Navigation Links
New method of DNA editing allows synthetic biologists to unlock secrets of a bacterial genome
Date:12/5/2013

A group of University of Illinois researchers, led by Centennial Chair Professor of the Department of Chemical and Biomolecular Engineering Huimin Zhao, has demonstrated the use of an innovative DNA engineering technique to discover potentially valuable functions hidden within bacterial genomes. Their work was reported in a Nature Communications article on December 5, 2013 (DOI: 10.1038/ncomms3894).

The genome of every bacterial species contains genes that can synthesize a diverse arsenal of compounds. These include natural antibiotics, antifungals, and other biochemicals that help the bacteria fight off unfriendly fellow microbes; such compounds are of potentially great medical importance. The genes encoding the enzymes a bacterium needs to create these compounds are often arranged in clusters. Each gene corresponds to one of a set of proteins that work together in a biochemical pathway to create one or a few products.

If a colony of bacteria is producing a biologically active compound, sometimes referred to as a natural product, scientists can isolate it, study its structure and function, and discover its potential uses. Many natural products have already been discovered by screening the compounds produced by different bacterial and other microbial species.

The compounds discovered so far, however, represent a small fraction of those that bacteria are capable of producing.

Bacteria are masters at survival; their genomes represent a set of contingency plans for a wide array of environmental situations. Like a painter laying out a palette with only the colors needed that day, a bacterium will only express the genes and synthesize the compounds that will help it thrive in its current setting. Constant expression of the gene clusters that aren't useful in a given situation would be energetically wasteful.

This conservation of energy is good for bacteria, but bad for researchers hoping to discover new natural products. This was the challenge that Zhao and colleagues hoped to address when they began their project. "Sequence analysis of bacterial genomes indicates that there are many cryptic or silent pathways that have not been discovered," Zhao said. " . . .they need the right signal to turn on expression of the whole gene cluster."

Several strategies have been employed to trick cells into activating their little-used, "cryptic" gene clusters, such as culturing bacteria in a variety of harsh conditions or inserting sets of genes from one species of bacteria into the genome of another species. These techniques involve labor-intensive trial and error, with no guarantee of success.

Zhao's group, rather than attempting to manipulate the environment, focused on reprogramming the control of gene expression within the cell. They used a genetic engineering method previously developed by Zhao's laboratory, called DNA assembler, to insert small sections of DNA between each gene in a cryptic gene cluster. The sections of DNA added were promoters, specialized regions that help control when and how much nearby genes are expressed. By adding the right promoters, Zhao and colleagues forced the cell to increase expression of every gene in the cluster.

What makes Zhao's strategy possible is the ability of the DNA assembler method to join many different fragments of DNA in a single step. Previous methods for DNA editing limited researchers to making a series of sequential changes; the number of experimental steps required to add a promoter to each gene in even a small cluster would have been prohibitive. In contrast, Zhao said, "we can actually build the whole cluster, so that gives us ultimate flexibility, because we can add different promoters," ensuring that every gene within the cluster is consistently activated.

For the study published in Nature Communications, Zhao and his coauthors modified a cryptic cluster of six genes from Streptomyces griseus, a species of soil bacterium. They added a promoter before each gene in the cluster to increase expression, and inserted the cluster into a related bacterial species, Streptomyces lividans, that is easier to grow in a laboratory setting.

The resulting bacterial strain expressed all the genes in the previously silent cluster, and produced several previously unknown compounds. These compounds belonged to a class of natural products called polycyclic tetramate macrolactams or PTMs, many of which have useful biomedical applications. By examining the compounds produced by strains missing one of the six genes in the cluster, the researchers were able to discover the function of each gene's encoded protein, leading to a better understanding of how bacteria synthesize PTMs.

Zhao sees the work as an important step toward a larger goal: to create a generalized, automated high-throughput method to reconstruct any biochemical pathway in a target experimental organism. Zhao is the leader of the recently formed Biosystems Design Research Theme at the Institute for Genomic Biology, University of Illinois, and development of this type of method is a major goal of the Theme.

"We want the technology platform established, then we can actually work on mammalian systems, on plant systems, on microorganisms," said Zhao. Yet his ultimate motivation is the discovery of potentially useful biochemicals: "It's very likely some of the compounds will turn into new drugs, and that's very exciting."


'/>"/>

Contact: Nicholas Vasi
nvasi@illinois.edu
Institute for Genomic Biology, University of Illinois at Urbana-Champaign
Source:Eurekalert

Related biology news :

1. New method for stabilizing hemoglobin could lead to stable vaccines, artificial blood
2. SU biologist develops method for monitoring shipping noise in dolphin habitat
3. UCSB biomedical scientist discovers a new method to increase survival in sepsis
4. New method to diagnose sepsis is faster, cheaper
5. Rice University method gives accurate picture of gas storage by microscopic cages
6. MU study finds more accurate method to diagnose pancreatic cancer
7. New methods improve quagga and zebra mussel identification
8. Laser technology sorting method can improve Capsicum pepper seed quality
9. Researchers develop rapid, cost-effective early detection method for organ transplant injury
10. Scientists develop method that ensures safe research on deadly flu viruses
11. UTSA, Southwest Research Institute to develop low-cost method to treat fracking water
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:2/2/2016)... YORK , Feb. 2, 2016 /PRNewswire/ ... facilities are primarily focused on medical screening ... measure point-of-care parameters. Wearable devices that facilitate ... user,s freedom of movement are being bolstered ... for human biomedical signal acquisition coupled with ...
(Date:2/2/2016)... --Technology Enhancements Accelerate Growth of X-ray Imaging This ... computed radiography markets in Thailand , ... (TIM). It provides an in-depth analysis of ... regional market drivers and restraints. The study offers revenue ... attractiveness, both for digital and computed radiography. Market participants ...
(Date:2/1/2016)... Canada , February 1, 2016 ... technological advancements to drive global touchfree intuitive gesture control ... --> Rising sales of consumer electronics coupled ... gesture control market size through ... consumer electronics coupled with new technological advancements to drive ...
Breaking Biology News(10 mins):
(Date:2/11/2016)... ... February 11, 2016 , ... Reichert Technologies, ... continues today to pursue the highest level of accuracy and quality with the ... Refractometer and the AR5 Refractometer. Accurate, reliable and tough enough for the ...
(Date:2/11/2016)... ... , ... Global Stem Cells Group, has announced ... new facility will provide advanced protocols and state-of-the-art techniques in cellular medicine, focusing ... The new GSCG clinic is headed by four prominent Ecuadorian physicians, including Pablo ...
(Date:2/10/2016)... 10, 2016 Early-career researchers from ... Peru , Uganda and Yemen ... health and nutrition   Indonesia , ... and Yemen are being honored for their ... are also celebrated for mentoring young women scientists who are pursuing careers ...
(Date:2/10/2016)... Feb. 10, 2016 NX Prenatal Inc., a ... NeXosome® technology for early warning of adverse pregnancy ... recent study by Dr. Thomas McElrath ... Maternal Fetal Medicine,s (SMFM) annual meeting held in ... , 2016.  The presentation reported initial positive top-line ...
Breaking Biology Technology: