Biochemistry, Biophysics, and Structural Biology Commons^™

A Multiple Species Approach To Biomass Production From Native Herbaceous Perennial Feedstocks, J. L. Gonzalez-Hernandez, Gautam Sarath, J. M. Stein, V. Owens, K. Gedye, A. Boe

Gautam Sarath Publications

Due to the rapid rate of worldwide consumption of nonrenewable fossil fuels, production of biofuels from cellulosic sources is receiving increased research emphasis. Here, we review the feasibility to produce lignocellulosic biomass on marginal lands that are not well-suited for conventional crop production. Large areas of these marginal lands are located in the central prairies of North America once dominated by tallgrass species. In this article, we review the existing literature, current work, and potential of two native species of the tallgrass prairie, prairie cordgrass (Spartina pectinata), and little bluestem (Schizachyrium scoparium) as candidates for commercial production of …

Two Distinct Waxy Alleles Impact The Granule-Bound Starch Synthase In Sorghum, Scott E. Sattler, Jaswinder Singh, Eric J. Haas, Lining Guo, Gautam Sarath, Jeffrey F. Pedersen

Gautam Sarath Publications

The granule-bound starch synthase (GBSS) is the enzyme responsible for amylose synthesis in starch granules. Loss of GBSS activity results in starch granules containing mostly amylopectin and little or no amylose, a phenotype described as waxy.

Eukaryotic Selenoproteins And Selenoproteomes, Alexey V. Lobanov, Dolph L. Hatfield, Vadim N. Gladyshev

Vadim Gladyshev Publications

Selenium is an essential trace element for which both beneficial and toxic effects in human health have been described. It is now clear that the importance of having adequate amounts of this micronutrient in the diet is primarily due to the fact that selenium is required for biosynthesis of selenocysteine, the twenty first naturally occurring amino acid in protein. In this review, we provide an overview of eukaryotic selenoproteins and selenoproteomes, which are sets of selenoproteins in these organisms. In eukaryotes, selenoproteins show a mosaic occurrence, with some organisms, such as vertebrates and algae, having dozens of these proteins, while …

Comparative Genomic Analyses Of Nickel, Cobalt And Vitamin B12 Utilization, Yan Zhang, Dmitry Rodionov, Mikhail Gelfand, Vadim N. Gladyshev

Vadim Gladyshev Publications

Background: Nickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B₁₂. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. Results: We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i) transport systems, and (ii) metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO …

Functions And Evolution Of Selenoprotein Methionine Sulfoxide Reductases, Byung Cheon Lee, Alexander Dikiy, Hwa-Young Kim, Vadim N. Gladyshev

Vadim Gladyshev Publications

Methionine sulfoxide reductases (Msrs) are thiol-dependent enzymes which catalyze conversion of methionine sulfoxide to methionine. Three Msr families, MsrA, MsrB, and fRMsr, are known. MsrA and MsrB are responsible for the reduction of methionine-S-sulfoxide and methionine-R-sulfoxide residues in proteins, respectively, whereas fRMsr reduces free methionine-R-sulfoxide. Besides acting on proteins, MsrA can addi¬tionally reduce free methionine-S-sulfoxide. Some MsrAs and MsrBs evolved to utilize catalytic selenocysteine. This includes MsrB1, which is a major MsrB in cytosol and nucleus in mammalian cells. Specialized machinery is used for insertion of selenocysteine into MsrB1 and other seleno¬proteins at in-frame UGA codons. Selenocysteine offers catalytic advantage …

Selenoproteins That Function In Cancer Prevention And Promotion, Dolph L. Hatfield, Min-Hyuk Yoo, Bradley A. Carlson, Vadim N. Gladyshev

Vadim Gladyshev Publications

Of the many health benefits attributed to selenium, the one that has received the most attention is its role in cancer prevention. Selenium-containing proteins (selenoproteins) have been shown in recent years to have roles in cancer prevention. However, selenoproteins have diverse functions and their view as antioxidants is oversimplified. Some selenoproteins appear to have a split personality in having roles both in preventing and promoting cancer. The contrasting roles of one selenoprotein, thioredoxin reductase 1, in cancer are discussed in detail, but as also noted, at least one other selenoprotein may also have such a dual function. In addition, we …

Identification Of A Novel System For Boron Transport: Atr1 Is A Main Boron Exporter In Yeast, Alaattin Kaya, Huseyin C. Karakaya, Dmitri E. Fomenko, Vadim N. Gladyshev, Ahmet Koc

