The Desire to Explain
Nutrition Properly

ProteinTyrosine

ProteinfoodProtein Amino acid

which led to rather interesting findings. When you
move labs, it can be difficult to continue using thesame food due to changes in procurement methods and budget-related issues.

foodamount of food they eat changes when their foodcomposition changes. Basically, during the larvalstage, the larvae need to grow bigger and will try
to consume a lot of proteins. So, they will eat
more if the amount of protein in the food isreduced, but the underlying mechanism is notwell understood.

the ingredients determined?

that they donʼt have enough protein and modify
their behavior to eat more.

was essential or non-essential was determined
simply by whether or not it was possible to growwithout it, and it had not been properly verified
whether or not sufficient levels of each amino acid
were maintained in the body. There is not much ofa difference in the outer appearance of the bodywhen flies do not eat tyrosine. But when we closely
examined the amount of tyrosine in the body, we
found that the tyrosine had been reduced to halfof normal levels.

K▶ For amino acids, this is determined by aK▶ Thatʼs right. I wanted to know what in theY▶ If it is non-essential, why not just increase themethod called exome matching.

food was causing the resulting behavior, so using
the food in which I knew exactly what was in it, I
tried removing, reducing, or adding each one of
the 20 amino acids in the food. This was probably
the first time anyone had done this.

Y▶ In that respect, I guess standardized food isYakushiji(Y)▶ You are doing research onnutrition using the fruit fly?

easy to handle. What is the composition of thefood?

Kosakamoto(K)▶ It may come as a surprise, butthere is a lot of research on nutrition being carriedout with flies and a great deal has been uncovered
about the nutrients that are essential for flies. It isestimated that humans consume over 26,000
different nutrients on a regular basis, but flies only
require 40 different nutrients. Food specific for fruit
flies containing only the minimal number of essential nutrients was developed fairly recently̶in fact,in 2014.

K▶ It contains the 20 amino acids as well asY▶ Thatʼs pretty recent.
K▶ Yes. Up until then, each laboratory would
make their own fly food from natural ingredientssuch as yeast, glucose, sucrose, cornmeal and cornflour. But it appeared that experiments yielded
different results when food recipes differed,leading to the development of standardized fly
food. Itʼs like the standard cell culture medium.

Y▶ Do differences in food really change theresults?

vitamins, minerals, nucleic acids and cholesterol,
totaling about 40 different types of nutrients. Oh,and carbohydrates.

Y▶ So, you are trying to link how the flies senseY▶ That all sounds normal. How are the ratios ofY▶ Exome matching! Iʼve never heard of that.
K▶ Exome is a general term referring to all theexons in the genome, the regions that encode
genes. Simply put, we used the genetic information encoded in the exons to determine theamounts of amino acids synthesized and theirratios.

Y▶ Wow, a steamroller approach!
K▶ Because we know the composition of thisfood, it is now possible to remove one nutrientfrom the food. Thus, it is easier to study the effectsof a nutrient on the fly.

Hina Kosakamoto
Special Postdoctoral Researcher in the Laboratory for Nutritional Biology. She received her
doctorate in pharmaceutical studies from The
University of Tokyo. She enjoys playing badminton and is the head of the RIKEN Badminton
Club. She also enjoys playing piano on occasion.
Solo karaoke in the laboratory on weekends isthe number one way she relieves stress.

Y▶ You mention so casually that what you did
was a world first.

K▶ When tyrosine was removed from the food, we
discovered that the larvae ate more. By the way,tyrosine is a non-essential amino acid.
Y▶ What? Itʼs not an essential amino acid? I
thought that we donʼt need to eat non-essential
amino acids because they can be synthesized byour body. And yet, they can affect behavior?

K▶ Yes, it does. In fact, I heard from one of myseniors who is working on hibernation researchusing hamsters that he experienced considerable
difficulties in reproducing his results when hemoved to a different lab and the food fed to thehamsters also changed. In the end he figured outthat the vitamin content in the food was different,×

A non-essential amino acid is essential for sensing protein scarcity

K▶ Interesting, isnʼt it? Itʼs likely that because it is a
non-essential amino acid, its importance has neverbeen recognized. From my research, when theamount of tyrosine in the body is reduced by half,
it is a sign of starvation.

