Max Raas

Our story on the kinetochore composition of the ciliate Tetrahymena thermophila is out now on bioRxiv! We find surprisingly many orthologs of conventional kinetochore components, but also components that have very different evolutionary origins. A 🧵 (1/11) Check it out here: tinyurl.com/4ectm9x4

@danieltamarit.bsky.social

Max Raas reposted

Daniel Tamarit

22 May

I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏

uu.nluu.nl

Max Raas reposted

Nature Astronomy

@natastron.nature.com

16 Mar

Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T, U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth. http://dlvr.it/TRWtVp ☄️

dlvr.itA complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu - Nature AstronomySamples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T and U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth.

Max Raas reposted

Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺

@ettema.bsky.social

5 Mar

Finally out in @natmicrobiol.nature.com: Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Great work by @stephkoe.bsky.social @kassipan.bsky.social @jvhooff.bsky.social www.nature.com/articles/s41...

Max Raas reposted

Thibaut Brunet

@thibautbrunet.bsky.social

28 Feb

Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating). A brief 🧵 (carried over from the old place)

Nature Portfolio@natureportfolio.nature.com

A study in Nature shows that the single-celled form of a tiny, aquatic organism can turn into a multicellular version by three different routes. The discovery adds insight to the possible origins of multicellular life, suggesting a previously unrecognized degree of flexibility. 🧪

go.nature.comClonal-aggregative multicellularity tuned by salinity in a choanoflagellate - NatureThe choanoflagellate Choanoeca flexa forms motile and contractile cell monolayers purely clonally, purely aggregatively or through a combination of both processes depending on environmental conditions.

Max Raas reposted

Eelco Tromer

@eelcotromer.bsky.social

26 Feb

We're on a roll here. Check out this cool paper by @scienceleah.bsky.social et al. on not one, but two types of sperm (!) in the silk worm Bombyx mori. Happy to have contributed. #meiosis4ever

Leah Rosin@scienceleah.bsky.social

New paper from the Rosin lab in collaboration with the Hawley lab 🎉 Spearheaded by postdoc Leif Benner. We use imaging and RNA-seq to better understand apyrene meiosis. Programmed meiotic errors facilitate dichotomous sperm production in the silkworm, Bombyx mori. www.pnas.org/doi/10.1073/...

pnas.orgPNASProceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

Max Raas reposted

Eelco Tromer

@eelcotromer.bsky.social

26 Feb

Now in Nature Comms w/ @ritatewari.bsky.social, Pushkar Sharma & @ryanase.bsky.social (thanks!). Aurora kinases fascinate me: single ancestor - parallel duplications in eukaryotes - paralogs with distinct functions. ARK1 is the CPC Aurora in the malaria parasite. rdcu.be/e5NRT #plasmodium #mitosis

rdcu.bePlasmodium ARK1 regulates spindle formation during atypical mitosis and forms a divergent chromosomal passenger complexNature Communications - This study reveals that the malaria parasite Plasmodium uses a unique Aurora kinase complex to control cell division. This divergent machinery regulates spindle formation...

Eelco Tromer@eelcotromer.bsky.social

New work on ARK1 (AURKB?) in Plasmodium (malaria parasite) with @ritatewari.bsky.social and Pushkar Sharma. CPC in Plasmodium is (ofcourse..) different compared to conventional models: two INCENPs, no borealin/survivin - mainly at spindle microtubules/MTOCs. Special thanks to @ryanase.bsky.social!

Max Raas reposted

Kops Lab

@kopslab.bsky.social

23 Feb

As a cell biology lab, we acknowledge the decades-long impressive efforts to uncover evolutionary relationships using advanced phylogenomics methods. These approaches undergo continuous improvements that lead to adjustments of data interpretation, as is the case in every scientific field. (1/3)

Bungo Akiyoshi@bungoakiyoshi.bsky.social

BTW when I talked to a cell biologist this week and explained that bacterial-origin proteins were used to determine the root of the eukaryotic tree of life, the person was surprised by that approach. So it's not just me who has issues with this approach.

Max Raas reposted

Andrew Roger

@andrewjroger.bsky.social

16 Feb

Replying to @bungoakiyoshi.bsky.social

The 'devil is in the details'. You have to look beyond author claims and try to understand why the various studies have come to different conclusions and read the explanations given by the authors themselves.

tinyurl.comThe LECA had a conventional kinetochore and the kinetoplastid kinetochore is a derived feature – a critical evaluation of Akiyoshi, 2025Summary:Akiyoshi, 2025 presented a hypothesis with implications for the early evolution of eukaryotes and eukaryotic cell division machinery. In this Correspondence, the authors conclude that this hyp...

