Systematic identification, classification, and characterization of the open reading frames which encode novel helicase-related proteins inSaccharomyces cerevisiae by gene disruption and Northern analysis

Abstract

Helicase‐related proteins play important roles in various cellular processes incuding DNA replication, DNA repair, RNA processing and so on. It has been well known that the amino acid sequences of these proteins contain several conserved motifs, and that the open reading frames (ORFs) which encode helicase‐related proteins make up several gene families. In this study, we have identified 134 ORFs that encode helicase‐like proteins in the Saccharomyces genome, based on similarity with the ORFs of authentic helicase and helicase‐related proteins. Multiple alignment of the ORF sequences resulted in the 134 ORFs being classified to 11 clusters. Seven out of 21 previously uncharacterized ORFs (YDL031w, YDL070w, YDL084w, YGL150c, YKL078w, YLR276c, and YMR128w) were identified by systematic gene disruption, to be essential for vegetative growth. Three (YDR332w, YGL064c, and YOL095c) out of the remaining 14 dispensable ORFs exhibited the slow‐growth phenotype at 30°C and 37°C. Furthermore, the expression profiles of transcripts from 43 ORFs were examined under seven different growth conditions by Northern analysis and reverse transcription‐polymerase chain reaction, indicating that all of the 43 tested ORFs were transcribed. Interestingly, we found that the level of transcript from 34 helicase‐like genes was markedly increased by heat shock. This suggests that helicase‐like genes may be involved in the biosynthesis of nucleic acids and proteins, and that the genes can be transcriptionally activated by heat shock to compensate for the repressed synthesis of mRNA and protein. Copyright © 1999 John Wiley & Sons, Ltd.

Bypassing of stems versus linear base-by-base inspection of mammalian mRNAs during ribosomal scanning

“…In any case, homology between these proteins is limited to their C‐terminal two thirds. YLR419w is not essential (Shiratori et al , 1999) and a YLR419w deletion strain has no apparent translational defect, YLR419w does not associate with 40S subunits in vivo , and purified YLR419w does not bind yeast or mammalian 40S subunits in vitro (VP, TP, A Komar, unpublished data). These data indicate that YLR419w is likely not a functional DHX29 orthologue.…”

Pif1p Helicase, a Catalytic Inhibitor of Telomerase in Yeast

“…4A). None o f the other 132 yeast ORFs with helicase motifs (18) had detectable similarity to Pif l p by the criterion o f a blast search (19). This search also identified Pif lp-like proteins in Candida maltosa, Caenorhabditis elegans, and Drosophila melanogaster (Fig.…”

Plasmodium falciparum specific helicase 2 is a dual, bipolar helicase and is crucial for parasite growth

“…Helicases separate double helix of the DNA strands or secondary structures of RNA by utilizing energy harnessed from ATP hydrolysis and therefore all the helicases contain intrinsic nucleic-acid-dependent ATPase activity 14 . The importance of helicases is further strengthened because they are encoded by a major fraction of the prokaryotic and eukaryotic genome 15,16 . On the basis of conserved amino acid signature motifs, the helicases have been divided into six superfamilies’ SF1-SF6 17 .…”