For long time it was thought that genetic language is consist of mere 4 letters and encode all the genetic information based on large combinations of these four letters. Graduate students would have often solved question based on this fact. However, to add to the pedagogical information provided in text books, I discuss addition of more bases into the genetic alphabet and thus we have many more combinations possible. Though, new bases were known since 80s, but recent advancements such as protein synthesis using 6 bp alphabet and also creation of semi synthetic organisms has drawn the attention once again.
In fact, the concept of epigenetic regulation largely relies on this new information. Its not a very new discovery but in the early 80s, a fifth base the methyl-cytosine (mC) derived from cytosine was already added. And it was in the late 90's when mC was recognized as the main cause of epigenetic mechanisms: it is able to switch genes on or off depending on the physiological needs of each tissue. But, it has been quite some time when the 6th base methyl-cytosine (mA) was added to this list.
However, this old information has gained recent attention of researchers primarily due to unique role of these bases in genetic control. Moreover, the creation of semi-synthetic organism utilizing all six letter code has added flavor to the domain.
The Fifth and Sixth Base
One of the bases, the 5th base, is cytosine with a methyl group on it (chemically, this would be -CH3), labeled “mC” above. Structurally, the methylated cytosine causes the DNA double helix to coil just a little tighter than its non-methylated counterpart, “C” above. This tighter coil likely “silences” genes — they are not transcribed. The lead author for the papers reporting on these bases, Yi Zhang, states that “5-methylcytosine [mC]…arises when a chemical tag or methyl group is tacked onto a cytosine. This methylation is associated with gene silencing, as it causes the DNA’s double helix to fold even tighter upon itself.” While this is an interesting discovery, his group also found that these cytosine derivatives are observed in mouse embryonic stem cells and may be implicated in stem cell reprogramming.
In recent years, interest in this fifth DNA base has increased by showing that alterations in the methyl-cytosine contribute to the development of many human diseases, including cancer
(Adapted from - https://evolutionnews.org/2011/08/four_more_dna_bases/)
5-Hydroxymethylcytosine (hmC) was recently discovered as a new constituent of mammalian DNA. Besides 5-methylcytosine (mC), it is the only other modified base in higher organisms. The discovery is of enormous importance because it shows that the methylation of cytosines to imprint epigenetic information is not a final chemical step that leads to gene silencing but that further chemistry occurs at the methyl group that might have regulatory function. Recent progress in hmC detection--most notably LC-MS and glucosyltransferase assays--helped to decipher the precise distribution of hmC in the body. This led to the surprising finding that, in contrast to constant mC levels, the hmC levels are strongly tissue-specific. The highest values of hmC are found in the central nervous system. It was furthermore discovered that hmC is involved in regulating the pluripotency of stem cells and that it is connected to the processes of cellular development and carcinogenesis.
(Read complete study at https://www.ncbi.nlm.nih.gov/pubmed/21688365)
Semi-synthetic bacteria with 6 bp alphabet
The team, led by Floyd Romesberg from the Scripps Research Institute in California, engineered synthetic nucleotides - molecules that serve as the building blocks of DNA and RNA - to create an additional base pair, and they’ve successfully inserted this into the E. coli’s genetic code. Romesberg and his team suspect that creation of world’s first semi-synthetic organism, with a genetic code made up of two natural base pairs and an additional 'alien' base pair, is just the beginning for this new form of life.
Read the complete article here
https://www.pnas.org/content/early/2017/01/17/1616443114
An extra two letters might not sound like a lot, but it now vastly expands the number of possible three-letter “words” that can be written in DNA. In fact, the expanded code boosts the number of possible codons and corresponding amino acids from 20 to 172 .
Six-Letter DNA Alphabet Produces Proteins in Cells
The presence of additional letters in the genetic alphabet is not merely a over representation of epigenetic modification and fleeting environmental modulations, but have been successfully realized into the protein encoding machinery. To expand the alphabet, York et al developed synthetic nucleotides that pair to form an unnatural base pair (UBP), and used it as the basis of a semisynthetic organism (SSO) that stores increased information. However, the SSO grew poorly and lost the UBP under a variety of standard growth conditions. Here, using chemical and genetic approaches, they reported the optimization of the SSO so that it is healthy, more autonomous, and able to store the increased information indefinitely. This SSO constitutes a stable form of semisynthetic life and lays the foundation for efforts to impart life with new forms and functions. (Read complete research here - https://www.pnas.org/content/early/2017/01/17/1616443114) . Additionally, three years ago, chemistry professor Floyd Romesberg of the Scripps Research Institute in California and colleagues also reported the creation of additional artificial nucleotides, X and Y, that could pair up within DNA and take part in replication within a living bacterial cell. This proof-of-principle advance now sets the stage for biochemists to generate proteins with entirely novel forms and functions to those that can be created by natural organisms (Read complete article here - https://www.nature.com/articles/nature24659)
The list is expanding..
Not limited to 5th and 6th base but recent discovereies revealed 7th and 8th base as well. A research published online in the July 21, 2011, issue of the journal Science, researchers from the UNC School of Medicine have discovered the seventh and eighth bases of DNA.
These last two bases – called 5-formylcytosine and 5 carboxylcytosine – are actually versions of cytosine that have been modified by Tet proteins, molecular entities thought to play a role in DNA demethylation and stem cell reprogramming. Thus, the discovery could advance stem cell research by giving a glimpse into the DNA changes – such as the removal of chemical groups through demethylation – that could reprogram adult cells to make them act like stem cells.
https://www.cell.com/cell/fulltext/S0092-8674(15)00438-9