bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Autographa californica Multiple Nucleopolyhedrovirus
ac83
Gene Contains a
cis
-Acting Element That Is Essential for Nucleocapsid Assembly
Authors: Huang Zhihong , Pan Mengjia , Zhu Silei , Zhang Hao , Wu Wenbi , Yuan Meijin , Yang Kai 
Published: December 2016

ABSTRACT

Baculoviridae
is a family of insect-specific viruses that have a circular double-stranded DNA genome packaged within a rod-shaped capsid. The mechanism of baculovirus nucleocapsid assembly remains unclear. Previous studies have shown that deletion of the
ac83
gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) blocks viral nucleocapsid assembly. Interestingly, the
ac83
-encoded protein Ac83 is not a component of the nucleocapsid, implying a particular role for
ac83
in nucleocapsid assembly that may be independent of its protein product. To examine this possibility, Ac83 synthesis was disrupted by insertion of a chloramphenicol resistance gene into its coding sequence or by deleting its promoter and translation start codon. Both mutants produced progeny viruses normally, indicating that the Ac83 protein is not required for nucleocapsid assembly. Subsequently, complementation assays showed that the production of progeny viruses required the presence of
ac83
in the AcMNPV genome instead of its presence in
trans
. Therefore, we reasoned that
ac83
is involved in nucleocapsid assembly via an internal
cis
-acting element, which we named the nucleocapsid assembly-essential element (NAE). The NAE was identified to lie within nucleotides 1651 to 1850 of
ac83
and had 8 conserved A/T-rich regions. Sequences homologous to the NAE were found only in alphabaculoviruses and have a conserved positional relationship with another essential
cis
-acting element that was recently identified. The identification of the NAE may help to connect the data of viral
cis
-acting elements and related proteins in the baculovirus nucleocapsid assembly, which is important for elucidating DNA-protein interaction events during this process.

IMPORTANCE
Virus nucleocapsid assembly usually requires specific
cis
-acting elements in the viral genome for various processes, such as the selection of the viral genome from the cellular nucleic acids, the cleavage of concatemeric viral genome replication intermediates, and the encapsidation of the viral genome into procapsids. In linear DNA viruses, such elements generally locate at the ends of the viral genome; however, most of these elements remain unidentified in circular DNA viruses (including baculovirus) due to their circular genomic conformation. Here, we identified a nucleocapsid assembly-essential element in the AcMNPV (the archetype of baculovirus) genome. This finding provides an important reference for studies of nucleocapsid assembly-related elements in baculoviruses and other circular DNA viruses. Moreover, as most of the previous studies of baculovirus nucleocapsid assembly have been focused on viral proteins, our study provides a novel entry point to investigate this mechanism via
cis
-acting elements in the viral genome.
Barriers to Infection of Human Cells by Feline Leukemia Virus: Insights into Resistance to Zoonosis
Authors: Terry Anne , Kilbey Anna , Naseer Asif , Levy Laura S. , Ahmad Shamim , Watts Ciorsdaidh , Mackay Nancy , Cameron Ewan , Wilson Sam , Neil James C. 
Published: December 2016

ABSTRACT

The human genome displays a rich fossil record of past gammaretrovirus infections, yet no current epidemic is evident, despite environmental exposure to viruses that infect human cells
in vitro
. Feline leukemia viruses (FeLVs) rank high on this list, but neither domestic nor workplace exposure has been associated with detectable serological responses. Nonspecific inactivation of gammaretroviruses by serum factors appears insufficient to explain these observations. To investigate further, we explored the susceptibilities of primary and established human cell lines to FeLV-B, the most likely zoonotic variant. Fully permissive infection was common in cancer-derived cell lines but was also a feature of nontransformed keratinocytes and lung fibroblasts. Cells of hematopoietic origin were generally less permissive and formed discrete groups on the basis of high or low intracellular protein expression and virion release. Potent repression was observed in primary human blood mononuclear cells and a subset of leukemia cell lines. However, the early steps of reverse transcription and integration appear to be unimpaired in nonpermissive cells. FeLV-B was subject to G→A hypermutation with a predominant APOBEC3G signature in partially permissive cells but was not mutated in permissive cells or in nonpermissive cells that block secondary viral spread. Distinct cellular barriers that protect primary human blood cells are likely to be important in protection against zoonotic infection with FeLV.

