bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Rearrangements of Tn
1546
-Like Elements in Vancomycin-Resistant
Enterococcus faecium
Isolates Collected from Hospitalized Patients over a Seven-Year Period
Authors: Park Il Joong , Lee Wee Gyo , Lim Young Ae , Cho Sung Ran 
Published: September 2007

ABSTRACT

The heterogeneity of Tn
1546
results from point mutations, deletions, and the integration of insertion sequence (IS) elements. Among these variations, the presence of IS elements accounts for much of the heterogeneity. Such a rearrangement could play a key role in the evolution of the
vanA
gene cluster, and hence, it may modify its transferability. In this study, we characterized the consequence of Tn
1546
in
vanA
-containing
Enterococcus faecium
isolates collected from patients over time. From 1998 to 2004, 57
vanA
-containing
E. faecium
isolates were collected from hospitalized patients at Ajou University Hospital in Korea. PCR amplification of internal regions of Tn
1546
was performed, and both DNA strands were directly sequenced by the dideoxy termination method. All isolates were divided into three main types, including the prototype, according to the distribution of IS elements integrated into Tn
1546
elements. Type I was characterized by an IS
1542
insertion in the
orf2-vanR
intergenic region and an IS
1216V
insertion in the
vanX-vanY
intergenic region. Type II was represented by the presence of two copies of IS
1216V
at the 3′ end of IS
1542
and in the
vanX-vanY
intergenic region, as well as IS
1542
in the
orf2-vanR
intergenic region. Seventeen strains isolated from 1998 to 2000 represented type I, and 38 strains isolated from 2000 to 2004 represented type II. The remaining two isolates were the prototype. The tendency for the rearrangement of Tn
1546
was that the sequences were shortened as time passed, especially at the left or the right end, and hence, this could gradually modulate their transferability.
Identification of an APOBEC3G Binding Site in Human Immunodeficiency Virus Type 1 Vif and Inhibitors of Vif-APOBEC3G Binding
Authors: Mehle Andrew , Wilson Heather , Zhang Chengsheng , Brazier Andrew Jay , McPike Mark , Pery Erez , Gabuzda Dana 
Published: September 2007

ABSTRACT
The APOBEC3 cytidine deaminases are potent antiviral factors that restrict replication of human immunodeficiency virus type 1 (HIV-1). HIV-1 Vif binds APOBEC3G and APOBEC3F and targets these proteins for ubiquitination by forming an E3 ubiquitin ligase with cullin 5 and elongins B and C. The N-terminal region of Vif is required for APOBEC3G binding, but the binding site(s) is unknown. To identify the APOBEC3G binding site in Vif, we established a scalable binding assay in a format compatible with development of high-throughput screens. In vitro binding assays using recombinant proteins identified Vif peptides and monoclonal antibodies that inhibit Vif-APOBEC3G binding and suggested involvement of Vif residues 33 to 83 in APOBEC3G binding. Cell-based binding assays confirmed these results and demonstrated that residues 40 to 71 in the N terminus of Vif contain a nonlinear binding site for APOBEC3G. Mutation of the highly conserved residues His42/43 but not other charged residues in this region inhibited Vif-APOBEC3G binding, Vif-mediated degradation of APOBEC3G, and viral infectivity. In contrast, mutation of these residues had no significant effect on Vif binding and degradation of APOBEC3F, suggesting a differential requirement for His42/43 in Vif binding to APOBEC3G and APOBEC3F. These results identify a nonlinear APOBEC3 binding site in the N terminus of Vif and demonstrate that peptides or antibodies directed against this region can inhibit Vif-APOBEC3G binding, validating the Vif-APOBEC3 interface as a potential drug target.
CD4+CCR5+T-Cell Dynamics during Simian Immunodeficiency Virus Infection of Chinese Rhesus Macaques
Authors: Monceaux V. , Viollet L. , Petit F. , Cumont M. C. , Kaufmann G. R. , Aubertin A. M. , Hurtrel B. , Silvestri G. , Estaquier J. 
Published: September 2007

