scholarly journals Bacterial expression and protein purification of mini-fluorescence-activating proteins

Author(s):  
Jason C. Klima ◽  
Cameron M. Chow ◽  
Jiayi Dou ◽  
Anastassia A. Vorobieva ◽  
Lauren Carter ◽  
...  

Abstract Bacterial expression and purification of de novo designed mini-fluorescence-activating proteins (mFAPs) are accomplished by genetically fusing mFAP variants to an N-terminal 6xHis tag and optionally to a Tobacco Etch Virus (TEV) protease epitope. The protocol can take less than 24 hours to complete, and allows for downstream in vitro characterization of photophysical properties of mFAPs by equilibration with exogenous fluorogenic compounds.

2011 ◽  
Vol 152 (3) ◽  
pp. 108-112 ◽  
Author(s):  
Gerd Lindner ◽  
Reyk Horland ◽  
Ilka Wagner ◽  
Beren Ataç ◽  
Roland Lauster

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Brent Townshend ◽  
Joy S. Xiang ◽  
Gabriel Manzanarez ◽  
Eric J. Hayden ◽  
Christina D. Smolke

AbstractBiosensors are key components in engineered biological systems, providing a means of measuring and acting upon the large biochemical space in living cells. However, generating small molecule sensing elements and integrating them into in vivo biosensors have been challenging. Here, using aptamer-coupled ribozyme libraries and a ribozyme regeneration method, de novo rapid in vitro evolution of RNA biosensors (DRIVER) enables multiplexed discovery of biosensors. With DRIVER and high-throughput characterization (CleaveSeq) fully automated on liquid-handling systems, we identify and validate biosensors against six small molecules, including five for which no aptamers were previously found. DRIVER-evolved biosensors are applied directly to regulate gene expression in yeast, displaying activation ratios up to 33-fold. DRIVER biosensors are also applied in detecting metabolite production from a multi-enzyme biosynthetic pathway. This work demonstrates DRIVER as a scalable pipeline for engineering de novo biosensors with wide-ranging applications in biomanufacturing, diagnostics, therapeutics, and synthetic biology.


2006 ◽  
Vol 81 (4) ◽  
pp. 1858-1871 ◽  
Author(s):  
Stephen W. B. Fullerton ◽  
Martina Blaschke ◽  
Bruno Coutard ◽  
Julia Gebhardt ◽  
Alexander Gorbalenya ◽  
...  

ABSTRACT Sapoviruses are one of the major agents of acute gastroenteritis in childhood. They form a tight genetic cluster (genus) in the Caliciviridae family that regroups both animal and human pathogenic strains. No permissive tissue culture has been developed for human sapovirus, limiting its characterization to surrogate systems. We report here on the first extensive characterization of the key enzyme of replication, the RNA-dependent RNA polymerase (RdRp) associated with the 3Dpol-like protein. Enzymatically active sapovirus 3Dpol and its defective mutant were expressed in Escherichia coli and purified. The overall structure of the sapovirus 3Dpol was determined by X-ray crystallography to 2.32-Å resolution. It revealed a right hand fold typical for template-dependent polynucleotide polymerases. The carboxyl terminus is located within the active site cleft, as observed in the RdRp of some (norovirus) but not other (lagovirus) caliciviruses. Sapovirus 3Dpol prefers Mn2+ over Mg2+ but may utilize either as a cofactor in vitro. In a synthetic RNA template-dependent reaction, sapovirus 3Dpol synthesizes a double-stranded RNA or labels the template 3′ terminus by terminal transferase activity. Initiation of RNA synthesis occurs de novo on heteropolymeric templates or in a primer-dependent manner on polyadenylated templates. Strikingly, this mode of initiation of RNA synthesis was also described for norovirus, but not for lagovirus, suggesting structural and functional homologies in the RNA-dependent RNA polymerase of human pathogenic caliciviruses. This first experimental evidence makes sapovirus 3Dpol an attractive target for developing drugs to control calicivirus infection in humans.


