Borgs: Genome and Climate Engineering

Welcome to the Axial podcast. Axial is an early-stage investment firm based in San Francisco. We partner with great founders and inventors investing in early-stage life science companies, often when they are no more than an idea. Axial is fanatical about helping the rare inventor who is compelled to build their own enduring business. Okay, Bassam, let me make you a moderator.

All right, sounds good. I'm sure.

Hey Bassam, how are you? How's your day been? Hello. Can you hear me?

Yeah. Hello.

Okay, cool. Let me do the introductions and then we can kind of get to it. Um, thanks for everyone for showing up today. I have a really awesome guest. Uh, Bassem Alshayeb from the University of California, Berkeley, and he's a graduate student in the Jill Banfield lab and also Jennifer Doudna's lab jointly, if I remember correctly.

Yes, that's correct.

And so Bassem is the lead author and he's wrapping up his thesis. I just got a text from my friend Rishi that you just— he's happy that you showed up and it works this time. But Bassem was the lead author on some really awesome preprint discovering a thing called BORGs, which we're going to discuss today. And he's wrapping up his thesis. And so, yeah, really excited just to talk to you and learn more about BORGs and kind of the future directions and the whole story too. So maybe we'll start off, maybe a quick introduction on you and your career, and then we can kind of dig in deep.

Yeah. And yeah, thanks for having me. I'm really excited to be talking about this work. So I'm currently a 5th-year NSF fellow at UC Berkeley conducting research with Jill Banfield and Jennifer Doudna. And the sort of theme of my thesis so far has been the discovery of new types of mobile elements, so new groups of viruses things like borgs, and also sort of developing new genome editing tools that could have applications in human health or agriculture or even diagnostics. So really, for me, the most exciting part has been the sort of basic science discovery through sort of curiosity-driven exploration of the world that we live in and then evaluating how those discoveries could be used as useful tools for society. So yeah, the latest of that has been this Borg paper that was really part of work that we stumbled upon while conducting research on these giant phages and different CRISPR systems.

Cool. I mean, maybe to like set the stage first, I think it's always important to not only understand the science but the person who discovered— did the science. And so what kind of got you interested in biology in the first place?

Yeah, so for me initially, I, I've always been fascinated with how different things in biology work. Obviously, I'm a big fan of tech and computational work, which is the basis of a lot of the work that I do. But at the end of the day, nature has been to me the most fascinating tech just because it's evolved for billions of years in ways that we could never have imagined. And for me, it's really rewarding to discover mechanistically how different things work in the natural world. So actually, my physics teacher in high school was really sad about me not going into physics and engineering and going instead into biology, because I, I really enjoyed, obviously, physics and engineering, and that's why I have still stuck with synthetic biology. But Biology still has always been my passion. And so I did my undergrad at University of Minnesota studying genetics, cell biology, and development, and also a major in microbiology with a minor in philosophy, looking at philosophy of science and how we interpret different kinds of data. So all of that has sort of culminated in the role that I have now, doing a PhD in microbiology at UC Berkeley on these different topics.

Cool, it seems like you're just a really well-rounded person. Physics, philosophy, and biology. And did you go to, you have the NASA logo in your background. Did you kind of go to space camp as a kid or what was kind of some formative? Were there any like formative scientific experiences? You mentioned the physics teacher kind of being a mentor and guiding you, but was there any kind of like formative experience that said, I'm gonna be a scientist?

I mean, space and astrobiology have also been big passions of mine. I worked for a little bit during undergrad and after undergrad for a bit at NASA Ames Research Center. With their space biosciences division. So I worked in April Ronca's lab where they study sort of that the theme is sort of future generations in space. So how spaceflight conditions could affect future generations. And for example, pregnancy under spaceflight conditions, pregnancy under hypergravity or microgravity conditions, how those things can affect, you know, if we end up going to space at some point, how we would essentially form a colony, how those things would affect future generations biologically. So that research, you know, there's a lot of qPCR, ELISAs, looking at different gene expressions and protein production and things like that under spaceflight conditions. And I'm still, you know, in touch with the different scientists that work in that division, looking at, you know, future collaborations and stuff. So it's definitely still a big, big passion of mine, space biosciences.

