| … construction and design of biological system parts or whole organisms artificially…|
Synthetic Biology currently encompasses a number of engineering strategies including applied
protein design, genome design and construction, natural product or synthetics drug synthesis,
vaccines, pollution censors, and even the creation of standardized parts to build circuits into cells.
i.e., the artificial creation of DNA, genes, viri, and cells that mimic, or surpass, natural systems.
| beneficial examples: a. synthesize any gene with 100% accuracy for $1.60 per base pair|
b. design a low cost synthetics drug to treat malaria
c. build DNA transistors
d. make a molecular “water wheel” for use in miniature medical pumps
e. engineer bacteria to do “work”
| harmful examples: a. environmental release of an artificial system with harmful consequences|
b. re-engineering of deadly viri, as smallpox, to cause epidemic
| Specific Virus Examples: |
Synthetic Polio Virus – July 12 ,2002 : Molecular Origin of Life Research or Bioterrorism?
| To construct the synthetic polio virus virus, lead scientist Eckard Wimmer of the State University of New York at Stony Brook used the poliovirus’ widely known genetic sequence to synthesize that virus from the building blocks of DNA and a broth of other chemicals. The followed a recipe they downloaded from the internet and used gene sequences from a mail-order supplier. Having constructed the virus, which appears to be identical to its natural counterpart, the researchers, from the University of New York at Stony Brook, injected it into mice to demonstrate that it was active. The animals were paralyzed and then died.|
Wimmer has worked on the genetics and replication of poliovirus for more than 3 decades. The virus stores genetic information in a long strand of ribonucleic acid (RNA) rather than DNA. In the new work, described in Science (see below), Wimmer and his colleagues used common laboratory machines to synthesize DNA strands harboring the same protein-encoding instructions that a typical poliovirus carries.
| Wimmer and his team then mixed the lab-made DNA with an enzyme that converts DNA into RNA.|
Next, they added the resulting strands to a mixture of chemicals similar to that in the cells that poliovirus typically invades. This brew generated whole polioviruses that subsequent tests in cells and animals confirmed as infectious.
To distinguish any synthesized viruses from lab contaminants, the investigators introduced subtle changes into the virus’ genetic code that didn’t alter the proteins it encodes. Unexpectedly, however, the newly created viruses turned out to be much less potent than the typical lab strain. Higher doses of the synthetic poliovirus were needed to kill mice, for example.
|Link||Cello, J., A.V. Paul, and E. Wimmer. Chemical synthesis of poliovirus cDNA: Generation of infections virus|
in the absence of natural template. Science. Abstract available at . Science OnLine – July 11, 2002
November 2003 Phi X-174 virus synthesized In 1978 Phi X, a virus that infects bacteria but is harmless to humans, was the first virus ever sequenced. By 2004 Craig Venter’s (of Genomic sequencing fame) and his research group (including longtime collaborators Nobel Laureate Hamilton O. Smith of the Institute for Biological Energy Alternatives (IBEA), and Clyde A. Hutchinson of the University of North Carolina, Chapel Hill) at in Rockville, Maryland , in just 14 days, created an artificial version of Phi X-174 by piecing together synthetic DNA ordered from a biotechnology company. They used a technique called polymerase cycle assembly (PCA) to link the strands of DNA together.
The sequence and assembly of the synthetic genome matches up nearly perfectly with the sequenced genome of the natural virus. Each strand of DNA neatly overlaps its neighboring strands by 20 letters of genetic code. The new virus also infects bacterial cells just like the natural virus does.
The goal of the IBEA research is to create a synthetic genome that would be 100 to 1,000 times larger than the phi X virus. Someday, researchers hope to engineer fleets of self-replicating microbes that do everything from scrubbing down emissions at coal plants to producing enough hydrogen to power cars and trucks run by hydrogen-fuel cells rather than gasoline.
| October 2005 The 1918 Spanish Flu Virus is Reconstructed|
Jeffery K. Taubenberger, a molecular pathologist at the Armed Forces Institute of Pathology in Rockville, MD at a CDC Bio-Safety–Level 3 CDC lab reconstructed the genome of the 1918 lethal virus as reported in the October 7, 2005 issue of Science. They successfully reconstructed the influenza A (H1N1) virus responsible for the 1918 “Spanish flu” pandemic (pic + pic). The influenza pandemic of 1918-19 killed an estimated 20 to 50 million people worldwide, many more than the subsequent pandemics of the 20th century. The Spanish flu virus of the 1918 pandemic was probably a strain that originated in birds. Scientists have found the 1918 virus shares genetic mutations with the bird flu virus now circulating in Asia.
