Reply to the letter to the editor

Abstract

I am responding to comment letter (IJC-06-0794––Thioredoxin-related protein-1 induced by prostaglandin E2) by Dr. Antonio Miranda-Vizuete. First of all, we greatly appreciate the Doctor's comments and agree in some senses. While we were doing experiments, we had similar thoughts on the results. However, the full-length cDNA sequence was exactly as we reported. We will begin responding to his comments with the findings of reviewer 2. When we prepared and submitted the manuscript, reviewer 2 had the following comments (28 Dec 2004, Ref: IJC-04-1969.R1): “I don't find it appropriate to call the identified novel gene and to provide a new name for it. A genome search with a bit of the sequence around ATG of TRP-1 reveals one single hit at the TMX2 locus. The same is true using a sequence around the stop codon. This TMX2 locus encodes cDNAs that have already been reported. One report refers to the gene product as the CGI-31 protein (mentioned in the manuscript). This gene product shows 92% identity with TRP-1. Another report uses the designation TMX2 (Thioredoxin-related transmembrane protein 2: Meng et al. Cloning and identification of a novel cDNA coding thioredoxin-related transmembrane protein 2. Biochem Genet 2003;41:99). The latter is not referred to in the manuscript, although the TMX2 was here described to contain both the thioredox-related domain and a Myb-related domain. It thus seems that TRX-1 is a variant of TMX2/CGI-31. Whether the small alterations in aa sequence observed is due to natural variations in sequence or to alternative splicing (or to cloning effects), remains to be determined. Curiously, the TRP-1 variant seems to have a better Myb-fit than TMX2/CGI-31 with three properly spaced in TRP-1 and only one found in TMX2/CGI-31′. Reviewer 2 suggested that TRP-1 is a variant of TMX2/CGI-31. After the revision of the manuscript, it is stressed in the revised manuscript (24 May 2005, Ref: IJC-04-1969.R2) “A novel gene in the previous version of the manuscript, the identified gene was called novel and designated TRP-1, which I didn't find appropriate since TRP-1 clearly is a variant of TMX2/CGI-31.” gi|8452480|emb|AL138752.5 Human DNA sequence from clone RP11-3J10 on chromosome 9p12-13.3 contains the 3′ end of the SHB gene for SHB (Src homology 2 domain containing) adaptor protein B, the MCART1 gene for mitochondrial carrier triple repeat 1 (MGC14836), a novel gene, a novel pseudogene, a phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS) pseudogene, a novel gene (MGC10765, FLJ23201), a mitochondrial ribosomal protein S10 (MRP-S10, FLJ10567, PNAS-122) (MRPS10) pseudogene, the gene for exosome component RRP40, a novel gene (FLJ31455) and four CpG islands, complete sequence. gi|50472125|emb|CR591318.1| full-length cDNA clone CS0DM001YD22 of Fetal liver of Homo sapiens (human) gi|21218128|dbj|AP001931.5| Homo sapiens genomic DNA, chromosome 11q clone:RP11-691N7, complete sequences With facts mentioned earlier, we suggest that TRP-1 is a variant of TMX2/CGI-31. I feel that this discrepancy is most accurately outlined in the comments of reviewer 2. Yours sincerely, Myeong J. Nam.