Reaction centers (RCs) are pigment-protein complexes that drive photosynthesis by converting light into chemical energy (electrons) to power the cell, possibly arising from a homodimeric protein. The symmetry of a homodimer is broken in heterodimeric rRC structures, while the 2.2-Angstrom resolution X-ray structure of the homodimeric RC-photosystem from the phototroph Heliobacterium modesticaldum exhibits perfect C2 symmetry. The core polypeptide dimer and two small subunits coordinate 54 bacteriochlorophylls and 2 carotenoids that capture and transfer energy to the electron-transfer chain at the center, which performs charge separation and comprises 6 (bacterio)chlorophylls and an iron-sulfur cluster; unlike other RCs, it lacks a bound quinone. This structure preserves characteristics of the ancestral reaction center, providing insight into the evolution of photosynthesis.
Enough sunlight hits the Earth to power the planet many times over—if energy capture were more efficient. Thus, scientists have looked at nature’s means to understand photosynthesis in a sun-loving, soil-dwelling bacterium. A team of scientists has gained a fundamental understanding of the inner workings of this vital process and how it differs among plant systems. Their discovery may provide a new template for beginning organic-based solar panel design (i.e., “artificial leaves”) or possibly renewable biofuel applications.
But the team’s structural biologists are capturing freeze-frame images of crystallized proteins throughout the whole process of the simplest form of photosynthesis, in the single-celled heliobacteria, which are fundamentally different than plants. Instead of using water like plants, for example, heliobacteria use hydrogen sulfide and grow without oxygen; after photosynthesis, they give off the foul-smelling sulfur gas in place of oxygen. The scientists grew the “perfect” X-ray diffracting crystal charge after many initial trials. In this breakthrough study, they found an almost perfect symmetry in the heliobacter RC, which helps it gather every available photon of near-infrared light to build chlorophylls.
Gisriel, C., et al. “Structure of a symmetric photosynthetic reaction center–photosystem,” Science 357(6355), 1021–1025 (2017). [DOI:10.1126/science.aan5611].
Instruments and Facilities Used: X-ray macromolecular crystallograpy at Biodesign Center for Applied Structural Discovery at Arizona State University. Advanced Light Source at Berkeley Center for Structural Biology at Lawrence Berkeley National Laboratory. Structural Biology Center–CAT beamline of the Advanced Photon Source at Argonne National Laboratory.
The simplest known bacterium able to drive photosynthesis is found in muddy soils near hot springs. Heliobacterium modesticaldum is a sun-loving, soil-dwelling, thermophilic bacterium that photosynthesizes near-infrared light, unlike plants, which use different parts of visible light. The photosynthesis reaction centers (RCs) of H. modesticaldum are thought to resemble the earliest common ancestor of all photosynthesis complexes, which evolved around three billion years ago. Thus, a clear, detailed picture of the H. modesticaldum RC would provide valuable insight into the early evolution of photosynthesis. However, successfully purifying an RC protein and growing the crystals needed for X-ray crystallography can be a lengthy, difficult process.
Researchers successfully capped 7 years of work by obtaining a high-resolution (2.2 Å) structure of the membrane protein at the heart of the photosynthetic RC of H. modesticaldum. The structure revealed details such as the interactions between light-harvesting “antenna” molecules and the electron-transfer chain, where the initial steps required to convert photon energy into chemical energy occurs. With this data, the research team was able to make comparisons to other types of RCs, gaining new perspectives on the early evolution of photosynthesis and how nature optimized light-driven energy collection. This work will help unlock the secrets of photosynthesis, possibly leading to the development of cleaner, solar-based renewable energy.
Gisriel, C., et al. “Structure of a Symmetric Photosynthetic Reaction Center–Photosystem.” Science357(6355), 1021–1025 (2017). [DOI:10.1126/science.aan5611].
Instruments and Facilities: Beamline 8.2.1 at Advanced Light Source at Lawrence Berkeley National Laboratory; Advanced Photon Source at Argonne National Laboratory.
Scientists have determined the molecular structures of a highly specialized set of proteins that a strain of Escherichia coli bacteria use to communicate and defend their turf. Ironically, loads of bacteria cover the devices humans use to communicate—even more than on toilet seats, according to one study. Bacteria appear to have their own form of social network that allows these single-cell creatures to attract and repel one another. This insight stems from new research that could lead to new biomedical strategies for overcoming pathogenic bacteria that cause infectious diseases such as pneumonia and food-borne illnesses.
