David Michael Kehoe, Ph.D.
Associate Professor

I provide guidance and oversight to a bright, enthusiastic group of young and developing scientists, who have linked summaries of their research below. Click here to see some of the meetings lab members have attended and awards they have won for their presentations. Former members of the Kehoe lab have gone on to great jobs in academia, medicine or industry, and the contributions of those alumni to our research effort are described below as well. Nowadays, it’s mostly only good for a laugh in the lab when I return to the bench to do a few experiments, so instead of a research summary, I’ve just provided a bit of information about my professional background below.

Education and Appointments
B.A. University of Washington
M.S. University of Washington/National Research Council of Canada
Ph.D. University of California, Los Angeles
NSF Postdoctoral Fellow, Carnegie Institution of Washington, Stanford University
Indiana University Molecular Biology Institute Fellow
Indiana University Center for Genomics and Bioinformatics Fellow

Fellowships and Awards
Japanese Ministry of Education Fellow, University of Tokyo, Japan
USDA Predoctoral Training Fellowship
University of California Biotechnology Research and Education Fellowship
NSF Postdoctoral Fellowship
Indiana University Trustees’ Teaching Award (3 times)
Indiana University Outstanding Junior Faculty Award
Indiana University Senior Class Award for Teaching Excellence in Biology and Dedication to Undergraduates

Ryan Bezy
(started 2003)
B.A. in Biology, DePauw University, Indiana

My research focuses on the regulation of the cpeCDESTR operon, a key player in the regulation of green light expressed genes during CCA. The light regulation of this operon is jointly provided by both the Rca and Cgi systems, and I have made significant progress in unraveling how both of these pathways control cpeCDESTR expression. These include both transcriptional and post-transcriptional regulatory mechanisms. Read more here.

Andrian Gutu
(started 2004)
B.S. and M.S. in Biology, Babes-Bolyai University, Romania

First of my two projects focuses on identifying Cgi regulatory pathway components. My genetic screen identified a gene encoding a core translational machinery protein that appears to be involved in post-transcriptional regulation of the cpeCDESTR operon by light. My second project, to unravel the regulation of the sulfur limitation response, focusess on how cpc3 is activated while cpc1 and cpc2 is down-regulated in condition of sulfur deprivation. Read more here.

Animesh Shukla
(started 2007)
B. Tech. in Biotechnology, MIET, Uttar Pradesh Tech University, India

I am combining functional genomics and molecular genetics to unravel CA4, a blue-green acclimation process that is prevalent in cyanobacteria throughout the world’s oceans. We have generated NimbleGen whole-genome tiling microarrays to a marine Synechococcus strain and identified many genes whose expression is CA4 regulated. We are currently developing this strain for molecular genetics studies. Read more here.

LaDonna Jones
(started 2007)
B.A. in Biology, Transylvania University, Kentucky

We know nothing about whether additional, non-PBS related changes in protein or gene expression are occurring during sulfur limitation. I am addressing this by analyzing the expression of genes that are predicted to encode sulfur transport proteins. I will extend this further using microarrays with a long-term goal of determining if such responses are controlled by the same pathway(s) that regulate PBS restructuring. Read more here.

Adam Bussell
(started 2007)
B.S. in Biology, North Central University, Illinois

Prokaryotic phytochromes are a superfamily of photoreceptors found in photosynthetic and non-photosynthetic microbes, but since most of these were identified by genome sequencing, little is known about the responses most control or with which downstream partners they interact. I am studying a very unusual prokaryotic phytochrome whose expression is controlled by another phytochrome-class photoreceptor. Read more here.

Cassey Crowell
(joined the lab in Winter 2009)

I have just recently begun to work in the Kehoe lab and am examining the sulfur responsive promoter, working to determine what specific sequence is crucial for the low sulfur transcriptional response. Sami Bashour and Andrian Gutu established that the critical sequence required for sulfur responsiveness is between -377 and -307, but the exact nucleotides are not yet known. I am making further deletions and substitutions and using reporter gene assays to identify these sequences.

