title: Assigning functions to genes: identification of S-phase expressed genes in Leishmania major based on post-transcriptional control elements.
abstract: Assigning functions to genes is one of the major challenges of the post-genomic era. Usually, functions are assigned based on similarity of the coding sequences to sequences of known genes, or by identification of transcriptional cis-regulatory elements that are known to be associated with specific pathways or conditions. In trypanosomatids, where regulation of gene expression takes place mainly at the post-transcriptional level, new approaches for function assignment are needed. Here we demonstrate the identification of novel S-phase expressed genes in Leishmania major, based on a post-transcriptional control element that was recognized in Crithidia fasciculata as involved in the cell cycle-dependent expression of several nuclear and mitochondrial S-phase expressed genes. Hypothesizing that a similar regulatory mechanism is manifested in L.major, we have applied a computational search for similar control elements in the genome of L.major. Our computational scan yielded 132 genes, of which 33% are homologues of known DNA metabolism genes and 63% lack any annotation. Experimental testing of seven of these genes revealed that their mRNAs cycle throughout the cell cycle, reaching a maximum level during S-phase or just prior to it. It is suggested that screening for post-transcriptional control elements associated with a specific function provides an efficient method for assigning functions to trypanosomatid genes.
authors.affiliation: Department of Parasitology, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
authors.forename: Aviad
authors.initials: A
authors.lastname: Zick
authors.forename: Itay
authors.initials: I
authors.lastname: Onn
authors.forename: Rachel
authors.initials: R
authors.lastname: Bezalel
authors.forename: Hanah
authors.initials: H
authors.lastname: Margalit
authors.forename: Joseph
authors.initials: J
authors.lastname: Shlomai
mesh_terms: D000818:Animals; D001483:Base Sequence; D002478:Cells, Cultured; D016831:Crithidia fasciculata / Q000235:genetics; D016054:DNA, Protozoan / Q000378:metabolism; D015870:Gene Expression; D017125:Genes, Protozoan; D023281:Genomics; D018320:Leishmania major / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D015800:Protozoan Proteins / Q000235:genetics / Q000502:physiology; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid; D016196:S Phase; D020506:Untranslated Regions / Q000737:chemistry*
chemical_list: D016054:DNA, Protozoan; D015800:Protozoan Proteins; D012333:RNA, Messenger; D038621:Regulatory Sequences, Ribonucleic Acid; D020506:Untranslated Regions