Degradation of Diatom Protein in Seawater: A Peptide-Level View
Degradation of Diatom Protein in Seawater: A Peptide-Level View
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DOI：
10.3389/fmars.2021.757245
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发表时间：
2022-01-21
影响因子：
3.7
通讯作者：
Keil, Richard G.
中科院分区：
文献类型：
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作者：
Duffy, Megan E.;Adams, Cheyenne M.;Keil, Richard G.
在受控实验室降解海洋硅藻 Thalassiosira weissflogii 的过程中，通过表面海水微生物组鉴定了肽和蛋白质。每个时间点的样品均使用或不使用蛋白酶胰蛋白酶进行处理，从而可以部分区分微生物酶促降解天然产生的肽和实验室消化完整蛋白质产生的肽。在 12 天的降解实验中，31% 的颗粒有机碳被耗尽，并且整个蛋白质库没有优先降解。然而，微生物产生的肽与实验室分解产生的肽在细胞位置、二级结构和修饰方面存在明显差异。在藻类快速腐烂和细菌生长的初期，细胞质中的细胞内成分首先被消耗，导致膜相关蛋白和肽在碎屑池中积累。随着膜蛋白材料的富集，α-螺旋基序的重要性也随之增加。甲基化精氨酸是细胞衰老中常见的一种翻译后修饰，在微生物产生的碎屑肽库中发现了大量的甲基化精氨酸，这表明细胞内修饰与对立即降解的抵抗力之间存在联系。另一种修饰——天冬酰胺脱酰胺——在碎屑肽中积累。蛋白质分类显示分解藻类物质的细菌群落富含变形菌，蛋白质注释显示溶解的碳水化合物和小肽跨膜的丰富运输。在成岩作用的早期阶段，没有观察到大量氨基酸（THAA）的变化，但蛋白质组学方法使我们能够通过使用氨基酸序列推断亚细胞位置、二级结构和翻译后修饰（PTM）来观察硅藻蛋白保存的选择性变化。
Peptides and proteins were identified during a controlled laboratory degradation of the marine diatom Thalassiosira weissflogii by a surface seawater microbiome. Samples from each time point were processed both with and without the protease trypsin, allowing a partial differentiation between peptides produced naturally by microbial enzymatic degradation and peptides produced from the laboratory digestion of intact protein. Over the 12-day degradation experiment, 31% of the particulate organic carbon was depleted, and there was no preferential degradation of the overall protein pool. However, there was distinct differentiation in the cellular location, secondary structure and modifications between peptides produced by microbial vs. laboratory breakdown. During the initial period of rapid algal decay and bacterial growth, intracellular components from the cytoplasm were consumed first, resulting in the accumulation of membrane-associated proteins and peptides in the detrital pool. Accompanying the enrichment of membrane protein material was an increase in the importance of alpha-helix motifs. Methylated arginine, a post-translational modification common in cell senescence, was found in high amounts within the microbially produced detrital peptide pool, suggesting a link between in-cell modification and resistance to immediate degradation. Another modification-asparagine deamidation-accumulated within the detrital peptides. Protein taxonomies showed the bacterial community decomposing the algal material was rich in Proteobacteria, and protein annotations showed abundant transportation of solubilized carbohydrates and small peptides across membranes. At this early stage of diagenesis, no changes in bulk amino acids (THAA) were observed, yet a proteomic approach allowed us to observe selective changes in diatom protein preservation by using amino acid sequences to infer subcellular location, secondary structures, and post-translational modifications (PTMs).