Origins of the nucleus

Today I’m talking about the origin of the nucleus. All cells have organelles, which are like the 
organs of a cell, specialised subunits that carry out specific tasks. The nucleus is a particularly 
important organelle because it houses all the genetic information of the cell.  Understanding how the nucleus came to be could unveil current mysteries surrounding the nucleus’ structure, function and why it sometimes goes wrong.

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Transcript

    Hello everyone, welcome to the second episode of ‘What We Don’t Know’, a podcast that explores the boundaries of human knowledge, investigating the unanswered questions and theories that unravel them at the frontiers of science. During this podcast I hope to get you interested in new areas of science, sociology and technology, teaching you about existing concepts and igniting a curiosity for the things we have yet to know.

    Today I’m talking about the origin of the nucleus. All cells have organelles, which are like the organs of a cell, specialised subunits that carry out specific tasks. The nucleus is a particularly important organelle because it houses all the genetic information of the cell. Cells are the building blocks of life, and the nucleus’ DNA is responsible for everything the cell does. It also regulates cell growth and reproduction. 

    Over 3 billion years ago there existed early life, but all organisms were prokaryotes – by definition, containing no nucleus. Around two billion years ago early life evolved into eukaryotes – by definition, having a nucleus. Understanding the shift from no-nucleus to nucleus is a fundamental question in evolutionary biology, yet we still do not have a definitive answer. This shift is called ‘eukaryogenesis’ – the beginning of eukaryotic life. 

    Well, why should we care about the nucleus event? There is, of course, the intrinsic value in understanding our own history. We as humans would not exist, nor would any animals, plants or mushrooms, if early life did not take that step of evolution. Life could not have reached its complexity were it not for the existence of membrane-bound organelles. However, there are also practical benefits: understanding how the nucleus came to be could unveil current mysteries surrounding the nucleus’ structure, function and why it sometimes goes wrong. Considering the importance of the nucleus in every one of our cells, think of the impacts this understanding could have in medicine!

    Although there are theories trying to solve the problem of eukaryogenesis, none yet account for every detail, and ultimately the answer is still not widely agreed. In this episode I will explain the background information around this topic, by explaining what prokaryotes and eukaryotes are, and the history we do understand. Then I’ll explore the existing theories and their problems.

    First, what actually are eukaryotes, and what separates them from prokaryotes? All living organisms are part of three distinct domains: eukarya, bacteria and archaea. Bacteria and archaea are prokaryotes, and eukarya are eukaryotes. The three domains are distinct due to genetic differences and cellular structure, but the cellular structural differences are most pronounced between the two prokaryotic domains and eukaryotes.

    Prokaryotic and eukaryotic cells both contain genetic material, but prokaryotes’s DNA is double-stranded and circular, whereas eukaryote DNA is double-stranded and linear. Prokaryotes are all unicellular and they’re usually much small and simpler cells than eukaryotes: prokaryotes measure around 0.1-5 μm (micrometers) in diameter whereas eukaryotes measure 10-100 μm. Eukaryotic cells can be unicellular or multicellular, and they range from simple protists to fungi, plants and complex animals such as humans. We are eukaryotes, and so are our pets, plants and potatoes.

     In terms of cell structure, both eukaryotes and prokaryotes have a plasma cell membrane, which is a phospholipid bilayer – two layers of phospholipids with a hydrophobic interior and hydrophilic exterior - surrounding the entire cell that holds it together and acts as a semi-permeable selective barrier to the outside world. This often regulates transport of material in and out of the cell. They also both have cytoplasm, a thick solution of water, salt and proteins within the cell membrane, and ribosomes, which are responsible for protein synthesis. Ribosomes are incredibly interesting, but we’ll likely look at them in more depth in another episode.

