Chytrid Opsin structure paper published

Great work by former graduate student Steven Ahrendt (@sahrendt0), visiting student and current Duke graduate student Edgar Medina (@WhippingFungi) on the publication of a manuscript describing a Type II Opsin found in the zoosporic fungi.  “Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling” in PeerJ! Thanks also to co-author and collaborator Chia-en Chang in Chemistry Dept at UCR who helped mentor Steven on homology modeling and docking analyses. I also learned a lot through this project and was excited to be able to merge evolutionary and computational approaches. The project lead to the surprising findings of a gene important for light sensing that is shared among just the zoosporic (fungi with a flagellate life stage) and animals.

This project has been going for a while … Edgar and I discovered this protein in ~2008 when we started independently analyzing the Batrachochytrium genome, the first chytrid fungus sequenced. Based on sequence similarity we realized it looked like an animal rhodopsin, a 7 transmembrane G-protein coupled receptor (GPCR). These rhodopsins are called type II opsins and typically respond to green light.  We went looking for this in the first place because of work published in 1997 from Ken Foster’s lab which showed that zoosporic chytrid fungi respond to green light and that likely this behavior is due to a rhodopsin or rhodopsin-like GPCR  We found longer intact copy in the genome of the chytrid S. punctatus, so decided to focus on that copy – though we later discovered additional modifications of the predicted gene structure appeared necessary. We decided to do some homology modeling with the solved structure of a squid rhodopsin as shown in Figure 1. This confirmed that the sequence was compatible with the Type II Opsin structure. The paper documents several other computational simulations to test for the likely binding chromophore and hypothesis testing about the stability of the protein structure. Overall this work provides confidence that the sequence encoded in the genome of the zoosporic fungus can fold into a structure compatible with an opsin.

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Figure 1A: Structural alignment of S. punctatus homology model (grey) with T. pacificus crystal structure (light purple)

It still remains to be tested if this opsin-like gene can biochemically function in this way. We hope to explore more of that with some additional work in the future. We have also nearly completed our manuscript analyzing the evolutionary history of this protein in fungi and related species to give a better picture of the timing of the emergence of this receptor-like protein. This project has helped advance some ideas about how zoosporic fungi interact with their environment based on genomic and computational analyses. This gene is a good candidate for future investigations into environmental sensing and signaling in zoosporic fungi.

Asilomar and beyond

Just back from another fantastic Fungal Genetics Conference at Asilomar. An amazing number of helpful tweets under the #Fungal17 hashtag. Sarah Unruh (@sau916) and I are talking about how to best archive or building a storify this so it is easier to read. Always a fun meeting to see friends and nosh at the smorgasbord of fungal genetics, epigenetics, genomics, ecology, evolution, and chemistry that is going on. Jason got to give a Plenary talk and express the utility of sequencing fungal genomes in studying their evolution. Lab Alumnus Steven Ahrendt won a poster award on his work on Cryptomycota fungi and also gave a talk. 


Also got some good news that our paper on structural analyses of a rhodopsin-like protein in the chytrid fungi has been accepted at PeerJ after some helpful revisions – (see the preprint).

Onward!

2016 Round Up – by the numbers

Quick post to sum up some of the news from 2016 and head into 2017.

  • Six manuscripts were published and an additional two were accepted and three more were submitted or being revised in 2016
  • Three graduate students survived another year in the lab: Sawyer, Nat, Derreck
  • Joined by one Microbiology graduate student Jesus Pena joined in Fall 2016.
  • Nine undergraduates worked in the lab Deane, Josh, Jericho, Dillon, Na, Justin, Serena, Leandra, George and Travis has been part of bioinformatics projects
  • One postdoc, Jinfeng has been the bioinformatics and genomics guru from genome assembly to transposon bioinformatics
  • One new assembly of a Citrus genome
  • At least 15 new genomes from our work with Zygolife and 1000 Fungal Genomes project were released or material processed. More than 100 cultures of some fungi are being examined in the lab.
  • One NSF grant started on systematics of anaerobic chytrid fungi and one new grant awarded as part of the UC MRPI http://ucop.edu/research-initiatives/programs/mrpi/2017-Awards.html program on the “UC Valley Fever Research Initiative” lead by UCSF and including several other UC campus.
  • Jason is on sabbatical in 2017 at Oregon State University.

MSA 2016

Some us from the lab took a trip up to Berkeley, CA for the MSA 2016 meeting. We road tripped by car from Riverside through the central valley up to Berkeley.

