Effective antibody production ‘falters’, new study finds

The central dogma of molecular biology posits a simple recipe for building the human body: a blueprint of DNA is transcribed into an RNA message, and the RNA message is translated into the proteins that make you up. Translating the mRNA message is a bit like an assembly line.

Individual nucleotide “letters” in mRNA form sequences of three letters called codons. Another type of RNA molecule, transfer RNA (tRNA), recognizes a specific codon at one end and attaches to a specific amino acid at the other end. Amino acids make up the final protein.

The extent of protein production varies greatly depending on the protein, the type of cell in which it is produced, and what that cell is doing at that particular time. One type of protein notable for its incredibly high production is the antibody family, which must be rapidly generated in large quantities to fight infection.

The job of producing proteins is stressful for cells, and antibody-producing B cells are known to undergo metabolic changes to support antibody secretion.

Sophie Giguère, an immunology student at Harvard Medical School who recently completed her Ph.D. in the Batista lab at the Ragon Institute, had another question: In simple organisms, and for some proteins in more complex multicellular organisms, high production levels are associated with unusual patterns of codon usage. How do antibodies compare?

Dr. Giguère’s interest in immunology and antibody-producing B cells was driven by her appreciation of the role vaccines play in public health. However, it was the intellectual excitement of the Cambridge technology center that motivated his interest in codon bias in immune cells. “My very good undergraduate friend was working on alternative genetic codes… At the same time, I had just heard a lecture on T cell differentiation and began to wonder if codon bias might vary in different cell states .”

His bioinformatics dive revealed a particular quirk of antibody sequences: They frequently use codons without a “matching” tRNA in the genome.

The problem of codons with no apparent decoding mechanism was an early puzzle of genetics, and Francis Crick, one of the discoverers of the DNA helix, proposed early on that this problem could be solved by “wobble.” of tRNA, an ability to translate multiple codons that is now a well-known quirk of genetics.

The codons that tRNAs can translate are affected by chemical modifications made to those tRNAs; Dr. Giguère discovered a particular modification known as the “super-wobbler,” inosine (I34), at higher levels in plasma cells, which produce high levels of antibodies.

There are 64 possible codon combinations and only 20 amino acids are used in human proteins. Since multiple codons can encode the same amino acid, Dr. Giguère genetically engineered cell lines to replace codons that require I34 with codons that do not require it, but encode the same amino acid, by changing the instructions but producing the same protein.

She found that antibody-producing cells were more efficient than non-antibody-producing cells when it came to translating I34-dependent codons. When she looked at mice with B cell receptors (essentially membrane-bound antibodies) that were identical to the proteins but encoded differently, Dr. Giguère observed that B cells expressing more I34-dependent receptors seemed to have a greater chance of to survive.

“This surprised me: The most commonly used codons in human antibody heavy chains were those without a corresponding tRNA gene in the genome,” says associate and researcher Professor Facundo D. Batista, Ph.D. scientist. Director of the Ragon Institute and holder of the doctorate of Dr Giguère. mentor. “I’ve worked on B cell receptors my entire career and had never considered this angle. Every immunologist I spoke to shared a similar reaction.”

The practical implications are immense: producing antibodies for therapeutic and laboratory use is a huge industry, and antibodies are key mediators of vaccine effectiveness. Professor Batista says: “I spend a lot of time working on the antibodies that we want rationally designed vaccines to produce: now I’m going to think about how these antibodies are coded. »

The work is published in the journal Science.