TY - JOUR
T1 - Translational machinery of channel catfish
T2 - I. A transcriptomic approach to the analysis of 32 40S ribosomal protein genes and their expression
AU - Karsi, Attila
AU - Patterson, Andrea
AU - Feng, Jinian
AU - Liu, Zhanjiang
N1 - Funding Information:
This project was supported by a grant from USDA NRICGP (#98-35205-6738) and by the Auburn University Competitive BioGrant (Biogrant J. Liu 99). We appreciate the support of Auburn University Department of Fisheries and Allied Aquacultures, College of Agriculture, and the Vice President for Research for their matching funds to USDA NRI Equipment Grants (98-35208-6540, 99-35208-8512). The authors wish to thank Dr. Ira Wool at the University of Chicago for his kind advice and review of the manuscript. We would also like to thank Dr. Bernhart Kaltenback for allowing us to use his DNAStar software and Dongfeng Cao, Arif Kocabas, Zhenlin Ju, and Ping Li for their contribution in the EST analysis.
PY - 2002/5/29
Y1 - 2002/5/29
N2 - Ribosomal protein (RP) genes have become widely used as markers for phylogenetic studies and comparative genomics. However, they have not been available for evolutionary studies in fish although teleosts are the largest group of vertebrates with more than 23,000 species. Using a transcriptomic approach, we have cloned and sequenced 32 40S RP complementary DNAs (cDNAs) from channel catfish (Ictalurus punctatus), making them one of the most complete sets of 40S RP gene sequences from a single organism. Most 40S RPs in channel catfish are highly similar to their orthologues in mammalian species, but S19, S21, and S25 are highly divergent. Only one type of cDNA was found for all RP genes except S26 and S27, for which two cDNAs were found in channel catfish. Alternatively spliced transcripts for the S3 and alternatively polyadenylated transcripts for S19 and S21 were found. The 32 40S RP genes are generally highly expressed and together they account for 5.33-11.42% of expression depending on the tissues. Expression levels of the RP genes were highly variable both within a single tissue among different RP genes and among tissues with regard to a single RP gene. Taken together, these data strongly suggest post-transcriptional regulation of RP gene expression, particularly in consideration of the stoichiometry of their representation in ribosomes.
AB - Ribosomal protein (RP) genes have become widely used as markers for phylogenetic studies and comparative genomics. However, they have not been available for evolutionary studies in fish although teleosts are the largest group of vertebrates with more than 23,000 species. Using a transcriptomic approach, we have cloned and sequenced 32 40S RP complementary DNAs (cDNAs) from channel catfish (Ictalurus punctatus), making them one of the most complete sets of 40S RP gene sequences from a single organism. Most 40S RPs in channel catfish are highly similar to their orthologues in mammalian species, but S19, S21, and S25 are highly divergent. Only one type of cDNA was found for all RP genes except S26 and S27, for which two cDNAs were found in channel catfish. Alternatively spliced transcripts for the S3 and alternatively polyadenylated transcripts for S19 and S21 were found. The 32 40S RP genes are generally highly expressed and together they account for 5.33-11.42% of expression depending on the tissues. Expression levels of the RP genes were highly variable both within a single tissue among different RP genes and among tissues with regard to a single RP gene. Taken together, these data strongly suggest post-transcriptional regulation of RP gene expression, particularly in consideration of the stoichiometry of their representation in ribosomes.
KW - EST
KW - Gene expression
KW - Ribosomal protein
KW - Teleost
KW - Transcriptome
KW - cDNA
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U2 - 10.1016/S0378-1119(02)00595-4
DO - 10.1016/S0378-1119(02)00595-4
M3 - Article
C2 - 12095691
AN - SCOPUS:0037193681
SN - 0378-1119
VL - 291
SP - 177
EP - 186
JO - Gene
JF - Gene
IS - 1-2
ER -