Perception of butenolides byBacillus subtilisvia the α/β-hydrolase RsbQ DOI Open Access
Kim T. Melville, Muhammad Kamran, Jiaren Yao

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 5, 2023

Summary The regulation of behavioural and developmental decisions by small molecules is common to all domains life. In plants, strigolactones karrikins are butenolide growth regulators that influence several aspects plant development, as well interactions with symbiotic fungi 1–3 . DWARF14 (D14) KARRIKIN INSENSITIVE2 (KAI2) homologous receptors perceive karrikins, respectively, hydrolyse their ligands effect signal transduction 4–7 RsbQ, a homologue D14 KAI2 from the Gram-positive bacterium Bacillus subtilis , regulates responses nutritional stress via alternative transcription factor SigmaB (σ B ) 8,9 However, molecular function RsbQ unknown. Here we show perceives compounds bioactive in plants. thermally destabilised synthetic strigolactone GR24 its desmethyl equivalent dGR24. We that, like KAI2, functional hydrolase undergoes covalent modification catalytic histidine residue. Exogenous application both dGR24 inhibited endogenous signalling vivo being 10-fold more potent. Application B. phenocopied loss-of-function rsbQ mutations led significant down-regulation σ -regulated transcripts. also discovered exogenous butenolides promoted transition planktonic biofilm growth. Our results suggest may serve inter-kingdom between plants bacteria help shape rhizosphere communities.

Language: Английский

NrdR in Streptococcus and Listeria spp.: DNA Helix Phase Dependence of the Bacterial Ribonucleotide Reductase Repressor DOI Creative Commons
Saher Shahid, Mateusz Bałka, Daniel Lundin

et al.

Molecular Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 18, 2025

ABSTRACT NrdR is a universal transcriptional repressor of bacterial genes coding for ribonucleotide reductases (RNRs), essential enzymes that provide DNA building blocks in all living cells. Despite its prevalence, the mechanism has been scarcely studied. We report biochemical, biophysical, and bioinformatical characterization binding sites from two major pathogens phylum Bacillota Listeria monocytogenes Streptococcus pneumoniae . consists Zn‐ribbon domain followed by an ATP‐cone domain. show it forms tetramers bind to when loaded with ATP dATP, but if only ATP, various oligomeric complexes unable DNA. The DNA‐binding site L. pair boxes separated 15–16 bp, whereas S. , are unusually long spacers 25–26 bp. This observation triggered comprehensive study four NrdRs Escherichia coli Streptomyces coelicolor series dsDNA fragments where were 12–27 vitro results confirmed vivo E. revealed binds most efficiently there integer number turns between center boxes. facilitates prediction genomes suggests conserved throughout It sheds light on RNR regulation since does not occur eukaryotes, opens way development novel antibiotics.

Language: Английский

Citations

1
Identification and characterization of new proteins crucial for bacterial spore resistance and germination DOI Creative Commons
Benjamin Yu,

Julia Kanaan,

Hannah Shames

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: April 11, 2023

2Duf, named after the presence of a transmembrane (TM) Duf421 domain and small Duf1657 in its sequence, is likely located inner membrane (IM) spores some Bacillus species carrying transposon with an operon termed spoVA 2mob . These are known for their extreme resistance to wet heat, 2Duf believed be primary contributor this trait. In study, we found that absence YetF or YdfS, both domain-containing proteins only wild-type (wt) B. subtilis more abundant, leads decreased heat agents can damage spore core components. The IM phospholipid compositions water calcium-dipicolinic acid levels YetF-deficient similar those wt spores, but deficiency could restored by ectopic insertion yetF , overexpression increased heat. addition, ydfS have germination rates as individuals populations germinant receptor-dependent germinants sensitivity during germination, potentially due proteins. data consistent model which YetF, YdfS homologs modify structure reduce permeability stabilize against damage. Multiple also present other forming Bacilli Clostridia, even asporogenous Firmicutes fewer species. crystal tetramer lacking TM helices has been reported features two distinct globular subdomains each monomer. Sequence alignment prediction suggest fold shared Duf421-containing proteins, including 2Duf. We identified naturally occurring 2duf Clostridia cereus not Notably, genomic organization around gene most these suggesting one was source genes on extremely resistant formers.