ABSTRACTSimian immunodeficiency virus (SIV) infection of rhesus macaques (RMs) provides a reliable model to study the relationship between lentivirus replication, cellular immune responses, and CD4+T-cell dynamics. Here we investigated, using SIVmac251-infected RMs of a Chinese genetic background (which experience a slower disease progression than Indian RMs), the dynamics of CD4+CCR5+T cells, as this subset of memory/activated CD4+T cells is both a preferential target of virus replication and a marker of immune activation. As expected, we observed that the number of circulating CD4+CCR5+T cells decreases transiently at the time of peak viremia. However, at 60 days postinfection, i.e., when set-point viremia is established, the level of CD4+CCR5+T cells was increased compared to the baseline level. Interestingly, this increase correlated with faster disease progression, higher plasma viremia, and early loss of CD4+T-cell function, as measured by CD4+T-cell count, the fraction of memory CD4+T cells, and the recall response to purified protein derivative. Taken together, these data show a key difference between the dynamics of the CD4+CCR5+T-cell pool (and its relationship with disease progression) in Chinese RMs and those described in previous reports for Indian SIVmac251-infected RMs. As the SIV-associated changes in the CD4+CCR5+T-cell pool reflect the opposing forces of SIV replication (which reduces this cellular pool) and immune activation (which increases it), our data suggest that in SIV-infected Chinese RMs the impact of immune activation is more prominent than that of virus replication in determining the size of the pool of CD4+CCR5+T cells in the periphery. As progression of HIV infection in humans also is associated with a relative expansion of the level of CD4+CCR5+T cells, we propose that SIV infection of Chinese RMs is a very valuable and important animal model for understanding the pathogenesis of human immunodeficiency virus infection.
HC-Pro Protein of
Potato Virus Y
Can Interact with Three
Arabidopsis
20S Proteasome Subunits In Planta
Authors: Jin Yongsheng , Ma Dongyuan , Dong Jiangli , Jin Jingchen , Li Daofeng , Deng Changwang , Wang Tao 
Published: September 2007

ABSTRACT

The multifunctional protein helper component proteinase (HC-Pro) is thought to interfere with the activity of the 20S proteasome; however, no sites of interaction have been identified for either protein. Here, we first show that the
Potato virus Y
(PVY) HC-Pro protein can interact with three
Arabidopsis
20S proteasome subunits (PAA, PBB, and PBE), using a yeast two-hybrid system and the bimolecular fluorescence complement assay. In addition, yeast two-hybrid analysis of the interaction between several mutant subunits of the 20S proteasome and PVY HC-Pro confirmed that residues 81 to 140 of PAA, 1 to 80 of PBB, and 160 to 274 of PBE are necessary for binding PAA, PBB, and PBE to PVY HC-Pro, respectively. Deletion mutant analysis of PVY HC-Pro showed that the N terminus (residues 1 to 97) is necessary for its interaction with three
Arabidopsis
20S proteasome subunits. The ability of HC-Pro to interact and interfere with the activity of the 20S proteasome may help explain the molecular basis of its multifunctional character.
Activation of the Human T-Cell Leukemia Virus Type 1 Long Terminal Repeat by the Ternary Complex Factor Elk-1
Authors: Winter Heather Y. , Dayaram Tajhal , Marriott Susan J. 
Published: September 2007

ABSTRACT
Serum response factor (SRF) was recently shown to bind and activate the human T-cell leukemia virus type 1 (HTLV-1) promoter at bases −116 to −125 relative to the transcription start site. In addition to the SRF binding site (CArG box), serum response elements (SRE) also typically contain a binding site for a member of the ternary complex factor (TCF) family. Here we demonstrate the presence of two TCF binding sites upstream of the viral CArG box. Binding of the TCF family member Elk-1 to these sites was shown to activate transcription of the promoter. Based on these results, the position of the previously described viral SRE (vSRE) within the HTLV-1 promoter can be extended from −116 to −157 to include the two newly identified TCF sites. Purified Elk-1 bound to a probe containing the vSRE, and this complex formed a ternary complex with SRF. In addition, the complex formed by nuclear extract on this probe contained Elk-1, as shown by electrophoretic mobility shift assay supershift. Both of the predicted TCF sites independently bound Elk-1. Elk-1 activated transcription of the HTLV-1 long terminal repeat (LTR), and mutations within either of the TCF sites or the CArG box reduced responsiveness of the LTR to Elk-1. Chromatin immunoprecipitation demonstrated that Elk-1 associates with the HTLV-1 LTR in vivo. These results identify a functional SRE within the HTLV-1 LTR and suggest that both Elk-1 and SRF play important roles in regulating basal HTLV-1 gene expression.
Virp1 Is a Host Protein with a Major Role in
Potato Spindle Tuber Viroid
Infection in
Nicotiana
Plants
Authors: Kalantidis K. , Denti M. A. , Tzortzakaki S. , Marinou E. , Tabler M. , Tsagris M. 
Published: September 2007