IMPORTANCE
Domestic exposure to gammaretroviruses such as feline leukemia viruses (FeLVs) occurs worldwide, but the basis of human resistance to infection remains incompletely understood. The potential threat is evident from the human genome sequence, which reveals many past epidemics of gammaretrovirus infection, and from recent cross-species jumps of gammaretroviruses from rodents to primates and marsupials. This study examined resistance to infection at the cellular level with the most prevalent human cell-tropic FeLV variant, FeLV-B. We found that blood cells are uniquely resistant to infection with FeLV-B due to the activity of cellular enzymes that mutate the viral genome. A second block, which appears to suppress viral gene expression after the viral genome has integrated into the host cell genome, was identified. Since cells derived from other normal human cell types are fully supportive of FeLV replication, innate resistance of blood cells could be critical in protecting against cross-species infection.
Binding of the Methyl Donor
S
-Adenosyl-
l
-Methionine to Middle East Respiratory Syndrome Coronavirus 2′-
O
-Methyltransferase nsp16 Promotes Recruitment of the Allosteric Activator nsp10
Authors: Aouadi Wahiba , Blanjoie Alexandre , Vasseur Jean-Jacques , Debart Françoise , Canard Bruno , Decroly Etienne 
Published: December 2016

ABSTRACT

The Middle East respiratory syndrome coronavirus (MERS-CoV) nonstructural protein 16 (nsp16) is an
S
-adenosyl-
l
-methionine (SAM)-dependent 2′-
O
-methyltransferase (2′-O-MTase) that is thought to methylate the ribose 2′-OH of the first transcribed nucleotide (N
1
) of viral RNA cap structures. This 2′-O-MTase activity is regulated by nsp10. The 2′-
O
methylation prevents virus detection by cell innate immunity mechanisms and viral translation inhibition by the interferon-stimulated IFIT-1 protein. To unravel the regulation of nsp10/nsp16 2′-O-MTase activity, we used purified MERS-CoV nsp16 and nsp10. First, we showed that nsp16 recruited N7-methylated capped RNA and SAM. The SAM binding promotes the assembly of the enzymatically active nsp10/nsp16 complex that converted
7m
GpppG (cap-0) into
7m
GpppG
2′Om
(cap-1) RNA by 2′-OH methylation of N
1
in a SAM-dependent manner. The subsequent release of SAH speeds up nsp10/nsp16 dissociation that stimulates the reaction turnover. Alanine mutagenesis and RNA binding assays allowed the identification of the nsp16 residues involved in RNA recognition forming the RNA binding groove (K46, K170, E203, D133, R38, Y47, and Y181) and the cap-0 binding site (Y30, Y132, and H174). Finally, we found that nsp10/nsp16 2′-O-MTase activity is sensitive to known MTase inhibitors, such as sinefungin and cap analogues. This characterization of the MERS-CoV 2′-O-MTase is a preliminary step toward the development of molecules to inhibit cap 2′-O methylation and to restore the host antiviral response.