    Now the differences begin. Most bacteria, which are prokaryotes, have a rigid cell wall made of peptidoglycan. Of the eukaryotes only algae, fungi and complex plants have multilayered cell walls made from cellulose or chitin. Some prokaryotes, especially bacteria, have a carbohydrate capsule layer surrounding the cell wall, and thin fimbriae, both of which help the bacterium attach to surfaces. They may also have pili, rod-shaped structures involved in cellular attachment and the exchange of genetic material in a process called conjugation. Conjugation can occur in bacteria, some fungi and some protists like protozoan and algae. Also, prokaryotic ribosomes are usually smaller than eukaryotic ribosomes. 

    Here’s the key difference: prokaryotes do not have membrane-bound organelles. This means that only eukaryotes have mitochondria (responsible for energy production), an endoplasmic reticulum (for protein maturation and transportation), and vesicles and vacuoles (for transportation and storage). Many eukaryotes also have a Golgi body, which modifies and moves products of the endoplasmic reticulum, chloroplasts for photosynthesis and lysosomes containing hydrolytic enzymes. 

    All this information is to give you an overview of eukaryotic cell structure: the key take-away is the fact that eukaryotes can be much more complex. They can engage in more processes and build to more advanced stages of life.

    Perhaps the most important difference between the groups is how their DNA is stored. Eukaryotic cells have a nucleus (the focus of this episode), that holds all the cell’s DNA. Moreover, all their DNA is organised into pieces called chromosomes, which, in cell division, replicate and separate into the daughter cells. In contrast, prokaryotes do not have membrane-bound organelles, so do not have a nucleus; instead, prokaryotic DNA is bundled in a membrane-less nucleoid region, free floating in the cell. Most consist of a single circular chromosome, although there are exceptions up to four chromosomes, such as the vibrio cholerae bacterium that has two circular chromosomes. 

    The transition from no-nucleus to a nucleus is particularly significant because it represents the separation of DNA transcription and translation. Transcription describes the production of mRNA from DNA, which gets translated into proteins in ribosomes. In prokaryotic cells, DNA has no membrane barrier, so transcription and translation occur next to each other in the cytoplasm. They may even be simultaneous. In contrast, DNA in eukaryotes is enclosed a membrane-bound nucleus, so has no access to ribosomes.

    How did life begin? How did life evolve? The Earth is dated at around 4.54 billion years old. This Earth had an anoxic atmosphere, meaning there was very little molecular oxygen, and was attacked by harsh solar radiation. Early life forms likely originated in protected regions such as deep in the ocean, but even in protected areas must have endured intense conditions: early Earth enjoyed geological turbulence and frequent volcanic activity as well as mutagenic radiation. 

    Prokaryotes existed as the first forms of cellular life. We have fossil evidence of microbial mats dated 3.5 billion years ago. These are multi-layered sheets of biofilm around a few centimetres thick, comprised of bacteria and archaea, held together by a sticky substance called extracellular matrix. Some mats remained dependant on hydrothermal vents for energy and food, whereas some evolved to be phototrophic. Simple phototrophic organisms could convert solar energy into chemical energy. Around a billion years later, cyanobacteria were developed, and these began the oxygenation of the atmosphere. Increased atmospheric oxygen concentration was vital for two reasons: one, it allowed more efficiency in oxygen-utilising catabolic pathways (catabolic referring to degrading molecules to release energy), and two, some O2 converted into O3, forming an ozone layer that would absorb mutagenic UV light from the sun. Ultimately this allowed the evolution of more and more complex life forms.

    At some point there was a major shift in evolutionary history, in the history of life, when prokaryotes evolved into eukaryotes. There is disagreement between scientists as to the specific date, though many believed it occurred around 2.7 billion years ago. There is also a lack of consensus over how it happened. Endosymbiosis is probably the most major theory of eukaryogenesis, which refers to the origins of eukaryotic cells. Now, I will explain endosymbiosis, the arguments for it and the theory’s flaws, as well as the distinctions between versions, each of which gives a different account of the details. Afterwards we’ll take a look at an alternative theory, that of viral eukaryogenesis, which asks: what if viruses are responsible for the development of the nucleus? 

