Tag Archives: rna

What is DNA: the blueprint of life

Credit: Pixabay.

Deoxyribonucleic acid (DNA) is a long molecule that contains the hereditary genetic code required to build and maintain an organism. DNA sequences (the instructions inside the code) are converted into molecular messages that can be used to produce proteins. The DNA molecule is easily recognizable due to its double helix shape, consisting of two strands that wind around one another.

Ever wondered how to build a human? Like a cookbook, DNA contains all the necessary instructions in order to assemble a new organism. Although there are over a trillion cells that compose the human body, with varying degrees of complexity from neurons to immune cells, almost every one of these cells contains the same 3 billion DNA base pairs that make up the human genome.

Every species has a unique DNA sequence, and every individual also has slightly different DNA from the rest of the population (as long as they’re not clones that reproduce asexually).

What is DNA made of?

Each of the two DNA strands has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four types of nitrogen bases: adenine (A), thymine (T), guanine (G), and cytosine (C). These three parts together — a phosphate group, a sugar group, and a nitrogen base — are known as nucleotides.

The DNA double helix can be pictured as a sort of chemical ladder where the sides of the ladder are strands of alternating sugar and phosphate groups while the”rungs” are made up of two nitrogen bases, paired together by hydrogen bonds.

Base A always pairs with base T, and likewise C with G. Together, these units are called base pairs.

The sequence of nitrogen bases matters a lot. It can mean the difference between blue eyes or brown, tall or short, healthy or afflicted by a hereditary disease.

Overall, the complete instructions for a human contain three billion bases and about 20,000 genes found on 23 pairs of chromosomes, all wrapped inside a single molecule just six microns across located inside the nucleus of virtually every cell in the body.

Additionally, a small amount of DNA is present in the mitochondria, the structures within the cells that are responsible for converting the energy in food into a form that the cell can use — it’s called mitochondrial DNA (mtDNA). Together, the sum of all the DNA and mtDNA sequences in the cell is known as the genome.

If you uncoiled and stretched the DNA in one cell all the way out, it would be about two meters long. But what’s truly mind-boggling is that all the DNA in all your cells put together would stretch over a distance about twice the diameter of the solar system.

What does DNA do?

DNA sequences are used to make proteins in a two-step process. Enzymes first read the instructions in the DNA molecules in order to transcribe them into an intermediary molecule called messenger ribonucleic acid (mRNA). Pfizer’s and Moderna’s vaccines are based on mRNA, if that sounds familiar.

Next, the sequences in the mRNA molecules are translated into instructions that ribosomes, the small cellular structures responsible for making proteins, can ‘understand’. The protein-making machinery follows these instructions to the letter to link specific amino acids (protein building blocks) in the precise order required to produce a specific protein. The amino acids involved and the way they are linked to form the protein are what allow it to carry out its very specific tasks.

When a cell divides, so does DNA. Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases, so it can replicate and make exact copies of itself in the new cell. This copying process isn’t always perfect. Sometimes there is an alteration in the nucleotide sequence of the genome, called a mutation.

Each DNA sequence that contains the instructions for the production of a certain protein is known as a gene. Depending on how complex these instructions are, the size of a gene can vary from as little as 1,000 bases to one million bases in humans.

After the Human Genome Project was completed in 2003, scientists found that there were around 20,000 genes within the genome, a number that some researchers had already predicted.

But despite their fame, genes only make up 1% of the genome. The other 99% are instructions that regulate when and how these proteins are made. Scientists call this non-coding DNA because these sequences do not code for proteins.

At face value, the small number of genes relative to the entire genome might seem odd. But it makes sense when you consider that each of the over 200 cell types in the human body interprets a set of identical instructions (the genome) very differently in order to perform equally different functions.

Besides, a large genome doesn’t mean much. Plants in the genus Allium, which includes onions and garlic, have genome sizes ranging from 10 to 20 billion base pairs, whereas the human genome is only 3 billion base pairs. Obviously, a human is much more complex than an onion. This suggests that perhaps much of the genome isn’t actually useful and the size of a genome says nothing about how complex the organism is.

How do we know about DNA?

Since ancient times, people were at least somewhat aware that there was some hereditary factor that is passed down from parents to offspring. But it wasn’t until Gregor Mendel, a 19th-century monk, laid out the fundamental laws of inheritance that this process was unraveled scientifically.

Mendel was the first to demonstrate using his now-famous pea plant experiments that “invisible factors” — now known as genes — predictably determined the traits of an organism. He also coined many of the concepts and terms used in the field to this day, such as “recessive” and “dominant”.

DNA was actually known during the time of Mendel. The molecule was first discovered by Swiss biochemist Frederich Miescher in the late 1800s inside the nuclei of human white blood cells, but no one suspected that it had a central role in biology.

In the early 1900s, Russian biochemist Phoebus Levene, the author of over 700 papers on the chemistry of biological molecules, made phenomenal contributions to the unraveling of DNA. He was the first to discover the order of the three major components of a single nucleotide (phosphate-sugar-base), the carbohydrate component of RNA (ribose), and the carbohydrate component of DNA (deoxyribose), as well as the first to correctly identify the way RNA and DNA molecules are put together.

Levene’s work was expanded by Erwin Chargaff, an Austrian biochemist, who made additional discoveries surrounding DNA. He made two important contributions. First, he noted that the nucleotide composition of DNA varies among species. Secondly, he found that in almost all DNA, regardless of the organism or tissue it comes from, the amount of adenine (A) is usually similar to the amount of thymine (T), and the amount of guanine (G) usually approximates the amount of cytosine (C) — this now known as Chargaff’s rule.

3-D structure of DNA. Credit: Wikimedia Commons.

These discoveries paved the way for the discovery of DNA’s double helix. In 1953, James Watson, Francis Crick, Maurice Wilkins, and Rosalind Franklin performed X-ray diffraction and built models showing the three-dimensional, double helix structure of DNA.

Watson and Crick used cardboard cutouts representing the individual chemical components of the four bases and other nucleotide subunits. The two scientists shifted the molecules around countless times, as though they were putting together a puzzle. However, the puzzle pieces never seemed to click until American scientist Jerry Donohue suggested that they make new cardboard cutouts for thymine and guanine. The different atomic configurations made all the difference and the two complementary bases finally fitted together perfectly. What’s more, the structure also reflected Chargaff’s rule.

Since then, the Watson and Crick model has suffered minor corrections, but its four main features remain the same to this day. These are:

  • DNA is a double-stranded helix, with the two strands connected by hydrogen bonds. A bases always pair with Ts, and Cs always pair with Gs, which is consistent with and accounts for Chargaff’s rule.
  • Most DNA double helices are right-handed, meaning the sugar-phosphate backbone curls around the axis of the helix counter-clockwise.
  • The DNA double helix is antiparallel, which refers to the fact that the head of one strand is always laid against the tail of the other strand of DNA.
  • Not only are the DNA base pairs connected via hydrogen bonding, but the outer edges of the nitrogen-containing bases are exposed and available for potential hydrogen bonding as well. These hydrogen bonds provide easy access to the DNA for other molecules, including the proteins that play vital roles in the replication and expression of DNA.

More recently, scientists have found that the precise geometries and dimensions of the double helix can vary. The most common configuration is the one outlined by Watson and Crick, known as B-DNA. But there is also A-DNA, a shorter and wider form that is usually found in dehydrated samples of DNA and rarely encountered under normal conditions. Lastly, there’s Z-DNA, which is a left-handed conformation and is a transient form of DNA that appears only during certain types of biological activity.

Scientists reverse-engineered the Moderna vaccine, post RNA sequence online for free

Researchers at Stanford University sequenced the RNA components of the initial Moderna and Pfizer-BioNTech COVID-19 vaccines, then posted the two-page-long sequences in their entirety on GitHub.

Credit: Flickr/ Marco Verch.

One of the few good things out of this pandemic was that urgency of the matter fast-tracked RNA-based vaccines, which could end up being far cheaper and quicker to make than traditional vaccines.

Unlike a normal vaccine, RNA vaccines work by introducing an mRNA sequence (the genetic molecule which instructs cells what to build) which is coded for a specific antigen. Once produced within the body, the antigen is recognized by the immune system, preparing it to fight the real thing. In the case of COVID, the antigen is the coronavirus spike protein, which it uses to attach itself to cells and infect people.

Besides COVID, mRNA vaccines could prove more effective against other rapidly evolving pathogens like influenza, Ebola, Zika, HIV, and even cancers.

Although RNA vaccines can be designed and produced much faster than conventional vaccines that contain inactivated disease-causing organisms or proteins made by the pathogen, the COVID-19 vaccines from Moderna and Pfizer-BioNTech still required a huge effort to bring to market. And now a team of researchers from Stanford have posted the two vaccines’ genetic sequences online.

