Abstract:
:Quantification of biology's central dogma (transcription and translation) is pursued by a variety of methods. Direct, immediate, and ongoing quantification of these events is difficult to achieve. Common practice is to use fluorescent or luminescent proteins to report indirectly on prior cellular events, such as turning on a gene in a genetic circuit. We present an alternative approach, PURExpress-ReAsH-Spinach In-vitro Analysis (PERSIA). PERSIA provides information on the production of RNA and protein during cell-free reactions by employing short RNA and peptide tags. Upon synthesis, these tags yield quantifiable fluorescent signal without interfering with other biochemical events. We demonstrate the applicability of PERSIA in measuring cell-free transcription, translation, and other enzymatic activity in a variety of applications: from sequence-structure-function studies, to genetic code engineering, to testing antiviral drug resistance.
journal_name
ACS Synth Bioljournal_title
ACS synthetic biologyauthors
Wick S,Walsh DI 3rd,Bobrow J,Hamad-Schifferli K,Kong DS,Thorsen T,Mroszczyk K,Carr PAdoi
10.1021/acssynbio.8b00450subject
Has Abstractpub_date
2019-05-17 00:00:00pages
1010-1025issue
5issn
2161-5063journal_volume
8pub_type
杂志文章abstract::The extracellular expression of recombinant proteins using laboratory strains of Escherichia coli is now routinely achieved using naturally secreted substrates, such as YebF or the osmotically inducible protein Y (OsmY), as carrier molecules. However, secretion efficiency through these pathways needs to be improved fo...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.6b00366
更新日期:2017-05-19 00:00:00
abstract::Multiplex Automated Genome Engineering (MAGE) allows simultaneous mutagenesis of multiple target sites in bacterial genomes using short oligonucleotides. However, large-scale mutagenesis requires hundreds to thousands of unique oligos, which are costly to synthesize and impossible to scale-up by traditional phosphoram...
journal_title:ACS synthetic biology
pub_type: 信件
doi:10.1021/sb5001565
更新日期:2015-01-16 00:00:00
abstract::Agricultural soils are often cocontaminated with multiple pesticides. Unfortunately, microorganisms isolated from natural environments do not possess the ability to simultaneously degrade different classes of pesticides. Currently, we can use the approaches of synthetic biology to create a strain endowed with various ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.6b00025
更新日期:2016-05-20 00:00:00
abstract::Materials synthesized by organisms, such as bones and wood, combine the ability to self-repair with remarkable mechanical properties. This multifunctionality arises from the presence of living cells within the material and hierarchical assembly of different components across nanometer to micron scales. While creating ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.8b00448
更新日期:2019-01-18 00:00:00
abstract::Bacterial biofilms are three-dimensional networks of cells entangled in a self-generated extracellular polymeric matrix composed of proteins, lipids, polysaccharides, and nucleic acids. Biofilms can establish themselves on virtually any accessible surface and lead to varying impacts ranging from infectious diseases to...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00192
更新日期:2019-07-19 00:00:00
abstract::To facilitate the construction of cell-free genetic devices, we evaluated the ability of 17 different fluorescent proteins to give easily detectable fluorescence signals in real-time from in vitro transcription-translation reactions with a minimal system consisting of T7 RNA polymerase and E. coli translation machiner...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/sb400003y
更新日期:2013-09-20 00:00:00
abstract::We developed a hybrid synthetic circuit that co-opts the genetic regulation of the native bacterial quorum sensing autoinducer-2 and imposes an extra external controller for maintaining tightly controlled gene expression. This dual-input genetic controller was mathematically modeled and, by design, can be operated in ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00179
更新日期:2020-10-16 00:00:00
abstract::DNA replication is one of the central functions of the cell. The complexity of modern DNA replication systems raises a question: is it possible to achieve a simpler continuous isothermal DNA replication using fewer proteins? Here, we searched such replication using an evolutionary approach. Through a long-term serial ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00137
更新日期:2020-07-17 00:00:00
abstract::Modern bioprocessing depends on superior cellular traits, many stemming from unknown genes and gene interactions. Tolerance to toxic chemicals is such an industrially important complex trait, which frequently limits the economic feasibility of producing commodity chemicals and biofuels. Chemical tolerance encompasses ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/sb400156v
更新日期:2014-07-18 00:00:00
abstract::The availability of different host chassis will greatly expand the range of applications in synthetic biology. Members of the Acetobacteraceae family of Gram-negative bacteria form an attractive class of nonmodel microorganisms that can be exploited to produce industrial chemicals, food and beverage, and biomaterials....
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.8b00168
更新日期:2019-04-19 00:00:00
abstract::Microbial mutualisms play critical roles in a diverse number of ecosystems and have the potential to improve the efficiency of bioproduction for desirable chemicals. We investigate the growth of a photosynthetic cyanobacterium, Synechococcus elongatus PCC 7942, and a diazotroph, Azotobacter vinelandii, in coculture. F...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.6b00107
更新日期:2016-09-16 00:00:00
abstract::In vitro transcription and translation reactions have become popular for a bottom-up approach to synthetic biology. Concentrations of the mRNA intermediate are rarely determined, although knowledge of synthesis and degradation rates could facilitate rational engineering of in vitro systems. We designed binary probes t...
