Dynamic Regulation of Histone Chaperone Nucleoplasmin

Small-angle X-ray scattering (SAXS) analysis of nucleoplasmin (Npm) Core+A2 truncation (1-145) bound to five H2A/H2B dimers. (Top) SAXs envelope of the pentameric complex (pink) with the best nuclear magnetic resonance (NMR)–restrained SAXS hybrid model inside. (Bottom) SAXS curve of the complex (purple dots). Simulated SAXS curve (black line) from the best-scoring structural model. [From Warren, C., et al. “Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.” Nat. Commun. 8, 2215 (2017). DOI:10.1038/s41467-017-02308-3. Reused under a Creative Commons license (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/​).]
Histones are eukaryotic cell nuclei proteins that package and order DNA into structural units called nucleosomes. Chromatin is the complex of DNA and proteins comprising the genome’s physiological form. As chromatin’s chief protein components, histones act as spools around which DNA winds, playing a role in gene regulation. A chaperone protein assists in the folding and unfolding of macromolecules, such as in the assembly of nucleosomes from folded histones and DNA. Nucleoplasmin (Npm) is a highly conserved embryonic histone chaperone, responsible for the maternal storage and zygotic release of histones H2A and H2B. Npm contains a pentameric N-terminal Core domain and an intrinsically disordered C-terminal Tail domain. Although intrinsically disordered regions are common among histone chaperones, their roles in histone binding and chaperoning have remained unclear.

This study, using the Xenopus laevis Npm Tail domain, unveils the architecture of the Npm histone complex and a mechanism of histone chaperone regulation. It demonstrates that intramolecular regulation of the histone chaperone Npm controls histone binding and release—a key process in the earliest stages of embryonic development. Structural analyses enabled model constructions of both the Npm Tail domain and the pentameric complex, revealing that the Tail domain controls the binding of histones through specific, electrostatic interactions. Functional analyses demonstrated that these competitive interactions negatively regulate Npm histone chaperone activity in vitro. Data from these studies establish a potentially generalizable mechanism of histone chaperone regulation via dynamic and specific intramolecular shielding of histone interaction sites.

Warren, C., et al. “Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.” Nat. Commun. 8, 2215 (2017). DOI:10.1038/s41467-017-02308-3.

Instruments and Facilities Used: Bruker 600 nuclear magnetic resonance (NMR) and Inova 600 NMR instruments in the Albert Einstein College of Medicine (AECM) Einstein Structural NMR Resource; and bio–small-angle X-ray scattering (bio-SAXS) beamline 4-2, SLAC National Accelerator Laboratory’s Stanford Synchrotron Radiation Lightsource (SSRL).

“Zip-code” Mechanism for Hormone Signaling Revealed

Crystal structure of multikinase inhibitor sKLB bound to fibroblast growth factor (FGF) FGF21CT reveals two distinct binding sites. Structure of extracellular domain of β-Klotho “longevity” protein (green ribbons) bound to FGF21 hormone (salmon ball-and-stick) unveils critical molecular interactions required for hormone binding and cell activation. Yellow sticks denote nitrogen (N)-linked glycans. Grey dashed lines denote regions that do not exhibit significant electron density. About 30 angsroms (Å) apart, the FGF binding sites on the β-Klotho D1 and D2 domains are located on the opposite side of the molecule from the flexible linker that connects the two glycosidase domains and may contribute to the interdomain dynamic properties that enable complex formation with ligands and FGF receptors (FGFRs). [Reprinted by permission from Springer Nature: Lee, S., et al. “Structures of β-klotho reveal a ‘zip code’-like mechanism for endocrine FGF signaling.” Nature 553, 501–505 (2018). DOI:10.1038/nature25010. Copyright 2018]
Named after the Greek goddess who spun the thread of life, Klotho proteins play an important role in the regulation of longevity and metabolism. Alpha-Klotho is a membrane-spanning protein expressed predominantly in the kidney, as well as in the brain. Mice lacking α-klotho exhibit a range of signs associated with aging and have elevated blood phosphate levels. Like α-klotho, β-klotho functions as a co-receptor for endocrine fibroblast growth factors (FGFs). FGF21 is secreted from the liver following fasting, acting in fat cells and the brain to induce metabolic adaptation to fasting and responses to stress. Although FGF receptors (FGFRs) are expressed in a wide range of tissues, expression of the β-klotho “longevity” protein in the liver, fat, and brain restricts the target organs of these endocrine FGFs.

In a recent Yale Medical School–led study, researchers revealed the three-dimensional (3D), high-resolution structure of β-Klotho, illuminating its intricate mechanism and potential for antiaging therapeutics, as well as for treating a wide range of medical conditions. X-ray crystallography data revealed critical molecular interactions required for hormone binding and cell activation. The specific “zip-code”–like interactions of β-klotho receptors appear to regulate critical metabolic processes in the liver, kidneys, and brain, among other organs. Analysis yielded several insights, including that β-Klotho is the primary receptor that binds to FGF21, a key hormone that stimulates insulin sensitivity and glucose metabolism, causing weight loss. The researchers believe this new understanding can guide the development of therapies by improving the biological activity of FGF21. Also found were a new variant of FGF21 that has 10 times higher potency and cellular activity and the evidence of how a structurally related enzyme (glycosidase) that breaks down sugars evolved into a receptor for a hormone that lowers blood sugar. Researchers believe the untangled β-Klotho structure presents a platform for exploring and developing agents that either enhance or block the pathway, enabling therapies for conditions such as liver cancer and bone diseases.

Lee, S., et al. “Structures of β-klotho reveal a ‘zip code’-like mechanism for endocrine FGF signaling.” Nature 553, 501–505 (2018). DOI:10.1038/nature25010.

Instruments and Facilities Used: X-ray data were collected from β-klotho–receptor crystals at Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, beamline 14-1 as part of the program to aid National Synchrotron Light Source (NSLS) users prior to NSLS-II operations.

Structure of a Flavoenzyme Assembly Intermediate

(a) The structure of the FrdA-SdhE flavoenzyme assembly intermediate: flavoprotein subunit FrdA (cyan), assembly factor SdhE (green), flavin adenine dinucleotide FAD (orange sticks), and malonate (yellow sticks). The boxed region highlights the covalent interaction between the FAD and the enzyme. (b) Overlay of the flavin-binding domains of the FrdA subunit from the FrdA-SdhE intermediate (cyan) and the FrdA subunit from the mature assembled FrdABCD complex (gray). A rotation of 10.8° is observed in the capping domain of the assembly intermediate when compared to assembled FrdABCD. [From Sharma, P., et al. “Crystal structure of an assembly intermediate of respiratory Complex II,” Nat. Commun. 9, 274 (2018). DOI:10.1038/s41467-017-02713-8. Reused under a Creative Commons license (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/​.)]
Enzymes frequently depend on an electron transport cofactor for executing catalytic functions such as reduction-oxidation (redox) reactions. For flavoenzymes, the cofactor is flavin adenine dinucleotide (FAD), whose binding type with the enzyme impacts the redox potential and thus reaction chemistry, such as for metabolism and detoxification. Researchers in this study discovered that the structure of an assembled flavoenzyme intermediate reveals the mechanism of covalent flavin binding in respiration. Assembly factors include SdhAF2 in humans, SdhE in Escherichia coli, and Sdh5 in yeast. Other revelations include that mitochondrial flavoenzymes drive both noncovalent and covalent redox reactions and that the assembly factor (SdhE, a small protein of ~90 to 140 amino acids, conserved in all kingdoms) in the structure of the SdhE:FrdA complex with covalent FAD stabilizes a conformation of the flavoprotein subunit FrdA that favors succinate oxidation.

