scholarly journals Tailoring Escherichia coli Chemotactic Sensing towards Cadmium by Computational Redesign of Ribose-Binding Protein

mSystems ◽  
2022 ◽  
Author(s):  
Hengyi Li ◽  
Changsheng Zhang ◽  
Xi Chen ◽  
Hantian You ◽  
Luhua Lai
Keyword(s):  
Escherichia Coli ◽  
New Technologies ◽  
Binding Protein ◽  
Environmental Problems ◽  
Cadmium Ions ◽  
Cadmium Pollution ◽  
Good Biocompatibility ◽  
Ribose Binding Protein

Cadmium pollution is one of the major environmental problems due to excessive release and accumulation. New technologies that can auto-detect cadmium ions with good biocompatibility are in urgent need.

Subcellular localization defects characterize ribose-binding mutant proteins with new ligand properties in Escherichia coli

2021 ◽  
Author(s):  
Diogo Tavares ◽  
Jan R. van der Meer
Keyword(s):  
Escherichia Coli ◽  
Subcellular Localization ◽  
Ligand Binding ◽  
Binding Proteins ◽  
Binding Protein ◽  
Binding Pocket ◽  
Binding Properties ◽  
General Properties ◽  
Periplasmic Binding Proteins ◽  
Ribose Binding Protein

Periplasmic-binding proteins have been previously proclaimed as a general scaffold to design sensor proteins with new recognition specificities for non-natural compounds. Such proteins can be integrated in bacterial bioreporter chassis with hybrid chemoreceptors to produce a concentration-dependent signal after ligand binding to the sensor cell. However, computationally designed new ligand-binding properties ignore the more general properties of periplasmic binding proteins, such as their periplasmic translocation, dynamic transition of open and closed forms, and interactions with membrane receptors. In order to better understand the roles of such general properties in periplasmic signaling behaviour, we study here the subcellular localization of ribose-binding protein (RbsB) in Escherichia coli in comparison to a recently evolved set of mutants designed to bind 1,3-cyclohexanediol. As proxies for localization we calibrate and deploy C-terminal end mCherry fluorescent protein fusions. Whereas RbsB-mCherry coherently localized to the periplasmic space and accumulated in (periplasmic) polar regions depending on chemoreceptor availability, mutant RbsB-mCherry expression resulted in high fluorescence cell-to-cell variability. This resulted in higher proportions of cells devoid of clear polar foci and of cells with multiple fluorescent foci elsewhere, suggesting poorer translocation, periplasmic autoaggregation and mislocalization. Analysis of RbsB mutants and mutant libraries at different stages of directed evolution suggested overall improvement to more RbsB-wild-type-like characteristics, which was corroborated by structure predictions. Our results show that defects in periplasmic localization of mutant RbsB proteins partly explains their poor sensing performance. Future efforts should be directed to predicting or selecting secondary mutations outside computationally designed binding pockets that take folding, translocation and receptor-interactions into account. Importance Biosensor engineering relies on transcription factors or signaling proteins to provide the actual sensory functions for the target chemicals. Since for many compounds there are no natural sensory proteins, there is a general interest in methods that could unlock routes to obtaining new ligand-binding properties. Bacterial periplasmic-binding proteins (PBPs) form an interesting family of proteins to explore to this purpose, because there is a large natural variety suggesting evolutionary trajectories to bind new ligands. PBPs are conserved and amenable to accurate computational binding pocket predictions. However, studying ribose-binding protein in Escherichia coli we discovered that designed variants have defects in their proper localization in the cell, which can impair appropriate sensor signaling. This indicates that functional sensing capacity of PBPs cannot be obtained solely through computational design of the ligand-binding pocket, but must take other properties of the protein into account, which are currently very difficult to predict.

Influence of tat mutations on the ribose-binding protein translocation in Escherichia coli

2003 ◽  
Vol 306 (3) ◽  
pp. 786-791 ◽  
Author(s):  
Nathalie Pradel ◽  
Claire-Lise Santini ◽  
Chang-Yun Ye ◽  
Léna Fevat ◽  
Fabien Gérard ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Translocation ◽  
Binding Protein ◽  
Ribose Binding Protein

scholarly journals Structures of revertant signal sequences of Escherichia coli ribose binding protein

1995 ◽  
Vol 69 (6) ◽  
pp. 2703-2709 ◽  
Author(s):  
S.W. Chi ◽  
G.S. Yi ◽  
J.Y. Suh ◽  
B.S. Choi ◽  
H. Kim
Keyword(s):  
Escherichia Coli ◽  
Binding Protein ◽  
Signal Sequences ◽  
Ribose Binding Protein

scholarly journals Complete alanine scanning of the Escherichia coli RbsB ribose binding protein reveals residues important for chemoreceptor signaling and periplasmic abundance

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Artur Reimer ◽  
Vitali Maffenbeier ◽  
Manupriyam Dubey ◽  
Vladimir Sentchilo ◽  
Diogo Tavares ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Binding Protein ◽  
Alanine Scanning ◽  
Ribose Binding Protein

scholarly journals Mutations that affect the folding of ribose-binding protein selected as suppressors of a defect in export in Escherichia coli

1991 ◽  
Vol 266 (18) ◽  
pp. 11789-11796
Author(s):  
C.M. Teschke ◽  
J. Kim ◽  
T. Song ◽  
S. Park ◽  
C. Park ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Binding Protein ◽  
Ribose Binding Protein

scholarly journals The amino acid sequence of D-ribose-binding protein from Escherichia coli K12.

1983 ◽  
Vol 258 (21) ◽  
pp. 12952-12956 ◽  
Author(s):  
J M Groarke ◽  
W C Mahoney ◽  
J N Hope ◽  
C E Furlong ◽  
F T Robb ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Binding Protein ◽  
Escherichia Coli K12 ◽  
Ribose Binding Protein
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