Cool, that's really— my old mentor Gary, he had this project. I don't know if he's done it yet, but he wants to send like a nanopore to Mars just to see if there's anything to measure. I don't know if that's happened. But yeah, I think totally agree. I think understanding the interplay between biology and space is a pretty interesting opportunity. And so maybe to shift gears a bit and go towards your experience at UC Berkeley and really understand the story of not only the story of how you discovered Borgs and then the meaning of it. Did you ever overlap with Brian Thomas or Dudu Bernstein by any chance?

A couple of months at the beginning of my PhD. Yeah. Cool.

Yeah. Dude is a great guy. I think he's at the Weizmann now, or I think he's somewhere in Israel, but he's a great guy.

Yeah, he is.

Cool. And so maybe for the Borgs, what was the kind of the— so you enter the lab, what was your project? What was your project? What was the kind of the initial hypothesis that you set upon and that led to ultimately led to Borgs?

Um, well, initially I was studying giant phages, so, you know, giant viruses that infect bacteria, and from a specific site where, um, it was really a spontaneous decision to sample initially. So we were just in this area that was near Jill's house And we thought, why not take some samples to sequence and look at in the lab? And that was sort of a very wet bog area in a forest that we didn't really think twice about. And then once we found that with very deep sequencing that they do have these giant phages, we decided, you know, the next year I'm going to go back and I'm going to collect a lot more samples, try and study these phages a bit more, and understand really more of the biology that's going on in that environment. And what we found was these giant sequences from the sort of computational assemblies of genomes in that sample are these giant sequences that looked more archaeal than bacterial. And for the first few months, we just called it the archaeal mystery. As I finished the sort of giant phage work, this was something that I was still trying to figure out. Is this a virus? Is this a plasmid? Until I found sort of the complete genome, that was something that was just like a weird sort of artifact or something that I, you know, shelved for a bit until I work on clearer research directions. And then we ended up with a complete sequence with more samples from, from the site. And it looked, as we saw, very archaeal. And that archaea are arguably the most understudied domain of life compared to bacteria and eukaryotes. So really, there are quite a lot of mysteries to still learn about them. I remember the, you know, I have a folder of most mind-blowing science videos that I've seen, and one of those videos is a video of an archaeal cell that instead of dividing into 2 cells, it divides into 3 cells. So it's this like triangular cell that looks like a Dorito and it divides into 3 daughter cells, which, you know, blew my mind.

That's pretty crazy. That's pretty crazy.

Yeah. It's, you know, in a folder along with like phage nuclei and different, different mind-blowing science things. But these archaea are very obviously understudied and there's quite a lot there that still needs exploration. There's not a lot of like model systems that are studied in labs. So, and obviously a lot of them are anaerobic. So that was something that I really aimed for in the second sampling that we did, was we got these tools to dig really deep holes in the ground. And I used that to make a hole and then stick my arm with gloves and stuff all the way, as far as I could reach with my arm, which was a lot colder than I expected. So like for me, I'm from Cairo, from a city. Doing these sort of sampling trips in greenery and forests was really exciting for me. And we— I dug my hand as deep as possible to get these really anaerobic samples with very little oxygen that were rich in different archaea. And these archaea specifically that we found to be the Borg hosts that we call methanoperidins, these were only recently discovered, and they are known to extract methane from the environment and metabolize it. So as soon as we found this element that sort of had genes similar to the methanoperidins, we thought, okay, maybe this is like a sibling lineage to the methanoperidins because it's linear and it seemed to have these inverted repeats at the ends. So they didn't look like, they didn't have any viral structural genes. They didn't have the canonical plasmid replication genes. We thought maybe this is a sibling lineage to Methanoperidins, especially that it had a ribosomal protein that obviously is used to make proteins in the cell. That ribosomal protein was really similar to the one from Methanoperidins, along with other genes that were really similar as well. But that was— we only found, you know, 1 or 2 ribosomal proteins in the complete genomes, which meant that it can't survive by itself as a sibling lineage. And a lot of other genes that you would consider essential for life were also not there. So through a process of elimination, essentially, we decided that this was an exochromosomal element of some kind and then started digging more into, into what other genes are encoded there. And there's this, you know, rich diversity of these methane-oxidizing organisms like methanoperidins, but right now we don't know fully how to grow them in the lab to study them in depth. So, but obviously there's a pressing need for us to study this biology since methane is a greenhouse gas that's 30 times more potent than carbon dioxide. So it obviously affects climate change in a drastic way. And this is methane that's produced is through transport of coal, of natural gas, of oil. There's obviously a lot from livestock and agriculture and from landfills. But right now all the focus is on capturing carbon dioxide. But even the biggest facilities that I know of that are in Iceland to capture carbon dioxide, they do, I think it was like 4,000 tons of carbon dioxide per year to capture, but that negates maybe 3 or 4 seconds of the global emissions. So obviously there's a pressing need to understand how something like methane is actually removed from the environment. And that's mostly currently done by microbes that we don't really know a lot about. So for us, instead of—