They used samples left in used vials that were supposed to be discarded after vaccine shots were portioned for immunization. Instead of throwing them into the bin, the Stanford scientists prepared and sequenced the RNA in the samples with FDA authorization for research use.

“Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin,” wrote the researchers in a document describing their procedure on GitHub.

The Stanford researchers added that anyone with access to their hardware could data-mine and filter the genetic sequences in these vaccines. Previously, another group used publicly available information about the Pfizer-BioNTech information to figure out its RNA sequence.

Having the mRNA code used in novel vaccines currently being rolled out to millions of people is like having access to the code of open source software. It means anyone can study the code and perhaps improve on it.

However, simply having access to this genetic sequence doesn’t mean you can make the vaccine at home. The manufacturing process is quite elaborate and involves hundreds of steps and machinery that costs hundreds of millions of dollars.

Resistance is futile: what viruses are, and why we’ll never ‘beat’ them

No other year in living memory has been as heavily influenced by a virus as 2020. But what exactly are viruses, what makes them tick, what about them made us all put our lives on hold?

Image via Pixabay.

The short of it is that viruses are biological machines, supremely well-adapted to a single survival strategy. And this strategy is quite simple — viruses find living cells, infect them, and hijack their biochemical machinery to reproduce. They’ve done away with (or perhaps never developed in the first place ) anything that doesn’t directly help them perform that task, all the way down to the most fundamental traits of living organisms: viruses aren’t really alive, but they’re not not-alive either.

Their simplicity works to make viruses easy to ‘build’ (so they’re plentiful) and hard to detect and destroy. In fact, we still have very few reliable medicines against viruses (they’re known as ‘antiviral’ compounds), and they often only work on particular kinds or lineages of viruses. We’ve managed to put a man on the moon and put stars inside a bomb, but for all our achievements, humanity’s best defense against these pathogens is still our own bodies and immune systems. This becomes a bit scary when you consider that viruses very definitely outnumber any and all living things on the planet.

But I’m getting ahead of myself. Let’s start from the beginning:

General viral structure

Viruses are acellular. This means they are not made from cells nor do they have a cellular structure. This also means that all those fancy components you may or may not have learned about in cellular bio 101 — organelles, plasma membranes, ribosomes, etc — have nothing to do with a virus. They’re also exceedingly tiny, typically around 20–300 nanometers in diameter, though a few are larger. To put things into perspective, if a bacterium was the size of a soccer field, a virus would be around the size of three soccer balls put side-by-side. An animal cell would be the town around it.

One such pathogen (an individual, fully-assembled virus is referred to as a ‘virion’) is about as simple a biological machine as you can make and still have it work. They include a core that houses their nucleic acid (genetic material), an outer coat of proteins or ‘capsid’, and that’s pretty much it. That’s all you need to make a working virion. However, some fancier models can have additional features, such as an outer membrane shamelessly stolen off a host cell, different proteins (or glycoproteins) that can help them infect targets, or other structural elements. Capsids are constructed from proteins known as capsomeres. Them, alongside any membrane viruses have, typically tend to be peppered with glycoproteins that serve as binding or access keys into certain cells.

These proteins form the distinctive corona-like (‘crown’) structure of the coronavirus. Image via Pixabay.

By and large, viruses are classified into one of four groups based on their structure: filamentous, isometric (or icosahedral), enveloped, and head and tail. We’ll be getting to them in a second. One interesting characteristic of viruses is that across all strains, their complexity seems to be in no way related to the complexity of their hosts. The most complex and intricate structures we’ve seen in viruses belong to bacteriophages, pathogens that infect bacteria (which are the simplest living organisms).

What shape a virion takes, as well as the presence or absence of an envelope, has little bearing on what species it can infect and what the symptoms would be, but they’re still very useful classification criteria because they’re relatively easy to check.

Viral morphology

The shape and size of viruses tends to be consistent among different lineages, and quite distinctive for each.

Filamentous viruses have long, cylindrical bodies; plant viruses often employ this shape, including the TMV (tobacco mosaic virus). Icosahedral or isometric viruses look pretty much like spheres, or spheres with flattened faces. They get their name from the icosahedron, a polygon with 20 faces (like the dice you use in Dungeons and Dragons), although they don’t necessarily have to have that exact shape. One icosahedral virus you may know personally is the rhinovirus (which causes the common cold). Enveloped viruses have a membrane that surrounds their capsid, which is produced from bits of a cell’s membrane modified with viral proteins. The HIV virus is an enveloped virus, as most animal viruses tend to be. Finally we have head and tail viruses, which have a ‘head’ similar to icosahedral viruses and a ‘tail’ that resembles filamentous ones — they often infect bacteria.

Filamentous viruses are also known as ‘helical’, as their capsomers are arranged around a coil of genetic material, forming a helix. Them, alongside icosahedral viruses are sometimes called ‘simple’ viruses, while head and tail ones (or other shapes) are known as ‘complex’ viruses.

Image credits ZMEScience.

The presence of a membrane can help facilitate infection and provide protection against the host’s immune system (as it’s made from pilfered parts of cells). Enveloped viruses tend to rely completely on their membrane for infection. Its glycoproteins exploit cells’ natural pathways through the membrane to allow infections. They act as ‘keys’ to the protein ‘locks’ that are typically employed to allow nutrients or other elements through the lipid layers of the membrane. But through this, they become vulnerable to inactivation by compounds that interact with fats, such as soap. This is the case for the coronavirus, for example, which is why handwashing is so effective against it.

All of this is very swell, to be sure, but why are viruses so interested in getting inside cells? So glad you asked — here’s why:

The viral life cycle

The central idea to keep in mind here is that viruses aren’t technically alive. They have some of the trappings of living things — genetic material, they’re made of organic matter — but they also lack most essential elements of life, most notably the ability to reproduce by themselves. But that’s all fine and dandy, as far as viruses are concerned, because everyone else can do it for them.

Think of viruses as weaponized USB sticks. For the most part, they’re inert. Viruses have no metabolism, they don’t expend energy, they don’t move on purpose and they don’t chase their prey. They just float around, and every infection begins with a random encounter between a virus and a host. Once they make contact with an appropriate cell, a six-step process unfolds: attachment, penetration, uncoating, replication, assembly, and release.

Attachment and penetration are pretty self-explanatory. They involve the virion coming into contact with and attaching to the host cell, and the subsequent penetration through its membrane. Attachment is governed by the type of binding proteins on the capsid and the transfer proteins on the cell wall — if they’re compatible, the process can unfold. Penetration involves the transfer of viral genetic material through the membrane, which leaves the capsid outside the cell; in this step, the virion basically injects its genetic data into the host cell. Note that some enveloped viruses use other tricks to get inside the cell, most notably by fusing their membranes with that of the cell or tricking it into eating the virus. Once inside, the capsid degrades and the genetic material is released, representing the Uncoating phase.

An example of an enveloped virus infecting a cell.

In regards to this genetic data, first know that it can be either DNA or RNA (some virions that carry RNA are known as ‘retroviruses’). Viruses can carry single or double strands of DNA (‘ssDNA’ or ‘dsDNA’ viruses respectively) or RNA (‘ssRNA’ or ‘dsRNA’). Single strands can be either sense or antisense. Sense strands are those used actively as instructions to create proteins (messenger RNA, or ‘mRNA’), while antisense RNA are their mirror complementaries and serve as a template to create strands of mRNA.

Now, the moment we’ve all been waiting for: what does this genetic material encode? Well, the complete information on how to build the virus, naturally! Once the viral material enters the cell, it will hijack its ‘code’ to make it produce more viral genetic material, capsid elements, and anything else that is needed to Replicate the original virus. DNA viruses typically use a cell’s biochemical machinery to create more DNA (for the new viruses) that is then transcribed into mRNA, and this mRNA is used to start protein synthesis. RNA viruses use their genetic code as a direct template for more RNA (for the new viruses) and mRNA that is consumed in protein synthesis. Retroviruses such as HIV contain RNA that must first be copy-pasted into the host’s DNA — but they also have the right protein, ‘reverse transcriptase’, for the job.

If a cell lacks the know-how required to build these various elements, the viral genome instructs it on what needs to be done. This is best exemplified by retroviruses. Reverse transcription or retrotranscription involves turning a strand of RNA into a double-strand of DNA which is then inserted into the host genome; in very broad lines, it’s reverse-engineering, like creating a full blueprint on how to build a car by just looking at the car. Very nifty. Bacteria and cells do use reverse transcription, but typically for what could be considered data maintenance work. It’s unclear whether this is a natural ability of all cells or if it was inherited from ancient viruses that grafted the needed genes into their hosts (which goes to show that viruses can be a driver of evolution).