    The Endosymbiont Theory was popularized in the 1960s by Lynn Margulis from Boston University. At the beginning, most biologists were highly sceptical, but over time evidence piled up and it’s now widely accepted for the existence of mitochondria and chloroplasts. The theory proposes that ancient prokaryotes engulfed certain other prokaryotes, and then developed a mutually beneficial relationship: hence, the endo- prefix indicating ‘containing’ and -symbiosis indicating the association between species.  

    Similarities between mitochondria and chloroplasts, called semiautonomous organelles, and known bacteria/archaea, are strong enough to suggest the truth in endosymbiosis. These similarities include genetic resemblance. The genome in a nucleus is linear and well-organized into distinct chromosomes; it has non-coding sequences of DNA called intron, and condensation of DNA in and around proteins called histones which helps package the DNA into chromatin. Mitochondria and chloroplasts have their own DNA, which is usually circular (with linear exceptions in plant mitochondria), but usually does not have intron nor histone proteins. This DNA structure is, however, very similar to that of prokaryotic cells. 

    Further genetic evidence presents itself in the DNA sequencing analysis of zea mays, a species of maize crop. This provided information on the evolutionary history of maize’s nuclear genome, mitochondrial DNA and chloroplastic DNA. It can be deduced that the nuclear DNA comes from eukaryota whereas mitochondrial and chloroplastic DNA come from the bacteria domain. This suggests a triple origin of the species, through endosymbiosis. 

    More properties in favour of the theory include how mitochondria and chloroplasts reproduce through binary fission like bacteria do, whereas their ‘host’ cells reproduce through meiosis and mitosis. They have the same protein synthesis machinery: free 70S ribosomes compared to the 80S ribosomes in eukaryotic cytoplasm. The sizes also factor in: archaea and bacteria are usually around 1 to 10 microns (though can be found up to 100 microns), whereas eukaryotic cytoplasm measures 10-500 microns (though can be smaller). Take a guess to the size of mitochondria and chloroplasts? 1 to 10 microns. Finally, eukaryotic cells have a cytoskeleton, a self-organised protein network regulating the placement of organelles in the cell. That cytoskeleton is absent or static in prokaryotes and poorly developed in mitochondria and chloroplasts. This list is by no means exhaustive, but a pattern is clear regardless. The mitochondrion and chloroplastic organelles in eukaryotes share more features with prokaryotes than their eukaryotic cells, implying an origin as prokaryotes themselves. 

    Indeed, the endosymbiosis theory puts names to the abstract. Current eukaryotes likely descended from an archaeal or bacterial ancestor who absorbed a proteobacteria, which developed into the mitochondrion, and cyanobacteria, which developed into chloroplasts. These chloroplasts would have allowed early plant cells to carry out photosynthesis. Over time, these new organelles would integrate with the host cell as genes were transferred, production of proteins was swapped around, and products were gifted. 

    As I’ve said, the details are controversial. The order of events is difficult to discover – largely because they occurred over two billion years ago. There is little fossil or genetic evidence about intermediary organisms. What type of cell was the original host? Was it an archaea or bacteria? Were there specific evolutionary pressures that forced endosymbiosis, or did it occur by chance, as species thrived in collaboration?

    The theory has different models describing these details. One is the classic Searcy’s and Hydrogen hypothesis. Others, the more recent Reverse Flow, and Entangle–Engulf–Endogenize models. The Syntrophy hypothesis suggests specific organisms like the methanotrophic alphaproteobacterium as being the precursor to mitochondria. The Syntrophy model has two versions, the original hydrogen and methane transfer based symbiosis, and the revised hydrogen and sulphur transfer based symbiosis. These are a few examples out of many more. 