sorry, exactly. I think like a big part of it is, you know, biogeochemical cycles aren't really, really well understood. And this is what made your research really exciting because then begin to understand how do we integrate microbial cycles with like, you know, these kind of carbon models of the Earth. But maybe to back it up, could you maybe describe borgs? You know, this kind of these large elements, they have these direct repeats. And also, who named— it's a great name. Who came up with the name borg?

Yeah, so like I said at the beginning, we just called it the archaeal mystery. And it stayed that way for a while. And then once Jill was telling her son actually about this research, because we found that these borgs, they're linear elements, they're up to a megabase in size, which is a third of the size of their host chromosomes, which is, it's pretty massive. It's bigger than any of the giant phages that we described. It's bigger than a lot of small bacteria. So this was, you know, really fascinating to us. But also, like I mentioned, it had a lot of genes from the host. So this, this transfer of genes through horizontal gene transfer from the host, Jill was describing to her son, and he just said, oh, so it's like Borgs from Star Trek. Um, because in Star Trek, Borgs are this cybernetic group that needs to assimilate technology from other species, uh, from like sort of hosts to keep up their collective. And so we found this to be a really nice analogy with studying these, um, linear genetic elements, because majority of the genes that are encoded on the Borg DNA, up to 80%, are currently unknown. We don't know, like, it's not similar to anything that we found outside the borgs, and obviously nothing characterized in, in the lab. And so we figured that this was a chromosomal element, extra-chromosomal element of some kind in the methanoperidin cells that seems to assimilate a lot of genes from the methanoperidins. And that includes, for example, the methane oxidation group of a cluster of genes. So that's how we came up with the board.

I think it's a great story. I think. And so you spent a lot, I mean, I'm sure it was a lot of work, just like legwork to get the samples and then analyze them and then reconstruct these elements and then really then hone in on saying these aren't megaplasmids, these aren't from phages, this is kind of something unique. How did you go about, you touched upon this in the preprint, around their potential function. And you have a nice little figure about trying to like, you know, figure out what they actually do in terms of augmenting methane oxidation. But you discovered borgs. How did you go about then trying to figure out what they do, or at least hypothesize what they could do in the environment?