The bits and pieces that the cell creates will spontaneously self-Assemble into new virions inside the cytoplasm. Finally, they Release (or ‘egress’) out of the cell. Exactly how this takes place varies from strain to strain. Some viruses (especially enveloped ones, including HIV) gradually exit the cell through budding — a process through which they also gain their membrane covering — which keeps the host cell alive. Most commonly, however, virions are released when the cell is so full of viruses that it bursts open (and dies in the process).

Lytic vs Lysogenic

Now, viruses may seem evil, but they’re not out to kill you. In fact, they will occasionally put in the effort to not hurt their host, especially during times when prey cells are rare and harder to find.

The process of a cell ripping apart, the breaking down of its membrane, is known as ‘lysis’. Under normal circumstances, virions follow the lytic cycle, which is the one described above that ends in the death of the cell. Such an event sees several hundred virions released from the dying cell, around 100 to 200 individual particles, as a rule of thumb.

The lysogenic cycle is a bit more covert — it produces something known as a ‘temperate’ or ‘non-virulent’ infection. Through the lysogenic cycle, a virion lies dormant and hidden inside the host cell genome, waiting for the right time to strike. During this time, it uses inhibitor genes so that the host cell doesn’t read the viral information, leaving it free to hang around unimpeded. The cell also profits by gaining immunity from reinfection with the same virus.

But when the cell experiences some kind of stressor (such as exposure to UV light or chemical agents) that weaken these inhibitors, its automatic DNA-repair systems detect the intruder, activate, and cut it out of the genome. After this point, the viral genetic material activates and the steps of replication, assembly, and release resumes as per normal conditions, and the infection spreads.

Why are viruses a thing?

We don’t really know. They’re too simple for us to reliably extract information on their evolutionary history from them. They’re not exactly alive, but they can and do evolve and mutate when reproducing in cells. They also have an annoying habit of copy-pasting genes from and onto their hosts, which further muddies the waters.

What we do know is that they are the single most successful group on the planet. A paper published in the journal Nature in 2011 puts their immense scale into perspective. Although it cautions that these estimates are “mostly based on ‘back of the envelope’ calculations and should therefore be viewed as they were intended: ballpark figures aiming to inspire”, they’re still no less impressive.

“If all the 1 × 1031 viruses on earth were laid end to end, they would stretch for 100 million light years. Furthermore, there are 100 million times as many bacteria in the oceans (13 × 1028) as there are stars in the known universe. The rate of viral infection in the oceans stands at 1 × 1023 infections per second, and these infections remove 20–40% of all bacterial cells each day.”

“There are about 200 megatonnes of carbon in viruses in the ocean, which is equal to about 75 million blue whales,” explains Curtis Suttle, a Distinguished University Scholar and Professor at the University of British Columbia in another paper. “In fact, in a litre of coastal seawater there are more viruses than there are people on the planet.”

“If aliens randomly sampled Earth they would see a planet dominated by microbial life, most of which would be viruses,” Suttle adds. “On average, there are about 10 million viruses and a million bacteria per litre of seawater or freshwater. If we compare the number of viruses in the oceans to the number of stars in the universe, there are about 1023 stars in the universe [and] about 10 million-fold more viruses in the ocean.”

These numbers showcase why humanity can never truly hope to ‘defeat’ viruses — it hasn’t ever been an option. But one of the best, and perhaps most chilling ways to illustrate this is the legacy viruses have left in us.

Viruses have, to the fullest extent of the word, become a part of us. It’s estimated that around 8% of the genome of modern humans is viral, meaning it has been passed from a virus into a cell, down through the generations, and we still carry that around. By contrast, only between 1% and 2% of our genome was inherited from the Neanderthals.

We are more ‘virus’ than we are our closest relatives.

Study finds new genetic editing powers in squids

Usually described as elusive, squids are highly skillful animals. They have bilateral symmetry, gills that are used for breathing, and skin covered with chromatophores, pigment-containing and light-reflecting cells through which they can camouflage to the environment.

Credit Wikipedia Commons

Now, scientists have discovered another surprising feature of squids. Not only they can edit their RNA or genetic instructions within the nucleus of their neurons but also within the axon, which are the neural projections that transmit electrical impulses to other neurons.

DNA and RNA are the most important molecules in cell biology, responsible for the storage and reading of genetic information that underpins all life. While DNA replicates and stores genetic information, RNA converts the genetic information contained within DNA to a format used to build proteins.

Back in 2015, a group of researchers discovered that squids were able to change their RNA instructions, fine-tuning the type of proteins to be produced. Now, they were able to dig deeper into their work and observe the edits outside the nucleus of the cell of the squids.

“We thought all the RNA editing happened in the nucleus, and then the modified messenger RNAs are exported out to the cell,” says Rosenthal, senior author. “Now we are showing that squid can modify the RNAs out in the periphery of the cell. That means, theoretically, they can modify protein function to meet the localized demands of the cell.”

In the past, Rosenthal and his group of researchers also worked in cuttlefish and octopus, which they discovered also rely on the editing of RNA to diversify the proteins they produce in the nervous system. Alongside the squid, this group of animals is known for its sophisticated behavior.

The findings could have implications not only for squids but also for humans, as the axon dysfunction is associated with neurological disorders. Researchers hope the study will help biotech companies use the RNA editing process in humans for therapeutic benefits.

“The idea that genetic information can be differentially edited within a cell is novel and extends our ideas about how a single blueprint of genetic information can give rise to spatial complexity. Such a process could fine-tune protein function to help meet the specific physiological demands of the different cellular region,” the researchers wrote.

The paper was published in Nucleic Acids Research.

How plants decide when to flower and when to grow

An ancestral plant could help researchers understand when and why plants start to blossom.

Depiction of liverworts from Ernst Hackel‘s Kunstformen der Natur, 1904.

It’s easy to think that flowers have been around forever, but they actually haven’t been around for that long — well, in geological time at least. Flowering plants have emerged some 130 million years ago, during a period called the Cretaceous; for comparison, sharks have been around for more than 3 times that period. However, although flowering plants appeared relatively late (the first land plants emerged more than 700 million years ago), they are the most diverse group of land plants.

The act of flowering (which is essentially producing the plant’s reproductive structure) is quite complicated though. The transition to flowering is one of the biggest changes that a plant makes during its lifecycle. The time needs to be right, the environmental conditions need to be right, and the plant needs to have sufficient resources to trigger the changes. Without the environmental cues that trigger changes in the plant’s hormones, without a cold period to trigger vernalization, plants just don’t flower.

In some cases, plants choose to invest the energy for flowering into growing bigger. It’s kind of like a fallback investment: you don’t get to reproduce, but you get bigger, you’ll presumably have access to more energy and nutrients, and you’ll reproduce more the next time.

But not only flowering plants have to make this decision. In order to assess when this happens, a team of researchers working in Japan studied liverwort, a descendant of the first plants to move out of the ancient oceans and onto land.

Liverwort grows all over the world. It looks a bit like moss and also prefers the shady and cool environments that moss thrives in. Liverwort and moss are part of a group called Bryophyta. They don’t produce flowers and instead reproduce through spores, but fundamentally, the decision they must make is the same — although there are major differences, reproduction is always “expensive” in the plant world.

Healthy female Marchantia polymorpha liverworts develop distinctive umbrella-shaped structures when they are ready to reproduce. Image by Caitlin Devor, University of Tokyo.

The reason why researchers studied liverwort is that it has a relatively simple genome structure, especially compared to the plants most commonly used in this sort of study, like tobacco and Arabidopsis. The entire genome of the liverwort species Marchantia polymorpha was also sequenced in 2017 which further aided this study.

“Liverworts have the maximum power with the least structure,” said Professor Yuichiro Watanabe from the University of Tokyo’s Department of Life Sciences, an expert in plant molecular biology.

The team looked at microRNA — small molecules which regulate the activity of other genes. They found over 100 types of this molecule, and 8 of them were almost identical to microRNA found in Arabidopsis (which is a flowering plant).

This is particularly interesting. Why would the same gene-regulating mechanisms be found in an ancestral plant like liverwort and also in a modern plant which evolved hundreds of millions of years later?

“So, why keep them? We want to know what those shared microRNAs are doing, and liverworts are now a convenient model for us to investigate,” said Watanabe.

They found that one of the common microRNAs was helping plants control the shift to the reproductive stage. To test that it was indeed responsible for this change, they engineered a modified version of this microRNA. This confirmed their theory, and what happened was pretty weird: these modified liverworts produced reproductive cells on their vegetative tissues, rather than exhibiting normal growth.

