The paradox of evolving to change but retain activity

Science Spotlight

The paradox of evolving to change but retain activity

July 18, 2016

APOBEC3A may have been born to restrict deleterious endogenous elements like the LINE-1 retrotransposon. However, over the span of primate evolution, APOBEC3A gained the ability to restrict other pathogens like infectious viruses. Though APOBEC3A probably gained restriction of several different viruses over this time period, all of the mutations necessary to encode these changing functions occurred in a precise manner that preserved the ability of APOBEC3A to restrict LINE-1.
Image provided by Dr. Rick McLaughlin Jr.

In 1950, an American biologist named Barbara McClintock published a paper describing her observations of mobile genes, pieces of DNA that could change position and spread throughout the genome without following any of the known rules of DNA repair, replication, or recombination2.  In 1983 she was awarded the Nobel Prize for her discoveries, which have changed biology at its very core and led to the 'selfish gene theory' of evolution.  Now, it is widely recognized that autonomous mobile elements make up a significant portion of the human genome. Long interspersed element1 (LINE-1) is one of these mobile elements, also called transposons.  Along with the non-autonomous elements that are also moved by its activity, LINE-1 retrotransposition accounts for 25% of the human genome 3,4.  These LINE-1 elements can be harmful to their host organisms, which include other primates as well as humans, because their movement can disrupt essential genes or cause sterility.  In fact, over one hundred cases of human disease have been associated with LINE-1 insertions5.

APOBEC3A (A3A) is an enzyme that changes the sequence of nucleic acids and has been found to restrict LINE-1 movement in a cell culture (cells grown in a petri dish) model system.   A recent study reported that some primate A3A enzymes do not have the ability to restrict LINE-1 retrotransposition.  In order to study the molecular mechanism and evolutionary history of A3A restriction of LINE-1 movement, researchers in the Malik Laboratory (Basic Sciences Division) and the Emerman Laboratory (Human Biology) characterized A3A from different primate species.  The results of their investigation were recently published in Molecular Biology and Evolution

In research led by postdoctoral fellow Dr. Richard McLaughlin Jr, the scientists began by determining the sequence of the A3A gene in different primate species by analyzing the sequences in public databases and performing some targeted sequencing of A3A in several species of Old World monkeys.  Upon close inspection, they noticed that primers that were used in a previous published investigation to amplify part of the A3A gene also matched sequence in a part of the APOBEC3G (A3G) gene.  When they sequenced A3A in several Old World monkey species using different, unique primers, they identified a novel sequence.  Therefore, several of the previous A3A sequences were in fact artifactual mixtures of the A3A and A3G genes.  Their reconstruction of A3A sequences allowed the researchers in the Malik Lab to construct an evolutionary tree of the primate A3A gene that more closely matched the evolutionary tree of primates in general. 

To get an idea of the evolutionary history of A3A, the scientists searched for evidence of positive selection, which causes innovative changes in protein sequence and results in more changes to a sequence that would be expected from random mutation alone.  After finding evidence of this in the A3A sequence, the scientists set out to determine whether pressure to evolve was exerted by the LINE-1 retrotransposon. If A3A were indeed co-evolving with LINE-1 to restrict its movement, one would expect that a given primate A3A might not be able to restrict the LINE-1 from a different species.  To test this, the researchers expressed the A3A enzyme from a diverse panel of primates in a cell culture model system and tested whether they could restrict the movement of human or mouse LINE-1.  The movement, called retrotransposition, of the LINE-1 can be measured in this system by the expression of a fluorescent reporter molecule.  Surprisingly, the scientists found that all of the A3A enzymes they tested could restrict human and mouse LINE-1.  They conclude that the LINE-1 retrotransposon did not drive the positive selection of A3A

Their findings that diverse primate A3A enzymes have retained the ability to combat LINE-1 retrotransposition suggest that the strong positive selection in A3A they detected is caused by at least one other pathogen.  A3A has been reported to restrict the replication of diverse viruses, including HIV-1.  The scientists tested the ability of a panel of A3A enzymes to inhibit HIV-1 replication.  They found that the A3A of some Old World monkeys such as African green monkey and the rhesus macaque could restrict HIV-1 infection while others, such as human and colobus monkey A3A, could not. Based on these findings, the authors hypothesized that the ability to restrict HIV-1 evolved in the common ancestor of African green monkeys and rhesus macaques, a group known as the Cercopithinae, after they diverged from Colobinae primates such as the colobus monkey.  The scientists reconstructed this ancestral A3A sequence and found that it could restrict HIV-1, lending support to this hypothesis.

Overall, this research demonstrates how diverse pathogenic challenges can shape the evolution of anti-viral proteins. Dr. McLaughlin comments, "We think that A3A is constantly changing to block constantly changing infectious viruses that come and go, but some pathogens reside in our genomes (transposons) and stay around for very long evolutionary time periods.  As a result, we think that A3A has evolved in a way that allows it to consistently block transposons but also change to block newly encountered viruses.  A sort of flexibility amidst rigidity." Studies like these of anti-pathogen 'restriction factors' inform our understanding of how nature fights pathogens and may help us develop preventative methods to fight evolving pathogens.    

1.  McLaughlin Jr. RN, Gable JT, Wittkopp CJ, Emerman M, Malik HS.  2016.  "Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution." Molecular Biology and Evolution

2.  McClintock B.  1950.  "The Origin and Behavior of Mutable Loci in Maize."  PNAS.  36(6): 344-355.

3.  Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. 2001. "Initial sequencing and analysis of the human genome." Nature. 409:860–921.

4.  de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD. 2011. "Repetitive elements may comprise over two-thirds of the human genome." PLoS Genet. 7:e1002384.

5.  Hancks DC, Kazazian HH Jr.  2012.  "Active human retrotransposons: variation and disease."  Curr Opin Genet Dev.  22:191-203.

This research was supported by the Helen Hay Whitney Foundation, the Howard Hughes Medical Institute, the National Institutes of Health, and the Lupus Research Institute.