Supercoil Levels in E. coli and Salmonella Chromosomes Are Regulated by the C-Terminal 35–38 Amino Acids of GyrA

Abstract

Prokaryotes have an essential gene—gyrase—that catalyzes negative supercoiling of plasmid and chromosomal DNA. Negative supercoils influence DNA replication, transcription, homologous recombination, site-specific recombination, genetic transposition and sister chromosome segregation. Although E. coli and Salmonella Typhimurium are close relatives with a conserved set of essential genes, E. coli DNA has a supercoil density 15% higher than Salmonella, and E. coli cannot grow at the supercoil density maintained by wild type (WT) Salmonella. E. coli is addicted to high supercoiling levels for efficient chromosomal folding. In vitro experiments were performed with four gyrase isoforms of the tetrameric enzyme (GyrA2:GyrB2). E. coli gyrase was more processive and faster than the Salmonella enzyme, but Salmonella strains with chromosomal swaps of E. coli GyrA lost 40% of the chromosomal supercoil density. Reciprocal experiments in E. coli showed chromosomal dysfunction for strains harboring Salmonella GyrA. One GyrA segment responsible for dis-regulation was uncovered by constructing and testing GyrA chimeras in vivo. The six pinwheel elements and the C-terminal 35–38 acidic residues of GyrA controlled WT chromosome-wide supercoiling density in both species. A model of enzyme processivity modulated by competition between DNA and the GyrA acidic tail for access to β-pinwheel elements is presented.

DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines

“…coli are >90% identical, and this is also the case for the SpeE protein. Therefore, these findings alongside others [ 30 , 52 , 53 ] demonstrate how phenotypic differences between closely related bacterial species can result from allelic differences in conserved genes and in their regulation, rather than from the presence of a gene(s) in one species and its absence from another.…”

“…Typhimurium vs. E . coli [ 30 ]. However, the latter experiments were carried out using both a different S .…”

“…coli GyrA protein exhibited decreased DNA supercoiling compared to wild-type S . Typhimurium [ 30 ]. Our findings raise the possibility of putrescine and spermidine interacting with the C-terminal region of GyrA to activate the S .…”

“…Typhimurium) supercoils its DNA less than E . coli under basal growth conditions [ 30 ]. This is surprising because these two bacterial species are closely related [ 31 ] and also because their TopA (topoisomerase I) proteins share 96% amino acid identity, and their GyrA and GyrB proteins, which constitute the two subunits of DNA gyrase, share 91% and 97% identity, respectively.…”

FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo

“…For example, DNA wrapped by histones tends to be silent ( 8 ). The tight control of DNA supercoiling is critical for cell function; for example, the bacterium Escherichia coli loses viability upon a 15% decrease in DNA supercoiling ( 9 ), human immunodeficiency virus DNA cannot integrate into sufficiently relaxed DNA ( 3 ), and DNA cleavage by CRISPR Cas12a is favored when DNA is negatively supercoiled ( 10 ).…”