Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone allosterically mediates substrate binding to the active site DOI Open Access
Ornella Bimaï, Ipsita A. Banerjee, Inna Rozman Grinberg

et al.

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

Published: June 20, 2023

Abstract A small, nucleotide-binding domain, the ATP-cone, is found at N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding ATP or dATP it regulates enzyme activity all classes RNR. Functional and structural work on aerobic RNRs has revealed a plethora ways in which inhibits by inducing oligomerization preventing productive radical transfer from one subunit to active site other. Anaerobic RNRs, other hand, store stable glycyl next basis for their dATP-dependent inhibition completely unknown. We present biochemical, biophysical information effects anaerobic RNR Prevotella copri . The exists dimer-tetramer equilibrium biased towards dimers when two molecules are bound ATP-cone tetramers bound. In presence ATP, P. NrdD fully ordered domain (GRD) monomer dimer. Binding results loss increased dynamics GRD, such that can not be detected cryo-EM structures. formed even dATP-bound form, but substrate does bind. structures implicate complex network interactions regulation involve GRD more than 30 Å away molecules, allosteric specificity conserved previously unseen flap over site. Taken together, suggest acts increasing flexibility thereby both mobilisation.

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
How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase DOI Creative Commons
Michael A. Funk, Christina M. Zimanyi, Gisele A. Andree

et al.

Biochemistry, Journal Year: 2024, Volume and Issue: 63(19), P. 2517 - 2531

Published: Aug. 20, 2024

Class Ia ribonucleotide reductases (RNRs) are allosterically regulated by ATP and dATP to maintain the appropriate deoxyribonucleotide levels inside cell for DNA biosynthesis repair. RNR activity requires precise positioning of β

Language: Английский

Citations

6
Bacterial transcriptional repressor NrdR – a flexible multifactorial nucleotide sensor DOI Creative Commons
Inna Rozman Grinberg, Ornella Bimaï, Saher Shahid

et al.

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

Published: March 3, 2025

NrdR is a bacterial transcriptional repressor consisting of zinc (Zn)‐ribbon domain followed by an ATP‐cone domain. Understanding its mechanism action could aid the design novel antibacterials. binds specifically to two “NrdR boxes” upstream ribonucleotide reductase operons, which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, in last we identified new box. We show that E. (EcoNrdR) similar binding strength all three sites when loaded with ATP plus deoxyadenosine triphosphate (dATP) or equivalent diphosphate combinations. No other combination adenine nucleotides promotes DNA. present crystal structures EcoNrdR–ATP–dATP EcoNrdR–ADP–dATP, are first high‐resolution NrdR. have also determined cryo‐electron microscopy DNA‐bound filaments EcoNrdR–ATP. Tetrameric forms EcoNrdR involve alternating interactions between pairs Zn‐ribbon domains ATP‐cones. The reveal considerable flexibility relative orientation ATP‐cones vs domains. structure shows significant conformational rearrangements Zn‐ribbons accompany DNA while retain same orientation. In contrast, ATP‐loaded sequester DNA‐binding residues such they unable bind Our results, previous structural biochemical study, point highly flexible that, correct nucleotides, adapt optimal promoter‐binding conformation.

Language: Английский

Citations

0
Structural insights into CDF1 accumulation on the CONSTANS promoter via a plant-specific DNA-binding domain DOI
Hirotake Furihata, Zhangliang Zhu,

Kaisei Nishida

et al.

Nature Plants, Journal Year: 2025, Volume and Issue: 11(4), P. 836 - 848

Published: April 22, 2025

Language: Английский

Citations

0
Bacterial transcriptional repressor NrdR - a flexible multifactorial nucleotide sensor DOI Creative Commons
Inna Rozman Grinberg, Ornella Bimaï, Saher Shahid

et al.

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

Published: Sept. 8, 2024

Abstract NrdR is a bacterial transcriptional repressor consisting of Zn-ribbon domain followed by an ATP-cone domain. Understanding its mechanism action could aid the design novel antibacterials. binds specifically to two “NrdR boxes” upstream ribonucleotide reductase operons, which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, where we identified new box. We show that E. (EcoNrdR) similar binding strength all three sites when loaded with ATP plus dATP or equivalent diphosphate combinations. No other combination nucleotides promotes DNA. present crystal structures EcoNrdR-ATP-dATP EcoNrdR-ADP-dATP, are first high-resolution NrdR. have also determined cryo-EM DNA-bound filaments EcoNrdR-ATP. Tetrameric forms EcoNrdR involve alternating interactions between pairs domains ATP-cones. The reveal considerable flexibility in relative orientation ATP-cones vs domains. structure shows significant conformational rearrangements Zn-ribbons accompany DNA while retain same orientation. In contrast, ATP-loaded sequester DNA-binding residues such they unable bind Our results, previous structural biochemical study, point highly flexible correct adapt optimal promoter conformation.

Language: Английский

Citations

2
Cyanophage-encoded auxiliary metabolic genes in modulating cyanobacterial metabolism and algal bloom dynamics DOI Creative Commons

Quratul Ain,

Kevin Wu, Xuan Wu

et al.

