Pool engineering using sequence-optimized ribosomes can significantly improve protein synthesis yields, thus lowering drug manufacturing costs, according to recent research from Northwestern University and Stanford University.

Beyond improving protein synthesis yields, “This work more broadly suggests that ribosome pools can be customized to maximize expression of specific proteins for biotechnology and synthetic biology applications,” Michael C. Jewett, PhD, at the department of chemical and biological engineering, Northwestern University, and department of bioengineering, Stanford University, tells GEN.

“This is a totally new way of thinking about biomanufacturing,” he says. “It holds the promise to transform the bioeconomy.”

Writing in ACS Central Science, Jewett and colleagues studied seven unique ribosomal RNA operons in Escherichia coli, a common host for recombinant protein synthesis, to understand how sequence differences in their RNA lead to functional changes in their ability to make proteins.

“While ribosomes are typically thought of as uniform molecular assemblies, protein synthesis in cells is performed by a pool of heterogeneous ribosomes whose differences arise from the unique ribosomal sequences that exist in the genome of all organisms,” Jewett says. The question for this group, then, was “whether these unique operon sequences lead to ribosomes that are functionally distinct in their protein synthesis abilities.”

Surprising findings

Their research revealed three unexpected findings:

  1. “The diversity of expression yields from the different ribosomal RNA operons was surprising,” Jewett says. For example, some polymorphisms in individual native coli ribosomal RNA operons cause significant functional changes in the resulting ribosomes, such as reducing their translation ability.
  2. “Expression yields from a best single operon performed better in making a panel of industrially relevant proteins than a heterologous pool of ribosomes,” he says. For example, single-operon lysates each produced more protein than those made from the parent strain. One, which contained only operon A rRNA, increased protein production by almost three-fold.
  3. “Ribosomes derived from one of the seven operons were essentially nonfunctional. This suggests the native coli ribosome pool may be diluted with low-performing variants under the lab conditions tested,” Jewett adds. Therefore, the ribosome pool could be strengthened by replacing weaker variants with more productive ones.

“Looking ahead,” notes Jewett, “our work suggests the ribosome sequences in the genomes of biomanufacturing strains could be manipulated to increase recombinant protein synthesis yields. It opens a whole new world of possibilities.”

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