“This was amazing to us. Those liverworts skipped some part of the reproductive process and the body itself becomes the reproductive organ,” said Watanabe.

Liverworts normally sprout distinctive male (top row, left) and female (bottom row, left) structures when they reproduce. When researchers genetically modify the plants to lack microRNA156/529, the plants develop reproductive organs on their vegetative structures, which are called thalli. Normal thalli (center) are solid green with smooth edges. MicroRNA156/529 knockout male thalli (top right) are transparent at the edges and microRNA156/529 knockout female thalli (bottom right) develop irregular edges. Image credit: Tsuzuki et al., 2019.

Watanabe imagines that in the future, farmers could measure the amount of microRNA in crops to predict harvest times.

“We hope our results inspire others to develop new applications for plant reproduction,” said Watanabe.

Journal Reference: Tsuzuki et al., 2019, DOI: 10.1016/j.cub.2019.07.084.

We’re all familiar with DNA, but what about its lesser-known brother, RNA? Close in concept, but very different in purpose, these two types of nucleic acid areessential to our biology. So, what is RNA, or, Ribonucleic acid?

A visual representation of RNA coding. Credit: Thomas Splettstoesser on Wikimedia Commons

RNA’s Purpose

While DNA encodes your genes, RNA is important for how those genes get expressed. During the process of transcription, RNA is created by reading DNA with something called RNA polymerase.

The most important subtype of RNA is mRNA, which stands for messenger RNA. This type of mRNA carries the information from the DNA and goes over to ribosomes in order to create proteins. And proteins are the molecules that actually go forth and make changes in the body.

The central dogma of molecular biology. Credit: Madprime on Wikimedia Commons.

So, it’s sort of like DNA is a booklet containing all possible instructions for how to make things in the body, RNA are copies of only the relevant information for what the body needs right now, and proteins are the workers that go out and make it happen. This is known as the central dogma of molecular biology.

RNA vs DNA

A visual representation of the primary differences between RNA and DNA. Credit: Verwendete Bilder on Wikimedia Commons.

RNA and DNA have a surprising number of similarities. And it makes sense: RNA is literally copying itself from that main template.

For example, RNA and DNA both are made up of four nucleotide building blocks. DNA is made up of G, T, A, and C. RNA is similar, but substitutes the T (thymine) for U (uracil). Uracil actually looks just like thymine but lacks one methyl (CH3) group that thymine has.

DNA is double-stranded, but RNA is just one strand (it can form double strands but this isn’t RNA’s normal state). It’s easier to stay this way because it’s a much shorter strand of molecules. Why? In its single-stranded form, it’s genetically cheaper to make (half the material) while still containing all of the information (after all, if one always pairs with the other then you know exactly what that other strand had to be). Also, it’s easier to read. We actually have to unzip the DNA helix in places in order to access the code within, while RNA already comes in a form that’s open and easy to read.

Finally, they have different backbones. DNA is held together by deoxyribose, the sugar-phosphate backbone holding all of those nucleotides in order. RNA’s backbone is made up of ribose. Ribose is a lot like deoxyribose but has an additional hydroxyl (OH) group. So, deoxyribose is just de-oxygenated ribose, because it doesn’t have that oxygen.

Special Types of RNA

When most people think of RNA, they think of mRNA. But there are several additional subtypes of RNA that each have special functions.

The process of creating mRNA wouldn’t be possible without other forms of RNA. Transfer RNA (tRNA) is required to bring amino acids to the ribosome. In the ribosome, ribosomal RNA (rRNA) links together amino acids so they can create proteins. Taken together, tRNA, rRNA, and mRNA are referred to as coding RNAs because they all work together to encode proteins.

A visual depiction of translation machinery. Credit: NHS HEE Genomics Education Programme on Flickr.

Most noncoding RNA performs regulatory functions. The most popular of this category are microRNA (called miRNA or miR). These miRNAs can pair with single-stranded mRNA. When it does so, these mRNAs are tagged to be degraded. Therefore, miRNA can tag mRNA and shut down protein translation. So miRNA is usually used to control the amount of protein being produced from mRNA.

There’s also a very similar subtype called small interfering RNA (siRNA) which tags RNA for degradation right after transcription. It can be used to prevent any protein from being created. In addition, siRNA is often artificially used in labs to prevent certain proteins from being created and then see how this affects other biological processes.

siRNA mechanism of action. Credit: Singh135 on Wikimedia Commons.

Enhancer RNA (eRNA) was only first discovered in 2010. They are transcribed from “enhancer” regions of DNA – regulatory sites known to enhance gene expression. These eRNAs are also used to up-regulate the amount of mRNA produced from that DNA segment.

Small nucleolar RNA, called snoRNA, helps chemically modify other groups of RNA. They may help add either a methyl group (CH3), a process called methylation. Or they can turn one of the nucleotides into a uridine, a process called pseudouridylation.

Finally, there are long non-coding RNAs (lncRNAs). They are thought to silence long stretches of DNA. They also are thought to be involved in regulating stem cell division very early on in life.

What is RNA? Now You Know!

Now you’ve learned all about the mysteries of RNA. While not as widely known as DNA and not as flashy as protein function, it still remains one of the three cores of molecular biology. Life couldn’t exist without it. In fact, RNA is often thought to potentially be responsible for forming all life.

Breast cancer cells. Credit: Wikimedia Commons.

Scientists find genetic kill switch that destroys cancer cells without the need for chemotherapy

Scientists say they’ve found a molecular kill switch that when activated destroys cancer cells. According to new research, microRNA can be used to send cancerous cells a self-destruct message which they cannot ignore. By incorporating this mechanism into a new treatment, it could be possible to rid the body of cancer without having to go through the pain of chemotherapy.

Breast cancer cells. Credit: Wikimedia Commons.

Breast cancer cells. Credit: Wikimedia Commons.

Cells are always created and destroyed in the human body. About 300 million cells die every minute in our bodies and are replaced with new ones. This is to protect the body against potentially malfunctioned aging cells or diseased cells. The problem is that cancer cells can survive because they have the ability to ignore the immune system’s self-destruct instructions. But that doesn’t necessarily mean that there’s no way to relay this message to cancer cells.

Previously, researchers at Northwestern University described a mechanism by which every cell in the body can be programmed for destruction. Now, the same research team has reported that they’ve managed to crack the ‘code’ required to initiate this sequence.

Writing in the journal Nature Communications, the authors reported that the instructions of cell death are available as information in ribonucleic acid (RNA) and in microRNAs. Specifically, they used small-interfering (si)RNAs to trigger toxicity in cancer cells, a process normally activated by chemotherapy. Before they arrived at the winning formula consisting of six nucleotides (6mers) present in small RNAs, the researchers tested 4,096 different combinations of nucleotide bases.

The molecules used in the study put stress on several genes in cancerous cells, initiating the self-destruct sequence for four tested human and mouse cell lines. Because the molecules simultaneously destroy multiple genes that the cells need to survive, the cancer is unable to develop resistance.

“Now that we know the kill code, we can trigger the mechanism without having to use chemotherapy and without messing with the genome. We can use these small RNAs directly, introduce them into cells and trigger the kill switch,” said lead author Marcus E. Peter, professor of cancer metabolism at NU Feinberg School of Medicine.

In 2018, an estimated 1,735,350 new cases of cancer will be diagnosed in the United States and 609,640 people will die from the disease. The most common cancers (listed in descending order according to estimated new cases in 2018) are breast cancer, lung and bronchus cancer, prostate cancer, colon and rectum cancer, melanoma of the skin, bladder cancer, non-Hodgkin lymphoma, kidney and renal pelvis cancer, endometrial cancer, leukemia, pancreatic cancer, thyroid cancer, and liver cancer.

To treat cancer, doctors usually turn to chemotherapy with one or more cytotoxic antineoplastic drugs. The problem with chemotherapy is that it leads to horrible side effects because it also damages healthy cells. 

By incorporating the molecular messengers identified by the new study into a new therapy, researchers hope to rid patients of cancers without having to deal with chemo’s debilitating side effects. It may take many years before this happens, but the promising results suggest that one-day cancer could be treated safely.

DNA structure.

CRISPR-Cas9 scissors can cut through both DNA and RNA

DNA structure.

Image: public domain.

CRISPR-Cas9 technology has the potential to dramatically alter our environment and livelihoods. This powerful tool can cut out portions of DNA — the molecule that contains the blueprint of life — with such precision that unwanted genes, and only those genes, can be removed from the genome.

The possibilities are virtually endless. Using CRISPR-Cas9, scientists can engineer crops faster and more efficiently than ever or even potentially eradicate genetic diseases in humans. It’s even spilled over into the designer babies topic, starting a whole ethical debate regarding the use of CRISPR.

