A pGpG-specific phosphodiesterase regulates cyclic di-GMP signaling in Vibrio cholerae

Heo, Kyoo; Lee, Jae Woo; Jang, Yongdae; Kwon, Sohee; Lee, Jun Ho; Seok, Chaok; Ha, Nam‐Chul; Seok, Yeong‐Jae

doi:10.1016/j.jbc.2022.101626

Cited by 10 publications

(8 citation statements)

References 56 publications

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“…In the genome of A. butzleri and related species, the nrn and corA genes are fused, suggestive of a close functional relationship. The closest predicted structural matches for B. fragilis NrN are to the pGpG-specific PDE PggH from Vibrio cholerae , which has a role in the turnover of the cyclic nucleotide c-di-GMP 18 and the GdpP PDE from Staphylococcus aureus , which degrades pApA molecules as a component of c-di-AMP signalling systems 19 . Analysis of the DEDD protein suggests structural matches to RNaseT 20 , oligoribonuclease 21 , and the mammalian REXO2 protein, which degrades linear RNA and DNA dinucleotides 22 .…”

Section: Mainmentioning

confidence: 99%

Antiviral type III CRISPR signalling via conjugation of ATP and SAM

Chi,

Hoikkala,

Grüschow

et al. 2023

Nature

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CRISPR systems are widespread in the prokaryotic world, providing adaptive immunity against mobile genetic elements1,2. Type III CRISPR systems, with the signature gene cas10, use CRISPR RNA to detect non-self RNA, activating the enzymatic Cas10 subunit to defend the cell against mobile genetic elements either directly, via the integral histidine–aspartate (HD) nuclease domain3–5 or indirectly, via synthesis of cyclic oligoadenylate second messengers to activate diverse ancillary effectors6–9. A subset of type III CRISPR systems encode an uncharacterized CorA-family membrane protein and an associated NrN family phosphodiesterase that are predicted to function in antiviral defence. Here we demonstrate that the CorA-associated type III-B (Cmr) CRISPR system from Bacteroides fragilis provides immunity against mobile genetic elements when expressed in Escherichia coli. However, B. fragilis Cmr does not synthesize cyclic oligoadenylate species on activation, instead generating S-adenosyl methionine (SAM)-AMP (SAM is also known as AdoMet) by conjugating ATP to SAM via a phosphodiester bond. Once synthesized, SAM-AMP binds to the CorA effector, presumably leading to cell dormancy or death by disruption of the membrane integrity. SAM-AMP is degraded by CRISPR-associated phosphodiesterases or a SAM-AMP lyase, potentially providing an ‘off switch’ analogous to cyclic oligoadenylate-specific ring nucleases10. SAM-AMP thus represents a new class of second messenger for antiviral signalling, which may function in different roles in diverse cellular contexts.

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Section: Mainmentioning

confidence: 99%

Antiviral type III CRISPR signalling via conjugation of ATP and SAM

Chi,

Hoikkala,

Grüschow

et al. 2023

Nature

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“…The level of c-di-GMP is controlled by two classes of enzymes, DGCs and PDEs, for the synthesis and degradation of c-di-GMP, respectively ( 41 ). Although PDEs were also up-regulated like DGCs during the bacterial filamentation, PDEs such as PdeF can be inhibited by its catalytic product of c-di-GMP, 5′-pGpG ( 42 ), indicating that their activity is mutually balanced. In our study, c-di-GMP was accumulated during bacterial filamentation and exhibited upregulation.…”

Section: Resultsmentioning

confidence: 99%

Molecular responses during bacterial filamentation reveal inhibition methods of drug-resistant bacteria

