bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of
hemF
Gene Function and Expression in
Rhodobacter sphaeroides
2.4.1
Authors: Zeilstra-Ryalls Jill H. , Schornberg Kathryn L. 
Published: December 2005

ABSTRACT

The
hemF
gene of
Rhodobacter sphaeroides
2.4.1 is predicted to code for an oxygen-dependent coproporphyrinogen III oxidase. We found that a HemF
−
mutant strain is unable to grow under aerobic conditions. We also determined that
hemF
expression is controlled by oxygen, which is mediated, at least in part, by the response regulatory protein PrrA.
Whole-Genome Comparison betweenPhotorhabdusStrains To Identify Genomic Regions Involved in the Specificity of Nematode Interaction
Authors: Gaudriault S. , Duchaud E. , Lanois A. , Canoy A.-S. , Bourot S. , DeRose R. , Kunst F. , Boemare N. , Givaudan A. 
Published: December 2005

ABSTRACTThe bacteriumPhotorhabdusestablishes a highly specific association withHeterorhabditis, its nematode host.Photorhabdusstrains associated withHeterorhabditis bacteriophoraorHeterorhabditis megidiswere compared using aPhotorhabdusDNA microarray. We describe 31 regions belonging to thePhotorhabdusflexible gene pool. Distribution analysis of regions among thePhotorhabdusgenus identified loci possibly involved in nematode specificity.
Low pH-Dependent Endosomal Processing of the Incoming Parvovirus Minute Virus of Mice Virion Leads to Externalization of the VP1 N-Terminal Sequence (N-VP1), N-VP2 Cleavage, and Uncoating of the Full-Length Genome
Authors: Mani Bernhard , Baltzer Claudia , Valle Noelia , Almendral José M. , Kempf Christoph , Ros Carlos 
Published: December 2005

ABSTRACT
Minute virus of mice (MVM) enters the host cell via receptor-mediated endocytosis. Although endosomal processing is required, its role remains uncertain. In particular, the effect of low endosomal pH on capsid configuration and nuclear delivery of the viral genome is unclear. We have followed the progression and structural transitions of DNA full-virus capsids (FC) and empty capsids (EC) containing the VP1 and VP2 structural proteins and of VP2-only virus-like particles (VLP) during the endosomal trafficking. Three capsid rearrangements were detected in FC: externalization of the VP1 N-terminal sequence (N-VP1), cleavage of the exposed VP2 N-terminal sequence (N-VP2), and uncoating of the full-length genome. All three capsid modifications occurred simultaneously, starting as early as 30 min after internalization, and all of them were blocked by raising the endosomal pH. In particles lacking viral single-stranded DNA (EC and VLP), the N-VP2 was not exposed and thus it was not cleaved. However, the EC did externalize N-VP1 with kinetics similar to those of FC. The bulk of all the incoming particles (FC, EC, and VLP) accumulated in lysosomes without signs of lysosomal membrane destabilization. Inside lysosomes, capsid degradation was not detected, although the uncoated DNA of FC was slowly degraded. Interestingly, at any time postinfection, the amount of structural proteins of the incoming virions accumulating in the nuclear fraction was negligible. These results indicate that during the early endosomal trafficking, the MVM particles are structurally modified by low-pH-dependent mechanisms. Regardless of the structural transitions and protein composition, the majority of the entering viral particles and genomes end in lysosomes, limiting the efficiency of MVM nuclear translocation.
Varicella-Zoster Virus ORF63 Inhibits Apoptosis of Primary Human Neurons
Authors: Hood Chantelle , Cunningham Anthony L. , Slobedman Barry , Arvin Ann M. , Sommer Marvin H. , Kinchington Paul R. , Abendroth Allison 
Published: December 2005

ABSTRACT
Virus-encoded modulation of apoptosis may serve as a mechanism to enhance cell survival and virus persistence. The impact of productive varicella-zoster virus (VZV) infection on apoptosis appears to be cell type specific, as infected human sensory neurons are resistant to apoptosis, yet human fibroblasts readily become apoptotic. We sought to identify the viral gene product(s) responsible for this antiapoptotic phenotype in primary human sensory neurons. Treatment with phosphonoacetic acid to inhibit viral DNA replication and late-phase gene expression did not alter the antiapoptotic phenotype, implicating immediate-early (IE) or early genes or a virion component. Compared to the parental VZV strain (rOKA), a recombinant virus unable to express one copy of the diploid IE gene ORF63 (rOkaΔORF63) demonstrated a significant induction of apoptosis in infected neurons, as determined by three methods: annexin V staining, deoxynucleotidyltransferase-mediated dUTP-biotin nick end label staining, and transmission electron microscopy. Furthermore, neurons transfected with a plasmid expressing ORF63 resisted apoptosis induced by nerve growth factor withdrawal. These results show that ORF63 can suppress apoptosis of neurons and provide the first identification of a VZV gene encoding an antiapoptotic function. As ORF63 is expressed in neurons during both productive and latent infection, it may play a significant role in viral pathogenesis by promoting neuron survival during primary and reactivated infections.
Interferon Regulatory Factor 3 Is Necessary for Induction of Antiviral Genes during Human Cytomegalovirus Infection
Authors: DeFilippis Victor R. , Robinson Bridget , Keck Thomas M. , Hansen Scott G. , Nelson Jay A. , Früh Klaus J. 
Published: December 2005