Language: Английский

Citations

21
Genome mining conformance to metabolite profile of Bacillus strains to control potato pathogens DOI Creative Commons

Arezoo Lagzian,

Roohallah Saberi Riseh, Sajjad Sarikhan

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Nov. 4, 2023

Abstract Biocontrol agents are safe and effective methods for controlling plant disease pathogens, such as Fusarium solani , which causes dry wilt, Pectobacterium spp., responsible potato soft rot disease. Discovering that can effectively control both fungal bacterial pathogens in potatoes has always presented a challenge. Biological controls were investigated using 500 strains isolated from rhizospheric microbial communities, along with two promising biocontrol strains: Pseudomonas (T17-4 VUPf5). Bacillus velezensis (Q12 US1) chlororaphis VUPf5 exhibited the highest inhibition of growth pathogenicity laboratory (48%, 48%, 38%) greenhouse (100%, 85%, 90%) settings. Q12 demonstrated better against vivo (approximately 50%). Whole-genome sequencing US1 revealed genome size approximately 4.1 Mb. had 4413 gene IDs 4300 coding sequences, while 4369 4255 sequences. higher number genes classified under functional subcategories related to stress response, cell wall, capsule, levansucrase synthesis, polysaccharide metabolism. Both contained eleven secondary metabolite clusters identified by antiSMASH RAST servers. Notably, possessed antibacterial locillomycin iturin A clusters, absent US1. This genetic information suggests may have more pronounced over compared Metabolic profiling superior strains, determined LC/MS/MS, validated our findings. The produced compounds A, bacillomycin D, surfactin, fengycin, phenazine derivatives, etc. These reduced spore production caused deformation hyphae F. . In contrast, B. UR1, lacked iturin, did not affect these structures failed inhibit any pathogens. Our findings suggest contribute enhanced pectolytic Q12.

Language: Английский

Citations

9
Perception of butenolides by Bacillus subtilis via the α/β hydrolase RsbQ DOI Creative Commons
Kim T. Melville, Muhammad Kamran, Jiaren Yao

et al.

Current Biology, Journal Year: 2024, Volume and Issue: 34(3), P. 623 - 631.e6

Published: Jan. 5, 2024

Language: Английский

Citations

2
Disentangling the contributions of initial heterogeneities and dynamic stress adaptation to nonlinearities in bacterial survival curves DOI Creative Commons
Leonidas Georgalis, Kah Yen Claire Yeak,

Christina Tsimpou

et al.

Food Research International, Journal Year: 2023, Volume and Issue: 173, P. 113385 - 113385

Published: Aug. 18, 2023

The deviations from log-linearity that are often observed in bacterial survivor curves can be explained using different arguments, both biological and experimental. In this study, we used Bacillus subtilis as a model organism to demonstrate the generally accepted vitalistic arguments (initial heterogeneities stress resistance of cells population) may fail describe microbial inactivation some situations. sense, showed how dynamic acclimation during an isothermal treatment provides alternative explanation for with upwards curvature. We also provided innovative experimental approach based on preadaptation experiments evaluate which hypothesis is more suitable response. Furthermore, our results define bounds possible take place treatments, concluding magnitude larger treatments than experiments. evaluated contribution SigB general response system heat by comparing survival wt ΔsigB mutant. Both strains survived better 51, 52.5 55 °C when were pre-adapted at 48 non-pre-adapted cells. However, was less resistant due missing system. Although these conclusions B. organism, study first step towards development novel methodology able estimate effects only This would improve models developed within predictive microbiology community, improving ability predict industrial most dynamic.

