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For success with heterologous genes, look beyond sequence

Scientists at the Technical University of Denmark upend conventional wisdom about introducing new genes into bacteria.

Why do some foreign genes work well in a new host and some do not? The reasons are critical for synthetic biologists who add heterologous genes to bacteria. The issue is clinically relevant, since bacteria gain antibiotic resistance through gene transfer. Postdoctoral fellow Andreas Porse and Professor Morten Sommer at the Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, have new answers in their Nature Communications paper.

“Our motivation was to systematically rank the parameters that determine heterologous gene integration,” Porse says.

Earlier studies, Sommer says, pointed to sequence factors such as the way amino acids are coded as important for introducing new genes into cells. Those studies, though, were based on in silico modeling or experiments with one or a few genes. Porse et al. tested 200 antibiotic-resistance genes from a range of species. The gene products targeted diverse antibiotics, using mechanisms from degrading drugs to pumping them from cells. The researchers used growth and resistance to 20 antibiotics as a measure of gene compatibility with the Escherichia coli host.

Mechanism over sequence

“One of our main conclusions,” Sommer says, “was the extent to which the function of the gene determines how well it integrates into the host.”

Genes for proteins that interact with host structures, such as pumps that insert into membranes, were less likely to work and tended to be a burden when expressed in a new host. Genes for proteins that act independently, for example by modifying or degrading drugs, tended to perform well. Porse et al. found that for an introduced gene to function in a new host, its biochemical mechanism matters more than its sequence.

“It’s important to think about how the encoded protein interacts with cell physiology.”

“Industry tends to focus on sequences and gene expression,” Porse says. “We showed that it’s important to think about how the encoded protein interacts with cell physiology.”

The scientists also found that phylogenetic relatedness between gene donor and host mattered, but only for genes whose products interact with cell components. For example, E. coli tended to grow better with genes from other gram-negative compared to gram-positive bacteria. The bottom line, Sommer says, is when adding new genes to cells, consider the activity and mechanism of the gene product—If it must interact with membranes, proteins, or complexes, find a gene from a species closely related to the host.

Porse is now studying why some heterologous genes integrate poorly and how cells compensate. Sommer is chief scientific officer of AntibioTx, which develops antibiotics, but says these studies are part of his group’s basic research. The overall goal, he says, is “generating data to develop models that can explain and predict antibiotic resistance.”

 

Sommer and Porse

Andreas Porse and Morten Sommer

REFERENCE

Porse A, Schou TS, Munck C, Ellabaan MMH, Sommer MOA. Biochemical mechanisms determine the functional compatibility of heterologous genes. Nature Communications. 2018;9:522