ABSTRACT

Viroids are small, circular, single-stranded RNA molecules that, while not coding for any protein, cause several plant diseases. Viroids rely for their infectious cycle on host proteins, most of which are likely to be involved in endogenous RNA-mediated phenomena. Therefore, characterization of host factors interacting with the viroid may contribute to the elucidation of RNA-related pathways of the hosts.
Potato spindle tuber viroid
(PSTVd) infects several members of the
Solanaceae
family. In an RNA ligand screening we have previously isolated the tomato protein Virp1 by its ability to specifically interact with PSTVd positive-strand RNA. Virp1 is a bromodomain-containing protein with an atypical RNA binding domain and a nuclear localization signal. Here we investigate the role of Virp1 in the viroid infection cycle by the use of transgenic lines of
Nicotiana tabacum
and
Nicotiana benthamiana
that either overexpress the tomato
Virp1
RNA or suppress the orthologous
Nicotiana
genes through RNA silencing. Plants of the
Virp1
-suppressed lines were not infected by PSTVd or
Citrus exocortis viroid
through mechanical inoculation, indicating a major role of Virp1 in viroid infection. On the other hand, overexpression of tomato Virp1 in
N. tabacum
and
N. benthamiana
plants did not affect PSTVd KF 440-2 infectivity or symptomatology in these species. Transfection experiments with isolated protoplasts revealed that
Virp1
-suppressed cells were unable to sustain viroid replication, suggesting that resistance to viroid infection in
Virp1
-suppressed plants is likely the result of cell-autonomous events.
The Conserved FRNK Box in HC-Pro, a Plant Viral Suppressor of Gene Silencing, Is Required for Small RNA Binding and Mediates Symptom Development
Authors: Shiboleth Yoel Moshe , Haronsky Elina , Leibman Diana , Arazi Tzahi , Wassenegger Michael , Whitham Steven A. , Gaba Victor , Gal-On Amit 
Published: September 2007

ABSTRACT

The helper component-proteinase (HC-Pro) protein of potyviruses is a suppressor of gene silencing and has been shown to elicit plant developmental-defect-like symptoms. In
Zucchini yellow mosaic virus
(ZYMV), a mutation in the highly conserved FR
180
NK box of HC-Pro to FI
180
NK causes attenuation of these symptoms. At 5 days postinoculation and before symptoms appear, virus accumulation, HC-Pro protein levels, and viral short interfering RNA (siRNA) levels are similar for the severe (FRNK) and attenuated (FINK) strains. At this stage, ZYMV
FRNK
caused greater accumulation of most microRNAs (miRNAs), and especially of their complementary miRNA “passenger” strands (miRNA*s), in systemically infected leaves than the attenuated ZYMV
FINK
did. HC-Pro
FRNK
specifically bound artificial siRNA and miRNA/miRNA* duplexes with a much higher affinity than the mutated HC-Pro
FINK
. Further analysis of the mutant and wild-type HC-Pro proteins revealed that suppressor activity of the ZYMV HC
FINK
mutant was not diminished. However, the FINK mutation caused a loss of HC-Pro suppressor function in other potyviruses. Replacement of the second positively charged amino acid in the ZYMV FRNK box to result in FRNA also caused symptom attenuation and reduced small RNA duplex-binding affinity without loss of suppressor activity. Our data suggest that the highly conserved FRNK box in the HC-Pro of potyviruses is a probable point of contact with siRNA and miRNA duplexes. The interaction of the FRNK box with populations of miRNAs directly influences their accumulation levels and regulatory functions, resulting in symptom development.
Plasma Cell-Specific Transcription Factor XBP-1s Binds to and Transactivates the Epstein-Barr Virus BZLF1 Promoter
Authors: Sun Chia Chi , Thorley-Lawson David A. 
Published: September 2007

