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Genetically encoded reporter proteins have been a mainstay of biotechnology research, allowing scientists to track gene expression, understand intracellular processes and debug engineered genetic circuits. But conventional reporting schemes that rely on fluorescence and other optical approaches come with practical limitations that could cast a shadow over the field's future progress. Now, researchers at the University of Washington and Microsoft have created a "nanopore-tal" into what is happening inside these complex biological systems, allowing scientists to see reporter proteins in a whole new light.

The team introduced a new class of reporter proteins that can be directly read by a commercially available nanopore sensing device. The new system ? dubbed "Nanopore-addressable protein Tags Engineered as Reporters" or "NanoporeTERs" can detect multiple protein expression levels from bacterial and human cell cultures far beyond the capacity of existing techniques.

The study was published Aug. 12, 2021 in Nature Biotechnology. "NanoporeTERs offer a new and richer lexicon for engineered cells to express themselves and shed new light on the factors they are designed to track. They can tell us a lot more about what is happening in their environment all at once," said co-lead author Nicolas Cardozo, a doctoral student with the UW Molecular Engineering and Sciences Institute.

"We're essentially making it possible for these cells to 'talk' to computers about what's happening in their surroundings at a new level of detail, scale and efficiency that will enable deeper analysis than what we could do before." For conventional labeling methods, researchers can track only a few optical reporter proteins, such as green fluorescent protein, simultaneously because of their overlapping spectral properties. For example, it's difficult to distinguish between more than three different colors of fluorescent proteins at once. In contrast, NanoporeTERs were designed to carry distinct protein "barcodes" composed of strings of amino acids that, when used in combination, allow at least ten times more multiplexing possibilities.

These synthetic proteins are secreted outside of a cell into the surrounding environment, where researchers can collect and analyze them using a commercially available nanopore array. Here, the team used the Oxford Nanopore Technologies MinION device.

The researchers engineered the NanoporeTER proteins with charged "tails" so that they can be pulled into the nanopore sensors by an electric field. Then the team uses machine learning to classify the electrical signals for each NanoporeTER barcode in order to determine each protein's output levels.

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"This is a fundamentally new interface between cells and computers," said senior author Jeff Nivala, a UW research assistant professor in the Paul G. Allen School of Computer Science & Engineering. "One analogy I like to make is that fluorescent protein reporters are like lighthouses, and NanoporeTERs are like messages in a bottle.

"Lighthouses are really useful for communicating a physical location, as you can literally see where the signal is coming from, but it's hard to pack more information into that kind of signal. A message in a bottle, on the other hand, can pack a lot of information into a very small vessel, and you can send many of them off to another location to be read. You might lose sight of the precise physical location where the messages were sent, but for many applications that's not going to be an issue."

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