5SRNAdb: an Information Resource for 5S Ribosomal RNAs

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2015 Oct 23

PMID 26490961

Citations 29

Authors

Maciej Szymanski

Andrzej Zielezinski

Jan Barciszewski

Volker A Erdmann

Wojciech M Karlowski

Affiliations

Soon will be listed here.

Abstract

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.

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References

Szymanski M, Barciszewska M, Erdmann V, Barciszewski J . 5S Ribosomal RNA Database. Nucleic Acids Res. 2001; 30(1):176-8. PMC: 99124. DOI: 10.1093/nar/30.1.176. View

Rinke J, Steitz J . Precursor molecules of both human 5S ribosomal RNA and transfer RNAs are bound by a cellular protein reactive with anti-La lupus antibodies. Cell. 1982; 29(1):149-59. DOI: 10.1016/0092-8674(82)90099-x. View

Allison L, North M, Neville L . Differential binding of oocyte-type and somatic-type 5S rRNA to TFIIIA and ribosomal protein L5 in Xenopus oocytes: specialization for storage versus mobilization. Dev Biol. 1995; 168(2):284-95. DOI: 10.1006/dbio.1995.1080. View

Leontis N, Westhof E . The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure. RNA. 1998; 4(9):1134-53. PMC: 1369688. DOI: 10.1017/s1355838298980566. View

Shpanchenko O, Dontsova O, Bogdanov A, Nierhaus K . Structure of 5S rRNA within the Escherichia coli ribosome: iodine-induced cleavage patterns of phosphorothioate derivatives. RNA. 1998; 4(9):1154-64. PMC: 1369689. DOI: 10.1017/s1355838298980359. View

Kiparisov S, Petrov A, Meskauskas A, Sergiev P, Dontsova O, Dinman J . Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae. Mol Genet Genomics. 2005; 274(3):235-47. PMC: 1276653. DOI: 10.1007/s00438-005-0020-9. View

Sloan K, Bohnsack M, Watkins N . The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress. Cell Rep. 2013; 5(1):237-47. PMC: 3808153. DOI: 10.1016/j.celrep.2013.08.049. View

Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M . Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes Dev. 2007; 21(20):2580-92. PMC: 2000323. DOI: 10.1101/gad.1569307. View

Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Sayers E . GenBank. Nucleic Acids Res. 2008; 37(Database issue):D26-31. PMC: 2686462. DOI: 10.1093/nar/gkn723. View

10.

Ciganda M, Williams N . Eukaryotic 5S rRNA biogenesis. Wiley Interdiscip Rev RNA. 2011; 2(4):523-33. PMC: 3278907. DOI: 10.1002/wrna.74. View

11.

Pruitt K, Tatusova T, Brown G, Maglott D . NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2011; 40(Database issue):D130-5. PMC: 3245008. DOI: 10.1093/nar/gkr1079. View

12.

Donati G, Peddigari S, Mercer C, Thomas G . 5S ribosomal RNA is an essential component of a nascent ribosomal precursor complex that regulates the Hdm2-p53 checkpoint. Cell Rep. 2013; 4(1):87-98. PMC: 3928573. DOI: 10.1016/j.celrep.2013.05.045. View

13.

Korepanov A, Gongadze G, Garber M, Court D, Bubunenko M . Importance of the 5 S rRNA-binding ribosomal proteins for cell viability and translation in Escherichia coli. J Mol Biol. 2007; 366(4):1199-208. PMC: 1939977. DOI: 10.1016/j.jmb.2006.11.097. View