Researchers fixed the E. coli FrdA-SdhE intermediate via site-specific crosslinking, resolving the structure to 2.6 angstroms (Å). This study identified that SdhE stabilizes an FrdA conformation that likely enables the mechanism of autocatalytic covalent flavinylation. FrdA’s FAD-binding domain and capping domain both interact with SdhE, but structural data revealed a 10.8° difference in their angles. The investigators believe that domain rotation affects flavinylation, showing that enzymes are tuned to catalyze reactions in different ways and that conformational diversity can directly relate to catalytic mechanism diversity.

Sharma, P., et al. “Crystal structure of an assembly intermediate of respiratory Complex II.” Nat. Commun. 9, 274 (2018). DOI:10.1038/s41467-017-02713-8.

Instruments and Facilities Used: Small angle X-ray scattering (SAXS) and diffraction and mass spectrometry analysis using beamline 9-2 at Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC National Accelerator Laboratory (SLAC).

A Regional Model for Uranium Redox and Mobility

Anoxic organic-enriched sediments strongly accumulate uranium as U(IV), sulfide, and other reduced species. Seasonal reduction-oxidation (redox) cycling triggered by changing water tables can intermittently mobilize these species. [Courtesy Vincent Noël and John Bargar, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory]
Uranium (U) contamination stubbornly persists as a challenging and costly water quality concern at former uranium ore processing sites across the Upper Colorado River Basin (UCRB). Plumes at these sites are not self-attenuating via natural flushing by groundwater as originally expected. Recent studies at the Rifle, Colo., legacy site suggest that organic-enriched anoxic sediments create conditions that promote reduction of U(VI) to relatively immobile U(IV), causing it to accumulate locally under persistently saturated and anoxic conditions. However, incursion of oxidants into reduced sediments could transform contaminants, allowing these sediments to act as secondary sources of uranium. Oxidant incursions take place during periods of changing water tables, which occur in UCRB throughout the year. If these sediments were regionally common in the UCRB and exposed to varying reduction-oxidation (redox) conditions, then they could contribute to maintaining the longevity of regional uranium plumes.

To investigate these issues, researchers examined the occurrence and distribution of reduced and oxidized iron (Fe), sulfur (S), and U species in sediment cores spanning dry and oxic to wet and reduced conditions at three different UCRB sites. Detailed molecular characterization involved chemical extractions, X-ray absorption spectroscopy (XAS), Mössbauer spectroscopy, and X-ray microspectroscopy. This work demonstrates that anoxic organic-enriched sediments occur at all sites, strongly accumulate sulfides and U, and are exposed to strong seasonal redox cycles. Uranium was found to be present as U(IV) complexed to sediment-associated organic carbon and possibly to mineral surfaces. This finding is significant because complexed U(IV) is relatively susceptible to oxidative mobilization. Sediment particle size, organic carbon content, and pore saturation control redox conditions in sediments and thus strongly influence Fe, S, and U biogeochemistry. These findings help to illuminate the mechanistic linkages between hydrology, sediment texture, and biogeochemistry. They further provide enhanced contextual and conceptual underpinnings to support reactive transport modeling of uranium, other contaminants, and nutrients in redox-variable floodplains—a subject of importance to BER research missions. Cyclic redox variability has major implications for mobility of carbon (C), nitrogen (N), and metal contaminants in groundwater and surface waters. Redox-variable, organic-enriched sediments mediate the mobility of C, N, Fe, S, U, and metal contaminants regionally in the UCRB. Organic-enriched sediments were established to regionally mediate groundwater quality within the UCRB.

Noël, V., et al. “Understanding controls on redox processes in floodplain sediments of the Upper Colorado River Basin.” Sci. Total Environ. 603–604, 663–675 (2017). DOI:10.1016/j.scitotenv.2017.01.109.

Noël, V., et al. “Redox constraints over U(IV) mobility in the floodplains of Upper Colorado River Basin.” Environ. Sci. Technol. 51(19), 10954–10964 (2017). DOI:10.1021/acs.est.7b02203.

Instruments and Facilities Used: X-ray absorption spectroscopy and X-ray microprobe mapping at Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory (SLAC), and Mössbauer spectroscopy at Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL).

