SCoC蛋白的特异性，尽管在后者中不是优选的。最后，为了鉴定候选人非凋亡共有序列，我们使用Monte Carlo分析来确定Degrabase中与SCoC胱天蛋白酶底物相关的基序和基序对，Degrabase是人类凋亡细胞系中切割位点的数据库。我们发现了11个与SCoC蛋白水解显著相关的基序，包括IXXD和GD。我们采用逐步方法来选择基序对，其针对SCoC切割事件的给定覆盖范围优化SCoC特异性，产生11个可能在SCoC指导的人非凋亡半胱天冬酶共有序列中优选的基序对。GD + IXXD是这些基序对之一，表明脊椎动物中非凋亡一致位点的保守性。
The auditory brainstem relies on precise circuitry to facilitate sound source localization. In the chick, the development of this specialized circuitry requires non-apoptotic activity of caspase-3, for which we previously identified several hundred proteolytic substrates. Here we tested whether the sequence of the caspase cleavage site differentially encodes proteolytic preference in apoptotic and non-apoptotic contexts. We constructed a consensus sequence for caspase activity in the non-apoptotic chick auditory brainstem comprising the four residues N-terminal to the cleavage site: IX(G/R)D↓ where X represents no significant enrichment and ↓ represents the cleavage site. We identified GO terms significantly enriched among caspase substrates containing motifs found in the above consensus sequence. (G/R)D↓ was associated with the term “Structural Constituent of Cytoskeleton” (SCoC), suggesting that SCoC proteins may be specifically targeted by caspase activity during non-apoptotic developmental processes. To ascertain whether this consensus sequence was specific to the non-apoptotic auditory brainstem at embryonic day (E) 10, we used protein mass spectrometry of brainstems harvested at a time when auditory brainstem neurons undergo apoptotic cell death (E13). The apoptotic motif VD was significantly enriched among E13 cleavage sites, indicating that motif preference at the P2 subsite had shifted toward the canonical caspase consensus sequence. Additionally, Monte Carlo simulations revealed that only the GD motif was associated with SCoC substrates in the apoptotic auditory brainstem, indicating that GD encodes specificity for SCoC proteins in both non-apoptotic and apoptotic contexts, despite not being preferred in the latter. Finally, to identify candidate human non-apoptotic consensus sequences, we used Monte Carlo analyses to determine motifs and motif pairs associated with SCoC caspase substrates in the Degrabase, a database of cleavage sites in human apoptotic cell lines. We found 11 motifs significantly associated with SCoC proteolysis, including IXXD and GD. We employed a stepwise method to select motif pairs that optimized SCoC specificity for a given coverage of SCoC cleavage events, yielding 11 motif pairs likely to be preferred in SCoC-directed human non-apoptotic caspase consensus sequences. GD + IXXD was among these motif pairs, suggesting a conservation of non-apoptotic consensus sites among vertebrates.
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影响因子：
4
作者：
Hill ME;MacPherson DJ;Wu P;Julien O;Wells JA;Hardy JA
通讯作者：
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影响因子：
2.7
作者：
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DOI：
10.1080/07391102.2018.1517611
发表时间：
2019-09-02
影响因子：
4.4
作者：
Bingol, Elif Naz;Sercinoglu, Onur;Ozbek, Pemra
通讯作者：
Ozbek, Pemra