The work builds on the 2005 discovery that the bacteria produce toxic proteins, which they can transfer to their neighbors through direct contact to either kill or control them, possibly to gain better access to nutrients in densely populated microbial communities through a process called contact-dependent growth inhibition (CDI). Learning how the bacteria interact and communicate is helping to resolve the possibly different activities of the toxins, which “may affect different bacteria differently.” Found in soil and gut bacteria, as well as in human pathogens, some of these toxins of CDI systems are present, for example, in Pseudomonas aeruginosa, which is involved in lung disease.
The team obtained the molecular structures of proteins that belong to a three-part system of the NC101 strain of E. coli, which consists of the CDI toxin, its immunity protein, and its elongation factor (EF). The latter, known as EF-Tu, is a protein that plays a key role in protein synthesis. Knowing the protein structures of all three parts helps scientists understand their function. Discovery of the immunity protein has led scientists to suspect that the system’s purpose includes competition and signaling (intracommunication), as well as killing and controlling other bacteria. Actually, only a few molecules of the toxin “get into the neighboring cell,” so perhaps the toxin is “not meant to kill, but rather to control and communicate.” It can act on the transfer ribonucleic acid (tRNA) only under highly specific circumstances, and it is the first case seen where the EF is “needed for the toxin to function.” Researchers used high-bright X-rays to characterize, or identify, biological proteins and inspect chemical processes at the nanoscale level (i.e., one billionth of a meter).
Michalska, K., et al. “Structure of a Novel Antibacterial Toxin That Exploits Elongation Factor Tu to Cleave Specific Transfer RNAs.” Nucleic Acids Res.45(17), 10306–10320 (2017). [DOI:10.1093/nar/gkx700].
Instruments and Facilities Used: Advanced Photon Source 19-ID beamline and Advanced Protein Characterization Facility at Argonne National Laboratory.
A research team has uncovered a new mechanism for enzyme-mediated carbon dioxide (CO2) capture and conversion. They have revealed new and unique elements of carboxylation chemistry (CC) that could be used in catalytic strategies for converting CO2 into chemical feedstock or biomass. The crystal structure of acetone carboxylase (AC; enzyme involved in biodegradation by bacteria) was solved using X-ray crystallographic data. The inactive, unbound (apo) structure shows a substrate channel blocked off from the manganese (Mn) active site where CO2 conversion takes place. An adenosine monophosphate (AMP)–bound structure contains large conformational changes that open the channel to the active site. Highly reactive intermediates in the channel are protected from outside solvent as they are transported to the Mn active site for CO2 conversion. Stepwise mechanisms of carboxylation reactions differ in essential ways with respect to co-substrate, co-factor, and metal requirements. Knowledge of these mechanisms provides the basis for an increased fundamental understanding of CC, contributing to future strategies for CO2 capture and conversion to biomass. These in turn may mitigate the effects of increasing concentrations of CO2 on the global climate.
Mus, F., et al. “Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation.” Nat. Sci. Rep. 7, Article 7234 (2017). [DOI:10.1038/s41598-017-06973-8].
Instruments and Facilities Used: X-ray crystallographic data from the Stanford Synchrotron Lightsource (SSLS) at SLAC National Accelerator Laboratory (SLAC). Structural data from macromolecular crystallography were measured on SSLS beamline 12-2; Advanced Photon Source (APS) at Argonne National Laboratory (ANL); and the Diamond Light Source, Oxfordshire, United Kingdom.
Each year in the United States, more than 57,000 children younger than 5 years old are hospitalized due to respiratory syncytial virus (RSV) infection, and about 14,000 adults older than 65 die from it. By age 2, most children have been infected with RSV, experiencing usually only mild cold symptoms. People with weakened immune systems, however, such as infants and the elderly, can face serious complications, including pneumonia and, in some cases, death. Now, scientists studying the virus using bright X-rays have found clues to how RSV causes disease. They mapped the molecular structure of an RSV protein that interferes with the body’s ability to fight off the virus. Knowing the structure of this protein will help them understand how the virus impedes immune response, potentially leading to a vaccine or treatment for this common infection.
With no approved vaccine and limited treatment for RSV, doctors prescribe the antiviral drug ribavirin only in the most severe cases because it is expensive and not very effective. Thus, most people with RSV receive only supportive care to make them more comfortable while their bodies fight off the virus. People with weakened immune systems face a tough fight with RSV. The researchers say that solving the structure of this elusive protein will enable them to see what the protein looks like and help them define what it does and how it does it. Ultimately, this capability and finding could lead to new targets for vaccine or drug development.
