MdBVe46 is an envelope protein that is required for virion formation by Microplitis demolitor bracovirus

Bracoviruses (BVs) are endogenized nudiviruses that braconid parasitoid wasps have coopted for functions in parasitizing hosts. Microplitis demolitor is a braconid wasp that produces Microplitis demolitor bracovirus (MdBV) and parasitizes the larval stage of the moth Chrysodeixis includens. Some BV core genes are homologs of genes also present in baculoviruses while others are only known from nudiviruses or other BVs. In this study, we had two main goals. The first was to separate MdBV virions into envelope and nucleocapsid fractions before proteomic analysis to identify core gene products that were preferentially associated with one fraction or the other. Results indicated that nearly all MdBV baculovirus-like gene products that were detected by our proteomic analysis had similar distributions to homologs in the occlusion-derived form of baculoviruses. Several core gene products unknown from baculoviruses were also identified as envelope or nucleocapsid components. Our second goal was to functionally characterize a core gene unknown from baculoviruses that was originally named HzNVorf64-like. Immunoblotting assays supported our proteomic data that identified HzNVorf64-like as an envelope protein. We thus renamed HzNVorf64-like as MdBVe46, which we further hypothesized was important for infection of C. includens. Knockdown of MdBVe46 by RNA interference (RNAi) greatly reduced transcript and protein abundance. Knockdown of MdBVe46 also altered virion morphogenesis, near-fully inhibited infection of C. includens, and significantly reduced the proportion of hosts that were successfully parasitized by M. demolitor.

Download Full-text

Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1912006116 ◽

2019 ◽

Vol 116 (39) ◽

pp. 19585-19592 ◽

Cited By ~ 32

Author(s):

Julien Guglielmini ◽

Anthony C. Woo ◽

Mart Krupovic ◽

Patrick Forterre ◽

Morgan Gaia

Keyword(s):

Phylogenetic Trees ◽

Dna Viruses ◽

Double Stranded Dna ◽

Virion Morphogenesis ◽

Eukaryotic Dna ◽

Dsdna Viruses ◽

Virion Formation ◽

Intense Debate ◽

Core Genes

Giant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution, and potential roles in the emergence of modern eukaryotes remain subjects of intense debate. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of 2 superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were transferred between 2 clades of NCLDVs and proto-eukaryotes, giving rise to 2 of the 3 eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.

Download Full-text

Evaluation of a Genome-ScaleIn SilicoMetabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

Applied and Environmental Microbiology ◽

10.1128/aem.01795-12 ◽

2012 ◽

Vol 78 (24) ◽

pp. 8735-8742 ◽

Cited By ~ 12

Author(s):

Yilin Fang ◽

Michael J. Wilkins ◽

Steven B. Yabusaki ◽

Mary S. Lipton ◽

Philip E. Long

Keyword(s):

Proteomic Analysis ◽

In Silico ◽

Field Experiments ◽

Metabolic Model ◽

Geobacter Metallireducens ◽

Content Type ◽

Proteomic Data ◽

Subsurface Environment ◽

A Genome ◽

Genome Scale

ABSTRACTAccurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within anin silicomodel using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model ofGeobacter metallireducens—specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-basedin silicomodelof G. metallireducensrelates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637G. metallireducensproteins detected during the 2008 experiment were associated with specific metabolic reactions in thein silicomodel. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through thein silicomodel reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in thein silicomodel that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.

Download Full-text

TMT-based Proteomic Analysis and Protein Expression During Excystation of Cryptosporidium Anderson

10.21203/rs.3.rs-892460/v1 ◽

2021 ◽

Author(s):

Dongfang Li ◽

Zhaohui Cui ◽

Luyang Wang ◽

Kaihui Zhang ◽

Letian Cao ◽

...