ABSTRACT
Viral infection activates interferon regulatory factor 3 (IRF3), a cofactor for the induction of interferon-stimulated genes (ISGs). The role of IRF3 in the activation of ISGs by human cytomegalovirus (HCMV) is controversial despite the fact that HCMV has consistently been shown to induce ISGs during infection of fibroblasts. To address the function of IRF3 in HCMV-mediated ISG induction, we monitored ISG expression and global gene expression in HCMV-infected cells in which IRF3 function had been depleted by small interfering RNA or blocked by dominant negative IRF3. A specific reduction of ISG induction was observed, whereas other transcripts were unaffected. We therefore conclude that IRF3 specifically regulates ISG induction during the initial phase of HCMV infection.
Rescue of Recombinant Marburg Virus from cDNA Is Dependent on Nucleocapsid Protein VP30
Authors: Enterlein Sven , Volchkov Viktor , Weik Michael , Kolesnikova Larissa , Volchkova Valentina , Klenk Hans-Dieter , Mühlberger Elke 
Published: December 2005

ABSTRACT
Here we report recovery of infectious Marburg virus (MARV) from a full-length cDNA clone. Compared to the wild-type virus, recombinant MARV showed no difference in terms of morphology of virus particles, intracellular distribution in infected cells, and growth kinetics. The nucleocapsid protein VP30 of MARV and Ebola virus (EBOV) contains a Zn-binding motif which is important for the function of VP30 as a transcriptional activator in EBOV, whereas its role for MARV is unclear. It has been reported previously that MARV VP30 is able to support transcription in an EBOV-specific minigenome system. When the Zn-binding motif was destroyed, MARV VP30 was shown to be inactive in the EBOV system. While it was not possible to rescue recombinant MARV when the VP30 plasmid was omitted from transfection, MARV VP30 with a destroyed Zn-binding motif and EBOV VP30 were able to mediate virus recovery. In contrast, rescue of recombinant EBOV was not supported by EBOV VP30 containing a mutated Zn-binding domain.
Mefloquine, an Antimalaria Drug with Antiprion Activity In Vitro, Lacks Activity In Vivo
Authors: Kocisko David A. , Caughey Byron 
Published: December 2005

ABSTRACT
In view of the effectiveness of antimalaria drugs inhibiting abnormal protease-resistant prion protein (PrP-res) formation in scrapie agent-infected cells, we tested other antimalarial compounds for similar activity. Mefloquine (MF), a quinoline antimalaria drug, was the most active compound tested against RML and 22L mouse scrapie agent-infected cells, with 50% inhibitory concentrations of ∼0.5 and ∼1.2 μM, respectively. However, MF administered to mice did not delay the onset of intraperitoneally inoculated scrapie agent, the result previously observed with quinacrine. While most anti-scrapie agent compounds inhibit PrP-res formation in vitro, many PrP-res inhibitors have no activity in vivo. This underscores the importance of testing promising candidates in vivo.
Longitudinal Analysis of Human Immunodeficiency Virus Type 1
nef
/Long Terminal Repeat Sequences in a Cohort of Long-Term Survivors Infected from a Single Source
Authors: Churchill Melissa J. , Rhodes David I. , Learmont Jennifer C. , Sullivan John S. , Wesselingh Steven L. , Cooke Ian R. C. , Deacon Nicholas J. , Gorry Paul R. 
Published: December 2005