Yeah, so once we had the complete genomes, we sort of went through and annotated everything as either something that was new and uncharacterized or as the 20% of genes that had similarities to existing proteins in the NCBI database and other databases. We went through those annotations to try and figure out which processes those genes are part of. And methane oxidation is one thing that We touched on— there was also clusters of genes for nitrogen fixation. So with something like nitrogen fixation, it's very important in these soils that we found them in. And these are also found in different rice paddies and in many different environments. And so nitrogen fixation is very important agriculturally since Plants require nitrogen compounds for growth, and they essentially have transferred this machinery to their own genome, but also different genes, for example, for transferring electrons outside the cell. So the way that they respire is by transferring their electrons to another compound, for example, different metals, something like methane. Instead of oxygen. So that's a sort of long way of saying that they breathe other things than oxygen. And this was something that, you know, I worked in a lab in undergrad with Jeff Gralnick who studies this pretty extensively. So it was really rewarding for me to sort of come full circle and touch upon those topics of transferring electrons outside the cell, that, you know, potentially this could be something that can be used to generate electricity, since electricity, all it is is transfer of electrons, whether it's through a wire to an electrode and so on. So these likely enhance their host's ability to metabolize different compounds, methane and other metals. So those are some features that we were most excited about, but they also have different defense systems. For example, they have their own CRISPRs. So analogous to the discoveries that we made in phages in my previous papers, we found that they have CRISPR systems that target also other mobile elements that are integrated in the host genome. So clearly they are competing maybe for the host or augmenting the host's defenses against different mobile elements that would inhabit the same cell. And the other like really fascinating thing that we saw was that different borgs could also exchange genetic material with each other and not just with the host. So there are, you know, blocks of 11,000 base pairs, for example, that are 100% identical in different borgs, which implies that those two borgs probably were in the same host cell at some point, and there was some recombination that happened that transferred that piece of DNA. So, and yeah, those are just the things that we already know the functions of. And there's, you know, 80% of the genome is still unknown. So there's a lot still to learn from that.

Really cool. When I read the paper, I'm like, my gosh, the SEM has a decade's worth of work ahead of him here. You can do so much. There's like, you know, just so much to explore. I remember, I think Jill's lab published a paper in 2016 2019, discovering the first CRISPR system in archaea. And so I think you're spot on. This is— archaea is so underexplored branch of life and there's probably so much cool biology and tools to be discovered there. And so then you made some—

Yeah, I mean, even the first CRISPR, like when CRISPR was first described back in the '80s, a lot of that was from archaea.

Oh, really? Interesting. I thought the first CRISPR systems were like from yogurt. From Dannon, maybe. Maybe.

I know. So that was, that was the first indication of what CRISPR could be doing. But the very first, like, when they came up with the word CRISPR, like, the discovery of the repeats was back in the '80s, um, that included archaea.

Wow, interesting. That's really cool. I didn't know, I did not know that. I need to go read up some history, but, um, So you made this discovery on borgs, and then you did a lot of hard work to infer their function. And now you and the whole lab probably hard at work right now trying to learn more about these borgs. But the really exciting part, and you alluded to this, is how they can modulate greenhouse gases, in particular methane. And microbes play a massive role in carbon dioxide flux. I think it's involved in at least half, maybe you can correct me on this, of fixation of carbon dioxide in our environment. But microbes play a really pivotal role in carbon cycles. And so maybe you touch upon maybe the interplay between borgs, biogeochemical cycles, and climate change. It's a pretty large space. But do you have any kind of ideas around the potential impact of, of borgs on, you know, the climate?

Yeah, I mean, for right now we're still even just trying to understand, um, what kind of diversity is there for borgs, where are they found, um, why are there, for example, specifically some methanoperidins that have borgs and some that don't. So Obviously, like I said, Methanoperidens was very recently described as a species of archaea, but going through that data, we couldn't find any borugs in their data. So why is it that they exist on the ones, the Methanoperidens that we found, but not in somewhere else like Australia? So there's still a lot to learn. With their, their impact and their distribution across the world. And also, this was just the first demonstration of the methane oxidation machinery being able to transfer two mobile elements, and with that also implying transfer across lineages. So that's something that would be really interesting to explore, how much of that is mobile across different lineages of these both archaea and bacteria that tend to metabolize methane.

But yeah, you're really interesting. Yeah, I think— is— I'm really horrible at pronouncing like species names, but that— so C. elegans is such a nice It's so easy, right? Drosophila, but Methanoperidens. Okay, I got it. Is it a heterotroph? Or is it something else?

I think it's, it's, I think it is a heterotroph. I don't think there is any evidence of it fixing its own carbon.