2020 ◽  
Author(s):  
Brent Townshend ◽  
Joy Xiang ◽  
Gabriel Manzanarez ◽  
Eric Hayden ◽  
Christina Smolke

AbstractBiosensors are key components in engineered biological systems, providing a means of measuring and acting upon the large biochemical space in living cells. However, generating small molecule sensing elements and integrating them into in vivo biosensors have been challenging. Using aptamer-coupled ribozyme libraries and a novel ribozyme regeneration method, we developed de novo rapid in vitro evolution of RNA biosensors (DRIVER) that enables multiplexed discovery of biosensors. With DRIVER and high-throughput characterization (CleaveSeq) fully automated on liquid-handling systems, we identified and validated biosensors against six small molecules, including five for which no aptamers were previously found. DRIVER-evolved biosensors were applied directly to regulate gene expression in yeast, displaying activation ratios up to 33-fold. DRIVER biosensors were also applied in detecting metabolite production from a multi-enzyme biosynthetic pathway. This work demonstrates DRIVER as a scalable pipeline for engineering de novo biosensors with wide-ranging applications in biomanufacturing, diagnostics, therapeutics, and synthetic biology.


1979 ◽  
Author(s):  
C.J.W. van Ginkel ◽  
J.A. van Mourik ◽  
J.I.H. Oh ◽  
J. Vreeken ◽  
W.U. van Aken

During short-terra culture monocytes (M) only, not granulocytes or lymphocytes, generate thromboplastin (TP) activity which is absent Immediately after isolation. To clarify the mechanism whereby M generate TP, J approaches were applied: I. To investigate the presence of hidden” TP, freshly Isolated M were subjected either to mechanical disruption, to enzymatic stripping or to dellpldation, followed by reconstitution of the lipoproteins with exogenous phospholipids. No TP activity could be detected after any of these treatments. II. Using an antiserum against human brain TP apoprotein which cross-reacted with monocyte TP, it was shown that intact and disrupted freshly Isolated M lack TP related antigen whereas cultured M display binding of anti-TP antibodies. However, M cultured in the presence of protein synthesis Inhibitors and cultured lymphocytes, lacked TP antigen. III. Using several agents known to affect cellular processes, TP generation was shown to be dependent on;protein and RNA synthesis, energy metabolism, cAMP metabolism, assemblage of microtubules and divalent cations. Inhibition of prostaglandin synthesis by indomethacln did not arrect TP generation. M from 3 patients with COD displayed normal TP generation. These two observations suggest that prostaglandin synthesis and oxygen radicals are not involved Is TP generation. In conelusion, our data indicates that de novo synthesis of TP apoprotein Is responsible for the in vitro generation of TP activity by monocytes.


2018 ◽  
Author(s):  
Anis Senoussi ◽  
Jonathan Lee Tin Wah ◽  
Yoshihiro Shimizu ◽  
Jérôme Robert ◽  
Alfonso Jaramillo ◽  
...  

AbstractRiboregulators are short RNA sequences that, upon binding to a ligand, change their secondary structure and influence the expression rate of a downstream gene. They constitute an attractive alternative to transcription factors for building synthetic gene regulatory networks because they can be engineered de novo and they have a fast turnover and a low metabolic burden. However, riboregulators are generally designed in silico and tested in vivo, which only provides a yes/no evaluation of their performances, thus hindering the improvement of design algorithms. Here we show that a cell-free transcription-translation (TX-TL) system provides valuable quantitative information about the performances of in silico designed riboregulators. In particular, we use the ribosome as an exquisite molecular machine that detects functional riboregulators, precisely measures their concentration and linearly amplifies the signal by generating a fluorescent protein. We apply this method to characterize two types of translational riboregulators composed of a cis-repressed (cr) and a trans-activating (ta) strand. At the DNA level we demonstrate that high concentrations of taDNA poisoned the activator until total shut off. At the RNA level, we show that this approach provides a fast and simple way to measure dissociation constants of functional riboregulators, in contrast to standard mobility-shift assays. Our method opens the route for using cell-free TX-TL systems for the quantitative characterization of functional riboregulators in order to improve their design in silico.


RSC Advances ◽  
2018 ◽  
Vol 8 (33) ◽  
pp. 18434-18441 ◽  
Author(s):  
Longgang Jia ◽  
Wenjuan Wang ◽  
Jinzhao Shang ◽  
Wenping Zhao ◽  
Wei Wei ◽  
...  

A novel high-yield expression and purification method for Aβ42 based on a fusion with maltose binding protein followed by the soluble polypeptide linker (NANP)3and a modified tobacco etch virus cleavage site before the Aβ42 was developed.


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