Now, scientists in Germany have shown that the genetic slicing tool can also target RNA, with potentially far-reaching ramifications.

The molecular scissor

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. Gene editing with CRISPR-Cas9 is still in its infancy despite its widespread use among the world’s foremost research institutes. It was only a couple years ago that scientists discovered that the foodborne pathogen Campylobacter jejuni has an ingenious immune system that recognizes and deletes foreign genomic material from invading viruses, protecting the bacteria’s genetic integrity.

Its immune system performs this feat with the help of guide-RNA, which leads the Cas9 protein to the site of foreign viral material. Once there, Cas9 targets and cuts the DNA. The guide-RNA and Cas9 can be pictured as a hand and scissors. Using artificial guides, scientists have been able to modify specific genes in bacteria, but also in plants and animals. There are already thousands of peer-reviewed papers focusing on CRISPR technology.

Researchers at the Julius-Maximilians-Universität Würzburg (JMU) and the Helmholtz Institute for RNA-based Infection Research (HIRI) recently showed that the CRISPR-Cas9 system isn’t limited to desoxyribonucleic acid (DNA). Instead, the protein can also target and cut related molecules such as ribonucleic acids (RNA).

“The finding was surprising, given that Cas9 is thought to naturally target DNA only,” said Prof. Chase Beisel, a researcher at HIRI and co-author of the new study, in a statement.

“We continue to be astounded by the many things that Cas proteins are capable of. They can target DNA, they can target RNA, they can target both at the same time. They can also do different things upon target recognition, such as activating domains that cleave any DNA or RNA they find or produce small molecules that can diffuse and interact with other proteins,” Beisel told ZME Science in an e-mail.

Due to its phenomenal versatility, Beisel likens Cas proteins to a swiss army knife. However, it wasn’t easy for the researchers to unlock this new capability.

“One of the challenges was that virtually all of the RNAs bound by Cas9 in Campylobacter jejuni exhibited only partial complementarity between the guide RNA and the bound RNA. There were few trends to predict which RNAs would be bound and then which would be cleaved. However, our moment of validation was designing synthetic guide RNAs and showing that they could predictably bind and cleave a target unrelated to any of the RNAs identified in Campylobacter,” Beisel said.

From the left: Prof. Dr. Cynthia Sharma, Sara Eisenbart, Thorsten Bischler, Belinda Aul from the Institute of Molecular Infection Biology (IMIB) and Prof. Dr. Chase Beisel from the Helmholtz-Institute of RNA-based Infection Research (HIRI) in Würzburg. Credit: Hilde Merkert, IMIB.

RNA is DNA’s discount cousin, but equally indispensable for life. Whereas DNA is double-stranded (the famous double helix), RNA is single-stranded. RNA’s primary role is to act as a messenger of genetic material within the cell. For instance, genes — information stored in DNA — are transcribed into RNA, which then serves as a template for the translation of the gene’s information into proteins. The ability to target both RNA and DNA with laser precision gives scientists access to all sorts of new opportunities, from controlling which genes are turned on or off, to annihilating RNA viruses.

This isn’t the first study that found Cas proteins can target RNA. Last year, two other research group reported similar findings, intriguingly using two different bacteria. This means that RNA-targeting is a general trait of the Cas9 protein, independent of the bacteria species from which it is sourced. What’s more, this new study goes a step forward because it uses Cas proteins that can target both DNA and RNA, which is a first, while the previously mentioned studies focused on proteins that exclusively targetted RNA, not DNA.

“This prior study worked with a different Cas protein called C2c2 (or Cas13a). This differs from our Cas9 protein because C2c2 only targets RNA, whereas our protein has the ability to target both DNA and RNA. In addition, C2c2 requires the presence of a flanking sequence, so it cannot target any sequence, whereas our protein did not have any requirements when targeting RNA,” Beisel wrote.

In the future, the researchers plan on investigating whether the CRISPR-Cas9 system plays others roles, apart from combating infection, in Campylobacter. For instance, is it also involved in turning genes on and off in the bacteria? The answer to this and other questions might reveal even more amazing insights about the most powerful genetic tool in our arsenal.

“Our work and that of other groups continue to find new capabilities — the equivalent of additional attachments within the swiss army knife — and I imagine that other capabilities await discovery,” Beisel concludes on an excited tone.

Scientific reference: Gaurav Dugar, Ryan T. Leenay, Sara K. Eisenbart, Thorsten Bischler, Belinda U. Aul, Chase L. Beisel, Cynthia M. Sharma: CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9; Molecular Cell, DOI: https://doi.org/10.1016/j.molcel.2018.01.032.

Novel cancer ‘assassin’ discovered: Huntington’s Disease

Researchers discovered a remarkable cancer cell poison: Huntington’s disease is exceptionally toxic to cancer.

Pictured: several neurons (yellow) that have a large central core with up to two dozen tendrils branching out of them. In Huntington’s disease, the core of the neuron in the foreground contains an orange blob about a quarter of its diameter. Credit: Wikipedia

Andrea Murmann, assistant professor of medicine at Northwestern University, had previously researched ancient kill-switches in all cells that destroy cancer. She found that repeating RNA sequences, known as small interfering RNAs (siRNAs), evolved in living organisms millions of years ago to fight cancer before the more complex adaptive immune system appeared.

Keeping this in mind, she started looking for diseases involving similar RNA mechanisms that also correspond with lower rates of cancer. Murmann and her team found that Huntington’s disease (HD) patients have up to 80 percent less cancer than the general population.

HD is caused by too many repeating RNA sequences in one gene, called Hungtin, present in every cell. These siRNAs attack genes that are critical for survival. Nervous cells had been considered the most vulnerable to this cellular attack, but this study shows that cancerous cells are even more vulnerable to siRNAs.

“I thought maybe there is a situation where this kill switch is overactive in certain people, and where it could cause loss of tissues,” says first author on the study Andrea Murmann in a press release. “These patients would not only have a disease with an RNA component, but they also had to have less cancer.”

The RNA molecules found in HD were very similar to the ones that the team had discovered in their previous research, so they thought: Why not test them and see if they have the same effect?

Researchers developed nanoparticles that were able to transport cancer-killing siRNAs through the bodies of mice with cancer. The results showed that tumors stopped growing in a huge variety of different cancer cell lines, such as ovarian, breast, prostate, liver, brain, lung, skin and colon cancer cells. Also, the tumors did not develop resistance to this form of cancer treatment.

“This molecule is a super assassin against all tumor cells,” say senior author Marcus Peter. “We’ve never seen anything this powerful.”

Now, researchers have to find out how to refine the nanoparticles, making them more target-accurate and more stable and storable. Of course, there is also the matter of neuron toxicity to be tackled by the scientists, although they believe that a short-term treatment with siRNAs would not affect brain tissue, mainly because in HD the patients are exposed to increased levels of siRNAs several decades until clinical signs show up. Usually, HD patients develop the first symptoms around the age of 40.

“We believe a short-term treatment cancer therapy for a few weeks might be possible, where we could treat a patient to kill the cancer cells without causing the neurological issues that Huntington’s patients suffer from,” says Marcus Peter.

The research was supported in part by funding from the National Institutes of Health/National Cancer Institute and The Northwestern University Feinberg School of Medicine Developmental Therapeutic Institute and was published in the journal EMBO Reports.

 

Artist impression of early Earth atmosphere. Credit: Peter Sawyer.

Experiment mimicked Earth’s early atmosphere hit by extraterrestrial impact. It produced all four RNA bases

Artist impression of early Earth atmosphere. Credit: Peter Sawyer.

Artist impression of early Earth atmosphere. Credit: Peter Sawyer.

Researchers from France and the Czech Republic put a spin on a seminal science experiment that recreates the conditions necessary for life to appear. They mimicked Earth’s early atmosphere as it was impacted by cosmic bodies like meteorites and found the interaction produced all the four based of RNA, which is chemically related to DNA and just as essential to life. The findings support the RNA World and the Origins of Life hypothesis, according to which RNA stored both genetic information and catalyzed the chemical reactions in primitive cells.

Back in the 1950s, two biochemists named Stanley Miller and Harold Urey sealed a mixture of gases that modeled Earth’s early atmosphere as scientists assumed it must have been like at the time, then zapped electricity through the brew. The experiment showed that several organic compounds could be formed spontaneously this way from inorganic compounds, including amino acids — which are the building blocks of proteins.

The Miller-Urey experiment was a total hit and the findings traveled the global instantly, as it was the first study to add some tangible evidence to the theory that life first appeared spontaneously.

Schematic of the Miller-Urey experiment.

