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In their paper, the researchers describe findings from analyzing the genome of Lactobacillus bulgaricus. They explain that the organism is worth studying because of its important role in producing yogurt. Furthermore, the genome of L. bulgaricus is interesting because of its unique GC content compared to the other members of the acidophilus complex, which is a group of lactobacilli. From their findings, the researchers made conjectures about the evolution of the organism and how it lives. In this review, the writer will summarize the main evidence which the researchers put forward to support the hypothesis that L. bulgaricus is undergoing evolution that is reducing its genome size.
The first thing the researchers talk about is the basic sequence characteristics of L. bulgaricus in comparison to that of other closely related species. As they expected, the GC content of L. bulgaricus was found to differ greatly from that of closely related species. Furthermore, they found that this difference was due to GC content in codon position 3 (GC3), which was unusually high compared to other bacteria. In figure 1, the researchers graphed the GC content in GC3 against the GC content of the entire genome for many different eubacterial species. The reader can see that there is an approximately linear relationship between the two characteristics and that the GC content at GC3 of L. bulgaricus is indeed high with respect to the GC content in its entire genome. Because the researchers found that GC3 evolves faster than GC 1 or GC2, they speculated that this feature was due to either active evolution of the genome towards a higher GC content or evolution that has caused increased GC content in codon position 3 specifically. While the data presented was convincing, figure 1 could have been modified to make it more obvious that L. bulgaricus was an outlier. Also, the researchers do not give any information about the size and location of GC3.
In the genome atlas in figure 2, the researchers showed that pseudogenes were evenly distributed throughout the genome except for a small region, in which there was very little pseudogenes. Furthermore, the researchers found that there is a high number of pseudogenes in the genome of L. bulgaricus, which they interpreted as suggesting the genome was evolving towards a smaller size. This interpretation makes sense, but the researchers neglect to give information about the number of pseudogenes in other closely related species. After all, how can we tell if the high number of pseudogenes is unusual if we have no other genome to compare it to? In addition, the researchers found that the numbers of tRNA and rRNA genes are high for the genome size of L. bulgaricus when compared to other firmicutes. Firmicutes are a good choice of comparison because it consists of many members including lactobacilli and many other genera. This information was clearly shown in figure 3, which consisted of two separate graphs, comparing the genome size to numbers of 16S rRNA and tRNA in different firmicutes. Reasonably, the researchers interpreted the data as indicating that the genome of L. bulgaricus has undergone a recent reduction in size.
Using GC skew and presence of DnaA boxes, the researchers located the origin of replication, from which they located the replication terminus. Within the replication terminus, they found an inverted repeat that was conserved in most strains of L. bulgaricus. However, there was variation among the different strains in the sequence between the two sequences of the repeat. The researchers suggested that this could represent evolution in the L. bulgaricus genome.
The researchers found that there was region in the genome that had no IS elements, which seem randomly distributed throughout the rest of the genome. This region overlapped with the previously discussed region which had decreased amount of pseudogenes. However, the researchers do not believe that the low amount of pseudogenes is due to lack of IS elements, since most other pseudogenes in the genome were not caused by IS element insertions.
By comparing the L. bulgaricus genome with the genomes of L. acidophilus and L. johnsonii, the researchers found that more than half of the genome was conserved among the three species. On figure 4, the genomes of L. bulgaricus and L. acidophilus are compared. The reader can see the conservation between the two species by looking at the ‘line’ of data points running at a 45 degree angle. Simultaneously, from looking at the data points that do not lie on the forty five degree ‘line’, it is also evident that there are many genes that are not conserved. The researchers could not find functions for most of the genes that were not conserved, but they do describe the functions of a few of the genes that were not conserved. These genes are discussed again in later sections of the paper.
There is presence of a restriction modification system, which the researchers believe is responsible for the difficulty to transform this strain of L. bulgaricus. It could be interesting to find out how highly conserved this is among different strains of the species, and if it has an inhibitory effect on horizontal gene transfer.
In the rest of the paper, the researchers focus on features of the genome which exemplify adaptations of L. bulgaricus to its dairy-rich environment. In a comparison of the genomes of L. bulgaricus and L. plantarum, the researchers found that the L. bulgaricus genome had significantly fewer transcriptional regulators. They attributed this feature to the stable milk environment which L. bulgaricus inhabits. This makes sense because L. bulgaricus will not need genes that give it versatility in adapting to changing environment conditions. The researchers also found that certain regulators may have broader roles in L. bulgaricus. They found that in L. bulgaricus, HrcA seems to regulate clp as well as dnaK and groESL, whereas clp is regulated by a separate regulator, CtsR, in L. plantarum.
In the next section of the paper, the researchers go back to the topic of pseudogenes and how they suggest that L. bulgaricus is undergoing evolution through specialization to its nutrient-rich environment. For some of the pseudogenes, there were paralogs within the organism, but for many of them there were no paralogs. The absence of paralogs suggests that the function of the gene is lost completely. There was a reduction in the number of metabolic pathways and sugar transport systems. This makes sense because the environment of L. bulgaricus is so stable and so rich in nutrients, the organism can survive by just specializing in processing certain nutrient sources. Conserving other metabolic pathways would be a waste of energy. Interestingly, L. bulgaricus has lost many amino acid synthesis pathways. L. bulgaricus has an extracellular protease, which allows it to obtain its amino acids by digesting the peptides in the milk it lives in.
Another feature of L. bulgaricus that deserves examination is its relationship with S. thermophilus in their habitat. Because of their reduced genomes, the two organisms each have certain limitations to their metabolic pathways. However, the genes that are present in each genome seem to compensate for the absence of certain genes in the genome of the other species. This kind of cooperative evolution allows both genomes to reduce in size but still be viable.
For the most part, this paper was well-written. The researchers did a good job of presenting their data on figures and explaining their reasoning. In their paper, the researchers not only wanted to show that the genome of L. bulgaricus has experienced reductive evolution, but also that this evolution is still going on. This hypothesis is supported by the elevated GC content in GC3, the high number of pseudogenes, the disproportionately high number of tRNA and rRNA, and the inverted repeat with the variable sequence in the middle. It makes sense that the genome of L. bulgaricus is being reduced, because it lives in milk, a stable and nutritious environment. Furthermore, there seems to be mutualism between L. bulgaricus and S. thermophilus, in which each species makes products that the genome of the other species can no longer code for.
van de Guchte, M, Penaud, S, Grimaldi, C, Barbe, V, Bryson, K, Nicolas, P, Robert, C, Oztas, S, Mangenot, S, Couloux, A, Loux, V, Dervyn, R, Bossy, R, Bolotin, A, Batto, JM, Walunas, T,Gibrat, JF, Bessières, P, Weissenbach, J, Ehrlich, SD and Maguin, E. 2006 Jun 13. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proceedings of the National Academy of Sciences of the United States of America 103: 9274-9279. Accessed Oct 9, 2008.
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