Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large
subunit of ribosomes in all known organisms. Due to its small size, abundance
and evolutionary conservation 5S rRNA for many years now is used as a model
molecule in studies on RNA structure, RNA–protein interactions and molecular
phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that
provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across
three domains of life. Here, we give an overview of new developments in the
database and associated web tools since 2002, including updates to database
content, curation processes and user web interfaces

Barciszewski, Jan

Erdmann, Volker A.

Karlowski, Wojciech M.

Szymanski, Maciej

Zielezinski, Andrzej

Nucleic Acids Research

PubMed

Maciej Szymanski

Andrzej Zielezinski

Jan Barciszewski

Volker A. Erdmann

Wojciech M. Karlowski

Crossref

5SRNAdb: an information resource for 5S ribosomal RNAs

Institutional Repository of the Freie Universität Berlin

D180–D183 Nucleic Acids Research, 2016, Vol. 44, Database issue Published online 20 October 2015doi: 10.1093/nar/gkv10815SRNAdb: an information resource for 5S ribosomalRNAsMaciej Szymanski1,*, Andrzej Zielezinski1, Jan Barciszewski2, Volker A. Erdmann3 andWojciech M. Karlowski1,*1Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University,61-614 Poznan, Poland, 2Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland and3Institute for Chemistry and Biochemistry, Free University Berlin, 14195 Berlin, GermanyReceived August 13, 2015; Revised September 25, 2015; Accepted October 07, 2015ABSTRACTRibosomal 5S RNA (5S rRNA) is the ubiquitous RNAcomponent found in the large subunit of ribosomesin all known organisms. Due to its small size, abun-dance and evolutionary conservation 5S rRNA formany years now is used as a model molecule instudies on RNA structure, RNA–protein interactionsand molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides ahigh quality reference set of ribosomal 5S RNAs (5SrRNA) across three domains of life. Here, we givean overview of new developments in the databaseand associated web tools since 2002, including up-dates to database content, curation processes anduser web interfaces.INTRODUCTIONThe 5S ribosomal RNA is a ubiquitous component of thelarge subunit of the cytoplasmic ribosomes of all organisms.Together with the ribosomal proteins uL5 (bacterial L5, eu-karyotic L11) and uL18 (bacterial L18, eukaryotic L5), 5SrRNA is located on the interface between ribosomal sub-units within the central protuberance (1). The role of 5SrRNA within the ribosome is not clear, but its presence aswell as that of the associated universal proteins L5 and L18was shown to be essential for translation in bacteria (2) andyeast (3).In eukaryotes, 5S rRNA binds two ribosomal proteinsuL5 and uL18 (4). Apart from the ribosomes, eukaryotic5S rRNAs are also present in the cell in complexes withnon-ribosomal proteins including La protein (5), transcrip-tion factor IIIA (TFIIIA) involved in 5S rRNAgene expres-sion (6) and several other proteins (7). Recently it has beendemonstrated that in mammalian cells, 5S RNP plays an es-sential role as an inhibitor of MDM2, an E3 ubiquitin lig-ase involved in the degradation of p53. A consequence of in-creased concentration of 5SRNP and its binding toMDM2is stabilization and activation of p53 regulated pathways(8,9).The small size, universal occurrence, conservation andabundance combined with relative ease of its isolationmade5S rRNA an ideal model molecule in studies on RNAsequence-structure relationship, RNA–protein interactionsand molecular evolution and phylogeny.The 5SRNAdb is a database dedicated to nucleotide se-quences of bacterial, archaeal and eukaryotic (cytoplasmicand organellar) 5S ribosomal RNAs and their genes.IMPROVEMENTS/NEW FEATURES IN 5SrRNAdbTable 1 lists the advancements and new features supportedin the 2016 5SRNAdb update. Major improvements in-clude: (i) over 10-fold increase in number of full length 5SrRNA sequences and in the number of taxonomic groups;(ii) development of advanced web tools that allow better ac-cess to the database content and data presentation (e.g. dy-namic customizable sequence alignments, secondary struc-ture diagrams, sortable tables) and (iii) new user interfaceincluding improved searching, browsing and downloadingtools. Major features of the database interface with instruc-tions are described in the Help section of the webpage.Updates to database contentIn the 2016 update, 11 419 unique nucleotide sequences of5S rRNAs and 5S rRNA genes including 7291 from Bacte-ria, 319 from Archaea and 3809 from Eukaryota. The ma-jority of the new sequences included in the current releaseof the