Category Archives: zygomycete

Myco-bio-diesel

Posted on by
Reply

Previously I posted on an article on making biodiesel using the fungus Gliocladium roseum. Here is a new study reporting conversion of lipids to biodiesel using the basidiomycete Cryptococcus curvatus. There has been also other progress in this area where Mucor circinelloides can also be used to produce oils suitable for biodiesel production as reported in the paper and the press release - though it is a pathogenic fungus with interesting spore size dimorphism.

Thiru M, Sankh S, & Rangaswamy V (2011). Process for biodiesel production from Cryptococcus curvatus. Bioresource technology PMID: 21930373

Horizontal gene transfer from Zygo to pea aphid

Posted on by
Reply

Pea AphidAnother result from the analysis of the recently published genome of the pea aphid, Acyrthosiphon pisum. Nancy Moran and Tyler Jarvik present a study of the origin of the carotenoid production gene in pea aphid. Animals typically cannot make carotenoids so they sought to discover how this is possible. They find that it is derived from a horizontal gene transfer event of a fungal gene into the aphid lineage. This gene is responsible for the red-green color polymorphism in the aphid. It appears the gene is derived from a ‘zygomycete’ or relative in the early branching lineage of the fungi. One gene, a carotenoid desaturase, is encoded in a 30kb genomic region that is missing in green aphids but present in the red morphs. The region is apparently maintained in the population by frequency dependent selection since each color has an advantage or disadvantage for evading detection by predators in different environments.

The reports of eukaryotic HGT event from fungi to animals is quite rare so this finding is surprising in that sense, but the authors argue that the important ecological role of carotenoids suggest we might see even more examples if we look harder.

Moran, N., & Jarvik, T. (2010). Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids Science, 328 (5978), 624-627 DOI: 10.1126/science.1187113

Methylation to the max!

Posted on by
Reply

A new paper from the Zilberman lab at UC Berkeley shows the application of high throughput sequencing to the study of DNA methylation in eukaryotes.  They generate an huge data set of whole genome methylation patterns in several plants, animals, and five fungi including early diverging Zygomycete.

The work was performed using Bisulfite sequencing (Illumina) to capture methylated DNA, RNA-Seq of mRNA. The also performed some ChIP-Seq of H2A.Z on pufferfish to look at the nucleosome positioning in that species. For aligning the reads, they used BowTie to align the bisulfite sequences (though I’d be curious how a new aligner, BRAT, designed for Bisulfite seq reads would perform) to the genome.  They also sequenced mRNA via RNA-Seq to assay gene expression for some of the species.

They find several interesting patterns in animal and fungal genomes.  I’ll highlight one in the fungi. They find an unexpected pattern in U. reesii of reduced CGs in repeats, which shows signatures of a RIP-like process, are also methylated.  This finding is also consistent with observations in Coccidioides (Sharpton et al, Genome Res 2009) that showed depleted CGs pairs in repeats.  Since the phenomenon is also found in Coccidioides genomes this methylation of some repeats is likely not unique to U. reesii but may be important in recent evolution of the Onygenales fungi or the larger Eurotiales fungi.  There are several other interesting findings with the first such study that shows methylation data for Zygomycete fungi and a basidiomycete close to my heart, Coprinopsis.  It will be interesting is to dig deeper into this data and see how the patterns of methylation compare to other genomic features and the mechanisms regulating methylation process.

Zemach, A., McDaniel, I., Silva, P., & Zilberman, D. (2010). Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation Science DOI: 10.1126/science.1186366

A cacophony of comparative genomics papers

Posted on by
Reply

A nice series of comparative genomics articles have been published in the last few weeks. The pace of genome sequencing has accelerated to the point that we have lots of sequencing projects coming from individual labs and small consortia not necessarily from genome centers. We are seeing a preview of what next (2nd) generation sequencing will enable and can start to imagine what happens when even cheaper 3rd generation sequencing technologies are applied. I’m behind in reviewing these papers for you, dear reader, but I hope you’ll click through and take a look at some of these papers if you are interested in the topics.

