Evolution of a core ribosomal innovation in octopus leading to less error prone proteins

Amazing stuff!

"Octopuses are among the strangest creatures on Earth—right down to their molecules. New research has found that octopuses of a certain lineage have a mutation not seen in any other organism that makes their cellular machinery extremely accurate at creating proteins. As a result, their proteins are less likely to form toxic clumps. ...

The team serendipitously discovered a change in the octopus gene encoding ribosomal RNA (rRNA), which is part of the cellular machinery that translates mRNA messages into proteins. This region of the rRNA sequence is identical in every other known organism, from humans to bacteria. But in octopuses, the mutation causes the rRNA to break into two fragments and occurs right at a crucial spot where the rRNA matches the right amino acid to the right genetic instruction. Ribosomes with this break made about 50% fewer errors than other species’ ribosomes when incorporating amino acids into a protein. ..."

From the abstract:

"Much of biology focuses on how genetic changes mediate new functions, but less attention is given to adaptations in other steps of the central dogma.

Octopuses exhibit complex nervous systems and sophisticated behaviors that rival vertebrates, but via an entirely divergent evolutionary history.

Here, we serendipitously discovered that octopus ribosomes contain a structural break in the core ribosomal RNA that is unique among all animals.

This break site enhances translation fidelity to reduce miscoding and subsequent protein aggregation, even when engineered into evolutionarily distant bacterial ribosomes.

Furthermore, high fidelity translation by octopus ribosomes supports proteomic stability during extensive RNA editing observed in cephalopods, suggesting synergy between distinct non-canonical modes of gene regulation.

This adaptation emerged in recently derived octopuses with expanded nervous systems, thereby revealing a mechanism that could broadly support the evolution of novel organismal traits."

ScienceAdviser

A molecular quirk unique to octopuses makes them better at building proteins

Adaptive Innovation in the Octopus Ribosome (PhD dissertation by one of the involved researchers, 2025)

Evolution of a core ribosomal innovation in octopus (preprint, open access)

Figure 1. The octopus has a unique structural adaptation in the conserved ribosomal core

The secret to nature’s toughest teeth

Amazing stuff! Unfortunately, these teeth are black colored.

When will humans finally get hardened teeth! No more cavities!

"... the teeth of chitons, marine mollusks that feed by scraping algae and other organisms off rocks. Scientists wanted to determine what makes their teeth nearly indestructible.

Researchers extracted proteins from the mineralized teeth of three chiton species and compared them with proteins from a giant chiton they’d previously studied. They identified a total of 22 proteins from the animals that were important for forming hard iron oxide on teeth, but narrowed in on one called radular teeth matrix protein 1 (RTMP1). The protein appears to be unique to chitons, leading the team to think it might be the secret to their tough chompers.

In ex vivo experiments with chiton teeth and engineered yeast, RTMP1 indeed promoted the formation of ferrihydrite, which can transform into a kind of iron oxide called magnetite that turns the animals’ teeth black and gives them their super strength. Meanwhile, in in vivo experiments to silence the RNA that codes for RTMP1, the animals’ teeth didn’t mineralize properly.

RTMP1 is the first known example of an animal protein that helps iron oxide form. Teasing out exactly how it does so might help in the design of new, hardened materials ... That might include “new designs of abrasion-resistant and self-sharpening materials,” ..."

From the abstract of the perspective:

"Animals from diverse evolutionary lineages possess body parts composed of mineralized structures such as teeth, bones, and shells. Their hardening, referred to as biomineralization, relies on precisely orchestrated macromolecular machineries that control the type, spatial placement, nucleation, and growth of inorganic crystalline phases in an organic matrix.

Identifying specific macromolecules involved in these processes helps to illuminate how nature’s complex inorganic structures are formed. In particular, chitons—a class of marine mollusks ... —have exceptionally hard and abrasion-resistant teeth made of iron-based minerals.

However, the underlying mechanism that governs the mineralization of iron phases in chiton teeth has been puzzling. ... that radular teeth matrix protein 1 (RTMP1) plays a central role in incorporating iron oxide mineral magnetite into chiton teeth. This points to molecular strategies that may be shared among magnetite-forming organisms that might be used in biomimetic materials chemistry."