database were extracted from DNA sequences ob-tained in genome sequencing projects. In the case of bacte-rial and archaeal genomes, the sequences of 5S rRNAs wereretrieved from the records for complete genomic sequencesdeposited in the RefSeq database (10) and the genomic*To whom correspondence should be addressed. Tel: +48 61 829 5843; Fax: +48 61 829 5949; Email: mszyman@amu.edu.plCorrespondence may also be addressed to Wojciech M. Karlowski. Tel: +48 61 829 5841; Fax:+48 61 829 5949; Email: wmk@amu.edu.plDedicated to the late Professor Volker A. ErdmannC© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), whichpermits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contactjournals.permissions@oup.com at Freie Universitaet Berlin on April 11, 2016http://nar.oxfordjournals.org/Downloaded from Nucleic Acids Research, 2016, Vol. 44, Database issue D181Table 1. The comparison of data and features between 5SRNAdb version 1.0 and 5SRNAdb version 2Features Previous version (2002) Current releaseSpecies 764 7174Manually curated unique 5S rRNA sequences 995 11 419Browsing 5S rRNA genes acrosshigher-ordered taxonsStatic browser Dynamic browserAnnotation of 5S rRNA genes (NCBI,genomic locations, etc.)No YesDynamic graphical visualization No secondary structures, sequence alignmentsGeneration of custom data sets (sequences,structure diagrams)No Yesassemblies archives available from the NCBI ftp site (ftp.ncbi.nlm.nih.gov/genomes/Bacteria). The coordinates of 5SrRNA genes were taken from the annotations of respectiverecords. In the case of unannotated contigs, the candidate5S rRNA sequences were identified using BLAST.The eukaryotic 5S rRNA genes were extracted fromgenomic assemblies available at the NCBI. The putativegenes were identified in the genomic sequences using a cus-tom pipeline that includes search for candidate regions byBLAST, followed by identification of conserved sequenceelements and quality steps to exclude sequences that are tooshort or those that do not meet the structural criteria of 5SrRNA.The database recordEach individual database record represents a unique 5SrRNA sequence identified for a particular species. Multiple5S rRNA sequence variants determined for a single speciesare distinguished by the ‘Sequence variant’ field. In additionto the source organism name and the nucleotide sequence,each record contains information on the phylogenetic po-sition of the organism linked to the taxonomy resources atthe NCBI. The primary sources of the sequence are listedas links to the original GenBank records. In the case of se-quences that were not deposited in the GenBank, the bib-liographic information of the publication from which theywere derived is given. In the ‘Molecule’ field of the record,we include information on whether the sequence was ob-tained by direct sequencing of RNAusing chemical or enzy-matic methods or derived from genomic sequences. More-over, the records contain information on the secondarystructure that is displayed as a diagram in the record view.The structure diagrams show nucleotide sequences in thecontext of the general secondary structure models contain-ing all positions in the alignments.When compared with the previous version of thedatabase (11), the requirement for uniqueness of the se-quence within a given species reduced the redundancy ofthe data. Identical sequences from the same species de-posited under distinct accession numbers in the GenBankdatabase were previously treated as separate records. In thecurrent version, these sequences are encapsulated into sin-gle records. To improve the data quality we also excluded 5SrRNA partial sequences.Structural alignmentsThe added value of the data in the database are the manu-ally curated structural sequence alignments in which eachcolumn corresponds to a particular position in the sec-ondary structure of 5S rRNA. All 5S rRNA sequences canbe folded into a conserved secondary structure consistingof five double stranded regions (I–V), and five loops: twohairpin loops (C and D), two internal loops (B and E) anda three-helix junction hinge region (loop A) (Figure 1). Thesequence and structure analyses show that closely relatedeukaryotic and archaeal type structures differ from the bac-terial structure, particularly within the internal loop E (12).Bacterial 5S rRNAs also show much greater variability inthe length of helix IV and the size of hairpin loop D. TheRNA sequences from several organisms revealed deviationsfrom the canonical model due to insertions and deletions.Secondary structure diagrams displayed in the single recordand sequence alignments views show themost general mod-els based on all sequences from a particular group or fromthe