Short project (few weeks): Diversity in sortase recognition sites

Title: Short project (few weeks): Diversity in sortase recognition sites

Description

Supervisor: Roland Siezen

Introduction

Interaction between bacteria and their environment appears to depend mainly on the activity of covalently attached surface proteins. One of the mechanisms for covalently attaching secreted proteins is the sortase-dependent LPxTG anchor. The anchoring system consists of an enzyme (sortase) that recognizes C-terminal transmembrane helices that, in general, are preceded by an LPxTG-like pattern. However, many bacteria have a sortase recognition site that deviates from this generic LPxTG consensus: in L. plantarum we find LPQTxE, while in Listeria species we find LPxTGD. We also know that the cell walls of the mentioned bacteria in particular (but also of other lactic acid bacteria) have a peptidoglycan composition that deviates from that of other bacteria

Project

In this project we try to find a link between the consensus LPxTG sequence and the peptidoglycan composition of bacteria.

Methods

This project will use HMMs to identify LPxTG like sequences. Data on peptidoglycan composition will be derived from literature.