Proteome analysis of chloroplasts from the moss Physcomitrella patens (Hedw.) B.S.G.

Intact chloroplasts were prepared from protoplasts of the moss Physcomitrella patens according to an especially developed method. They were additionally separated into stroma and thylakoid fractions. The proteomes of intact plastids, stroma, and thylakoids were analyzed by 1D-electrophoresis under denaturing conditions followed by protein digestion and nano-LC-ESI-MS/MS of tryptic peptides from gel bands. A total of 624 unique proteins were identified, 434 of which were annotated as chloroplast resident proteins. The majority of proteins belonged to a photosynthetic group (21.3%) and to the group of proteins implicated in protein degradation, posttranslational modification, folding, and import (20.6%). Among proteins assigned to chloroplasts, the following groups are prominent combining proteins implicated in metabolism of: amino acids (6.9%), nucleotides (2.5%), lipids (2.2%), carbohydrates (2.4%), hormones (1.5%), isoprenoids (1.25%), vitamins and cofactors (1%), sulfur (1.25%), and nitrogen (1%); as well as proteins involved in the pentose-phosphate cycle (1.75%), tetrapyrrole synthesis (3.7%), and redox processes (3.6%). The data can be used in physiological and photobiological studies as well as in further studies of P. patens chloroplast proteome including structural and functional specifics of plant protein localization in organelles.