journal_title:ACS synthetic biology
pub_type: 信件
doi:10.1021/sb300104f
更新日期:2013-08-16 00:00:00
abstract::Dissimilatory metal-reducing bacteria, particularly those from the genus Shewanella, are of importance for bioremediation of metal contaminated sites and sustainable energy production. However, studies on this species have suffered from a lack of effective genetic tools for precise and high throughput genome manipulat...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00188
更新日期:2019-08-16 00:00:00
abstract::The development of a synthetic transcription factor that responds to intracellular calcium signals enables analyzing cellular events at the single-cell level or "rewiring" the intracellular information networks. In this study, we developed the calcium-dependent transcription factor (CaTF), which was cleaved by calpain...
journal_title:ACS synthetic biology
pub_type: 信件
doi:10.1021/sb500070c
更新日期:2014-10-17 00:00:00
abstract::The ATLAS of Biochemistry is a repository of both known and novel predicted biochemical reactions between biological compounds listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG). ATLAS was originally compiled based on KEGG 2015, though the number of KEGG reactions has increased by almost 20 percent since the...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00052
更新日期:2020-06-19 00:00:00
abstract::Directed evolution requires the creation of genetic diversity and subsequent screening or selection for improved variants. For DNA mutagenesis, conventional site-directed methods implicitly utilize the Boolean AND operator (creating all mutations simultaneously), producing a combinatorial explosion in the number of ge...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00063
更新日期:2019-06-21 00:00:00
abstract::Heterochiral DNA strand-displacement reactions enable sequence-specific interfacing of oligonucleotide enantiomers, making it possible to interface native d-nucleic acids with molecular circuits built using nuclease-resistant l-DNA. To date, all heterochiral reactions have relied on peptide nucleic acid (PNA), which p...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00335
更新日期:2019-12-20 00:00:00
abstract::In order to match our ability to conceive of and construct cells with enhanced function, we must concomitantly develop facile, real-time methods for elucidating performance. With these, new designs can be tested in silico and steps in construction incrementally validated. Electrochemical monitoring offers the above ad...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.5b00073
更新日期:2016-01-15 00:00:00
abstract::Author: Recently, increasing research in siderophores has been dedicated to their possible medical applications in diagnostics and therapeutics for human pathogenic infections. Fusarinine C (FsC) is a natural hydroxamate siderophore that harbors three amino groups, which allow the easy chemical modification of FsC for...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00026
更新日期:2019-08-16 00:00:00
abstract::To spatially control biochemical functions at specific sites within a genome, we have engineered a synthetic switch that activates when bound to its DNA target site. The system uses two CRISPR-Cas complexes to colocalize components of a de novo-designed protein switch (Co-LOCKR) to adjacent sites in the genome. Coloca...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00012
更新日期:2020-09-18 00:00:00
abstract::Many Gram-negative pathogens encode type 3 secretion systems, sophisticated nanomachines that deliver proteins directly into the cytoplasm of mammalian cells. These systems present attractive opportunities for therapeutic protein delivery applications; however, their utility has been limited by their inherent pathogen...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.5b00002
更新日期:2015-05-15 00:00:00
abstract::The Design-Build-Test-Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and biobased products. Here, ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00020
更新日期:2019-06-21 00:00:00
abstract::Recent advances in the design and construction of synthetic multicelled systems in E. coli and S. cerevisiae suggest that it may be possible to implement sophisticated distributed algorithms with these relatively simple organisms. However, existing design frameworks for synthetic biology do not account for the unique ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/sb300034m
更新日期:2012-08-17 00:00:00
abstract::Robust and precise ratio control of heterogeneous phenotypes within an isogenic population is an essential task, especially in the development and differentiation of a large number of cells such as bacteria, sensory receptors, and blood cells. However, the mechanisms of such ratio control are poorly understood. Here, ...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.9b00030
更新日期:2019-06-21 00:00:00
abstract::Lignans are plant secondary metabolites with a wide range of reported health-promoting bioactivities. Traditional routes toward these natural products involve, among others, the extraction from plant sources and chemical synthesis. However, the availability of the sources and the complex chemical structures of lignans...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00354
更新日期:2020-11-20 00:00:00
abstract::RNA parts often serve as critical components in genetic engineering. Here we report a design of translational activators which is composed of an RNA endoribonuclease (Csy4) and two exchangeable RNA modules. Csy4, a member of Cas endoribonuclease, cleaves at a specific recognition site; this cleavage releases a cis-rep...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.5b00130
更新日期:2016-01-15 00:00:00
abstract::A streamlined approach toward the rapid fabrication of streptavidin-biotin-based protein microarrays was investigated. First, using our engineered versatile plasmid (pBADcM-tBirA) and an optimal coexpression strategy for biotin ligase and biotin acceptor peptide (BAP) chimeric recombinant protein, an autogeneration sy...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00343
更新日期:2020-09-18 00:00:00
abstract::Streptomycetes are Gram-positive mycelial bacteria, which synthesize a wide range of natural products including over two-thirds of the currently available antibiotics. However, metabolic engineering in Streptomyces species to overproduce a vast of natural products are hampered by a limited number of genetic tools. Her...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.6b00263
更新日期:2017-03-17 00:00:00
abstract::Most of the current methods for controlling the formation rate of a key protein or enzyme in cell factories rely on the manipulation of target genes within the pathway. In this article, we present a novel synthetic system for post-translational regulation of protein levels, FENIX, which provides both independent contr...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.8b00345
更新日期:2018-11-16 00:00:00
abstract::Synonymous mutation of the N-terminal coding sequence (NCS) has been used to regulate gene expression. We here developed a statistical model to predict the effect of the NCSs on protein expression in Bacillus subtilis WB600. First, a synonymous mutation was performed within the first 10 residues of a superfolder green...
journal_title:ACS synthetic biology
pub_type: 杂志文章
doi:10.1021/acssynbio.0c00309
更新日期:2021-01-19 00:00:00