scholarly journals SynBio and the Boundaries between Functional and Pathogenic RepA-WH1 Bacterial Amyloids

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Rafael Giraldo
Keyword(s):  
Dna Replication ◽  
Synthetic Biology ◽  
Protein Engineering ◽  
Biofilm Formation ◽  
Protein Domain ◽  
Bacterial Plasmids ◽  
Allosteric Effectors ◽  
Amyloidogenic Protein ◽  
Functional States ◽  
Whole Tree

ABSTRACT Amyloids are protein polymers that were initially linked to human diseases. Across the whole Tree of Life, many disease-unrelated proteins are now emerging for which amyloids represent distinct functional states. Most bacterial amyloids described are extracellular, contributing to biofilm formation. However, only a few have been found in the bacterial cytosol. This paper reviews from the perspective of synthetic biology (SynBio) our understanding of the subtle line that separates functional from pathogenic and transmissible amyloids (prions). In particular, it is focused on RepA-WH1, a functional albeit unconventional natural amyloidogenic protein domain that participates in controlling DNA replication of bacterial plasmids. SynBio approaches, including protein engineering and the design of allosteric effectors such as diverse ligands and an optogenetic module, have enabled the generation in RepA-WH1 of an intracellular cytotoxic prion-like agent in bacteria. The synthetic RepA-WH1 prion has the potential to develop into novel antimicrobials.

scholarly journals Streamlined Construction of the Cyanobacterial CO2-Fixing Organelle via Protein Domain Fusions for Use in Plant Synthetic Biology

2015 ◽  
Vol 27 (9) ◽  
pp. 2637-2644 ◽  
Author(s):  
C. Raul Gonzalez-Esquer ◽  
Tyler B. Shubitowski ◽  
Cheryl A. Kerfeld
Keyword(s):  
Synthetic Biology ◽  
Protein Domain ◽  
Plant Synthetic Biology

scholarly journals Converting a Periplasmic Binding Protein into a Synthetic Biosensing Switch through Domain Insertion

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Lucas F. Ribeiro ◽  
Vanesa Amarelle ◽  
Liliane F. C. Ribeiro ◽  
María-Eugenia Guazzaroni
Keyword(s):  
Protein Engineering ◽  
Ligand Binding ◽  
Conformational Changes ◽  
Protein Function ◽  
Cellular Response ◽  
Protein Domain ◽  
Signal Molecule ◽  
Synthetic Protein ◽  
Periplasmic Binding Proteins ◽  
Domain Insertion

All biosensing platforms rest on two pillars: specific biochemical recognition of a particular analyte and transduction of that recognition into a readily detectable signal. Most existing biosensing technologies utilize proteins that passively bind to their analytes and therefore require wasteful washing steps, specialized reagents, and expensive instruments for detection. To overcome these limitations, protein engineering strategies have been applied to develop new classes of protein-based sensor/actuators, known as protein switches, responding to small molecules. Protein switches change their active state (output) in response to a binding event or physical signal (input) and therefore show a tremendous potential to work as a biosensor. Synthetic protein switches can be created by the fusion between two genes, one coding for a sensor protein (input domain) and the other coding for an actuator protein (output domain) by domain insertion. The binding of a signal molecule to the engineered protein will switch the protein function from an “off” to an “on” state (or vice versa) as desired. The molecular switch could, for example, sense the presence of a metabolite, pollutant, or a biomarker and trigger a cellular response. The potential sensing and response capabilities are enormous; however, the recognition repertoire of natural switches is limited. Thereby, bioengineers have been struggling to expand the toolkit of molecular switches recognition repertoire utilizing periplasmic binding proteins (PBPs) as protein-sensing components. PBPs are a superfamily of bacterial proteins that provide interesting features to engineer biosensors, for instance, immense ligand-binding diversity and high affinity, and undergo large conformational changes in response to ligand binding. The development of these protein switches has yielded insights into the design of protein-based biosensors, particularly in the area of allosteric domain fusions. Here, recent protein engineering approaches for expanding the versatility of protein switches are reviewed, with an emphasis on studies that used PBPs to generate novel switches through protein domain insertion.

scholarly journals RNase I regulates Escherichia coli 2′,3′-cyclic nucleotide monophosphate levels and biofilm formation

2018 ◽  
Vol 475 (8) ◽  
pp. 1491-1506 ◽  
Author(s):  
Benjamin M. Fontaine ◽  
Kevin S. Martin ◽  
Jennifer M. Garcia-Rodriguez ◽  
Claire Jung ◽  
Laura Briggs ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Cyclic Nucleotide ◽  
Biofilm Formation ◽  
Physiological Role ◽  
Rna Degradation ◽  
Bacterial Biofilm ◽  
Biological Functions ◽  
Salvage Pathway ◽  
E Coli