In the following set of papers we have some nice examples of comparative genomics of closely related species and among a clade of species. The papers mentioned below include our work on the human pathogens Coccidioides and Histoplasma (Sharpton et al) studied at several evolutionary distances, a study on Saccharomycetaceae (Souciet et al) clade of yeast species, and a comparison of two species of Candida (Jackson et al): the commensal and opportunistic fungal pathogen Candida albicans with a very closely related species Candida dubliensis.  There is also a nice comparison of strains of Saccharomyces cerevisiae looking at effects of domestication and examples of horizontal transfer.

There is also a report of de novo sequencing of a filamentous fungus using several approaches, traditional Sanger sequencing, 454, and Illumina/Solexa (DiGuistini et al).

Finally, a paper from a few months ago (Ma et al), gives a fantastic look at one of the early branches in the fungal tree – the Mucorales (formerly Zygomycota) – via the genome of Rhizopus oryzae.  This paper is a really excellent example of what we can learn about a group of species by contrasting genomic features in the early branches in the tree with the more well studied Ascomycete and Basidiomycete fungi.  More genome sequences will help us build on these findings and clarify if some of the observations are unique to the lineage or universal aspects of the earliest fungi.

I hope you enjoy!

Novo, M., Bigey, F., Beyne, E., Galeote, V., Gavory, F., Mallet, S., Cambon, B., Legras, J., Wincker, P., Casaregola, S., & Dequin, S. (2009). Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118 Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0904673106 (via J Heitman)

Jackson, A., Gamble, J., Yeomans, T., Moran, G., Saunders, D., Harris, D., Aslett, M., Barrell, J., Butler, G., Citiulo, F., Coleman, D., de Groot, P., Goodwin, T., Quail, M., McQuillan, J., Munro, C., Pain, A., Poulter, R., Rajandream, M., Renauld, H., Spiering, M., Tivey, A., Gow, N., Barrell, B., Sullivan, D., & Berriman, M. (2009). Comparative genomics of the fungal pathogens Candida dubliniensis and C. albicans Genome Research DOI: 10.1101/gr.097501.109

DiGuistini, S., Liao, N., Platt, D., Robertson, G., Seidel, M., Chan, S., Docking, T., Birol, I., Holt, R., Hirst, M., Mardis, E., Marra, M., Hamelin, R., Bohlmann, J., Breuil, C., & Jones, S. (2009). De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biology, 10 (9) DOI: 10.1186/gb-2009-10-9-r94 (open access)

Sharpton, T., Stajich, J., Rounsley, S., Gardner, M., Wortman, J., Jordar, V., Maiti, R., Kodira, C., Neafsey, D., Zeng, Q., Hung, C., McMahan, C., Muszewska, A., Grynberg, M., Mandel, M., Kellner, E., Barker, B., Galgiani, J., Orbach, M., Kirkland, T., Cole, G., Henn, M., Birren, B., & Taylor, J. (2009). Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives Genome Research DOI: 10.1101/gr.087551.108 (open access)

Souciet, J., Dujon, B., Gaillardin, C., Johnston, M., Baret, P., Cliften, P., Sherman, D., Weissenbach, J., Westhof, E., Wincker, P., Jubin, C., Poulain, J., Barbe, V., Segurens, B., Artiguenave, F., Anthouard, V., Vacherie, B., Val, M., Fulton, R., Minx, P., Wilson, R., Durrens, P., Jean, G., Marck, C., Martin, T., Nikolski, M., Rolland, T., Seret, M., Casaregola, S., Despons, L., Fairhead, C., Fischer, G., Lafontaine, I., Leh, V., Lemaire, M., de Montigny, J., Neuveglise, C., Thierry, A., Blanc-Lenfle, I., Bleykasten, C., Diffels, J., Fritsch, E., Frangeul, L., Goeffon, A., Jauniaux, N., Kachouri-Lafond, R., Payen, C., Potier, S., Pribylova, L., Ozanne, C., Richard, G., Sacerdot, C., Straub, M., & Talla, E. (2009). Comparative genomics of protoploid Saccharomycetaceae Genome Research DOI: 10.1101/gr.091546.109 (open access)

