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 degradation of toxic chemicals. Biofilms exhibit high mechanical stiffness and are inherently tolerant to adverse conditions including the presence of antibiotics, pollutants, detergents, high temperature, changes in pH, etc. These features make biofilms resilient, which is beneficial for applications in dynamic environments such as bioleaching, bioremediation, materials production, and wastewater purification. We have recently described an easy and cost-effective method for 3D printing of bacteria and have extended this technology for 3D printing of genetically engineered Escherichia coli biofilms. Our 3D printing platform exploits simple alginate chemistry for printing of a bacteria-alginate bioink mixture onto calcium-containing agar surfaces, resulting in the formation of bacteria-encapsulating hydrogels with varying geometries. Bacteria in these hydrogels remain intact, spatially patterned, and viable for several days. Printing of engineered bacteria to produce inducible biofilms leads to formation of multilayered three-dimensional structures that can tolerate harsh chemical treatments. Synthetic biology and material science approaches provide the opportunity to append a wide range of useful functionalities to these 3D-printed biofilms. In this article, we describe the wide range of future applications possible for applying functional 3D-printed biofilms to the construction of living biofilm-derived materials in a large-scale and environmentally stable manner.
journal_name
ACS Synth Bioljournal_title
ACS synthetic biologyauthors
Balasubramanian S,Aubin-Tam ME,Meyer ASdoi
10.1021/acssynbio.9b00192subject
Has Abstractpub_date
2019-07-19 00:00:00pages
1564-1567issue
7issn
2161-5063journal_volume
8pub_type
杂志文章abstract：:Living organisms employ endogenous negative feedback loops to maintain homeostasis despite environmental fluctuations. A pressing open challenge in Synthetic Biology is to design and implement synthetic circuits to control host cells' behavior, in order to regulate and maintain desired conditions. To cope with the hig...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.6b00220
更新日期：2017-03-17 00:00:00
abstract：:Transform-MinER (Transforming Molecules in Enzyme Reactions) is a web application facilitating the exploration of chemical biosynthetic space, guiding the user toward promising start points for enzyme design projects or directed evolution experiments. Two types of search are possible: Molecule Search allows a user to ...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.9b00105
更新日期：2019-11-15 00:00:00
abstract：:Gene expression noise arises from stochastic variation in the synthesis and degradation of mRNA and protein molecules and creates differences in protein numbers across populations of genetically identical cells. Such variability can lead to imprecision and reduced performance of both native and synthetic networks. In ...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.8b00279
更新日期：2018-11-16 00:00:00
abstract：:Feedback control allows cells to dynamically sense and respond to environmental changes. However, synthetic controller designs can be challenging because of implementation issues, such as determining optimal expression levels for circuit components within a feedback loop. Here, we addressed this by coupling rational d...
journal_title：ACS synthetic biology
pub_type： 信件
doi：10.1021/acssynbio.7b00260
更新日期：2018-01-19 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：: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：:Biosensors are important components of many synthetic biology and metabolic engineering applications. Here, we report a second generation of Saccharomyces cerevisiae digoxigenin and progesterone biosensors based on destabilized dimeric ligand-binding domains that undergo ligand-induced stabilization. The biosensors, c...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.8b00242
更新日期：2018-10-19 00:00:00
abstract：:Movement of molecules across membranes in response to a stimulus is a key component of cellular programming. Here, we characterize and manipulate the response of a protein-based piston capable of puncturing membranes in a pH-dependent manner. Our protein actuator consists of modified R bodies found in a bacterial endo...
journal_title：ACS synthetic biology
pub_type： 信件
doi：10.1021/acssynbio.5b00237
更新日期：2016-04-15 00:00:00
abstract：:The structural complexity of nonribosomal peptides (NRPs) impeding economic chemical synthesis and poor cultivability of source organisms limits the development of bioprocesses for novel bioactive compounds. Since nonribosomal peptide synthetases (NRPSs) assemble NRPs from simple amino acid building blocks, heterologo...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/sb400082j
更新日期：2014-07-18 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：: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：:Due to autotrophic growing capacity and extremely rich secondary metabolism, plants should be preferred targets of synthetic biology. However, developments in plants usually run below those in other taxonomic groups. In this work we engineered genetic circuits capable of logic YES, OR and AND Boolean computation in pl...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.8b00214
更新日期：2018-10-19 00:00:00
abstract：:In this work we report synthetic adhesins (SAs) enabling the rational design of the adhesion properties of E. coli. SAs have a modular structure comprising a stable β-domain for outer membrane anchoring and surface-exposed immunoglobulin domains with high affinity and specificity that can be selected from large repert...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/sb500252a
更新日期：2015-04-17 00:00:00
abstract：:A bacterial flavin transferase (ApbE) was recently employed for flavin mononucleotide (FMN) modification on the Na+-translocating NADH:quinone oxidoreductase C (NqrC) protein in the pathogenic Gram-negative bacterium Vibrio cholerae. We employed this unique post-translational modification in mammalian cells and found ...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.6b00284
更新日期：2017-04-21 00:00:00
abstract：:Improved plants are necessary to meet human needs. Agrobacterium-mediated transformation is the most common method used to rewire plant capabilities. For plant gene delivery, DNA constructs are assembled into binary T-DNA vectors that rely on broad host range origins for bacterial replication. Here we present pLX vect...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.6b00354
更新日期：2017-10-20 00:00:00
abstract：:Transcription activator-like effectors (TALEs) are proteins secreted by Xanthomonas bacteria to aid the infection of plant species. TALEs assist infections by binding to specific DNA sequences and activating the expression of host genes. Recent results show that TALE proteins consist of a central repeat domain, which ...