ABSTRACT

We studied the evolution of human immunodeficiency virus type 1 (HIV-1) in a cohort of long-term survivors infected with an attenuated strain of HIV-1 acquired from a single source. Although the cohort members experienced differing clinical courses, we demonstrate similar evolution of HIV-1
nef
/long-terminal repeat (LTR) sequences, characterized by progressive sequence deletions tending toward a minimal
nef
/LTR structure that retains only sequence elements required for viral replication. The in vivo pathogenicity of attenuated HIV-1 is therefore dictated by viral and/or host factors other than those that impose a unidirectional selection pressure on the
nef
/LTR region of the HIV-1 genome.
ATP Hydrolysis and AMP Kinase Activities of Nonstructural Protein 2C of Human Parechovirus 1
Authors: Samuilova Olga , Krogerus Camilla , Fabrichniy Igor , Hyypiä Timo 
Published: December 2005

ABSTRACT

The highly conserved picornavirus 2C proteins, thought to be involved in genome replication, contain three motifs found in NTPases/helicases of superfamily III. We report that human parechovirus 1 2C displays Mg
2+
-dependent ATP diphosphohydrolase activity in vitro, whereas other nucleoside triphosphates are not substrates for the hydrolysis. We also found that the 2C protein has an enzymatic activity that converts AMP to a corresponding diphosphate using ADP or ATP as a phosphate donor. In addition, we observed that ATP hydrolysis results in 2C autophosphorylation. These findings indicate that the parechovirus 2C protein has enzymatic activities, which may contribute to several functions in the viral replication cycle.
Nucleocytoplasmic Shuttling of Bovine Herpesvirus 1 UL47 Protein in Infected Cells
Authors: Verhagen Janneke , Hutchinson Ian , Elliott Gillian 
Published: December 2005

ABSTRACT
Previous studies with transfected cells have shown that the herpes simplex virus type 1 (HSV-1) and bovine herpesvirus 1 (BHV-1) UL47 proteins shuttle between the nucleus and the cytoplasm. HSV-1 UL47 has also been shown to bind RNA. Here we examine the BHV-1 UL47 protein in infected cells using a green fluorescent protein-UL47-expressing virus. We show that UL47 is detected in the nucleus early in infection. We use fluorescence loss in photobleaching to show that nuclear UL47 undergoes rapid nucleocytoplasmic shuttling. Furthermore, we demonstrate that actinomycin D inhibits the reaccumulation of UL47 in the nuclei of infected cells. These results suggest that UL47 exhibits behavior similar to that of previously characterized RNA-transporting proteins.
Characterization of a Vaccinia Virus Mutant with a Deletion of the D10R Gene Encoding a Putative Negative Regulator of Gene Expression
Authors: Parrish Susan , Moss Bernard 
Published: December 2005

ABSTRACT

The D9 and D10 proteins of vaccinia virus are 25% identical to each other, contain a
mutT
motif characteristic of nudix hydrolases, and are conserved in all sequenced poxviruses. Previous studies indicated that overexpression of D10 and, to a lesser extent, D9 decreased the levels of capped mRNAs and their translation products. Here, we further characterized the D10 protein and showed that only trace amounts are associated with purified virions and that it is expressed exclusively at late times after vaccinia virus infection. A viable deletion mutant (vΔD10) produced smaller plaques and lower virus yields than either wild-type virus or a D9R deletion mutant (vΔD9). Purified vΔD10 virions appeared normal by microscopic examination and biochemical analysis but produced 6- to 10-fold-fewer plaques at the same concentration as wild-type or vΔD9 virions. When 4 PFU per cell of wild-type or vΔD9 virions or equal numbers of vΔD10 virions were used for inoculation, nearly all cells were infected in each case, but viral early and late transcription was initiated more slowly in vΔD10-infected cells than in the others. However, viral early transcripts accumulated to higher levels in vΔD10-infected cells than in cells infected with the wild type or vΔD9. In addition, viral early and late mRNAs and cellular actin mRNA persisted longer in vΔD10-infected cells than in others. Furthermore, analysis of pulse-labeled proteins indicated prolonged synthesis of cellular and viral early proteins. These results are consistent with a role for D10 in regulating RNA levels in poxvirus-infected cells.
Evolution of Broad Host Range in Retroviruses Leads to Cell Death Mediated by Highly Cytopathic Variants
Authors: Rainey G. Jonah A. , Coffin John M. 
Published: December 2005

ABSTRACT

The ability of many retroviruses to cause disease can be correlated to their cytopathic effect (CPE) in tissue culture characterized by an acute period of cell death and viral DNA accumulation. Here, we show that mutants of a subgroup B avian retrovirus (
Alpharetrovirus
) cause a very dramatic CPE in certain susceptible avian cells that is coincident with elevated levels of apoptosis, as measured by nuclear morphology, and persistent viral DNA accumulation. These mutants also have a broadly extended host range that includes rodent, cat, dog, monkey, and human cells (31). Previously, we have shown that the mutants exhibit diminished resistance to superinfection. The results presented here have important implications for the process of evolution of retroviruses to use distinct cellular receptors.
Sequence Homology Required by Human Immunodeficiency Virus Type 1 To Escape from Short Interfering RNAs
Authors: Sabariegos Rosario , Giménez-Barcons Mireia , Tàpia Natalia , Clotet Bonaventura , Martínez Miguel Angel 
Published: December 2005

