Novel protein manufacturing process could pave way for new drugs

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Researchers have developed a novel way of manufacturing proteins using which it will become easier for students to learn how proteins work and how to fix them when they are broken and also pave way for novel drugs that could target a myriad of diseases, including cancer.

Researchers at Northwestern University and Yale University used a special strain of E. coli bacteria to build a cell-free protein synthesis platform technology that can manufacture large quantities of human phosphoproteins for scientific study. The technology holds promise of letting scientists learn in greater detail the structure of phosphoproteins, how they function, and which ones are involved with diseases.

Scientist involved with the study explain that our bodies have a nifty way of turning its proteins on and off to alter their function and activity in cells. This process called phosphorylation is a reversible attachment of phosphate groups to proteins. This attachment provide an enormous variety of function and are essential to all forms of life. However, researchers have known little about how the dynamic process works in humans.

“This innovation will help advance the understanding of human biochemistry and physiology,” said Michael C. Jewett, a biochemical engineer who led the Northwestern team.

a) Schematic of the production and utilization of an S30 crude extract containing the Sep-OTS for phosphoprotein biosynthesis. The plasmid-based Sep-OTS is induced during cell growth in the presence of Sep supplemented to the culture media. Cells expressing the Sep-OTS are then collected, lysed and processed to generate S30 extracts. CFPS reactions are supplemented with nucleoside triphosphates (NTPs), amino acids, T7 RNA polymerase and template plasmid DNA to direct the transcription and translation of a desired phosphoprotein product. (b) Schematic of the Sep-OTS. tRNASep is aminoacylated with Sep by SepRS. EF-Sep then delivers Sep-tRNASep to the ribosome. Site-specific incorporation of Sep at UAG (amber codon) is directed via the CUA anticodon of tRNASep. (c) Time-course and endpoint analysis of sfGFP-S2TAG with sfGFP-S2TAG DNA template added (dark grey) and as a control with no template DNA added (white). Expression of wild-type sfGFP-S2S (black) in the presence of the Sep-OTS. Error bars represent s.d. from three independent samples. (d) Annotated tandem mass spectrum from sfGFP-S2TAG confirming the site-specific incorporation of Sep at position S2. Doubly charged ions and fragments that have lost ammonia are marked by ++ and * respectively.
a) Schematic of the production and utilization of an S30 crude extract containing the Sep-OTS for phosphoprotein biosynthesis. The plasmid-based Sep-OTS is induced during cell growth in the presence of Sep supplemented to the culture media. Cells expressing the Sep-OTS are then collected, lysed and processed to generate S30 extracts. CFPS reactions are supplemented with nucleoside triphosphates (NTPs), amino acids, T7 RNA polymerase and template plasmid DNA to direct the transcription and translation of a desired phosphoprotein product. (b) Schematic of the Sep-OTS. tRNASep is aminoacylated with Sep by SepRS. EF-Sep then delivers Sep-tRNASep to the ribosome. Site-specific incorporation of Sep at UAG (amber codon) is directed via the CUA anticodon of tRNASep. (c) Time-course and endpoint analysis of sfGFP-S2TAG with sfGFP-S2TAG DNA template added (dark grey) and as a control with no template DNA added (white). Expression of wild-type sfGFP-S2S (black) in the presence of the Sep-OTS. Error bars represent s.d. from three independent samples. (d) Annotated tandem mass spectrum from sfGFP-S2TAG confirming the site-specific incorporation of Sep at position S2. Doubly charged ions and fragments that have lost ammonia are marked by ++ and * respectively.

Researchers explain that the problem starts when there is trouble in the phosphorylation process. Such trouble is known to cause a range of diseases including cancer, inflammation and Alzheimer’s disease. With proteins being phosphorylated at more than 100,000 unique sites, scientists have a huge and daunting task at hand when it comes to understanding their role in disease.

This is where the new cell-free protein synthesis platform technology comes to aid as researchers can make the special proteins at unprecedented yields all the while being free from the constraints of a living organisms.

“The consequence of this innovative strategy is enormous”, Jewett says.

The Northwestern team worked with a team from Yale led by Jesse Rinehart for this study. They combined state-of-the-art genome engineering tools and engineered biological “parts” into a “plug-and-play” protein expression platform that is cell-free. Cell-free systems activate complex biological systems without using living intact cells. Crude cell lysates, or extracts, are employed instead.

Specifically, the researchers prepared cell lysates of genomically recoded bacteria that incorporate amino acids not found in nature. This allowed them to harness the cell’s engineered machinery and turn it into a factory, capable of on-demand biomanufacturing new classes of proteins.

“This manufacturing technology will enable scientists to decrypt the phosphorylation ‘code’ that exists in the human proteome,” said Javin P. Oza, the lead author of the study and a postdoctoral fellow in Jewett’s lab.

To demonstrate their cell-free platform technology, the researchers produced a human kinase that is involved in tumor cell proliferation and showed that it was functional and active. Kinase is an enzyme (a protein acting as a catalyst) that transfers a phosphate group onto a protein. Through this process, kinases activate the function of proteins within the cell. Kinases are implicated in many diseases and, therefore, of particular interest.

“The ability to produce kinases for study should be useful in learning how these proteins function and in developing new types of drugs,” Jewett said.

The study has been published in journal Nature Communications.