Y▶ So you are using that food in your research?
K▶ I am using fly larvae in my research and theY▶ How did you investigate whether or not they
were in a state of starvation?

Exome matchingK▶ There is a transcription factor that is activat-st encode
nces thancode for protein
euq
sefoesteohncot
st reat dContains ins and those thfor prote

ed when they enter a state of starvation. We useda genetically modified reporter fly line that will
fluoresce red when this factor is activated. Thisbecomes a marker. When protein is restricted, thefly will fluoresce red. If you add one amino acid ata time, sometimes this red fluorescence willdisappear.

me protein
Intron Does not beco

Exon Becomes protein
E.g.

where I spent a lot of time reading recipe books,
which naturally led me to becoming interested in(Other)

Changing the food willchange the results

Y▶ I see, so that indicates what was lacking in the fly.
K▶ Thatʼs right. We also discovered that theRequires amino acids(Threonine)

All of the exons = exome
Counting by reading ACGTs in exons as amino acids

Can determine the essential amino acids

phenomenon only occurs in a specific tissue, thefat body.

Hideki Yakushiji
Business developer based in Kobe, and aRIKEN alumni. He has a broad background inareas such as analytical chemistry, optics,biotechnology and IT. He is involved in a wide
range of activities to assist in commercializing
technologies and ideas born from academia,including setting up opportunities for idea
sharing, finding investors, and strategicplanning.

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amount synthesized in the body?

K▶ The synthesis system does not appear to be asophisticated one and thus, even if the amount oftyrosine intake is reduced, tyrosine synthesis does
not increase. On the other hand, there is also a
regulatory mechanism involved in tyrosine breakdown which is tightly controlled. But even withthis mechanism, the level of tyrosine in the bodyis insufficient, and requires increased dietaryintake of tyrosine or the body shifts to anenergy-conserving state by slowing down
processes that require a lot of energy.

Detecting shortages
Y▶ So, being non-essential doesnʻt mean that you
do not have to eat it.

K▶ The classification of whether an amino acid
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nutrition.

Y▶ So thatʼs where it started.
K▶ Around that time, about 2017, there was ahealth craze with many TV programs touting
things like, “Eat this and you will be healthy.” But
when I watched those programs, I often thought,“Is that really true?” Itʼs not as if a single ingredientcan do something to improve health, and even if it
could, the mechanism of how it improved healthwas presented very simply. I began this researchbecause I wanted to be able to explain the mechanism of action at the molecular level.

Y▶ Thatʼs a pretty clear-cut goal.
K▶ At the beginning of my masterʼs program,
however, my research environment was notsuitable for nutrition research, so I was doing
research on development. It was only in thesecond half of my masterʼs program that myresearch environment was finally favorable fornutrition research, so I changed my theme midway
through.

Y▶ The masterʼs program is two years, right? Isnʼtit difficult to change your research theme with only
one year left?
K▶ Yes, it is. My advisor told me that if I was going
to change my theme at that point, I should do sowith the intent of going on to pursue a doctoral
degree. That was when I made up my mind̶if I
am going to get a PhD, I am going to become aresearcher.

Y▶ How does the body sense that levels oftyrosine are insufficient?

I want to beable toproperly talkabout nutrition.

K▶ I think there is something like a tyrosine
sensor, which I would like to investigate further,but it is extremely difficult. A method for analyzingprotein-protein binding has been established, but
we havenʼt yet fully established a technique forextracting proteins that are bound to metabolites.
In this case, it is particularly challenging as the it isbound to amino acids, which are quite small.
Y▶ Do you have a strategy in mind?
K▶ I can think of a few techniques. A simple way
would be to coat beads with metabolites andcollect the proteins that attach to these metabolites. Or, since the stability of proteins that are
attached to metabolites can easily change, we canlook at the changes in stability when heat is
applied to proteins on its own and those that areattached to metabolites. I believe there's a way, soI'd like to keep at it a bit longer.

