NORMAL GENOMIC

• Menichini P, Linial M
• SUVi and BACH1: a new subfamily of mammalian helicases?
• Mutat Res. 2001; 487: 67-71
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• The RecQ family of DNA helicases have been shown to be important for themaintenance of genomic integrity in prokaryotes and eukaryotes. Members ofthis family are genes responsible for cancer predisposition disorders likeBloom's syndrome, Werner's syndrome and Rothmund-Thomson syndrome. Here,we show the sequence homologies between two recently identified mammalianhelicases, namely SUVi and BACH1. These two genes also share stronghomologies with other members of the RecQ family. On the basis ofpublished data and sequence analysis we suggest that SUVi/BACH1 mayrepresent a novel subfamily of mammalian helicases, functioning in theprocessing of lesions induced by different genotoxic agents.

• Okanami M, Meshi T, Iwabuchi M
• Characterization of a DEAD box ATPase/RNA helicase protein of Arabidopsisthaliana.
• Nucleic Acids Res. 1998; 26: 2638-43
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• We have isolated cDNAs encoding a novel member of the DEAD box RNAhelicase family from Arabidopsis. The protein, named AtDRH1, is composedof 619 amino acids and the central portion has high similarity with thehelicase core region of a prototypic RNA helicase, the human nuclearprotein p68. The N- and C-terminal regions are considerably diverged fromthe animal and yeast p68 homologs at the amino acid sequence level, butlike the p68 subfamily members, an RGG box-like domain is present near theC-terminus. RNA blot analysis showed that the AtDRH1 transcriptaccumulates at a high level and almost equally in every part of theArabidopsis plant. The purified, recombinant AtDRH1 was capable ofunwinding double-stranded RNA in the presence of ATP or dATP and ofhydrolyzing ATP. The ATPase activity was stimulated by somesingle-stranded RNAs and DNAs, including poly(A) and poly(dT), but not bypoly(dA). The ability of the polynucleotides to stimulate the ATPaseactivity was largely consistent with their affinity for AtDRH1. Theseresults show that AtDRH1 is a novel type of ATP/dATP-dependent RNAhelicase and polynucleotide-dependent ATPase.

• Du J, Nasir I, Benton BK, Kladde MP, Laurent BC
• Sth1p, a Saccharomyces cerevisiae Snf2p/Swi2p homolog, is an essentialATPase in RSC and differs from Snf/Swi in its interactions with histonesand chromatin-associated proteins.
• Genetics. 1998; 150: 987-1005
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• The essential Sth1p is the protein most closely related to the conservedSnf2p/Swi2p in Saccharomyces cerevisiae. Sth1p purified from yeast has aDNA-stimulated ATPase activity required for its function in vivo. Thefinding that Sth1p is a component of a multiprotein complex capable ofATP-dependent remodeling of the structure of chromatin (RSC) in vitro,suggests that it provides RSC with ATP hydrolysis activity. Three sth1temperature-sensitive mutations map to the highly conservedATPase/helicase domain and have cell cycle and non-cell cycle phenotypes,suggesting multiple essential roles for Sth1p. The Sth1p bromodomain isrequired for wild-type function; deletion mutants lacking portions of thisregion are thermosensitive and arrest with highly elongated buds and 2CDNA content, indicating perturbation of a unique function. The pleiotropicgrowth defects of sth1-ts mutants imply a requirement for Sth1p in ageneral cellular process that affects several metabolic pathways.Significantly, an sth1-ts allele is synthetically sick or lethal withpreviously identified mutations in histones and chromatin assembly genesthat suppress snf/swi, suggesting that RSC interacts differently withchromatin than Snf/Swi. These results provide a framework forunderstanding the ATP-dependent RSC function in modeling chromatin and itsconnection to the cell cycle.

• Webster PJ, Liang L, Berg CA, Lasko P, Macdonald PM
• Translational repressor bruno plays multiple roles in development and iswidely conserved.
• Genes Dev. 1997; 11: 2510-21
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• oskar (osk) mRNA is tightly localized to the posterior pole of theDrosophila oocyte, where the subsequent expression of Osk protein directsabdomen and germ-line formation in the developing embryo. Misplacedexpression of Osk protein leads to lethal body patterning defects. The Oskmessage is translationally repressed before and during the localizationprocess, ensuring that Osk protein is only expressed after the mRNA hasreached the posterior. An ovarian protein, Bruno (Bru), has beenimplicated as a translational repressor of osk mRNA. Here we report theisolation of a cDNA encoding Bru using a novel approach to the expressioncloning of an RNA-binding protein, and the identification of previouslydescribed mutants in the arrest (aret)-locus as mutants in Bru. The mutantphenotype, along with the binding properties of the protein and itspattern of accumulation within the oocyte, indicate that Bru regulatesmultiple mRNAs involved in female and male gametogenesis as well as earlyin embryogenesis. Genetic experiments provide further evidence that Brufunctions in the translational repression of osk. Intriguingly, we findthat Bru interacts physically with Vasa (Vas), an RNA helicase that is apositive regulator of osk translation. Bru belongs to an evolutionarilyconserved family of genes, suggesting that Bru-mediated translationalregulation may be widespread. Models for the molecular mechanism of Brufunction are discussed.

• Eberl DF, Lorenz LJ, Melnick MB, Sood V, Lasko P, Perrimon N
• A new enhancer of position-effect variegation in Drosophila melanogasterencodes a putative RNA helicase that binds chromosomes and is regulated bythe cell cycle.
• Genetics. 1997; 146: 951-63
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• In Drosophila melanogaster, position-effect variegation of the white genehas been a useful phenomenon by which to study chromosome structure andthe genes that modify it. We have identified a new enhancer of variegationlocus, Dmrnahel (hel). Deletion of mutation of hel enhances whitevariegation, and this can be reversed by a transformed copy of hel+. Inthe presence of two endogenous copies, the transformed hel+ behaves as asuppressor of variegation. hel is an essential gene and functions bothmaternally and zygotically. The HEL protein is similar to known RNAhelicases, but contains an unusual variant (DECD) of the DEAD motif commonto these proteins. Potential HEL homologues have been found in mammals,yeast and worms. HEL protein associates with salivary gland chromosomesand locates to nuclei of embryos and ovaries, but disappears in mitoticdomains of embryos as chromosomes condense. We propose that the HELprotein promotes an open chromatin structure that favors transcriptionduring development by regulating the spread of heterochromatin, and thatHEL is regulated by, and may have a role in, the mitotic cell cycle duringembryogenesis.

• Yura T et al.
• Systematic sequencing of the Escherichia coli genome: analysis of the0-2.4 min region.
• Nucleic Acids Res. 1992; 20: 3305-8
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• A contiguous 111,402-nucleotide sequence corresponding to the 0 to 2.4 minregion of the E. coli chromosome was determined as a first step tocomplete structural analysis of the genome. The resulting sequence wasused to predict open reading frames and to search for sequence similarityagainst the PIR protein database. A number of novel genes were found whosepredicted protein sequences showed significant homology with knownproteins from various organisms, including several clusters of genessimilar to those involved in fatty acid metabolism in bacteria (e.g.,betT, baiF) and higher organisms, iron transport (sfuA, B, C) in Serratiamarcescens, and symbiotic nitrogen fixation or electron transport (fixA,B, C, X) in Azorhizobium caulinodans. In addition, several genes and ISelements that had been mapped but not sequenced (e.g., leuA, B, C, D) wereidentified. We estimate that about 90 genes are represented in this regionof the chromosome with little spacer.

• Koonin EV
• A new group of putative RNA helicases.
• Trends Biochem Sci. 1992; 17: 495-7