scholarly journals Chlorovirus PBCV-1 Multidomain Protein A111/114R Has Three Glycosyltransferase Functions Involved in the Synthesis of Atypical N-Glycans

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 87
Author(s):  
Eric Noel ◽  
Anna Notaro ◽  
Immacolata Speciale ◽  
Garry A. Duncan ◽  
Cristina De Castro ◽  
...  
Keyword(s):  
Major Capsid Protein ◽  
Hydrolytic Activity ◽  
Conserved Residues ◽  
The Core ◽  
Domains Of Life ◽  
Domain 3 ◽  
Glycosylation Pathway ◽  
Additional Support ◽  
Complex Glycan ◽  
Cellular Organelles

The structures of the four N-linked glycans from the prototype chlorovirus PBCV-1 major capsid protein do not resemble any other glycans in the three domains of life. All known chloroviruses and antigenic variants (or mutants) share a unique conserved central glycan core consisting of five sugars, except for antigenic mutant virus P1L6, which has four of the five sugars. A combination of genetic and structural analyses indicates that the protein coded by PBCV-1 gene a111/114r, conserved in all chloroviruses, is a glycosyltransferase with three putative domains of approximately 300 amino acids each. Here, in addition to in silico sequence analysis and protein modeling, we measured the hydrolytic activity of protein A111/114R. The results suggest that domain 1 is a galactosyltransferase, domain 2 is a xylosyltransferase and domain 3 is a fucosyltransferase. Thus, A111/114R is the protein likely responsible for the attachment of three of the five conserved residues of the core region of this complex glycan, and, if biochemically corroborated, it would be the second three-domain protein coded by PBCV-1 that is involved in glycan synthesis. Importantly, these findings provide additional support that the chloroviruses do not use the canonical host endoplasmic reticulum–Golgi glycosylation pathway to glycosylate their glycoproteins; instead, they perform glycosylation independent of cellular organelles using virus-encoded enzymes.

scholarly journals Chlorovirus PBCV-1 protein A064R has three of the transferase activities necessary to synthesize its capsid protein N-linked glycans

2020 ◽  
Vol 117 (46) ◽  
pp. 28735-28742
Author(s):  
Immacolata Speciale ◽  
Maria Elena Laugieri ◽  
Eric Noel ◽  
Sicheng Lin ◽  
Todd L. Lowary ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Major Capsid Protein ◽  
Hydroxyl Group ◽  
Bacterial Proteins ◽  
Chlorella Variabilis ◽  
Double Stranded Dna ◽  
Unicellular Green Alga ◽  
Domains Of Life ◽  
Domain 3 ◽  
Spontaneous Mutants

Paramecium bursariachlorella virus-1 (PBCV-1) is a large double-stranded DNA (dsDNA) virus that infects the unicellular green algaChlorella variabilisNC64A. Unlike many other viruses, PBCV-1 encodes most, if not all, of the enzymes involved in the synthesis of the glycans attached to its major capsid protein. Importantly, these glycans differ from those reported from the three domains of life in terms of structure and asparagine location in the sequon of the protein. Previous data collected from 20 PBCV-1 spontaneous mutants (or antigenic variants) suggested that thea064rgene encodes a glycosyltransferase (GT) with three domains, each with a different function. Here, we demonstrate that: domain 1 is a β-l-rhamnosyltransferase; domain 2 is an α-l-rhamnosyltransferase resembling only bacterial proteins of unknown function, and domain 3 is a methyltransferase that methylates the C-2 hydroxyl group of the terminal α-l-rhamnose (Rha) unit. We also establish that methylation of the C-3 hydroxyl group of the terminal α-l-Rha is achieved by another virus-encoded protein A061L, which requires an O-2 methylated substrate. This study, thus, identifies two of the glycosyltransferase activities involved in the synthesis of theN-glycan of the viral major capsid protein in PBCV-1 and establishes that a single protein A064R possesses the three activities needed to synthetize the 2-OMe-α-l-Rha-(1→2)-β-l-Rha fragment. Remarkably, this fragment can be attached to any xylose unit.

scholarly journals Crystal Structure of African Swine Fever Virus pS273R Protease and Implications for Inhibitor Design

2020 ◽  
Vol 94 (10) ◽  
Author(s):  
Guobang Li ◽  
Xiaoxia Liu ◽  
Mengyuan Yang ◽  
Guangshun Zhang ◽  
Zhengyang Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Information ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Hydrolytic Activity ◽  
Viral Disease ◽  
Fever Virus ◽  
Dna Virus ◽  
Core Domain ◽  
The Core

