- Press Release Distribution

Scientists uncover a multibillion-year epic written into the chemistry of life

Study demonstrates that just a handful of "forgotten" biochemical reactions are needed to transform simple geochemical compounds into the complex molecules of life

Scientists uncover a multibillion-year epic written into the chemistry of life

The origin of life on Earth has long been a mystery that has eluded scientists. A key question is how much of the history of life on Earth is lost to time. It is quite common for a single species to "phase out" using a biochemical reaction, and if this happens across enough species, such reactions could effectively be "forgotten" by life on Earth. But if the history of biochemistry is rife with forgotten reactions, would there be any way to tell? This question inspired researchers from the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology, and the California Institute of Technology (CalTech) in the USA. They reasoned that forgotten chemistry would appear as discontinuities or "breaks" in the path that chemistry takes from simple geochemical molecules to complex biological molecules.

The early Earth was rich in simple compounds such as hydrogen sulfide, ammonia, and carbon dioxide – molecules not usually associated with sustaining life. But, billions of years ago, early life relied on these simple molecules as a raw material source. As life evolved, biochemical processes gradually transformed these precursors into compounds still found today. These processes represent the earliest metabolic pathways.

In order to model the history of biochemistry, ELSI researchers – Specially Appointed Associate Professor Harrison B. Smith, Specially Appointed Associate Professor Liam M. Longo and Associate Professor Shawn Erin McGlynn, in collaboration with Research Scientist Joshua Goldford from CalTech  – needed an inventory of all known biochemical reactions, to understand what types of chemistry life is able to perform. They turned to the Kyoto Encyclopedia of Genes and Genomes database, which has catalogued more than 12,000 biochemical reactions. With reactions in hand, they began to model the stepwise development of metabolism.

Previous attempts to model the evolution of metabolism in this way had consistently failed to produce the most widespread, complex molecules used by contemporary life. However, the reason was not entirely clear. Just as before, when the researchers ran their model, they found that only a few compounds could be produced. One way to circumvent this problem is to nudge the stalled chemistry by manually providing modern compounds. The researchers opted for a different approach: They wanted to determine how many reactions were missing. And their hunt led them back to one of the most important molecules in all of biochemistry: adenosine triphosphate (ATP).

ATP is the cell's energy currency because it can be used to drive reactions – like building proteins – that would otherwise not occur in water. ATP, however, has a unique property: The reactions that form ATP themselves require ATP. In other words, unless ATP is already present, there is no other way for today's life to make ATP. This cyclic dependency was the reason why the model was stopping.

How could this "ATP bottleneck" be resolved? As it turns out, the reactive portion of ATP is remarkably similar to the inorganic compound polyphosphate. By allowing ATP-generating reactions to use polyphosphate instead of ATP – by modifying just eight reactions in total – nearly all of contemporary core metabolism could be achieved. The researchers could then estimate the relative ages of all common metabolites and ask pointed questions about the history of metabolic pathways.

One such question is whether biological pathways were built up in a linear fashion – in which one reaction after another is added in a sequential fashion – or if the reactions of pathways emerged as a mosaic, in which reactions of vastly different ages are joined together to form something new. The researchers were able to quantify this, finding that both types of pathways are nearly equally common across all of metabolism.

But returning to the question that inspired the study – how much biochemistry is lost to time? "We might never know exactly, but our research yielded an important piece of evidence: only eight new reactions, all reminiscent of common biochemical reactions, are needed to bridge geochemistry and biochemistry, says Smith." "This does not prove that the space of missing biochemistry is small, but it does show that even reactions which have gone extinct can be rediscovered from clues left behind in modern biochemistry," concludes Smith.



Joshua E. Goldford1,2,3,*,#, Harrison B. Smith3,4,#, Liam M. Longo3,4,#, Boswell A. Wing5, and Shawn Erin McGlynn3,4,6,*, Primitive purine biosynthesis connects ancient geochemistry to modern metabolism, Nature Ecology & Evolution, DOI: 10.1038/s41559-024-02361-4

Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA Physics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA, USA Blue Marble Space Institute of Science, Seattle, WA, USA Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan Department of Geological Sciences, University of Colorado, Boulder, CO, USA Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Wako, Japan

#Co-first authorship


More information

Tokyo Institute of Technology (Tokyo Tech) stands at the forefront of research and higher education as the leading university for science and technology in Japan. Tokyo Tech researchers excel in fields ranging from materials science to biology, computer science, and physics. Founded in 1881, Tokyo Tech hosts over 10,000 undergraduate and graduate students per year, who develop into scientific leaders and some of the most sought-after engineers in industry. Embodying the Japanese philosophy of "monotsukuri," meaning "technical ingenuity and innovation," the Tokyo Tech community strives to contribute to society through high-impact research.

