Well begun is half done? Skoltech researchers study the recipe for efficient protein synthesis

May 28, 2020

Skoltech scientists and their colleagues have studied more than 30 thousand variants of genetic sequences encoding two fluorescent proteins in order to determine which characteristics of mRNA and of the first dozen or so codons in it can increase the efficiency of translation. Among other things, they found that rare codons at the beginning of the sequence do not seem to enhance translation, contrary to some hypotheses.

Translation is one of the fundamental processes in any cell: decoding a newly minted messenger RNA (produced from DNA during transcription), a ribosome builds an amino acid chain that then folds into a protein, which goes on to perform various vital functions in the cell. Each amino acid is represented by a codon, a triplet of nucleotides in the mRNA chain. There are 61 codons for amino acids but only 20 amino acids that a ribosome can make, which means that some codons are, in effect, synonymous -- they encode the same amino acid.

After decades of research, scientists still aren't sure what makes the work of a cellular "protein plant" more or less efficient. For instance, there is evidence suggesting that some particular secondary structures of mRNA, i.e. how the coding sequence is folded spatially at its start, can prevent the ribosome from binding to the mRNA and doing its job. Another factor might have to do with those synonymous codons: earlier research hinted at the possibility that codons that are statistically used more rarely can enhance the efficiency of translation if placed at the beginning of an open reading frame. These codons make the ribosome move slower along the mRNA at its beginning so that ribosome queues do not form downstream.

This is not an idle line of inquiry. Studying the efficiency of translation will help us understand gene expression better and aid biotechnology by making sure our protein-producing workhorses are at their best. That is why Ilya Osterman and Zoe Chervontseva of Petr Sergiev, Olga Dontsova and Mikhail Gelfand groups at Skoltech and Lomonosov MSU and their colleagues decided to run a competition of sorts: they tested more than 30,000 variants of mRNA encoding the same protein to see which ones will lead to a more efficient translation. The researchers were interested in the role of codons number 2 to 11 (the first codon is always the ATG start codon, much like the first line of code in some programming languages that tells the computer that a program will follow).

They used Escherichia coli and plasmids -- rings of DNA encoding what's called a dual fluorescent protein reporter (the "duo" are RFP and CER, two fluorescent proteins). The randomized 30-nucleotide sequences were inserted right after the start codon so that they would become codons number 2 to 11 in an mRNA. After growing the modified E. coli to make the CER and RFP proteins and sorting the cells by how efficient they were at it, scientists used the so-called flowseq method to determine which coding sequences turned out to be better for efficient protein production.

"Flowseq is a combination of flow cytometry, a technique where physical and chemical characteristics of cells are measured via the scattering of light from a laser beam, with sequencing of the separated fractions. This method allows to assess the efficiency of protein synthesis in a massively parallel setup, analyzing thousands of variants at a time," Ilya Osterman, principal research scientist at Skoltech, comments.

While the secondary structure of mRNA did indeed inhibit translation, the researchers were unable to show that rare codons at the beginning of a coding sequence affected it in a positive way. However, they found that additional start codons are beneficial for translation, while additional Shine-Dalgarno boxes --sequences that help recruit the ribosome to the mRNA -- are inhibitory.

Among other things, researchers believe their results will help design more efficient artificial gene constructs that can be used to turn common bacteria such as E. coli into potent biotechnological instruments.
Other organizations involved in this research include the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, and A. A. Kharkevich Institute for Information Transmission Problems.

Skolkovo Institute of Science and Technology (Skoltech)

Related Amino Acids Articles from Brightsurf:

Igniting the synthetic transport of amino acids in living cells
Researchers from ICIQ's Ballester group and IRBBarcelona's Palacín group have published a paper in Chem showing how a synthetic carrier calix[4]pyrrole cavitand can transport amino acids across liposome and cell membranes bringing future therapies a step closer.

Microwaves are useful to combine amino acids with hetero-steroids
Aza-steroids are important class of compounds because of their numerous biological activities.

New study finds two amino acids are the Marie Kondo of molecular liquid phase separation
a team of biologists at the Advanced Science Research Center at The Graduate Center, CUNY (CUNY ASRC) have identified unique roles for the amino acids arginine and lysine in contributing to molecule liquid phase properties and their regulation.

Prediction of protein disorder from amino acid sequence
Structural disorder is vital for proteins' function in diverse biological processes.

A natural amino acid could be a novel treatment for polyglutamine diseases
Researchers from Osaka University, National Center of Neurology and Psychiatry, and Niigata University identified the amino acid arginine as a potential disease-modifying drug for polyglutamine diseases, including familial spinocerebellar ataxia and Huntington disease.

Alzheimer's: Can an amino acid help to restore memories?
Scientists at the Laboratoire des Maladies Neurodégénératives (CNRS/CEA/Université Paris-Saclay) and the Neurocentre Magendie (INSERM/Université de Bordeaux) have just shown that a metabolic pathway plays a determining role in Alzheimer's disease's memory problems.

New study indicates amino acid may be useful in treating ALS
A naturally occurring amino acid is gaining attention as a possible treatment for ALS following a new study published in the Journal of Neuropathology & Experimental Neurology.

Breaking up amino acids with radiation
A new experimental and theoretical study published in EPJ D has shown how the ions formed when electrons collide with one amino acid, glutamine, differ according to the energy of the colliding electrons.

To make amino acids, just add electricity
By finding the right combination of abundantly available starting materials and catalyst, Kyushu University researchers were able to synthesize amino acids with high efficiency through a reaction driven by electricity.

Nanopores can identify the amino acids in proteins, the first step to sequencing
While DNA sequencing is a useful tool for determining what's going on in a cell or a person's body, it only tells part of the story.

Read More: Amino Acids News and Amino Acids Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.