Research Emphasis: Huatao Guo, PhD researches the biology and practical applications of Diversity‐Generating Retroelements (DGRs). DGRs are molecular evolution machines that are widely distributed in bacteria, archaea, and their viruses. They use an RNA-guided, reverse transcriptase (RT)-mediated mechanism to diversify protein-encoding sequences. This facilitates the adaption of their hosts to changing environments. In addition, DGRs are abundant in human gut viromes, suggesting that they play important roles in the dynamic regulation of human gut microbiomes. The prototype DGR was discovered in a bacteriophage (BPP-1) that infects Bordetella species. These are gram-negative bacterial pathogens that colonize the respiratory tracts of humans and mammals.
Recently, Dr. Guo’s research showed that mutagenic homing of the BPP-1 DGR occurs through a template RNA-primed reverse transcription (TRPRT) mechanism, in which the RNA sequence downstream of TR folds back to anneal to the 3′ end of TR and is site-specifically cleaved to initiate cDNA synthesis. Adenine‐specific mutagenesis occurs during minus-strand cDNA synthesis and is a result of error-prone incorporation of standard deoxyribonucleotides when the RT protein copies adenine residues in the template RNA. It remains unknown how the primer RNA sequence is cleaved for cDNA initiation and how the mutated cDNA sequence replaces the parental VR. In addition, the mechanism of adenine-specific misincorporation by the BPP-1 DGR RT is also unknown. Dr. Guo’s research is meant to provide solutions for and improved treatment of bacterial and retroviral infectious diseases.
Wu L, Gingery M, Abebe M, Arambula D, Czornyj E, Handa S, Khan H, Liu M, Pohlschröder M, Shaw K, Du A, Guo H, Ghosh P, Miller JF, Zimmerly S. Diversity-Generating Retroelements: Natural Variation, Classification and Evolution Inferred from a Large-Scale Genomic Survey. Nucleic Acids Res, Accepted.
Naorem SS, Han J, Wang S, Lee WR, Heng X, Miller JF, Guo H. DGR mutagenic transposition occurs via hypermutagenic reverse transcription primed by nicked template RNA. Proc Natl Acad Sci U S A, doi: 10.1073/pnas.1715952114.
Zhang, X., Guo, H., Jin, L., Czovnyj, E., Hodes, A., Hui, W.H., Nieh, A.W., Miller, J.F., and Zhou, Z.H. A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 A resolution. eLife. 2:e01299.
Guo, H.*, Arambula, D., Ghosh, P., and Miller, J.F.* 2014. Diversity-generating Retroelements in Phage and Bacterial Genomes. Microbiol. Spectrum. 2(6): MDNA3-0029-2014. (Online publication of a book chapter in Mobile DNA, 3rd edition) (*Co-corresponding author)
Arambula D., Wong W., Medhekar B.A., Guo H., Gingery M., Czornyj E., Liu M., Dey S., Ghosh P., and J.F. Miller. 2013. Surface display of a massively variable lipoprotein by a Legionella diversity-generating retroelement. Proc Natl Acad Sci U S A 110(20):8212-8217.
Alayyoubi, M.*, Guo, H.*, Dey, S., Golnazarian, T., Brooks, G.A., Rong, A., Miller, J.F., and P. Ghosh. 2013. Structure of the essential diversity-generating retroelement protein bAvd and its functionally important interaction with reverse transcriptase. Structure 21(2):266-76. (*Co-first author)
Guo, H., Tse, L.V., Nieh, A.W., Czovnyj, E., Williams, S., Oukil, S., Liu, V.B., and J.F. Miller. 2011. Target site recognition by a diversity-generating retroelement. PLoS Genet 7(12): e1002414
Guo, H., Tse, L.V., Barbalat, R., Sivaamnuaiphorn, S., Xu, M., Doulatov, S., and J.F. Miller. 2008. Diversity-generating retroelement homing regenerates target sequences for repeated rounds of codon rewriting and protein diversification. Mol Cell 31(6):813-823.
Karberg, M., Guo, H., Zhong, J., Coon, R., Perutka, J., and A.M. Lambowitz. 2001. Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria. Nature Biotechnol 19(12):1162-1167.