Schematic of the Miller-Urey experiment.

As years past, however, the Miller-Urey experiment passed out of favor among scholars, though to this day it’s one of the most widely enacted experiments in high schools and universities around the world. Fred Hoyle, an astrophysicist, once compared the likelihood of life appearing on Earth by chemical reactions “as equivalent to the possibility that a tornado sweeping through a junkyard might assemble a Boeing 747 from the materials therein”. Critics have argued that even though amino acids can provide the necessary primitive biochemistry for proteins to form, you need more than just proteins to activate a cell’s catalytic chemistry. Miller and Urey couldn’t have known at the time, but both RNA and DNA seem to be heavily involved in biochemistry.

Another problem with the Miller-Urey experiment was that it assumed Earth’s early atmosphere was ‘reducing’, the opposite of today’s ‘oxidizing’ one. Since then, researchers now largely presume our planet’s early atmosphere was neutral, somewhere in between reducing and oxidizing.

But this textbook experiment isn’t done yet. Researchers gave a new spin on the experiment to add something Miller and Urey hadn’t originally considered: impacts from cosmic bodies, an extremely common occurrence on primordial Earth.

In the new study, the researchers argued that Earth’s atmosphere from 3.6 billion years ago was a bit on the reducing side, which is somewhat different from the atmosphere used by Millet-Urey but still relevant. The aim of the study was to monitor the gases for formamide, a compound made of carbon, nitrogen, and oxygen, with hydrogen in between. Previously, research showed that under the right conditions, formamide can react with itself to produce all the four RNA bases.

To mimic the shockwaves produced by an extraterrestrial impact, the researchers turned to the Prague Asterix Laser System which can generate Terawatt-sized pulses. The shock waves caused chemical reactions that went on to form formamide and, eventually, all the four RNA bases, albeit in minute quantities — barely above the detectable limit, but that’s Ok since a real impact would have been much more powerful.

“We show that RNA nucleobases are synthesized in these experiments, strongly supporting the possibility of the emergence of biologically relevant molecules in a reducing atmosphere. The reconstructed synthetic pathways indicate that small radicals and formamide play a crucial role, in agreement with a number of recent experimental and theoretical results,” the team wrote.

The findings published in PNAS support the RNA World theory, which posits bacterial cells cannot form from nonliving chemicals in one step. Instead, there must be intermediate forms, “precellular life,” and RNA is the leading contender because it has the ability to act both as an enzyme and encode genes. This offers a way around the “chicken-and-egg” problem (Genes require enzymes; enzymes require genes). While the sort of atmosphere assumed by the study is debatable, it’s exciting to hear about a plausible route for producing the basic building blocks of RNA and life eventually.

[via ArsTechnica]

 

A major difference between DNA and RNA could explain why one is the go-to blueprint for life

A new study could finally explain why our cells rely on DNA, and not its molecular relative RNA, to store and pass on genetic data. The findings show that RNA breaks apart when it tries to incorporate changes — such as chemical damage to the molecule — while DNA can twist and bend its shape to allow for changes.

Image via pixabay

The most important thing for any living thing on Earth is to pass on its genes to offspring. Life everywhere feeds, fights and flees all in the hopes that it can eventually bring about more life in its image. But all that effort would be for nothing if genetic information couldn’t be safely stored for when it’s needed. Two molecules are responsible for carrying this information — RNA, which is a simpler single-strand molecule, and DNA which is a more complex double-strand molecule.

But up to now no one really knew why most cells favor DNA to store this genetic data over RNA. But a new study lead by Hashim Al-Hashimi from the Duke University School of Medicine might have found the answer: DNA can accommodate damage in its structure which would cause RNA to break down.

“For something as fundamental as the double helix, it is amazing that we are discovering these basic properties so late in the game,” said lead researcher .

“We need to continue to zoom in to obtain a deeper understanding regarding these basic molecules of life.”

You’re probably familiar with the double-helix model of DNA. When they first proposed it in 1953, Watson and Crick predicted how the base pairs ( A&T. C&G ) bind to form up the whole. Two strands of DNA line up and link by bonding these pairs, and end up looking kind of like a ladder with the bonds being the rungs.

So these bonds were called Watson-Crick base pairs. But researchers struggled to find evidence that the pairs were binding in the way Watson and Crick predicted. Then in 1959, biochemist Karst Hoogsteen took a picture of an A–T base pair, finding a more skewed geometry than expected, with one base rotated 180 degrees relative to the other — and these were called Hoogsteen pairs. In more recent times, researchers have observed both Watson-Crick and Hoogsteen base pairs in images of DNA.

Al-Hashimi and his team stumbled onto something five years ago that no one has ever observed before: DNA pairs that shift back and forth between Watson-Crick and Hoogsteen bonds. They found that DNA employs Hoogsteen bonds when there’s a protein bond to a DNA site – or the bases suffered chemical damage. Once the damage is fixed or the protein is released, the DNA goes back to Watson-Crick bonds. The discovery was big in itself, but now the team has shown that RNA doesn’t have the ability. This could explain why DNA forms the blueprint — it can absorb chemical changes and repair damage, RNA becomes too stiff and falls apart.

“In DNA this modification is a form of damage, and it can readily be absorbed by flipping the base and forming a Hoogsteen base pair. In contrast, the same modification severely disrupts the double helical structure of RNA,” said one of the team, Huiqing Zhou.

“The finding will likely rewrite textbook coverage of the difference between the two purveyors of genetic information, DNA and RNA,” said a Duke University press release.

DNA (left) can form Hoogsteen bonding to incorporate damaged base-pairs, while RNA (right) falls apart in the same case.
Image credits Huiqing Zhou.

The team figured this out by using RNA and DNA molecules to create double-helices, then observed how their base pairs form bonds using advanced imaging techniques. At any one time, around 1 percent of DNA bases were shifting into Hoogsteen pairs, they found. The RNA strands however didn’t do the same.

They tested RNA double-helices under a host of conditions, but couldn’t determine them to naturally form Hoogsteen pairs. When they forced the molecules to form such pairs, the RNA strands fell apart completely. This happens because RNA double-helices are more tightly packed than DNA, and can’t change direction without hitting something or shifting atoms around, which makes the structure critically unstable.

“There is an amazing complexity built into these simple beautiful structures, whole new layers or dimensions that we have been blinded to because we didn’t have the tools to see them, until now,” said Al-Hashimi.

Further research is needed to determine if DNA’s flexibility compared to RNA is what lead to it becoming the go-to molecule for storing genetic data, but if confirmed, it could help us understand why life on Earth evolved into what we see today.

The full paper, “Scientists have just uncovered a major difference between DNA and RNA” has been published in the journal Nature Structural & Molecular Biology.

Key findings help unravel journey from inanimate chemistry to life

In the beginning, the Earth’s surface was a lifeless, hot, but chemically rich place. In these harsh conditions, the first amino acids synthesized from inorganic compounds, and from them, proteins formed. They built the first single cells, which went on to form plants and animals. Recent research helps us understand the process that created amino acids, and there is a widespread consensus in the scientific community as to the path cells took to evolve to complex life as we know it today. But there is a missing link in the chain of events that ties lifeless to life: how and why did amino acids form the proteins that underpin the functions of every cell?

University of North Carolina scientists Richard Wolfenden and Charles Carter have shed new light on how the building blocks came together to form life some 4 billion years ago.

“Our work shows that the close linkage between the physical properties of amino acids, the genetic code, and protein folding was likely essential from the beginning, long before large, sophisticated molecules arrived on the scene,” said Carter, professor of biochemistry and biophysics at the UNC School of Medicine. “This close interaction was likely the key factor in the evolution from building blocks to organisms.”

Their findings, published in companion papers in the Proceedings of the National Academy of Sciences, contravene the traditional yet problematic “RNA world” theory, which posits that RNA -implicated in various biological roles in coding, decoding, regulation, and expression of genes- came into existence from the primordial pool, created the first simple proteins, peptides, and thus led to the creation of the first cells; in fact, they argue, it’s just as likely that peptides catalyzed the creation of RNA as the polymeric molecule was to lead to the formation of these simple proteins.

A strand of RNA Image via: miltenyibiotec.com

A strand of RNA, the first records of genetic information.
Image via: miltenyibiotec.com

The scientific community places the last universal common ancestor of all life on Earth, dubbed LUCA, at about 3.6 billion years ago. LUCA was most likely a single-cell organism, had a few hundred genes which stored the blueprints for DNA replication, protein synthesis, and RNA transcriptions. It had the basic components that modern organisms have, such at lipids. In other words, it had all the traits we expect to find in complex life today. After LUCA, it’s relatively easy to see how modern life evolved. But there is little hard evidence of how LUCA came into being.