Scientists have long known that a nonstructural RSV protein (known as NS1) is key to the virus’s ability to evade the body’s immune response. However, its structure was unknown, so scientists were unable to determine exactly how the enigmatic NS1 interfered with the immune system. Using X-ray crystallography, the scientists determined the three-dimensional (3D) structure of NS1, and, in a detailed analysis of the structure, they identified a piece of the protein known as the alpha 3 helix, possibly critical for suppressing the immune response.
The researchers created different versions of this NS1 protein, with some having an intact and some with a mutated alpha 3 helix region. They tested the functional impact of helix 3 and created a set of viruses containing either the original or the mutant NS1 genes, measuring the effect on the immune response when they infected cells with these viruses. They found that viruses with the mutated helix region did not suppress the immune response, while the ones with the intact helix region did, globally modulating the immune response.
The findings also showed that the protein’s alpha 3 helix region was necessary for the virus to dial down the body’s immune response, giving the virus a better chance of surviving and multiplying—in other words, causing disease. Thus, a vaccine or treatment that targets the alpha 3 helix may supply what is needed to prevent immune suppression.
Chatterjee, S., et al. “Structural Basis for Human Respiratory Syncytial Virus NS1-Mediated Modulation of Host Responses.” Nat. Microbiol. 2, Article 17101 (2017). [DOI:10.1038/nmicrobiol.2017.101].
Instruments and Facilities Used: X-ray crystallography at the Advanced Photon Source at Argonne National Laboratory.
Plants caught in the act, changing chemistry thought to be immutable because necessary for life
Plants are the chemists of the living world, producing hundreds of thousands of small molecules that provide protection—to screen sunrays, to poison plant eaters, to scent the air, to color flowers, and for much other vegetative business.
Called “secondary metabolites,” these chemicals are distinguished from “primary metabolites,” which are the essential building blocks of proteins, fats, sugars, and DNA. Secondary metabolites just smooth the way in life, but failure to make primary metabolites correctly and efficiently is fatal. Genes for enzymes in the molecular assembly lines of primary metabolism have duplicates, allowing more tolerance of mutations that might have destabilized the primary pathways because the originals were still on the job. With evolutionary constraints thus relaxed, synthetic machinery was able to accumulate enough mutations to do new chemistry.
Widely conserved, primary metabolism it was thought to remain unchanged across many different groups of organisms because it operates correctly and efficiently and because its products are necessary for life. But now, a collaborative team of scientists has caught primary metabolism in the act of evolving. In a comprehensive study of a primary-metabolism assembly line in plants, they discovered a key enzyme evolving from a canonical form possessed by most plants, through noncanonical forms in tomatoes, to a switch-hitting form found in peanuts, and finally committing to the novel form in some strains of soybeans. This feat is comparable to pulling the tablecloth out from under the dishes without breaking any of them. A collaborative study of this biochemical pathway resulted in the crystallization of the soybean enzyme to reveal how nature changed the way the protein works, also capturing plants “building a pathway that links the primary to the secondary metabolism,” to reveal evolutionary machinery that creates new molecules.
A new pathway discovered for making tyrosine is much less constrained than the old one, raising the possibility that carbon flow could be directed away from lignin to increase the yields of drugs or nutrients to levels that would allow them to be produced in commercial quantities. Though the scientists have found two different assembly lines for tyrosine, they have not determined why except in general terms. This work is important because it demonstrates that primary metabolism does evolve.
Schenck, C. A., et al. “Molecular Basis of the Evolution of Alternative Tyrosine Biosynthetic Routes in Plants.” Nat. Chem. Biol.13, 1029–1035 (2017). [DOI:10.1038/nchembio.2414].
Instruments and Facilities Used: X-ray macromolecular crystallography; diffraction data collected at beamline 19-ID of the Advanced Photon Source at Argonne National Laboratory Structural Biology Center.
Peanuts have a secret. It is a subtle one, but the peanut and its legume kin have not one, but two ways to make the tyrosine amino acid—one of 20 required to make all of this family’s proteins—an essential plant and human nutrient. Though a seemingly small feat, this unique way of making such an important chemical building block has been a mystery since its discovery in the 1960s. New research abetted by high-brightness X-ray beams is revealing how this second tyrosine pathway emerged in the legume family. Plant chemistry has evolved to make many different chemical compounds, many of which are important to human society, such as food, fiber, feed, fuel, and medicine. Starting from simpler compounds like tyrosine, these important molecules are precursors of countless interesting and useful chemicals such as morphine. The recently determined structure of the new plant enzyme could be a useful tool for biotechnologists trying to control the production of tyrosine and its derivatives. The team has tied this major evolutionary change in plant metabolism to a single mutation in the new enzyme.
