Research

HSV 2 Oral Infection

People get very sick from HSV 2 (Herpes Simplex Virus Serotype 2) oral infections, which are quickly becoming universal in the human population. Physicians conflate HSV 1 and HSV 2 infections, although HSV 2 infections are much more serious. By choice and training, physicians are incompetent to identify, diagnose and treat HSV 2 oral infections. Contrary to physician beliefs, in people with intact immune systems, HSV 2 oral infections can become chronic and progress to meningitis and death. Physicians and Public Safety have turned a blind eye to a serious and lethal epidemic hiding in plain sight.  

Burton, ZF. “Herpes Simplex Virus Serotype 2 Oral Infection.” JSM Biochem Mol Biol (2016) 3(1):1015.

https://www.nytimes.com/2017/02/04/opinion/sunday/what-happens-when-a-rape-goes-unreported.html?_r=0

Double-Ψ-β-barrels

Multi-subunit RNA polymerases are of the two double-Y-b-barrel type. This explains much of RNA polymerase evolution, function and dynamics.  

Burton ZF, Opron K, Wei G, Geiger JH. “A model for genesis of transcription systems.” Transcription. (2016) Jan 6:0. doi:10.1080/21541264.2015.1128518

Burton ZF. “The Old and New Testaments of gene regulation. Evolution of multi-subunit RNA polymerases and co-evolution of eukaryote complexity with the RNAP II CTD.” Transcription.(2014);5(3):e28674. doi:10.4161/trns.28674

Burton SP, Burton ZF. “The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs.” Transcription.(2014);5(4):e967599. doi:10.4161/21541264.2014.967599

A primordial initiation factor and helix-turn-helix (HTH) repeats

A primordial initiation factor (>4-HTH) gave rise to archaeal TFB (2-HTH) and bacterial sigma factors (sigma70/sigmaA (4-HTH); sigma54/sigmaN (~6-7-HTH). This homology and divergence of general transcription factors appears to explain the divergence of archaea and bacteria. This homology and divergence also permits reasonable modeling of the evolution of transcription systems and promoters.

Burton ZF, Opron K, Wei G, Geiger JH. “A model for genesis of transcription systems.” Transcription. (2016) Jan 6:0. doi:10.1080/21541264.2015.1128518

Burton SP, Burton ZF. “The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs.” Transcription.(2014);5(4):e967599. doi:10.4161/21541264.2014.967599

Transfer RNA as a molecular archetype

tRNA is a molecular archetype around which translation systems evolved. The tRNA cloverleaf has a 75 nucleotide core sequence plus 3’-CCA, where the specified amino acid is attached. tRNA evolved by ligation of three 31 nucleotide minihelices followed by two symmetrical deletions of 9 nucleotides (93-18=75 nucleotides). Acceptor stems and acceptor stem remnants evolved from a GCG repeat and its complement. The D loop evolved from a UAGCC repeat. The anticodon and the T loop evolved from a non-contiguous 17 nucleotide ~CCGGGUUCAAAACCCGG microhelix repeat. A 31 nucleotide minihelix is a 17 nucleotide microhelix + 2 x 7 nucleotide paired acceptor stems (31=17 + 14 nucleotides). Every nucleotide in the 75 nucleotide core sequence of the tRNA cloverleaf is accounted for by the model. Statistical tests support the model. The model describes the evolution of the 3 nucleotide genetic code, which required cloverleaf tRNA. Other models based on a 72 nucleotide tRNA cloverleaf core (caused by a 3 nucleotide deletion in the D loop) that do not consider anticodon loop and T loop homology are incomplete and/or incorrect.   

Root-Bernstein R, Kim Y, Sanjay A, Burton ZF. “tRNA evolution from the proto-tRNA minihelix world.” Transcription. (2016) Sep 16;. doi:10.1080/21541264.2016.1235527     

Pak, D, Root-Bernstein R and Burton, ZF. tRNA structure and evolution and standardization to the three nucleotide genetic code. Transcription (2017) submitted.

Ancient evolution

If you understand evolution of transcription systems and translation systems (see above), you understand much about the inception of living systems on earth.

Burton, ZF. Evolution Since Coding. Academic Press (Elsevier). Coming 2017.