ABSTRACT African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs that is responsible for serious economic and production losses. It is caused by the African swine fever virus (ASFV), a large and complex icosahedral DNA virus of the Asfarviridae family. Currently, there is no effective treatment or approved vaccine against the ASFV. pS273R, a specific SUMO-1 cysteine protease, catalyzes the maturation of the pp220 and pp62 polyprotein precursors into core-shell proteins. Here, we present the crystal structure of the ASFV pS273R protease at a resolution of 2.3 Å. The overall structure of the pS273R protease is represented by two domains named the “core domain” and the N-terminal “arm domain.” The “arm domain” contains the residues from M1 to N83, and the “core domain” contains the residues from N84 to A273. A structure analysis reveals that the “core domain” shares a high degree of structural similarity with chlamydial deubiquitinating enzyme, sentrin-specific protease, and adenovirus protease, while the “arm domain” is unique to ASFV. Further, experiments indicated that the “arm domain” plays an important role in maintaining the enzyme activity of ASFV pS273R. Moreover, based on the structural information of pS273R, we designed and synthesized several peptidomimetic aldehyde compounds at a submolar 50% inhibitory concentration, which paves the way for the design of inhibitors to target this severe pathogen. IMPORTANCE African swine fever virus, a large and complex icosahedral DNA virus, causes a deadly infection in domestic pigs. In addition to Africa and Europe, countries in Asia, including China, Vietnam, and Mongolia, were negatively affected by the hazards posed by ASFV outbreaks in 2018 and 2019, at which time more than 30 million pigs were culled. Until now, there has been no vaccine for protection against ASFV infection or effective treatments to cure ASF. Here, we solved the high-resolution crystal structure of the ASFV pS273R protease. The pS273R protease has a two-domain structure that distinguishes it from other members of the SUMO protease family, while the unique “arm domain” has been proven to be essential for its hydrolytic activity. Moreover, the peptidomimetic aldehyde compounds designed to target the substrate binding pocket exert prominent inhibitory effects and can thus be used in a potential lead for anti-ASFV drug development.

Hot and sweet: protein glycosylation in Crenarchaeota

2013 ◽  
Vol 41 (1) ◽  
pp. 384-392 ◽  
Author(s):  
Benjamin H. Meyer ◽  
Sonja-Verena Albers
Keyword(s):  
Living Cell ◽  
Protein Glycosylation ◽  
Haloferax Volcanii ◽  
Present Review ◽  
Sulfolobus Acidocaldarius ◽  
Glycosylphosphatidylinositol Anchor ◽  
Sweet Protein ◽  
Domains Of Life ◽  
Glycosylation Pathway ◽  
Sugar Chains

Every living cell is covered with a dense and complex array of covalently attached sugars or sugar chains. The majority of these glycans are linked to proteins via the so-called glycosylation process. Protein glycosylation is found in all three domains of life: Eukarya, Bacteria and Archaea. However, on the basis of the limit in analytic tools for glycobiology and genetics in Archaea, only in the last few years has research on archaeal glycosylation pathways started mainly in the Euryarchaeota Haloferax volcanii, Methanocaldococcus maripaludis and Methanococcus voltae. Recently, major steps of the crenarchaeal glycosylation process of the thermoacidophilic archaeon Sulfolobus acidocaldarius have been described. The present review summarizes the proposed N-glycosylation pathway of S. acidocaldarius, describing the phenotypes of the mutants disrupted in N-glycan biosynthesis as well as giving insights into the archaeal O-linked and glycosylphosphatidylinositol anchor glycosylation process.

scholarly journals The Amino-Terminal Region of Major Capsid Protein P3 Is Essential for Self-Assembly of Single-Shelled Core-Like Particles of Rice Dwarf Virus

2004 ◽  
Vol 78 (6) ◽  
pp. 3145-3148 ◽  
Author(s):  
Kyoji Hagiwara ◽  
Takahiko Higashi ◽  
Naoyuki Miyazaki ◽  
Hisashi Naitow ◽  
R. Holland Cheng ◽  
...  
Keyword(s):  
Self Assembly ◽  
Major Capsid Protein ◽  
Core Protein ◽  
Terminal Region ◽  
Dwarf Virus ◽  
Rice Dwarf Virus ◽  
Amino Terminal ◽  
The Core ◽  
Baculovirus System ◽  
Terminal Amino

ABSTRACT The core protein P3 of Rice dwarf virus constructs asymmetric dimers, one of which is inserted by the amino-terminal region of another P3 protein. The P3 proteins with serial amino-terminal deletions, expressed in a baculovirus system, formed particles with gradually decreasing stability. The capacity for self-assembly disappeared when 52 of the amino-terminal amino acids had been deleted. These results demonstrated that insertion of the amino-terminal arm of one P3 protein into another appears to play an important role in stabilizing the core particles.