Charles Clark
(joined the lab in Fall 2009)

I am working with Andrian Gutu in isolating and identifing mutants of F. diplosiphon defficient in PC3 production in low sulfur conditions. I am also involved in the fine characterization of the existing mutants already identified in the lab.

Caitlynn Miller
(joined the lab in Fall 2008)

I am helping to figure out how the Cgi system functions to repress gene expression in red light. We are accomplishing this by mutating F. diplosiphon cells that do not have a functional Rca system (such cells are greenish-black). This means that phycoerythrin expression is only being controlled by the Cgi system in these cells. If mutated cells have a red phenotype when grown in red light, the Cgi system may have been altered. I am introducing a wild type genomic DNA plasmid library into several such mutants and screening for complementation by selecting cells with reversion to normal phycoerythrin repression (a greenish-black color). I am then isolating and sequencing the genomic DNA within the putatively complementing plasmid.  Genes encoded in this sequence will be further studied in order to establish whether they produce a protein that is part of the Cgi system.

David Rollo
Senior Research Associate

It is time for humans to use energy sources that are environmentally clean and sustainable. We believe that the capacity of cyanobacteria to efficiently convert the energy in sunlight into chemical bond energy through photosynthesis provides us with an excellent way to harness solar power in an ecologically benign manner. We are modifying the light harvesting capabilities of the unicellular cyanobacterium Synechocystis sp. PCC 6803 in order to make its capture and use of photon energy during photosynthesis very efficient. We are collaborating with other groups across the country in a combined effort to engineer 6803 cells that both produce large amounts of hydrogen and utilize ambient light extremely efficiently.

Nicholas White
Junior Research Associate

The Kehoe laboratory has defined the Rca pathway from the RcaE photoreceptor to the L Box binding site for the transcription factor RcaC. We are working to transfer this entire system into Escherichia coli in order to create a transcriptional regulatory system for light responsive control of gene expression in this organism. The long term use of such a system will be for commercial over expression of proteins using different colors of light for the activation and inactivation of transcription. This will provide several advantages related systems that are currently being used, including lowered cost for activation, absence of physiological side effects during activation, clean control of activation by precise control of the number of photons applied, and instant reversibility of activation through a simple shift in ambient light color.

Victoria Neely
Laboratory Assistant

I am the lab assistant and chief bottle washer. My job is to make sure no one runs out of pipette tips, microcentrifuge tubes, clean flasks, media, or sterile culture tubes. (DMK Note: Victoria is the single most important person in our laboratory!)

Graduate Students

Dr. Richard M. Alvey
Ph.D. Student
B.S. in Microbiology, Virginia Tech
Currently a Postdoctoral Fellow at The Pennsylvania State University

Doctoral Dissertation Title: " The Coordination of Apo-protein and Bilin Biosynthetic Enzyme Expression in Response to Light Color and Sulfur Availability in Fremyella diplosiphon'

Rick identified and uncovered the mechanisms underlying the light-regulated expression of the genes encoding the bilin chromophore biosynthetic enzymes that are used for light absorption within F. diplosiphon phycobilisomes. These were pebA and pebB, which encode proteins responsible for the production of the green-light absorbing chromophore phycoerythrobilin, and pcyA, which produces the enzyme that makes phycocyanobilin, a red-light absorbing chromophore. He also identified the L Box, the DNA promoter element that is bound by RcaC, as functionally critical for the activation of red-light activated genes. Finally, he also carried out the initial detailed studies of the sulfur limitation response in this organism.

Barbara Balabas
Masters student from 2000-2003
Currently practicing Optometry

Masters thesis title:  “Characterization of cyanobacterial mutants defective in phycoerythrin synthesis”

Barbara discovered a gene called cotB that is required for normal accumulation of phycoerythrin during growth in green light. The CotB protein may be part of a family of proteins called lyases, which are responsible for the covalent attachment of chromophores to proteins. The loss of cotB leads to a large drop in phycoerythrin mRNA, suggesting a possible feedback loop between phycoerythrin  protein and mRNA production.

