NORMAL GENOMIC

• Pioszak AA et al.
• Structures of a putative RNA 5-methyluridine methyltransferase, Thermusthermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine.
• Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005; 61: 867-74
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• The Thermus thermophilus hypothetical protein TTHA1280 belongs to a familyof predicted S-adenosyl-L-methionine (AdoMet) dependent RNAmethyltransferases (MTases) present in many bacterial and archaealspecies. Inspection of amino-acid sequence motifs common to class IRossmann-fold-like MTases suggested a specific role as an RNA5-methyluridine MTase. Selenomethionine (SeMet) labelled and nativeversions of the protein were expressed, purified and crystallized. Twocrystal forms of the SeMet-labelled apoprotein were obtained: SeMet-ApoIand SeMet-ApoII. Cocrystallization of the native protein withS-adenosyl-L-homocysteine (AdoHcy) yielded a third crystal form,Native-AdoHcy. The SeMet-ApoI structure was solved by the multipleanomalous dispersion method and refined at 2.55 A resolution. TheSeMet-ApoII and Native-AdoHcy structures were solved by molecularreplacement and refined at 1.80 and 2.60 A, respectively. TTHA1280 formeda homodimer in the crystals and in solution. Each subunit folds into athree-domain structure composed of a small N-terminal PUA domain, acentral alpha/beta-domain and a C-terminal Rossmann-fold-like MTasedomain. The three domains form an overall clamp-like shape, with theputative active site facing a deep cleft. The architecture of the activesite is consistent with specific recognition of uridine and catalysis ofmethyl transfer to the 5-carbon position. The cleft is suitable in sizeand charge distribution for binding single-stranded RNA.

• Balaji S, Babu MM, Iyer LM, Aravind L
• Discovery of the principal specific transcription factors of Apicomplexaand their implication for the evolution of the AP2-integrase DNA bindingdomains.
• Nucleic Acids Res. 2005; 33: 3994-4006
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• The comparative genomics of apicomplexans, such as the malarial parasitePlasmodium, the cattle parasite Theileria and the emerging human parasiteCryptosporidium, have suggested an unexpected paucity of specifictranscription factors (TFs) with DNA binding domains that are closelyrelated to those found in the major families of TFs from other eukaryotes.This apparent lack of specific TFs is paradoxical, given that theapicomplexans show a complex developmental cycle in one or more hosts anda reproducible pattern of differential gene expression in course of thiscycle. Using sensitive sequence profile searches, we show that theapicomplexans possess a lineage-specific expansion of a novel family ofproteins with a version of the AP2 (Apetala2)-integrase DNA bindingdomain, which is present in numerous plant TFs. About 20-27 members ofthis apicomplexan AP2 (ApiAP2) family are encoded in differentapicomplexan genomes, with each protein containing one to four copies ofthe AP2 DNA binding domain. Using gene expression data from Plasmodiumfalciparum, we show that guilds of ApiAP2 genes are expressed in differentstages of intraerythrocytic development. By analogy to the plant AP2proteins and based on the expression patterns, we predict that the ApiAP2proteins are likely to function as previously unknown specific TFs in theapicomplexans and regulate the progression of their developmental cycle.In addition to the ApiAP2 family, we also identified two other novelfamilies of AP2 DNA binding domains in bacteria and transposons. Usingstructure similarity searches, we also identified divergent versions ofthe AP2-integrase DNA binding domain fold in the DNA binding region of thePI-SceI homing endonuclease and the C-terminal domain of the pleckstrinhomology (PH) domain-like modules of eukaryotes. Integrating thesefindings, we present a reconstruction of the evolutionary scenario of theAP2-integrase DNA binding domain fold, which suggests that it underwentmultiple independent combinations with different types of mobileendonucleases or recombinases. It appears that the eukaryotic versionshave emerged from versions of the domain associated with mobile elements,followed by independent lineage-specific expansions, which accompaniedtheir recruitment to transcription regulation functions.

• Korber P, Stahl JM, Nierhaus KH, Bardwell JC
• Hsp15: a ribosome-associated heat shock protein.
• EMBO J. 2000; 19: 741-8
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• We are analyzing highly conserved heat shock genes of unknown or unclearfunction with the aim of determining their cellular role. Hsp15 haspreviously been shown to be an abundant nucleic acid-binding protein whosesynthesis is induced massively at the RNA level upon temperature upshift.We have now identified that the in vivo target of Hsp15 action is the free50S ribosomal subunit. Hsp15 binds with very high affinity (K(D) <5 nM) tothis subunit, but only when 50S is free, not when it is part of the 70Sribosome. In addition, the binding of Hsp15 appears to correlate with aspecific state of the mature, free 50S subunit, which contains boundnascent chain. This provides the first evidence for a so far unrecognizedabortive event in translation. Hsp15 is suggested to be involved in therecycling of free 50S subunits that still carry a nascent chain. Thisgives Hsp15 a very different functional role from all other heat shockproteins and points to a new aspect of translation.