title: PPR proteins of green algae.
abstract: Using the repeat finding algorithm FT-Rep, we have identified 154 pentatricopeptide repeat (PPR) proteins in nine fully sequenced genomes from green algae (with a total of 1201 repeats) and grouped them in 47 orthologous groups. All data are available in a database, PPRdb, accessible online at http://giavap-genomes.ibpc.fr/ppr. Based on phylogenetic trees generated from the repeats, we propose evolutionary scenarios for PPR proteins. Two PPRs are clearly conserved in the entire green lineage: MRL1 is a stabilization factor for the rbcL mRNA, while HCF152 binds in plants to the psbH-petB intergenic region. MCA1 (the stabilization factor for petA) and PPR7 (a short PPR also acting on chloroplast mRNAs) are conserved across the entire Chlorophyta. The other PPRs are clade-specific, with evidence for gene losses, duplications, and horizontal transfer. In some PPR proteins, an additional domain found at the C terminus provides clues as to possible functions. PPR19 and PPR26 possess a methyltransferase_4 domain suggesting involvement in RNA guanosine methylation. PPR18 contains a C-terminal CBS domain, similar to the CBSPPR1 protein found in nucleoids. PPR16, PPR29, PPR37, and PPR38 harbor a SmR (MutS-related) domain similar to that found in land plants pTAC2, GUN1, and SVR7. The PPR-cyclins PPR3, PPR4, and PPR6, in addition, contain a cyclin domain C-terminal to their SmR domain. PPR31 is an unusual PPR-cyclin containing at its N terminus an OctotricoPeptide Repeat (OPR) and a RAP domain. We consider the possibility that PPR proteins with a SmR domain can introduce single-stranded nicks in the plastid chromosome.
authors.affiliation: UMR 7141 CNRS/UPMC; Institut de Biologie Physico-Chimique; F-75005 Paris, France.
authors.forename: Nicolas J
authors.initials: NJ
authors.lastname: Tourasse
authors.affiliation: UMR 7141 CNRS/UPMC; Institut de Biologie Physico-Chimique; F-75005 Paris, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Choquet
authors.affiliation: UMR 7141 CNRS/UPMC; Institut de Biologie Physico-Chimique; F-75005 Paris, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Vallon
mesh_terms: D020418:Algal Proteins / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D001483:Base Sequence; D000460:Chlorophyta / Q000235:genetics / Q000378:metabolism*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012333:RNA, Messenger / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D020418:Algal Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins
keywords: chloroplast; cyclin; evolution; green algae; mitochondrion; pentatricopeptide repeat; small MutS-related; tRNA methyltransferase
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