"The result shows absence of intragenomic variation among 16S rDNA gene and presence of variable regions among the 16S rDNA sequences (intergenomic variation), noticing for example high variability around 800, 900, and 1000 bp and a large conserved region between 1150 and 1350 bp. This information allowed us to discard the restriction enzymes FnuII, AsuI, FokI, Eco57I that recognized some restriction sites contained within variable regions, since they are more susceptible of acquiring future nucleotidic variations and with this, the potential generation of different band patterns." [1]
I add that the article mentioned that these discarded enzymes were targeting conserved sites in the study species.
[1]Mandakovic D, Glasner B, Maldonado J, Aravena P, González M, Cambiazo V, Pulgar R. Genomic-Based Restriction Enzyme Selection for Specific Detection of Piscirickettsia salmonis by 16S rDNA PCR-RFLP. Front Microbiol. 2016 May 9;7:643. doi: 10.3389/fmicb.2016.00643. PMID: 27242682; PMCID: PMC4860512.
Is my reading right that the article implies that there is such potential? If yes, what are the possible mechanisms?
More important, what's the time frame of this "future nucleotidic variation", is it an evolutionary time frame that could take thousands of years?
Edit: i think my question can be thought of as: How common are new 16s rRNA gene variants in bacterial species?
Conserved restriction sites that are found in variable regions of DNA are not always reliable, as they can mutate over time.
Yes, your reading is correct. The article implies that there is potential for future nucleotide variations within the conserved restriction sites that are located in variable regions of the 16S rDNA gene.
The possible mechanisms for such variations are mutations, insertions, deletions, or recombinations, which can occur spontaneously or as a result of exposure to environmental factors, such as UV radiation, chemicals, or antibiotics. These changes can accumulate over time and result in differences in the sequence and/or length of the conserved restriction sites, leading to the generation of different band patterns upon restriction digestion.
The time frame for such variations can vary depending on the bacterial species, its population size, its growth rate, and the selective pressures it faces. Some bacterial species have high mutation rates and/or frequent horizontal gene transfer events, which can result in rapid evolution and diversification. Others have lower mutation rates and/or stable environments, which can lead to slower evolution and conservation of certain traits. However, even slow evolution can accumulate changes over time, and it is difficult to predict the exact time frame for future nucleotide variations within conserved restriction sites.
Regarding your edited question, the frequency of new 16S rRNA gene variants in bacterial species can also vary depending on the factors mentioned above. Some bacterial species have high genetic diversity and high rates of recombination and horizontal gene transfer, leading to frequent emergence of new variants. Others have low genetic diversity and low rates of recombination and horizontal gene transfer, resulting in slower emergence of new variants. However, the 16S rRNA gene is generally considered to be a stable and conserved marker for bacterial identification and classification, and many conserved regions within this gene are used as targets for PCR amplification and sequencing.
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