Vadim Gladyshev Publications

Boron is a micronutrient in plants and animals, but its specific roles in cellular processes are not known. To understand boron transport and functions, we screened a yeast genomic DNA library for genes that confer resistance to the element in Saccharomyces cerevisiae. Thirty boron-resistant transformants were isolated, and they all contained the ATR1 (YML116w) gene. Atr1 is a multidrug resistance transport protein belonging to the major facilitator superfamily. C-terminal green fluorescent protein-tagged Atr1 localized to the cell membrane and vacuole, and ATR1 gene expression was upregulated by boron and several stress conditions. We found that atr1Δ mutants were …

A Structure-Based Approach For Detection Of Thiol Oxidoreductases And Their Catalytic Redox-Active Cysteine Residues, Stefano M. Marino, Vadim N. Gladyshev

Vadim Gladyshev Publications

Cysteine (Cys) residues often play critical roles in proteins, for example, in the formation of structural disulfide bonds, metal binding, targeting proteins to the membranes, and various catalytic functions. However, the structural determinants for various Cys functions are not clear. Thiol oxidoreductases, which are enzymes containing catalytic redox-active Cys residues, have been extensively studied, but even for these proteins there is little understanding of what distinguishes their catalytic redox Cys from other Cys functions. Herein, we characterized thiol oxidoreductases at a structural level and developed an algorithm that can recognize these enzymes by (i) analyzing amino acid and secondary structure …

Resolving The Lateral Component Of Blood Flow Velocity Based On Ultrasound Speckle Size Change With Scan Direction And Speed, Tiantian Xu, Greg R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional blood flow velocity measurement using ultrasound is capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these Doppler-based methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. In this paper, we introduce a method which estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to the blood reflectors (typically red blood cells) stretches (i.e., is “smeared”) if …

Further Progress On Lateral Flow Estimation Using Speckle Size Variation With Scan Direction, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional blood flow velocity measurement using ultrasound is capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these Doppler-based methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. In this paper, we report additional data on a new method recently introduced. This method estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to the blood reflectors (typically red …

Single Molecule Diffusion Coefficient Estimation By Image Analysis Of Simulated Ccd Images To Aid High-Throughput Screening, Pengfei Song, Lloyd M. Davis, Greg Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Extension of one-dimensional signal analysis to two-dimensional image analysis could accelerate conventional methods of high-throughput screening in the discovery of new pharmaceutical agents. This work describes a first step taken towards this goal – the evaluation of image-analysis based estimation strategies of the diffusion coefficient of a single molecule transported within a microfabricated flowcell. A computer simulation of single-molecule imaging by a charge-coupled device (CCD) camera is used to determine if it is possible to distinguish three different types of molecules with different diffusion coefficients. The Gaussian fitting algorithm finds the variance of the transverse trajectory, which increases linearly with …

Optimal Thresholds Of Feature Tracking For Blood Velocity And Tissue Motion Estimation, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Feature tracking is an algorithm for estimating blood flow velocity and tissue motion using pulse-echo ultrasound. In contrast to cross-correlation speckle-tracking techniques, feature tracking identifies features at discrete locations and corresponds them from frame to frame. Prior studies have demonstrated that feature-tracking estimates exhibit lower variance than those obtained by the conventional autocorrelation method and require less computational complexity than either speckle tracking or autocorrelation. To date, not much attention has been paid to the process by which trackable features (normally local maxima) are selected from the set of all available features. In the selection process, it is desired to …

Spontaneous Idiopathic Arteritis Of The Testicular Artery In Raccoons (Procyon Lotor), A. N. Hamir, M. V. Palmer, H. Li, J. Stasko, D. G. Rogers

School of Veterinary and Biomedical Sciences: Faculty Publications

The testes and the spermatic cord of raccoons (Procyon lotor, kits to adult breeders; n = 48) were examined. Segmental arteritis confined to the extratesticular portions of the testicular artery was present in raccoons of all ages. The arterial changes were seen in laboratory-confined experimental and control animals as well as in wild-caught raccoons. The lesions consisted of proliferative endarteritis with presence of inflammatory cells within the intima, media, and the adventitial regions of most affected vessels. Some aspects of the proliferative arterial lesions were reminiscent of systemic necrotizing vasculitis (polyarteritis nodosa), an immunologically mediated condition of animals and humans. …

