Chloroplast research in the genomic age

Dario Leister
<span title="">2003</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/alw4ab5u3vdqlgfh3smvbfnjqu" style="color: black;">Trends in Genetics</a> </i> &nbsp;
Chloroplast research takes significant advantage of genomics and genome sequencing, and a new picture is emerging of how the chloroplast functions and communicates with other cellular compartments. In terms of evolution, it is now known that only a fraction of the many proteins of cyanobacterial origin were rerouted to higher plant plastids. Reverse genetics and novel mutant screens are providing a growing catalogue of chloroplast protein -function relationships, and the characterization of
more &raquo; ... tid-to-nucleus signalling mutants reveals cell-organelle interactions. Recent advances in transcriptomics and proteomics of the chloroplast make this organelle one of the best understood of all plant cell compartments. Plastids are organelles characteristic of plant cells. As endosymbiotic remnants of a free-living cyanobacterial progenitor, plastids have, over evolutionary time, lost the vast majority of their genes. Indeed, depending on the organism, contemporary plastomes contain only 60 -200 open reading frames (ORFs). The plastomes of green algae and flowering plants are remarkably similar in the sequences of their genes, whereas the organization of genes on the plastid chromosome differs drastically. Although identical plastome copies are contained in each cell of a plant, the organelles themselves can vary to a large extent in their morphology and function. In fact, proplastids can develop into green chloroplasts, red or yellow chromoplasts, or other variants specialized for the storage of starch, lipids or proteins. The photosynthetically active chloroplasts are characterized by high rates of transcription and translation, allowing the synthesis of large amounts of the enzyme ribulose bisphosphate carboxylase (Rubisco) and a rapid renewal (through turnover) of electron transfer components, features necessary for efficient photosynthetic CO 2 fixation. Besides photosynthesis, chloroplasts carry out other essential plant functions, such as the synthesis of amino acids, fatty acids and lipids, plant hormones, nucleotides, vitamins and secondary metabolites. Technological developments in the genomics of Arabidopsis thaliana, including the sequencing of its genome, have recently stimulated the initiation of projects aimed at systematically identifying the functions of chloroplast proteins and their encoding genes, and elucidating their evolution. This article highlights the new findings, focusing on screens for novel chloroplast mutants, systematic reverse genetics, bioinformatics, transcriptomics and proteomics, in A. thaliana and other plant species. Size, composition and phylogeny of the chloroplast proteome The vast majority of chloroplast proteins are nucleusencoded and, with the exception of the outer envelope proteins, require N-terminal presequences, termed 'chloroplast transit peptides' (cTPs), to target them to the chloroplast. Between 2100 and 3600 distinct proteins are estimated to be located in the Arabidopsis chloroplast [1,2]. These estimates are based on the computational identification of cTPs in the predicted protein-coding regions of the Arabidopsis genome. In general, for almost all chloroplast proteins identified by experimental proteomic analysis in pea or Arabidopsis, and for ,90% of orthologous proteins from other plant species, coding regions for precursor proteins have been correctly predicted by computer programs through the identification of a cTP [3] [4] [5] . Prediction of the intraorganellar location of these proteins, after import into the chloroplast and cleavage of the cTP, is more difficult. The proteins of the stroma, inner envelope and stromal side of thylakoid membranes, as well as most integral proteins of the thylakoid membrane, have no additional transit peptides. By contrast, proteins destined for the thylakoid lumen are targeted and translocated via a second Nterminal sequence, which is located directly C-terminal of the cTP (Box 1). Two different mechanisms are known to facilitate translocation of such lumenal proteins across the thylakoid membrane, the Sec pathway and the twin-arginine translocation (TAT) pathway. The latter requires a specific amino acid sequence, the TAT motif. In A. thaliana, the protein content of the thylakoid lumen has been characterized by two-dimensional electrophoresis and mass spectrometry, as well as by genome-wide searches for the TAT motif. Thirty to 35 lumenal proteins, identified by experimental proteome analysis, and 30 -56 additional proteins encoded by the Arabidopsis nuclear genome and containing a tentative TAT motif, are listed by the groups of van Wijk and Kieselbach, respectively [4, 5] . This allows the prediction that the thylakoid lumen should contain at least 80 different proteins [5] . Based on the annotation of the novel lumenal proteins, new functions, in addition to the accumulation of protons necessary for ATP synthesis and the equilibration of ion currents through the thylakoid membrane, can be associated with the thylakoid lumen. A large group of peptidyl-prolyl cis-trans isomerases (rotamases) and proteases, a family of proteins related to the P subunit Corresponding author: Dario Leister (leister@mpiz-koeln.mpg.de).
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