Doubling the DNA alphabet

Implications for life in the universe and DNA storage

Life on Earth is dictated by the DNA alphabet comprised of only four DNA bases or letters: A, T, G and C. It has long been of interest to understand whether there is something very special about the four letters that comprise DNA and whether this is the only code that could support life. At a basic level, this question can be addressed by examining an expanded alphabet and determining the properties of DNA including additional synthetic letters. This study impacts our current understanding of terrestrial DNA and suggests that extraterrestrial life forms could have evolved using a different genetic code than found here on Earth. The work has immediate applications in synthetic biology for the creation of new molecules and greatly expands the ability to store information in DNA.

Now, in breakthrough work, funded by NASA, NSF and NIGMS, Dr. Steven Benner at the Foundation for Applied Molecular Evolution, in collaboration with Dr. Millie Georgiadis at the Indiana University School of Medicine, and colleagues at biotechnology companies and other universities, have provided evidence that the standard DNA code can be expanded to include eight letters forming “hachimoji DNA” (“hachi” eight and “moji” letter in Japanese) using four novel synthetic nucleobases (B, S, P and Z) in addition to A, T, C and G and still retain critical features of natural DNA1,2. Structurally, hachimoji DNA can adopt a standard double helical form of DNA and retain Watson-Crick complementary base pairing, which allows the expanded DNA to be faithfully replicated and transcribed by polymerases to produce hachimoji DNA copies and hachimoji RNA. These properties are essential for a genetic system that can support life.

>Read more on the Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC website

Image: Crystal structure of a double helix built from eight hachimoji building blocks, G (green), A (red), C (dark blue), T (yellow), B (cyan), S (pink), P (purple), and Z (orange). The first four building blocks are found in human DNA; the last four are synthetic, and possibly present in alien life. Each strand of the double helix has the sequence CTTAPCBTASGZTAAG. Notable is the geometric regularity of the pairs, a regularity that is needed for evolution.

Structural insights into tiny bacterial harpoons

Bacteria produce complex nano-harpoons on their cell surface. One of their functions is to harpoon and inject toxins into cells that are close by. Producing such a complex weapon requires lots of different moving components that scientists are still trying to understand. Researchers from the University of Sheffield have been using some of Diamond’s crystallography beamlines to understand a particularly enigmatic piece of this tiny puzzle. The team led by David Rice and Mark Thomas worked on a protein component of the harpoon called TssA which they already knew was an integral piece of the machinery. However, unlike the other components of the harpoon, there are distinct variants of the TssA protein that contain radically different amino acid sequences at one end of the protein. The team showed that the structures of the variable region of two different TssA subunits were completely unrelated and they could assemble into distinctly different multisubunit complexes in terms of their size and geometry. This begged the question as to how different bacteria could use this protein with different structures to produce a harpoon with the same function across all species. They found that despite these differences, there was a very specific conserved region at the other end of the protein. They hypothesise that the conserved region is the part that does the work and helps the harpoon to function whereas the variable region acts as a scaffold. They used I02, I03 and I24 in their study and plan to do follow up work using X-ray crystallography and Cryo-EM such as those at the eBIC centre at Diamond. The research was published in Nature Communications.

>Read more on the Diamond Light Source website

Image: Macromolecular Crystallography (MX) at Diamond reveals the shape and arrangement of biological molecules at atomic resolution, knowledge of which provides a highly accurate insight into function. 

First users on VMXm

First users from the University of Southampton investigated proteins involved in nutrient uptake of photosynthetic or cyanobacteria to understand how these phytoplankton thrive under scarce nutrient conditions.

The work has immense global significance for biofuels production and biotechnology. This beamline marks the completion of Diamond’s original Phase III funding on time and within budget.

First users have now been welcomed by Diamond Light Source, the UK’s national synchrotron light source on its new VMXm beamline. The Versatile Macromolecular Crystallography micro/nanofocus (VMXm) beamline becomes the 32nd operational beamline to open its doors to users, completing the portfolio of seven beamlines dedicated to macromolecular crystallography.
The unique VMXm beamline represents a significant landmark for Diamond. It is a specialist tuneable micro/nanofocus macromolecular crystallography (MX) beamline, with an X-ray beam size of less than 0.5 microns, allowing even the tiniest of samples to be analysed. Integrated into the ‘in vacuum’ sample environment is a scanning electron microscope, making VMXm a hybrid X-ray/cryoEM instrument for detecting and measuring data from nanocrystals. VMXm is aimed at research applications where the production of significant quantities of protein and crystals is difficult.

>Read more on the Diamond Light Source website

Image: Principal Beamline Scientist Dr Gwyndaf Evans with his team Dr Jose Trincao, Dr Anna Warren, Dr Emma Beale and Dr Adam Crawshaw. First users – Dr Ivo Tews from Biological Sciences at the University of Southampton and joint Diamond-Southampton PhD student Rachel Bolton investigating proteins involved in nutrient uptake of photosynthetic or cyanobacteria.

Snaphot of molecular mechanism at work in lethal virus

X-ray crystallography at the Australian Synchrotron contributed to major research findings.

Data collected on the macromolecular crystallography beamlines at the Australian Synchrotron has contributed to major research findings on two deadly viruses, Hendra and Nipah, found in Australia, Asia and Africa. The viruses can be transmitted to humans not directly by the bat which is the natural carrier but by an infected animal like horses or pigs.