journal_title：ACS synthetic biology
pub_type： 杂志文章,评审
doi：10.1021/sb400137b
更新日期：2014-10-17 00:00:00
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：:Simple computation can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be describ...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.5b00275
更新日期：2016-08-19 00:00:00
abstract：:Cellobiose phosphorylase (CBP) cleaves cellobiose-abundant in plant biomass-to glucose and glucose 1-phosphate. However, the pentose sugar xylose, also abundant in plant biomass, acts as a mixed-inhibitor and a substrate for the reverse reaction, limiting the industrial potential of CBP. Preventing xylose, which lacks...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.6b00211
更新日期：2017-02-17 00:00:00
abstract：:In this work, we develop methodologies for analyzing and cross comparing metabolic models. We investigate three important metabolic networks to discuss the complexity of biological organization of organisms, modeling, and system properties. In particular, we analyze these metabolic networks because of their biotechnol...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/sb300102k
更新日期：2013-05-17 00:00:00
abstract：:The CRISPR-Cas9 nuclease has been repurposed as a tool for gene repression (CRISPRi). This catalytically dead Cas9 (dCas9) variant inhibits transcription by blocking either initiation or elongation by the RNA polymerase complex. Conditional control of dCas9-mediated repression has been achieved with inducible promoter...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.8b00347
更新日期：2019-02-15 00:00:00
abstract：:Exploiting the ability of proteins to self-assemble into architectural templates may provide novel routes for the positioning of functional molecules in nanotechnology. Here we report the engineering of multicomponent protein templates composed of distinct monomers that assemble in repeating orders into a dynamic func...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.8b00241
更新日期：2018-10-19 00:00:00
abstract：:As engineering foundations such as standards and abstraction begin to mature within synthetic biology, it is vital that genetic design automation (GDA) tools be developed to enable synthetic biologists to automatically select standardized DNA components from a library to meet the behavioral specification for a genetic...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/sb400135t
更新日期：2014-08-15 00:00:00
abstract：:DNA circuits have been widely used to develop biological computing devices because of their high programmability and versatility. Here, we propose an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement. The elementary gates in our architecture include ad...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.6b00144
更新日期：2016-08-19 00:00:00
abstract：:An RNA-dependent RNA polymerase ribozyme that was highly optimized through in vitro evolution for the ability to copy a broad range of template sequences exhibits promiscuity toward other nucleic acids and nucleic acid analogues, including DNA, threose nucleic acid (TNA), and arabinose nucleic acid (ANA). By operating...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.9b00044
更新日期：2019-05-17 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：:Light-switchable proteins enable unparalleled control of molecular biological processes in live organisms. Previously, we have engineered red/far-red and green/red photoreversible two-component signal transduction systems (TCSs) with transcriptional outputs in E. coli and used them to characterize and control syntheti...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/sb500273n
更新日期：2014-11-21 00:00:00
abstract：:As a product of a multistep enzymatic reaction, accumulation of poly(3-hydroxybutyrate) (PHB) in Escherichia coli (E. coli) can be achieved by overexpression of the PHB synthesis pathway from a native producer involving three genes phbC, phbA, and phbB. Pathway optimization by adjusting expression levels of the three ...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.6b00083
更新日期：2016-11-18 00:00:00
abstract：:Eukaryotic transcriptional factors (TFs) typically recognize short genomic sequences alone or together with other proteins to modulate gene expression. Mapping of TF-DNA interactions in the genome is crucial for understanding the gene regulatory programs in cells. While chromatin immunoprecipitation followed by sequen...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.6b00358
更新日期：2017-06-16 00:00:00