set defined by the user. The positions corresponding togaps in the alignment are shown as dots.The alignments containing selected sequences, togetherwith consensus structure diagrams, can be produced fromrecords found by search or browse tools. Full alignmentsfor all sequences from three domains of life are availablethrough the ‘Download’ page.The sequences selected from the results table are usedto generate secondary structure model for the consensussequence derived from the current alignment and the ta-ble with the nucleotide statistics at each position. To makethe comparison of alignments and general structure modelspossible, both the alignments and secondary structure dia-grams include all positions present in the master alignmentof all sequences from respective taxonomic domains (i.e. Ar-chaea, Bacteria and Eukaryota). The secondary structurediagram is interactive––the nucleotides or base pairs statis-tics are displayed by pointing at a nucleotide or base pairsymbol, respectively.To customize the content of the alignment, it is possi-ble to add and remove sequences on the fly from the cur-rent view using the panel, listing records or by providingthe record identifier. The new nucleotide statistics and thesecondary structure models are dynamically recalculated tomatch the current set of sequences in the alignment. Thecustom alignment can also be built from scratch by addingsubsequent search results.All customized sequence alignments can be downloadedin FASTA format. In addition to nucleotide sequences, the at Freie Universitaet Berlin on April 11, 2016http://nar.oxfordjournals.org/Downloaded from D182 Nucleic Acids Research, 2016, Vol. 44, Database issueFigure 1. Diagrams of the secondary structure models of 5S rRNAs fromBacteria (A), Archaea (B) and Eukaryota (C). The structures are basedon the multiple sequence alignments of all 5S rRNAs in the current re-lease of the database. The numbering of nucleotides in the structures cor-responds to numbering of the positions in the alignments. The nucleotidesymbols used in diagrams are according to IUBMB nomenclature. N–anynucleotide; Y–pyrimidine R–purine; W–A or U/T; S–G or C; M–A or C;K–G or U/T. The diagrams were produced using tools available from thedatabase.files also contain the secondary structure information inbracket notation.Database accessThe updated version of 5S rRNA database offers a new,modern graphical interface that allows querying and ex-ploring of all contained information. The data from thedatabase can be accessed in three different ways: (i) textsearch, (ii) taxonomic browser and (iii) similarity BLASTsearch. The individual records from the database can be re-trieved by querying for a particular record identifier, speciesor a higher taxon name. Many of the sequences were origi-nally published under different species names than reportedin the current GenBank records. To address this, in the cur-rent version of the database the search supports primary sci-entific names as well as their synonyms and common namesas listed in the NCBI Taxonomy database (13). The recordsmatching the query are shown in a tabular form providingrecord identifier, organism name, sequence length and thetype of sequencedmolecule (RNAorDNA). By turning the‘RNAonly’ option on, the database search can be limited torecords containing sequences that were obtained by direct(enzymatic or chemical) RNA sequencing methods.Another novel feature in the updated user interface in-cludes an improved taxonomic browser that allows retrievalof individual sequences from a particular organism as wellas sets of sequences from related species. The classificationof organisms used by the browser is based on theNCBITax-onomy Database (www.ncbi.nlm.nih.gov/taxonomy).The numbers shown along with taxon name indicate thequantity of species and records associated with each node.The tree-based interface allows a user to select either thesingle species (last node) or any intermediate junction toretrieve records for all species included within a particulartaxonomic branch.A new user interfaceThe user interface of the 5S rRNA database was completelyredesigned to incorporate several user-oriented solutionsenhancing the efficiency of the data mining experience. Allbrowsing and searching results are now presented as sepa-rate, clearly named windows with both graphical elementsproviding contextual clues as well as mouse-over tooltips.Users can adjust the amount of information that is presenton each page, as any window can be dynamically wrappedup or expanded. Depending on the data type, each of thewindows may contain tools for data presentation like sort-ing, filtering and changing data source allowing user to gen-erate