George Sensabaugh, Professor

Closed (1) Phylogenomic analysis of genes controlling the synthesis of pigment in species of Staphylococcus.

Applications for fall 2021 are now closed for this project.

The pathogen Staphylococcus aureus takes its name from its gold color. The color pigment, staphyloxanthin, has been demonstrated to protect the bacterium against oxidative stress, thus contributing to the survival of the organism. However S. aureus is not unique with regard to pigmentation: many other species of staphylococci also express similar yellow to orange pigmentation. Previous studies in my laboratory have shown that other staphylococci carry the same gene complex that controls the synthesis of staphyloxanthin in S. aureus. Phylogenetic analysis has shown that genes in this complex are related to the genes in aureus but form a phylogenetically distinct group. The overall objective of this research project is to address the evolutionary origin (or origins) of the genes in this group.
The pathway of staphyloxanthin synthesis is mediated by 6 enzymes, 5 of which are encoded in a single operon, the crt operon, and the 6th elsewhere in the microbial genome. For a reference on this pathway and the roles of the 6 enzymes, see Kim SH, Lee PC. Functional expression and extension of staphylococcal staphyloxanthin biosynthetic pathway in Escherichia coli. (2012) J Biol Chem. 287(26):21575-83. Don’t get hung up on the procedures used in the paper – you can get most of what you want to know from the illustrations.
The central question regarding the evolutionary origins of the crt operon genes is whether (a) they have evolved from a single ancestral origin and have evolved in parallel with the evolution of staphylococcal species or (b) have jumped between staph species in separate species lineages. To address this question, we will pursue the following specific aims:
• Complete a survey of the species distribution of the crt operon by searching on the microbial genome database. The operon may be ubiquitous in some species but partially present in some or absent in others.
• Perform phylogenetic analyses on the crt genes to characterize genetic relationships among them and compare this to the overall phylogenetic tree of staph species.
• Prior surveys we have done show that the operon is carried in some plasmids; these may be vehicles for horizontal gene transfer between species. We need to know where these fit into the general picture.
• Is there evidence of recombination between species?
• Complete genome sequences are known for most staph species. Comparison of genome environments, both proximal to the crt operon and positional relative to other genomic elements, may provide corroborative support for one or another hypothesis.

The student participating in this project will be responsible for organizing sequence data from research files and the NCBI Microbial Genome database. The sequence data will be characterized using standard software programs to test hypotheses suggested by the data. The software to be used is either web based or can be downloaded from the web and run on PCs or Macs (the software I am most familiar with is PC based).
Students will be able to work on this project on their own time and place. We will review progress weekly through the term by video chat.

Qualifications: Knowledge of the basic concepts underlying DNA sequence analysis and of phylogenetic analysis is essential. Students must be meticulous in managing data and in recording work; sloppiness, losing control of operations, and failure to maintain good documentation may mean having to start all over again.

Weekly Hours: 3-5 hrs

Off-Campus Research Site: Communication between student and faculty will be done by email and a weekly zoom meeting. If circumstances allow, we can meet in person as well.