A Herpesvirus Encoded Deubiquitinase Is A Novel Neuroinvasive Determinant, Joy I. Lee, Patricia J. Sollars, Scott B. Baver, Gary E. Pickard, Mindy Leelawong, Gregory A. Smith

School of Veterinary and Biomedical Sciences: Faculty Publications

The neuroinvasive property of several alpha-herpesviruses underlies an uncommon infectious process that includes the establishment of life-long latent infections in sensory neurons of the peripheral nervous system. Several herpesvirus proteins are required for replication and dissemination within the nervous system, indicating that exploiting the nervous system as a niche for productive infection requires a specialized set of functions encoded by the virus. Whether initial entry into the nervous system from peripheral tissues also requires specialized viral functions is not known. Here we show that a conserved deubiquitinase domain embedded within a pseudorabies virus structural protein, pUL36, is essential for initial …

Regulation Of Innate Immune Responses By Bovine Herpesvirus 1 And Infected Cell Protein 0 (Bicp0), Clinton Jones

School of Veterinary and Biomedical Sciences: Faculty Publications

Bovine herpesvirus 1 (BoHV-1) infected cell protein 0 (bICP0) is an important transcriptional regulatory protein that stimulates productive infection. In transient transfection assays, bICP0 also inhibits interferon dependent transcription. bICP0 can induce degradation of interferon stimulatory factor 3 (IRF3), a cellular transcription factor that is crucial for activating beta interferon (IFN-β) promoter activity. Recent studies also concluded that interactions between bICP0 and IRF7 inhibit trans-activation of IFN-β promoter activity. The C3HC4 zinc RING (really important new gene) finger located near the amino terminus of bICP0 is important for all known functions of bICP0. A recombinant virus that contains a single …

The Selenoproteome Of Clostridium Sp. Ohilas: Characterization Of Anaerobic Bacterial Selenoprotein Methionine Sulfoxide Reductase A, Hwa Young, Yan Zhang, Byung Cheon Lee, Jae-Ryong Kim, Vadim N. Gladyshev

Vadim Gladyshev Publications

Selenocysteine (Sec) is incorporated into proteins in response to UGA codons. This residue is frequently found at the catalytic sites of oxidoreductases. In this study, we characterized the selenoproteome of an anaerobic bacterium, Clostridium sp. (also known as Alkaliphilus oremlandii) OhILA, and identified 13 selenoprotein genes, five of which have not been previously described. One of the detected selenoproteins was methionine sulfoxide reductase A (MsrA), an antioxidant enzyme that repairs oxidatively damaged methionines in a stereospecific manner. To date, little is known about MsrA from anaerobes. We characterized this selenoprotein MsrA which had a single Sec residue at the catalytic …

X-Ray Fluorescence Microscopy Reveals The Role Of Selenium In Spermatogenesis, Sebastian Kehr, Mikalai I. Malinouski, Lydia Finney, Stefan Vogt, Vyacheslav M. Labunskyy, Marina V. Kasaikina, Bradley A. Carlson, You Zhou, Dolph L. Hatfield, Vadim N. Gladyshev

Vadim Gladyshev Publications

Selenium (Se) is a trace element with important roles in human health. Several selenoproteins have essential functions in development. However, the cellular and tissue distribution of Se remains largely unknown because of the lack of analytical techniques that image this element with sufficient sensitivity and resolution. Herein, we report that X-ray fluorescence microscopy (XFM) can be used to visualize and quantify the tissue, cellular and subcellular topography of Se. We applied this technique to characterize the role of Se in spermatogenesis and identified a dramatic Se enrichment specifically in late spermatids, a pattern that was not seen in any other …

Overexpression Of Methionine-R-Sulfoxide Reductases Has No Influence On Fruit Fly Aging, Valentina A. Shchedrina, Gerd Vorbrüggen, Byung Cheon Lee, Hwa-Young Kim, Hadise Kabil, Lawrence G. Harshman, Vadim N. Gladyshev

Vadim Gladyshev Publications

Methionine sulfoxide reductases (Msrs) are enzymes that repair oxidized methionine residues in proteins. This function implicated Msrs in antiox¬idant defense and the regulation of aging. There are two known Msr types in animals: MsrA specific for the reduction of methionine-S-sulfoxide, and MsrB that catalyzes the reduction of methionine-R-sulfoxide. In a previous study, overexpression of MsrA in the nervous system of Drosophila was found to extend lifespan by 70%. Overexpression of MsrA in yeast also extended lifespan, whereas MsrB overexpression did so only under cal¬orie restriction conditions. The effect of MsrB overexpression on lifespan has not yet been characterized in animal …

