oxygen – Lightsources.org

Protein family shows how life adapted to oxygen

2022/10/042022/10/12

Cornell scientists have created an evolutionary model that connects organisms living in today’s oxygen-rich atmosphere to a time, billions of years ago, when Earth’s atmosphere had little oxygen – by analyzing ribonucleotide reductases (RNRs), a family of proteins used by all free-living organisms and many viruses to repair and replicate DNA.

“By understanding the evolution of these proteins, we can understand how nature adapts to environmental changes at the molecular level. In turn, we also learn about our planet’s past,” said Nozomi Ando, associate professor of chemistry and chemical biology in the College of Arts and Sciences and corresponding author of the study. “Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade” published in eLife Digest Oct. 4.

Co-first authors of the study are Audrey Burnim and Da Xu, doctoral students in chemistry and chemical biology, and Matthew Spence, Research School of Chemistry, Australian National University, Canberra. Colin J. Jackson, professor of chemistry, Australian National University, Canberra, is a corresponding author.

This undertaking involved a large dataset of 6,779 RNR sequences; the phylogeny took several high-performance computers a combined seven months (1.4 million CPU hours) to calculate. Made possible by computing advances, the approach opens up a new way to study other diverse protein families that have evolutionary or medical significance.

RNRs have adapted to changes in the environment over billions of years to conserve their catalytic mechanism because of their essential role for all DNA-based life, Ando said. Her lab studies protein allostery – how proteins are able to change activity in response to the environment. The evolutionary information in a phylogeny gives us a way to study the relationship between the primary sequence of a protein and its three-dimensional structure, dynamics and function.

Read more on the CHESS website

Image: Tree inference on a ribonucleotide reductase (RNR) sequence dataset as included in the original report, “Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade“.

Beryllium configuration with neighbouring oxygen atoms revealed

2019/06/252019/06/26

High-pressure experiments prove 50-year-old theoretical prediction.

In high-pressure experiments at DESY’s X-ray light source PETRA III, scientists have observed a unique configuration of beryllium for the first time: At pressures nearly a million times the average atmospheric pressure, beryllium in a phosphate crystal acquires six neighbouring atoms instead of the usual four. This six-fold coordination had been predicted by theory more than 50 ago, but could not be observed until now in inorganic compounds. DESY scientist Anna Pakhomova and her collaborators report their results in the journal Nature Communications.
“Originally, chemistry textbooks stated that elements like beryllium from the second period of the periodic table could never have more than four neighbours, due to their electron configuration”, explains Pakhomova. “Then around 50 years ago theorists discovered that higher coordinations could actually be possible, but these have adamantly evaded experimental proof in inorganic compounds.” Inorganic compounds are typically those without carbon – apart from a few exceptions like carbon dioxide and carbon monoxide.

Image: Transformation of the usual fourfold coordination of beryllium to five- and sixfold with increasing pressure. (Credit: DESY, Anna Pakhomova)

Did plate tectonics aid the development of life on Earth?

2018/01/242018/01/29

The appearance of plate tectonics 2.5 billion years ago, favouring the internal dynamics of the Earth, would have allowed a significant release of oxygen in the atmosphere inducing the development of life on our planet, according to a study published by the journal Geochemical Perspectives.

The Earth’s atmosphere remained anoxic for two billion years after the formation of our planet. Then, its oxygen content increased drastically during a well-identified Great Oxygenation Event. It is generally believed that the release of free oxygen was due to the biosphere itself, in relation with the evolution of life on Earth. An international team of researchers from Laboratoire Magmas et Volcans (Université Clermont-Ferrand, CNRS-IRD-OPGC), Géosciences Montpellier (Université de Montpellier, CNRS), the laboratory Conditions Extrêmes et Matériaux: Haute Température et Irradiation (CNRS), and involving five scientists from the ESRF propose a completely different scenario. Based on the experimental observation of a significant amount of ferric iron in the deep Earth’s mantle, they suggest an ascent toward the Earth’s surface of a primordial oxidised-mantle material, inducing the arrival of oxygen into the atmosphere. The upwelling movements would have been hampered during the Archean eon, which was dominated by floating micro-plates at the Earth’s surface. Then, major mantle mixing started when modern plate tectonics and deep slab subduction were established about 2.5 billion years ago, enabling the release of oxygen to the Earth’s surface.

>Read more on the ESRF website