Bacteriophage synthetic biology pdf

Bacteriophages have formed the backbone of molecular biology, having championed the demonstration of dna as genetic material, the proof of darwinian natural selection, and the ubiquitous use of phagederived enzymes for common laboratory protocols. This science use the knowledge about the genetic circuits that have been obtained by the systems biology to design and implement new synthetic genetic circuits that have the properties that are desired for the application 3. Phages are obligate intracellular parasites that multiply inside bacteria by making. Continuous advancements in dna synthesis and sequencing technologies coupled with new techniques for genomic modification and assembly have opened the door for. The earliest known observation of what we would now. Here, we discuss the use of phage as therapeutics, as well as how synthetic biology can create bacteriophage with desirable attributes. Bacteriophage t7 transcription system an enabling tool in. Phages also exhibit significant medical potential as antibacterial agents and bacterial diagnostics due to their extreme. In this timeline, salmond and fineran discuss a century of phage. Recent advances in the synthetic biology field have enabled the development of new molecular biology techniques used to build specialized bacteriophages with new functionalities. Modulating resource allocation in bacteria to redirect metabolic building blocks to the formation of recombinant proteins rather than biomass formation remains a grand challenge in biotechnology. These synthetic biology advances coupled with our growing ability to engineer bacteriophage with expanded host range, antiresistance mechanisms, and immune evasion capabilities may lower the number of phages and cost of production to a level attractive to regulators and commercial entities merril et al. Cite this article as cold spring harb perspect biol doi. Engineered bacteriophage targeting gene networks as.

Bacteriophagebased synthetic biology for the study of. Synthetic biology to engineer bacteriophage genomes. Pdf bacteriophagebased synthetic biology for the study. The continued advancement of synthetic biology calls for the construction of larger and more complex synthetic gene circuits, which in turn necessitates the development of additional parts and component libraries with which to build these circuits. Collinsb,1 aharvardmassachusetts institute of technology division of health sciences and technology, cambridge, ma 029. What they all have in common, however, is that they see synthetic biology as the design and construction of new biological functions and systems not found in nature. Assessing the synergy between phages and antibiotics. Bacteriophages have been engineered towards a wide range of applications including pathogen control and detection, targeted drug delivery, or even assembly of new. Modern synthetic biology offers pioneering approaches to accelerate and finetune the detection process, subsequently enabling clinicians to offer fast, targeted treatments. Lieberman, jon rodriguez, adrian sierra, drew endyn department of bioengineering, y2e2269b, 473 via ortega, stanford, ca 943054201, usa. Phage derived t7 rnap is an important molecular tool for the study of synthetic gene circuits.

A plaqueis a small, clear area on an agar plate where the host bacteria have been lysed as a result of the lytic life cycle of the infecting bacteriophages. Bacteriophages, in short, are the viruses that infect bacteria. Our synthetic phage design can be extended to target nonsos gene networks and overexpress multiple factors to produce additional effective antibiotic adjuvants. Synthetic biology is an emerging engineering field focused on designing artificial biological systems with novel functionalities for use in therapeutics, basic science, biotechnology, and diagnostics 1,2. Dispersing biofilms with engineered enzymatic bacteriophage.

Synthetic biology synbio is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature it is a branch of science that encompasses a broad range of methodologies from various disciplines, such as biotechnology, genetic engineering, molecular biology, molecular engineering, systems biology. This article is dedicated to the special collection of synthetic biology. Defining the indirect antimicrobial properties and antibiofilm activity of phage. Synthetic biology has enabled technologies for nextgeneration phage engineering.

Genome replication, synthesis, and assembly of the. Koeris1,2 1sample6 2 technologies, 27 drydock avenue, boston, ma 02210, usa department of electrical engineering and computer science and department of biological engineering, massachusetts institute of. Thus, bacteriophage can be viewed as model systems for animal cell viruses. However, a lack of consistency in application and observed efficacy during their early use meant that upon the discovery of antibiotic compounds research in the field of phage therapy quickly slowed. Synthetic biology, equipped with the engineeringdriven approaches of modularization, rationalization and modelling, has. Phages were discovered 100 years ago, and since then phage research has transformed fundamental and translational biosciences. Phagebased applications in synthetic biology annual. It is a multidisciplinary research field at the intersection of virology, synthetic biology, computational biology, and dna nanotechnology, from which it borrows and integrates its concepts and methodologies.

Bacteriophage based synthetic biology for the study of infectious 1 diseases robert j citorik,25, mark mimee 1and timothy k lu 3 4 since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Bacteriophagebased synthetic biology for the study of infectious diseases article pdf available in current opinion in microbiology 19c1. Similarly, bacteriophage components constitute a core set of parts in the toolbox of a. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions.

