RecJ from <i>Bacillus halodurans</i> possesses endonuclease activity at moderate temperature

Wen, Wang; Ma, Liya; Zheng, Lirong; Zheng, Minggang

doi:10.1002/1873-3468.13809

Cited by 5 publications

(3 citation statements)

References 24 publications

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“…Unlike typical members of the GdpP family, such as B. subtilis GdpP, MbovGdpP is only characterized by a GGDEF-like motif and a DHH-DHHA1 domain, but no PAS motif ( Figure 1 ). Yet, sequence comparison with other members of the DHH superfamily revealed similarity with prokaryotic subfamily I members including cyclic nucleotide phosphodiesterase, nanoRNases, and exonuclease RecJ ( Srivastav et al, 2019 ; Wang et al, 2020 ). In particular, MbovGdpP sequence alignment with RecJ and RecJ-like proteins revealed an important level of similarity ( Supplementary Figure S1 ).…”

Section: Resultsmentioning

confidence: 99%

An atypical GdpP enzyme linking cyclic nucleotide metabolism to osmotic tolerance and gene regulation in Mycoplasma bovis

Zhu,

Baranowski,

Hao

et al. 2023

Front. Microbiol.

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Nucleotide second messengers play an important role in bacterial adaptation to environmental changes. Recent evidence suggests that some of these regulatory molecular pathways were conserved upon the degenerative evolution of the wall-less mycoplasmas. We have recently reported the occurrence of a phosphodiesterase (PDE) in the ruminant pathogen Mycoplasma bovis, which was involved in c-di-AMP metabolism. In the present study, we demonstrate that the genome of this mycoplasma species encodes a PDE of the GdpP family with atypical DHH domains. Characterization of M. bovis GdpP (MbovGdpP) revealed a multifunctional PDE with unusual nanoRNase and single-stranded DNase activities. The alarmone ppGpp was found unable to inhibit c-di-NMP degradation by MbovGdpP but efficiently blocked its nanoRNase activity. Remarkably, MbovGdpP was found critical for the osmotic tolerance of M. bovis under K+ and Na+ conditions. Transcriptomic analyses further revealed the biological importance of MbovGdpP in tRNA biosynthesis, pyruvate metabolism, and several steps in genetic information processing. This study is an important step in understanding the role of PDE and nucleotide second messengers in the biology of a minimal bacterial pathogen.

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Section: Resultsmentioning

confidence: 99%

An atypical GdpP enzyme linking cyclic nucleotide metabolism to osmotic tolerance and gene regulation in Mycoplasma bovis

Zhu,

Baranowski,

Hao

et al. 2023

Front. Microbiol.

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“…A novel class of RecJ nucleases, distinct from the classic RecJ nucleases and derived from Bacillus alcalophilus, Bacillus cereus, and Bacillus halodurans, exhibit not only the exonuclease activity of RecJ but also endonuclease activity (Ma et al, 2021;Wang et al, 2020;Zheng et al, 2020;Srivastav et al, 2019;Makarova et al, 2012). Based on the combined exo-and endonuclease activities of the RecJ (BaRecJ) nuclease from B. alkaliphilic, we established a novel global in vivo mutagenesis method, differentiating it from current global in vivo mutagenesis mechanisms (Luan et al, 2013;Badran and Liu, 2015).…”

Section: Introductionmentioning

confidence: 99%

Highly efficient in vivo mutagenesis method based on the endonuclease and exonuclease activity of Bacillus alcalophilus RecJ (BaRecJ)

