Elsevier

Drug Discovery Today

Volume 10, Issue 18, 15 September 2005, Pages 1245-1252
Drug Discovery Today

Review
Using microarray gene signatures to elucidate mechanisms of antibiotic action and resistance

https://doi.org/10.1016/S1359-6446(05)03566-XGet rights and content

Microarray analyses reveal global changes in gene expression in response to environmental changes and, thus, are well suited to providing a detailed picture of bacterial responses to antibiotic treatment. These responses are represented by patterns of gene expression, termed expression signatures, which provide insight into the mechanism of action of antibiotics as well as the general physiological responses of bacteria to antibiotic-related stresses. The complexity of such signatures is challenging the notion that antibiotics act on single targets and this is consistent with the concept that there are multiple targets coupled with common stress responses. A more detailed knowledge of how known antibiotics act should reveal new strategies for antimicrobial drug discovery.

Section snippets

Antimicrobial drug discovery and screening approaches

Since Alexander Fleming's discovery of the antimicrobial activity of penicillin [1], the field of antimicrobial drug discovery has been largely dominated by whole-cell screening assays, wherein new antimicrobial compounds are chosen for their ability to inhibit the growth of actively multiplying bacteria. Although the mechanism of action of such compounds is not always clear, this approach was successful in the early days of antibiotic development. Whereas this approach still holds potential

Complex modes of action

A perusal of medical and microbiology textbooks leads one to believe that all antibiotics work by simple mechanisms, involving single targets. This, however, does not appear to be correct, at least for the bactericidal antibiotics. For example, Ī²-lactams, the class of antibiotics utilized most often in clinical setting, are known to have several molecular targets [13]. Ī²-lactams inhibit the activity of penicillin-binding proteins (PBPs), a group of enzymes important for cell-wall synthesis, and

Expression signatures of bacteria interacting with antimicrobials

Whole-genome expression profiling, facilitated by the development of DNA microarrays [25, 26], provides a comprehensive portrait of the bacterial response to any given condition because it allows simultaneous analysis of the expression of all genes in an organism. Microarrays are cDNA- or oligonucleotide-based platforms containing probes to every open reading frame in a given genome. Labeled mRNA samples from an organism grown under a given condition, or cDNAs made therefrom, are hybridized to

Signatures characteristic of direct target inhibition

Global transcription profiles of bacteria following antimicrobial exposure reveal that the bacterial response to a particular antibiotic often reflects the ā€˜directā€™ response of the cell to inhibition of a particular physiological function as targeted by the antimicrobial (Table 1, Group 1). As an example, DNA-gyrase inhibitors of the quinolone class elicit the bacterial SOS DNA-repair response as a consequence of the DNA damage caused by the interaction of these agents with DNA gyrase [27, 28,

Signatures beyond direct target inhibition

Bacterial responses, and thus bacterial expression profiles following antibiotic treatment, typically contain substantially more genes than those directly targeted by the antibiotic. Among these, there are numerous genes ā€˜indirectlyā€™ affected by the antibiotic (Table 1, Group 2) but nonetheless relevant to the response of the organism to the antibiotic-induced stress (i.e. genes involved in general stress responses). For example, the heat-shock response which helps the cell survive the

Towards expression signature libraries

With these signature groupings in mind, investigators have started to develop compendia of gene-expression signatures for a range of antimicrobials [27, 39, 40]. Although in some instances modes of action for novel compounds can be predicted on the basis of this compendium, difficulties in prediction arise if the database does not contain expression profiles for a broad enough complement of antibiotics.

The Bacillus subtilis database compiled by Hutter et al. [27], for example, is extensive and

Potential use of expression signatures in drug discovery

Detailed expression signatures contain an immense amount of information and arguably might open up avenues for antimicrobial drug discovery. For example, the comparison of gene-expression signatures will continue to be useful in predicting mechanisms of action for novel compounds. Such data mining will also be useful in identifying potential novel antimicrobial targets among the plethora of uncharacterized genes present in expression signatures. For a given class of antibiotics, recurrence of

Conclusions

Genomics and its associated technologies are not only providing the tools to drive antimicrobial drug discovery as it applies to whole-cell based and target-screening approaches, but are providing new insights into antimicrobial mechanisms of action. Although such analyses have exposed our limited understanding of the mechanisms of action of even well-known antimicrobials, they also open up new avenues for antimicrobial drug discovery. Expression signatures gathered from an array of antibiotics

Acknowledgements

The authors own microarray studies on antibiotic action were supported by the Canadian Cystic Fibrosis Foundation (CCFF) and a grant from Genome Prairie and Genome British Columbia, with ancillary support from Inimex Pharmaceuticals. R.E.W. Hancock has a Canada Research Chair in genomics and human health; M.D. Brazas was supported by CCFF and Natural Sciences and Engineering Research Council (NSERC) studentships.

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