New publication utilizing metagenomic data for understanding the evolution of translation

Complex evolutionary history of translation Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids

This is the product of a great collaboration with some excellent labs and people.

Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key-residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.

GBE paper figure 3

Graduation

The lab feels like it’s emptying out, with 1 PhD, 1 MS, and 2 BS graduates this May. Congratulations to:
Dr. Adrienne Narrowe, PhD (with both the College of Liberal Arts and Sciences and the Department of Integrative Biology outstanding Defense awards)
David Banks-Richardson, MS Biology
Maria Nikulkova, BS Biology
Connor Jacobs, BS Biology

A great accomplishment for each of them, and I can’t wait to see what each accomplishes next.

New freshwater wetlands / methane publication

Our Old Woman Creek Wetlands team has a new publication out revealing that much of the methane in this wetland appears to come from a novel methanogen residing in surface, oxygenated soils.  Congratulations and thanks to the Wrighton and Bohrer labs, who led this work.

Angle, J.C., Morin, T.H., Solden, L.M., Narrowe, A.B., Smith, G.J., Borton, M.A., Rey-Sanchez, C., Daly, R.A., Mirfenderesgi, G., Hoyt, D.W., Riley, W.J., Miller, C.S., Bohrer, G. & Wrighton, K.C., 2017. Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions. Nature Communications, 8(1), p.1567.

https://www.nature.com/articles/s41467-017-01753-4

Figure 2 explains why this archaea is called Candidatus Methanothrix paradoxum.  This paper is the whole enchilada: genomics, transcriptomics, extensive in situ methane measurements, emissions modeling, 16S and biogeography.

 

Mallika Iyer, MS

Congratulations to Mallika, who successfully defended her MS Thesis, “Prediction of Prokaryotic Optimum Growth Temperature Based on Genomic And Proteomic Features.”  Mallika did a great job, showing her mastery of her research and the literature.

Mallika is off to the Burnham Institute to pursue her PhD with Adam Godzik.