Improving protein extraction for metaproteomic analysis of marine sediment with high clay content

Marine sediments harbor highly diverse microbial communities that contribute to global biodiversity and play essential roles in the ecosystem functioning. However, the metaproteome of marine sediments remains poorly understood. Extracting proteins from environmental samples can be challenging, especially in marine sediments due to their complex matrix. Few studies have been conducted on improving protein extraction methods from marine sediments. To establish an effective protein extraction workflow for clay-rich sediments, we compared, combined and improved several protein extraction methods. The presented workflow includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis via ultra-sonication, and the electro-elution and simultaneous fractionation of proteins. Using this workflow, we were able to recover 100% of the previously added Escherichia coli proteins from the sediment.

海洋沉积物中栖息着高度多样的微生物群落，这些群落不仅维系全球生物多样性，更在生态系统功能运行中发挥关键作用。然而，目前对海洋沉积物的宏蛋白质组（metaproteome）仍缺乏深入认知。从环境样品中提取蛋白质本就颇具挑战，而海洋沉积物因其基质复杂，这一难题尤为突出。目前针对优化海洋沉积物蛋白质提取方法的研究仍较为匮乏。为构建适用于富黏土沉积物的高效蛋白质提取流程，我们对多款蛋白质提取方法进行了对比、整合与改良。本次提出的提取流程包含以下步骤：以高浓度氨基酸封闭沉积物颗粒表面的蛋白质结合位点、通过超声破碎实现高效细胞裂解，以及对蛋白质进行电洗脱与同步分级分离。借助该流程，我们可从沉积物中完全回收此前添加的大肠杆菌(Escherichia coli)蛋白质。