Keyword(s):

Proteomic Analysis ◽

Vaccine Development ◽

Protein Composition ◽

Tandem Mass ◽

Liquid Chromatograph ◽

Control Of Gene Expression ◽

Proteomic Data ◽

Cryptosporidium Andersoni ◽

New Information ◽

Infected Adult

Abstract Background: Cryptosporidium andersoni (C. andersoni) initiates infection by the release of sporozoites through excystation. However, the proteins involved in excystation remain unknown. Researching the proteins that participate in the excystation of C. andersoni oocysts will fill the gap in our understanding of the excystation system of this parasitic pathogen. Methods: In this study, C. andersoni oocysts were collected and purified from the feces of naturally infected adult cows. Tandem mass tags (TMT) coupled with liquid chromatograph- tandem mass spectrometry (LC-MS/MS) proteomic analysis was used to investigate the proteomic expression profile of C. andersoni oocysts during excystation. Results: Our proteomic analysis identified a total of 1586 proteins, of which 17 were identified as differentially expressed proteins (DEPs), with 10 upregulated and 7 downregulated proteins. Each of those 17 proteins had multiple biological functions associated with control of gene expression at the level of transcription and biosynthetic and metabolic processes. Quantitative real-time PCR of eight selected genes validated the proteomic data.Conclusions: Our findings provide new information on the protein composition of C. andersoni oocysts as well as possible excystation factors. These data may help us to better understand the pathology of C. andersoni and thus may be useful in diagnosis, vaccine development, and immunotherapy for Cryptosporidium.

Download Full-text

Detection of hepatitis B virus core gene products in sera and liver of HBV-infected individuals

Journal of Hepatology ◽

10.1016/0168-8278(89)90165-7 ◽

1989 ◽

Vol 8 (1) ◽

pp. 77-85 ◽

Cited By ~ 2

Author(s):

Lorenz Theilmann ◽

Eberhard Pfaff ◽

Burkhard Kommerell ◽

Karl Gmelin ◽

Heinz Schaller ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Core Gene ◽

Gene Products ◽

Virus Core ◽

B Virus

Download Full-text

Characterization of the VP39 envelope protein from Singapore grouper iridovirus

Canadian Journal of Microbiology ◽

10.1139/cjm-2015-0118 ◽

2015 ◽

Vol 61 (12) ◽

pp. 924-937 ◽

Cited By ~ 8

Author(s):

Honglian Zhang ◽

Sheng Zhou ◽

Liqun Xia ◽

Xiaohong Huang ◽

Youhua Huang ◽

...

Keyword(s):

Envelope Protein ◽

Core Gene ◽

Immunofluorescence Assay ◽

Current Data ◽

Viral Envelope ◽

Economic Losses ◽

Immunogold Electron Microscopy ◽

Viral Envelope Protein ◽

Drug Inhibition

Singapore grouper iridovirus (SGIV) is a major pathogen that causes heavy economic losses to the grouper aquaculture industry in China and Southeast Asian countries. In the present study, a viral envelope protein, VP39, encoded by SGIV ORF39L, was identified and characterized. SGIV ORF39L was found in all sequenced iridoviruses and is now considered to be a core gene of the family Iridoviridae. ORF39L was classified as a late gene during in vitro infection using reverse transcription–polymerase chain reaction, western blotting, and a drug inhibition analysis. An indirect immunofluorescence assay revealed that the VP39 protein was confined to the cytoplasm, especially at viral assembly sites. Western blot and matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry analyses suggested that VP39 is an envelope protein. Immunogold electron microscopy further confirmed that VP39 is a viral envelope protein. Furthermore, a mouse anti-VP39 polyclonal antibody exhibited SGIV-neutralizing activity in vitro, suggesting that VP39 is involved in SGIV infection. Taken together, the current data suggest that VP39 represents a conserved envelope protein of iridoviruses that contributes to viral infection.

Download Full-text

Proteomic data in meningiomas: post-proteomic analysis can reveal novel pathophysiological pathways

Journal of Neuro-Oncology ◽

10.1007/s11060-010-0526-9 ◽

2011 ◽

Vol 104 (2) ◽

pp. 401-410 ◽

Cited By ~ 7

Author(s):

A. Herrmann ◽

J. Ooi ◽

S. Launay ◽

J. L. Searcy ◽

R. F. Deighton ◽

...