The Earth-Life Science Institute (ELSI) is one of Japan's ambitious World Premiere International research centers, whose aim is to achieve progress in broadly inter-disciplinary scientific areas by inspiring the world's greatest minds to come to Japan and collaborate on the most challenging scientific problems. ELSI's primary aim is to address the origin and co-evolution of the Earth and life.

The World Premier International Research Center Initiative (WPI) was launched in 2007 by Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT) to foster globally visible research centers boasting the highest standards and outstanding research environments. Numbering more than a dozen and operating at institutions throughout the country, these centers are given a high degree of autonomy, allowing them to engage in innovative modes of management and research. The program is administered by the Japan Society for the Promotion of Science (JSPS).



[Attachments] See images for this press release:
Scientists uncover a multibillion-year epic written into the chemistry of life Scientists uncover a multibillion-year epic written into the chemistry of life 2 Scientists uncover a multibillion-year epic written into the chemistry of life 3


Monitoring diseases through sweat becomes accessible to everyone

Monitoring diseases through sweat becomes accessible to everyone
Sweat contains biomarkers that can monitor various health conditions, from diabetes to genetic disorders. Sweat sampling, unlike blood collection, is preferred by users due to its painless nature. However, to obtain sufficient nutrients or hormones from sweat for testing, intense physical activity was previously required to induce sweat. This method posed challenges for individuals with limited mobility. Dr. Kim Joohee from the Bionics Research Center at the Korea Institute of Science and Technology (KIST, Director Oh Sangrok) and Professor John A. Rogers from Northwestern University jointly announced the development ...

Mathematical model driven evolutionary therapy dosing exploiting cancer cell plasticity

Mathematical model driven evolutionary therapy dosing exploiting cancer cell plasticity
Cancer poses significant challenges due to the development of resistance and the likelihood of relapse. Resistance may arise from permanent genetic changes in cancer cells or non-genetic alterations in cancer cell behavior induced by treatment. Standard of care in cancer treatments typically involves administering the maximum tolerated dose of a drug to eradicate drug-sensitive cells effectively. However, this approach often fails in the long term because drug-resistant cancer cells can grow more rapidly when all drug-sensitive cancer ...

Biodiversity in the margins: Merging farmlands affects natural pest control

Biodiversity in the margins: Merging farmlands affects natural pest control
A new study published in the Journal of Applied Ecology demonstrates how the diversity and abundance of arthropods decrease when hedgerows and field margins covered by wild grass and flowers are removed. Researchers from the UK, Netherlands and China studied 20 rice fields in China for six years to see how the changing agricultural landscape affects the diversity and abundance of rice pests and their natural enemies, as well as the effect on rice yield. Traditional Chinese smallholder fields are irregularly shaped and separated by areas of hedgerows, wild grass, and flowers. Using large-scale machinery in these farmlands is difficult, so there is low agricultural ...

1 in 8 pregnant people have a disability, but significant gaps exist in the provision of accessible care

Toronto, ON, May 28, 2024 – People with disabilities account for 13% of all pregnancies in Ontario, but a new report shows that this population was more likely to experience pregnancy complications such as emergency department visits, hospitalizations, and preterm birth.  Researchers from ICES, the University of Toronto Scarborough, and the Centre for Addiction and Mental Health (CAMH) have released a landmark report detailing findings from one of the largest studies to date on disability and pregnancy.   Funded by the US National Institutes of Health, the Disability and Pregnancy Study used healthcare ...

Statins associated with decreased risk for CVD and death, even in very old adults

Embargoed for release until 5:00 p.m. ET on Monday 27 May 2024     Annals of Internal Medicine Tip Sheet      @Annalsofim     Below please find summaries of new articles that will be published in the next issue of Annals of Internal Medicine. The summaries are not intended to substitute for the full articles as a source of information. This information is under strict embargo and by taking it into possession, media representatives are committing to the terms of the embargo not only on their own behalf, but also on behalf of the organization they represent.     ----------------------------     1. Statins associated with ...

Climate change is moving tree populations away from the soil fungi that sustain them

Climate change is moving tree populations away from the soil fungi that sustain them
As our planet warms, many species are shifting to different locations as their historical habitats become inhospitable. Trees are no exception – many species’ normal ranges are no longer conducive to their health, but their shift to new areas that could better sustain them has been lagging behind those of other plants and animals. Now, scientists show that the reason for this lag might be found belowground. A study published in PNAS on May X, shows that trees, especially those in the far ...

