The A Team

Principle Investigator:
Audrey L. Atkin

Postdoctoral Associate:
Bessie Kebaara

Graduate Students:
Pushpita Sarkar
Melanie Langford

Undergraduate Students:
Chris Cummings
Kingsley Okafor
Rachel Gubbels
Sam Majumder


Current Research

Gene regulatory mechanisms in two fungal model organisms, Saccharomyces cerevisiae and Candida albicans, to study regulation of cell and developmental biology.

A second important role for the Nonsense-mediated mRNA decay pathway in decay of normal cellular mRNAs

Nonsense-mediated mRNA decay is a highly conserved mRNA decay pathway that serves an RNA surveillance mechanism by ridding cells of premature termination codon-containing mRNAs encoding potentially harmful truncated proteins. It also regulates the accumulation of approximately five percent of the normal cellular mRNAs in yeast ( S. cerevisiae), fruit flies (Drosphila melanogaster) and humans. Further it is essential for mammalian viability. Thus nonsense-mediated mRNA decay serves an important cellular function in normal regulation of gene expression. Our long-term goal is to understand the molecular mechanisms responsible for recognition and targeting of wild-type mRNAs for degradation by this pathway and the contributions of this pathway to gene regulation.

We have shown that the normal cellular mRNA, PPR1 mRNA, is targeted for nonsense-mediated mRNA decay by a unique mechanism that depends on 1) the same cellular factors that are involved in the decay of nonsense mRNAs and 2) a specific region of the PPR1 mRNA. PPR1 encodes a transcription activator and increasing PPR1 mRNA levels by inhibiting nonsense-mediated mRNA decay in turn results in an increase in the expression of Ppr1-activated genes. From the lessons learned studying PPR1 mRNA decay, we have developed a novel bioinformatics approach to identify other mRNAs regulated by the yeast nonsense-mediated mRNA decay pathway.

Currently we are examining the role of nonsense-mediated mRNA decay in regulation of normal cellular mRNA decay. We are: (1) Identifying additional normal cellular mRNAs that are degraded by the nonsense-mediated mRNA and investigating the mechanisms targeting these mRNAs for decay; (2) Examining the conservation of normal cellular mRNA decay by nonsense-mediated mRNA decay. This work is funded by a grant from the National Science Foundation (MCB-0444333).

Photographs of the double-labelled yeast cells showing Upf1p (left), DNA stained with DAPI (center), and yeast cells (right). This approach was used to show that Upf1p is primarily found in the cytoplasm. See Atkin et al., 1995 for more details.

Regulation of Candida albicans morphogenesis by quorum sensing

Candida albicans is an important opportunistic human pathogen. It normally resides in the gastrointestinal and genitourinary tract and to a lesser extent on the skin of most humans. However, given the opportunity, it can cause candidemia where it invades host tissues, progresses to growth of fungal masses in the kidney, heart or brain, and ultimately can cause death.   Candida morphogenesis is important for development of candidemia.   Patients with compromised immune systems are at high risk for candidemia.   Many patients with candidemia die by the time laboratory diagnosis is made.   Further, there is still substantial mortality of patients who receive antifungal treatment.   Consequently there is a need for development of molecular probes that facilitate earlier clinical diagnosis and new classes of antifungal drugs.  

Candida can grow vegetatively as yeast, hyphae or pseudohyphae. It posesses the ability to interconvert between these different morphological forms in response to its environment. There is a strong correlation between morphological interconversion and pathogenicity. The morphological transition is regulated, in part, by farnesol. Farnesol is synthesized by Candida and it blocks the conversion of yeast to hyphae or pseudohyphae in response to most, if not all, of the chemical and environmental morphogenesis inducers. Farnesol also acts as a virulence factor for systematic Candida infections in a mouse model, and the response to farnesol is unique to Candida because it does not block the morphological transition in the other dimorphic fungal species we have tested.   We are part of a multidisciplinary team studying the role of farnesol.   We are determining how Candida interprets signaling by farnesol at the level of gene regulation and expression, and then executes this regulation through changes in cell structure, dynamics and function.

