A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes.
The proteins harboring RING finger motif(s) have been shown to mediate protein-protein interactions that are relevant to a variety of cellular processes. In an effort to elucidate the evolutionary dynamics of the rice RING finger protein family, we have attempted to determine their genomic locations, expression diversity, and co-expressed genes via in silico analysis and semi-quantitative RT-PCR. A total of 425 retrieved genes appear to be distributed over all 12 of the chromosomes of rice with different distributions, and are reflective of the evolutionary dynamics of the rice genome. A genome-wide dataset harboring 155 gene expression omnibus sample plates evidenced some degree of differential evolutionary fates between members of RING-H2 and RING-HC types. Additionally, responses to abiotic stresses, such as salinity and drought, demonstrated that some degree of expression diversity existed between members of the RING finger protein genes. Interestingly, we determined that one RING-H2 finger protein gene (Os04g51400) manifested striking differences in expression patterns in response to abiotic stresses between leaf and culm-node tissues, further revealing responses highly similar to the majority of randomly selected co-expressed genes. The gene network of genes co-expressed with Os04g51400 may suggest some role in the salt response of the gene. These findings may shed further light on the evolutionary dynamics and molecular functional diversity of these proteins in complex cellular regulations.
Lim
Sung Don
SD
Plant Genomics Lab, Department of Applied Plant Sciences Technology, Kangwon National University, Chuncheon, 200-713, Korea.
Yim
Won Cheol
WC
Moon
Jun-Cheol
JC
Kim
Dong Sub
DS
Lee
Byung-Moo
BM
Jang
Cheol Seong
CS
D000595:Amino Acid Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D015870:Gene Expression; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D054829:RING Finger Domains / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism
D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant