Protein extraction and database construction in tea rhizosphere soil

Abstract

Soil protein extraction and database construction are the key points of soil proteomics research. In this paper, tea tree rhizosphere soil was used as material. The soil proteins were extracted three times by citrate, SDS, and mixture of citrate and SDS, respectively. The total proteins were separated by 2-DE electrophoresis and identified by Data Dependent Acquisition (DDA). The DDA data collection was further separated by High-Performance Liquid Chromatography (HPLC) and identified by LC–MS/MS, then to build the database of soil protein and microbial species using fungus and bacteria databases. The result showed soil protein was identified and reached 2741 points, and the molecular weight was mainly distributed in between 2.64 and 338.33 kDa, and Isoelectric point (pI) is mainly distributed in between 3.78 and 12.15. The soil protein was mainly from 138 families, 346 species of microorganisms. This optimization method could obtain more proteins than previous methods, with a wider range of molecular weight and pI. This study lays an important foundation for the research and development of soil metaproteomics.