Photosynthesis Research 153R1: 1–13, 2003. © 2003 Kluwer Academic Publishers. Printed in the Netherlands. 1 Minireview Update on chloroplast proteomics Wolfgang P. Schröder 1,2 & Thomas Kieselbach 3 1 Departments of Chemistry and Biochemistry, Umeå University, 901 87 Umeå, Sweden; 2 Umeå Plant Science Center, Sweden; 3 Departments of Medical Nutrition and Biosciences, Karolinska Institute, 141 86 Huddinge, Sweden; * Author for correspondence (e-mail: wolfgang.schroder@chem.umu.se; fax: +46-90-7867661) Received 1 August 2003; accepted in revised form 9 August 2003 Key words: ■■■ Abstract Currently, relatively few proteomics studies of chloroplast have been published, but the field has just started emerging and is likely to develop more rapidly in the future. While the complex membrane structure of the chloroplast makes it difficult to study its entire proteome by global approaches, proteomics has considerably increased our knowledge of the proteins of single compartments such as, for instance, the envelope and the thylakoid lumen. Proteomics has also succeeded in the subunit characterisation of select protein complexes such as the ribosomes and the cytochrome b 6 f complex. In addition, proteomics was successfully applied to find new potential target pathways for thioredoxin-mediated signal transduction. In this review, we present an overview of the latest developments in the field of chloroplast proteomics and discuss their impact on photosynthesis research. In addition, we summarise the current state of research in proteomics of the photosynthetic cyanobactrium Synechocystis sp. PCC 6803. Abbreviations: 2-DE – two-dimensional electrophoresis; LC-MS/MS – liquid chromatography-MS/MS; LHC II – light harvesting complex II; MS/MS – fragmentation analysis of a selected peptide by mass spectrometry; PS II – Photosystem II; Rubisco – Ribulose bisphosphate carboxylase; SDS-PAGE – sodium dodecylsulfate polyacrylamide electrophoresis; TIGR – The Institute for Genomic Research Introduction The field of proteomics has developed rapidly during recent years, and the general objectives and meth- ods in proteomics research have been covered in numerous excellent reviews (Graves and Haystead 2002; Aebersold and Mann 2003; Tyers and Mann 2003). Originally, the term proteomics was coined at a 2-D electrophoresis meeting in Siene in 1994 (Williams and Hochstrasser 1997) and stands liter- ally for Proteins expressed by a genome. Today proteomics has become a broad research field that not only focuses on protein expression but also in- tegrates many complementary disciplines. Figure 1 shows a simplified overview of the different research areas that meet in proteomics. The spectrum of dis- ciplines includes screening of mutants, and RNA expression studies as well as protein expression, the analysis of protein–protein interactions, studies of post-translational modifications and protein structure determination. As the field of proteomics research has grown very fast, there is so far no strict definition of what is meant by the word ‘proteomics’. Differ- ent researchers have different views on this subject, and the line between proteomics and functional ge- nomics is blurred. Some typical questions addressed in proteomics deal with the expression of proteins in certain physiological states, their subcellular loca- tion, the study of splice variants and post-translational modifications. Many researchers use proteomics in a sense of high-throughput protein chemistry, but oth- ers count also studies in a smaller scale such as the analysis of protein complexes as proteomics. How- ever, what distinguishes proteomics from conventional 153r1.tex; 1/10/2003; 15:26; p.1 Thomson Press (I) Ltd., PIPS No. 5150826 (preskap:bio2fam) v.1.2 UNCORRECTED PROOF! PDF OUTPUT!