ComFB, a new widespread family of c-di-NMP receptor proteins DOI Creative Commons

Sherihan Samir,

Abdalla A. Elshereef, Vikram Alva

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 10, 2024

ABSTRACT Cyclic dimeric GMP (c-di-GMP) is a widespread bacterial second messenger that controls variety of cellular functions, including protein and polysaccharide secretion, motility, cell division, development, biofilm formation, contributes to the virulence some important pathogens. While genes for diguanylate cyclases c-di-GMP hydrolases (active or mutated) can be easily identified in microbial genomes, list receptor domains quite limited, only two them, PliZ MshEN, are found across multiple phyla. Recently, new protein, named CdgR ComFB, has been cyanobacteria shown regulate their size and, more recently, natural competence. Sequence structural analysis indicated part ComFB family, after “late competence development ComFB” from Bacillus subtilis . This prompted suggestion ComFB-like proteins could also receptors. Indeed, we revealed Gram-positive B. Thermoanaerobacter brockii were able bind with high-affinity. The ability was demonstrated clinically relevant Gram-negative bacteria Vibrio cholerae Treponema denticola These observations indicate family serves as yet another Incidentally, capable c-di-AMP binding, identifying them unique c-di-NMP proteins. overexpression comFB subtilis, combined an elevated concentration c-di-GMP, suppressed attesting biological relevance binding protein. IMPORTANCE content controlled by synthases (GGDEF domains) (EAL HD-GYP domains), whose activities, turn, respond signals perceived upstream sensory domains. Cyclic-di-GMP transmits its targets, which may contain inactivated GGDEF, EAL, domains, PilZ MshEN various lineage-specific Many organisms encode GGDEF but few c-di-GMP-binding proteins, suggesting existence still unidentified Here, demonstrate include recently characterized cyanobacterial CdgR/ComFB, constitute We additionally show bacillar motility c-di-GMP-dependent manner.

Language: Английский

Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins DOI Creative Commons
Shai Zilberzwige‐Tal, Han Altae-Tran, Soumya Kannan

et al.

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

3
COG database update 2024 DOI Creative Commons
Michael Y. Galperin, Roberto Vera Alvarez, Svetlana Karamycheva

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D356 - D363

Published: Nov. 4, 2024

The Clusters of Orthologous Genes (COG) database, originally created in 1997, has been updated to reflect the constantly growing collection completely sequenced prokaryotic genomes. This update increased genome coverage from 1309 2296 species, including 2103 bacteria and 193 archaea, most cases, with a single representative per genus. set covers all genera archaea that included organisms 'complete genomes' as NCBI databases November 2023. number COGs expanded 4877 4981, primarily by protein families involved bacterial secretion. Accordingly, COG pathways functional groups now include secretion systems types II through X, well Flp/Tad type IV pili. These groupings allow straightforward identification examination lineages encompass-or lack-a particular system. Other developments improved annotations for rRNA tRNA modification proteins, multi-domain signal transduction some previously uncharacterized families. new version is available at https://www.ncbi.nlm.nih.gov/research/COG, on FTP site https://ftp.ncbi.nlm.nih.gov/pub/COG/, which also provides archived data previous releases.

Language: Английский

Citations

7
Bacterial cell volume regulation and the importance of cyclic di-AMP DOI
Alexander J. Foster, Marco van den Noort, Bert Poolman

et al.

Microbiology and Molecular Biology Reviews, Journal Year: 2024, Volume and Issue: 88(2)

Published: June 10, 2024

SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most their functionality is associated with general lifestyle and metabolic adaptations, often response to environmental fluctuations physical parameters. the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide many prokaryotic lineages, including Firmicutes, Actinobacteria, Cyanobacteria. Its importance highlighted by fact that both lack overproduction affect viability prokaryotes utilize di-AMP, it generates a strong innate immune eukaryotes. bacteria produce messenger, molecular targets cell volume control. Besides, other evidence links messenger wall remodeling, DNA damage repair, sporulation, central metabolism, regulation glycogen turnover. this review, we take biochemical, quantitative approach address main cellular processes directly regulated show these very connected require similar set proteins which binds. Altogether, argue master regulator can be through core function. We further highlight directions field develop gain full understanding network why some regulated, while others not.