Shang,

Zhang,

et al. 2024

Preprint

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With the continual advancement of technologies such as microbial cultivation, DNA sequencing, bioinformatics, and genetic engineering, methods for microbial breeding have become increasingly diverse. We identified a RecJ enzyme (BaRecJ) with both endonuclease and exonuclease activities from B. alcalophilus. Differing from traditional physical-chemical mutagenesis approaches and the methods based on perturbation factor. this research established a novel mutagenesis method utilizing the endonuclease and exonuclease activities of BaRecJ. Mutagenesis of E. coli was conducted using the BaRecJ method, followed by screening for rifampicin-resistant mutants, rpoB sequencing results demonstrated a broader, more uniform spectrum of mutations and a higher frequency of substitution mutations with this mutagenesis approach. Furthermore, this mutagenesis method was applied to S cerevisiae, resulting in mutants with enhanced tolerance to acetic acid and ethanol, exhibiting improved fermentation performance and flocculation abilities Genomic resequencing analysis summarized genes possibly associated with the tolerance of mutants. Therefore, this approach not only holds immense potential in microbial mutagenesis breeding and adaptive evolution but also, when coupled with genomic resequencing, allows for the rapid identification of genetic loci associated with specific traits.

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“…RecJ enzymes function in DNA repair and recombination, nucleotide recycling, stress tolerance, and the final stages of chromosome duplication ( 28 - 33 ). In bacteria, such as Escherichia coli , RecJ is a single-stranded (ss) DNA-specific 5′−3′ exonuclease that is processive ( 26 , 27 ), while other bacterial RecJ enzymes are identified that cleave dsDNA ( 34 ). Archaea have an expanded repertoire of RecJ homologs related to bacterial RecJ and eukaryal Cdc45, the latter a non-catalytic subunit of the CMG complex.…”

Section: Introductionmentioning

confidence: 99%

RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii

Jia

Dantuluri

Margulies

et al. 2023

mBio

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Nucleases are strictly regulated and often localized in the cell to avoid the uncontrolled degradation of DNA and RNA. Here, a new type of nuclease complex, composed of RecJ3, RecJ4, and aRNase J, was identified through its ATP-dependent association with the ubiquitin-like SAMP1 and AAA-ATPase Cdc48a. The complex was discovered in Haloferax volcanii , an archaeon lacking an RNA exosome. Genetic analysis revealed aRNase J to be essential and RecJ3, RecJ4, and Cdc48a to function in the recovery from DNA damage including genotoxic agents that generate double-strand breaks. The RecJ3:RecJ4:aRNase J complex (isolated in 2:2:1 stoichiometry) functioned primarily as a 3′−5′ exonuclease in hydrolyzing RNA and ssDNA, with the mechanism non-processive for ssDNA. aRNase J could also be purified as a homodimer that catalyzed endoribonuclease activity and, thus, was not restricted to the 5′−3′ exonuclease activity typical of aRNase J homologs. Moreover, RecJ3 and RecJ4 could be purified as a 560-kDa subcomplex in equimolar subunit ratio with nuclease activities mirroring the full RecJ3/4-aRNase J complex. These findings prompted reconstitution assays that suggested RecJ3/4 could suppress, alter, and/or outcompete the nuclease activities of aRNase J. Based on the phenotypic results, this control mechanism of aRNase J by RecJ3/4 is not necessary for cell growth but instead appears important for DNA repair. IMPORTANCE Nucleases are critical for various cellular processes including DNA replication and repair. Here, a dynamic type of nuclease complex is newly identifiedidentifiedidentifiedin the archaeon Haloferax volcanii , which is missing the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, functions primarily as a 3′−5′ exonuclease and was discovered through its ATP-dependent association with the ubiquitin-like SAMP1 and Cdc48a. aRNase J alone forms a homodimer that has endonuclease function and, thus, is not restricted to 5′−3′ exonuclease activity typical of other aRNase J enzymes. RecJ3/4 appears to suppress, alter, and/or outcompete the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for recovery against DNA damage. These biological distinctions may correlate with the regulated nuclease activity of aRNase J in the RecJ3/4-aRNaseJ complex.

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RecJ from Bacillus halodurans possesses endonuclease activity at moderate temperature

Cited by 5 publications

References 24 publications

An atypical GdpP enzyme linking cyclic nucleotide metabolism to osmotic tolerance and gene regulation in Mycoplasma bovis

An atypical GdpP enzyme linking cyclic nucleotide metabolism to osmotic tolerance and gene regulation in Mycoplasma bovis

Highly efficient in vivo mutagenesis method based on the endonuclease and exonuclease activity of Bacillus alcalophilus RecJ (BaRecJ)

RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii

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