ABSTRACT
Epstein-Barr virus (EBV) in vivo is known to establish persistent infection in resting, circulating memory B cells and to productively replicate in plasma cells. Until now, the molecular mechanism of how EBV switches from latency to lytic replication in vivo was not known. Here, we report that the plasma cell differentiation factor, XBP-1s, activates the expression of the master regulator of EBV lytic activation, BZLF1. Using reporter assays, we observed that XBP-1s was able to transactivate the BZLF1 promoter, Zp, in a plasma cell line and other lymphoid cell lines but, interestingly, not in epithelial cell lines. We have identified an XBP-1s binding site on the ZID/ZII region of Zp, which when abolished by site-directed mutagenesis led to abrogation of XBP-1s binding and promoter activation. Using the chromatin immunoprecipitation assay, we observed direct binding of XBP-1s to endogenous Zp in an EBV-infected plasma cell line. Finally, in the same cell line, we observed that overexpression of XBP-1s resulted in increased expression of BZLF1, while knockdown of XBP-1s with short hairpin RNA drastically reduces BZLF1 expression. We suggest that EBV harnesses the B-cell terminal differentiation pathway via XBP-1s as a physiological signal to reactivate and begin viral replication. We are currently investigating other signals, such as the endoplasmic reticulum stress response proteins, which act upstream of XBP-1s, to identify other interacting factors that initiate and/or amplify the lytic switch.
The Human Papillomavirus Type 16 E7 Oncoprotein Activates the Fanconi Anemia (FA) Pathway and Causes Accelerated Chromosomal Instability in FA Cells
Authors: Spardy Nicole , Duensing Anette , Charles Domonique , Haines Nathan , Nakahara Tomomi , Lambert Paul F. , Duensing Stefan 
Published: September 2007

ABSTRACTFanconi anemia (FA) patients have an increased risk for squamous cell carcinomas (SCCs) at sites of predilection for infection with high-risk human papillomavirus (HPV) types, including the oral cavity and the anogenital tract. We show here that activation of the FA pathway is a frequent event in cervical SCCs. We found that FA pathway activation is triggered mainly by the HPV type 16 (HPV-16) E7 oncoprotein and is associated with an enhanced formation of large FANCD2 foci and recruitment of FANCD2 as well as FANCD1/BRCA2 to chromatin. Episomal expression of HPV-16 oncoproteins was sufficient to activate the FA pathway. Importantly, the expression of HPV-16 E7 in FA-deficient cells led to accelerated chromosomal instability. Taken together, our findings establish the FA pathway as an early host cell response to high-risk HPV infection and may help to explain the greatly enhanced susceptibility of FA patients to squamous cell carcinogenesis at anatomic sites that are frequently infected by high-risk HPVs.
Identification of Five Major and Two Minor Genotypes of Varicella-Zoster Virus Strains: a Practical Two-Amplicon Approach Used To Genotype Clinical Isolates in Australia and New Zealand
Authors: Loparev Vladimir N. , Rubtcova Elena N. , Bostik Vanda , Govil Dhwani , Birch Christopher J. , Druce Julian D. , Schmid D. Scott , Croxson Margaret C. 
Published: September 2007

ABSTRACT
Whole genome phylogenetic analysis in this study resolved a total of five major genotypes among the 22 varicella-zoster virus (VZV) strains or isolates for which complete genomic sequences are available. Consistent with earlier publications we have designated these genotypes European 1 (E1), European 2 (E2), Japanese (J), mosaic 1 (M1), and mosaic 2 (M2). Single nucleotide polymorphism (SNP) analysis performed in a whole-genome alignment revealed that VZV isolates of all five genotypes can be accurately genotyped using SNPs from two amplicons: open reading frame 22 (ORF22) and either ORF21 or ORF50. This modified approach identifies all of the genotypes observed using any of the published genotyping protocols. Of 165 clinical varicella and zoster isolates from Australia and New Zealand typed using this approach, 67 of 127 eastern Australian isolates were E1, 30 were E2, 16 were J, 10 were M1, and 4 were M2; 25 of 38 New Zealand isolates were E1, 8 were E2, and 5 were M1. VZV strain diversity in eastern Australia is thus broader than has been described for any other region, including Europe, Africa, and North America. J strains were far more prevalent than previously observed in countries other than Japan. Two-amplicon typing was in complete accord with genotypes derived using SNP in multiple ORFs (ORFs 1, 21, 22, 38, 50, 54, and 62). Two additional minor genotypes, M3 and M4, could also be resolved using two-amplicon typing.
FoxP3+CD25+CD8+T-Cell Induction during Primary Simian Immunodeficiency Virus Infection in Cynomolgus Macaques Correlates with Low CD4+T-Cell Activation and High Viral Load
Authors: Karlsson Ingrid , Malleret Benoît , Brochard Patricia , Delache Benoît , Calvo Julien , Le Grand Roger , Vaslin Bruno 
Published: September 2007