Y▶ Incidentally, are essential amino acids thesame in flies and humans?
K▶ They are basically the same. They have beenBD RIt started with thequestion “Is that true?”Y▶ Why did you decide to study nutrition?
K▶ I really love to cook, and there was a period

foodDr. Chika Takahashi who talked about her research using the short-lived
killiﬁsh, introduced me to Dr. Hina Kosakamoto, who works with the fruit ﬂy,. As the name of the lab she works in includes thewords ʻnutritional biology,ʼ I went to the interview hoping that I would be able
to learn something that might be useful for dieting.

Dive intoBDRʼs intriguing
research

Fluoresces red State of starvation

Cell

conserved from an ancient ancestor, and in fact,
they are also the same for C. elegans. Our bodies
do not need to synthesize those amino acids wecan intake from our diet, so this synthetic pathway
was discarded a long time ago and it hasremained the same since then.

Postscript

The fly that was mentioned in this interview is
Drosophila melanogaster, an organism widelyused in life science research. It is a type of fruit
fly that on occasion can be spotted flying
around your kitchen. When they are well nourished, they can on average lay two eggs perhour and these eggs will develop to adultstages in 10 days, and those adults will thenstart laying eggs. Learning this fact has renewed
my determination to regularly clean up messes.

BDR Research Highlights■

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Research highlights articles and press releases between May 2023 to November 2023.
Read these and other articles on the BDR website.

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How a widely used antimalarial drug
affects zinc levels in a malarial parasite

Unlocking the rhythms behind thegrowth of zigzag hair

Fumiaki Obata and his co-workers in the Labfor Nutritional Biology reveal how, a gut bacterium, shortens the lifespanof fruit flies. A component in the bacterium's
cell wall triggers a receptor in the fly's gut,
enhancing immunity and causing early death.
This 'live fast, die young' tradeoff raises
possibilities for health-beneficial 'postbiotics.'
Future research will explore the involved
genes and potential applicability to otheranimals.
Onuma T, Yamauchi T, Kosakamoto H, et al. PLoS
Genet 19, e1010709 (2023)

Akira Wada and his co-workers at the RIKEN
BDR uncover the crucial role of zinc depletionin the action of the antimalarial drug dihydroartemisinin (DHA) against the parasite,. DHA was found to induce
pyknosis, a state of developmental arrest, in red
blood cells, reduce glutathione concentrationand disrupt zinc homeostasis leading to asynergistic inhibition of parasite growth. Thesefindings offer insights for developing new
antimalarial drugs to combat drug-resistantstrains.

A team led by Takashi Tsuji of the Lab for
Organ Regeneration has been investigating
the molecular mechanisms responsible for thedistinctive bending pattern observed inʻzigzag hairsʼ found in the underfur of mice.
They found that these hairs develop kinks
every three days during the follicle maturation
process and uncovered a molecular rhythm
responsible for this phenomenon. These findings could pave the way for novel anti-aging
solutions in humans.

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Towards organ preservation:
Animal resistance to cold reflectedin stem cells
Researchers led by Genshiro Sunagawa in theLab for Hibernation Biology have shown that ananimalʼs stem cells possess the same level ofcold resistance as the animal itself. Examiningmice with different hibernation-like characteristics, they show that those with the best
resistance to cold temperatures have stem cells
that generate energy differently than others.
Beyond these immediate findings, the study
establishes mouse stem cells as a practicalmodel system for further research into organ
preservation and even human hibernation.
Suita K, Ishikawa K, Kaneko M, et al. Cell Rep 42,112954 (2023)■■

Bridges to RIKEN Kobe Campus

On thecover!

