Topoisomerase IV can functionally replace all type 1A topoisomerases in Bacillus subtilis

Reuß, Daniel R.; Faßhauer, Patrick; Mroch, Philipp Joel; Ul-Haq, Inam; Koo, Bon Chul; Pöhlein, Anja; Gross, Carol A.; Daniel, Rolf; Brantl, Sabine; Stülke, Jörg

doi:10.1093/nar/gkz260

Cited by 33 publications

(32 citation statements)

References 58 publications

(77 reference statements)

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“…With the initiation of global mRNA degradation as the (quasi)-essential function of RNases E and Y in E. coli and B. subtilis, respectively, one might expect that the overexpression of other RNases might compensate for their loss. By analogy, such a compensation has been observed for the essential DNA topoisomerase I of B. subtilis, which could be replaced by overexpression of topoisomerase IV (44).…”

Section: Discussionmentioning

confidence: 81%

“…In Salmonella typhimurium, rrn operons have been shown to be a hotspot of gene duplications or amplifications (67). Since evolution of such a genomic duplication is dependent on homologous recombination, we performed the PCR also on the recA mutant GP2542, which is defective in homologous recombination and thus unable to amplify chromosomal regions (44,45). Indeed, in this case we did not obtain even a faint band.…”

Section: Genomic Separation Of the Genes Encoding The Core Subunits Omentioning

confidence: 96%

“…Mapping of the reads was performed using the Geneious software package (Biomatters Ltd., New Zealand) (43). Frequently occurring hitchhiker mutations (44) and silent mutations were omitted from the screen. The resulting genome sequences were compared to that of our in-house wild type strain.…”

Section: Dna Manipulation and Genome Sequencingmentioning

confidence: 99%

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Quasi-essentiality of RNase Y inBacillus subtilisis caused by its critical role in the control of mRNA homeostasis

Benda

Woelfel

Gunka

et al. 2020

Preprint

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RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase -α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β' subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed massive decreases in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.If the continued activity of a protein may become harmful to the bacteria, it is important not only to prevent expression of the corresponding gene but also to take two important measures: (i) switch off the protein's activity and (ii) degrade the mRNA to exclude further production of the protein. The inactivation or even degradation of proteins is well documented in the model bacteria. For example, in both E. coli and B. subtilis the uptake of toxic ammonium is limited by a regulatory interaction of the ammonium transporter with GlnK, a regulatory protein of the PII family (1,2). Similarly, the uptake of potentially toxic potassium can be prevented by inhibition of potassium transporters at high environmental potassium concentrations, either by the second messenger cyclic di-AMP or by interaction with a dedicated modified signal transduction protein, PtsN (3,4,5). To prevent the accumulation of potentially harmful mRNAs, bacteria rely on a very fast mRNA turnover. Indeed, in E. coli and B. subtilis more than 80% of all transcripts have average half-lives of less than 8 minutes, as compared to about 30 minutes and 10 hours in yeast or human cells, respectively (6,7,8,9). Thus, the mRNA turnover is much faster than the generation time. The high mRNA turnover rate in bacteria contributes to the fast adaptation even in rapidly growing cells. The rapid mRNA turnover is therefore a major factor to resolve the apparent growth speed-adaptation trade-off. 4RNases are the key elements to achieve the rapid mRNA turnover in bacteria. Theses enzymes can degrade bulk mRNA in a rather unspecific manner, just depending on the accessibility of the RNA molecules as well as perform highly specific cleavages that serve to process an RNA molecule to its mature form. In all organisms, RNA degradation involves an interplay ...

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Section: Discussionmentioning

confidence: 81%

Section: Genomic Separation Of the Genes Encoding The Core Subunits Omentioning

confidence: 96%

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Quasi-essentiality of RNase Y inBacillus subtilisis caused by its critical role in the control of mRNA homeostasis

Benda

Woelfel

Gunka

et al. 2020

Preprint

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“…It is possible that S. flexneri is unable to amplify the region encompassing the parC and parE genes [32]. In a very recent study, B. subtilis topA null mutants that were able to form colonies were shown to carry parC parE amplifications [15]. However, no compensatory mutations were found in gyrA or gyrB.…”

Section: Viability Of Single Topa Null Mutants and The Role Of Topo Imentioning

confidence: 99%

“…In this reaction RecQ, or its eukaryotic homologs Sgs1 and BLM act on the recombination intermediate to generate a hemicatenane, a structure that can only be resolved by a type 1A topo [2]. However, recent results have shown that both E. coli and B. subtilis cells lacking type 1A topos can survive when they overproduce topo IV [14,15]. Topo IV is a type II enzyme and therefore cannot resolve hemicatenanes.…”

Section: Introductionmentioning

confidence: 99%

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

Brochu

Breton

Drolet

2020

Genes

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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.

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DNA topoisomerases: Advances in understanding of cellular roles and multi‐protein complexes via structure‐function analysis

Neuman²,

2021

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DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA‐topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single‐molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase interactions with accessory proteins and other DNA‐associated proteins, supporting the idea that they often function as part of multi‐enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini‐A. These new findings are advancing our understanding of DNA‐related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism.

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Topoisomerase IV can functionally replace all type 1A topoisomerases in Bacillus subtilis

Cited by 33 publications

References 58 publications

Quasi-essentiality of RNase Y inBacillus subtilisis caused by its critical role in the control of mRNA homeostasis

Quasi-essentiality of RNase Y inBacillus subtilisis caused by its critical role in the control of mRNA homeostasis

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

DNA topoisomerases: Advances in understanding of cellular roles and multi‐protein complexes via structure‐function analysis

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