Keyword(s):

Proteomic Analysis ◽

Proteomic Data

Download Full-text

Deep learning with evolutionary and genomic profiles for identifying cancer subtypes

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720019400055 ◽

2019 ◽

Vol 17 (03) ◽

pp. 1940005 ◽

Cited By ~ 2

Author(s):

Chun-Yu Lin ◽

Peiying Ruan ◽

Ruiming Li ◽

Jinn-Moon Yang ◽

Simon See ◽

...

Keyword(s):

Breast Cancer ◽

Deep Learning ◽

Evolutionary Conservation ◽

Core Gene ◽

Breast Cancer Subtypes ◽

Gene Set ◽

Cancer Subtypes ◽

The Core ◽

Cancer Types ◽

Core Genes

Cancer subtype identification is an unmet need in precision diagnosis. Recently, evolutionary conservation has been indicated to contain informative signatures for functional significance in cancers. However, the importance of evolutionary conservation in distinguishing cancer subtypes remains largely unclear. Here, we identified the evolutionarily conserved genes (i.e. core genes) and observed that they are primarily involved in cellular pathways relevant to cell growth and metabolisms. By using these core genes, we developed two novel strategies, namely a feature-based strategy (FES) and an image-based strategy (IMS) by integrating their evolutionary and genomic profiles with the deep learning algorithm. In comparison with the FES using the random set and the strategy using the PAM50 classifier, the core gene set-based FES achieved a higher accuracy for identifying breast cancer subtypes. The IMS and FES using the core gene set yielded better performances than the other strategies, in terms of classifying both breast cancer subtypes and multiple cancer types. Moreover, the IMS is reproducible even using different gene expression data (i.e. RNA-seq and microarray). Comprehensive analysis of eight cancer types demonstrates that our evolutionary conservation-based models represent a valid and helpful approach for identifying cancer subtypes and the core gene set offers distinguishable clues of cancer subtypes.

Download Full-text

Determination of Critical Requirements for Classical Swine Fever Virus NS2-3-Independent Virion Formation

Journal of Virology ◽

10.1128/jvi.00679-19 ◽

2019 ◽

Vol 93 (18) ◽

Cited By ~ 2

Author(s):

D. Dubrau ◽

S. Schwindt ◽

O. Klemens ◽

H. Bischoff ◽

N. Tautz

Keyword(s):

Classical Swine Fever Virus ◽

Classical Swine Fever ◽

Rna Replication ◽

Fever Virus ◽

Genome Packaging ◽

Gain Of Function ◽

Diarrhea Virus ◽

Virion Production ◽

Virion Morphogenesis ◽

Virion Formation

ABSTRACTFor members of theFlaviviridae, it is known that, besides the structural proteins, nonstructural (NS) proteins also play a critical role in virion formation. Pestiviruses, such as bovine viral diarrhea virus (BVDV), rely on uncleaved NS2-3 for virion formation, while its cleavage product, NS3, is selectively active in RNA replication. This dogma was recently challenged by the selection of gain-of-function mutations in NS2 and NS3 which allowed virion formation in the absence of uncleaved NS2-3 in BVDV type 1 (BVDV-1) variants encoding either a ubiquitin (Ubi) (NS2-Ubi-NS3) or an internal ribosome entry site (IRES) (NS2-IRES-NS3) between NS2 and NS3. To determine whether the ability to adapt to NS2-3-independent virion morphogenesis is conserved among pestiviruses, we studied the corresponding NS2 and NS3 mutations (2/T444-V and 3/M132-A) in classical swine fever virus (CSFV). We observed that these mutations were capable of restoring low-level NS2-3-independent virion formation only for CSFV NS2-Ubi-NS3. Interestingly, a second NS2 mutation (V439-D), identified by selection, was essential for high-titer virion production. Similar to previous findings for BVDV-1, these mutations in NS2 and NS3 allowed for low-titer virion production only in CSFV NS2-IRES-NS3. For efficient virion morphogenesis, additional exchanges in NS4A (A48-T) and NS5B (D280-G) were required, indicating that these proteins cooperate in NS2-3-independent virion formation. Interestingly, both NS5B mutations, selected independently for NS2-IRES-NS3 variants of BVDV-1 and CSFV, are located in the fingertip region of the viral RNA-dependent RNA polymerase, classifying this structural element as a novel determinant for pestiviral NS2-3-independent virion formation. Together, these findings will stimulate further mechanistic studies on the genome packaging of pestiviruses.IMPORTANCEForFlaviviridaemembers, the nonstructural proteins are essential for virion formation and thus exert a dual role in RNA replication and virion morphogenesis. However, it remains unclear how these proteins are functionalized for either process. In wild-type pestiviruses, the NS3/4A complex is selectively active in RNA replication, while NS2-3/4A is essential for virion formation. Mutations recently identified in BVDV-1 rendered NS3/4A capable of supporting NS2-3-independent virion morphogenesis. A comparison of NS3/4A complexes incapable/capable of supporting virion morphogenesis revealed that changes in NS3/NS4A surface interactions are decisive for the gain of function. However, so far, the role of the NS2 mutations as well as the accessory mutations additionally required in the NS2-IRES-NS3 virus variant has not been clarified. To unravel the course of genome packaging, the additional sets of mutations obtained for a second pestivirus species (CSFV) are of significant importance to develop mechanistic models for this complex process.

