Mechanism of Type IA Topoisomerases
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molecules Review Mechanism of Type IA Topoisomerases Tumpa Dasgupta 1,2,3, Shomita Ferdous 1,2,3 and Yuk-Ching Tse-Dinh 1,2,* 1 Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; tdasg002@fiu.edu (T.D.); sferd001@fiu.edu (S.F.) 2 Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA 3 Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA * Correspondence: yukching.tsedinh@fiu.edu; Tel.: +1-305-348-4956 Academic Editor: Dagmar Klostermeier Received: 21 September 2020; Accepted: 15 October 2020; Published: 17 October 2020 Abstract: Topoisomerases in the type IA subfamily can catalyze change in topology for both DNA and RNA substrates. A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. Type IA topoisomerases have since evolved to catalyze the resolution of topological barriers encountered by genomes that require the passing of nucleic acid strand(s) through a break on a single DNA or RNA strand. Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. Active site residues assist in the nucleophilic attack of a phosphodiester bond between two nucleotides to form a covalent intermediate with a 50-phosphotyrosine linkage to the cleaved nucleic acid. A divalent ion interaction helps to position the 30-hydroxyl group at the precise location required for the cleaved phosphodiester bond to be rejoined following the passage of another nucleic acid strand through the break. In addition to type IA topoisomerase structures observed by X-ray crystallography, we now have evidence from biophysical studies for the dynamic conformations that are required for type IA topoisomerases to catalyze the change in the topology of the nucleic acid substrates. Keywords: topoisomerase; type IA; DNA supercoiling; RNA topology; decatenation 1. Introduction Normal cell growth requires replication of the genome and regulated transcription. Certain enzymes play crucial roles in these vital cellular processes. For example, DNA polymerase enzymes are essential for DNA replication [1] and RNA polymerases are required for transcription [2]. Because cellular genomes exist as very long double-stranded DNA, topoisomerases are needed for their unique role as master regulators of DNA topology during DNA replication, transcription, recombination, chromosome remodeling and many other genomic processes [3–7]. Topoisomerases catalyze the interconversion of different topological forms of DNA by creating transient breaks on one or both strands of the DNA duplex [8,9]. 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 [6,10,12–14]. In addition to the relaxation of negatively supercoiled DNA and preventing hypernegative supercoiling, type IA topoisomerases can also catalyze the decatenation of replication intermediates [15–19] and the knotting or unknotting of single-stranded DNA circles or nicked duplex DNA [20,21]. Every living organism has at least one type IA topoisomerase that can resolve topological barriers, including replication and recombination Molecules 2020, 25, 4769; doi:10.3390/molecules25204769 www.mdpi.com/journal/molecules Molecules 2020, 25, 4769 2 of 16 Molecules 2020, 25, x FOR PEER REVIEW 2 of 16 intermediatesreplication and or recombination other entangled intermediates DNA structures, or other by entangled passing DNA DNA through structures, a transient by passing break DNA in a singlethrough strand a transient of DNA break [7]. in The a single ability strand to unknot of DNA single-stranded [7]. The ability RNA to unknot circles was single-stranded first observed RNA for Escherichiacircles was colifirsttopoisomerase observed for Escherichia III [22]. This coli RNA topoisomerase topoisomerase III [22]. activity This might RNA have topoisomerase been related activity to the similaritymight have between been relatedE. coli totopoisomerase the similarity IIIbetween (TOP3) E. and coli an topoisomerase ancestral type III IA (TOP3) topoisomerase and an ancestral present intype the IA RNA topoisomerase world. The interestpresent inin thethe physiologicalRNA world. The significance interest ofin RNAthe physiological topoisomerase significance activity was of greatlyRNA topoisomerase heightened by activity the findings was greatly that human heighten topoisomeraseed by the findings IIIβ (TOP3B) that human has both topoisomerase DNA and RNA IIIβ topoisomerase(TOP3B) has both activities DNA and [23 ,RNA24]. Furthermore,topoisomerase mutations activities [23,24]. in human Furthermore, TOP3B are mutations linked to in disorders human inTOP3B neurodevelopment are linked to disorders and mental in neurodevelopment health [23–27]. 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[23–25] and Potential may play roles a role of TOP3B in translation. in unlinking Potential molecules roles ofof mRNATOP3B orin overcomingunlinking molecules torsional stressof mRNA of mRNA or overcoming have been torsional proposed stress [29], of but mRNA the exact have cellular been functionsproposed of[29], the but RNA the topoisomerase exact cellular activityfunctions remain of the toRNA be fullytopoisomerase elucidated. activity Remarkably, remain TOP3Bto be fully has elucidated. recently been Remarkably, demonstrated TOP3B tobe has a hostrecently factor been hijacked demonstrated for the e toffi cientbe a host viral factor replication hijacked of positive-sensefor the efficient single-stranded viral replication RNA of positive- viruses thatsense include single-stranded flaviviruses RNA and viruses coronaviruses that include [35]. flav Figureiviruses1 shows and coronaviruses some of the potential [35]. Figure topological 1 shows barrierssome of the occurring potential during topological the life barriers cycle of occurring a positive-sense during the single-stranded life cycle of a positive-sense RNA virus that single- may requirestranded the RNA RNA virus topoisomerase that may require activity the of RNA human topoisomerase TOP3B. TDRD3 activity plays of anhuman important TOP3B. role TDRD3 in the stabilizationplays an important and activation role in ofthe the stabilization DNA and RNA and topoisomeraseactivation of the activities DNA ofand human RNA andtopoisomerase Drosophila TOP3Bactivities [28 of,31 human,36]. CRISPR and Drosophila/Cas9-based TOP3B deletion [28,31,3 that6]. targetedCRISPR/Cas9-based the TOP3B–TDRD3 deletion complexthat targeted did notthe aTOP3B–TDRD3ffect Flavivirus translationcomplex did and not replication, affect Flavivirus but was translation found to diminish and replication, the late-stage but was production found ofto infectiousdiminish the virus late-stage particles production [37]. It is notof infectious known yet virus if the particles TOP3B–TDRD3 [37]. It is complexnot known is involvedyet if the similarlyTOP3B– inTDRD3 the di complexfferent stages is involved of the coronavirussimilarly in lifethe cycle.different stages of the coronavirus life cycle. Figure 1. Some of the potential topological problems during the life cycle of a positive-sense single- Figure 1. Some of the potential topological problems during the life cycle of a positive-sense single- stranded RNA virus that may require the RNA topoisomerase activity of human TOP3B. Genome stranded RNA virus that may require the RNA topoisomerase activity of human TOP3B. Genome circularization can be mediated by RNA–RNA interactions and proteins binding to the 5 and 3 ends. circularization can be mediated by RNA–RNA interactions and proteins binding to the 50′ and 3′0 ends. Decatenation of the catenated circular viral genome by TOP3B is required to remove blocks of (A) viral Decatenation of the catenated circular viral genome by TOP3B is required to remove blocks of (A) protein translation, (B) viral RNA transport and packaging. (C) When a translating ribosome or a viral protein translation, (B) viral RNA transport and packaging. (C) When a translating ribosome or helicase unwinds a duplex region in a viral RNA hairpin, and if the hairpin is bound to an immobile a helicase unwinds a duplex region in a viral RNA hairpin, and if the hairpin is bound to an immobile RNP or cellular matrix, the helical torsion will need to be relaxed by TOP3B. The figure is modified RNP or cellular matrix, the helical torsion will need to be relaxed by TOP3B. The