Frontiers in Virology, Journal Year: 2024, Volume and Issue: 4

Published: Oct. 1, 2024

Cyanophages play a pivotal role in controlling cyanobacterial populations aquatic environments. These dsDNA viruses harbor auxiliary metabolic genes (AMGs) that modulate the key processes of their hosts, such as Photosynthesis, nutrient uptake for optimization viral replication. Recently, pan1~pan5 and pam1~pam5 cyanophages have been isolated from fifth largest water resource China; Lake Chaohu. Detailed genomic analysis these phages revealed especially Pan1, Pam2 Pam3 possess unique AMGs significantly enhance activities potentially leading to suppression bloom formation stabilization ecological dynamics Our findings provide concrete evidence encoding could serve effective biocontrol agents against harmful algal blooms, offering targeted approach manage environmental threats. The integration cyanophage-based management therapies with traditional methods advance efficiency sustainability outbreaks, paving way novel applications management. This review emphasizes importance critical need further exploration phage-host fully harness potential ecosystem regulation.

Language: Английский

Citations

2
Pooled CRISPR Interference Screening Identifies Crucial Transcription Factors in Gas-Fermenting Clostridium ljungdahlii DOI
Huan Zhang, Huibao Feng,

Xin‐Hui Xing

et al.

ACS Synthetic Biology, Journal Year: 2024, Volume and Issue: 13(6), P. 1893 - 1905

Published: June 3, 2024

Gas-fermenting Clostridium species hold tremendous promise for one-carbon biomanufacturing. To unlock their full potential, it is crucial to unravel and optimize the intricate regulatory networks that govern these organisms; however, this aspect currently underexplored. In study, we employed pooled CRISPR interference (CRISPRi) screening uncover a wide range of functional transcription factors (TFs) in ljungdahlii, representative gas-fermenting Clostridium, with special focus on TFs associated utilization carbon resources. Among 425 TF candidates, identified 75 68 genes affecting heterotrophic autotrophic growth C. respectively. We focused our attention two screened TFs, NrdR DeoR, revealed pivotal roles regulation deoxyribonucleoside triphosphates (dNTPs) supply, fixation, product synthesis thereby influencing strain performance gas fermentation. Based this, proceeded expression deoR ljungdahlii by adjusting its promoter strength, leading an improved rate ethanol when utilizing syngas. This study highlights effectiveness CRISPRi species, expanding horizons genomic research industrially important bacteria.

Language: Английский

Citations

1
Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site DOI Open Access
Ornella Bimaï, Ipsita A. Banerjee, Inna Rozman Grinberg

et al.

Published: Aug. 16, 2023

A small, nucleotide-binding domain, the ATP-cone, is found at N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding ATP or dATP it regulates enzyme activity all classes RNR. Functional and structural work on aerobic RNRs has revealed a plethora ways in which inhibits by inducing oligomerization preventing productive radical transfer from one subunit to active site other. Anaerobic RNRs, other hand, store stable glycyl next basis for their dATP-dependent inhibition completely unknown. We present biochemical, biophysical information effects anaerobic RNR Prevotella copri . The exists dimer-tetramer equilibrium biased towards dimers when two molecules are bound tetramers bound. In presence ATP, P. NrdD fully ordered domain (GRD) monomer dimer. Binding ATP-cone results loss disordering GRD. formed even dATP-bound form, but substrate does not bind, suggesting that acts GRD more than 30 Å away molecule, thereby both mobilisation. structures implicate complex network regulation involving GRD, allosteric specificity conserved previously unseen flap over site.

Language: Английский

Citations

1
Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding DOI Creative Commons
Ornella Bimaï, Ipsita A. Banerjee, Inna Rozman Grinberg

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Aug. 16, 2023

A small, nucleotide-binding domain, the ATP-cone, is found at N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine (dATP) it regulates enzyme activity all classes RNR. Functional and structural work on aerobic RNRs has revealed a plethora ways in which dATP inhibits by inducing oligomerisation preventing productive radical transfer from one subunit to active site other. Anaerobic RNRs, other hand, store stable glycyl next basis for their dATP-dependent inhibition completely unknown. We present biochemical, biophysical, information effects ATP anaerobic RNR Prevotella copri. The exists dimer-tetramer equilibrium biased towards dimers when two molecules are bound ATP-cone tetramers bound. In presence ATP, P. copri NrdD fully ordered domain (GRD) monomer dimer. Binding results loss increased dynamics GRD, such that cannot be detected cryo-EM structures. formed even dATP-bound form, but substrate does not bind. structures implicate complex network interactions regulation involve GRD more than 30 Å away molecules, allosteric specificity conserved previously unseen flap over site. Taken together, suggest acts increasing flexibility thereby both mobilisation.

Language: Английский

Citations

1
Pooled CRISPR interference screening identifies crucial transcription factors in gas-fermentingClostridium ljungdahlii DOI Open Access
Huan Zhang, Huibao Feng,

Xin‐Hui Xing

et al.

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

Published: Feb. 20, 2024

Abstract Gas-fermenting Clostridium species hold tremendous promise for one-carbon biomanufacturing. To unlock their full potential, it is crucial to unravel and optimize the intricate regulatory networks that govern these organisms; however, this aspect currently underexplored. In study, we employed pooled CRISPR interference (CRISPRi) screening uncover a wide range of functional transcription factors (TFs) in ljungdahlii , representative gas-fermenting with special focus on TFs associated utilization carbon resources. Among 425 TF candidates, identified 75 68 genes affecting heterotrophic autotrophic growth C. respectively. We directed our attention two screened TFs, NrdR DeoR, revealed pivotal roles regulation deoxyribonucleotides (dNTPs) supply, fixation, product synthesis thereby influencing strain performance gas fermentation. Based this, proceeded expression deoR by adjusting its promoter strength, leading improved rate ethanol when utilizing syngas. This study highlights effectiveness CRISPRi species, expanding horizons genomic research industrially important bacteria.

Language: Английский

Citations

0