HIGHLIGHTS

GENOME WATCH of non- Matthew Holden, Lisa Crossman, Ana Cerdeño-Tárraga and

Analysing the of non-pathogenic appears to be well endowed with potential secretion system and some genes similar to microorganisms, in addition to its basic and adhesins capable of binding specific host mol- those found in Salmonella typhimurium applied scientific interest, can also shed ecules, it does not contain the ica operon, invasion loci. Insecticidal, nematocidal and considerable light on the study of pathogenic which is required for polysaccharide-mediated antibiotic synthesis genes are also present, microorganisms. Two of the three adhesion and formation in some giving some indication of the diversity of the microorganisms described here are rarely strains of S. epidermidis.The region of the environment inhabited by this organism. pathogenic, but carry genetic determinants ATCC 12228 chromosome that is similar to the Finally, Gloeobacter violaceus PCC 7421is a that have previously been identified as being flanking regions of the ica operon appears to unicellular cyanobacterium whose important for the pathogenicity of other contain signs of genetic rearrangements, leading consists of a single chromosome of just over microorganisms. This underlines the growing the authors to suggest that the absence of this 4.5 Mb5.Key differences have been found in its understanding that many so-called ‘ operon is the result of a genetic defect. genome that set this bacterium apart from the genes’ are probably involved in more general The comparison of this genome with those rest of the cyanobacterial group it belongs to; interactions between the microorganism and of the clinical S. aureus isolates reveals that this this reflects a considerable phylogenetic distance the host or the environment. strain’s virulence arsenal is not as well stocked. as the Gloeobacter lineage was the earliest to However, as this strain is a non-clinical isolate diverge within the radiation of cyanobacteria Staphylococcus epidermidis is generally a rela- with low virulence in an animal model, the and chloroplasts. One of the main differences tively benign resident of human skin and real significance of the arsenal’s remaining reflects an ancestral characteristic: G. violaceus mucosal surfaces. However, over recent decades, contents in virulence and colonization is has the necessary genes for photosystems I and the increased use of invasive devices and unclear. The apparent loss of the ica operon II, which are both required for oxygenic photo- implants, such as catheters, has contributed to also raises the question as to whether any synthesis6,however this process occurs in the the rise of this bacterium as a hospital-acquired virulence functions, or indeed additional cytoplasmic membrane and not in the thylakoid . The severity and diversity of the biofilm genes, could also be missing. To this membrane, as thylakoids are not present in caused by this pathogen are not as end, the publication of the complete genome G. violaceus.Therefore, although the photosyn- great as those associated with its more notori- of the biofilm-forming, clinically isolated thetic structures present in other cyanobacteria ous cousin ,but its ability S. epidermidis strain RP62A is keenly awaited. face the lumen of the thylakoids, in this bac- to form on artificial surfaces means The genome sequence of Chromobacterium terium they face the periplasmic space and that it is often recalcitrant to antimicrobial violaceum ATCC 12472 reveals a 4.75 Mb single hence co-exist with the respiratory system. The therapy and therefore difficult to treat. chromosome with 65% G+C content4.This other main difference is related to circadian S. epidermidis strain ATCC 12228 is a non- unusual free-living microorganism was isolated rhythm. G. violaceus lacks the major genetic biofilm-forming, non--associated from a tropical soil and water environment. elements of the circadian clock, the kai genes, isolate that has previously been used for anti- Approximately one-third of the predicted genes which are involved in controlling cell division biotic detection in food products. In their encode transport proteins, which are thought in other cyanobacteria, suggesting that this publication, Zhang et al.1 present the complete to be highly specific and permit efficient scav- system could have been acquired after the genome sequence, and use previously published enging of very low concentrations of nutrients. divergence of the Gloeobacter lineage. 2,3 genome sequences of clinical S. aureus isolates C. violaceum can adapt quickly to harsh envi- Matthew Holden, Lisa Crossman, Ana Cerdeño- to identify components of the ATCC 12228 ronmental stress using alternative metabolic Tárraga and Julian Parkhill are at the Sanger Institute, genome involved in virulence, pathways for growth depending on the nutri- Genome Campus, Hinxton, and regulation. The authors found that the ents available. Tight transcriptional control is Cambridge CB10 1SA, UK. ATCC 12228 genome contains fewer virulence achieved by many regulators, including several e-mail: [email protected] doi:10.1038/nrmicro825 determinants than the clinical S. aureus isolates sigma factors. The organism produces violacein — it lacks orthologues of pyrogenic toxins — a purple pigment with antimicrobial 1. Zhang, Y. Q. et al. Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis with superantigen activity, and the only toxins properties against major pathogens such as strain (ATCC 12228). Mol. Microbiol. 49, 1577–1593 (2003). identified were the membrane-active β- and Mycobacterium — and its produc- 2. Baba, T. et al. Genome and virulence determinants of high δ virulence community-acquired MRSA. Lancet 359, -haemolysins. This strain also lacks the viru- tion is under quorum-sensing control. The 1819–1827 (2002). lence-associated extracellular enzymes staphy- considerable biotechnological potential of 3. Kuroda, M. et al. Whole genome of methicillin- resistant Staphylococcus aureus. Lancet 357, 1225–1240 lokinase, staphylocoagulase and hyaluronidase. C. violaceum has been explored with its use in (2001). It is better equipped with genes encoding methods to synthesize polyhydroxyalkanoates 4. BNGP Consortium. The complete genome sequence of Chromobacterium violaceum reveals remarkable and adhesins: in addition to previously character- (PHAs), hydrolyze plastic films and solubilize exploitable bacterial adaptability. Proc. Natl Acad. Sci. ized S. epidermidis adhesin genes (altE, fbe and gold without mercury. C. violaceum occa- USA 100, 11660–11665 (2003). 5. Nakamura, Y. et al. Complete genome structure of embP), the genome contains orthologues of sionally infects humans but the genome Gloeobacter violaceus PCC 7421, a cyanobacterium that several S. aureus MSCRAMMs that have been has no obvious pathogenicity islands; it is lacks thylakoids. DNA Res. 10, 137–145 (2003). 6. Hervas, M., Navarro, J. A. & De La Rosa, M. A. Electron shown to modulate host-cell interactions. suggested that these could be isolate-specific. transfer between membrane complexes and soluble proteins Although the ATCC 12228 isolate therefore However, there is an almost-complete type III in photosynthesis. Acc. Chem. Res. 36, 798–805 (2003).

NATURE REVIEWS | VOLUME 2 | FEBRUARY 2004 | 91 ONLINE

Online links

Entrez S. epidermidis strain ATCC 12228 http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=genome&g i=271

Chromobacterium violaceum ATCC 12472 http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=genome&g i=321

Gloeobacter violaceus PCC 7421 http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=genome&g i=346

NATURE REVIEWS | MICROBIOLOGY VOLUME 2 | JANUARY 2004 | 92