Thursday, September 12, 2013

Story behind the paper guest post by Corey Nislow (w/ Metka Lenassi) on "Genomics w/o Borders"

Below is another in the "Story behind the paper" series of guest posts here.  This one is from Corey Nislow w/ Metka Lenassi.  If anyone else has published an open access paper on anything relating to this blog and would like to write a guest post on the Story behind the paper, please let me know.


Genomics without Borders: Genome Sequence of the Extremely Halotolerant Yeast Hortaea werneckii 

by Corey Nislow (with Metka Lenassi)



In this guest post (thank you Jonathan!) I wanted to tell the story behind a paper that my colleagues and I published two weeks ago in PLoS ONE. The story also offers an opportunity to talk about what role, if any, a middle author can play in a scientific study.

The story is set in Slovenia a beautiful country which was part of the former Yugoslavia and which is home to about 2 million inhabitants, 2400+ fungal species (thanks Wikipedia) and some very interesting environments. One of these environments is the Secovlje Salterns where one can find the yeast Hortaea werneckii.
A worker harvests sea salt in the Secovlje salterns, July 17, 2010. Some 2600 tons of salt is expected to be produced during the two and a half month season at the salterns.(Xinhua/Reuters Photo)

I hadn't heard of Hortaea until I started googling around looking for a yeast extremophile that I can grow in the lab to dissect out its nucleosomes to ask questions regarding nucleosome occupancy and transcription in the face of extreme environments. Turns out it was not a crazy idea--

13 years ago a peculiar black yeast Hortaea werneckii was isolated from its natural habitat: waters containing so much salt, it would kill most living organisms instantly. Since then, two small (but enthusiastic) Slovenian groups have tried to understand its halotolerance. This demanded field trips to the beautiful Slovenian coast, but also a lot of hard work and inventiveness to optimizing protocols used for other organisms – and to do it on a low budget. The first important obstacle was actually cultural - to persuade the scientific community that such extreme yeast even exists in nature! You can see it below. We now have ample evidence as Hortaea has been isolated from many seawater-related environments, saline lakes, but also from surface layers of tropical microbial mats in salterns and even from spider webs in Atacama Desert caves. All these different Hortaea strains are now waiting in their freezer (the Ex culture collection) to be analyzed.

Hortaea werneckii growing happily on 2M salt.


The figure below summarizes what was known about halotolerance of Hortaea before the genome sequence was decoded. In brief, high salinity is detected by sensors of the HOG signaling pathway (green arrows), which modulate the expression of salt-responsive genes (underlined green). The expression of other genes also varies; genes with higher expression at high salinity are written in red, repressed genes in blue). The impact of a hyperosmolar environment is countered by increasing the energy supply to drive energy-demanding processes such as export of Na+ and H+, import of glycerol andthe synthesis of compatible solutes. Melanization of the cell wall reduces the leaking of solutes from the cells and restructuring of membrane lipids helps preserve the integrity of the cells. Read this paper if you want to know more: GostinĨar et al, Adv Appl Microbiol. 2011;77:71-96 .

GostinĨar et al, Adv Appl Microbiol. 2011;77:71-96

This critter, as our recent paper reports, is as interesting genotypically as it is phenotypically. The full genome sequence reported in the PLoS ONE paper shows that genome size is 51mB quite a bit larger than its closest relatives, and given the number of gene models detected (20,000!), for all intents and purposes it looks like Hortaea underwent whole genome duplication last weekend!

Piquing my interest, I immediately started searching for the the genome sequence to have a reference to map nucleosome sequencing reads. Turns out, I had requested the strain from Metka years ago, only to find that one of our lab mates, Uros, with whom I was collaborating at the University of Toronto, had performed some of the groundwork on Hortaea for his PhD. But the network connections don't stop here, I moved to the University of British Columbia last year, and as it happened Hortaea is popular in Vancouver too! Our new colleagues at UBC were working together with the Slovenian team on sequencing and analyzing the Hortaea genome. In fact, the collaboration started in 2005, catalyzed by a poster at the Budapest FEBS conference were Metka, at that time still a PhD student, and Ivan Sadowski started a discussion about the interesting phenotypic switch that Hortaea undergoes between yeast and filamentous forms. So, by virtue of a convergence of curiosity, good luck and generous collaborators I had the good fortune of being an active participant in the study.

So how does this have anything to do with what a middle author does or doesn't do on a manuscript? And why do I care? 

Well, I recently re-read the comments section of a fellowship application, and ginned up the guts to read the “supervisor/training environment” section. The chief criticism was that I have a lot of papers on which I am not the senior author. So to the skeptics, I would say- even middle authors play important roles in bringing a study to an audience. In my case my self-interests guided my actions, but along the way, I had the chance to learn about an extraordinary critter, and an amazing group of Slovenian scientists. Yeah, I needed the genome sequence, but I was also excited to help drafting the manuscript, have our sequencing facility prepare additional libraries to close some gaps, and now to bring attention to this extraordinary critter.

The genome sequence offers an exciting new start in studies of Hortaea werneckii. Going forward, the Slovenians want to study its transcriptome and proteome in response to increasing salinity. Preparing knock-out mutants is also a must, to find key genes important for halotolerance. We definitely want to take a closer look at all those cation transporters and their functions. It would also be fun to find its mating partner in one of those frozen Hortaea samples. And now that the genome sequence is available to everybody, the research on this extremely interesting species may start to gain more appeal even to researchers beyond the two stubborn Slovenian groups.

Although I might not get to Slovenia in the foreseeable future, I wouldn't be surprised if one of my graduate students will meet up with the group at an upcoming yeast meeting. This particular student is dragging our lab into evolutionary genomics by trying to see if he can't get Hortaea to lose some of its genome in long-term culture (I can't help but think of “Amadeus” where Salieri is telling Mozart that the composition is fine but it has too many notes....). I'm sure the results will be surprising, and am also encouraged to see what our future collaboration will bring.

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