Classification And Cluster Analysis Of Complex Time-Of-Flight Secondary Ion Mass Spectrometry For Biological Samples, Stephen E. Reichenbach, Xue Tian, Qingping Tao, Alex Henderson

CSE Conference and Workshop Papers

Identifying and separating subtly different biological samples is one of the most critical tasks in biological analysis. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is becoming a popular and important technique in the analysis of biological samples, because it can detect molecular information and characterize chemical composition. ToF-SIMS spectra of biological samples are enormously complex with large mass ranges and many peaks. As a result the classification and cluster analysis are challenging. This study presents a new classification algorithm, the most similar neighbor with a probability-based spectrum similarity measure (MSN- PSSM), which uses all the information in the entire ToF- SIMS …

Targeting The Fatty Acid Transport Proteins (Fatp) To Understand The Mechanisms Linking Fatty Acid Transport To Metabolism, Paul N. Black, Angel Sandoval, Elsa Arias-Barrau, Concetta C. Dirusso

Department of Biochemistry: Faculty Publications

One principal process driving fatty acid transport is vectorial acylation, where fatty acids traverse the membrane concomitant with activation to CoA thioesters. Current evidence is consistent with the proposal that specific fatty acid transport (FATP) isoforms alone or in concert with specific long chain acyl CoA synthetase (Acsl) isoforms function to drive this energy-dependent process. Understanding the details of vectorial acylation is of particular importance as disturbances in lipid metabolism many times leads to elevated levels of circulating free fatty acids, which in turn increases fatty acid internalization and ectopic accumulation of triglycerides. This is associated with changes in fatty …

Copper Transport Activity Of Yeast Ctr1 Is Down-Regulated Via Its C Terminus In Response To Excess Copper, Xiaobin Wu, Devis Sinani, Heejeong Kim, Jaekwon Lee

Department of Biochemistry: Faculty Publications

Copper is an essential yet toxic trace element. The Ctr1 family of proteins plays a critical role for copper uptake in eukaryotes. However, the mechanisms of action of Ctr1 are largely unknown. Our previous data demonstrated that copper transport induces conformational changes in the cytosolic C terminus of the yeast Saccharomyces cerevisiae Ctr1. To define the physiological significance of this molecular event and gain better insights into the mechanism of Ctr1-mediated copper uptake, we have characterized the functional roles of the Ctr1 C terminus.ACtr1 mutant lacking the entire C-terminal cytosolic tail is functional in high affinity copper uptake; however, yeast …

Sdh5, A Gene Required For Flavination Of Succinate Dehydrogenase, Is Mutated In Paraganglioma, Huai-Xiang Hao, Oleh Khalimonchuk, Margit Schraders, Noah Dephoure, Jean-Pierre Bayley, Henricus Kunst, Peter Devilee, Cor W.R.J. Cremers, Joshua D. Schiffman, Brandon G. Bentz, Steven P. Gygi, Dennis R. Winge, Hannie Kremer, Jared Rutter

Department of Biochemistry: Faculty Publications

Mammalian mitochondria contain about 1100 proteins, nearly 300 of which are uncharacterized. Given the well-established role of mitochondrial defects in human disease, functional characterization of these proteins may shed new light on disease mechanisms. Starting with yeast as a model system, we investigated an uncharacterized but highly conserved mitochondrial protein (named here Sdh5). Both yeast and human Sdh5 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Germline …

Functional Aspects Of The Hyaluronan And Chondroitin Sulfate Receptors, Ed Harris, Paul H. Weigel

Department of Biochemistry: Faculty Publications

Glycosaminoglycans (GAGs) are distinct from other sugars/oligosaccharides in that they are polymers of disaccharide units composed of an amino sugar, N-acetylglucosamine (GlcNAc), or N-acetylgalactosamine (GalNAc), and uronic acid, glucuronic acid (GlcUA), or iduronic acid (IdUA). The exception is keratan sulfate (KS) in which the uronic acid is replaced by the neutral sugar galactose. Initially, GAGs were thought to be just part of an extracellular glue or ground substance that held tissues together and provided a liquid-like space between cells for the transport of nutrients. However, research using new technologies and techniques over the last two decades has revealed that the …