We know a lot about LUCA and we are beginning to learn about the chemistry that produced building blocks like amino acids, but between the two there is a desert of knowledge,” Carter said. “We haven’t even known how to explore it.”

Dr. Wolfenden’s and Dr. Carter’s research aims to bridge the knowledge gap. It creates a model where RNA did not have to just pop into existance, and shows how even before there were cells, it seems more likely that there were interactions between amino acids and nucleotides that led to the co-creation of proteins and RNA.

“Dr. Wolfenden established physical properties of the twenty amino acids, and we have found a link between those properties and the genetic code,” Carter said. “That link suggests to us that there was a second, earlier code that made possible the peptide-RNA interactions necessary to launch a selection process that we can envision creating the first life on Earth.”

In order to function properly, proteins must fold in certain ways. The first PNAS paper, led by Wolfenden, shows that both the polarities of the amino acids (how they arrange themselves between water and oil) and their sizes help explain the complex process of protein folding – how a chain of connected amino acids arranges itself to form a particular 3-dimensional structure that has a specific biological function.

“Our experiments show how the polarities of amino acids change consistently across a wide range of temperatures in ways that would not disrupt the basic relationships between genetic coding and protein folding,” said Wolfenden, Alumni Distinguished Professor of Biochemistry and Biophysics.

This is an important piece of information, as when life started to form, in early-Earth conditions, temperatures were much hotter than when the first plants and animals appeared. If amino acid interaction changed with temperature in such a way as to interfere with genetic coding, the system would have stopped working when the planet cooled down.  Life could not had evolved based on these principles.

A series of lab experiments with amino acids showed that two properties, namely size and polarity of amino acids, were necessary but also sufficient to explain how they behaved in folded proteins and that the relationship between the two held at the temperatures Earth had 4 billion years ago.

In their second PNAS paper, lead by Carter, they analyse how aminoacyl-tRNA synthetases recognized the enzymes that translate the genetic code, named transfer ribonucleic acid or tRNA. It shows that each one of the two ends of the L-shaped tRNA molecule has specific rules on what amino acid to tie to. The end that carried the amino-acid selects the molecule based on size. The other end, named an anticodon, selects it based on polarity:

“Think of tRNA as an adapter,” Carter said. “One end of the adapter carries a particular amino acid; the other end reads the genetic blueprint for that amino acid in messenger RNA. Each synthetase matches one of the twenty amino acids with its own adapter so that the genetic blueprint in messenger RNA faithfully makes the correct protein every time.”

“Translating the genetic code is the nexus connecting pre-biotic chemistry to biology”, he added.

Their findings imply that the relationships between tRNA and the sizes and polarities of amino acids were crucial during the Earth’s early days. And basing on Carter’s work with the active cores of tRNA synthetases, called Urzymes, it seems likely that selection by size preceded selection after polarity. Because of this ordered selection, the earliest proteins did not have to fold into unique shapes, which evolved later. This would help explain two paradoxes: how complex structures arose from simple conditions, and how biology divided the work between proteins and nucleic acids, two very different structures.

The structure of DNA, RNA, and proteins.
Image via: exploringorigins.org

“The fact that genetic coding developed in two successive stages — the first of which was relatively simple — may be one reason why life was able to emerge while the earth was still quite young,” Wolfenden noted.

“The collaboration between RNA and peptides was likely necessary for the spontaneous emergence of complexity,” Carter added. “In our view, it was a peptide-RNA world, not an RNA-only world.”

An earlier structure, that would enable coded peptides to bind RNA, would have provided a decisive selective advantage. This simple system would then undergo a natural selection process, paving the way for new and more biological forms of evolution.

 

 

 

 

starvation

Genetic response to starvation is passed down to at least three generations

starvation

Photo: newgrounds.com

In 1944, the Nazis caused widespread famine in Western Netherlands after they blocked food supplies. A group of pregnant women living in the Netherlands, labouring under starvation conditions imposed by a harsh winter and food embargo, gave birth to relatively small babies. When their children grew up, in relative prosperity, to have children of their own their babies were unexpectedly small. This was the birth place of epigenetics – the study of genetic changes sparked by external factors that become passed down to subsequent generations. A new study may have discovered underlying  mechanism that transfers starvation response to future generations, after they studied food-deprived worms.

The famine that lingers

“There are possibly several different genetic mechanisms that enable inheritance of traits in response to changes in the environment. This is a new field, so these mechanisms are only now being discovered,” said Dr. Oded Rechavi of Tel Aviv University’s Faculty of Life Sciences and Sagol School of Neuroscience. “We identified a mechanism called ‘small RNA inheritance’ that enables worms to pass on the memory of starvation to multiple generations.”

RNA (ribonucleic acid) molecules differ from DNA molecules in several ways. RNA molecules are single-stranded, and their nucleotides contain ribose rather than deoxyribose sugar. Like DNA, RNA nucleotides each contain one of four organic bases, but whereas adenine, cytosine, and guanine nucleotides occur in both DNA and RNA, thymine nucleotides are found only in DNA. In place of thymine nucleotides, RNA molecules contain uracil nucleotides. A type of RNA, messenger RNA molecules (mRNA) instruct the production of certain proteins that allows cells to function properly. Basically, all RNA have a regulatory function with different types of RNA being involved in different types regulatory activity. Small RNAs are maybe the most intriguing – short molecules, hence the name, that regulate gene expression by shutting them on or off.

Dr. Rechavi first became interested in studying starvation-induced epigenetic responses following a discovery made as a post doctorate in Prof. Hobert’s lab at Columbia University Medical Center in New York. “Back then, we found that small RNAs were inherited, and that this inheritance affected antiviral immunity in worms. It was obvious that this was only the tip of the iceberg,” he said.

The researchers grew common worms (C.elegans nematodes) in a food-deprived environment and followed their genetic markup. They noticed the starved worms  responded by producing small RNAs, which function by regulating genes through a process that is known as RNA interference (RNAi). The researchers discovered that the starvation-responsive small RNAs target genes that are involved in nutrition and that these became inherited by at least three subsequent generations of worm specimens.

“We were also surprised to find that the great-grandchildren of the starved worms had an extended life span,” said Dr. Rechavi. “To the best of our knowledge, our paper provides the first concrete evidence that it’s enough to simply experience a particular environment — in this case, an environment without food — for small RNA inheritance and RNA interference to ensue. In this case, the environmental challenge is starvation, a very physiologically relevant challenge, and it is likely that other environments induce transgenerational inheritance of small RNAs as well.

“We identified genes that are essential for production and for the inheritance of starvation-responsive small RNAs. RNA inheritance could prove to be an important genetic mechanism in other organisms, including humans, acting parallel to DNA. This could possibly allow parents to prepare their progeny for hardships similar to the ones that they experience,” Dr. Rechavi said.

There are many reasons why this research is really important. It shows yet again how important external factors are to development and how quickly responses to significant changes or events in our lives are passed on to offspring. For instance, we know that fear and trauma are transmitted to our children and children’s children – even sexual promiscuity.

The findings were reported in the journal Cell.

Sperm RNA carries marks of trauma

Scientists have shown that trauma can leave epigenetic marks – chemical changes that affect how DNA is expressed without altering its sequence. Basically, your traumatic experiences genetically affect your offspring.

tiripero/iStock/Thinkstock

Scientists have recently focused on the long term after effects of trauma, finding them to be numerous and diverse. The offspring of traumatized people are at a high risk of depression and anxiety, may have higher suicide rates – but this is difficult to explain genetically; one could argue that the traumatized parent is indirectly responsible for this, through his/her behavior, which is in turn influenced by the trauma. Now, researchers found that stress in early life alters the production of small RNAs, called microRNAs, in the sperm of mice. The mice show depressive behavior for a long time, and so do their offspring.

The study is notable for showing that sperm can be influenced by the father’s mental state, says Stephen Krawetz, a geneticist at Wayne State University School of Medicine in Detroit, Michigan, who studies microRNAs in human sperm and was not involved with this study.

“Dad is having a much larger role in the whole process, rather than just delivering his genome and being done with it,” he says. He adds that this is one of a growing number of studies to show that subtle changes in sperm microRNAs “set the stage for a huge plethora of other effects”.

Isabelle Mansuy, a neuroscientist at the University of Zurich, Switzerland, and her colleagues periodically separated mother mice from their young pups and exposed the mothers to stressful situations. They subjected the mice to this torturous experience every day, but at erratic times, so that the mothers couldn’t comfort their children in advance – morally, I find this disturbing, but from a strictly scientific point of view, you can’t argue with the method they used.

