For Dr. Kotaro Fujii, assistant professor in the Department of Molecular Genetics and Microbiology, it all comes back to the ribosome: the organelle that produces nearly everything needed for life to function.

“My research interests have always centered on ribosomes and mRNA translation. I began asking biological questions using a single cell model organism, particularly how to maintain functional gene regulation. I then moved onto a multicellular model organism to understand the impact of the gene regulation at the step of mRNA translation during embryonic development and the maintenance of human health.”

Since high school, the field of genetics and the central dogma of molecular biology has been Dr. Fujii's favorite topic- particularly the translation from nucleic acid language in RNA to amino acids in protein by the ribosome. His interests evolved into exploring how gene expression and billions of ribosomes contribute to developmental processes in the human body. He received his PhD from Kyoto University, Japan for his research on ribosome biochemistry and genetics to understand how the functional gene expression and ribosome are maintained as cellular homeostasis. During his postdoctoral research, he carried over his ribosome biochemistry expertise into the field of developmental biology.

“I’ve always been interested to understand how the information contained in the genome produces our complex bodies and how dynamic gene expression regulation can maintain homeostasis.”

Dr. Fujii joined the UFGI last December and is also a member in the Center for Neurogenetics. One of his papers was recently accepted into the journal Developmental Cell and was published on November 8th, 2021. It can be seen here.

Ribosomes and Protein Translation Fidelity

Proteins are the building blocks of our body and the amount and quality of these blocks are tightly regulated. Dr. Fujii is particularly interested in protein synthesis and the machinery that produces protein: the ribosome. This protein synthesis, known as mRNA translation, is the final step of gene expression and one single machine can produce all the hundreds of thousands of different proteins.

Each cell in our body contains several millions of ribosomes. A ribosome is a complex protein synthesis machine made up of four ribosomal RNAs and 80 ribosomal proteins.

Dr. Fujii’s research interests involve understanding how ribosomes regulate the fidelity of protein synthesis, and how the quantity and quality of protein production is regulated and affects the organism at large.

Measuring how accurately protein synthesis occurs, and not just how much is being produced, is a field about which little is known. Dr. Fujii’s research aims to reveal how ribosomes maintain this balance of fidelity in protein construction.

All ribosomes in a cell have traditionally been considered identical in structure and function, but this is not the case.

“People start to realize that ribosomes are not the same. My postdoctoral research in Maria Barna’s laboratory revealed that ribosomes are heterogeneous at the level of core ribosomal proteins. There are ribosomes missing specific ribosomal proteins and each ribosome has slightly different preference for the transcripts to translate. Other research also shows diversity in the sequence of ribosomal RNAs,” Dr. Fujii explained.

When proteins are not accurately produced by a ribosome, it might cause a buildup of nonfunctional proteins and lead to a host of problems. With millions of ribosomes in a single cell working around the clock, errors are bound to occur.

“We don’t know yet how the accuracy of protein synthesis correlates with aggregation, but we do know that the error rate of protein synthesis is quite high and increasing translation error produces protein aggregation.”

Dr. Fujii explained that each amino acid chain constructed by a ribosome has an error rate of 10^-4, or .0001%. When compared to DNA replication, which has a more stable 10^-8 chance for mistakes, protein synthesis carries a much more notable margin of error.

Until fairly recently, detecting mRNA translation steps directly has proved to be difficult for researchers like Dr. Fujii. In 2009, a new technology was developed called ribosome profiling. This novel process allows researchers to take a snapshot of all of the ribosomes active in a cell at a given time and what proteins they are producing.

“The invention of [ribosome profiling] brings the field in the right direction to begin identifying mRNA regulation and understanding these dynamics. The next outstanding question at least for me is to understand when and where the translation errors occur and what is the consequence of these errors and the impact to our health,” he stated.

Even though every cell in a multicellular organism contains the same genome, the spectrum of mRNA molecules present within a cell varies widely and is dependent on cell type and function. This has to be the same for protein synthesis. The demand for protein and synthesis varies between cell types. To satisfy such cell type specific demands, cells might have different properties of translation such as speed and fidelity.

The Ribosome’s Role in Neurodegenerative Diseases

Ribosomes support both their individual cells as well as the multicellular environment in which they reside. For example: in pancreatic cells ribosomes create insulin, while in neurons they manufacture neurotransmitters.

Many neural cells build extremely long structural proteins, which, due to their length, have a higher likelihood of translation errors. Dr. Fujii commented that the fidelity of this process in a neuron could be naturally higher to compensate for this.

“Ribosomes generally have a long half-life such as a week, but we don’t know the half-life of a ribosome in the brain. They might have a longer half-life to match with the longer average lifespan of neurons. There is so much we don’t understand yet.”

As individuals age, the fidelity of their ribosomes’ mRNA translation might be reduced. As errors become more frequent, unused and inaccurate proteins can build up over time in the brain. This protein aggregation is a hallmark of many late onset neurodegenerative disorders such as Alzheimer’s, Parkinson's, Huntington's, ALS, and others.

“We are working to understand fidelity and accuracy of protein synthesis. Right now, we don’t even know the full impact of fidelity regulation within ribosomes, let alone in neurons. As we begin to monitor the dynamics of fidelity in protein synthesis, we can begin to understand the mechanism of regulation and how ribosomes can lose their accuracy,” Dr. Fujii explained.

Fidelity in mRNA translation could be preserved, or even improved, within neurons and related cells by selectively eliminating ribosomes that produce higher levels of erroneous proteins. In the future, these devastating neural disorders’ symptoms may be able to be reduced through therapeutic, ribosomal means. Dr. Fujii is hopeful his lab’s research will make a positive difference in furthering the understanding of these processes.

mRNA Research in the Wake of COVID

With the world still being affected by Covid-19, Dr. Fujii hopes that people will see how RNA and ribosome centered research can positively impact their lives.

“Now that so many people are taking the Pzifer and Moderna vaccines, both of which are mRNA vaccines, I hope that more people will see real value in the ribosome research that is being done all around the world.”

Technological advances in the last decade have allowed for certain scientific processes to be sped up, but he agrees it is still important for the general public to recognize that science takes time and can change, and to not expect quality results right away.

“Basic science literacy is really important. If the general populace could be more patient, so much good can get done. Science is full of errors. Sometimes 80% of the time! But that other 20%, you can get some real solutions from it.”

"The ribosome is a really critical molecule everywhere in your body. By researching it and understanding the molecules in the vicinity of the organelle, it can benefit many areas of study. No matter the outcome of my research, the results can still be broadly utilized across many fields. Having that knowledge is most important.” ∎