A database of mutant phenotypes of nuclear-encoded chloroplast proteins
This database provides easy access to all-inclusive knowledge data, including the information of Arabidopsis knockout mutant resources and their phenotypes for nuclear-encoded chloroplast proteins.
Chloroplast Function Database III April 2019 Update release
The Chloroplast Function Database was first opened in December 2009, and updated as the Chloroplast Function Database II in November 2012. The former update brought a number of new features to the original Chloroplast Function Database. The Chloroplast Function Database II has been used for functional analysis of chloroplast proteins.
In the Chloroplast Function Database III updated on April 2019, useful information was added for the functional analysis of nuclear genes for chloroplast proteins including membrane proteins. There are many useful new features like a new sorting system, enhancement of search functions, and direct link to a request of seeds in RIKEN BRC. Moreover, this updated database provides a user-friendly database with additional 450 tagged mutant lines of nuclear genes for chloroplast membrane proteins. We defined 791 chloroplast proteins having a transmembrane alpha motif in the protein as "chloroplast membrane proteins", which were estimated by computational prediction of the ARAMEMNON plant membrane protein database v7.0 (Schwacke et al., Plant Physiol. (2003) 131: 16-26). The database provides 70% tagged mutant lines of chloroplast membrane proteins estimated in the ARAMEMNON database.
The chloroplast is the most important organelle in plants and is involved in photosynthesis and the production of numerous metabolites such as sugars, lipids, amino acids, vitamins, etc., that are important for agriculture and nutrition. However, most of the proteins in the chloroplast are encoded by the nuclear genome and are targeted to the chloroplast. Richly and Leister (2004) identified 2,090 chloroplast proteins by computational prediction of the N-terminal chloroplast transit peptides (cTPs) and demonstrated that at least 3 of the 4 different prediction softwares (iPSORT, PCLR, Predotar, and TargetP) can identify proteins with cTPs. We defined these proteins as "nuclear-encoded chloroplast proteins," and we systematically collected tagged lines that that Ds/Spm transposon or transferred DNA (T-DNA) inserted into Arabidopsis. Based on the databases of tagged mutant lines such as RIKEN Ds, JIC GT/SM, Wisconsin T-DNA, CSHL genetrap, and SALK T-DNA lines, we collected 3,246 transposon or T-DNA-tagged lines that encode 1,369 chloroplast proteins. We observed the visible phenotypes of these tagged lines on agar plates at the seedling stage; we then collected homozygous lines that had no clear phenotypes (see Methods). Mutants with heterozygotes but no homozygous knockouts were also identified in our collection, suggesting that the responsible genes of these mutants encode the essential genes in embryogenesis.
The chloroplast function database provides easy access to a collected tagged mutant data of Arabidopsis nuclear genes encoding chloroplast proteins and their phenotypes for the analysis of functions of nuclear-encoded chloroplast proteins. Our collection of homozygous mutants, in particular, is a powerful tool for screening chloroplast mutants with cryptic abnormalities (e.g., abnormal biotic or abiotic stress response, parameters of photosynthesis, etc.) and is easy to identify the mutated gene as compared to screening after ethylmethanesulfonate (EMS) mutagenesis; further, it can newly identify mutants that are yet to be identified experimentally.
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