From the editor's summary and abstract:

"Editor’s summary

The major lateral radula teeth of chitons are formed from magnetite and other biominerals in a way that makes them very hard and wear resistant. As the cusps wear out, they are replaced by newly formed teeth from behind. Nemoto et al. expanded on prior studies of these organisms by exploring the molecular mechanism of magnetite biomineralization ... The authors demonstrate that one protein, which they call radular teeth matrix protein 1 (RTMP1), controls iron oxide deposition and differs from other magnetite-precipitating proteins found in magnetotactic bacteria. ...

Abstract

Nature builds multiscale mineral structures with impressive mechanical properties through spatially and temporally orchestrated organic-mineral assembly. One example of regulated mineralization is found in hypermineralized and ultrahard magnetic teeth of chiton, which grind on rock to feed on algae. At early stages of tooth formation, iron oxide deposition is controlled using a chiton-specific radular teeth matrix protein 1 (RTMP1), which is transported into teeth through microvilli. RTMP1 spatially and temporally guides and enhances mineralization on chitinous fibers within the tooth, providing a hard, tough, and strong architecture that enables the organism to perform repetitive abrasive events to survive."

ScienceAdviser

Hardening nature’s toughest teeth (no public access) "A protein that underlies the mineralization of chiton teeth is revealed"

Radular teeth matrix protein 1 directs iron oxide deposition in chiton teeth (no public access)

Radular teeth matrix protein 1 directs iron oxide deposition in chiton teeth (preprint, open access)

Fig. 1 A transcriptomic comparison of radular tissues revealed that RTMP1 and its homologs are chiton-specific proteins.

Fig. 4 The recombinant RTMP1 exhibited iron ion binding and iron oxide precipitation activity.

Mollusk menagerie/family tree from whole genome sequencing of 13 species and detailed genomic analysis of 77 species

Amazing stuff!

The first author, i.e. Zeyuan Chen, of this study works at the Senckenberg Research Institute and Natural History Museum Frankfurt, in my hometown Frankfurt am Main, Germany. 

"... To create an accurate evolutionary ‘tree’ for the phylum, researchers sequenced whole genomes from 13 species, allowing them to look at genetic markers from 77 species in total, including members of every major subgroup of mollusks.

The findings revealed that monoplacophorans were one of the first offshoots of the Conchifera, a group within mollusks that includes almost all the highly recognizable types, including octopuses and their relatives as well as clams and snails.

The analyses also revealed just how genomically diverse mollusks are, with lots of rearrangements and repetitive sequences—features that may have allowed the group’s physical diversity to emerge. ..."

"... In their new study, scientists analysed the genomes of 77 mollusc species, representing all eight major living groups, including lesser-known forms like deep-sea monoplacophorans and worm-like solenogasters. Using cutting-edge genomic techniques, the team reconstructed a detailed evolutionary tree and confirmed key hypotheses about mollusc ancestry. ..."

From the editor's summary and abstract:

"Editor’s summary

Genome sequencing has allowed for a much greater understanding of how species relate to one another than did earlier morphology-based approaches. A particularly difficult phylum to study using genomic data has been mollusks, which encompass species ranging from squid to sea snails, in part due to their high levels of heterozygosity and repetitiveness. Chen et al. sequenced 13 new complete genomes from across the phylum to assemble a new phylogeny for Mollusca. They resolved several highly debated nodes and provide additional genomes for future study of this highly diverse and genomically complex phylum. ...

Abstract

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups—gastropods, bivalves, and cephalopods—each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations.

The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution.

In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success."

ScienceAdviser

Cracking the Mollusc Code: Genomes Reveal the Ancient Ancestor of Your Garden Snail (original news release) "An international team of scientists has cracked a longstanding evolutionary mystery surrounding molluscs, one of the most diverse groups of animals on Earth. The groundbreaking research, published today in Science, resolves the family tree for molluscs, bringing long-awaited clarity on their evolutionary history and resolving debates that have persisted for decades."

A genome-based phylogeny for Mollusca is concordant with fossils and morphology (open access)

Nudibranchs like this Flabellina affinis are among the varied forms of mollusks.

Fig. 1. Mollusca timetree.

Why did it take so long to find giant squids?

Very recommendable! Amazing stuff! There are hundreds of species of squid!

Anatomy

Living depth in the twilight zone habitat

Population

The colossal squid is still largely unknown, believed to live in the polar regions

The one thing stopping jellyfish from taking over

Recommendable!