The CRISPR Target-Recognition Mechanism

Cas1-Cas2 complexSurface representation of the Cas1-Cas2 complex, consisting of four Cas1 proteins (light and dark green) and two Cas2 proteins (yellow). Donor DNA (brown) is being integrated into the target DNA (blue), at a precise location in the CRISPR array, following a short leader sequence (red). [From Wright, A. V., et al.  “Structures of the CRISPR Genome Integration Complex,” Science 357(6356), 1113–1118 (2017). [DOI:10.1126/science.aao0679. Reprinted with permission from AAAS*.]

* Readers may view, browse, and/or download material for temporary copying purposes only, provided these uses are for noncommercial personal purposes. Except as provided by law, this material may not be further reproduced, distributed, transmitted, modified, adapted, performed, displayed, published, or sold in whole or in part, without prior written permission from the publisher.

 

 

Bacterial DNA is characterized by regions of clustered regularly interspaced short palindromic repeats (CRISPRs) and associated Cas proteins (CRISPR-associated endonucleases). The CRISPR-Cas system has revolutionized gene editing by vastly simplifying the insertion of short snippets of new (“donor”) DNA into very specific locations of target DNA. Researchers in this study have discovered how Cas proteins recognize their target locations with such great specificity. They used x-ray crystallography to solve the structures of Cas1 and Cas2—responsible for DNA-snippet capture and integration—as the proteins were bound to synthesized DNA strands designed to mimic different stages of the process. The research also demonstrated how the system works in its native context as part of a bacterial immune system and how Cas proteins act as general-purpose molecular recording devices—tools for encoding information in genomes.

Cas1 appears to have evolved from a more “promiscuous” (less selective) type of enzyme that catalyzes the movement of DNA sequences from one position to another (a transposase). At some point, Cas1 acquired an unusual degree of specificity for a particular location in the bacterial genome, the CRISPR array. This specificity is critical to the bacteria, both for acquiring immunity and for avoiding genome damage caused by the insertion of viral fragments at the wrong location. The researchers wanted to learn how Cas1-Cas2 proteins recognize the target sequence to enable comparison with previously studied transposases and integrases (i.e., enzymes that catalyze the integration of donor DNA into target DNA) and to determine whether the proteins can be altered to recognize new sequences for custom applications.

The researchers crystallized Cas1-Cas2 in complex with preformed DNA strands that mimicked reaction intermediates and products. X-ray crystallography revealed that the structures showed substantial distortions in the target DNA, but there were surprisingly few sequence-specific contacts with the Cas1-Cas2 complex, and the DNA’s resulting flexibility produced disorder in the crystals. Attempts to model the DNA across the disordered sections showed that the DNA had to be even more distorted. Cryoelectron microscopy experiments, coupled with the crystallography data, confirmed that an accessor protein called the integration host factor (IHF) introduces an additional sharp bend in the DNA, bringing an upstream recognition sequence into contact with Cas1 to increase both the specificity and efficiency of integration. The architecture of the CRISPR integration complex suggests that subtle adjustment of the distance between Cas1 active sites could reprogram the system to recognize different target sites. Changes in its architecture could be exploited, thereby, for genome tagging applications and also may explain the natural divergence of CRISPR arrays in bacteria.

Wright, A. V., et al. “Structures of the CRISPR Genome Integration Complex,” Science 357(6356), 1113–1118 (2017). [DOI:10.1126/science.aao0679].

Instruments and Facilities Used: X-ray macromolecular crystallography; beamline 8.3.1; protein crystallography (PX); and scattering/diffraction at the Advanced Light Source at Lawrence Berkeley National Laboratory; Stanford Synchrotron Radiation Light Source 9-2 beamline.