Zhang

Yin

Qin

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Bacterial antimicrobial resistance (AMR) is among the most significant challenges to current human society. Exposing bacteria to antibiotics can activate their self-saving responses, e.g., filamentation, leading to the development of bacterial AMR. Understanding the molecular changes during the self-saving responses can reveal new inhibition methods of drug-resistant bacteria. Herein, we used an online microfluidics mass spectrometry system for real-time characterization of metabolic changes of bacteria during filamentation under the stimulus of antibiotics. Significant pathways, e.g., nucleotide metabolism and coenzyme A biosynthesis, correlated to the filamentation of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL- E. coli ) were identified. A cyclic dinucleotide, c-di-GMP, which is derived from nucleotide metabolism and reported closely related to bacterial resistance and tolerance, was observed significantly up-regulated during the bacterial filamentation. By using a chemical inhibitor, ebselen, to inhibit diguanylate cyclases which catalyzes the synthesis of c-di-GMP, the minimum inhibitory concentration of ceftriaxone against ESBL- E. coli was significantly decreased. This inhibitory effect was also verified with other ESBL- E. coli strains and other beta-lactam antibiotics, i.e., ampicillin. A mutant strain of ESBL- E. coli by knocking out the dgcM gene was used to demonstrate that the inhibition of the antibiotic resistance to beta-lactams by ebselen was mediated through the inhibition of the diguanylate cyclase DgcM and the modulation of c-di-GMP levels. Our study uncovers the molecular changes during bacterial filamentation and proposes a method to inhibit antibiotic-resistant bacteria by combining traditional antibiotics and chemical inhibitors against the enzymes involved in bacterial self-saving responses.

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“…Nor has it been determined whether different subclasses of NrnA-like proteins may exhibit different substrate preferences and cellular purposes. Interestingly, a recent study demonstrated that a DHH-DHHA1 homolog from Vibrio cholera acts specifically on GG, at the exclusion of other dinucleotides and other short RNA species ( 55 ). This important publication demonstrates proof-of-principle that certain bacteria may have evolved specialized versions of DHH-DHHA1 proteins, and that still more cellular roles for DHH-DHHA1 proteins are likely to await discovery.…”

Section: Resultsmentioning

confidence: 99%

NrnA is a 5′-3′ exonuclease that processes short RNA substrates in vivo and in vitro

Weiss

Myers

et al. 2022

Nucleic Acids Research

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Bacterial RNases process RNAs until only short oligomers (2–5 nucleotides) remain, which are then processed by one or more specialized enzymes until only nucleoside monophosphates remain. Oligoribonuclease (Orn) is an essential enzyme that acts in this capacity. However, many bacteria do not encode for Orn and instead encode for NanoRNase A (NrnA). Yet, the catalytic mechanism, cellular roles and physiologically relevant substrates have not been fully resolved for NrnA proteins. We herein utilized a common set of reaction assays to directly compare substrate preferences exhibited by NrnA-like proteins from Bacillus subtilis, Enterococcus faecalis, Streptococcus pyogenes and Mycobacterium tuberculosis. While the M. tuberculosis protein specifically cleaved cyclic di-adenosine monophosphate, the B. subtilis, E. faecalis and S. pyogenes NrnA-like proteins uniformly exhibited striking preference for short RNAs between 2–4 nucleotides in length, all of which were processed from their 5′ terminus. Correspondingly, deletion of B. subtilis nrnA led to accumulation of RNAs between 2 and 4 nucleotides in length in cellular extracts. Together, these data suggest that many Firmicutes NrnA-like proteins are likely to resemble B. subtilis NrnA to act as a housekeeping enzyme for processing of RNAs between 2 and 4 nucleotides in length.

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A pGpG-specific phosphodiesterase regulates cyclic di-GMP signaling in Vibrio cholerae

Cited by 10 publications

References 56 publications

Antiviral type III CRISPR signalling via conjugation of ATP and SAM

Antiviral type III CRISPR signalling via conjugation of ATP and SAM

Molecular responses during bacterial filamentation reveal inhibition methods of drug-resistant bacteria

NrnA is a 5′-3′ exonuclease that processes short RNA substrates in vivo and in vitro

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