Antibiotics are one of the most important advances in medical science, but
today, antibiotic-resistant bacteria threaten this legacy. We risk losing our ability to treat
acute infections, perform invasive surgeries, and exploit immunosuppressive therapies like
transplantation and cancer chemotherapy. The antibiotics we use today have ancient roots
and have been produced by microbial denizens of the soil for millions of years before we
adopted them in the 20th century. This history has modern consequences, as strategies to
resist these compounds have evolved in concert for millions of years. The result is a vast
reservoir of antimicrobial resistance that exists in environmental bacteria, which have the
potential to be mobilized into human pathogens and cripple our antibiotic arsenal. Here, I
set out to deepen our understanding of the environmental resistome, focusing on the
rifamycin antibiotics. These compounds inhibit bacterial RNA polymerase and are
frontline agents for treating tuberculosis. Environmental bacteria from the phylum
Actinobacteria induce the production of resistance enzymes in response to these
compounds. Although mechanistic questions remain, we demonstrate that this induction
stems from the inhibition of RNA polymerase by rifamycins. The induction process is
known to require a specific DNA motif; here, I identify additional sequences as part of this
motif and use this information to map inducible rifamycin resistance across the entire
phylum. The most common rifamycin-inducible gene was an uncharacterized family of
proteins annotated as DNA helicases. I investigated these proteins and discovered that they
bind to RNA polymerase and displace rifamycin antibiotics, a novel mechanism of
rifamycin resistance. Lastly, we repurposed this inducible system to develop an assay to
screen for novel RNA polymerase inhibitors. From this screen, we identified a rifamycin
immune to a common environmental resistance enzyme and a new family of rifamycin
antibiotics. / Thesis / Doctor of Philosophy (PhD) / Our antibiotic arsenal consists primarily of metabolites produced by soil microbes,
which humanity repurposed into life-saving medicines in the 20th century. As a direct result
of the natural origin of antibiotics, resistant bacteria exist in these same environments,
independent of human use. Individual genetic determinants from this reservoir can emerge
in pathogenic bacteria without warning and render antibiotics ineffective. The aim of this
work was to understand how environmental bacteria resist the rifamycin class of
antibiotics. Firstly, I investigated the ability of some bacteria to sense the presence of
rifamycins, and in response produce proteins to protect themselves. I discovered that this
process requires specific DNA sequences nearby resistance genes. Using this DNA
sequence as a guide I cataloged resistance genes in thousands of bacterial genomes and
discovered a new mechanism of rifamycin resistance. Lastly, I exploited this rifamycin
sensing system to discover new antibiotics from soil microbes.
| Identifer | oai:union.ndltd.org:mcmaster.ca/oai:macsphere.mcmaster.ca:11375/28498 |
| Date | January 2023 |
| Creators | Surette, Matthew |
| Contributors | Wright, Gerard, Biochemistry and Biomedical Sciences |
| Source Sets | McMaster University |
| Language | English |
| Detected Language | English |
| Type | Thesis |
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