customizable and integrated results.Through a new ‘Comment’ feature, users can remark onany 5S rRNA record present in the database and start dis-cussions. Our goal is to encourage feedback from the bio-science community in terms of verifying the information weprovide, as well as obtaining relevant data either from theongoing research or from the previous research, both pub-lished and unpublished.CONCLUSIONWith the addition in the new version of the novel data aswell as advanced mining and visualization tools, 5SRNAdbcontinues to be the most comprehensive and integrated re-source of up-to-date information on 5S ribosomal genesand structural profiling. These new data and web tools willbe valuable for comparative sequence analysis and develop-ment of bettermethods of the annotation of 5S rRNAgenes at Freie Universitaet Berlin on April 11, 2016http://nar.oxfordjournals.org/Downloaded from Nucleic Acids Research, 2016, Vol. 44, Database issue D183and 5S rRNA-like sequences. In the future, we plan to ex-pand the scope of the 5SrRNAdb by incorporating the 5SrRNA-binding proteins.AVAILABILITY5SRNAdb is freely available at http://www.combio.pl/5srnadb/. All data that have been used to create the databasecan be downloaded from the web page and from interactivewindows, and can be used in subsequent data-mining appli-cations.ACKNOWLEDGEMENTThis work was supported by the KNOW RNA ResearchCentre in Poznan´ (No. 01/KNOW2/2014) and the Facultyof Biology Adam Mickiewicz University in Poznan. Theauthors wish to acknowledge critical comments from theanonymous reviewers that were helpful for improving thedatabase and the web interface.FUNDINGKNOW RNA Research Centre in Poznan´ [No. 01/KNOW2/2014]; Faculty of BiologyAdamMickiewiczUni-versity in Poznan. Funding for open access charge: KNOWRNA Research Centre in Poznan´ [No. 01/ KNOW2/2014]and the Faculty of Biology AdamMickiewicz University inPoznan.Conflict of interest statement.None declared.REFERENCES1. Shpanchenko,O.V., Dontsova,O.A., Bogdanov,A.A. andNierhaus,K.H. (1998) Structure of 5S rRNA within the Escherichiacoli ribosome: iodine-induced cleavage patterns of phosphorothioatederivatives. RNA, 4, 1154–1164.2. Korepanov,A.P., Gongadze,G.M., Garber,M.B., Court,D.L. andBubunenko,M.G. (2007) Importance of the 5 S rRNA-bindingribosomal proteins for cell viability and translation in Escherichiacoli. J. Mol. Biol., 366, 1199–1208.3. Kiparisov,S., Petrov,A., Meskauskas,A., Sergiev,P.V., Dontsova,O.A.and Dinman,J.D. (2005) Structural and functional analysis of 5SrRNA in Saccharomyces cerevisiae.Mol. Genet. Genomics, 274,235–247.4. Zhang,J., Harnpicharnchai,P., Jakovljevic,J., Tang,L., Guo,Y.,Oeffinger,M., Rout,M., Hiley,S., Hughes,T. and Woolford,J. (2007)Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomalproteins rpL5 and rpL11 into nascent ribosomes. Genes Dev., 21,2580–2592.5. Rinke,J. and Steitz,J.A. (1982) Precursor molecules of both human 5Sribosomal RNA and transfer RNAs are bound by a cellular proteinreactive with anti-La lupus antibodies. Cell, 29, 149–159.6. Allison,L.A., North,M.T. and Neville,L.A. (1995) Differentialbinding of oocyte-type and somatic-type 5S rRNA to TFIIIA andribosomal protein L5 in Xenopus oocytes: specialization for storageversus mobilization. Dev. Biol., 168, 284–295.7. Ciganda,M. and Williams,N. (2011) Eukaryotic 5S rRNA biogenesis.Wiley Interdiscip. Rev. RNA, 2, 523–533.8. Sloan,K.E., Bohnsack,M.T. and Watkins,N.J. (2013) The 5S RNPcouples p53 homeostasis to ribosome biogenesis and nucleolar stress.Cell Rep., 5, 237–247.9. Donati,G., Peddigari,S., Mercer,C.A. and Thomas,G. (2013) 5Sribosomal RNA is an essential component of a nascent ribosomalprecursor complex that regulates the Hdm2–p53 checkpoint. CellRep., 4, 87–98.10. Pruitt,K.D., Tatusova,T., Brown,G.R. and Maglott,D.R. (2012)NCBI Reference Sequences (RefSeq): current status, new features andgenome annotation policy. Nucleic Acids Res., 40, D130–D135.11. Szymanski,M., Barciszewska,M.Z., Erdmann,V.A. andBarciszewski,J. (2002) 5S Ribosomal RNA Database. Nucleic AcidsRes., 30, 176–178.12. Leontis,N.B. and Westhof,E. (1998) The 5S rRNA loop E: chemicalprobing and phylogenetic data versus crystal structure. RNA, 4,1134–1153.13. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. andSayers,E.W. (2009) GenBank. Nucleic Acids Res., 37, D26–D31. at Freie Universitaet Berlin on April 11, 2016http://nar.oxfordjournals.org/Downloaded from 

https://refubium.fu-berlin.de/bitstream/fub188/14879/1/Nucl.xAcidsxRes.-2016-Szymanski-D180-3.pdf

5SRNAdb: an information resource for 5S ribosomal RNAs

Abstract

Similar works

Full text

Available Versions

Crossref

Institutional Repository of the Freie Universität Berlin