However, very few phage genomes have been wellcharacterized, the tailed phage t4 genome being one of them. Phage therapy in the era of synthetic biology ncbi. Similarly, bacteriophage components constitute a core set of parts in the toolbox of a synthetic biologist. In addition, our synthetic phage act as strong adjuvants for other bactericidal antibiotics, improve the killing of antibioticresistant bacteria, and reduce the number of antibiotic. Here, we discuss bacteriophagebased technologies and their application to the study of infectious diseases. There is a wide range of applications for synthetic viral. Furthermore, bacteriophages have provided many tools that have advanced the. Bacteriophage phage are obligate intracellular parasites that multiply inside bacteria by making use of some or all of the host biosynthetic machinery i.

Here, we present a novel approach for improved recombinant protein production rpp using escherichia coli e. Using a cellfree transcriptiontranslation system as a molecular programming platform, we show that the bacteriophage t7, encoded by a 40 kbp dna program composed of about 60 genes, can be entirely synthesized from its genomic dna in a test tube. Synthetic biology is a new open access journal which covers all aspects of synthetic biology. Pdf bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic biology. Bacteriophagebased synthetic biology for the study of infectious diseases 4232014 congratulations to lior nissim, sam perli, and team for their work on multiplexed gene circuits with rnai and crisprcas. Pdf phagebased applications in synthetic biology researchgate. In this study, we make a proof of principles in the simplest and realistic condition. Starting the 1940s, phages became model organisms that facilitated the birth of molecular biology and were utilized to derive the most basic. Bacteriophages attacking escherichia coli are called coliphages or tphages. Bacteriophagebased synthetic biology for the study of infectious 1 diseases robert j citorik,25, mark mimee 1and timothy k lu 3 4 since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Bacteriophagebased synthetic biology for the study of infectious. Engineered bacteriophage to combat bacterial biofilms and antibioticresistant bacteria, invited talk, frontiers in synthetic biology. Max delbruck 1938 numbered coliphages as teven phages t2, t4, t6 etc.

Synthetic biology and genetic engineering to improve or better understand phage properties. Many phagederived technologies have been adapted for building gene circuits to program biological systems. In this article we will discuss about bacteriophage. Bacteriophage means to eat bacteria, and are called so because virulent bacteriophage can cause the compete lysis of a susceptible bacterial culture. Advancing bacteriophagebased microbial diagnostics with. Synthetic virology is a branch of virology engaged in the study and engineering of synthetic manmade viruses. For more than a century, bacteriophage or phage research has enabled some of the most important discoveries in biological sciences and has equipped. Similarly, bacteriophage components constitute a core set of parts in. The therapeutic potential of bacteriophages has been debated since their first isolation and characterisation in the early 20th century. Bacteriophages likely constitute the largest biomass on earth.

Using a cellfree transcriptiontranslation system as a molecular programming platform, we show that the bacteriophage t7, encoded by a 40 kbp dna program composed of about 60 genes, can be entirely synthesized from its genomic dna in a test tube reaction. The classical genetic strategies are tedious, compounded by genome modifications such as cytosine hydroxylmethylation and glucosylation which. Phages also exhibit significant medical potential as antibacterial agents and bacterial diagnostics due to their extreme specificity for their. As the bacteria replicate on the plate they form a lawn of confluent growth. Phage therapy in the era of synthetic biology advanced online article. Furthermore, bacteriophages have provided many tools that have advanced the fields of genetic engineering and synthetic biology. Engineering synthetic bacteriophage to combat antibiotic. For more than a century, bacteriophage or phage research has enabled some of the most important discoveries in biological sciences and has equipped scientists with many of the molecular biology tools that have advanced our understanding of replication, maintenance, and expression of genetic material. Even in t4, much of the genome remained uncharacterized.

Some phage genomes can be rebooted either using cellfree systems in vitro transcriptiontranslation 20, 21 or in e. Timeline i a brief history of synthetic biology earliest combinatorial synthesis of genetic networksn synthetic circuits used to study transcriptional noise during this sb 1. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy timothy k. Understanding the relationship between bacterial virulence and phage resistance. One intriguing option is the reactivation of synthetic bacteriophage dna, a process also known as genome rebooting.

Engineered phages and derived parts constitute a new. Pdf bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic. The synthesis of living entities in the laboratory is a standing challenge that calls for innovative approaches. Bacteriophage inspired growthdecoupled recombinant. There are many similarities between bacteriophages and animal cell viruses. Advancing bacteriophagebased microbial diagnostics with synthetic biology timothy k. Cellfree txtl synthesis of infectious bacteriophage t4 in. Synthetic biology synbio is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature it is a branch of science that encompasses a broad range of methodologies from various disciplines, such as biotechnology, genetic engineering, molecular biology, molecular. Synthetic biology is a broad and interdisciplinary filed involving chemistry, physics, mathematics, and biology with the ultimate aims of creating functional parts, devices, circuits, systems and organisms that possess novel, predictable and useful functions of value from catalogued and standardized biological building blocks cameron et al. Synthetic biology is a new area of biological research that combines science and engineering. Today you will infect the bacterium escherichia coli b with its specific bacteriophage, coliphage t4 in the first part of the lab you will perform a plaque count. Engineering of bacteriophage t4 genome using crisprcas9.