|
Facts on lactic acid bacteria that have been discovered through genome sequencing
Surprising facts on lactic acid bacteria that have been discovered through genome sequencing
Since 2001, large amounts of information on sequenced lactic acid bacteria genomes have been published one after another, shedding light on the true nature of lactic acid bacteria. This is causing a paradigm shift of the unknown.
This section explains two key surprising discoveries.
Previously, scientists thought that lactic acid bacteria did not breathe in the traditional sense of using oxygen, and would typically become weak when exposed to oxygen. This was the common understanding at the time. However, when some genome sequencing was done on Lactococcus lactis (i.e., one of the first lactic acid bacteria whose genome was sequenced), it was discovered that the genus possessed almost all the genes necessary to sustain life by breathing oxygen. When researchers fed proteins containing the heme iron to the bacteria and cultured them in an oxygen-rich environment, the bacteria actually began oxygen breathing. In this experiment, the bacteria’s genes previously found to be involved in oxygen breathing apparently manifested, while the genes involved in the fermentation function under anaerobic conditions were suppressed, halting their lactic acid production. As lactic acid bacteria were previously known as non-breathing organisms, which was considered one of their defining characteristics, the revelation that they could actually breathe by altering their metabolism under certain conditions shocked scientists around the world.
The second discovery concerns lactic acid bacteria’s hidden capacity. As lactic acid bacteria are unable to produce all amino acids that are necessary to stay alive, they source the amino acids from the outside environment (i.e., amino acid requirement). This is a well-known fact. However, after their genomes were decoded, it was found that many lactic acid bacteria had almost all the genes necessary for producing amino acids themselves. Research has also shown that there are certain lactic acid bacteria that completely lack any genes for producing various types of amino acids, although this is still limited to a small number of cases. Based on all these facts, it is inferred that the lactic acid bacteria that obtain amino acids from external sources to stay alive can be classified into two different types, i.e., those that possess the amino-acid-producing genes with their function being suppressed, and those that lack such genes completely.
As the genetic data of lactic acid bacteria continues to be revealed through genome sequencing, scientists are altering their conceptual understanding of what lactic acid bacteria are, and offering a novel image of the bacterial order.
How can the information obtained from genome sequencing be used?
Even if fragments of genetic information obtained about an organism by decoding its genome is made available, such as its base sequences and gene quantities, they alone provide no clue as to the function of each of the organism’s genes. To determine the functions of the organism’s genes, new experiments must be conducted using the obtained genome data. While there are several different methods of conducting such experiments, the one that has become most popular for its simplicity and accuracy is called microarray analysis.
This experimental method works as follows. First, it must be understood that the genes existing in any given organism’s genome are not directly producing the proteins necessary for sustaining its life. Instead, only the genes that are essential under the current conditions get copied to the RNA (this process is known as “transcription”), and then proteins are produced through the RNA acting as an intermediary. Therefore, to precisely understand how certain genes function under specific conditions, one only needs to know the amount of RNA (transcription) produced by each gene involved.
But how exactly is microarray analysis conducted? It might be difficult to understand, but the following is a simple outline.
- (1) First, DNA containing strands of roughly 2000 genes making up the genome of a lactic acid bacterium is placed on a small glass plate, one by one, in precise spots to form a microarray.
- (2) Next, all RNA is extracted from the lactic acid bacterium’s cells that have been cultured under certain conditions.
- (3) The objective here is to measure the amount of RNA (transcription) in each gene contained in this RNA collection, but it is impossible to measure as is. Therefore, complementary DNA (abbreviated “cDNA”) is synthesized through enzyme reaction based on all the RNA. In this process, fluorescent pigments are added as markings for future reference to all the DNA on the glass plate (microarray) until the desired reaction is achieved.
- (4) Finally, when the fluorescence intensity of each cDNA is measured, it reveals which genes are functional under certain experimental conditions (i.e., promoted transcription) or suppressed (suppressed transcription).
This enables simultaneous observation of the changes occurring in all the genes (roughly 2000 of them) in each lactic acid bacterium, and also increases the chance of finding genes that are often missed by other conventional methods. As a result, this microarray analysis is useful for diverse applications as an important tool for facilitating the advancement of genome research.
Genome research leads to a holistic understanding of what lactic acid bacteria really are.
This final section explains the unique characteristics of a lactic acid bacterium that have been discovered through microarray analysis.
Lactobacillus gasseri, a species of lactic acid bacterium, has strong resistance to stomach acid not seen in any other species of lactic acid bacteria. This characteristic is considered an important aspect of effective probiotics, as it allows them to avoid being damaged by stomach acid and to perform their positive functions in the stomach, in addition to reaching the intestines alive. Therefore, much attention has been paid to elucidating this mechanism.
When L. gasseri was stimulated with acid in experiments, and its approx. 1600 genes were examined in microarray form, it was revealed that over 100 of those genes would start moving quite actively. Further analysis of the data indicated that the bacterium’s ability to withstand acid was actually a function of a number of bacterial mechanisms working in concert with each other. Examples of such mechanisms include neutralization of incoming acid, discharge of incoming acid, repair of the nucleic acid and proteins that have been damaged by acid, etc., all working simultaneously. Meanwhile, as energy is required for the acid-resisting capacity to manifest itself, research has shown that the activities of certain gene groups are apparently suppressed to halt the process of cellular proliferation.
The capacity of each lactic acid bacterium is manifested strictly in accordance with the genetic data contained in its entire genome. Therefore, conducting genome research on lactic acid bacteria involves understanding what they are in a holistic manner.
Since human beings started walking the earth, lactic acid bacteria have provided us with tremendous benefits for millennia. To keep reaping benefits from these amazing microorganisms and improve our diets and health, it is crucial to gain a better understanding of what lactic acid bacteria truly are, based on their genome data, and to constantly endeavor to harness their full potential.
|
