Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation DOI Creative Commons
Takayuki Ohnuma,

Jun Tsujii,

Chikara Kataoka

et al.

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

Published: Nov. 23, 2023

Abstract Periplasmic solute-binding proteins (SBPs) specific for chitooligosaccharides, (GlcNAc) n (n = 2, 3, 4, 5 and 6), are involved in the uptake of chitinous nutrients negative control chitin signal transduction Vibrios . Most translocation processes by SBPs across inner membrane have been explained thus far two-domain open/closed mechanism. Here we propose three-domain mechanism based on experiments using a recombinant Vc CBP, SBP from Vibrio cholerae X-ray crystal structures unliganded or 3 -liganded CBP solved at 1.2–1.6 Å revealed three distinct domains, Upper1, Upper2 Lower domains this protein. Molecular dynamics simulation indicated that motions independent state Upper2/Lower interface fluctuated more intensively, compared to Upper1/Lower interface. The bound two GlcNAc residues tightly, while appeared loosen release sugar molecule. proposed here was fully supported binding data obtained thermal unfolding ITC, may be applicable other systems involving belonging same cluster.

Language: Английский

A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus DOI Creative Commons
Yasuhiro Oda, William Nelson, William G. Alexander

et al.

Applied and Environmental Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: March 10, 2025

ABSTRACT Rhodopseudomonas are a group of phototrophic microbes with marked metabolic versatility and flexibility that underpins their potential use in the production value-added products, bioremediation, plant growth promotion. Members this have an average genome size about 5.5 Mb, but two closely related strains sizes 4.0 Mb. To identify types genes missing reduced strain, we compared strain DSM127 other isolates at genomic phenotypic levels. We found can grow as well members genus retains most versatility, it has many fewer associated high-affinity transport nutrients, iron uptake, nitrogen metabolism, biodegradation aromatic compounds. This analysis indicates be deleted reduction campaigns suggests could favorable choice for biotechnology applications using or engineered further to reside specialized natural environment. IMPORTANCE cohort bacteria broad versatility. present diverse soil water environments, some plants growth-promoting activity. Motivated by idea may possible design genomes survive only specific environment more metabolically efficient, typical Mb From this, concluded is part identity group, apparent redundant function dispensed with.

Language: Английский

Citations

0
Sensing preferences for prokaryotic solute binding protein families DOI Creative Commons
Jean Paul Cerna‐Vargas, Beatriz Sánchez‐Romera, Miguel A. Matilla

et al.

Microbial Biotechnology, Journal Year: 2023, Volume and Issue: 16(9), P. 1823 - 1833

Published: Aug. 7, 2023

Solute binding proteins (SBPs) are of central physiological relevance for prokaryotes. These present substrates to transporters, but they also stimulate different signal transduction receptors. SBPs form a superfamily at least 33 protein Pfam families. To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all three-dimensional structures deposited in data bank retrieved 748 prokaryotic that been solved complex with bound ligand. were classified into 26 The analysis ligands recognized revealed most families possess preference compound class. There three each bind preferentially saccharides amino acids. In addition, identified purines, quaternary amines, iron iron-chelating compounds, oxoanions, bivalent metal ions or phosphates. Phylogenetic analyses suggest convergent evolutionary events lead same functional link chemotaxis uptake is reflected similarities by chemoreceptors. Associating profiles will be help design experimental strategies aimed identification uncharacterized SBPs.

Language: Английский

Citations

10
Exploring solute binding proteins in Pseudomonas aeruginosa that bind to γ‐aminobutyrate and 5‐aminovalerate and their role in activating sensor kinases DOI Creative Commons
Jean Paul Cerna‐Vargas, Tino Krell

MicrobiologyOpen, Journal Year: 2024, Volume and Issue: 13(3)

Published: May 23, 2024

The standard method of receptor activation involves the binding signals or signal-loaded solute proteins (SBPs) to sensor domains. Many histidine kinases (SHKs), which are activated by SBP binding, encoded adjacent their corresponding sbp gene. We examined three SBPs Pseudomonas aeruginosa PAO1, near genes for AgtS (PA0600) and AruS (PA4982) SHKs, determine how common this arrangement is. Ligand screening microcalorimetric studies revealed that PA0602 PA4985 preferentially bind GABA (KD = 2.3 0.58 μM, respectively), followed 5-aminovalerate 30 1.6 respectively) ethanoldiamine respectively). In contrast, AgtB (PA0604) exclusively recognizes 5-aminovaleric acid 2.9 μM). However, titrations did not show any between domain PA0602, regardless presence ligands. Similarly, bacterial two-hybrid assays demonstrate an interaction domain. Therefore, shk located nearby always functionally linked. previously identified PA0222 as a GABA-specific SBP. may be linked GABA's role trigger P. virulence.

Language: Английский

Citations

1
Molecular mechanism underlying high-affinity terephthalate binding and conformational change of TBP from Ideonella sakaiensis DOI
Seul Hoo Lee, Hogyun Seo, Hwaseok Hong

et al.

