Year: 2022

STOP CODONS. “Because the code governs the translation of nucleotide to amino acid sequences, a code can in principle only be confirmed when both the gene and protein sequences are known. Stop codons stick out as a sore thumb in DNA sequence because they disrupt the coding region in a way that is difficult to overlook or misinterpret, so these codes can be strongly inferred from DNA sequence.” https://lnkd.in/d87ZWbH View in LinkedIn

STILL TO FIND. “In contrast, a code where two amino acid-encoding codons were altered would appear in DNA sequence to be slightly divergent, but not obviously translated by a different genetic code. But it is therefore possible, even likely, that non-canonical genetic codes involving switches between amino acids have been observed but escaped our detection.” https://lnkd.in/d87ZWbH View in LinkedIn

MORE EXCEPTIONS. “It was the stand-out nature of stop codons that first alerted Zahonova et al. to the presence of the new non-canonical codes in Blastocrithidia. But digging deeper they encountered something more interesting. The most frequent nuclear code change is UAR=Q (stop codons UAA and UAG to encode glutamine). Zahonova et al. found instead that UAR=E and that UGA=W (which is common in bacteria).” https://lnkd.in/d87ZWbH View in LinkedIn

PREDICTION FULFILLED. “Swart et al. recently reported evidence for just such a context-dependent process linked to a similar genetic code change in a ciliate, where UAR=Q and UGA=W or stop, depending on the downstream sequence. These codes are also exciting because they fulfill a central prediction of one of the models for how the genetic code evolves, the Ambiguous Intermediate model.” https://lnkd.in/d87ZWbH View in LinkedIn

INTERMEDIATE FORM. “While we must bear in mind that most non-canonical codes evolved independently from the others, and so may have evolved through different steps, it is nevertheless intriguing to have an extant nuclear genome with an ambiguous intermediate.” https://lnkd.in/d87ZWbH View in LinkedIn

PARADIGM WRECKERS. “Further study of how translation functions in Blastocrithidia will cast a unique light on how the code works, which will certainly be challenging since it is not only an uncultured symbiont, but also a trypanosome, a lineage which is notorious for re-writing the rule books of molecular biology and genomics.” https://lnkd.in/d87ZWbH View in LinkedIn

ARTIFICIAL CODE. “New methods of synthetic biology have recently allowed substantial artificial alteration of the code in bacteria. Although the fitness of the bacteria with altered codes has not been thoroughly studied, their viability itself seems to support the view that the fitness of different codes might not differ dramatically, so that the (near) universality of the standard genetic code is likely to stem from high fitness barriers separating it from other codes, or in other words, low fitness of the intermediates.” https://lnkd.in/dKTqJpY View in LinkedIn

HORIZONTAL EXPLANATION. “Then, why only one frozen accident, assuming that the actual codon assignments are indeed (quasi) accidental? To put it even more generally, why a single last universal common ancestor only? Only one code survived because extensive horizontal gene transfer was an aspect of early evolution without which the transition to the cellular level of complexity would not have been possible. Even a small change in the code has a prohibitive effect on horizontal gene transfer.” https://lnkd.in/dKTqJpY View in LinkedIn

CONSERVING FORCES. “Conceivably, frozen accident and the requirement of horizontal gene transfer were major, complementary factors that have kept the code universal.” https://lnkd.in/dKTqJpY View in LinkedIn

NEW CELLULAR DNA. “Australian researchers have identified a new DNA structure -- called the i-motif -- inside cells. A twisted 'knot' of DNA, the i-motif has never before been directly seen inside living cells. The new shape looks entirely different to the double-stranded DNA double helix. We think the coming and going of the i-motifs is a clue to what they do. It seems likely that they are there to help switch genes on or off, and to affect whether a gene is actively read or not." https://lnkd.in/dC4Eqkg View in LinkedIn