In the 1960s and 1970s, scientists observed that plants used one pathway, known as arogenate dehydrogenase (ADH), to make tyrosine. They found that the legume family (i.e., peas, beans, and peanuts), however, had uniquely added a second, called prephenate dehydrogenase (PDH), previously known to be only in microbes. Two years ago, part of this team discovered the genes responsible for making tyrosine, learning that before peanuts and peas evolved into separate lineages, the legumes had evolved PDH enzymes from their existing ADH ones. These sister enzymes are very similar, so only a small number of changes could account for how ADH enzymes evolved into PDH ones. But there were still too many changes to test. The international collaborating teams purified the PDH enzyme of the soybean legume and determined its three-dimensional (3D) structure, which revealed that only a couple of mutations had occurred at the site where the chemical reactions take place. Instead of dozens of possible mutations, there were only two. Thus, changing a single amino acid in the center of the enzyme largely converted the soybean PDH enzyme back into its ancestor ADH enzyme, and this crucial switch also worked in reverse and for enzymes from multiple species. The scientists believe the legume PDH insensitivity to tyrosine could help to produce more tyrosine, and its useful derivatives, in systems like yeast or engineered plants.
Schenck, C. A., et al. “Molecular Basis of the Evolution of Alternative Tyrosine Biosynthetic Routes in Plants,” Nat. Chem. Biol. 13, 1029–1035 (2017). [DOI:10.1038/nchembio.2414].
Instruments and Facilities Used: Structural Biology Center (SBC)–CAT beam 19-ID of the Advanced Photon Source at Argonne National Laboratory.
Many populations in developing countries rely on plants for dietary iron (Fe)—essential for plant growth, crop yields, and human health, but, due to its low or limited solubility, Fe is sparingly available in neutral or basic soils and thus not readily accessible in the rhizosphere. Leading to a restricted Fe content in many plants, this low solubility is a major factor contributing to the widespread prevalence of Fe deficiency anemia in people with plant-based diets. Thus, increasing plant Fe acquisition and storage may have profound impacts on plant and human nutrition and can be achieved by manipulating genes and related mechanisms governing Fe homeostasis in plants. However, understanding the balance between positive and negative regulation of the Fe deficiency response is essential for efforts to engineer plants having a sufficient but not toxic level of Fe. Although plants often are challenged with Fe deficiency, no environment remains constant, making Fe availability in the rhizosphere dependent on many factors. When sufficient Fe is available, plants must effectively suppress Fe-deficiency response to avoid excessive uptake.
A research team has identified a novel Fe-binding domain allele called BTS in a mutagenesis screen for altered Fe accumulation (bts-3). Data showed that bts-3 is more tolerant than wild type to Fe-deficient conditions and that bts-3 is sensitive to Fe-sufficient conditions and accumulates excessive Fe. A triple mutant with loss of both BTS paralogs and a partial loss of BTS expression exhibits even greater tolerance to Fe-deficient conditions and increased Fe accumulation without any resulting Fe toxicity effects, with the mutations also changing their uptake of important minerals such as zinc (Zn) and manganese (Mn). Genetic knockdowns and modifications of the proteins have been implicated in regulating plant uptake of Fe. This work will lead to greater understanding of plant Fe homeostasis to inform efforts for improved crops. Identifying natural variants of these genes in crop species may lead to traditional breeding efforts to generate higher-Fe cultivars.
Hindt, M. N., et al. “BRUTUS and its Paralogs, BTS LIKE1 and BTS LIKE2, Encode Important Negative Regulators of the Iron Deficiency Response in Arabidopsis thaliana.” Metallomics9(7), 876–890 (2017). [DOI:10.1039/C7MT00152E].
Instruments and Facilities Used: PerkinElmer LAS Ltd, Seer Green, United Kingdom, and Elemental Scientific Inc., Omaha, Neb.; synchrotron X-ray fluorescence (SXRF) at National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory; Stanford Synchrotron Lightsource (SSLS) at SLAC National Accelerator Laboratory (SLAC); real-time quantitative PCR (Step One Plus Real Time PCR System using Applied Biosystems Version 2.2.3; Advanced Photon Source (APS) at Argonne National Laboratory (ANL); and Australian Synchrotron, Victoria. Two-dimensional SXRF analysis was performed at various X-ray microprobe beamlines: microarray analysis and X-ray fluorescence imaging (XFI) on SSLS beamline 2-3 at SLAC; X26A and X27A of NSLS; XFM beamline of the Australian Synchrotron; APS beamline 2-ID-D. Microarray analysis performed at Geisel School of Medicine in the Genomics Shared Resource at Dartmouth College. Elemental concentration analysis (inductively coupled plasma-mass spectrometry (ICP-MS, PerkinElmer NexION 300D equipped with Elemental Scientific Inc. autosampler and Apex HF sample introduction system at PerkinElmer LAS Ltd, Seer Green, U.K., and Elemental Scientific Inc., Omaha, Neb., respectively, in the standard mode.