An understanding of how Candida responds to farnesol is important because it will reveal a whole new layer of fungal morphogenesis control that, in turn, should provide a series of new target sites for the design of antifungal drugs. Further, the specificity of farnesol for control of the Candida morphological transition suggests that the genes for farnesol response may be unique to Candida and thus these genes are candidates for molecular probes for rapid clinical diagnosis.  

Relevant Publications:

Kebaara, B. W., M. L. Langford, D. H. M. L. P. Navarathna, R. Dumitru, K. W. Nickerson and A. L. Atkin, 2008. Candida albicans Tup1 is involved in farnesol-mediated inhibition of filamentous-growth induction. Eukarytic Cell 7: in press. [Abstract]

Dumitru, R., D. H. M. L. P. Navarathna, C. P. Semighini, C. G. Elowsky, R. V. Dumitru, D. Dignard, M. Whiteway, A. L. Atkin, and K. W. Nickerson, 2007. In vivo and in vitro anaerobic mating in Candida albicans. Eukaryotic Cell 6:465-472. [Abstract]

Nickerson, K. W., A. L. Atkin, and J. M. Hornby, 2006. Quorum Sensing in Dimorphic Fungi: Farnesol and Beyond. Applied and Environmental Microbiology, 72:3805-3813. [Abstract]

Kebaara, B. W., L. E. Nielsen, K. W. Nickerson, and A. L. Atkin, 2006. Determination of mRNA half-lives in Candida albicans using thiolutin as a transcription inhibitor. Genome, 49:894-899. [Abstract]

Jensen, E. C., J. M. Hornby, N. E. Pagliaccetti, C. M. Wolter, K. W. Nickerson, and A. L. Atkin, 2006. Farnesol restores wild-type colony morphology to 96% of Candida albicans colony morphology varients recovered following treatment with mutagens. Genome, 49:346-353. [Abstract]

Taylor, R., B. W. Kebaara, T. Nazarenus, A. Jones, R. Yamanaka, R. Uhrenholdt, J. P. Wendler, and A. L. Atkin, 2005. Gene sets co-regulated by the Saccharomyces cerevisiae nonsense-mediated mRNA decay pathway. Eukaryotic Cell, 4:2066-2077. [Abstract]

Mosel, D. D., R. Dumitru, J. M. Hornby, A. L. Atkin, and K. W. Nickerson, 2005. Farnesol concentrations required to block germ tube formation in Candida albicans in the presence and absence of serum. Applied and Environmental Microbiology, 71:4938-4940. [Abstract]

Nazarenus, T., R. Cedarberg, R. Bell, J. Cheatle, A. Forch, A. Haifley, A. Hou, B. W. Kebaara, C. Shields, K. Stoysich, R. Taylor, and A. L. Atkin, 2005. Upf1p, a highly conserved protein required for nonsense-mediated mRNA decay, interacts with the nuclear pore proteins Nup100p and Nup116p. Genes 345:199-212. [Abstract]

Kebaara, B., T. Nazarenus, R. Taylor, A. Forch, and A. L. Atkin, 2003. The Upf-dependent decay of wild-type PPR1 mRNA depends on its 5'-UTR and first 92 ORF nucleotides. Nucleic Acids Research, 31(12):3157-3165. [Abstract]

Kebaara, B., T. Nazarenus, R. Taylor, and A. L. Atkin, 2003. Genetic background affects relative nonsense mRNA accumulation in wild-type and upf mutant yeast strains. Current Genetics, 43:171-177. [Abstract]

The Beadle Center

We are part of the School of Biological Sciences at the Univerity of Nebraska in Lincoln, NE. Our lab is located in the George W. Beadle Center for Genetics and Biomaterials Research.

The Center for Biotechnology is also located in the Beadle Center. The Center for Biotechnology manages the UNL Core Research Facilities. We have easy access to the following state of the art facilities for:

Links to Other Sites

School of Biological Sciences at the University of Nebraska-Lincoln

The mRNA Decay Resource Page

Saccharomyces Genome Database

Contact infomation:


Audrey L. Atkin Ph.D.
School of Biological Sciences
University of Nebraska-Lincoln
E146 Beadle Center
Lincoln, Nebraska 68588-0666

Telephone: (402) 314-5571