Recently, a Hypothesis was posed in @jcellsci.bsky.social in which the root of eukaryotes was placed between kinetoplastids and all other eukaryotes. From this, it was implied that LECA did not have a kinetochore. We argue this is highly unlikely. A 🧵(1/12) Read our reply here: tinyurl.com/n87myhpr

We are grateful to @jcellsci.bsky.social for providing the opportunity to express our views on this matter and for the smooth handling of our correspondence piece. (11/12)

nature.comGenomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist - Nature CommunicationsThe mechanisms for replicating and segregating DNA are highly conserved across eukaryotes. A comparative genomic analysis of a free-living protist finds a surprising lack of protein complexes involved...

Finally, I'd like to thank my co-authors @jvhooff.bsky.social, Julius Lukeš, Thomas Richards, @andrewjroger.bsky.social, Bill Wickstead, @kopslab.bsky.social, Berend Snel & @eelcotromer.bsky.social for their valuable contributions and support. (12/12) #protistsonsky

Furthermore, kinetoplastids are not the only known lineage to lack (almost) all components of the conventional kinetochore, as the metamonad Carpediemonas membranifera also was found to not encode many kinetochore subunits in its genome. See: www.nature.com/articles/s41... (9/12)

We conclude that the kinetoplastid kinetochore is the result of a replacement of an ancestral conventional kinetochore. This negates the idea that kinetoplastids branched off from all other eukaryotes directly after LECA and before the origin of the kinetochore. (10/12)

By contrast, maintaining the monophyly of euglenids and kinetoplastids directly results in the inference of a conventional kinetochore in LECA, as euglenids possess numerous components of this system. Thus, the absence of a conventional kinetochore in kinetoplastids must be derived. (7/12)

Instead of a conventional kinetochore, kinetoplastids have an analogous system. In our reply, we point out that the replacement of core cell biological machinery by non-homologous proteins is known to have happened on multiple occasions across diverse eukaryotic lineages. (8/12)

Placing the LECA root within Euglenozoa, as @bungoakiyoshi.bsky.social proposes, is problematic because it implies that LECA itself was a Euglenozoan-like cell. This scenario necessitates the loss of many Euglenozoa-specific features in the branch leading to all other eukaryotes. (5/12)

Unfortunately, @bungoakiyoshi.bsky.social responded to our reply without acknowledging these points. Instead, he argues that even in his proposed root placement, euglenids can be closely-related to kinetoplastids, despite their paraphyly. We stress that these notions are mutually exclusive.(6/12)

This scenario places the root of the eukaryotic tree of life between kinetoplastids and all other eukaryotes. However, no phylogenetic support exists for this idea. (3/12)

Critically, the proposed scenario would mean that euglenids are more closely-related to all other eukaryotes, including humans, than they are to kinetoplastids. This is dubious as there is a lot of evidence showing the close relation between euglenids and kinetoplastids, together Euglenozoa. (4/12)

In their Hypothesis, @bungoakiyoshi.bsky.social interprets the fact that kinetoplastids lack a conventional kinetochore, a core machinery for cell division, as evidence for these organisms having split-off before the emergence of the conventional kinetochore system. (2/12)

All in all, we find that T. thermophila has a unique kinetochore combining both highly-divergent, but ancient, as well as more recently-evolved components into a functional whole. (10/11)

This work would not have been possible without Emine Ali, my co-first author and resident Tetrahymena expert, and co-authors @lauraelse.bsky.social , Harmjan, Paula, and of course my supervisors @eelcotromer.bsky.social, Berend Snel and @kopslab.bsky.social. Thanks to all! (11/11)

We find three unconventional components localising to the inner kinetochore, a known hub for evolutionary novelty. Our homology searches revealed that they have very diverse origins despite likely co-orchestrating the various functions of the inner kinetochore. (8/11)

Finally, we identified one unconventional component to be a highly-divergent member of the kinesin-6 family. So far, no kinesin-6 family member has been reported at the kinetochore in model organisms, but its presence in T. thermophila may suggest an ancestral function here. (9/11)

There were also proteins without homology to known kinetochore components. Further searches revealed that they have a wide range of evolutionary backgrounds, some neofunctionalised, others arose through lineage-specific gene birth and yet others may be unrecognised ancestral kinetochore units.(6/11)

To uncover how the different components assemble in the T. thermophila kinetochore, we performed nanometer-scale intra-kinetochore measurements. This revealed that the T. thermophila kinetochore assembles much like the human kinetochore despite high levels of divergence. (7/11)

Using deep-homology searches with sequence-based methods as well as AlphaFold-based structural searches, we found a set of highly-diverse orthologs of known kinetochore components. Combined, these constitute a primary axis of the kinetochore: CENP-C, the MIS12 complex and the NDC80 complex. (4/11)

Surprisingly, we found no orthologs of either the Dam1 nor the Ska complexes, and also a large number of spindle assembly checkpoint proteins remained elusive. (5/11)

The kinetochore composition of ciliates has long been elusive, as they seemed to lack many known components. Moreover, they have a unique cell division process, as are binucleated but only one undergoes mitosis. We wanted to find out how they segregate their chromosomes during cell division. (2/11)