    Notably, there is more mystery surrounding the origins of the nucleus. Most work on endosymbiosis appeals to mitochondria and chloroplasts, since they have the most evidence in favour of archaeal-bacterial symbiosis. Despite suggestions for the nucleus – for example, the Syntrophy hypothesis involves a methanogenic archaeon (methanogenic organisms produce methane waste products in low-oxygen conditions) – there is less convincing evidence in favour of one argument or another. Indeed, saying that nuclei came from prokaryotes may not account for some of their features.

    Every nucleus has a nuclear envelope made from an inner and outer membrane, with pores to allow molecules to travel between the nucleus and cytoplasm. Inside is the nucleolus, almost the ‘nucleus of the nucleus’, which is the largest structure in the nucleus. This is the central nuclear location where ribosomal RNA is synthesised and collected with ribosomal proteins; in a sense, it’s machinery for the production of ribosomes. Although that is known as the nucleolus’ primary function, recently it’s been discovered to have other functions, such as mitosis regulation, cell-cycle regulation, forms of stress response and production of ribonucleoproteins. 

    The nucleus compartmentalises the cell’s DNA, and in doing so separates transcription from translation. Messenger RNA produced in transcription travels through the nuclear pores into the cytoplasm, so it can find ribosomes for translation. The ideal origin story for the nucleus would not only explain its unique structures, but also give evolutionary reasoning for the closing-up of DNA from the rest of the cell.

    One idea is an ‘outside-in’ approach. This suggests that an archaeal cell membrane gradually turned inward to create internal compartments, which fused to form the nuclear compartment and endomembrane system. DNA naturally collected inside the nuclear compartment. An opposite idea was proposed by Buzz Baum and David Baum in June 2020. They suggested an ‘inside-out’ approach, where the archaeal membrane formed outward protrusions that became the outer nuclear membrane, endomembrane system and cell surface membrane. The archaeal membrane became the inner nuclear membrane, and other bacteria, such as those to be mitochondria, were engulfed in this process. From there, the new cell evolved into higher complexity.

    Viral eukaryogenesis is a completely different approach. It’s still on the edge of evolutionary theories because it credits viruses with the nucleus, rather than archaea. The theory was proposed by two scientists independently, Masaharu Takemura and Philip Bell, each of which prefer a different version of the theory. Both versions start with the infection of a giant virus into an ancient prokaryote, and the formation of a ‘viral factory’ within the cell that isolates viral DNA and produces new viral particles. Takemura argues that the host cell then created its own DNA compartment, providing protection from the virus, and did this using stolen genes from the virus. It took the virus’ barrier-building trick, and this semipermanent form of defence evolved into the nucleus over time. Bell argues that instead, the viral factory stole genes from the cell which helped with virus production, keeping the cell alive. This viral factory evolved into a nucleus as the viral functions were lost, but the DNA compartment remained. He says this version is a more accurate reflection of the behaviour of viruses that infect prokaryotes today. Either way, the virus strongly influenced eukaryotic evolution.

    There are several reasons why this theory is appealing. Takemura’s early analysis of DNA polymerases revealed that poxviruses had similar DNA polymerases to one major class of eukaryotic polymerases, which suggests a contribution from one to another. Bell believed there were too many differences between bacterial and eukaryotic genomes for the nucleus to start as a bacterial endosymbiont. In contrast, he saw genomic similarities between poxviruses and eukaryotes.

    Both scientists updated their hypotheses recently after the discovery of giant viruses. Giant viruses’ genomes are bigger than usual, made of over a million base pairs, which compares with small bacteria, and they include viral versions of genes responsible for important cellular processes. Examples of giant viruses include the mimivirus and tupanvirus. Most notably, they are, like poxviruses, classified as NCLDVs, which stands for nucleocytoplasmic large DNA viruses. This means they replicate inside self-contained compartments like the viral factories aforementioned. These factories are as large as the nucleus, have inner and outer membranes like the nucleus, and some, like the double-membrane compartments of coronaviruses, even have pores. 

