Analysis of an Unusual Transcript with a non AUG translation initiation codon in Giardia Lamblia

RIOS, DIEGO N; MERINO, GABRIELA; SERRADELL, MARIANELA; RUPIL LUCIA; SAURA, ALICIA; MARTINA, MARIANA; FERNÁNDEZ, ELMER ANDRÉS; LUJAN, HUGO DANIEL; GARGANTINI, PABLO R

Mar del Plata

Congreso; X Congreso de Protozoologia y enfermedades parasitarias; 2014

Sociedad Argentina de Protozoología

Giardia lamblia is a protozoan parasite that is found worldwide and has both medical and veterinary importance. The availability of second-generation sequencers has made it easier and less expensive to study the gene expression profile of Giardia, improving our understanding of the unique features of these parasites and allowing us to identify expressed genes and verify annotated ones. We used the data from a RNA-seq study to analyze the correct identification and quantitation of expression for a putative Non-AUG translation initiation gene first described in this parasite. Visual inspection of the alignment obtained with the Integrative Genomics Viewer (IGV), revealed the presence of readings in the previous genomic region to the ATG site annotated in the public database. Transcript levels were calculated from the mapped sequences as fragments per kilobase per million fragments mapped (FPKM), using Cufflinks v.2.0.0. Another analysis revealed the presence of a putative downstream box (DB) in this transcript, we used a 15 nt sequence (5´-CAGGCGCGGGGGCUC-3´) as a query that complements precisely the 15 nt putative anti-DB sequence at the 3´-end of the Giardia 16S-like rRNA. We also examined this transcript looking for a frequent transcription-initiation site consensus, which could be upstream of the Non-AUG start codon previously identified by 5´RACE. All this in silico analysis complement others molecular experiments that could explain the unique mechanism of translation initiation that probably falls somewhere between that of a prokaryote and a eukaryote with a potentially close link with that in the Archaea.