Fungal lytic polysaccharide monooxygenases (LPMOs) are known to enhance the efficiency of cellulose-hydrolyzing enzymes through oxidative cleavage of the glycosidic bonds. For this study, PMO-2 from Neurospora crassa was heterologously expressed from Pichia pastoris, purified, and crystallized for high-resolution X-ray crystal structures that revealed “prebound” molecular oxygen in the resting state and a dioxo species in complex with the catalytic copper (Cu2+) ion, which is the first structural description of molecular oxygen (O2) activation by a LPMO. In addition, neutron diffraction studies and density functional theory calculations have identified a role for a conserved histidine in promoting oxygen activation. Extension of these studies to the enzyme-substrate complex could provide a complete picture of the enzymatic mechanism for the potential benefit of applications such as bioethanol production.
O’Dell, W. B., et al. “Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase.” Angew. Chem. Int. Ed.129(3), 785–788 (2017). [DOI:10.1002/anie.201610502].
Instruments and Facilities Used: Neutron crystallography. Joint X-ray/neutron refinement at Center for Structural Molecular Biology at Oak Ridge National Laboratory (ORNL). Diffraction data were collected at SER-CAT 22-ID at the Advanced Photon Source at Argonne National Laboratory and at CG-4D IMAGINE (NSF MRI 09229719) at the High Flux Isotope Reactor at ORNL.
Scientists have captured the three-dimensional (3D) detail of the structure of a molecule implicated in Alzheimer’s disease. Knowing the shape of this molecule—and how that shape may be disrupted by certain genetic mutations—can help in understanding how Alzheimer’s and other neurodegenerative diseases develop and how to prevent and treat them.
From past studies, scientists think that the molecule TREM2 possibly is involved in cognitive decline, the hallmark of neurodegenerative diseases, because certain mutations that alter the structure of TREM2 are associated with an increased risk of developing late-onset Alzheimer’s, frontal temporal dementia, Parkinson’s disease, and sporadic amyotrophic lateral sclerosis (ALS). Other TREM2 mutations are linked to Nasu-Hakola disease, a rare inherited condition that causes progressive dementia and death in most patients by age 50.Although its exact contribution is unknown, dysfunctional TREM2 does relate to neurodegeneration, and “inflammation is the common thread in all these conditions.” The scientists investigated what TREM2 mutations do to the structure of the protein itself to impact its function, so ways can be found to correct it.
Structural analysis of TREM2 revealed that the mutations associated with Alzheimer’s alter the surface of the protein, while those linked to Nasu-Hakola influence the “guts” of the protein. The difference in location could explain the severity of Nasu-Hakula, in which signs of dementia begin in young adulthood. The internal mutations totally disrupt the structure of TREM2, resulting in fewer TREM2 molecules. The surface mutations, in contrast, leave TREM2 intact but likely make it harder for the molecule to connect to proteins or send signals as normal TREM2 molecules would.
TREM2 lies on the surface of immune cells called microglia, which are thought to be important “housekeeping” cells involved in, for example, maintaining healthy brain biology via a process called phagocytosis that cleans cellular waste, including the amyloid beta that is known to accumulate in Alzheimer’s disease. If the microglia lack TREM2 or the TREM2 is dysfunctional, these cellular housekeepers can’t perform their cleanup tasks. Though the exact function of TREM2 is still unknown, mice without TREM2 have defects in their microglia. With these structural data, scientists can study how TREM2 works, or doesn’t work, in these neurodegenerative diseases, as well as other inflammatory conditions including chronic obstructive pulmonary disease and stroke. The structure of TREM2 could be important for understanding many chronic and degenerative diseases.
Kober, D. L., et al. “Neurodegenerative Disease Mutations in TREM2 Reveal a Functional Surface and Distinct Loss-of-Function Mechanisms,” eLife5, e20391 (2016). [DOI:10.7554/eLife.20391].
Instruments and Facilities Used: X-ray Facility at the Advanced Photon Source (APS) at Argonne National Laboratory
Funding Acknowledgements (from publication): NIH, Knight Alzheimer’s Disease Research Center, Alzheimer’s Association Research Grant, Burroughs-Wellcome Fund Career Award for Medical Scientists, and American Heart Association Predoctoral Fellowship.