Ma, L., Ibrahim, A., Skory, C., Grabherr, M., Burger, G., Butler, M., Elias, M., Idnurm, A., Lang, B., Sone, T., Abe, A., Calvo, S., Corrochano, L., Engels, R., Fu, J., Hansberg, W., Kim, J., Kodira, C., Koehrsen, M., Liu, B., Miranda-Saavedra, D., O’Leary, S., Ortiz-Castellanos, L., Poulter, R., Rodriguez-Romero, J., Ruiz-Herrera, J., Shen, Y., Zeng, Q., Galagan, J., Birren, B., Cuomo, C., & Wickes, B. (2009). Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication PLoS Genetics, 5 (7) DOI: 10.1371/journal.pgen.1000549 (open access)

Mucor circinelloides genome and annotation available

Posted on by
1

The Mucormycotina (formerly Zygomycota) fungus Mucor circinelloides Genome Portal is now publicly available at http://genome.jgi-psf.org/Mucci1/Mucci1.home.html.

If you are planning to attend the Fungal Conference in Asilomar, there will be a JGI Workshop on March 19, 2009 at noon in Chapel to show how to use the manual curation tools.

Escaping the dung pile quickly: Speedy Pilobolus spores

Posted on by
2

ResearchBlogging.orgSporangiophore discharge in the fungus <em/>Pilobolus kleinii captured with high speed video.” width=”300″ /> In a paper appearing today in PLoS One, “The Fastest Flights in Nature: High-Speed Spore Discharge Mechanisms among Fungi” <a href=Nicholas Money and colleagues including 6 undergraduates and 3 graduate students, have measured the speed of flight of spores discharging from several Ascomycete and Zygomycete dung fungi including Pilobolus kleinii, Basidiobolus ranarum, Podospora anserina, and Ascobolus immersus. The team used high speed cameras that recorded at 250,000 frames per second and were able to capture spores being launched at 25 meters per second at accelerations of 180,000 g. The publication also provides multimedia including a video of the spore discharge slowed down and set to music. Nik and Mark Fisher both presented portions of the work at the Mycological Society of America 2008 meeting this summer and showed clips of these dramatic videos, so it was great to see this in print shortly following the meeting.

By way of the press release the major findings from this work show that

… the discharge mechanisms in fungi are powered by the same levels of pressure that are characteristic of the cells that make up the feeding colonies of fungi. Therefore, the long flights enjoyed by spores result not from unusually high pressure, but from the way in which explosive pressure loss is linked to the propulsion of the spores. There appear to be some similarities between the escape of the spores and the expulsion of ink droplets through nozzles on inkjet printers. 

As Dr Money has described in a humorous and humble manner before in his Mr Bloomfield’s Orchard, some of the coolest and fundamental observations about spore flight and discharge, from Buller to the present, have come from simple and careful observations of fungi. In this case they have used a new tools of ultra high speed photography to capture events. Some of the previous work from the Money lab on this front include a demonstration that conidia are actively launched and rather than being passively released by low velocity airflow in the toxic indoor mold Stachybotrys (Tucker et al FGB 2007; free at PMC)

Yafetto L, Carroll L, Cui Y, Davis DJ, Fischer MWF,Henterly AC,, Kessler JD, Kilroy HA, Shidler JB, Stolze-Rybczynski JL, Sugawara Z, Money NP (2008). The Fastest Flights in Nature: High-Speed Spore Discharge Mechanisms among Fungi PLoS One, 3 (9) DOI: 10.1371/journal.pone.0003237

Papers on our desk

Posted on by
2

A quick post of some recent comparative genomics papers on our desk that are worth a look.

  • Khaldi N, Wolfe KH (2008) Elusive Origins of the Extra Genes in Aspergillus oryzae. PLoS ONE 3(8): e3036. doi:10.1371/journal.pone.0003036. This was a cool but somewhat controversal finding presented at Fungal Genetics last year.
  • Casselton, LA. Fungal sex genes – searching for the ancestors. doi: 10.1002/bies.20782. A review of recent findings about the Zygomycete MAT locus.
  • Soanes DM, Alam I, Cornell M, Wong HM, Hedeler C, et al. (2008) Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis. PLoS ONE 3(6): e2300. doi:10.1371/journal.pone.0002300
  • Lee DW, Freitag M, Selker EU, Aramayo R (2008) A Cytosine Methyltransferase Homologue Is Essential for Sexual Development in Aspergillus nidulans. PLoS ONE 3(6): e2531. doi:10.1371/journal.pone.0002531

Will a zygomycete help solve our energy woes?