Download Full-text

Comparative proteomic analysis of chestnut blight fungus,Cryphonectria parasitica, under tannic-acid-inducing and hypovirus-regulating conditions

Canadian Journal of Microbiology ◽

10.1139/w2012-065 ◽

2012 ◽

Vol 58 (7) ◽

pp. 863-871 ◽

Cited By ~ 8

Author(s):

Jung-Mi Kim ◽

Jin-Ah Park ◽

Dae-Hyuk Kim

Keyword(s):

Tannic Acid ◽

Proteomic Analysis ◽

Cryphonectria Parasitica ◽

Chestnut Blight ◽

Gene Products ◽

Glutathione S Transferase ◽

Chestnut Blight Fungus ◽

Shock Proteins ◽

Related Proteins ◽

Hypothetical Genes

Chestnut blight fungus, Cryphonectria parasitica , and its hypovirus present a useful model system for investigating the mechanisms of hypoviral infection. To identify gene products associated with fungal pathogenicity and hypoviral regulation, we attempted a proteomic analysis of the virus-free EP155/2 strain and its isogenic virus-infected UEP1 strain in response to tannic acid (TA), which is abundant in the bark of chestnut trees. In this study, pretreatment of mycelia grown on TA-supplemented media was developed for proteomic analysis. Approximately 704 proteins from the mycelia of the EP155/2 strain were reproducibly present in 3 independent extractions. Among these, 111 and 79 spots were found to be responsive to hypovirus infection and TA supplementation, respectively. The TA-grown UEP1 strain yielded 28 spots showing an expression pattern different from that of untreated UEP1. Thirty protein spots showing considerable differences in spot density were selected for further analysis. Hybrid tandem LC-MS/MS spectrometry of the 30 selected protein spots revealed that 29 were identified while 1 was unidentified. Among the identified 29 proteins, 15 were metabolic enzymes; 5 were stress-related, of which 4 were heat-shock proteins and 1 was glutathione S-transferase; 5 were signaling and cellular process-related proteins; 2 were structural proteins; and 2 matched proteins of hypothetical genes.

Download Full-text

Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

Open Biology ◽

10.1098/rsob.140133 ◽

2015 ◽

Vol 5 (1) ◽

pp. 140133 ◽

Cited By ~ 83

Author(s):

Nitin Kumar ◽

Ganesh Lad ◽

Elisa Giuntini ◽

Maria E. Kaye ◽

Piyachat Udomwong ◽

...

Keyword(s):

Rhizobium Leguminosarum ◽

Bacterial Population ◽

Population Genomics ◽

Bacterial Species ◽

Core Gene ◽

Biological Species ◽

Ecological Groups ◽

Genetic Isolation ◽

Taxonomic Framework ◽

Core Genes

Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum , they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny.

Download Full-text