Projects

Dr. Austin’s Projects:

Phytochrome isolation and characterization:

P. heparinus has a light-sensing protein, a phytochrome, which enables it to detect light even though this bacterium is non-photosynthetic. So, this raises a variety of questions: What are the key properties of this light-detecting protein? Why does the protein detect light? How does it use the light? I try to answer these questions through a combination of laboratory work and bioinformatics.

One of things we have learned through gene annotation is that the phytochrome is different from other bacterial phytochromes. It appears to be smaller than related bacterial species. It is missing a specific section that is found all other bacterial proteins. One of my goals is to isolate and characterize this phytochrome to determine why it is unique.

Impact of glyphosate on P. heparinus:

P. heparinus lives in soil at moderate temperatures. It has been shown to associate with such plants as rice and a morning glory. This organism is likely to be found living near other plants, including agricultural one.  On farms, Roundup® has been used in the United States for a few decades. The key ingredient in this herbicide is glyphosate, a molecule similar in structure to the amino acid, glycine. When applied to growing plants, glyphosate binds an enzyme that is important in synthesizing aromatic amino acids, such as tyrosine. When this enzyme is bound with glyphosate it is inactivated and can not produced these necessary amino acids. The result is that the plant dies.

Bacteria have a similar enzyme to that of plants and, hence, are susceptible to glyphosate as well. Some bacteria are able to degrade this herbicide and use the breakdown products as nutrients. P. heparinus appears to be one of these bacteria, at least at certain points in its growth cycle. At early periods of growth new bacteria are killed when in contact with glyphosate. If applied later in its life cycle the impact appears to be minimal even at high concentration. 

My work on this project is to determine how and when P. heparinus is impacted by glyphosate.  If the organism can thrive in the herbicide’s presence, what features allow this to happen? Could the bacteria excrete an enzyme to degrade and inactivate glyphosate?

Dr. Essig’s Projects:

My research with undergraduate students strives to connect P. heparinus genome structure/function with integrated organismal functions.  

A. One major ongoing project is to improve the annotation of genes within the Pedobacter heparinus genome.   Of the approximately 5,000 genes, roughly 1,000 code for proteins which have no predicted function.  These genes are often referred to as hypothetical.  Through a combination of bioinformatic tools and experimental procedures, undergraduate students from BIO 319 Genetics gather additional evidence to uncover the function of the protein products for these hypothetical genes.  Genes for which a product name can be assigned are featured in the GENI-ACT website http://geni-act.org/. 

B. Another project seeks to determine the sequence motif upstream of start codons which facilitates ribosomal binding to the mRNA in P. heparinus.  Typically this includes a Shine Dalgarno consensus sequence which binds to the 16S rRNA.  Preliminary data based on sequence signature analysis suggest that genes in P. heparinus and other related organisms do not have a Shine Dalgarno sequence. This suggests that an alternative and novel mechanism must exist to stabilize ribosome binding to the mRNA.

C. I also direct hypothesis driven research projects based on findings of previous bioinformatic studies. These include:

1. Biosynthesis of plant hormones by P. heparinus.  Hypothesis:  Plant hormones produced by P. heparinus will positively influence the growth of the model plant organism Arabidopsis thaliana. 
2. Transcriptome regulation during colony spreading.  Hypothesis:  Multiple operons will be transcriptionally upregulated.  These will include genes which assemble the gliding motility apparatus and regulate cell division.
3. Interspecies competition and expression of anti-microbial peptides.  Hypothesis:  Operons previously shown to encode novel anti-microbial peptides and transport machinery will be be upregulated in the presence of competitive bacterial species.   Some of the anti-microbial peptides may have therapeutic applications.
4. Transcriptome regulation during environmental stress: Hypothesis: Light and other environmental stressors will upregulate a carotenoid biosynthesis operon and other stress protection operons through a phytochrome independent mechanism involving the transcription factor MarR.
5. Transcriptome regulation during growth on pectin:  Hypothesis: Growth on pectin will cause selective upregulation of genes in the pectin PUL.