    Furthermore, researchers in 2017 discovered that a Pseudomonas bacteriophage – which is a virus – assembled a nucleus-like compartment within a bacterial cell. This was enclosed by a protein shell and DNA replication and transcription happened within, whereas translation and viral assembly happened outside. Before, viral compartments such as this seemed exclusive to eukaryotic cells, but now there is convincing evidence they could have formed in ancient prokaryotes. Unfortunately, the structure is not membrane-based.

    There is also the argument around intrinsically disordered proteins, or IDPs. These are stretches of flexible amino acids that allow fluid and rapid response to varied cellular instructions. Most proteins are highly structured. In 2012 Keith Dunker found that IDP content in prokaryotes capped off at 28%, whereas eukaryotes had 32% at minimum. Interestingly, viral proteomes (proteomes are the entire set of proteins that can be expressed in an organism) have an IDP range from 7.3 to 77.3 percent. Dunker suggests that viruses could bridge the gap between prokaryotic and eukaryotic IDP contents, and thus viral eukaryogenesis could explain why there is such a jump. 

    Takemura and Bell see viral eukaryogenesis as best explaining the separation of transcription from translation. Takemura says other theories do not account for why the genome was compartmentalised and why protein-making was excluded from this compartmentalisation.

    However, there are, of course, flaws in their theory. A lot of its evidence stems from genetic similarities between viruses and eukaryotes. But viruses are known for stealing, and they consistently take genes from their hosts. It is difficult to prove which way the genetic transfer occurred: did viruses donate their barrier-building techniques to host cells, or did viruses steal the compartmentalisation from an existing nucleus? Did viral DNA help build the first nucleus, or did the virus engage in its expected kleptomania. As I’ve said, it’s difficult to know, especially since phylogeny, which addresses evolutionary history, often has trouble in realising directionality of gene flow. 

    There may be a way to make the theory more convincing. In 2020, Japanese researchers have finally isolated and cultured Lokiarcheaota from deep sea sediments. The first eukaryote is believed to have been formed out of a collaboration with that archaea. Giant viruses from the same area were also sequenced. If any of these viruses can infect the archaea, then build the right viral factories, it would make viral eukaryogenesis a theory impossible to ignore. 

    To summarise this episode, I first explained what prokaryotes and eukaryotes were, their similarities and especially their differences. I highlighted the key difference as being the respective absence and presence of membrane-bound organelles, and the significance of that for DNA. Then I briefly considered the evolutionary history of prokaryotes before asking how the transition between domains occurred. I explained what endosymbiosis was and the convincing evidence behind it being responsible for mitochondria and chloroplasts, as well as touching on the details between theory distinctions. This contrasted with the more controversial nucleus. After explaining key features of the nucleus and requirements of a successful origin story, I dived into the viral eukaryogenesis theory, which explores the link between viral factories and nuclei. I considered its successes and shortcomings, then finished with the promise of future experiments.

    Evolutionary history is the ultimate form of history. History of humanity considers the rise and fall of civilisations, the motives of leaders and everyday people in shaping the last two hundred thousand years. Evolutionary history considers a different kind of progress. It seeks to understand how we came to be on the molecular level, the cellular level; it pieces together a mess of genetic and fossilised fragments into a tapestry spanning billions of years, the greatest tapestry of all. 

    Part of the reason to study history is to understand the present. Exploring why wars were fought and peace was agreed upon, why cultures shifted, and societies grew, gives insight into the events occurring today. 

    Exploring and, hopefully, reaching conclusions on how life evolved should give people greater understanding about how and why life works today. For example, knowing how the nucleus originated may tell us important secrets about the nucleus, about genetics.

    The further back you go, the harder it becomes to understand evolution. The furthest back of all, the complete origin of life, is the hardest problem of all.

    But doesn’t that make it more interesting?

    Thank you for listening.