42. Isolation and structural analysis of the YABBY gene family in rice

Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657 Japan

YABBY genes have been found to encode a new class of transcription factor and constitute a small gene family in the plant genome. The proteins encoded by YABBY genes contain a zinc finger domain in the N-terminal region and the YABBY domain, which is likely to form helix-turn-helix structure, in the C-terminal region. The YABBY gene family includes CRABS CLAW (CRC), FILAMENTOUS FLOWER (FIL), and INNER NO OUTER (INO) in Arabidopsis. CRC controls nectary development and is partially responsible for carpel development (Bowman and Smyth 1999). FIL controls leaf dorsoventral patterning and maintenance of flower meristem activity (Sawa et al. 1999). We have isolated the DROOPING LEAF (DL) gene from rice, which plays essential roles for carpel development in the flower and midrib formation in the leaf (Hirano and Yamaguchi, in press). DL encodes a protein with the zinc-finger and YABBY domains. Thus, YABBY genes play essential functions in plant development.

To elucidate the function of the YABBY genes in rice development, we have isolated cDNA clones and characterized them.

First, we determined the nucleotide sequences of two cDNAs (OsFIL1 and OsFIL2) that had been registered in the rice EST database. Second, we isolated rice cDNAs homologous to the YABBY genes. A cDNA library was constructed from young rice panicles including flower primordia. Fifty-five clones were obtained by screening about 2 x 105 cDNA clones using DNA fragments of highly conserved regions of DL and OsFIL2 as probes. These clones were classified into seven groups including DL, OsFIL1 and OsFIL2. We named the four remaining cDNAs, which were newly identified in this study, OsYABBY3, OsYABBY4, OsYABBY5 and OsYABBY6.

The proteins predicted from these cDNAs share two conserved regions in the C- and N-terminal regions. These conserved amino acids correspond to the zinc finger and YABBY domains. No significant homology was found in other regions.

Multiple bands were detected by genomic Southern blot analysis using a fragment corresponding to the YABBY domain in OsFIL2 as a probe. This result indicates that genes encoding the YABBY domain form a multi-gene family in the rice genome, which agrees with the cDNA screening results.

A molecular phylogenic tree was constructed by comparing amino acid sequences in the zinc finger and YABBY domains. OsYABBY3, OsYABBY4 and OsYABBY5 form one cluster with Arabidopsis FIL and YABBY3. OsYABBY6, OsFIL1 and OsFIL2 form another cluster. DL and CRC are distantly related to these genes, suggesting that they should be classified into another subfamily.

Organ-specific expression patterns of each YABBY gene were analyzed by RT-PCR

analysis. OsFIL1 and OsFIL2 are highly expressed in almost all organs except root. On the other hand, OsYABBY3 and OsYABBY4 are expressed in the young panicle and immature flower and not expressed in other organs. OsYABBY5 is predominantly expressed in the flower. To elucidate the functions of these genes in rice development, we are now analyzing the spatial expression pattern of each YABBY gene by in situ hybridization, and are trying to make transgenic plants overexpress some of the YABBY genes.


Bowman, J.L. and D.R. Smyth, 1999. CRABS CLAW, a gene that regulates carpel and nectary development in Arabidopsis, encodes a novel protein with zinc finger and helix-loop-helix domains. Development 126: 2387-2396.

Hirano, H.-Y. and T. Yamaguchi, 1999. Isolation of the DROOPINGLEAF gene that regulates carpel development and midrib formation in rice. Gamma Field Symp. 38 (in press).

Sawa, S., K. Watanabe, K. Goto, E. Kanaya, E.H. Morita and K. Okada, 1999. FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains. Genes Dev. 13: 1079-88.