Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome.
BACKGROUND
Understanding the functional role(s) of the more than 20,000 proteins of the vertebrate genome is a major next step in the post-genome era. The approximately 4,000 co-translationally translocated (CTT) proteins - representing the vertebrate secretome - are important for such vertebrate-critical processes as organogenesis. However, the role(s) for most of these genes is currently unknown.


RESULTS
We identified 585 putative full-length zebrafish CTT proteins using cross-species genomic and EST-based comparative sequence analyses. We further investigated 150 of these genes (Figure 1) for unique function using morpholino-based analysis in zebrafish embryos. 12% of the CTT protein-deficient embryos resulted in specific developmental defects, a notably higher rate of gene function annotation than the 2%-3% estimate from random gene mutagenesis studies.


CONCLUSIONS
This initial collection includes novel genes required for the development of vascular, hematopoietic, pigmentation, and craniofacial tissues, as well as lipid metabolism, and organogenesis. This study provides a framework utilizing zebrafish for the systematic assignment of biological function in a vertebrate genome.
Pickart
Michael A
MA
Department of Oral Sciences and Minnesota Craniofacial Research Training Program (MinnCResT), University of Minnesota, Minneapolis, Minnesota, United States of America.
Klee
Eric W
EW
Nielsen
Aubrey L
AL
Sivasubbu
Sridhar
S
Mendenhall
Eric M
EM
Bill
Brent R
BR
Chen
Eleanor
E
Eckfeldt
Craig E
CE
Knowlton
Michelle
M
Robu
Mara E
ME
Larson
Jon D
JD
Deng
Yun
Y
Schimmenti
Lisa A
LA
Ellis
Lynda B M
LB
Verfaillie
Catherine M
CM
Hammerschmidt
Matthias
M
Farber
Steven A
SA
Ekker
Stephen C
SC
D000595:Amino Acid Sequence; D000818:Animals; D030801:Animals, Genetically Modified; D016375:Antisense Elements (Genetics) / Q000235:genetics; D001483:Base Sequence; D001808:Blood Vessels / Q000196:embryology; D019295:Computational Biology; D016678:Genome; D023281:Genomics; D006410:Hematopoiesis; D050356:Lipid Metabolism / Q000235:genetics; D008969:Molecular Sequence Data; D020543:Proteome; D040901:Proteomics; D016415:Sequence Alignment; D014714:Vertebrates / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D015027:Zebrafish / Q000196:embryology / Q000235:genetics / Q000502:physiology; D029961:Zebrafish Proteins / Q000235:genetics / Q000502:physiology
D016375:Antisense Elements (Genetics); D020543:Proteome; D029961:Zebrafish Proteins