Students in my courses and research lab studied the marine bacterium Cellulophaga lytica, the unofficial “Microbial Mascot” of Northwestern. We took on the job of interpreting the genome (complete DNA sequence) of C. lytica in collaboration with the Joint Genome Institute of the US Department of Defense. Students taking microbiology and genetics received training and hands on experience in bioinformatics and used a suite of computer programs to further understand C. lytica genes and their functions. Genetics students studied 13 genes predicted to be involved in the ability of the bacterium to glide across surfaces and their work suggested that C. lytica gliding is similar to that in the related bacterium Flavobacterium johnsoniae. Beyond bioinformatics, research students have performed laboratory experiments to investigate the ability of C. lytica to degrade cellulose – the main component of plant cell walls. Cellulose degrading bacteria may help in the development of new technologies to produce ethanol from plant material, with the goal of reducing reliance on fossil fuels and addressing current limitations of producing ethanol from corn. Students in my lab cloned a cellulase gene from C. lytica and expressed it in E. coli. Future work will measure the enzymatic activity of this protein. 

The study of bacterial genetics is a critical component of biomedical research. Bacteria associated with the human body number in the trillions, with varying levels of consequence.  While the relationship between human and microbe is largely mutualistic, a seemingly simplistic single-cell organism such as a bacterium does have the power to overcome its host.  Ultimately, this ability is encoded within the genetic information, the DNA, of the bacteria. In addition to understanding the workings of a particular bacterium, the study of bacterial genetics often increases our understanding of basic biological principles found in complex organisms, thus serving as a model organism. My research harnesses the power of bacterial genetics to both understand a family of bacteria known as the lactic acid bacteria, and the potential to understand a basic genetic process in higher organisms. My research deals with the very fundamental issue of how genetic information is processed in a cell to ultimately express particular characteristics. The process I study is called splicing, and is the removal of seemingly unimportant genetic information (called introns) from genes that are critical for cell function. Bacterial introns splice by a relatively novel mechanism that is still poorly understood. In addition, bacterial introns are mobile and can enter into a new region of DNA. My research objective is to identify and characterize important features required for intron splicing and explore the incidence and consequences of intron mobility.

Specifically, the purpose of my research is to locate and characterize regions of the Ll.ltrB intron in the gram positive bacterium Lactococcus lactis that are important for its splicing ability. I use a genetic screen to identify mutations that disrupt intron function. The screen takes advantage of the fact that the intron is present on a plasmid that undergoes bacterial conjugation. The Ll.ltrB intron disrupts a gene required for plasmid transfer. In the normal situation, the intron is able to splice from this gene and plasmid transfer can occur. However, mutations in the intron that disrupt splicing also prevent plasmid transfer; therefore, splicing ability can be measured using a simple assay for plasmid transfer. By generating mutations throughout the intron and screening for loss of plasmid transfer ability, potential splicing mutants are identified. Interesting mutants are further analyzed for splicing ability using RT-PCR analysis and sequenced to determine the location of the mutation. Data that is collected provides new information about the structure and function of the Ll.ltrB intron and may increase our understanding of splicing in higher organisms.