Work of Southeast Scientists Makes Cover of Worldwide Science Journal
Years of fungal genetic research by two
Southeast Missouri State University biology professors is currently
featured on the cover of one of the world’s most influential science
journals.
“Genome Evolution in Mushrooms” is the title of the article published
in the June 30 issue of the Proceedings of the National Academy of
Sciences of the United States of America. The article also features
a guest commentary on the significance of the research by two
scientists at the University of California Berkeley.
The journal article is the culmination of nearly six years of work by
Dr. Allen Gathman and Dr. Walt Lilly, Southeast professors of biology,
on the genome of the mushroom Coprinopsis cinerea.
“The paper makes a major contribution to our understanding of
evolution in the phylum Basidiomycota, which includes all mushrooms as
well as numerous fungal pathogens that cause disease in plants and
animals, including humans,” Gathman said. The research is important, he
says, because it shows how “the organization of genes on chromosomes
contributes to the functioning of the organism.”
Lilly and Gathman, along with more than a dozen Southeast students
over the past six years, have worked to assemble and characterize the
genome sequence for a mushroom called Coprinopsis cinerea.
Their work was funded by a $744, 055 grant they received from the
National Science Foundation to collaborate on research with scientists
at Duke University and the University of North Carolina-Chapel Hill. The
project was part of the Microbial Genome Sequencing Program of the
National Science Foundation.
Gathman said the Southeast research group with their cadre of
undergraduate researchers sequenced more than 6,000 gene transcripts
from the organism and used those sequences to help define the structure
of genes in the genome. In addition the Southeast team performed
genome-level sequencing and computational biology to close the nearly
435 gaps in the original sequence to allow for assembly of the entire 30
million DNA bases into 13 chromosomes.
“You can think of the genome as a book, and each gene as a sentence
in that book. Those sentences are arranged into chapters, the
chromosomes,” Lilly said. “Imagine starting with something like 60,000
sentence fragments and assembling those into a book with 13 chapters
with interesting characters and a plot.”
Pat Pukkila, the primary investigator on the project at the
University of North Carolina, has worked with Coprinopsis cinerea for
many years. Lilly and Pukkila became acquainted several years ago while
collaborating on a project. Pukkila was a primary proponent for getting
the initial draft sequence of the Coprinus genome which was completed
in 2003 by the Whitehead institute at MIT. Pukkila coordinated the
project and mapped the genes to the 13 chromosomes of Coprinopsis
cinerea. In addition, over 40 other scientists from institutions
in the US, Europe and Asia contributed to the genome characterization
described in the paper.
Fungi like Coprinopsis produce a large spectrum of oxidative
and degradative enzymes that are of industrial interest. Some of those
enzymes may prove to be important as detergent additives, in
remediation processes for contaminated soil and water, or in
pharmaceutical production, Lilly says.
Gathman says their research may be significant in controlling grain
pathogens, which currently limit food production in many parts of the
world. Plant pathogens such as rust and smut fungi impose major limits
on the production of wheat, corn and rice, he said.
“All cereal grains have problems with basidiomycete pathogens,” he
said.
“The information we came up with will help with knowing how all
members of the basidiomycetes grow and function,” Gathman said. “This is
a step towards understanding how this group of fungi has evolved, and
how different species have adapted to specific environments.”
As a result of their work, the Southeast researchers developed and
continue to maintain an interactive Coprinopsis cinerea worldwide
genetics/genome database located at Southeast at http://genome.semo.edu/ccin/.
Former Southeast students who have worked on the project over the
years include 2009 graduate Hannah Korte of St. Joseph, Mo.; 2008
graduates Nathalie Pogue of St. Louis, Noriko Inoguchi of Makinohara
Shizuoka, Japan, Miranda Koester of O’Fallon, Mo., and Erica Young of
Valley Park, Mo; 2006 graduate Nicole Arnold of St. Louis; and 2005
graduates Sarah Wilke of Carrboro, N.C., Alex Guerrero of St. Peters,
Mo., Michelle Carlson of Eden Prairie, Minn., and Amber Smith of
Sikeston, Mo. Former students Bruno Murphy of Jackson, Mo., and
Christian Barr of Seattle, Wash., also worked on the project.
Lilly said the project “provided students with experience at the
forefront molecular biology. This is as ‘cutting edge’ as students can
get at any university in the country,” he said.
Southeast alumna Sarah Wilke of Carrboro, N.C., began working on the
project as an undergraduate in the lab, continued as a paid lab tech,
and then moved to the University of North Carolina as a lab tech under
Pukkila, Gathman said.
“Sarah’s contributions were so important that she is second author on
the paper,” he said.
Gathman and Lilly will continue their work in this area. Currently
they are examining changes in the expression of genes in Coprinopsis
cinerea based on nutritional resources the fungus has. They also
have projects aimed at understanding one important group of enzymes
produced by the fungus, those that break down proteins. Lilly said, “by
comparing proteases of Coprinopsis to other fungi that live in
different environments, the importance of individual enzymes may be
discovered.” Lilly and Gathman are involved in characterizing other
basidiomycete genomes as well. The description of the genome of Schizophyllum
commune, a wood decaying fungus which they have studied for
decades is scheduled to be published soon. Because it is also a
basidiomycete, the gene order along chromosomes is similar. He said
their earlier work with Coprinopsis cinerea will serve as a
guide and make it easier in the future to assemble full chromosomes of Schizophyllum
commune and other fungi.