Takeo M, Toyoshima K, Fujimoto R, et al. Nat Commun
14, 4478 (2023)

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Using cryo-electron microscopy, Shun-ichi
Sekine and his colleagues in the Lab for Transcription Structural Biology unveil three-dimensional images detailing how key viralproteins of the dengue virus interact with RNA
at various stages during viral replication. Thisatomic exploration sheds light on the part ofthe mechanism by which the virus propagatesin infected cells, including the suppression ofimmune responses. These finding could pave
the way for development of more effective
antiviral drugs against dengue and related
flaviviruses.
Osawa T, Aoki M, Ehara H, Sekine S. Mol Cell 83,2781-2791 (2023)

Stolen genes allow parasitic
control of behavior

Mishina T, Chiu MC, Hashiguchi Y, et al. Curr Biol 33,4988-4994 (2023)(Chuo Ward, Kobe)

Atomic picture of dengue
replication could transform
antiviral approaches

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A team led by Tappei Mishina in the Lab for
Chromosome Segregation has discovered that aparasite, horsehair worm, can manipulate thebehavior of their mantis host using stolen genesthat they likely acquired through a phenomenon
called horizontal gene transfer allowing themto complete its reproductive life cycle.

Kobe Bridge and Portopia Bridge

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How a gut microbe causes flies tolive fast and die young

Asahi H, Niikura M, Inoue S, et al. ACS Infect Dis 9,1303-1309 (2023)

Introducing interesting research equipment and devices as well as favorite
spots at BDR campuses in Kobe, Osaka, and Yokohama.

BDR Photo Tour■

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Signaling molecule from cancer cells
induces metabolic changes to fruit-fly larvae
Morihiro Okada, Sa Kan Yoo and co-workers in
the Lab for Homeodynamics have discoveredthat cancer-induced stress in fruit-fly larvae
produces a protein known as Netrin, which
reprograms the metabolism of the larvae. This is
the first time that Netrin, also known to guidecell migration during development, has been
implicated in spreading the effects of cancer
systemically. Inhibiting Netrin expression
increased larvae survival rates, suggesting
potential new ways to treat for cancer-induced
complications in humans. The team plans toextend their investigation to mice next.

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Put the blocks throughthe holes

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Dissecting the structural secrets of
the inactive X chromosome
One of the two X chromosomes carried byfemale cells is inactivated early in embryogenesis, becoming an inactive X chromosome
and suppressing gene expression. Rawin
Poonperm, Ichiro Hiratani and others in theLab for Developmental Epigenetics have analyzed the regulation of DNA replication
timing of the inactive X chromosome in
mammalian females and uncovered newfeatures regarding its three-dimensionalstructure. Their findings are expected to leadto a better understanding of how the highly
condensed chromosome structure, called
heterochromatin, stably represses geneexpression.

Kobeʼs city center of Sannomiya is connected to the man-made Port Island by two bridges and one undersea tunnel. This photo of
the illuminated Kobe Bridge was taken from the Port Island side.

This is an experiment showing the technology allowing
scientists to build 3D structures of actin, a protein acting
as the cell skeleton. Whenvarious subcellular-sizedshapes (pink) were drawn on
a sheet mimicking the cell
membrane (blue), actin(green) was self-assembled
into pillars with maintaining
the drawn shapes.
Credit: Lab for Bottom-up
Cell Biology

BDR TIMES vol.15
2024 SPRING
Issued March 01, 2024

Poonperm R, Ichihara S, Miura H, et al. Nat Struct Mol
Biol 30, 1224-1237 (2023)

Published by RIKEN
Center for Biosystems
Dynamics Research (BDR)
E-mail: bdr-riken@ml.riken.jp

The Portopia Bridge (right) running parallel to the Kobe Bridge

https://www.bdr.riken.jp/en/(left) is a bridge specifically for the Port Liner train operated by
Kobe New Transit.

The two bridges are connected directly with
Kobe Port Terminal, an international port.
Blue laser beams light up the sky on bothends of the bridges when large passenger

Okada M, Takano T, Ikegawa Y, et al. EMBO J 42,e111383 (2023)

ships sail into the port.
RIKEN 2024-007

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BD R

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