Copper Transport Into The Secretory Pathway Is Regulated By Oxygen In Macrophages, Carine White, Taiho Kambe, Yan G. Fulcher, Sherri W. Sachdev, Ashley I. Bush, Kevin Fritsche, Jaekwon Lee, Thomas P. Quinn, Michael J. Petris

Department of Biochemistry: Faculty Publications

Copper is an essential nutrient for a variety of biochemical processes; however, the redox properties of copper also make it potentially toxic in the free form. Consequently, the uptake and intracellular distribution of this metal is strictly regulated. This raises the issue of whether specific pathophysiological conditions can promote adaptive changes in intracellular copper distribution. In this study, we demonstrate that oxygen limitation promotes a series of striking alterations in copper homeostasis in RAW264.7 macrophage cells. Hypoxia was found to stimulate copper uptake and to increase the expression of the copper importer, CTR1. This resulted in increased copper delivery to …

Polyploidy Creates Higher Diversity Among Cynodon Accessions As Assessed By Molecular Markers, Osman Gulsen, Songul Sever-Mutlu, Nedim Mutlu, Metin Tuna, Osman Karaguzel, Robert C. Shearman, Terrance P. Riordan, Tiffany M. Heng-Moss

Department of Biochemistry: Faculty Publications

Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions’ genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an …

Crystal Structure Of Acivicin-Inhibited Γ-Glutamyltranspeptidase Reveals Critical Roles For Its C-Terminus In Autoprocessing And Catalysis, Kristin Williams, Sierra Cullati, Aaron Sand, Ekaterina I. Biterova, Joseph J. Barycki

Department of Biochemistry: Faculty Publications

Helicobacter pylori γ-glutamyltranspeptidase (HpGT) is a general γ-glutamyl hydrolase and a

demonstrated virulence factor. The enzyme confers a growth advantage to the bacterium, providing essential amino acid precursors by initiating the degradation of extracellular glutathione and glutamine. HpGT is a member of the N-terminal nucleophile (Ntn) hydrolase superfamily and undergoes autoprocessing to generate the active form of the enzyme. Acivicin is a widely used γ-glutamyltranspeptidase inhibitor that covalently modifies the enzyme, but its precise mechanism of action remains unclear. The time-dependent inactivation of HpGT exhibits a hyperbolic dependence on acivicin concentration with kmax = 0.033 ± 0.006 sec^{−1 …}

Glucose Promotes Stress Resistance In The Fungal Pathogen Candida Albicans, Alexandra Rodaki, Iryna M. Bohovych, Brice Enjalbert, Tim Young, Frank C. Odds, Neil A.R. Gow, Alistair J.P. Brown

Department of Biochemistry: Faculty Publications

Metabolic adaptation, and in particular the modulation of carbon assimilatory pathways during disease progression, is thought to contribute to the pathogenicity of Candida albicans. Therefore, we have examined the global impact of glucose upon the C. albicans transcriptome, testing the sensitivity of this pathogen to wide-ranging glucose levels (0.01, 0.1, and 1.0%). We show that, like Saccharomyces cerevisiae, C. albicans is exquisitely sensitive to glucose, regulating central metabolic genes even in response to 0.01% glucose. This indicates that glucose concentrations in the bloodstream (approximate range 0.05–0.1%) have a significant impact upon C. albicans gene regulation. However, in contrast …

Modulation Of The Heme Electronic Structure And Cystathionine Β-Synthase Activity By Second Coordination Sphere Ligands: The Role Of Heme Ligand Switching In Redox Regulation, Sangita Singh, Peter Madzelan, Jay Stasser, Colin L. Weeks, Donald F. Becker, Thomas G. Spiro, James Penner-Hahn, Ruma Banerjee

Department of Biochemistry: Faculty Publications

In humans, cystathionine β-synthase (CBS) is a hemeprotein, which catalyzes a pyridoxal phosphate (PLP)-dependent condensation reaction. Changes in the heme environment are communicated to the active site, which is ~20 Å away. In this study, we have examined the role of H67 and R266, which are in the second coordination sphere of the heme ligands, H65 and C52 respectively, in modulating the heme's electronic properties and in transmitting information between the heme and active sites. While the H67A mutation is comparable to wild-type CBS, interesting differences are revealed by mutations at the R266 site. The pathogenic mutant, R266K, is moderately …