Molecular evolution of dihydrouridine synthases

BackgroundDihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus enhance its conformational flexibility. D is generated post-transcriptionally by the reduction of the 5,6-double bond of a uridine residue in RNA transcripts. The reaction is carried out by dihydrouridine synthases (DUS). DUS constitute a conserved family of enzymes encoded by the orthologous gene family COG0042. In protein sequence databases, members of COG0042 are typically annotated as “predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family”.ResultsTo elucidate sequence-structure-function relationships in the DUS family, a comprehensive bioinformatic analysis was carried out. We performed extensive database searches to identify all members of the currently known DUS family, followed by clustering analysis to subdivide it into subfamilies of closely related sequences. We analyzed phylogenetic distributions of all members of the DUS family and inferred the evolutionary tree, which suggested a scenario for the evolutionary origin of dihydrouridine-forming enzymes. For a human representative of the DUS family, the hDus2 protein suggested as a potential drug target in cancer, we generated a homology model. While this article was under review, a crystal structure of a DUS representative has been published, giving us an opportunity to validate the model.ConclusionsWe compared sequences and phylogenetic distributions of all members of the DUS family and inferred the phylogenetic tree, which provides a framework to study the functional differences among these proteins and suggests a scenario for the evolutionary origin of dihydrouridine formation. Our evolutionary and structural classification of the DUS family provides a background to study functional differences among these proteins that will guide experimental analyses.

[1]  Yutaka Kuroda,et al.  POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions , 2007, Bioinform..

[2]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[3]  David E. Kim,et al.  Physically realistic homology models built with ROSETTA can be more accurate than their templates. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[4]  J Lundström,et al.  Pcons: A neural‐network–based consensus predictor that improves fold recognition , 2001, Protein science : a publication of the Protein Society.

[5]  Jenn-Kang Hwang,et al.  Predicting subcellular localization of proteins for Gram‐negative bacteria by support vector machines based on n‐peptide compositions , 2004, Protein science : a publication of the Protein Society.

[6]  E. Phizicky,et al.  A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. , 2002, RNA.

[7]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[8]  Yusuke Nakamura,et al.  A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis. , 2005, Cancer research.

[9]  R. Y. Morita,et al.  Posttranscriptional modification of tRNA in psychrophilic bacteria , 1997, Journal of bacteriology.

[10]  Tal Pupko,et al.  Structural Genomics , 2005 .

[11]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[12]  Haruki Nakamura,et al.  PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences , 2010, Nucleic Acids Res..

[13]  J. Kowalak,et al.  Posttranscriptional Modification of the Central Loop of Domain V in Escherichia coli 23 S Ribosomal RNA (*) , 1995, The Journal of Biological Chemistry.

[14]  J. McCloskey,et al.  Conformational flexibility in RNA: the role of dihydrouridine. , 1996, Nucleic acids research.

[15]  B. Palfey,et al.  Mechanism of Dihydrouridine Synthase 2 from Yeast and the Importance of Modifications for Efficient tRNA Reduction* , 2009, Journal of Biological Chemistry.

[16]  BMC Bioinformatics , 2005 .

[17]  Kengo Kinoshita,et al.  PrDOS: prediction of disordered protein regions from amino acid sequence , 2007, Nucleic Acids Res..

[18]  S. Whelan,et al.  A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. , 2001, Molecular biology and evolution.

[19]  J. Bujnicki,et al.  Computational methods for prediction of protein-RNA interactions. , 2012, Journal of structural biology.

[20]  K. Gajiwala,et al.  The 1.59 Å resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima , 2004, Proteins.

[21]  Jack Y. Yang,et al.  BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features , 2010, BMC Systems Biology.

[22]  P. Radivojac,et al.  PROTEINS: Structure, Function, and Bioinformatics Suppl 7:176–182 (2005) Exploiting Heterogeneous Sequence Properties Improves Prediction of Protein Disorder , 2022 .

[23]  S. Brunak,et al.  Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.

[24]  Hagit Shatkay,et al.  SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. , 2007, Bioinformatics.

[25]  Zsuzsanna Dosztányi,et al.  IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content , 2005, Bioinform..

[26]  K. Chou,et al.  Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. , 2007, Journal of proteome research.

[27]  Arne Elofsson,et al.  Prediction of global and local model quality in CASP7 using Pcons and ProQ , 2007, Proteins.

[28]  T. Hughes,et al.  The Specificities of Four Yeast Dihydrouridine Synthases for Cytoplasmic tRNAs*[boxs] , 2004, Journal of Biological Chemistry.

[29]  G. Schneider,et al.  Crystal Structure of the Productive Ternary Complex of Dihydropyrimidine Dehydrogenase with NADPH and 5-Iodouracil , 2002, The Journal of Biological Chemistry.

[30]  Andrei N. Lupas,et al.  CLANS: a Java application for visualizing protein families based on pairwise similarity , 2004, Bioinform..

[31]  Anthony C. Bishop,et al.  Molecular determinants of dihydrouridine synthase activity , 2006, FEBS letters.

[32]  Shuichi Hirose,et al.  BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm330 Structural bioinformatics , 2022 .

[33]  A Keith Dunker,et al.  Intrinsic disorder and protein function. , 2002, Biochemistry.

[34]  T. Gibson,et al.  Protein disorder prediction: implications for structural proteomics. , 2003, Structure.

[35]  M. Nei,et al.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.

[36]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[37]  Sergey Steinberg,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 2004, Nucleic Acids Res..

[38]  Kristian Rother,et al.  MODOMICS: a database of RNA modification pathways, update 2008 , 2009, Nucleic Acids Res..

[39]  Janusz M. Bujnicki,et al.  MetaMQAP: A meta-server for the quality assessment of protein models , 2008, BMC Bioinformatics.

[40]  Anthony C. Bishop,et al.  Identification of the tRNA-Dihydrouridine Synthase Family* , 2002, The Journal of Biological Chemistry.

[41]  Janusz M. Bujnicki,et al.  GeneSilico protein structure prediction meta-server , 2003, Nucleic Acids Res..

[42]  John Hawkins,et al.  Predicting nuclear localization. , 2007, Journal of proteome research.

[43]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Arne Elofsson,et al.  Automatic consensus‐based fold recognition using Pcons, ProQ, and Pmodeller , 2003, Proteins.

[45]  Paul Horton,et al.  Nucleic Acids Research Advance Access published May 21, 2007 WoLF PSORT: protein localization predictor , 2007 .

[46]  T. Spector,et al.  Inactivation of dihydropyrimidine dehydrogenase by 5-iodouracil. , 1991, The Journal of biological chemistry.

[47]  Janusz M. Bujnicki,et al.  MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins , 2012, BMC Bioinformatics.

[48]  Sine Larsen,et al.  The crystal structure of lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function , 1998, Protein science : a publication of the Protein Society.

[49]  I. Tanaka,et al.  Molecular basis of dihydrouridine formation on tRNA , 2011, Proceedings of the National Academy of Sciences.

[50]  Gajendra P.S. Raghava,et al.  Prediction of RNA binding sites in a protein using SVM and PSSM profile , 2008, Proteins.

[51]  Marcin Feder,et al.  MODOMICS: a database of RNA modification pathways , 2005, Nucleic Acids Res..

[52]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[53]  Zheng Rong Yang,et al.  RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins , 2005, Bioinform..