Dr. Lina Li
Ph.D. Student
B.A. in Biology, Sichuan University, China
Currently a Postdoctoral Fellow at The University of California, Los Angeles

Doctoral Dissertation Title: " Regulation and Role of the Complex Response Regulator RcaC During Complementary Chromatic Adaptation in Fremyella diplosiphon"

Lina carried out detailed studies of the complex response regulator RcaC. Using site directed mutagenesis, she identified the key amino acids within this protein that are required for the CCA response and obtained data suggesting that RcaC is phosphorylated when cells are exposed to red light. Lina also determined that this protein is a transcription factor that binds to the L Box of the cpc2 promoter, and found that it is six times more abundant in red light than in green light. She demonstrated that these abundance changes are at least partially required for the proper regulation of CCA, although she found that phosphorylation of this response regulatory also appears to be needed.

Laura Ort-Seib
Research Associate from 1998-2000
Masters student from 2000-2002
Currently operating her own small business

Masters thesis title: “The role of CpeR in the regulation of phycobiliprotein gene expression”

Laura discovered the gene encoding CpeR (link to Laura’s paper), a small protein that has been found to be critical for the expression of a number of genes that are activated by green light. She was also the first to clearly outline the role of a second photoreception system in controlling green light responses during CCA, which we call the Cgi (Control of green light induction) system.

Postdoctoral Fellows

Dr. Emily Stowe Evans
National Science Foundation Postdoctoral Fellow in Microbiology from 2002-2004
Currently an Assistant Professor at Bucknell University

Emily created and utilized DNA microarrays in studies that greatly expanded our understanding of the scope and regulation of CCA in F. diplosiphon. This included the identification of 17 genes not previously known to be CCA controlled. The majority of these do not apparently encode phycobilisome components and a number of these provide new insights into the cellular physiology of the CCA response.

Dr. Beronda Montgomery
National Science Foundation Postdoctoral Fellow in Microbiology from 2001-2004
Currently an Assistant Professor at Michigan State University

Beronda characterized an the first of a new family of proteins called AplA, which is similar to proteins found in phycobilisomes and contains a covalently attached bilin chromophore in vivo. However, AplA is larger than the related phycobilisome proteins and, although made in the cell, does not appear to be associated with phycobilisomes. The specific role of this pioneer protein is not yet clear.

Dr. Nadya Lebedeva
MetaCyte PostDoctoral Fellow from 2004-2005
M.S. in Microbiology , Moscow State University, Russia
Ph.D. in Plant Physiology, Russian Academy of Sciences, Russia
Currently a Research Associate at the Russian Academy of Sciences, Russia

Nadya's research was designed to define the mechanisms through which F. diplosiphon deals with sulfur limitation. She worked to establish growth rates in the presence and absence of sulfur and compare these with growth in the absence of nitrogen and phosphate. Nadya found that limiting nutrients led to changes in cell morphology.

Dr. Kazuki Terauchi
Postdoctoral Fellow from 1999-2000
Currently an Associate Professor at Ritsumeikan University, Japan

Kazuki worked with the phytochrome-class photoreceptor RcaE. After making high-quality antibodies for RcaE, she demonstrated that it contained a covalently attached bilin chromophore in vivo, was equally abundant during growth in red and green light, and controlled both red and green light CCA responses.

Undergraduate Researchers

We have been fortunate to have a number of outstanding undergraduate students work in our laboratory over the past decade. Most have gone on the graduate or medical school. They are, starting with the most recent and listed chronologically:

Sami Bashour
Andrew Nejad
Matthew Careskey
Peter Gracheck
Emma Hollingsworth
Lenny Weiss
Noyan Olcum
Coral Maldonado
Bobby Huang
Chandler Walker
Erin Klenk
Patricia Odom
Bikram Malhi
Joshua Littlejohn
Coraline Haitjema
Jason Fox
Elicia Roos
Lee Peeples
Cydryce Carter
Katherine Shockley