Another month, another awesome Protein Structure Evolution talk! Register here if you like cool science: tinyurl.com/prose-seminar2

Jointly organized by @lacholt.bsky.social, @caro-rocha.bsky.social, @claudiaalcar.bsky.social, @zachary-ardern.bsky.social and myself.

(Starts in half an hour!)

In case y'all are interested in cool science about protein evolution—join our monthly seminar series! tinyurl.com/prose-seminar2

Organized by @lacholt.bsky.social @caro-rocha.bsky.social @claudiaalcar.bsky.social and myself.

(Stephen Fried is set to deliver this week's seminar in half an hour!)

@zachary-ardern.bsky.social and myself suggested just that hypothesis in our commentary on a yeast paper from the @carvunis.bsky.social lab—I don't think this has been tested yet!

Generally, I think by "non-functional" people mean "when you knock out that one protein, it doesn't affect fitness"

I understand "pervasive/spurious translation" to mean "the protein is non-functional". See the example below from Stringer et al (2021)—I think this is the common usage.

Do people disagree with this? Are there other ways of using this phrase in the literature that I'm not familiar with?

But I guess if the goal is to fill in gaps in annotation for less studied organisms, mass spec can be of some help. Here's a sampling of proteogenomics-based studies that makes the general point.

(Table from the same paper) (4/4)

In cases where people have tried to validate RiboSeq-supported non-annotated proteins with mass spec in the same study—generally, very few could be confirmed.

See the highlighted rows from the table below, taken from our recent review paper: genome.cshlp.org/content/earl... (3/4)

Similar conclusions have previously been reached by Fijalkowski et al (2021), and for eukaryotes, Wacholder & Carvunis @carvunis.bsky.social (2023).

These proteins are either way too small, or not expressed enough, or generate "bad" (hard to detect) peptides—mass spec doesn't like them. (2/4)

After testing virtually all reasonable permutations of sample prep, spectra acquisition, database selection, data processing...

This team (convincingly, I think) demonstrates that ~85% of the small, *annotated* bacterial proteins are undetectable by mass spec—much less non-annotated ones. (1/4) 🧵

...How inert, non-expressed parts of the genomes can gain expression.

This proposed first step of gene birth has been studied extensively in bacteria, with no sign of stopping—see attached table for a sampling.

In our previous work... (6/7)

One, they're highly diverged versions of coding or non-coding sequences already "native" to the genome,

Two, they're "foreign" genes—deposited in their current habitats from sources unknown.

We review the evidence for and against these hypotheses, and conclude... (3/7)

Where do "orphan genes" in bacteria come from—and how do we know? (Do we even?)

I've been thinking about this problem over the course of my PhD, and our review paper is now out in Genome Research!

genome.cshlp.org/content/earl...

Here are some plot points (1/7) 🧵

I was looking for this paper but couldn't remember the exact title, so I googled "effective population size for complete dumbasses" and it worked

I got my PhD commencement at @utaustin.bsky.social before GTA 6

If you enjoy cool science about the origin of life, join us May 13 (9 AM central time). Registration link - tinyurl.com/prose-seminar2

Having followed Dr. Hlouchová's work for a long time, I can say with confidence that this will be one of the most exciting episodes we've had yet.

Cool new seminar series alert: in tomorrow's session (March 11, 3PM GMT), @zachary-ardern.bsky.social will be discussing long-term trends in protein structure evolution.

To sign up for the series: tinyurl.com/prose-seminar2

@lacholt.bsky.social @caro-rocha.bsky.social @claudiaalcar.bsky.social

I don't quite understand how this happened, but I recently completed my PhD at UT Austin! On that note, I thought I should acknowledge what I think are some of the best papers in my field of research - De Novo gene birth.

@vakirlis.bsky.social @caraweisman.bsky.social @carvunis.bsky.social

This paper from the @carvunis.bsky.social lab went under my radar for a while, likely because it seems to report "negative" results. I've since realized this is essential reading for anyone attempting to detect novel proteins using mass spectrometry. Definitely cleared up a lot of my misgivings!