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At the conference we had a great chance to meet with other mycologists, ecologists, and fungal enthusiasts. The meeting was fantastic from the Clark Kerr campus at UC Berkeley we had dorm life living so everyone was close by and could eat meals together. The talks and posters were really outstanding and such fun to talk about interesting research in fungi. Clearly genomics, next generation sequencing are at the forefront of tools used by the community but new approaches to visualizing communities and exploring the interactions between fungi and partners like bacteria and plants were very well explored in the meeting. Some great work on microbiomes and mycobiomes of insects and amphibians also made for some fascinating new results.  There was a MSA session dedicated to some results from the ZyGoLife project and our team also had a one day meeting earlier in the week at the Joint Genome Institute to catch up on all the different team projects (a long post on this will appear on the zygolife project page soon). It was also fun to catch up with former lab member Steven Ahrendt who now works at JGI on early diverging fungi genome projects.

The meeting also featured Arturo Casadevall as the Karling lecture – an honor to bring in a scientist who is likely an outside member of the MSA community to speak about fungi. Dr Casadevall gave a lecture that covered the importance of collaboration, the impact of the pressure to publish in ‘one word journals’, and reviewed his provocative hypothesis about the link in the success of fungi, dinofall of dinosaurs, and rise of mammals. He also paid tribute to Thomas Taylor, a Zygolife collaborator who sadly passed away this Spring but who would have been the Karling lecturer this year.

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Jason spoke on new population genomics work on Candida and Fusarium, while Sawyer presented a poster on Rhizopus stolonifer resequencing and population genomics; Derreck presented a poster on Bacteria-Fungi interactions on Serratia and zygomycete fungi; Nat presented his poster on data from first environmental sequencing of desert biological soil crusts from Joshua Tree National Park. On the way back we stopped for an overnight in Pinnacles National Park. Much fun, science, and discussions were had throughout the week.

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We also stopped to take our first lab album cover photo while in Pinnacles. More to come!

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Desert Crust collecting, Summer edition

On August 4th, 2016, Nat, Derreck, Sawyer, and Jericho went to Joshua Tree National Park to collect more Biological Soil Crusts samples. They were lucky to find some Lichen crusts which we could not find in our last sampling trip. Here are some pictures of our sampling team.

Stajich lab sampling team: Derreck, Nat, Sawyer, and Jericho
Stajich lab sampling team: Derreck, Nat, Sawyer, and Jericho
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Our first collection of Lichen crust from Joshua Tree National Park
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Derreck measured crust surface temperature, while Jericho was getting ready for sampling

New funding, new papers, new data

We celebrated a few events in April and May.

  • A new NSF grant was funded and started in April on rumen fungi “Phylogenomics and evolutionary history of the anaerobic fungal group, Neocallimastigomycota“. This is a collaboration with Noha Youssef and Mostafa Elshahed at Oklahoma State University and will give the opportunity to work on systematics of these anaerobic gut fungi.
  • Raúl Castanera who came to the lab for a short stay last year, authored a paper that was accepted this week on transposable elements in the Pleurotus (oyster mushroom) genome and comparisons in proliferation rates and impact on gene expression. Castanera R et al. PLoS Gen doi: 10.1371/journal.pgen.1006108
  • We just started to get our first microbial diversity (16S and ITS) results for rock and soil communities from California desert environments and Antarctica as part of project by visiting student Claudia Coleine and Nat Pombubpa. Claudia is a PhD student with Laura Selbmann of Tuscia University and visited for nine months, but we processed isolates the lab collected from Antartica expeditions. We are also sequencing genomes of a handful of cultured fungal species from Antarctic locations and the first assemblies look pretty good (200-400 contigs for these 25-40Mb genomes) for a MiSeq only assembly.
  • Nat is collecting samples from Joshua Tree National Park and in collaboration with other desert crust researchers Paul De Ley and Nicole Pietrasiak examining fungal and bacterial distribution.

French connection

Jason was at the European Conference on Fungal Genetics in Paris this April and had a chance to deliver a lecture. It was a great meeting of science and there was a lot of social media coverage by participants.

Jason and Ousmane also attended the 1st conference on multicellular development in fungi where Ousmane presented his work on the Neolecta genome and comparative biology of the Taphrinomycotina fungi.

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An ascus of Neurospora biologists…
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It was a bit imposing to be on stage with bright colored backdrop
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I showed some colorful trees
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Little Jason and big slides

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Mural at a school with a mushroom little red riding hood and mushrooms in the forest
Mural at a school with a mushroom little red riding hood and mushrooms in the forest

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