 

Revealing How Bacterial Organelles Assemble

Kerfeld and Sutter

Cheryl Kerfeld and Markus Sutter handle crystallized proteins at Berkeley National Laboratory’s Advanced Light Source. [Image courtesy Marilyn Chung, Lawrence Berkeley National Laboratory]
Structure of microcompartment’s protein shell could help research in bioenergy, pathogenesis, and biotechnology

Scientists are providing the clearest view yet of an intact bacterial microcompartment, revealing the structure and assembly of the organelle’s protein shell at atomic-level resolution. They studied the “photogenic” organelle shell of an ocean-dwelling slime bacteria Haliangium ochraceum. Providing the first view of the shell of an intact bacterial organelle membrane, this full structural view can help provide important information for beneficial use in fighting pathogens or bioengineering bacterial organelles. The research team said these organelles, or bacterial microcompartments (BMCs), are used by some bacteria to fix carbon dioxide. Thus, understanding how the microcompartment membrane is assembled, as well as how it lets some compounds pass through while impeding others, could contribute to research in enhancing carbon fixation and, more broadly, bioenergy. This class of organelles also helps many types of pathogenic bacteria metabolize compounds that are not available to normal, nonpathogenic microbes, giving the pathogens a competitive advantage.

Sutter, M., et al. “Assembly Principles and Structure of a 6.5-MDa Bacterial Microcompartment Shell.” Science 23(6344), 1293–1297 (2017). [DOI:10.1126/science.aan3289].

Instruments and Facilities Used: Michigan State University–DOE Plant Research Laboratory and the Molecular Biophysics and Integrated Bioimaging Division at Lawrence Berkeley National Laboratory; Stanford Synchrotron Radiation Lightsource.

Probing S-layer Protein Structural Dynamics by SAXS

Biophysical Journal Cover Image
Calcium mediates the structural state of the Caulobacter crescentus surface layer protein, RsaA. Image featured on the cover of Biophysical Journal.

All archaea, and many bacteria, possess a protein shell referred to as a surface layer (S-layer), which usually consist of a single protein that self-assembles into a two-dimensional (2D) crystal lattice.  Studies have revealed the structural dynamics of this S-layer protein from the model bacterium Caulobacter crescentus, called RsaA. Using small angle scattering and diffraction (SAXS/D) techniques, multiple structural states of RsaA were successfully characterized including monomeric, aggregated, and crystalline states (see figure), with only monomeric Rssa forming 2D crystals. Enabling differentiation of the discrete states, these results rationalize physiological data implicating RsaA as a player in environmental adaptation of C. crescentus. The findings also provide a biochemical and physiological basis for RsaA’s calcium (Ca)-binding behavior, which extends far beyond Ca’s usual role in S-layer biology of aiding biogenesis or oligomerization, and demonstrate a connection to cellular fitness. Further characterization using slow and fast time-resolved SAXS/D methods is ongoing.

SAXS/D data
Small angle X-ray scattering and diffraction (SAXS/D) data of five solutions with different concentrations of the Caulobacter crescentus S-layer protein, RsaA, in the presence of calcium (Ca). Scattering profiles indicate concentration-dependent crystallization. Automatic indexing of the numbered peaks yielded a hexagonal crystal lattice consistent with predictions and denoted by Miller indices. (Top) The diffraction pattern obtained for the highest concentration used (8 mg/ml) shows powder rings. (Bottom) Transmission electron microscopy of the 8 mg/ml RsaA in the presence of 10 millimole per Liter (mm/L) of calcium chloride (CaCl2) (scale bar 200 nm). [Reprinted from Herrmann, J., et al. “Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer.” Biophys. J. 112(9), 1841–1851 (2017). DOI:10.1016/j.bpj.2017.04.003. Copyright 2017, with permission from Elsevier.]
Herrmann, J., et al. “Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer,” Biophys. J. 112(9), 1841–1851 (2017). [DOI:10.1016/j.bpj.2017.04.003].

Instruments and Facilities Used: Stanford ChEM-H Macromolecular Structure Knowledge Center,  Stanford Department of Structural Biology Electron Microscopy Center, Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC National Accelerator Laboratory (SLAC). Beamlines or instruments used: transmission electron microscopy (TEM) and small angle X-ray scattering and diffraction (SAXS/D) at SSRL beamline 4-2 at SLAC.

