Researchers at NCBS gain key insights into the role of whole genome duplication in the evolution of the vesicle trafficking system
The mechanisms of how life evolved on earth have intrigued scientists for decades. Despite our broader understanding of eukaryotic evolution from prokaryotes, our knowledge of how key eukaryotic functions came about still remains fuzzy.
A new study from the National Centre for Biological Sciences (NCBS) sheds light on how genome doublings have played a key role in the evolution of vesicle trafficking pathways in eukaryotes. Mukund Thattai, a faculty member at the Simons Centre for the Study of Living Machines at NCBS and his then graduate student, Ramya Purkanti (now a post-doc at the Vastenhouw Lab, MPI-CBG and Junior Lecturuer at Université de Lausanne), were interested in understanding what kinds of selective pressures led to the rapid emergence of hallmark eukaryotic functions.
To probe further, they choose to look at yeast. Yeast cells are extensively used as model organisms in biology and have a rich trove of bioinformatic information about their cellular processes readily available.
Thattai and Purkanti found that whole genome duplication events within yeast cells played a key role in the expansion of the vesicular trafficking system – a key eukaryotic adaptation that allows cells to package and transport intracellular cargo.
Vesicular Trafficking System
Vesicles are small membrane-bounded entities that help package and transport cellular metabolites from one organelle to another in eukaryotes. The vesicle trafficking system is akin to a cellular courier service: cargo is loaded at one location, appropriately packaged and tagged, transported to its respective destination, and then finally unpacked and used.
To enable the precise delivery of cellular cargo, vesicles have recognition markers or tags (proteins such as Rab GTPases and v-SNAREs) that only bind to specific readers on their respective target organelles (receptors such as tethers and t-SNAREs). These unique receptor-ligand pairings serve as cellular barcodes that provide specificity to vesicular transport processes and ensure streamlined and error-proof delivery of cellular cargo.
The evolution of the vesicular trafficking system over time has been critical in enabling several hallmark functions within eukaryotic cells, including secretion, signalling, and formation of cellular compartments.
But how exactly did the vesicle trafficking system evolve in the first place? Thattai & Purkanti were curious about this question and strongly suspected that genome duplication might have a role to play here.
The Eukaryotic Genome
A genome represents the entire collection of genes present within an organism. These genes are nothing but stretches of DNA sequences that can code for a variety of functions including regulatory, secretory or structural proteins (such as those involved in the vesicle trafficking system) or comprise portions of non-coding DNA with hitherto unknown functions.
Understanding the evolution of such a complex array of functions within eukaryotic cells, starting from relatively simpler prokaryotic cells is of great interest to scientists. Our current understanding dictates that eukaryotes may have formed when a few prokaryotes were engulfed by another prokaryotic cell, leading to the formation of membrane-bound organelles like mitochondria within the cell. This is widely known as the endosymbiotic theory. The study at NCBS specifically constructs a timeline of events that could have led to the diversification of eukaryotic functions such as vesicle trafficking, after the first membrane-bound organelles were formed.
Constructing such a timeline of events requires a careful study of genome inheritance patterns over thousands of years. The authors specifically chose to look at available bioinformatic data on genome doubling events in yeast for approximately the last 100 million years.
Genome doubling
Gene duplications are key drivers of evolutionary novelty. Genome doubling creates two copies of every gene in an organism. Extra gene copies can take on new functions, allowing cells to adapt in the face of selective pressures. The vesicle traffic system contains many examples of duplicated genes. Thattai & Purkanti wanted to know if these arose sporadically, by the duplication of single genes, or via a global genome duplication.
Genome duplications can lead to the loss or gain of new capabilities in eukaryotes, which might eventually be beneficial, detrimental or neutral for the cell. Thattai explains that “having two copies of every gene is mostly useless if they just do the same thing. So you lose 90% [of these duplicated genes], but the ones that stick around, give you some sense of what seems to be selected”. Duplicate gene copies may be initially redundant, but they can diverge over time, but can also allow for new variations to be selected.
Specfically, Thattai and Purkanti found that proteins involved in later endocytic steps and intra-Golgi traffic in yeast are highly enriched in gene duplicates arising from a genome doubling event. Their analysis shows that across many species of yeast, the same genes acting at the same parts of the vesicle traffic system are repeatedly retained as duplicates. These findings demonstrate that whole genome duplications had a key role to play in the expansion and diversification of the yeast vesicle trafficking apparatus.
The research journey
Talking about their motivations behind this study, Thattai shares that “this project actually started a long time ago, when my student Rohini and I made a model of how vesicle traffic systems evolve”. Around this time, Ramya joined his lab and started working on gene duplication events for her PhD. Soon, they wanted to see if gene duplications occurring via genome doubling played a role in the evolution of vesicular transport systems.
However, their research journey was met with several roadblocks, including the COVID-19 pandemic, which delayed their work significantly. Soon after, Ramya also moved to the USA as a postdoctoral fellow. However, Ramya and Thattai continued to collaborate. They decided to use available bioinformatic data on yeast gene duplications to start this project anew in late 2020 and carefully went through the genome sequence of the whole budding yeast clade – the entire set of organisms that have evolved from a common yeast ancestor.
Thattai & Purkanti found through their bioinformatic models that an ancestral genome duplication appeared to have similar outcomes across descendant species, with multiple lineages retaining specific sets of duplicated genes which coded for functions involved in vesicle trafficking apparatus. This was direct proof of convergent evolution since different yeast species’ vesicle trafficking functions changed in a similar way over the course of time.
The authors were able to claim this as being an instance of convergence evolution since they used a systematic approach to compare different yeast species within the clade and were able to rule out alternative explanations such as shared ancestral events. “It's one of those cases where if you see something in biology, typically you can't tell if it's convergence or ancestry. But because you have many species now, you can distinguish those two things. Having a nice simple demonstration of that, for me, was quite satisfying”, concludes Thattai.
The road ahead
Thattai’s lab continues to work further on understanding the intricacies of vesicle trafficking systems and their origins. Thattai & Purkanti’s theoretical approach to this biological problem not only highlights the need for future interdisciplinary collaborations but also paves the way for the academic community to look more deeply into the effects of whole genome duplication on cellular processes.
“To my knowledge, it's the first time that there's some sort of evidence, indirect evidence, that selection is acting on a particular part of the vesicle traffic system. That means that some aspect of secretion was beneficial for the cells to survive. And it'll be interesting to check [this] through experiments”, explains Thattai.
Thattai & Purkanti’s work was a unique combination of perseverance, calculated guesswork and a robustly designed research method. The big questions in biology need all of these (and more) to be answered. What lies ahead is the fascinating world of eukaryotic evolution, with even more nuances waiting to be unravelled.
Read more about their study at https://www.nature.com/articles/s41598-022-15419-9
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