ABSTRACTThe early immune response fails to prevent the establishment of chronic human immunodeficiency virus (HIV) infection but may influence viremia during primary infection, thereby possibly affecting long-term disease progression. CD25+FoxP3+regulatory T cells may contribute to HIV/simian immunodeficiency virus (SIV) pathogenesis by suppressing efficient antiviral responses during primary infection, favoring high levels of viral replication and the establishment of chronic infection. In contrast, they may decrease immune activation during chronic infection. CD4+regulatory T cells have been studied in the most detail, but CD8+CD25+FoxP3+T cells also have regulatory properties. We monitored the dynamics of CD25+FoxP3+T cells during primary and chronic SIVmac251 infection in cynomolgus macaques. The number of peripheral CD4+CD25+FoxP3+T cells paralleled that of memory CD4+T cells, with a rapid decline during primary infection followed by a rebound to levels just below baseline and gradual depletion during the course of infection. No change in the proportion of CD25+FoxP3+T cells was observed in peripheral lymph nodes. A small number of CD4+CD25+FoxP3+T cells at set point was associated with a high plasma viral load. In contrast, peripheral CD8+CD25+FoxP3+T cells were induced a few days after peak plasma viral load during primary infection. The number of these cells was positively correlated with viral load and negatively correlated with CD4+T-cell activation, SIV antigen-specific proliferative responses during primary infection, and plasma viral load at set point, with large numbers of CD8+CD25+FoxP3+T cells being indicative of a poor prognosis.
Entry of Hepatitis Delta Virus Requires the Conserved Cysteine Residues of the Hepatitis B Virus Envelope Protein Antigenic Loop and Is Blocked by Inhibitors of Thiol-Disulfide Exchange
Authors: Abou-Jaoudé Georges , Sureau Camille 
Published: September 2007

ABSTRACT
Hepatitis delta virus (HDV) particles are coated with the envelope proteins (large, middle, and small) of the hepatitis B virus (HBV). The large protein bears an infectivity determinant in its pre-S1 domain, whereas a second determinant has been proposed to map to the cysteine-rich antigenic loop (AGL) within the S domain of all three envelope proteins (G. Abou Jaoudé and C. Sureau, J. Virol. 79:10460-10466, 2006). In this study, the AGL cysteines were substituted by serine or alanine, and the mutants were evaluated for their function at viral entry using HDV particles and susceptible HepaRG cells. Mutations of cysteines 121 to 149 were tolerant of the production of HDV virions. The mutations altered the structure and antigenicity of the conserved “a” determinant of the AGL, as measured by conformation-sensitive antibodies, and they created a block to infectivity. Substitution of Cys-90 or Cys-221, located outside of the AGL, had no impact on the “a” determinant or viral entry. Furthermore, infectivity was maintained when the AGL CxxC motif at position 121 to 124 was modified by single-amino-acid deletion or insertion, suggesting that cysteines 121 and 124 are not catalyzers of thiol/disulfide exchange. However, membrane-impermeable inhibitors of thiol/disulfide isomerazation demonstrated a dose-dependent inhibition of infection in an in vitro assay when applied to the virus prior to inoculation or during the virus-cell interaction period. Overall, the results demonstrate the essential role of the AGL cysteines at viral entry, and they establish a correlation between the cysteine disulfide network, the conformation of the “a” determinant, and infectivity.
A High Viral Burden Predicts the Loss of CD8 T-Cell Responses Specific for Subdominant Gag Epitopes during Chronic Human Immunodeficiency Virus Infection
Authors: Geldmacher Christof , Gray Clive , Nason Martha , Currier Jeffrey R. , Haule Antelmo , Njovu Lilian , Geis Steffen , Hoffmann Oliver , Maboko Leonard , Meyerhans Andreas , Cox Josephine , Hoelscher Michael 
Published: September 2007

ABSTRACTHuman immunodeficiency virus (HIV)-specific CD8 T-cell responses targeting products encoded within the Gag open reading frame have frequently been associated with better viral control and disease outcome during the chronic phase of HIV infection. To further clarify this relationship, we have studied the dynamics of Gag-specific CD8 T-cell responses in relation to plasma viral load and time since infection in 33 chronically infected subjects over a 9-month period. High baseline viral loads were associated with a net loss of breadth (P< 0.001) and a decrease in the total magnitude of the Gag-specific T-cell response in general (P= 0.03). Most importantly, the baseline viral load predicted the subsequent change in the breadth of Gag recognition over time (P< 0.0001,r2= 0.41). Compared to maintained responses, lost responses were low in magnitude (P< 0.0001) and subdominant in the hierarchy of Gag-specific responses. The present study indicates that chronic exposure of the human immune system to high levels of HIV viremia is a determinant of virus-specific CD8 T-cell loss.