Regulatory roles of MarA in flagellar biosynthesis in Escherichia coli: a novel mechanism for transcription initiation

Klimova, Ksenia (2024). Regulatory roles of MarA in flagellar biosynthesis in Escherichia coli: a novel mechanism for transcription initiation. University of Birmingham. Ph.D.

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Abstract

Multiple antibiotic resistance is one of the main threats to human health in the modern world. Multiple antibiotic resistance (mar) locus provides resistance to a wide range of antibiotics and phenolic compounds in gram-negative bacteria Escherichia coli. The transcription factor MarA encoded in this locus is mainly required for activation and expression of the AcrAB- TolC encoded efflux pump, which plays a primary role in active antibiotic transport out of the cell. However, recent studies suggest that MarA is also involved in lipid trafficking, DNA repair and biofilm formation in E. coli.
The current work shows that MarA can also regulate flagellar gene expression, suggesting an interplay between flagellar biosynthesis and intrinsic response to antibiotics. New σ28- dependent promoter regions were found upstream of the flgBCDEFGHIJ/KL and flgAMN operons, which were known as σ70- and FlhDC-dependent only. Both operons are located in close proximity to each other on opposite DNA strands, and share an FlhDC binding site. Another σ28-dependent promoter was also found upstream of the flgJ gene, which is a part of the flgBCDEFGHIJ/KL operon. A new σ70-dependent promoter was found upstream of the flgM gene, which also has a σ28-dependent promoter, and can also be transcribed as part of the flgAMN operon. Marboxes were identified upstream of the flgA, flgB, flgJ and flgM genes.
MarA has been known as an activator that assists only σ70-dependent transcription in a Class I or Class II manner. In the current study, MarA activates both flgA and flgB σ70-dependent promoters in an FlhDC-dependent manner in vivo via an unknown indirect mechanism. However, in vitro MarA assists the novel σ28-dependent flgB promoter in a Class III manner. MarA binds between the -10 and -35 elements of σ28-dependent flgB promoter, and distort conserved -11A base, where unwinding of the open complex nucleates. At the same time, MarA represses open complex formation on flgA promoter.
This regulatory mechanism suggests that MarA plays a role in redirecting transcription to favor partial flagellar biosynthesis during antibiotic stress, potentially enabling E. coli to escape hazardous environments. The novel finding that MarA can assist RNAPσ28 expands our understanding of transcription regulation and suggests a broader regulatory interactions in bacterial adaptive responses.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

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