1 School of Molecular and Microbial Biosciences, Biochemistry and Microbiology Building, University of Sydney, NSW 2006, Australia
2 Centre for Infectious Diseases and Microbiology, University of Sydney, Westmead Hospital, Sydney, NSW 2145, Australia
3 Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
Correspondence
H. W. Stokes
(hstokes{at}rna.bio.mq.edu.au)
The term integron is legitimately used in a number of ways (Hall, 2001, 2002
). It describes the configuration of features that are characteristic of integrons, namely an intI gene, encoding the IntI site-specific recombinase responsible for capturing the small mobile elements known as gene cassettes, an attI site into which the cassettes are inserted and a promoter (Pc) that drives expression of cassette-associated genes. Integron describes such structures both when no cassettes are present and when there are integrated cassettes as, in the latter case, the cassettes are viewed as part of the integron. Granted that each gene cassette found in an integron is a mobile element (Collis & Hall, 1992
; Recchia & Hall, 1995
), variability in the number of gene cassettes found in any class of integron is to be expected. Hence, while the ability to capture gene cassettes is a definitive feature of integrons, the number and nature of the cassettes present is not.
The term super integron was coined by Mazel et al. (1998) in response to use of the term mega-integron by Clark et al. (1997)
. Both groups were referring to the fact that the recently discovered integron found in the small chromosome of Vibrio cholerae has a very large array of gene cassettes incorporated within it. Though super integron has never been clearly defined, it appears to have subsequently been used to refer to all integrons that are or might be found in a bacterial genome or chromosome, perhaps assuming that they will all include large arrays of cassettes. However, there is no a priori reason why this should be so. Indeed, an integron in the Shewanella oneidensis chromosome that contains only three cassettes has been reported recently, yet the term super integron has been used to describe it (Drouin et al., 2002
). An integron containing only 30 cassettes and whose location is currently unknown, but possibly chromosomal, found in a Pseudomonas alcaligenes strain that carries three different integrons has also been called a super integron (Vaisvila et al., 2001
). In reality, while there is a single integron type in V. cholerae, known as class 4, after the intI gene which is intI4 (Mazel et al., 1998
), there is no single integron when cassettes are also considered because individual strains of V. cholerae have different cassette arrays (Clark et al., 2000
) and class 4 integrons with short arrays of gene cassettes or even no cassettes may be found in the future.
The terms antibiotic resistance integron or antibiotic resistant integron or multiresistance integron have also been used by Mazel and co-workers (see Rowe-Magnus et al., 2002) and these integrons are said to have fewer cassettes than super integrons. Again, the basis of the distinction is not clear as antibiotic resistance is generally a property conferred by the gene cassettes rather than the integron scaffold. Furthermore, amongst the cassettes in the sequenced strain of V. cholerae there is at least one that confers resistance to an antibiotic (Heidelberg et al., 2000
; Rowe-Magnus et al., 2002
). Indeed, it is obvious that chromosomally located integrons in the Vibrionaceae and in other organisms are the likely source of gene cassettes that confer resistance to antibiotics, and it might be expected that more such cassettes will be found in integrons from bacterial chromosomes in the future.
The ability to distinguish integrons that are an intrinsic part of bacterial chromosomes and found in most members of a species or genus, as appears to be the case for Vibrio and Listonella, from integrons that are found in the chromosome of only some or few strains in a species, as is the case for P. alcaligenes (Vaisvila et al., 2001) and Pseudomonas stutzeri (Holmes et al., 2003
), and from those that are part of the mobile gene pool, such as the extensively studied class 1 integrons (Hall & Collis, 1995
; Collis et al., 2002
), is undoubtedly useful in the context of genome evolution. But, super integron and antibiotic resistance integron do not adequately fulfil this role. We believe that use of these terms should not continue. The term integron has a clear definition which uses only conserved features, namely the intI gene, attI site, Pc promoter and the ability to incorporate gene cassettes (Hall, 2001
, 2002
). This definition is sufficient to encompass all integrons, whatever the number of cassettes they harbour and whatever their location.
REFERENCES
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Clark, C. A., Purins, L., Keawrakon, P., Focareta, T. & Manning, P. A. (2000). The Vibrio cholerae O1 chromosomal integron. Microbiology 146, 26052612.
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Collis, C. M., Kim, M.-J., Stokes, H. W. & Hall, R. M. (2002). Integron-encoded IntI integrases preferentially recognize the adjacent cognate attI site in recombination with a 59-be site. Mol Microbiol 46, 14151427.[CrossRef][Medline]
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Holmes, A. J., Holley, M. P., Mahon, A., Nield, B., Gillings, M. & Stokes, H. W. (2003). Recombination activity of a distinctive integron-gene cassette system associated with Pseudomonas stutzeri populations in soil. J Bacteriol 185, 918928.
Mazel, D., Dychinco, B., Webb, V. A. & Davies, J. (1998). A distinctive class of integron in the Vibrio cholerae genome. Science 280, 605608.
Recchia, G. D. & Hall, R. M. (1995). Gene cassettes: a new class of mobile element. Microbiology 141, 30153027.[Medline]
Rowe-Magnus, D. A., Guerout, A.-M. & Mazel, D. (2002). Bacterial resistance evolution by recruitment of super-integron gene cassettes. Mol Microbiol 43, 16571679.[CrossRef][Medline]
Vaisvila, R., Morgan, R. D., Posfai, J. & Raleigh, E. A. (2001). Discovery and distribution of super-integrons among pseudomonads. Mol Microbiol 42, 587601.[CrossRef][Medline]
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