Scientists scratch new universe of miniproteins with variable functions

Researchers have been exploring the new universe of mini proteins with variable functions

A DNA double helix is seen in an undated artist's illustration released by the National Human Genome Research Institute to Reuters on May 15, 2012. A group of 25 scientists June 2, 2016, proposed an ambitious project to create a synthetic human genome, or genetic blueprint, in an endeavor that is bound to raise concerns over the extent to which human life can or should be engineered. Reuters

Biologists are beginning to delve into the world of micro proteins, micro peptides or mini proteins, which perform a number of functions such as bolstering the immune system, controlling destruction of faulty RNA molecules, protecting bacteria from heat and cold, dictating when plants flower, as well as, providing the toxic punch for many types of venom. Their small size, however, also seems to allow them to jam the intricate workings of larger proteins, inhibiting some cellular processes while unleashing others, scientists have found through experiments.

"There's probably going to be small [proteins] involved in all biological processes. We just haven't looked for them before," biochemist Alan Saghatelian from the Salk Institute for Biological Studies in San Diego, California, said. These molecules also promise to revise the current understanding of the genome as many are encoded in stretches of DNA and RNA that were earlier not thought to help build proteins of any sort.

Scientists have also been speculating that the short stretches of DNA can be newborn genes on their way to evolving into larger genes that make full-size proteins."We need to rethink what genes are," said microbiologist and molecular biologist Gisela Storz from the National Institute of Child Health and Human Development in Maryland.

Dystrophin, a structural protein whose gene can carry mutations that cause muscular dystrophy, has more than 3,600 amino acids, while Titin that acts like a spring to give muscle elasticity is the biggest known protein with more than 34,000 amino acids.

Muscle biologist Eric Olson of the University of Texas Southwestern Medical Center in Dallas and colleagues in an experiment came up with an extraordinary mouse, who on a treadmill could scurry up a steep 10 percent grade for about 90 minutes before faltering, which is 31 percent longer than other rodents that can log 10 km or more per night on the exercise wheel.

Researchers had genetically altered the mice to lack tiny muscle protein called myoregulin that unleashed superior muscle performance. "It's like you've taken the brakes off," American Association for the Advancement of Science quoted Olson as saying.Scientists now realize their initial rules for analyzing genomes discriminated against identifying those pint-size molecules and have now been uncovering minuscule proteins not just in mice but in many other species, including humans.

Researchers are testing potential uses for the molecules, with one company already selling insecticides derived from small proteins in the poison of an Australian funnel-web spider. Another clinical trial is evaluating an imaging agent based on another minute protein in scorpion venom that highlights the borders of tumors so that surgeons can remove them more precisely.

Small proteins came to light about 20 years ago when scientists while analyzing an organism's genome scanned for open reading frames (ORFs), which are DNA sequences demarcated by signals that tell the cell's ribosomes, its protein-making assembly lines, where to start and stop. Researchers in the past typically excluded any ORF that would yield a protein smaller than 100 amino acids in eukaryotes or 50 amino acids in bacteria.

Stanford postdoc Hila Sberro Livnat, microbial genomicist Ami Bhatt of Stanford University in Palo Alto, and colleagues earlier this year trawled genome fragments from the microbes that inhabit four parts of the human body, including the gut and skin, and identified about 4,000 families of potential microproteins by searching for small ORFs that could encode proteins between five and 50 amino acids long.

"For the first time, we are about to explore this universe of new proteins," said biochemist Jonathan Weissman of the University of California in San Francisco, who along with colleagues found microproteins through a method they invented to determine which proteins cells made. He and his team in a 2011 Cell study applied a ribosome profiling method called Ribo-seq to mouse embryonic stem cells and discover the cells were making thousands of unexpected proteins, including many that would fall below the 100–amino-acid cutoff.

Biochemist Alan Saghatelian from the Salk Institute for Biological Studies in San Diego discovered a trove of microproteins in human cells by using mass spectrometry that involved breaking up proteins into pieces sorted by mass to produce a distinctive spectrum for each protein.Chemist Julio Camarero of the University of Southern California in Los Angeles said, being small limited a protein's capabilities, while larger proteins folded into complex shapes suited for a particular function such as catalyzing chemical reactions.

Because of their attraction to larger proteins, small proteins may give cells a reversible way to switch larger proteins on or off, suggested a 2016 study published in PLOS Genetics in which plant developmental biologist Stephan Wenkel of the University of Copenhagen and colleagues genetically altered Arabidopsis plants to produce extra amounts of two small proteins.

The tiny proteins delayed flowering in the plants, which normally flower when the days are long enough. Slavoff, Saghatelian, and colleagues in 2016 revealed that human cells manufacture a 68–amino-acid protein named NoBody that managed the destruction of faulty or unneeded mRNA molecules. NoBody's name reflects its role in preventing the formation of processing bodies (P-bodies), mysterious clusters in the cytoplasm where RNA breakdown may occur. "It shows that small proteins can have massive effects in the cell," Slavoff says.

Storz and her team in 2012 suggested a previously undiscovered 49–amino-acid protein called AcrZ helps intestinal bacterium Escherichia coli survive antibiotics by stimulating a pump that expels the drugs. Many components in venom produced by a variety of organisms, including spiders, centipedes, scorpions, and poisonous mollusks, disable or kill by blocking the channels for sodium or other ions that are necessary for the transmission of nerve impulses.

Cancer researchers are trying to capitalize on the poison of African and Middle Eastern deathstalker scorpion (Leiurus quinquestriatus) microprotein which has a mysterious attraction to tumors. The small proteins appear to have a huge potential in the field of medicine, but the DNA sequences for tiny proteins occur in unconventional locations as some lie near the ORFs for bigger proteins.

Those genomic surprises could illuminate how new genes arise, said evolutionary systems biologist Anne-Ruxandra Carvunis of the University of Pittsburgh in Pennsylvania, who believed microproteins suggested protogenes could form when mutations created new start and stop signals in a noncoding portion of the genome.