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Staphylococcus aureus N315

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close this sectionAbout this Microorganism


Courtesy of Dr. Hiramatsu, Juntendo Univ.

Staphylococcus aureus N315 was isolated as an MRSA (methicillin-resistant S. aureus) that was a major pathogen causing hospital-acquired infections in 1982. This bacterium is easy to acquire antibiotic-resistance, even to vancomycin that is said to be a last hope of drug to cure MRSA-infected patients. Analysis of the genome of S. aureus N315 is expected to enhance the accuracy of detection of Staphylococcal infections as well as to reduce the time for detection. Furthermore, it is expected that the mechanisms of antibiotic-resistance will be further investigated so as to develop new methods and techniques to combat with MRSA.

Results of the genome analysis of S. aureus N315 indicate that it contains a plasmid of 25 kb in size. Its genome size is 2.81 Mb with a 32.8 % G+C content, 20 copies of insertion sequences and five transposons. There are three 'pathogenicity islands' within the genome. With a few characteristic exceptions such as the genes involved in sporulation in Bacillus subtilis or those involved in toxin production in S. aureus N315, the numbers of genes in various functional categories are very similar between the two bacteria.

close this sectionProject history

close this date 2007-04-06 ..... 1
2007-04-06 Staphylococcus aureus N315 database was updated (We changed gene and product information of several ORFs)
imageList of ORFs updated in annotation
We thank Dr. Enrique D. Vines, University of Western Ontario for letting us know about his study.

product
IDoldnew
SA0109lipoproteiniron-regulated ABC transporter siderophore permease protein SirC
SA0110lipoproteiniron-regulated ABC transporter siderophore permease protein SirB
SA0111lipoproteiniron-regulated ABC transporter siderophore-binding protein SirA
SA0113hypothetical protein, similar to ornithine cyclodeaminaseputative ornithine cyclodeaminase
SA0114conserved hypothetical proteinsiderophore biosynthesis protein SbnC
SA0115hypothetical protein, similar to multi-drug resistance efflux pumphypothetical efflux protein
SA0116hypothetical protein, similar to rhizobactin siderophore biosynthesisprotein RhsCsiderophore biosynthesis protein SbnE
SA0117hypothetical protein, similar to rhizobactin siderophore biosynthesisprotein RhsFsiderophore biosynthesis protein SbnF
SA0118hypothetical protein, similar to various aldolaseputative 2-dehydro-3-deoxyglucarate aldolase
SA0119hypothetical protein, similar to diaminopimelate decarboxylaseputative diaminopimelate decarboxylase
SA0602ferrichrome transport ATP-binding proteiniron-hydroxamate transport ATP-binding protein
SA0603ferrichrome transport permeaseiron-hydroxamate transport permease
SA0604ferrichrome transport permeaseiron-hydroxamate transport permease
SA2079hypothetical protein, similar to ferrichrome ABC transporter fhuD precursorhydroxamate siderophore binding lipoprotein


gene
IDoldnew
SA0112sbnA
SA0113sbnB
SA0114sbnC
SA0115sbnD
SA0116sbnE
SA0117sbnF
SA0118sbnG
SA0119sbnH
SA0120sbnI
SA0602fhuAfhuC
SA2079fhuD2

close this sectionSummary of the genomic data

N315
Genomic size 2,839,469 bp
G+C content 32.81 %
Number of ORFs assigned 2,624
Percentage of the coding regions 84.34 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 16
5S16S23S
655
Number of tRNA genes 62
AlaArgAsnAspCysGln
443412
GluGlyHisIleLeuLys
352353
MetPheProSerThrTrp
422531
TyrValpseudo
231
Number of other features
(misc_RNA,misc_feature,repeat)
0

close this sectionGeneral Procedure

The entire nucleotide sequence of the S. aureus N315 genome was determined by the whole-genome shotgun (WGS) method as described below.

  1. A WGS clone library was prepared in E. coli DH5-alpha-MCR by preparing genomic DNA fragments of S. aureus N315 and cloning them into pUC18 plasmid.

  2. The WGS clones were randomly sequenced by using the dye-terminator kit and analyzed in PRISM 3700 DNA Analyzers of ABI.

  3. The raw sequence data thus obtained were assembled by using Phred/Phrap. The assembled sequencing data were subsequently split into 50-kb regions and reassembled and edited by Sequencher.

  4. Gaps between contigs were amplified by PCR using primers placed at the ends of individual contigs and sequenced.

  5. Confirmation of the nucleotide sequence was achieved by performing PCR walking of every 18-kb region of the genome.
Criteria for ORF assignment and annotation
  1. ORFs encoding proteins with 30 aa or more were identified with GAMBLER (http://bio.mki.co.jp/en/) and GLIMMER.

  2. The predicted ORFs were examined with respect to their start-codon assignment and some overlapping ORFs were removed.

  3. The homology of the ORFs were then searched for against a non-redundant protein database using BLAST.

  4. Functional motifs and domains of the deduced proteins were searched for against Prosite, Blocks, Pfam and PSORT.

  5. The tRNA and tmRNA genes were identified, respectively, by tRNAscan-SE or by the procedure described (http://www.indiana.edu/~tmrna/).

close this sectionRelated links to external databases