Posted on by
Reply

I found the headline today, “Biofuels: Fungus Use Improves Corn-to-ethanol Process” and I was curious to find out what fungus they were talking about in the article. It turns out that researchers at Iowa State University found that Rhizopus microsporus is able to grow off part of the leftovers of ethanol production called thin stillage. The reason this is so exciting is explained below:


(Rhizopus sporangium, picture taking during PMB 110L @ UC Berkeley)

The fuel is recovered by distillation, but there are about six gallons of leftovers for every gallon of fuel that’s produced. Those leftovers, known as stillage, contain solids and other organic material. Most of the solids are removed by centrifugation and dried into distillers dried grains that are sold as livestock feed, primarily for cattle.
The remaining liquid, known as thin stillage, still contains some solids, a variety of organic compounds from corn and fermentation as well as enzymes. Because the compounds and solids can interfere with ethanol production, only about 50 percent of thin stillage can be recycled back into ethanol production. The rest is evaporated and blended with distillers dried grains to produce distillers dried grains with solubles.
The researchers added a fungus, Rhizopus microsporus, to the thin stillage and found it would feed and grow. The fungus removes about 80 percent of the organic material and all of the solids in the thin stillage, allowing the water and enzymes in the thin stillage to be recycled back into production.
The fungus can also be harvested. It’s a food-grade organism that’s rich in protein, certain essential amino acids and other nutrients. It can be dried and sold as a livestock feed supplement. Or it can be blended with distillers dried grains to boost its value as a livestock feed and make it more suitable for feeding hogs and chickens.

The idea of being more efficient by saving water and producing nutritious animal feed that can produce healthier animals that produce more meat is very interesting and worthwhile. But the article never mentions that many Rhizopus species are considered pathogens and R. microsporus when paired with Burkholderia rhizoxinia, a endosymbiont that produces rhizoxin, essentially becomes the pathogen responsible for rice seedling blight. Rhizopus also can cause serious mycoses in humans (The non squeamish can search for rhizopus mycoses on google).

I am curious if this Rhizopus has any endosymbionts that could be helping it grow on stillage or what other fungi that may not be potential pathogens might be out there that could also grow on the thin stillage.

Some links

Posted on by
2

ResearchBlogging.org

I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.

Schmitt, I., Partida-Martinez, L.P., Winkler, R., Voigt, K., Einax, E., Dölz, F., Telle, S., Wöstemeyer, J., Hertweck, C. (2008). Evolution of host resistance in a toxin-producing bacterial–fungal alliance. The ISME Journal DOI: 10.1038/ismej.2008.19

LEVASSEUR, A. (2008). FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2008.01.004

Shivaji, S., Bhadra, B., Rao, R.S., Pradhan, S. (2008). Rhodotorula himalayensis sp. nov., a novel psychrophilic yeast isolated from Roopkund Lake of the Himalayan mountain ranges, India. Extremophiles DOI: 10.1007/s00792-008-0144-z

Sex in fungi: MAT locus cloned from a Zygomycete

Posted on by

On the cover of this week’s Nature is a picture of Phycomyces blakesleeanus Nature Coverhighlighting the discovery of the MAT locus in this Zygomycete fungus from Alex Idnurm and Joe Heitman and colleagues. While it was previously known that Zygomycetes (the Orange lineage represented by R. oryzae in the tree below) mate, the specific locus has until now, never been discovered. The authors in this study identified the MAT locus through a sequence search looking for HMG-box genes knowing that these are found the Mating Type locus in Basidiomycetes and Ascomycetes. They confirmed the identity through a through set of experiments that included PCR, sequencing and crosses of (+) and (-) strains of P. blakesleeanus, and Southern blots.

Continue reading →