scholarly journals The non-power model of the genetic code: a paradigm for interpreting genomic information

2016 ◽  
Vol 374 (2063) ◽  
pp. 20150062 ◽  
Author(s):  
Diego Luis Gonzalez ◽  
Simone Giannerini ◽  
Rodolfo Rosa
Keyword(s):  
Genetic Code ◽  
Power Model ◽  
Mathematical Framework ◽  
Genomic Information ◽  
Unified Framework ◽  
Hidden Symmetries ◽  
Protein Coding ◽  
The Core ◽  
Domains Of Life ◽  
Mitochondrial Code

In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries. Also, it provides us with new tools for the analysis of genomic sequences. We review briefly three main areas: (i) the Euplotid nuclear code, (ii) the vertebrate mitochondrial code, and (iii) the main coding/decoding strategies used in the three domains of life. In every case, we show how the non-power model is a natural unified framework for describing degeneracy and deriving sound biological hypotheses on protein coding. The approach is rooted on number theory and group theory; nevertheless, we have kept the technical level to a minimum by focusing on key concepts and on the biological implications.

scholarly journals Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea

2021 ◽  
Vol 12 ◽  
Author(s):  
Anchal ◽  
Vineeta Kaushik ◽  
Manisha Goel
Keyword(s):  
Structural Alignment ◽  
Protein Structures ◽  
Peptide Bond ◽  
Basic Function ◽  
Isomerization Reaction ◽  
Prolyl Isomerase ◽  
Peptidyl Prolyl Isomerase ◽  
Conserved Residues ◽  
Domains Of Life

Cis-trans isomerization of the peptide bond prior to proline is an intrinsically slow process but plays an essential role in protein folding. In vivo cis-trans isomerization reaction is catalyzed by Peptidyl-prolyl isomerase (PPIases), a category of proteins widely distributed among all the three domains of life. The present study is majorly focused on the distribution of different types of PPIases in the archaeal domain. All the three hitherto known families of PPIases (namely FKBP, Cyclophilin and parvulin) were studied to identify the evolutionary conservation across the phylum archaea. The basic function of cyclophilin, FKBP and parvulin has been conserved whereas the sequence alignment suggested variations in each clade. The conserved residues within the predicted motif of each family are unique. The available protein structures of different PPIase across various domains were aligned to ascertain the structural variation in the catalytic site. The structural alignment of native PPIase proteins among various groups suggested that the apo-protein may have variable conformations but when bound to their specific inhibitors, they attain similar active site configuration. This is the first study of its kind which explores the distribution of archaeal PPIases, along with detailed structural and functional analysis of each type of PPIase found in archaea.

scholarly journals The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains

2019 ◽  
Author(s):  
Pablo Ricardo Arantes ◽  
Conrado Pedebos ◽  
Marcelo D. Poleto ◽  
Laércio Pol-Fachin ◽  
Hugo Verli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Membrane Lipid ◽  
Membrane Dynamics ◽  
En Bloc ◽  
Future Studies ◽  
Head Groups ◽  
Domains Of Life ◽  
Glycosylation Pathway ◽  
Dynamics Simulations

<div> <div> <div> <p>Lipid-linked oligosaccharides (LLOs) plays an important role in the N-glycosylation pathway as the donor substrate of oligosaccharyltransferases (OSTs), which are respon- sible for the en bloc transfer of glycan chains onto a nascent polypeptide. The lipid component of LLO in both eukarya and archaea consists of a dolichol, and an unde- caprenol in prokarya, whereas the number of isoprene units may change between species. Given the potential relevance of LLOs and their related enzymes to diverse biotechno- logical applications, obtaining reliable LLO models from distinct domains of life could support further studies on complex formation and their processing by OSTs, as well as protein engineering on such systems. In this work, molecular modeling, such as quantum mechanics calculations, molecular dynamics simulations, and metadynamics were employed to study eukaryotic (Glc3-Man9-GlcNAc2-PP-Dolichol), bacterial (Glc1- GalNAc5-Bac1-PP-Undecaprenol) and archaeal (Glc1-Man1-Gal1-Man1-Glc1-Gal1-Glc1- P-Dolichol) LLO in membrane bilayers. Microsecond molecular dynamics simulations and metadynamics calculations of LLOs revealed that glycan chains are more prone to interact with the membrane lipid head groups, while the PP linkages are positioned at the lipid phosphate head groups level. Dynamics of isoprenoid chains embedded within the bilayer are described and membrane dynamics and its related properties are also investigated. Overall, there are similarities regarding the structural and dynamics of the eukaryotic, the bacterial and the archaeal LLOs in bilayers, which can support the comprehension of their association with OSTs. This data may support future studies on the transferring mechanism of the oligosaccharide chain to an acceptor protein. </p> </div> </div> </div>

scholarly journals Autophagy in Neurons

2019 ◽  
Vol 35 (1) ◽  
pp. 477-500 ◽  
Author(s):  
Andrea K.H. Stavoe ◽  
Erika L.F. Holzbaur
Keyword(s):  
Endoplasmic Reticulum ◽  
Cell Biology ◽  
Neuronal Development ◽  
Selective Autophagy ◽  
The Core ◽  
Differentiated Cells ◽  
Neuronal Homeostasis ◽  
Core Components ◽  
Cellular Organelles