Language: Английский

Citations

4
Quantitative Aspect of <em>Bacillus subtilis</em> σB Regulatory Network on a Proteome Level – a Computational Simulation DOI Open Access
Jiří Vohradský

Published: June 19, 2024

Bacillus subtilis is a model organism used to study molecular processes in Gram-positive bacteria. Sigma factor B, which associates with RNA polymerase, one of the transcriptional regulators involved cell’s response environmental stress. Experiments have proven that amounts free σB (SigB) are controlled by system anti- (RsbW) and anti-anti-sigma (RsbV) factors expressed from same operon as SigB. Moreover, phosphorylation state RsbV phosphatases RsbP RsbU, directly dephosphorylates RsbV. A set chemical equations describing network controlling levels SigB was converted differential quantifying dynamics network. The solution these allowed simulation kinetic behavior its components under real conditions. In this study, time series protein expression measured mass spectrometry were utilized investigate role RsbU/RsbP transmitting signal. Additionally, influence constants other on functioning investigated. comparison performed using transcriptomic dataset showed while between proteomic datasets) not correlated, results same. This indicates when modeling done within dataset, it does matter whether data come mRNA or level. summary, computational based experimental provide quantitative insight into SigB-dependent circuit offer template for similar systems.

Language: Английский

Citations

1
Functional characterization and mechanism of the multidrug resistance transport potein YoeA in Bacillus subtilis DOI

Mengxi Wang,

Wenqing Li,

Siwei Li

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: 291, P. 139115 - 139115

Published: Dec. 23, 2024

Language: Английский

Citations

1
Insights into effects of salt stress on the oil-degradation capacity, cell response, and key metabolic pathways of Bacillus sp. YM1 isolated from oily food waste compost DOI
Xia Zhang, Muhammad Khalid,

Saiqa Menhas

et al.

Chemosphere, Journal Year: 2023, Volume and Issue: 341, P. 140092 - 140092

Published: Sept. 5, 2023

Language: Английский

Citations

3
8-OxoG-Dependent Regulation of Global Protein Responses Leads to Mutagenesis and Stress Survival in Bacillus subtilis DOI Creative Commons
Lissett E. Martínez,

Gerardo Gómez,

Norma Ramírez Ramírez

et al.

Antioxidants, Journal Year: 2024, Volume and Issue: 13(3), P. 332 - 332

Published: March 8, 2024

The guanine oxidized (GO) system of Bacillus subtilis, composed the YtkD (MutT), MutM and MutY proteins, counteracts cytotoxic genotoxic effects nucleobase 8-OxoG. Here, we report that in growing B. subtilis cells, genetic inactivation GO potentiated mutagenesis (HPM), subsequent hyperresistance, contributes to damaging hydrogen peroxide (H2O2) (HPHR). mechanism(s) connect accumulation mutagenic lesion 8-OxoG with ability evolve survive noxious oxidative stress were dissected. Genetic biochemical evidence indicated synthesis KatA was exacerbated, a PerR-independent manner, transcriptional coupling repair factor, Mfd, contributed HPHR HPM ΔGO strain. Moreover, these phenotypes are associated wider pleiotropic effects, as revealed by global proteome analysis. results upregulated production KatA, it reprograms proteins involved distinct types cellular stress; this has direct impact on (i) cysteine catabolism, (ii) iron–sulfur clusters, (iii) reorganization cell wall architecture, (iv) activation AhpC/AhpF-independent organic resistance, (v) increased resistance transcription-acting antibiotics. Therefore, contend derived from 8-OxoG, activates belonging regulons respond wide, diverse range stressors.

Language: Английский

Citations

0
Strong conservation of spacer lengths in NrdR repressor DNA binding sites DOI Creative Commons
Saher Shahid, Mateusz Bałka, Daniel Lundin

et al.

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

Published: May 27, 2024

Abstract The ribonucleotide reductase-specific repressor NrdR, from the human pathogens Listeria monocytogenes and Streptococcus pneumoniae , form tetramers that bind to DNA when loaded with dATP ATP. If only ATP they different oligomeric complexes cannot DNA. binding site in L. is a pair of NrdR boxes separated by 15-16 bp, whereas are 25-26 bp. However, binds stronger related thermophilus sites This observation triggered comprehensive study four NrdRs monocytogenes, pneumoniae, Escherichia coli Streptomyces coelicolor series synthetic dsDNA fragments where were 12-27 All bound well 14-17 also 24-27 worst occurred 20 vitro results confirmed vivo E. for spacer distances We conclude repressors most efficiently there an integer number turns between center two boxes.

Language: Английский

Citations

0