ABSTRACTShort interfering RNAs (siRNAs) targeting viral or cellular genes can efficiently inhibit human immunodeficiency virus type 1 (HIV-1) replication. Nevertheless, the emergence of mutations in the gene being targeted could lead to the rapid escape from the siRNA. Here, we simulate viral escape by systematically introducing single-nucleotide substitutions in all 19 HIV-1 residues targeted by an effective siRNA. We found that all mutant viruses that were tested replicated better in the presence of the siRNA than in the presence of the wild-type virus. The antiviral activity of the siRNA was completely abolished by single substitutions in 10 (positions 4 to 11, 14, and 15) out of 16 positions tested (substitution at 3 of the 19 positions explored rendered nonviable viruses). With the exception of the substitution observed at position 12, substitutions at either the 5′ end or the 3′ end (positions 1 to 3, 16, and 18) were better tolerated by the RNA interference machinery and only in part affected siRNA inhibition. Our results show that optimal HIV-1 gene silencing by siRNA requires a complete homology within most of the target sequence and that substitutions at only a few positions at the 5′ and 3′ ends are partially tolerated.
The MC160 Protein Expressed by the Dermatotropic Poxvirus Molluscum Contagiosum Virus Prevents Tumor Necrosis Factor Alpha-Induced NF-κB Activation via Inhibition of I Kappa Kinase Complex Formation
Authors: Nichols Daniel Brian , Shisler Joanna L. 
Published: December 2005

ABSTRACT
The pluripotent cytokine tumor necrosis factor alpha (TNF-α) binds to its cognate TNF receptor I (TNF-RI) to stimulate inflammation via activation of the NF-κB transcription factor. To prevent the detrimental effects of TNF-α in keratinocytes infected with the molluscum contagiosum virus (MCV), this poxvirus is expected to produce proteins that block at least one step of the TNF-RI signal transduction pathway. One such product, the MC160 protein, is predicted to interfere with this cellular response because of its homology to other proteins that regulate TNF-RI-mediated signaling. We report here that expression of MC160 molecules did significantly reduce TNF-α-mediated NF-κB activation in 293T cells, as measured by gene reporter and gel mobility shift assays. Since we observed that MC160 decreased other NF-κB activation pathways, namely those activated by receptor-interacting protein, TNF receptor-associated factor 2, NF-κB-inducing kinase, or MyD88, we hypothesized that the MC160 product interfered with I kappa kinase (IKK) activation, an event common to multiple signal transduction pathways. Indeed, MC160 protein expression was associated with a reduction in in vitro IKK kinase activity and IKK subunit phosphorylation. Further, IKK1-IKK2 interactions were not detected in MC160-expressing cells, under conditions demonstrated to induce IKK complex formation, but interactions between the MC160 protein and the major IKK subunits were undetectable. Surprisingly, MC160 expression correlated with a decrease in IKK1, but not IKK2 levels, suggesting a mechanism for MC160 disruption of IKK1-IKK2 interactions. MCV has probably retained its MC160 gene to inhibit NF-κB activation by interfering with signaling via multiple biological mediators. In the context of an MCV infection in vivo, MC160 protein expression may dampen the cellular production of proinflammatory molecules and enhance persistent infections in host keratinocytes.
Point Mutations Upstream of Hepatitis B Virus Core Gene Affect DNA Replication at the Step of Core Protein Expression
Authors: Guarnieri Michael , Kim Kyun-Hwan , Bang Genie , Li Jisu , Zhou Yonghong , Tang Xiaoli , Wands Jack , Tong Shuping 
Published: December 2005