Beamline scientist, Dr David Aragao (pictured above), a co-author on the paper in Nature Communications, said that obtaining a clear motion picture of key biological process at the molecular level of viruses is often not available with current biomedical techniques.
“However, using X-ray crystallography from data collected on both MX1 and MX2 beamlines at the Australian Synchrotron, we were able to obtain  8  ‘photograph-like’ snapshots of the molecular process that allows the Hendra and Nipah virus to replicate.“

Two authors of the paper, PhD students Kate Smith and Sofiya Tsimbalyuk, who are co-supervised by Aragao and his collaborator Professor of Biochemistry Jade Forwood of the Graham Centre for Agricultural Innovation Charles Sturt University, used the Synchrotron extensively collecting multiple data sets that required extensive refinements over two years to isolate the mechanism of interest.

>Read more on the Australian Synchrotron website

Image: Beamline scientist, Dr David Aragao.

New high-precision instrument enables rapid measurements of protein crystals

A team of scientists and engineers at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory have developed a new scientific instrument that enables ultra-precise and high-speed characterization of protein crystals at the National Synchrotron Light Source II (NSLS-II)—a DOE Office of Science User Facility at Brookhaven, which generates high energy x-rays that can be harnessed to probe the protein crystals. Called the FastForward MX goniometer, this advanced instrument will significantly increase the efficiency of protein crystallography by reducing the run time of experiments from hours to minutes.

Protein crystallography is an essential research technique that uses x-ray diffraction for uncovering the 3D structures of proteins and other complex biological molecules, and understanding their function within our cells. Using this knowledge about the basic structure of life, scientists can advance drug design, improve medical treatments, and unravel other environmental and biochemical processes governing our everyday lives.

>Read more on the NSLS-II website

Image: Yuan Gao, Wuxian Shi, Evgeny Nazaretski, Stuart Myers, Weihe Xu and, Martin Fuchs designed and implemented the new goniometer scanner system for ultra-fast and efficient serial protein crystallography at the Frontier Microfocusing Macromolecular Crystallography (FMX) beamline at the National Synchrotron Light Source II.

The proteins that bind

Researchers reveal the structure of a protein that helps bacteria aggregate

Serine-rich repeat proteins (SRRPs), which help bacteria attach to surfaces, have been structurally characterised in pathogenic bacteria but not in beneficial bacteria such as those present in the gut. Dr Nathalie Juge’s team at the Quadram Institute Bioscience has previously identified SRRP as a main adhesin in Lactobacillus reuteri strains from pigs and mice. Now, together with colleagues at the University of East Anglia, they have described the structure and activity of the binding region of L. reuteri SRRPs in a paper published in PNAS. Using the Macromolecular Crystallography beamlines (I03 and I04) at Diamond Light Source, they discovered that the structure of these proteins is unique among characterised SRRPs and is surprisingly similar to pectin degrading enzymes. Molecular simulations and binding experiments revealed a pH-dependent binding to pectin and to proteins from the epithelium known as mucins. Altogether, these findings shed light on the activity of a key protein in these bacteria and may help guide the development of more targeted probiotic interventions.

>Read more on the Diamond Light Source website

Figure: (Left) Cartoon representation of crystal structures of the binding region of SRRP53608. (Right) Cartoon representation of crystal structures of the binding region of SRRP100-23. The N-terminus is shown with blue balls and the C-terminus is shown with red balls.

Solution to plastic pollution on the horizon

Engineering a unique plastic-degrading enzyme

The inner workings of a recently discovered bacterium with a fascinating ability to use plastic as an energy source have been recently revealed in PNAS. The world’s unique Long-Wavelength Macromolecular Crystallography (MX) beamline here at Diamond Light Source was used to successfully solve the structure of the bacterial enzyme responsible for chopping up the plastic. This newly evolved enzyme could be the key to tackling the worldwide problem of plastic waste.

Plastic pollution is a global threat that desperately needs addressing. Plastics are rarely biodegradable and they can remain in the environment for centuries. One of the most abundant plastics that contributes hugely to this dire situation is poly(ethylene terephthalate) (PET).

PET is used largely in textiles, where it is commonly referred to as polyester, but it is also used as packaging for liquids and foodstuffs. In fact, PET’s excellent water-repellent properties led to it being the plastic of choice for soft drink bottles. However, once plastic bottles are discarded in the environment the water resistance of PET means that they are highly resistant to natural biodegradation. PET bottles can linger for hundreds of years and plastic waste like this will accumulate over time unless a solution is found to degrade them.

A recent breakthrough came in the discovery of a unique bacterium, Ideonella sakaiensis 201-F6, which was found feeding on waste from an industrial PET recycling facility. PET has only been widely used since the 1970s, so the bacterium had evolved at breakneck speed to be able to take advantage of the new food source.

The bacterium had the amazing ability to degrade PET and use it to provide carbon for energy. Central to this ability was the production of a PET-digesting enzyme, known as PETase.

>Read more on the Diamond Light Source website

 

Hijacker parasite blocked from infiltrating blood

A major international collaboration led by Melbourne researchers has discovered that the world’s most widespread malaria parasite infects humans by hijacking a protein the body cannot live without.

The researchers were then able to successfully develop antibodies that disabled the parasite from carrying out this activity.
The study, led by the Walter and Eliza Hall Institute’s Associate Professor Wai-Hong Tham and Dr Jakub Gruszczyk, found that the deadly malaria parasite Plasmodium vivax (P. vivax) causes infection through latching onto the human transferrin receptor protein, which is crucial for iron delivery into the body’s young red blood cells.

Published today in Science, the discovery has solved a mystery that researchers have been grappling with for decades.
The MX and SAXS beamline staff at the Australian Synchrotron assisted with data collection.

Associate Professor Tham, who is also a HHMI-Wellcome International Research Scholar, said the collective efforts of teams from Australia, New Zealand, Singapore, Thailand, United Kingdom, United States, Brazil and Germany had brought the world closer to a potential effective vaccine against P.vivax malaria.

>Read more on the Australian Synchrotron website