Autophagy is the major cellular pathway to degrade dysfunctional organelles and protein aggregates. Autophagy is particularly important in neurons, which are terminally differentiated cells that must last the lifetime of the organism. There are both constitutive and stress-induced pathways for autophagy in neurons, which catalyze the turnover of aged or damaged mitochondria, endoplasmic reticulum, other cellular organelles, and aggregated proteins. These pathways are required in neurodevelopment as well as in the maintenance of neuronal homeostasis. Here we review the core components of the pathway for autophagosome biogenesis, as well as the cell biology of bulk and selective autophagy in neurons. Finally, we discuss the role of autophagy in neuronal development, homeostasis, and aging and the links between deficits in autophagy and neurodegeneration.

Evidence from the Historical Record

2020 ◽  
pp. 67-114
Author(s):  
Rupal N. Mehta
Keyword(s):  
Statistical Tests ◽  
Panel Study ◽  
Historical Record ◽  
Leadership Change ◽  
The Core ◽  
Additional Support ◽  
Special Circumstances ◽  
The Impact ◽  
Significant Support ◽  
Nuclear Reversal

This chapter provides a series of quantitative, large-n analyses of nuclear reversal that test the core propositions and hypotheses derived in Chapter 2. It expands on existing work to systematically examine all states that engaged in nuclear weapons activity. It overviews the data on rewards (political, military, or economic) and punishments (economic or military) for analysis. It presents several statistical tests of the six hypotheses derived in Chapter 2. Using a time-series panel study that incorporates a variety of model specifications examining the impact of inducements on nuclear reversal, it finds significant support for the theoretical framework introduced earlier. Further, it finds support for the probabilistic conditions that examines special circumstances of leadership change and nuclear reversal among allies and adversaries. Appendix 3.1 presents a battery of robustness checks to provide additional support for the findings.

scholarly journals Flexibility of the petunia strigolactone receptor DAD2 promotes its interaction with signaling partners

2020 ◽  
Vol 295 (13) ◽  
pp. 4181-4193 ◽  
Author(s):  
Hui Wen Lee ◽  
Prachi Sharma ◽  
Bart J. Janssen ◽  
Revel S. M. Drummond ◽  
Zhiwei Luo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Root Development ◽  
Binding Sites ◽  
Hydrolytic Activity ◽  
Shoot Branching ◽  
Scf Complex ◽  
The Core ◽  
Hydrolase Fold ◽  
Dynamics Simulations ◽  
F Box Protein

Strigolactones (SLs) are terpenoid-derived plant hormones that regulate various developmental processes, particularly shoot branching, root development, and leaf senescence. The SL receptor has an unusual mode of action. Upon binding SL, it hydrolyzes the hormone, and then covalently binds one of the hydrolytic products. These initial events enable the SL receptor DAD2 (in petunia) to interact with the F-box protein PhMAX2A of the Skp-Cullin-F-box (SCF) complex and/or a repressor of SL signaling, PhD53A. However, it remains unclear how binding and hydrolysis structurally alters the SL receptor to enable its engagement with signaling partners. Here, we used mutagenesis to alter DAD2 and affect SL hydrolysis or DAD2's ability to interact with its signaling partners. We identified three DAD2 variants whose hydrolytic activity had been separated from the receptor's interactions with PhMAX2A or PhD53A. Two variants, DAD2N242I and DAD2F135A, having substitutions in the core α/β hydrolase-fold domain and the hairpin, exhibited hormone-independent interactions with PhMAX2A and PhD53A, respectively. Conversely, the DAD2D166A variant could not interact with PhMAX2A in the presence of SL, but its interaction with PhD53A remained unaffected. Structural analyses of DAD2N242I and DAD2D166A revealed only small differences compared with the structure of the WT receptor. Results of molecular dynamics simulations of the DAD2N242I structure suggested that increased flexibility is a likely cause for its SL-independent interaction with PhMAX2A. Our results suggest that PhMAX2A and PhD53A have distinct binding sites on the SL receptor and that its flexibility is a major determinant of its interactions with these two downstream regulators.

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