Regulation of nucleotide and nucleoside concentrations is critical for faithful DNA replication, transcription, and translation in all organisms, and has been linked to bacterial biofilm formation. Unusual 2′,3′-cyclic nucleotide monophosphates (2′,3′-cNMPs) recently were quantified in mammalian systems, and previous reports have linked these nucleotides to cellular stress and damage in eukaryotes, suggesting an intriguing connection with nucleotide/nucleoside pools and/or cyclic nucleotide signaling. This work reports the first quantification of 2′,3′-cNMPs in Escherichia coli and demonstrates that 2′,3′-cNMP levels in E. coli are generated specifically from RNase I-catalyzed RNA degradation, presumably as part of a previously unidentified nucleotide salvage pathway. Furthermore, RNase I and 2′,3′-cNMP levels are demonstrated to play an important role in controlling biofilm formation. This work identifies a physiological role for cytoplasmic RNase I and constitutes the first progress toward elucidating the biological functions of bacterial 2′,3′-cNMPs.

scholarly journals Polymer Adhesin Domains in Gram-Positive Cell Surface Proteins

2020 ◽  
Vol 11 ◽  
Author(s):  
Michael A. Järvå ◽  
Helmut Hirt ◽  
Gary M. Dunny ◽  
Ronnie P.-A. Berntsson
Keyword(s):  
Protein Function ◽  
Biofilm Formation ◽  
Lipoteichoic Acid ◽  
Surface Proteins ◽  
Protein Domain ◽  
Gram Positive ◽  
Surface Attachment ◽  
Gram Positive Bacteria ◽  
Different Types ◽  
Host Cell Interactions

Surface proteins in Gram-positive bacteria are often involved in biofilm formation, host-cell interactions, and surface attachment. Here we review a protein module found in surface proteins that are often encoded on various mobile genetic elements like conjugative plasmids. This module binds to different types of polymers like DNA, lipoteichoic acid and glucans, and is here termed polymer adhesin domain. We analyze all proteins that contain a polymer adhesin domain and classify the proteins into distinct classes based on phylogenetic and protein domain analysis. Protein function and ligand binding show class specificity, information that will be useful in determining the function of the large number of so far uncharacterized proteins containing a polymer adhesin domain.

Advances in protein engineering and its application in synthetic biology

2022 ◽  
pp. 147-158
Author(s):  
Rongming Liu ◽  
Liya Liang ◽  
Maria Priscila Lacerda ◽  
Emily F. Freed ◽  
Carrie A. Eckert
Keyword(s):  
Synthetic Biology ◽  
Protein Engineering

scholarly journals Inhibition of curli assembly and Escherichia coli biofilm formation by the human systemic amyloid precursor transthyretin

2017 ◽  
Vol 114 (46) ◽  
pp. 12184-12189 ◽  
Author(s):  
Neha Jain ◽  
Jörgen Ådén ◽  
Kanna Nagamatsu ◽  
Margery L. Evans ◽  
Xinyi Li ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Biofilm Formation ◽  
Bacterial Species ◽  
Amyloid Β ◽  
Amyloid Formation ◽  
Amyloid Fibers ◽  
Amyloidogenic Protein ◽  
Aβ Aggregation ◽  
Antibiotic Efficacy

During biofilm formation, Escherichia coli and other Enterobacteriaceae produce an extracellular matrix consisting of curli amyloid fibers and cellulose. The precursor of curli fibers is the amyloidogenic protein CsgA. The human systemic amyloid precursor protein transthyretin (TTR) is known to inhibit amyloid-β (Aβ) aggregation in vitro and suppress the Alzheimer’s-like phenotypes in a transgenic mouse model of Aβ deposition. We hypothesized that TTR might have broad antiamyloid activity because the biophysical properties of amyloids are largely conserved across species and kingdoms. Here, we report that both human WT tetrameric TTR (WT-TTR) and its engineered nontetramer-forming monomer (M-TTR, F87M/L110M) inhibit CsgA amyloid formation in vitro, with M-TTR being the more efficient inhibitor. Preincubation of WT-TTR with small molecules that occupy the T4 binding site eliminated the inhibitory capacity of the tetramer; however, they did not significantly compromise the ability of M-TTR to inhibit CsgA amyloidogenesis. TTR also inhibited amyloid-dependent biofilm formation in two different bacterial species with no apparent bactericidal or bacteriostatic effects. These discoveries suggest that TTR is an effective antibiofilm agent that could potentiate antibiotic efficacy in infections associated with significant biofilm formation.

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