Taubenberger and his colleagues were able to piece together the virus’s genes from two unusual sources. One source was fingernail-size pieces of lung tissue removed at autopsy from a 21-year-old soldier who died in 1918 at Fort Jackson in South Carolina. He was among the pandemic’s 675,000 American victims and he provided intact pieces of viral RNA that could be analysed and sequenced.. The other source was the frozen body of an Inuit woman who died of influenza in November 1918 and was buried in the permafrost.
The virus’s eight “RNA gene segments” were in pieces. Using gene sequencing and the polymerase chain reaction they reassembled the virus. Two of the 8 genes are considered to be of greatest importance for the virulence of the virus: the genes for hemagglutinin (HA) and neuraminidase (NA). Hemagglutinin type 5 [H5] and Neuraminidase type 1 [N1] are protein surface coatings of the virus. Hemagglutinin A is a glycoprotein that binds the virus to the host cell. There are at least 16 different HA antigens. Neuraminidase is an antigenic glycoprotein enzyme found on the surface of the flu virus. Nine neuraminidase subtypes are known, many occurring only in various species of ducks and chickens. Subtypes N1 and N2 have been positively linked to epidemics in man. The neuraminidases aid in the efficiency of virus release from infected cells.
The reconstruction of the 1918 virus is expected to provide insights that are immediately useful to the virologists and epidemiologists charting the flow of hundreds of flu strains through dozens of species. Researchers hope to identify the mutations that are necessary for adaptation to a human host. It will be especially useful to compare the similarities between the Spanish flu virus 1918 virus gene sequence to the H5N1 of the current “Avian Flu”, as well as to those of the “Asian flu”, which emerged in 1957, and the “Hong Kong flu”, which circled the globe in 1968. Hybrid viruses containing genetic features of each in different combinations can then be constructed and studied in the laboratory.
The biological properties that confer virulence to pandemic influenza viruses are poorly understood. Evaluating the biological properties of the individual genes that make up this virus (CDC has examined four of the virus’ eight genes so far). Scientists will continue to study the hemagglutinin (HA) gene to better understand the role of HA in causing inflammation of the lung, a factor that may contribute to the overall increased levels of illness and death associated with this virus.
The strain of avian influenza that has led to the deaths of 140 million birds and 60 people in Asia in the past two years appears to be slowly acquiring the genetic changes characteristic of the “Spanish flu” virus that killed 50 million people nearly a century ago.
How far “bird flu” has traveled down the evolutionary path to becoming a pandemic virus is unknown. Nor is it certain the worrisome strain, designated influenza A-H5N1, will ever acquire all the genetic features necessary for rapid, worldwide pandemic spread.
| A bacterial example of Synthetic Biology |
J. Craig Venter, a principle investigator (P.I.) of the Human Genome Project is attempting
to make a synthetic new type of bacterium using DNA manufactured in the lab; using the sequenced the genes of a bacterium called Mycoplasma genitalium, a gram-positive parasitic bacterium, whose primary infection site may be the human urogenital tract. It probably causes non-gonococcal urethritis. The complete nucleotide sequence is 580,073 base pairs, the smallest known genome of any free-living organism, has been determined. A total of only 517genes (480 encoding for proteins; the rest for RNAs) were identified that included genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism.
> researchers began systematically removing genes to determine how many genes
are essential for life. In 1999, they published the narrowed the needs of M. genitalium
to between 265 & 350 genes.
> How many genes does it take to make an organism? What is the minimum genes a cell needs?
The scientists at The Institute for Genomic Research (TIGR) who determined the Mycoplasma
genitalium sequence followed this work by systematically destroying its genes (by mutating them
with insertions) to see which ones are essential to life and which are dispensable. Of the 480
protein-encoding genes, they conclude that only 265–350 of them are essential to life.
> The next step is to artificially assemble these 300+ genes to create a SYNTHETIC CELL.