But yeah, because my understanding of like how I took this class over a decade ago, a guy named Peter Gerges. So he's really— Oh yeah. He's awesome. I don't know where he's at. I haven't kept in touch with the guy, but he's a really—

He's been at Harvard. Well, I know because he's another fellow Egyptian.

Oh, he is? Oh, cool, man. He's a cool guy. I think he used to work at Monterey and then went to Harvard. I took a class of his. I was really fascinated with microbes in the ocean. I love history. And so I think a very romantic part of biology is like Darwin on the Beagle. Rather than being in lab all day, he could be on the ship. That's much more attractive to me, I think. But, and from my understanding of how biogeochemical cycles work, heterotrophs are really involved in oxidation and production of CO2, and then photoautotrophs are really involved in fixation, and maybe production of oxygen. So just something I'm not— I'm so— I've been out of science for so long. So I'm not on the cutting edge anymore, unfortunately. But maybe that's the— maybe there's some sort of Borgs play some element in terms of oxidation. And, but to be determined.

Yeah, I mean, the Methanoperidins, I think, would be considered like chemolithotrophs. So using like inorganic sources, like different metals, for example, for respiration, but obviously they also use methane.

Interesting. Yeah. So much, so much to be done. I think not only do great science, but probably go on some really cool adventures. Metagenomics, definitely the cool part about metagenomics is you get really cool data, but then you get to go on cool trips. Whoever went to that mercury mine in Napa, that must have been scary. To be honest, I would've have— I can see why you didn't want to go to that mercury mine. I wouldn't have gone. I'd have been terrified. Cool. Maybe then we can also touch upon the just searching nature for new inventions and borgs is something in nature. And in the beginning of the conversation, you touched upon this of being fascinated with nature and nature invented CRISPR. And Joe Banfield, you can argue, invented or was a key inventor of CRISPR. And her dataset was what enabled Jennifer to make her awesome discoveries. I think Patrick Schrew just published some cool papers around integrases. But do you have any thoughts around why nature has been such a great inventor? I think the arms race between phages and microbes seems to be it, but yeah, any thoughts around nature as an inventor?

Yeah, I mean, to me, that has always been my driving force for, you know, research interests. And that's sort of why I decided I wanted to be co-advised between Jill and Jennifer is Jill has this innate curiosity towards nature and sort of the discovery of new basic science.. And Jennifer is always asking me, you know, so what, how can you use this for something useful? So that has been a very strong combination in my thesis research. And for me, looking at nature, like arms races have always produced some of our best tools, even something like antibiotics. That's, you know, the arms race of different microbes against each other. The same site where we studied all these giant phages and also the, the borugs, the same site a colleague of mine was using to look at different antibiotics that the preprint came out for pretty recently as well. And so this, this, you know, plot of dirt near Jill's backyard was really the driving force for, or the site for a lot of my thesis research and my colleagues' research. That it just goes to show that everyone has this sort of universe lurking near them, waiting to be explored. And obviously, like, as I said, I'm really excited about, you know, space exploration and astrobiology and all of that. But there's also this incredible diversity just here near all of us that is just waiting to be explored. And that's what really excites me about microbiology and about science.

Well, it's really powerful, Bassem. Like, the next great discovery might just be in your backyard.

That's a great—

Exactly. That's a great line. Anybody in the audience have any questions around the topic of science and Borgs? Please raise your hand. But maybe to kind of then kind of wrap up this conversation, and I know you're doing your thesis, so I don't want to talk about things that are unpublished, but what kind of new research are you doing, kind of exploring Borg research and also maybe going beyond Borgs and trying to find new types of elements in these samples?

Yeah, I mean, of course, a lot of that work is being done. And for me, mobile elements are some of the most fascinating things in biology ever since I think Barbara McClintock got a Nobel Prize for transposons. It's always been, you know, elements that do things somewhat differently than life because they have this selfish need to want to replicate as much as possible and spread everywhere regardless of, you know, what different life forms might have to say about that. And I think that there's a lot of untapped tools that can be developed from that. And obviously, that's what I've focused my thesis research on. And that's, you know, a lot more unpublished stuff that I'm hoping to get out soon as well to touch on that.

