Seminar: Dr. Barbara MacGregor, UNC Marine Sciences

“Heptamer repeats in the genomes of giant sulfur bacteria: Where did they come from and what are they doing?”

The bacteria currently designated Orange Guaymas “Maribeggiatoa” are conspicuous members of microbial mats at hydrothermal sites in Guaymas Basin, a heavily sedimented ocean spreading center between Baja California and mainland Mexico. Individual cells are disk-shaped, with a large central vacuole, and grow as long multicellular filaments visible to the naked eye. A single filament was isolated with a toothpick, cleaned of epibionts, and a draft genome sequence obtained. Its predicted genes are consistent with the expected sulfide-oxidizing, nitrate-reducing physiology, and the orange color is attributable to a multiheme cytochrome that may be a nitrite reductase. There is evidence of horizontal gene transfer with a variety of distantly related species, Cyanobacteria in particular.

In this seminar, after a brief overview of molecular biology basics, I will discuss a puzzling genomic feature also visible to the naked eye. Over 160 of the ~5000 predicted genes have two to six consecutive direct repeats of the sequence TAACTGA just upstream of their start codons, usually covering the expected ribosome-binding site. These include genes for presumably essential products such as ribosomal proteins. Given their distribution in our genome, those of close relatives, and the larger database, the repeats are definitely not random, and may have been spread by horizontal transfer. But, what do they do? How are the downstream genes translated? Are leaderless mRNAs produced, is there a protein that can bind these sequences, are they somehow recognized by standard ribosomes? Are these genes coregulated? If so, what might the regulatory signal be? There are laboratory methods for addressing these questions in cultivated bacteria, but with an uncultivated species that can be collected at best every few years, it is a challenge. Suggestions are welcome.