The males which were raised this way showed depressive behaviours and tended to underestimate risk, the study found. Their sperm also showed abnormally high expression of five microRNAs. One of these, miR-375, has been linked to stress and regulation of metabolism. When it came to the following generation, they were also more depressive than their control counterparts, even though they were never subjected to any trauma. To rule out the possibility that the effects of stress were transmitted socially, the researchers also collected RNA from the F1 males’ sperm and injected it into freshly fertilized eggs from untraumatized mice. This resulted in similar depressive behaviors which were passed onto the next generation.

While there is still much to be discovered about the biological underlying mechanisms, this is the first study to show that traumatized mammals affect their offspring directly through the sperm.

Source: Nature.

Research suggests we use 4 times more DNA than previously believed

Less than 1.5 percent of our DNA is used in a conventional way, that is to encode for proteins – this was the common sense around this issue 10 years ago; recently, previous research has shown that 5-8% of the genome is conserved at the level of DNA sequence, indicating that it is functional, but we don’t really know exactly what it does. However, a new study conducted by Australian geneticisits suggests that much more (possibly up to 30%) is conserved, and actually used at the level of RNA structure.

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Credit: © Maridav / Fotolia

At a very basic level, DNA is the blueprint for our bodies – but it must be copied into another instance before it is actualised. The DNA molecule encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. Through a process called ‘transcription’, DNA is copied into RNA, some of which encodes the proteins that carries out various tasks required by our cells. Just like very small Lego blocks, RNA molecules bind with each other in very specific ways, creating a very complex 3D structure. Dr Martin Smith and Professor John Mattick, from Sydney’s Garvan Institute of Medical Research, have created a very complicated method of predicting these RNA structures.

“Genomes accumulate mutations over time, some of which don’t change the structure of associated RNAs. If the sequence changes during evolution, yet the RNA structure stays the same, then the principles of natural selection suggest that the structure is functional and is required for the organism,” explained Dr Martin Smith.

Using this method, they ultimately concluded that we actively use much more DNA for coding than previously believed.

“Our hypothesis is that structures conserved in RNA are like a common template for regulating gene expression in mammals – and that this could even be extrapolated to vertebrates and less complex organisms.”

“We believe that RNA structures probably operate in a similar way to proteins, which are composed of structural domains that assemble together to give the protein a function.”

“We suspect that many RNA structures recruit specific molecules, such as proteins or other RNAs, helping these recruited elements to bond with each other. That’s the general hypothesis at the moment – that non-coding RNAs serve as scaffolds, tethering various complexes together, especially those that control genome organization and expression during development.”

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Synthetic DNA and RNA that mimics chemistry of life can encode genetic information and evolve

Scientists at UK Medical Research Council’s Laboratory of Molecular Biology have successfully managed to create an artificial version of both DNA and RNA, fundamental biomolecules crucial to life. The synthetic nucleic acids are capable of encoding information and passing it on to the next generation, even with changes in the code with the help of an intermediate molecule, thus proving that these can also evolve! Besides the obvious implications in the field of synthetic biology, this breakthrough might greatly help scientists how life may form outside our solar system, as well as how the very first primitive life forms came to be on Earth.

DNAThe classic double-helix structure of DNA is like a twisted ladder, where the steps are made from paired nucleobases (RNA is typically a single helix). Its sides are chains of a sugar called deoxyribose (the D in DNA), connected by phosphate groups. The researchers’ synthetic versions use the same bases and the same phosphate groups, however their ladders were made using different sugars. Thus, Dr. Philipp Holliger and colleagues from the MRC Laboratory of Molecular Biology have developed six alternative polymers called xeno-nucleic acids, XNAs, that  can share information with DNA – and one, anhydrohexitol nucleic acid,or HNA, that can undergo directed evolution and fold into biologically useful forms.

“There’s a lot of chemisty that seeks to build alternative nucleic acids, and people have been modifying the bases, the sugars and the backbone, but what we were focusing on was the type of nucleic acid or polymers that would retain the ability to communicate with the natural DNA,” Dr Holliger  said.

Dr Holliger and his colleagues have tweaked  a natural enzyme called polymerase that efficiently transcribes the code of their synthetic DNA to natural DNA and then from that back to another synthetic DNA. The scientists started with a varied pool of polymerases, all slightly different, and all mixed with their own corresponding gene. Researchers observed  some were better at building nucleic acids with the weird sugar backbones than others. By selecting and filtering out the inefficient ones, the scientist quickly evolved enzymes that could assemble XNA strands from DNA ones.

“We’ve been able to show that both heredity – information storage and propagation – and evolution, which are really two hallmarks of life, can be reproduced and implemented in alternative polymers other than DNA and RNA,” Dr Holliger explained.

“There is nothing ‘Goldilocks’ about DNA and RNA – there is no overwhelming functional imperative for genetic systems or biology to be based on these two nucleic acids.”

DNA and RNA form the absolute basis of life, however its still unclear how they were first formed, as it is unlikely a primitive mixture of chemical elements would have suffice without some kind of intermediate stage. What this remarkable research proves is that the two nucleic acids aren’t unique in their abilities and variations could exist somewhere else in the Universe as well, which could branch in life forms significantly different than the ones encountered on Earth. Also, as the researchers conclude, the “construction of genetic systems based on alternative chemical platforms may ultimately lead to the synthesis of novel forms of life”.

Their findings were published in the journal Science.

BBC source

 

Biologists use DNA for calculating square roots

Biological systems have recently attracted the attention of mathematicians and computer scientists, who have been turning everything from quantum processes to RNA into logic gates. But before you get paranoid about DNA controlling Skynet, you have to know that these systems have only been successful on a small scale, calculating square roots on four-bit numbers, and each calculation took over five hours.

Today’s issue of Science jumps over small scale demonstrations, going directly into showing how a form of DNA computing can perform a calculation with up to 130 different types of DNA molecules involved. Despite its lack of speed, the system is incredibly flexible – flexible enough to allow the use of compilers and debugging circuitry.

Thing is, even though this technology isn’t exactly well suited for calculations, it can be integrated into biological systems, taking their input from a cell and feeding the output into biochemical processes. The authors of the papers are a biologist and a computer scientist from Caltech.

The system relies on what they have called “seesaw” logic gates, displayed above. The central feature of these gates is a stretch of DNA that can base-pair with many different molecules, allowing them to compete for binding. Even once a molecule is base-paired, it can be displaced; short “landing” sequences on either side allow a different molecule to attach, after which it can displace the resident one.

Because of the simplicity of logical operations and the fact that the rules of DNA base pairing are so straightforward they were able to generate a computerized model that told them what DNA molecules to acquire. In order to prove that it works, they constructed a system which calculated the floor of the square root of a four-bit binary number. The operation required 74 different single-stranded molecules of DNA, and during the time in which the operation was running, 130 different double stranded molecules existed in the same test tube.

A large number of biomolecules could be used as input here, including DNA, RNA, and small molecules. The authors also indicate that they have an idea on how to dramatically speed the process up – by using arge DNA scaffolds to assemble gates in close proximity to each other, ensuring that reactions take place quickly and require far less DNA to be used.

Via Wired, pictures via Ars Technica

Lifeless prions are capable of evolution

prionsup35Researchers from the Scripps Research Institute have determined for the first time that prions, which are just bits of infectious protein without any DNA or RNA that can cause fatal degenerative diseases are capable of Darwinian evolution.

This study shows that prions do develop significant large numbers of mutations at a protein level as a response to external influences, and through natural selection, they can eventually lead to mutations such as drug resistance.

“On the face of it, you have exactly the same process of mutation and adaptive change in prions as you see in viruses,” said Charles Weissmann, M.D., Ph.D., the head of Scripps Florida’s Department of Infectology, who led the study. “This means that this pattern of Darwinian evolution appears to be universally active. In viruses, mutation is linked to changes in nucleic acid sequence that leads to resistance. Now, this adaptability has moved one level down — to prions and protein folding — and it’s clear that you do not need nucleic acid for the process of evolution.”

This also started another discussion, well actually restarted it, that of the quasi-species. First launched 30 years ago, this idea basically suggest a complex, self-perpetuating population of diverse and related entities that act as a whole.

“The proof of the quasi-species concept is a discovery we made over 30 years ago,” he said. “We found that an RNA virus population, which was thought to have only one sequence, was constantly creating mutations and eliminating the unfavorable ones. In these quasi-populations, much like we have now found in prions, you begin with a single particle, but it becomes very heterogeneous as it grows into a larger population.”

“It’s amusing that something we did 30 years has come back to us,” he said. “But we know that mutation and natural selection occur in living organisms and now we know that they also occur in a non-living organism. I suppose anything that can’t do that wouldn’t stand much of a chance of survival.”