Strategies to boost archaea sulfolobus solfataricus P2 proteome coverage and predict new genes

Bing Wang, Lin Yang, Yuyue Zhan, Junhui Hao,Cuihong Wan

Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China.

Abstract

Archaea are well-known for their ability to adapt to harsh environments, which are too severe for the growth of bacteria and Eukaryotes. So far, the studies of Archaea proteomics haven’t achieved satisfying proteome coverage yet. In this work, S. solfataricus P2, a typical model Archaea was chosen for proteogenomic analysis to further characterize the proteome. Among 2938 predicted protein-coding genes, 2122 proteins (>72%) were identified. Furthermore, 48 peptides out of 549 genome search-specific peptides were mapped to regions of the genome where no genes were annotated. 31 previously unidentified protein-coding regions were matched by these 48 peptides using FgenesB and 7 of these regions were assigned by at least two unique genome search-specific peptides. Findings in this work suggest the effectiveness of proteogenomics pipeline in expanding the depth of proteome and genome annotation.

Graphical abstract

Keywords: Sulfolobus solfataricus, Archaea, Proteomics, Database search, Proteogenomics.