Maize Genetics Cooperation Newsletter

maize gene review

Author: DOI/

Review: pending

Pub date: May 2009

Name: caf2--CRS2 associated factor2

Synonyms: chloroplast group II intron splicing factor

Chromosome 3S bin 3.04.
Genome Browser via BAC c0529P01/AC199526

Function: chloroplast group II intron splicing

image of corn mutant

Summary: CAF2 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. CAF2/CRS2 complexes bind in vivo specifically to those introns whose splicing they promote. CAF2 is paralogous to CAF1, 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 caf2 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 on a seedling leaf color scale

First report: Ostheimer et al 2003.

Key Allele

caf2-1::Mu. Mu insertion in the first exon. Ivory, seedling lethal phenotype. Mutant seedlings tend to be much smaller than wildtype siblings.

Map location

No recombination data. Chromosome location is based on sequence similarity to the B73 Reference Genome Sequence Version 1.

Gene Product

RNA-binding, CRM-domain subunit of a heterodimeric chloroplast group II intron splicing complex.

Paralogous locus

caf1; promotes splicing of chloroplast class II introns, with specificity distinct from caf2.

Related locus

crs2; encodes the other subunit of the chloroplast group II intron splicing complex.

Genotyping Primers

caf2-1, 150 bp product; 5' primer a 1:1 a mix of: 5'-GCCTCCATTTCGTCGAATCCC-3' and 5'-GCCTCTATTTCGTCGAATCCG-3'; 3' primer, 5'-GTTGTGTGAAATGTGCGGCTTGA-3'.

Caf2 (functional allele); 603 bp product that spans caf2-1 insertion site;5'-Primer 5'-CCCAAGAAGCACTCCCAGCAG-3'; 3' -Primer, 5'-GTTGTGTGAAATGTGCGGCTTGA-3'


Asakura Y, 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, and 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

Ostheimer GJ, Rojas M, Hadjivassiliou H, Barkan A. (2006) Formation of the CRS2-CAF2 group II intron splicing complex is mediated by a 22-amino acid motif in the COOH-terminal region of CAF2. J Biol Chem 281: 4732-4738. PUBMED

Links: MGDB caf2 NCBI: caf2 UniProt: Q84N48