Abstract
Genomes of the month the good, the bad and the ugly
The sequences of three bacterial genomes have been published in the month since the last Genome Update was written, with each representing bacteria with different and interesting lifestyles. The three genomes include that of a member of the acidophilus group of intestinal lactobacilli (a good bacterium), that of a pathogen that causes a highly contagious respiratory disease in cattle (a bad bacterium, certainly from the perspective of the ranchers) and that of a bacterial predator that invades and consumes other bacteria (ugly from the point of view of its prey).
The genome of Lactobacillus johnsonii strain NCC 533 (Pridmore et al., 2004) is just under 2 Mbp in size, has an AT content of 65 % and encodes about 1800 proteins (see Table 1). Surprisingly, this genome is missing key enzymes for the biosynthesis of amino acids, many co-factors and purine nucleotides (Pridmore et al., 2004). However, this appears to be compensated for by extra amino acid permeases, peptidases and small-molecule transporters, which bring in the necessary molecules from the environment. Perhaps this is not surprising for a bacterium which is known for living as an intestinal commensal, living in the rich and relatively constant intestine environment. L. johnsonii is a probiotic bacterium and, as such, is claimed to be involved in pathogen inhibition, epithelial cell attachment and immunomodulation. Several large adhesion proteins have been found in this genome, as well as bile salt hydrolases and transporters, which are likely to be involved in persistence in the gastrointestinal tract (Pridmore et al., 2004). Obviously it is better, from a human's perspective, to have one's intestinal tract populated by a healthy population of lactobacilli which can prevent the growth of potential pathogens.