Maize Genetics Cooperation Newsletter

maize gene review

Author: Alice Barkan, University of Oregon, Eugene, OR. USA 97403


Review: pending

Pub date: May 2009

Name: caf1-- CRS2 associated factor1

Synonyms: chloroplast splicing factor

Chromosome 7L bin 7.02
Genome Browser via BAC c0040M18/ AC205396

Function: chloroplast intron II splicing.

image of corn mutant

Summary: CAF1 functions in the context of a heterodimeric complex with the peptidyl-tRNA hydrolase homolog CRS2 to promote the splicing of a subset of chloroplast group II introns. CAF1/CRS2 complexes bind in vivo specifically to those introns whose splicing they promote. CAF1 is paralogous to CAF2, which also promotes chloroplast group II intron splicing in concert with CRS2. CAF1 and CAF2 promote the splicing of distinct intron subsets. CAF1 and CAF2 both harbor “CRM” domains, an RNA binding domain found in various mitochondrial and chloroplast splicing factors. Null alleles of caf1 are albino and seedling lethal due to the failure to splice several plastid tRNAs and ribosomal protein mRNAs: these splicing defects block the biogenesis of the plastid translation machinery, which in turn leads to the loss of all plastid-encoded proteins.

Images: mutant leaf color depicted on a seedling color scale

First reported: Ostheimer et al. 2003.

Key Alleles

caf1-1::Mu. Mu insertion in exon 1. Ivory, seedling lethal phenotype.

caf1-2::Mu. Mu insertion in exon 1. very pale yellow green, seedling lethal phenotype. Often has small revertant sectors.

Map Location

Determined by NCBI BLAST and Version 1 of the B73 pseudomolecule.

Gene Product

Subunit of a heterodimeric chloroplast group II intron splicing protein required to process several plastid tRNAs and ribosomal protein mRNAs (Barkan et al. 2007, Ostheimer et al. 2003, Schmitz-linneweber et al. 2005).

Paralogous locus

caf2, which promotes splicing of distinct intron subset (Asakura and Barkan 2006)

Related locus

crs2; the CRS2 polypeptide forms an active complex with the CAF1 polypeptide (Ostheimer et al. 2003).


Asakura Y and Barkan A. (2006) Arabidopsis orthologs of maize chloroplast splicing factors promote splicing of orthologous and species-specific group II introns. Plant Physiology 142: 1656-1663. PUBMED

Barkan A, Klipcan L, Ostersetzer O, Kawamura T, Asakura Y, Watkins K. (2007) The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein. RNA 13:55-64. PUBMED

Ostheimer GJ, Williams-Carrier R, Belcher S, Osborne E, Gierke J, Barkan A. (2003) Group II Intron Splicing Factors Derived by Diversification of an Ancient RNA Binding Domain. EMBO J. 22: 3919-3929. PUBMED

Schmitz-Linneweber C, Williams-Carrier R, Barkan A. (2005) RNA immunoprecipitation and microarray analysis shows a chloroplast PPR protein to be associated with the 5'- region of mRNAs whose translation it activates. Plant Cell, 17: 2791-2804. PUBMED

Links: MGDB: caf1 NCBI:caf1 UniProt: Q84N49