International Journal of Biological Macromolecules, Journal Year: 2023, Volume and Issue: 243, P. 125252 - 125252

Published: June 7, 2023

Language: Английский

Citations

3
The Cellular Abundance of Chemoreceptors, Chemosensory Signaling Proteins, Sensor Histidine Kinases, and Solute Binding Proteins of Pseudomonas aeruginosa Provides Insight into Sensory Preferences and Signaling Mechanisms DOI Open Access
Miguel A. Matilla, Roberta Genova, David Martín‐Mora

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(2), P. 1363 - 1363

Published: Jan. 10, 2023

Chemosensory pathways and two-component systems are important bacterial signal transduction systems. In the human pathogen Pseudomonas aeruginosa, these control many virulence traits. Previous studies showed that inorganic phosphate (Pi) deficiency induces virulence. We report here abundance of chemosensory signaling proteins P. aeruginosa grown in Pi deficient sufficient media. The cellular chemoreceptors differed greatly, since a 2400-fold difference between most least abundant receptors was observed. For chemoreceptors, their amount varied with growth condition. did not correlate magnitude chemotaxis to cognate chemoeffectors. Of four pathways, Che pathway were little variation different conditions. solute binding indicates sensing preference for amino acids polyamines. There an excess response regulators over sensor histidine kinases contrast, ratios CheY CheB kinase CheA all below 1, indicative mechanisms. This study will serve as reference exploring preferences mechanisms other bacteria.

Language: Английский

Citations

2
Characterization of the l-arabinofuranose-specific GafABCD ABC transporter essential for l-arabinose-dependent growth of the lignocellulose-degrading bacterium Shewanella sp. ANA-3 DOI

Konstantinos Drousiotis,

Reyme Herman,

Judith A. Hawkhead

et al.

Microbiology, Journal Year: 2023, Volume and Issue: 169(3)

Published: March 15, 2023

Microbes that have evolved to live on lignocellulosic biomass face unique challenges in the effective and efficient use of this material as food. The bacterium Shewanella sp. ANA-3 has potential utilize arabinan arabinoxylan, uptake monosaccharide, l -arabinose, derived from these polymers, is known be mediated by a single ABC transporter. We demonstrate substrate binding protein system, GafA Sw , binds specifically -arabinofuranose, which rare furanose form -arabinose found biomass. structure was resolved 1.7 Å comparison Escherichia coli YtfQ (GafA Ec ) revealed site adaptations confer specificity for over pyranose forms monosaccharides, while selecting arabinose another related galactose. discovery with natural predilection sugar abundantly certain materials suggests an intimate connection enzymatic release sugar, perhaps prevent other microbes scavenging nutrient before it mutarotates -arabinopyranose. This biological also provides clear route engineer more utilization plant components industrial biotechnology.

Language: Английский

Citations

1
Unraveling the full impact of SPD_0739: a key effector in S. pneumoniae iron homeostasis DOI Creative Commons
Edroyal Womack,

Melina Antone,

Zehava Eichenbaum

et al.

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 29, 2024

ABSTRACT Streptococcus pneumoniae is a common member of the nasopharynx commensal microflora and leading etiological agent bacterial pneumonia in young children aging adults. SPD_0739, highly expressed lipoprotein, predicted substrate-binding component an ABC transporter linked to uptake nucleosides heme by independent studies (named PnrA or Spbhp-37, respectively). Here, we demonstrate that SPD_0739 binds vitro contributes binding hemoglobin. A ∆ spd_0739 strain exhibited growth attenuation was relieved inactivation piuBCDA transporter. Knocking out wild type, Δ resulted accumulation, higher sensitivity toxicity, small reduction compared medium supplemented with nucleoside mixture. In addition, loss results iron- heme-related gene expression lower H 2 O production. Altogether, data are consistent role import show does not heme. Instead, it indirectly influences iron metabolism, linking status S. e. IMPORTANCE obtains essential from hemoglobin other host hemoproteins. Still, mechanisms involved only partially understood, there inconsistent reports regarding function several transporters implicated uptake. this study, clarified PnrA/Spbhp-37, ligand-binding protein previously different studies. We present supporting scavenging rather than reveal PnrA/Spbhp-37 modulates uptake, likely influencing cellular pool. Hence, work provides new understanding process critical pathophysiology significant human pathogen. Moreover, abundant immunogenic surface conserved. study also clarifies promising vaccine target.

Language: Английский

Citations

0
Characterization of the involvement of the plant cell wall and its derived compounds in the virulence of Dickeya dadantii 3937 DOI Creative Commons

Clara Gálvez Roldán

Published: March 6, 2023

Citation Gálvez Roldán, Clara (2023). Characterization of the involvement plant cell wall and its derived compounds in virulence Dickeya dadantii 3937. Thesis (Doctoral), E.T.S. de Ingeniería Agronómica, Alimentaria y Biosistemas (UPM). https://doi.org/10.20868/UPM.thesis.73540.

Language: Английский

Citations

0
Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation DOI Creative Commons
Takayuki Ohnuma,

Jun Tsujii,

Chikara Kataoka

et al.

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

Published: Nov. 23, 2023

Abstract Periplasmic solute-binding proteins (SBPs) specific for chitooligosaccharides, (GlcNAc) n (n = 2, 3, 4, 5 and 6), are involved in the uptake of chitinous nutrients negative control chitin signal transduction Vibrios . Most translocation processes by SBPs across inner membrane have been explained thus far two-domain open/closed mechanism. Here we propose three-domain mechanism based on experiments using a recombinant Vc CBP, SBP from Vibrio cholerae X-ray crystal structures unliganded or 3 -liganded CBP solved at 1.2–1.6 Å revealed three distinct domains, Upper1, Upper2 Lower domains this protein. Molecular dynamics simulation indicated that motions independent state Upper2/Lower interface fluctuated more intensively, compared to Upper1/Lower interface. The bound two GlcNAc residues tightly, while appeared loosen release sugar molecule. proposed here was fully supported binding data obtained thermal unfolding ITC, may be applicable other systems involving belonging same cluster.

Language: Английский

Citations

0