高粘土含量海洋沉积物元蛋白质组学分析中蛋白质提取的系统评价。

IF 5.1 Q1 ECOLOGY
ISME communications Pub Date : 2025-05-22 eCollection Date: 2025-01-01 DOI:10.1093/ismeco/ycaf074
Anne Ostrzinski, Benoit J Kunath, André Rodrigues Soares, Cédric C Laczny, Rashi Halder, Jens Kallmeyer, Rolando di Primio, Paul Wilmes, Alexander J Probst, Anke Trautwein-Schult, Dörte Becher
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引用次数: 0

摘要

海洋沉积物中蕴藏着极其多样化的微生物群落,它们为全球生物多样性做出了贡献,并在生态系统的功能中发挥着至关重要的作用。然而,海洋沉积物的元蛋白质组仍然知之甚少。由于基质的复杂性,从环境样品中提取蛋白质仍然是一个挑战,特别是从海洋沉积物中。因此,从海洋沉积物中提取蛋白质的方法需要改进。为了建立有效的粘土沉积物蛋白质提取流程,我们对不同的蛋白质提取方法进行了比较、组合和增强。这里介绍的工作流程包括用高浓度氨基酸阻断沉积物颗粒上的蛋白质结合位点,通过超声波捕获有效的细胞裂解,电洗脱和同时分离蛋白质。为了测试该方案的有效性,我们在提取蛋白质之前将大肠杆菌细胞添加到沉积物样品中。通过使用我们完善的工作流程,我们能够从补充的沉积物中鉴定出与纯大肠杆菌培养物相当数量的大肠杆菌蛋白。这一新方案将使未来的研究能够识别富含粘土的海洋沉积物中的活性参与者,并根据其各自的蛋白质补体准确确定功能生物多样性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Systematic evaluation of protein extraction for metaproteomic analysis of marine sediment with high clay content.

Marine sediments harbor extremely diverse microbial communities that contribute to global biodiversity and play an essential role in the functioning of ecosystems. However, the metaproteome of marine sediments is still poorly understood. The extraction of proteins from environmental samples is still a challenge, especially from marine sediments, due to the complexity of the matrix. Therefore, methods for protein extraction from marine sediments need to be improved. To develop an effective workflow for protein extraction for clayey sediments, we compared, combined and enhanced different protein extraction methods. The workflow presented here includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis by ultrasonic capture, electro-elution, and simultaneous fractionation of proteins. To test the protocol's efficacy, we added Escherichia coli cells to sediment samples before protein extraction. By using our refined workflow, we were able to identify a comparable number of E. coli proteins from the supplemented sediment to those from pure E. coli cultures. This new protocol will enable future studies to identify active players in clay-rich marine sediments and accurately determine functional biodiversity based on their respective protein complements.

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