Language: Английский

Citations

5
Cyclic-di-AMP hydrolase GdpP is critical for stress response of Lactiplantibacillus plantarum WCFS1 DOI

Zhaoqing Yu,

Zhuqing Dai, Xinyi Pang

et al.

Food Bioscience, Journal Year: 2025, Volume and Issue: 64, P. 105883 - 105883

Published: Jan. 10, 2025

Language: Английский

Citations

0
Bioinformatics Analysis of Diadenylate Cyclase Regulation on Cyclic Diadenosine Monophosphate Biosynthesis in Exopolysaccharide Production by Leuconostoc mesenteroides DRP105 DOI Creative Commons

Wenna Yu,

Liansheng Yu,

Tao Li

et al.

Fermentation, Journal Year: 2025, Volume and Issue: 11(4), P. 196 - 196

Published: April 7, 2025

Lactic acid bacteria exopolysaccharides (EPS) have a variety of excellent biological functions and are widely used in the food pharmaceutical industries. The complex metabolic system lactic mechanism EPS biosynthesis not been fully analyzed, which limits wider application EPS. synthesis is regulated by cyclic diadenosine monophosphate (c-di-AMP), but exact remains unclear. Dac pde c-di-AMP anabolic genes, gtfA, gtfB gtfC gene clusters, among was key for Leuconostoc mesenteroides DRP105. In order to explore whether diadenylate cyclase (DAC) can catalyze from ATP, sequence DAC analyzed bioinformatics based on whole genome sequence. CdaA type containing classical domain DisA_N DGA RHR motifs. secondary structure mainly composed α-helices, AlphaFold2 model 3D protein evaluate rationality model. A total 8 salt bridges, 21 hydrogen bonds 221 non-bonded interactions were found between GtfC. Molecular docking simulations revealed ATP1 ATP2 occupied binding pocket interacted directly with site residues DAC. molecular dynamics showed that ATP molecules relatively stable. Gene enzyme correlation analysis dac expression significantly positively correlated activity, content production, had no significant PDE activity responsible degradation. Bioinformatics regulatory role helpful reveal biosynthetic provide theoretical basis large-scale industrial production

Language: Английский

Citations

0
The Bacterial Second Messenger Cyclic di-AMP and Inflammation DOI
Tiffany M. Zarrella, Guangchun Bai

Inflammation, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 17

Published: Jan. 1, 2025

Language: Английский

Citations

0
The many roles of cyclic di-AMP to control the physiology of Bacillus subtilis DOI Creative Commons
Christina Herzberg,

Janek Meißner,

Robert Warneke

et al.

microLife, Journal Year: 2023, Volume and Issue: 4

Published: Jan. 1, 2023

Abstract The dinucleotide cyclic di-AMP (c-di-AMP) is synthesized as a second messenger in the Gram-positive model bacterium Bacillus subtilis well many bacteria and archaea. possesses three diadenylate cyclases two phosphodiesterases that synthesize degrade molecule, respectively. Among messengers, c-di-AMP unique since it essential for B. on one hand but toxic upon accumulation other. This role an “essential poison” related to function of control potassium homeostasis. C-di-AMP inhibits expression activity uptake systems by binding riboswitches transporters activates exporters. In this way, allows adjustment export achieve balanced intracellular concentration. also binds dedicated signal transduction proteins, DarA DarB. Both proteins seem interact with other their apo state, i.e. absence c-di-AMP. For DarB, (p)ppGpp synthetase/hydrolase Rel pyruvate carboxylase PycA have been identified targets. interactions trigger synthesis alarmone acceptor molecule citric acid cycle, oxaloacetate, c-di-AMP, amino acids inhibit growth subtilis. feature can be used identify novel players review, we discuss different functions physiological relevance.