ABSTRACTThe pregenomic RNA directs replication of the hepatitis B virus (HBV) genome by serving both as the messenger for core protein and polymerase and as the genome precursor following its packaging into the core particle. RNA packaging is mediated by a stem-loop structure present at its 5′ end designated the ε signal, which includes the core gene initiator AUG. The precore RNA has a slightly extended 5′ end to cover the entire precore region and, consequently, directs the translation of a precore/core protein, which is secreted as e antigen (HBeAg) following removal of precore-derived signal peptide and the carboxyl terminus. A naturally occurring G1862T mutation upstream of the core AUG affects the bulge of the ε signal and generates a “forbidden” residue at the −3 position of the signal peptide cleavage site. Transfection of this and other mutants into human hepatoma cells failed to prove their inhibition of HBeAg secretion but rather revealed great impairment of genome replication. This replication defect was associated with reduced expression of core protein and could be overcome by a G1899A covariation, or by nonsense or frameshift mutation in the precore region. All these mutations antagonized the G1862T mutation on core protein expression. Cotransfection of the G1862T mutant with a replication-deficient HBV genome that provides core protein intransalso restored genome replication. Consistent with our findings in cell culture, HBV genotype A found in African/Asian patients has T1862 and is associated with much lower viremia titers than the European subgroup of genotype A.
Inhibition of Protease-Resistant Prion Protein Formation in a Transformed Deer Cell Line Infected with Chronic Wasting Disease
Authors: Raymond Gregory J. , Olsen Emily A. , Lee Kil Sun , Raymond Lynne D. , Bryant P. Kruger , Baron Gerald S. , Caughey Winslow S. , Kocisko David A. , McHolland Linda E. , Favara Cynthia , Langeveld Jan P. M. , van Zijderveld Fred G. , Mayer Richard T. , Miller Michael W. , Williams Elizabeth S. , Caughey Byron 
Published: December 2005

ABSTRACT

Chronic wasting disease (CWD) is an emerging transmissible spongiform encephalopathy (prion disease) of North American cervids, i.e., mule deer, white-tailed deer, and elk (wapiti). To facilitate in vitro studies of CWD, we have developed a transformed deer cell line that is persistently infected with CWD. Primary cultures derived from uninfected mule deer brain tissue were transformed by transfection with a plasmid containing the simian virus 40 genome. A transformed cell line (MDB) was exposed to microsomes prepared from the brainstem of a CWD-affected mule deer. CWD-associated, protease-resistant prion protein (PrP
CWD
) was used as an indicator of CWD infection. Although no PrP
CWD
was detected in any of these cultures after two passes, dilution cloning of cells yielded one PrP
CWD
-positive clone out of 51. This clone, designated MDB
CWD
, has maintained stable PrP
CWD
production through 32 serial passes thus far. A second round of dilution cloning yielded 20 PrP
CWD
-positive subclones out of 30, one of which was designated MDB
CWD2
. The MDB
CWD2
cell line was positive for fibronectin and negative for microtubule-associated protein 2 (a neuronal marker) and glial fibrillary acidic protein (an activated astrocyte marker), consistent with derivation from brain fibroblasts (e.g., meningeal fibroblasts). Two inhibitors of rodent scrapie protease-resistant PrP accumulation, pentosan polysulfate and a porphyrin compound, indium (III) meso-tetra(4-sulfonatophenyl)porphine chloride, potently blocked PrP
CWD
accumulation in MDB
CWD
cells. This demonstrates the utility of these cells in a rapid in vitro screening assay for PrP
CWD
inhibitors and suggests that these compounds have potential to be active against CWD in vivo.
Restriction of Foamy Viruses by APOBEC Cytidine Deaminases
Authors: Delebecque Frédéric , Suspène Rodolphe , Calattini Sara , Casartelli Nicoletta , Saïb Ali , Froment Alain , Wain-Hobson Simon , Gessain Antoine , Vartanian Jean-Pierre , Schwartz Olivier 
Published: December 2005

ABSTRACT

Foamy viruses (FVs) are nonpathogenic retroviruses infecting many species of mammals, notably primates, cattle, and cats. We have examined whether members of the apolipoprotein B-editing catalytic polypeptide-like subunit (APOBEC) family of antiviral cytidine deaminases restrict replication of simian FV. We show that human APOBEC3G is a potent inhibitor of FV infectivity in cell culture experiments. This antiviral activity is associated with cytidine editing of the viral genome. Both molecular FV clones and primary uncloned viruses were susceptible to APOBEC3G, and viral infectivity was also inhibited by murine and simian APOBEC3G homologues, as well as by human APOBEC3F. Wild-type and
bet
-deleted viruses were similarly sensitive to this antiviral activity, suggesting that Bet does not significantly counteract APOBEC proteins. Moreover, we did not detect FV sequences that may have been targeted by APOBEC in naturally infected macaques, but we observed a few G-to-A substitutions in humans that have been accidentally contaminated by simian FV. In infected hosts, the persistence strategy employed by FV might be based on low levels of replication, as well as avoidance of cells expressing large amounts of active cytidine deaminases.