Cool, man. I'll be— if you have Transcripts, I'll be your first reader. I love reading paper. I'm very good at reading papers. I'm not so good at doing the science. So I think I seriously, I used to, I went to grad school at Berkeley. I could, we can go get drinks, but I can tell you my scientific career and I'm definitely a bad at the bench. But yeah, I think I've read your preprint at least 10 times. It's not that long, so it's not that impressive. What are you thinking about after grad school? So you're gonna wrap up your thesis. Are you thinking about professorship? Are you thinking about entrepreneurship? You're thinking about joining NASA and doing space biology? What kind of, what do you think your next steps are?

I mean, I'm keeping doors open right now. All I know is that I'm really excited about creative research to sort of explore the world and come up with sort of translational tools that could be helpful from that. So whatever context I can do that in is hopefully what I would pursue as my next step. That might mean academia, but I also know that at least in the entrepreneurial space, it seems people are a lot more receptive to more high-risk, high-reward ideas than maybe they used to be. So I'm keeping that option open as well.

Cool. Yeah, we live in the age of the inventor, right? So just, if you can invent something new, the money's there. I remember I met Brian Thomas. You should start a company. You should join Metagenome. That's a really cool company. I met Brian when he started the company and I did not invest, I didn't invest like an idiot. I should have invested. But Brian's done an incredible job. I think maybe serving as an example, I think he was in Jill's lab for a long time and now he has an incredible business. So I think the future is bright and I think you're going to have a lot of great options. I think Borgs is a real big breakthrough in connecting microbes with our environment, understanding the mechanism by which carbon and nitrogen and, you know, various other chemicals are kind of recycled. Because biogeochemical cycles are really underappreciated in, like, climate models. And so if we can kind of, you know, hone in on that, we might have different ways to engineer the environment and maybe solve climate change.

But absolutely.

But any final thoughts? I think I had a great time. Great time. I think, but any final thoughts you want to part to everyone?

Maybe just that, you know, none of this work would have been possible without sort of curiosity-driven basic research. Like we didn't really set out to find a tool that might help with climate change, but that sort of came to be from the curiosity-driven research that we did on other things. And the same can be said about CRISPR, for example, where nobody really set out to invent a gene editing tool. That just sort of happened as we studied why these elements have repeats in them, and what are these genes that tend to co-occur with the CRISPR, you know, CRISPR-associated proteins that are now Cas proteins. So yeah, there's a lot to be learned from just basic science, I think. If you want to sit and invent something new, it's always a good idea to look at nature and how nature has done it because that took billions of years of evolution.

But yeah. Totally agree. I think we're on the same page. Well, Bassem, I had an awesome time talking. I was really just curious to have a conversation with you since you— I read your paper a lot and it was really— I think it's a big— I think it's a massive breakthrough and it's going to unlock a a lot of different elements in terms of biology and climate. But yeah, when you get your thesis done, send me an email. We'll go for a walk. We'll go to Jupiter or go for some cheese board or something. But good luck on the thesis. I think you probably have a lot of writing ahead of you. How long is your thesis going to be? Is it 100 pages or 300 pages or how long?

I can tell you I've already passed 100.

Louise.

That's a lot.

Oh man, how do you edit that thing?

Yeah, that's the struggle.

Well, Bissem, get some sleep and congratulations on all the success. I'm sure the best is yet to come though. And so I'm really excited to just send me an email and we'll go for a nice little walk around Berkeley. But thanks for taking the time to talk to us. And I I learned a ton and I think we all look forward to kind of what you're gonna do next and kind of the impact you're gonna have on science and more. So I really appreciate everyone and Bassam, thank you for the time. I really appreciate it.

Yeah, thanks so much for having me. That was fun.

Cool, let me, I'll end the room and we'll talk soon, Bassam.

Well, have a great day. Thanks, you too.