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The characterisation of novel secreted Ly‐6 proteins from rat urine by the combined use of two‐dimensional gel electrophoresis, microbore high performance liquid chromatography and expressed sequence tag data
Author(s) -
Southan Christopher,
Cutler Paul,
Birrell Helen,
Connell John,
Fantom Kenneth G. M.,
Sims Matthew,
Shaikh Narjis,
Schneider Klaus
Publication year - 2002
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/1615-9861(200202)2:2<187::aid-prot187>3.0.co;2-a
Subject(s) - biology , peptide sequence , peptide , amino acid , gel electrophoresis , protein sequencing , biochemistry , microbiology and biotechnology , gene
A proteomic study of rat urine was undertaken using two‐dimensional gel electrophoresis, microbore high performance liquid chromatographhy, mass spectrometry and N ‐terminal sequencing. Five known urinary proteins were identified but two novel peptide fragments matched a large number of rat expressed sequence tags (ESTs) from a liver library. By combining protein chemical and nucleotide data, two 101‐residue open reading frames with 90% amino acid identity were determined, rat urinary protein 1 (RUP‐1) and RUP‐2. The data established signal peptide removal and provided evidence for N ‐glycosylation. A third related sequence, rat spleen protein (RSP‐1) was confirmed from EST searches. These three proteins have been submitted to SWISS‐PROT as P81827, P81828 and Q9QXN2, respectively. A fourth novel homologue was found in porcine and bovine ESTs from embryo libraries. Alignment with known homologues showed conserved cysteine positions characteristic of a secreted subfamily of Ly‐6 proteins. In two cases, antineoplastic urinary protein and caltrin, these homologues have unverified functional annotations. The RUP sequences showed high scoring matches to three unrelated rat mRNAs subsequently established to be chimeric. Two of these share extended sectional identity to RUP‐1 but the third may represent another novel Ly‐6 homologue. These chimeras have caused serious annotation errors in secondary databases.