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Amazon Inspire Digital Educational Resources. Amazon Rapids Fun stories for kids on the go. Amazon Restaurants Food delivery from local restaurants. ComiXology Thousands of Digital Comics. As of July there are only five such cases among cellular organisms, three bacteria Borrelia burgdorferi [ 23 , 24 ], Buchnera aphidicola str.
Cc [ 25 ] and Ureaplasma urealyticum [ 26 , 27 ] and two eukaryotes Entamoeba histolytica [ 28 , 29 ] and Giardia lamblia [ 30 , 31 ]. These are all parasites or obligate intracellular endosymbionts, and absence of RNRs indicates that all must rely on salvage of hostderived deoxyribonucleotides. There are numerous large-scale sequence databases that provide annotations and classifications of proteins and protein families. In some cases, the process of annotation is approached systematically [ 32 - 34 ] while in others, e.
GenBank, annotations are made by those depositing information, using a variety of methodologies. Specialist databases, in contrast, can serve to collate all available information on a given protein or protein family, and are small enough to allow detailed, expert curation. It is for these reasons that we were originally motivated to build RNRdb. That said, there is only any real value in such an endeavour if expert curation results in significant improvements in accuracy over existing resources.
To this end, we compared our annotations to those recorded in GenBank entries for all sequences in RNRdb on the basis of the following criteria: In addition, over group I introns and ca 80 inteins have been manually curated from the entries. This serves to highlight the potential value of manual curation, given the complexities of annotation [ 20 , 36 ]. While manual curation is not infallible see previous section , we nevertheless believe that our annotations are significantly improved over existing publicly available annotations.
GenBank definitions of proteins in RNRdb. Four different aspects of RNR functional annotation have been investigated: RNR class, protein role subunit identity , general function involved with ribonucleotides and single domain identification the ATP cone [ 35 ] that regulates activity in many enzymatic subunits. Only NCBI entries for full-length sequences were used, and nine sequences that were difficult to classify were excluded.
We have focused the user interface of the database on tools for exploration of RNR diversity and distribution and to serve as an annotation resource for specialists.
There are four main access points to RNR sequences in the database:. By scrolling down the page or using the browser to search for text strings, the user can explore the distribution of RNRs in the three cellular domains as well as among viruses. Proteins with additional attributes solved structure, mutagenised forms, selfsplicing introns and inteins and fully sequenced genomes are indicated by red superscript abbreviations; clicking on these superscripts links to explanations. Following an organism or protein hyperlink presents the user with all RNR sequences for that organism or the chosen protein respectively, together with classification information and cross-references to other databases.
It is also possible to retrieve proteins with specific annotated attributes e.
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All three aspects of searches can also be combined, allowing searches for, e. The BLAST search interface can be used to annotate unknown sequences, or to investigate annotations in other databases.
For complete genomes, all combinations of RNR classes are summed for each domain likewise viruses and across domains; clicking on sums generates a detailed list of species and proteins e. Combinations of RNR classes in the cellular domains and viruses. This table only contains data from fully sequenced genomes.
We have exhaustively verified absence of RNRs in organismal, but not in viral genomes. To facilitate data acquisition for comparative analyses, sequences including those returned by a specific search can be downloaded in FASTA or NEXUS format via the protein detail pages. Subsets of sequence data from returned searches or from the "RNRs by organism" page can also be selected manually via checkboxes and downloaded as above. Our knowledge of the distribution of ribonucleotide reductases has expanded rapidly over the last few years.
Until recently, the distribution of the three classes was considered rather limited, and, as a domain, only bacteria were thought to possess the full gamut of classes. Moreover, a number of genomes carry clear misannotations, and protein family databases do not always correctly categorise RNRs. Searching Pfam [ 32 ], for instance, returns adequate descriptions of two of the structural domains "ATP cone" and "Glycine radical" of the Escherichia coli K12 catalytic subunit class III protein, but no family or structural domain with clear reference to RNRs.
Searching with the E. Although other protein family databases have broader coverage e. Pfam [ 32 ], InterPro [ 33 ] and PhyloFacts [ 34 ] , our approach with HMM profiles followed by manual curation yields more accurate descriptions unpublished observations. RNRdb thus offers a first clear overview of the distribution of the three classes of ribonucleotide reductase.
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The data curated in RNRdb make it clear that all three classes of ribonucleotide reductase are found in all three organismal domains. Around half of all sequenced species carry genes for only one class of RNR, but among those with more than one RNR class, two eukaryotes, one archeon, and 54 7. Evolutionary genomic analyses support this view Lundin et al.
The diverse distribution of ribonucleotide reductases was poorly appreciated prior to the genomic era in biological research. Prior to the establishment of RNRdb this information was difficult to navigate due to incomplete and misleading annotation regarding class membership and subcomponent information in databases. We demonstrate that manual curation of protein sequences leads to significant improvements over existing annotations, and that there is therefore value in generating such annotation sets.
Indeed, there are ongoing efforts to try and integrate such approaches to large-scale annotation [ 38 ]. Our plans for the next major release of the database, RNRdb 2. Specifically, we are developing tools to complement the current BLAST search feature with a service that matches user submitted sequences to our set of HMM profiles, allowing a more precise and fine-grained annotation. Interestingly, ribonucleotide reductases are the most abundant enzyme family identified in metagenomic sequencing projects [ 39 ], and the potential utility of relating the biochemical attributes of RNRs to environmental parameters such as oxygen levels or iron availability is clear.
Our vision for RNRdb 2. We will continue to expand the content and scope of RNRdb, in order to further deepen our understanding of this fascinating enzyme, and to explore its utility in the metagenomic analyses of diverse microbial environments. RNRdb is freely available at http: BMS collated the initial dataset.
DL designed and programmed the database and candidate search programs. BMS and ET curated the data. All authors read and approved the final version. The authors wish to thank Pernilla Larsson Birgander, Ernst Furrer and Margareta Sahlin for their valuable help in the initial curation process, and David Nord for help with structural identification of group I introns. National Center for Biotechnology Information , U. Published online Dec 8. Received Jul 14; Accepted Dec 8. This article has been cited by other articles in PMC.
Abstract Background Ribonucleotide reductases RNRs catalyse the only known de novo pathway for deoxyribonucleotide synthesis, and are therefore essential to DNA-based life. Conclusion RNRdb is a specialist database that provides a reliable annotation and classification resource for RNR proteins, as well as a tool to explore distribution patterns of RNR classes.
Background Ribonucleotide reductases RNRs form a universal enzyme family that catalyse the reduction of ribonucleotides to their corresponding deoxyribonucleotides. Table 1 General characteristics of RNR classes. NrdE, NrdF specific activase: Open in a separate window. Table 2 Distribution of RNR proteins.
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Utility of RNRdb Motivation for building a specialist RNR database There are numerous large-scale sequence databases that provide annotations and classifications of proteins and protein families. Table 3 RNR annotation. There are four main access points to RNR sequences in the database: Table 4 RNR distribution. Discussion Our knowledge of the distribution of ribonucleotide reductases has expanded rapidly over the last few years.
Conclusion and future directions The diverse distribution of ribonucleotide reductases was poorly appreciated prior to the genomic era in biological research. Availability and requirements RNRdb is freely available at http: Authors' contributions BMS collated the initial dataset. Acknowledgements The authors wish to thank Pernilla Larsson Birgander, Ernst Furrer and Margareta Sahlin for their valuable help in the initial curation process, and David Nord for help with structural identification of group I introns.