Long-Ignored Microproteins Play Important Roles in Biological Processes
Photo: Chia-Chi Charlie Chang
The smallest proteins play some of biology’s most important roles. However, they’ve been overlooked because identifying something so tiny is challenging, said Dr. Gisela Storz, who recently delivered the G. Burroughs Mider Lecture in Lipsett Amphitheatre.
“There are thousands of microproteins waiting to be discovered. We’re missing many, many proteins. They serve as regulators in all domains of life,” said Storz, an NIH Distinguished Investigator in the section on environmental gene regulation in NIH’s Eunice Kennedy Shriver National Institute of Child Health and Human Development.
Proteins—the building blocks of life—play pivotal roles in all biological processes. Scientists have studied protein activity, determined the shape and structure of millions of proteins and can accurately predict the function of many proteins.
“Despite all that we’ve learned, there’s a class of proteins that have long been ignored,” she said.
This class, known as microproteins, measures 50 amino acids or less in bacteria and 100 amino acids or less in eukaryotes. Standard-sized proteins are several times larger, for comparison. What’s undiscovered make up the “dark proteome.”
Most techniques to identify and characterize proteins do not work for the smallest proteins, Storz said. Researchers also face challenges in annotation, the process of identifying and assigning biological information to specific locations within a genome’s DNA sequence.
“It’s hard to convey how difficult it is to work on these small proteins,” she said. “There’s a reason people didn’t work on them.”
The first microproteins were discovered serendipitously, Storz said. Now, there are new approaches for detecting microproteins. One method is ribosome profiling. This technique allows researchers to precisely determine which messenger RNAs are actively being translated into proteins in cells. Computational approaches for detecting microproteins have also advanced.
Storz and her lab have been searching for microproteins in bacteria like Escherichia coli using these techniques. The microproteins they’ve identified perform important roles in cell function.
One microprotein that is 15 amino acids long binds to the cAMP receptor (CRP), a transcription factor that helps turn specific genes on or off by binding to nearby DNA. CRP regulates genes involved in energy metabolism. Typically, E. coli cells prefer glucose as a energy source. However, bacteria live in ever-changing conditions, so glucose is not always available. In E. coli, CRP activates when glucose is absent. This allows the bacteria to use other energy sources.
“I wonder how many other transcription factors are out there in other bacteria or eukaryotic cells whose activity is modulated by such a small protein,” Storz said.
Photo: Chia-Chi Charlie Chang
The majority of microproteins that have been discovered are located in cell membranes. One binds to glycerol 3-phosphate dehydrogenase, an enzyme that’s located on the outer surface of a cell’s inner membrane. It’s crucial for lipid metabolism and energy production. “Interestingly, another small protein that binds a different dehydrogenase is specifically induced under conditions of heat shock,” Storz said.
One microprotein that’s 48 amino acids long is induced when cells are exposed to antibiotics or other harmful chemicals and modifies the specificity of a drug efflux pump, she said. Microproteins like this one could explain why bacteria are resistant to so many drugs. Further study might one day help scientists develop new therapies against antibiotic-resistant bacteria.
A microprotein that’s 31 amino acids long binds to a larger protein that transports magnesium through an E. coli cell’s membrane. Magnesium is important for many cellular functions. Storz thinks the smaller protein helps stabilize the transporter. Right now, her lab is searching for more microproteins that aid other proteins in transporting critical ions, including calcium and zinc.
There are many unanswered questions about the vast and largely unexplored potential of small proteins in cellular processes, Storz concluded. Further research is needed to understand how these proteins function.
The G. Burroughs Mider Lecture was established in 1968 in honor of the first NIH director of laboratories and clinics. It is presented by an NIH intramural scientist to recognize and appreciate outstanding contributions to biomedical research. This lecture, part of the NIH Research Festival, was the first Wednesday Afternoon Lecture of the 2025-2026 season.