Language: Английский

Citations

7
Bacterial second messenger cyclic di‐AMP in streptococci DOI Open Access
Michael Wright, Guangchun Bai

Molecular Microbiology, Journal Year: 2023, Volume and Issue: 120(6), P. 791 - 804

Published: Oct. 28, 2023

Abstract Cyclic dimeric adenosine monophosphate (c‐di‐AMP) has been well studied in bacteria, including those of the genus Streptococcus , since first recognition this dinucleotide 2008. Streptococci possess a sole diadenylate cyclase, CdaA, and distinct c‐di‐AMP phosphodiesterases. Interestingly, cdaA is required for viability some streptococcal species but not all when streptococci are grown standard laboratory media. Bacteria also have effector proteins, diverse c‐di‐AMP‐signaling pathways, subsequent biological outcomes. In streptococci, may influence bacterial growth, morphology, biofilm formation, competence program, drug resistance, pathogenesis. secreted by shown to interact with mammalian host induces immune responses type I interferon production. review, we summarize reported networks seven which cause clinical manifestations, propose future perspectives investigate signaling molecule these pathogens.

Language: Английский

Citations

4
Characterization of c‐di‐AMP signaling in the periodontal pathobiont, Treponema denticola DOI Creative Commons

Aidan D. Moylan,

Dhara T. Patel, Claire O’Brien

et al.

Molecular Oral Microbiology, Journal Year: 2024, Volume and Issue: 39(5), P. 354 - 367

Published: March 4, 2024

Pathobionts associated with periodontitis, such as Treponema denticola, must possess numerous sensory transduction systems to adapt the highly dynamic subgingival environment. To date, signaling pathways utilized by T. denticola rapidly sense and respond environmental stimuli are mainly unknown. Bis-(3'-5') cyclic diadenosine monophosphate (c-di-AMP) is a nucleotide secondary messenger that regulates osmolyte transport, central metabolism, biofilm development, pathogenicity in many bacteria but uncharacterized denticola. Here, we studied c-di-AMP understand how it contributes physiology. We demonstrated produces identified enzymes function synthesis (TDE1909) hydrolysis (TDE0027) of c-di-AMP. investigate may impact cellular processes, screening assay was performed identify putative receptor proteins. This approach TDE0087, annotated potassium uptake protein, first binding protein. As homeostasis critical for maintaining turgor pressure, concentrations impacted osmolarity, suggesting negatively hypoosmotic solutions. Collectively, this study demonstrates utilizes signaling, identifies metabolism proteins, correlates osmoregulation.

Language: Английский

Citations

1
c-di-AMP accumulation impairs toxin expression of Bacillus anthracis by down-regulating potassium importers DOI Creative Commons
Jia Hu,

Junmin Yao,

Chengfeng Lei

et al.

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: 12(8)

Published: June 20, 2024

ABSTRACT The Gram-positive bacterium Bacillus anthracis is the causative agent of anthrax and a bioterrorism threat worldwide. As crucial second messenger in many bacterial species, cyclic di-AMP (c-di-AMP) modulates various key processes for homeostasis pathogenesis. Overaccumulation c-di-AMP alters cellular growth reduces toxin expression as well virulence by unresolved underlying mechanisms. In this report, we discovered that binds to series receptors involved potassium uptake B. . By analyzing Kdp Ktr mutants osmotic stress, gene expression, also showed inhibits operon through binding KdpD ydaO riboswitch; up-regulating intracellular promotes accumulated Decreased at high occurs inhibition uptake. Understanding molecular basis how affects has potential provide new insight into control anthracis. IMPORTANCE conserved global regulator homeostasis. How regulates unknown. With study, link between accumulation might inhibit suppressing

Language: Английский

Citations

1