New Protein Discovered That Is A Mechanism For Adaptations In Bacteria

Spy Protein

Molecular model of the Spy protein

A new discovery has just been made by biochemist James Bardwell and his team from the University of Michigan, Howard Hughes Medical Institute, McGill University and the National Research Council of Canada’s Biotechnology Research Institute. Their findings include a model of the protein obtained from the Canadian Light Source.   The research paper, entitled Genetic selection designed to stabilize proteins uncovers a chaperone called Spy” was published in the journal Nature Structural and Molecular Biology, DOI:10.1038/nsmb.2016.

The researchers challenged Escherichia coli to stabilize (survive) against a penicillin forcing the bacteria to either fold proteins or die.  The result was a massively overproduced periplasmic protein called Spy. The abstract of the research paper states,

“The structure of Spy is unlike that of any previously solved chaperone, making it the prototypical member of a new class of small chaperones that facilitate protein refolding in the absence of energy cofactors.”

A prototype is a selective breeding term based upon Gregor Mendelian genetics.   Identical replicas of life forms that are deemed to be a perfect display of quality physical traits can be reproduced by bioengineering the offspring to be an exact phenotype match appearing identical to the prototype model.  This is typically accomplished by inbreeding offspring back to a parent.  Show dogs and thoroughbred race horses are examples of prototypes.

Overall Experimental Scheme

Overall Experimental Scheme

The fact that there are prototypes in nature are evidence of design.  Cladistically, phylogenetically, and taxonomically, the first life form representing each clade, genus, phylum, or taxon is a genetic prototype model of that genre of life.

According to Mendelian laws of genetics, variations of species are somewhat limited to the information in the genome of that population.  The laws that apply to inheritance pull the genotype of each new generation back to the original prototype ancestral model of that lineage.  It’s a force in nature to preserve original design models by recessive genes being overpowered by the dominant genes of the prototype, which according to ID Theory was predicted to be the original design of that genre of life form.

The SPY Protien

Crystal structure of the Spy dimer shown in three orientations rotated by 90° along the vertical axis.

Dr. Bardwell described the experiment to, “We gave the bacteria a pretty stark choice – fold proteins or die.”  He explained the researchers linked making a stable target protein in strains of E. coli to their resistance to penicillin.  “The bacteria could survive only if they could also fold the target protein really well.”

Molecular biologists classify the protein “Spy” as a molecular chaperone, which means it is a type of molecule that facilitates the folding of other proteins.  Spy (short for spheroplast protein Y) had been previously identified inside bacteria, but its function wasn’t understood until this research.  The amount of Spy normally present in cells is infinitesimally small, but in response to stress it is made in huge amounts.

“A lot of people were surprised that such well-studied bacteria as E. coli had a chaperone that had remained undiscovered,” said Dr. Bardwell. “But many assay tests that look for chaperones wouldn’t find Spy; then again, no one else has tried to genetically select for protein folding like we did.”

A dual fusion selection for enhancing in vivo protein stability.

A dual fusion selection for enhancing in vivo protein stability.

Spy increases the steady-state levels of a set of unstable protein mutants by an impressive 700 times in quantity.  Spy protein functions without any dependence on ATP Synthase, suppresses protein aggregation, and aids protein refolding.  The research team offers strategy to facilitate future chaperone discoveries. 

Spy also forms thin, apparently flexible cradle-shaped dimers.  The article describes Spy as one of the thinnest chaperone molecues ever found, “the same thickness, roughly, of nine hydrogen atoms.”

The Spy’s cradle-shape may allow it to surround larger proteins, enabling them to fold properly while protecting them from harmful influences.  “It kind of acts like Teflon or a candy wrapper, covering the proteins and keeping them from clumping and sticking together,” Dr. Bardwell noted.

Protein folding is also evidence of design as noted in this research paper entitled, “The Case Against a Darwinian Origin of Protein Folds” – It is discussed further in the ID blog linked here,

Spy is a newly discovered protein that provides bacteria their remarkable ability to adapt and evolve into new impressive strains, such as nylonase.  Many proteins used in pharmaceuticals, such as insulin, have been able to be manufactured in the past by bacteria that have had the instructions for making the desired protein inserted into their genetic code.

Spy is a molecule that operates as a simple engine that powerfully facilitates the folding of proteins, finally offering us an explanation as to how bacteria are capable of so readily adapting to new conditions.  This molecular machinery has been equipping bacteria for billions of years to adapt and with terms like “prototypical” have undoubtedly existed before the existence of the first cell.  That such complexity existed at the very origin of life itself testifies as evidence for design.

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