Ebola Virus

In the Ebola virus one of the proteins, VP40, has the ability to refold to achieve new functions;  three structural forms of VP40 have been determined, with each structure conferring a separate and essential function in the virus life cycle.  The image illustrates (top) a butterfly-shaped dimer critical for membrane trafficking; (middle) a rearranged hexameric structure essential for building and releasing nascent virions; (bottom) an RNA-binding octameric ring that controls transcription in infected cells

Bornholdt, T. Noda, D.M. Abelson, P. Halfmann, M.R. Wood, Y. Kawaoka, E. Ollmann Saphire, Cell 154, 763 (2013) [DOI: 10.1016/j.cell.2013.07.015]

Finding Manganese Reduction-Oxidation Drives Plant Debris Decomposition

cross-sectioned Douglas-fir needle
Fluorescence microscope image showing a cross-sectioned Douglas-fir needle prepared for this work and analyzed using ALS beamlines 1.4.3, 10.3.2 and 9.0.2. [Courtesy Marco Keiluwit]
Microbial decomposition of plant debris (“litter”) regulates nutrient availability, ecosystem productivity, and carbon (C) cycling. Historically, scientists thought climate (primarily temperature and precipitation) regulated the rate of litter decomposition, which then influenced the rate at which nutrients become available and C contained in the litter was released back into the atmosphere as the greenhouse gas carbon dioxide (CO2). Recently, evidence has shown that geochemical factors also influence litter decomposition rates. A research team has shown that long-term litter decomposition rates in forest ecosystems are closely related to the process of manganese (Mn) reduction-oxidation (redox) in a variety of forest ecosystems. A strong correlation had been observed previously between litter Mn content and decomposition rates, but the underlying mechanisms were not well understood. In redox cycling, redox governs Mn reactions, frequently mediated by microbes, which accumulate and oxidize Mn in the litter, then using the oxidized Mn species to break down plant cells.

By pairing high-resolution chemical imaging analysis with a long-term litter decomposition experiment under field conditions, the researchers discovered that litter decomposition is tightly coupled to redox cycling of Mn. The researchers discovered why Mn exerts such a strong control on litter decomposition rates and the mechanism of the underlying biogeochemical process, observing molecular changes within the litter as it decomposed over the years and probing structural changes within the very large biomolecules present in litter that frequently are not directly detectable by other means. This tunable technique also allowed the scientists to selectively ionize different biopolymers present in the litter, such as lignin, which is an important biopolymer because it lends rigidity to plant cell walls and protects litter from microbial decay.

In microenvironments within the litter, microbes actively cycle Mn as they colonize and break down the litter, and research indicates that biogeochemical constraints on bioavailability, mobility, and Mn reactivity in the plant-soil system may have a profound impact on litter decomposition rates. Understanding more about the mobility and reactivity of Mn in the plant-soil system also helps researchers improve their ability to accurately predict carbon cycling trends in ecosystems, contributing to greater insights into climate change patterns.

Keiluweit, M.. et al. “Long-Term Litter Decomposition Controlled by Manganese Redox Cycling,” PNAS 12(38), E5253–E5260 (2015). [DOI:10.1073/pnas.1508945112].

Instruments and Facilities Used: Beamlines 10.3.2 (X-ray microprobe capabilities) and 1.4.3 (Fourier transform infrared spectromicroscopy) at Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory; beamline 4-3 at Stanford Synchrotron Radiation Light Source (SSRLS).

Modular Construction on a Biomolecular Scale

The spherical protein ferritin was used to synthesize a porous 3-D crystalline framework material, and further engineered to have metal hubs on its surface.  Organic molecules bridge these hubs, and in a controlled way create a porous material with potential uses from efficient fuel storage to carbon capture and conversion.  The study shows the great potential for proteins as building blocks with exquisite properties of electron transfer and bioinspired catalysis.

A. Sontz, J. B. Bailey, S. Ahn and F. A. Tezcan, “A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals”, J. Am. Chem. Soc. 137, 11598 (2015), doi: 10.1021/jacs.5b07463