Supercoiling, R-Loops, Replication and the Functions of Bacterial Type 1A Topoisomerases

Abstract

Type 1A topoisomerases (topos) are the only topos that bind single-stranded DNA and the only ones found in all cells of the three domains of life. Two subfamilies, topo I and topo III, are present in bacteria. Topo I, found in all of them, relaxes negative supercoiling, while topo III acts as a decatenase in replication. However, recent results suggest that they can also act as back-up for each other. Because they are ubiquitous, type 1A enzymes are expected to be essential for cell viability. Single topA (topo I) and topB (topo III) null mutants of Escherichia coli are viable, but for topA only with compensatory mutations. Double topA topB null mutants were initially believed to be non-viable. However, in two independent studies, results of next generation sequencing (NGS) have recently shown that double topA topB null mutants of Bacillus subtilis and E. coli are viable when they carry parC parE gene amplifications. These genes encode the two subunits of topo IV, the main cellular decatenase. Here, we discuss the essential functions of bacterial type 1A topos in the context of this observation and new results showing their involvement in preventing unregulated replication from R-loops.

Mechanism of Type IA Topoisomerases

“…The protein–protein interactions with other cellular proteins are relevant for the physiological functions and regulation of type IA topoisomerase activities [ 38 ]. Basic residues in the C-terminal domains of E. coli topoisomerase I [ 100 ] and the C-terminal tail of M. smegmatis topoisomerase I [ 101 ] have been proposed to interact directly with the β′ subunit of RNA polymerase for the function of topoisomerase I in transcription elongation [ 14 , 102 , 103 ] to suppress hypernegative supercoiling and R-loop accumulation [ 14 , 104 , 105 ].…”

“…The twin supercoiling domain model proposed by Liu and Wang described the topological problems encountered during transcription that would require topoisomerase action ahead and behind the elongating RNA polymerase complex [ 10 , 11 ]. In bacteria, topoisomerase I belonging to the type IA subfamily relaxes the negative supercoiling generated by transcription behind the RNA polymerase complex to prevent the formation of DNA–RNA hybrids/R-loops that in turn can inhibit the transcription process [ 6 , 10 , 12 , 13 , 14 ]. In addition to the relaxation of negatively supercoiled DNA and preventing hypernegative supercoiling, type IA topoisomerases can also catalyze the decatenation of replication intermediates [ 15 , 16 , 17 , 18 , 19 ] and the knotting or unknotting of single-stranded DNA circles or nicked duplex DNA [ 20 , 21 ].…”

“…Two recent reviews on type IA topoisomerases have discussed the essential functions of bacterial type IA topoisomerase [ 14 ] and the many versatile collaborations engaged by eukaryotic TOP3 to carry out different topological transactions [ 38 ]. This review on the mechanism of type IA topoisomerases will focus more on the results from recent structural, biophysical, biochemical and genetic studies that help us gain a better understanding of how type IA topoisomerases can act as magicians to manipulate the topology of both DNA and RNA, in addition to key remaining questions on the catalytic mechanism.…”

Type IA Topoisomerases as Targets for Infectious Disease Treatments

“…DNA topoisomerases are well known targets for antibacterial drug discovery [ 7 , 21 , 22 , 23 , 24 , 25 ]. Topoisomerases are responsible for controlling the topology of the genome, including local and global DNA supercoiling [ 26 , 27 ]. DNA topology and topoisomerase functions play important roles in replication, transcription, and genome stability [ 21 , 27 , 28 , 29 , 30 , 31 , 32 ].…”

Bacterial type 1A topoisomerases maintain the stability of the genome by preventing and dealing with R-loop-and nucleotide excision repair-dependent topological stress

“…Class A enzymes are the only ubiquitous topos (3,4). Furthermore, unlike other topos, they use ssDNA as substrates and many of them possess RNA topo activity (5,6).…”