Secrets of sargassum: Scientists advance knowledge of seaweed causing chaos in the Caribbean and West Africa

Secrets of sargassum: Scientists advance knowledge of seaweed causing chaos in the Caribbean and West Africa
Researchers have been working to track and study floating sargassum, a prolific seaweed swamping Caribbean and West African shorelines, and causing environmental and economic harm.   The stranded seaweed blocks fishing boats; threatens tourism; disrupts turtle nesting sites, reefs and mangroves, and releases toxic gas, which impacts human health and damages electrical equipment.   First reported by Christopher Columbus in the 15th century, floating mats of sargassum have long been present in the North Atlantic. However, since 2011, a floating population has established ...

Bioinformatics approach could help optimize soldiers’ training for improved readiness and recovery

Bioinformatics approach could help optimize soldiers’ training for improved readiness and recovery
Of the many perils facing members of the military, injuries incurred in training or on deployment repeatedly sideline elite operators. “It’s a pervasive problem,” says Dhruv Seshadri, an assistant professor of bioengineering in Lehigh University’s P.C. Rossin College of Engineering and Applied Science. “We’re looking at how we can integrate physiological data, biomechanical data, and subjective assessments to help reduce the risk of these injuries happening in the first place, and when they do happen, how we can use those data to accelerate the soldier’s return to operation.”  Seshadri ...

Earth scientists describe a new kind of volcanic eruption

No two volcanic eruptions are exactly alike, but scientists think a series of explosive eruptions at Kīlauea volcano fit into a whole new category. By analyzing the dynamics of 12 back-to-back explosions that happened in 2018, researchers describe a new type of volcanic eruption mechanism. The explosions were driven by sudden pressure increases as the ground collapsed, which blasted plumes of rock fragments and hot gas into the air, much like a classic stomp-rocket toy. Researchers from the University of Oregon, United States Geological Survey and China’s Sichuan University report their findings in a paper published May 27 in Nature Geoscience. The ...

Warmer wetter climate predicted to bring societal and ecological impact to the Tibetan Plateau

While recent reports have stated that more than half the world’s largest lakes, including lakes in the Tibetan plateau, are drying up, a paper in Nature Geoscience today (27/5/24 DOI  10.1038/s41561-024-01446-w ) suggests that, by the end of this century, land-locked lakes on the Tibetan Plateau are set to increase exponentially, resulting in major land loss and related economic, environmental and climatic impacts. Climate and weather predictions suggest that increased rainfall due to climate change will enlarge these lakes, and see water levels rise by up to 10 metres. The volume of water caught in these land-locked lakes is estimated to ...


Discovery of spontaneous inflow and outflow states of high-temperature plasma by energetic ions

Tax the rich, say a majority of adults across 17 G20 countries surveyed

Semaglutide leads to greater weight loss in women than men with HF, improves HF symptoms in both sexes

12.5, the 1st Impact Factor of COMMTR released!

Circadian clock impact on cluster headaches funded by $2.4M NIH grant for UTHealth Houston research

Study identifies first drug therapy for sleep apnea

How old is your bone marrow?

Boosting biodiversity without hurting local economies

ChatGPT is biased against resumes with credentials that imply a disability — but it can improve

Simple test for flu could improve diagnosis and surveillance

UT Health San Antonio researcher awarded five-year, $2.53 million NIH grant to study alcohol-assisted liver disease

Giving pre-med students hands-on clinical training

CAMH research suggests potential targets for prevention and early identification of psychotic disorders

Mapping the heart to prevent damage caused by a heart attack

Study challenges popular idea that Easter islanders committed ‘ecocide’

Chilling discovery: Study reveals evolution of human cold and menthol sensing protein, offering hope for future non-addictive pain therapies.

Elena Beccalli, new rector of Università Cattolica del Sacro Cuore, takes office on 1st July

Pacific Northwest Research Institute uncovers hidden DNA mechanisms of rare genetic diseases

Empowering older adults: Wearable tech made easier with personalized support

Pennington Biomedical researchers partner on award-winning Long Covid study

Cooling ‘blood oranges’ could make them even healthier – a bonus for consumers

Body image and overall health found important to the sexual health of older gay men, according to new studies

Lab-grown muscles reveal mysteries of rare muscle diseases

Primary hepatic angiosarcoma: Treatment options for a rare tumor

Research finds causal evidence tying cerebral small-vessel disease to Alzheimer’s, dementia

Navigating the Pyrocene: Recent Cell Press papers on managing fire risk

Restoring the Great Salt Lake would have environmental justice as well as ecological benefits

Cannabis, tobacco use, and COVID-19 outcomes

A 5:2 intermittent fasting meal replacement diet and glycemic control for adults with diabetes

Scientists document self-propelling oxygen decline in the oceans

[] Scientists uncover a multibillion-year epic written into the chemistry of life
Study demonstrates that just a handful of "forgotten" biochemical reactions are needed to transform simple geochemical compounds into the complex molecules of life