IMPORTANCE
MERS-CoV codes for a cap 2′-
O
-methyltransferase that converts cap-0 into cap-1 structure in order to prevent virus detection by cell innate immunity mechanisms. We report the biochemical properties of MERS-CoV 2′O-methyltransferase, which is stimulated by nsp10 acting as an allosteric activator of the nsp16 2′-
O
-methyltransferase possibly through enhanced RNA binding affinity. In addition, we show that SAM promotes the formation of the active nsp10/nsp16 complex. Conversely, after cap methylation, the reaction turnover is speeded up by cap-1 RNA release and nsp10/nsp16 complex dissociation, at the low intracellular SAH concentration. These results suggest that SAM/SAH balance is a regulator of the 2′-
O
-methyltransferase activity and raises the possibility that SAH hydrolase inhibitors might interfere with CoV replication cycle. The enzymatic and RNA binding assays developed in this work were also used to identify nsp16 residues involved in cap-0 RNA recognition and to understand the action mode of known methyltransferase inhibitors.
Association of Human Papillomavirus 16 E2 with Rad50-Interacting Protein 1 Enhances Viral DNA Replication
Authors: Campos-León Karen , Wijendra Kalpanee , Siddiqa Abida , Pentland Ieisha , Feeney Katherine M. , Knapman Alison , Davies Rachel , Androphy Elliot J. , Parish Joanna L. 
Published: December 2016

ABSTRACT

Rad50-interacting protein 1 (Rint1) associates with the DNA damage response protein Rad50 during the transition from the S phase to the G
2
/M phase and functions in radiation-induced G
2
checkpoint control. It has also been demonstrated that Rint1 is essential in vesicle trafficking from the Golgi apparatus to the endoplasmic reticulum (ER) through an interaction with Zeste-White 10 (ZW10). We have isolated a novel interaction between Rint1 and the human papillomavirus 16 (HPV16) transcription and replication factor E2. E2 binds to Rint1 within its ZW10 interaction domain, and we show that in the absence of E2, Rint1 is localized to the ER and associates with ZW10. E2 expression results in a disruption of the Rint1-ZW10 interaction and an accumulation of nuclear Rint1, coincident with a significant reduction in vesicle movement from the ER to the Golgi apparatus. Interestingly, nuclear Rint1 and members of the Mre11/Rad50/Nbs1 (MRN) complex were found in distinct E2 nuclear foci, which peaked during mid-S phase, indicating that the recruitment of Rint1 to E2 foci within the nucleus may also result in the recruitment of this DNA damage-sensing protein complex. We show that exogenous Rint1 expression enhances E2-dependent virus replication. Conversely, the overexpression of a truncated Rint1 protein that retains the E2 binding domain but not the Rad50 binding domain acts as a dominant negative inhibitor of E2-dependent HPV replication. Put together, these experiments demonstrate that the interaction between Rint1 and E2 has an important function in HPV replication.

IMPORTANCE
HPV infections are an important driver of many epithelial cancers, including those within the anogenital and oropharyngeal tracts. The HPV life cycle is tightly regulated and intimately linked to the differentiation of the epithelial cells that it infects. HPV replication factories formed in the nucleus are locations where viral DNA is copied to support virus persistence and amplification of infection. The recruitment of specific cellular protein complexes to these factories aids efficient and controlled viral replication. We have identified a novel HPV-host interaction that functions in the cellular response to DNA damage and cell cycle control. We show that the HPV E2 protein targets Rad50-interacting protein 1 (Rint1) to facilitate virus genome replication. These findings add to our understanding of how HPV replicates and the host cell pathways that are targeted by HPV to support virus replication. Understanding these pathways will allow further research into novel inhibitors of HPV genome replication.
Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance
Authors: Hove-Jensen Bjarne , Andersen Kasper R. , Kilstrup Mogens , Martinussen Jan , Switzer Robert L. , Willemoës Martin 
Published: December 2016

SUMMARYPhosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.
XYZ-like spectra from Laplace sum rule at N2LO in the chiral limit
Authors: Albuquerque R. , Narison S. , Fanomezana F. , Rabemananjara A. , Rabetiarivony D. , Randriamanatrika G. 
Published: December 2016

We present new compact integrated expressions of QCD spectral functions of heavy-light molecules and four-quark [Formula: see text]-like states at lowest order (LO) of perturbative (PT) QCD and up to [Formula: see text] condensates of the Operator Product Expansion (OPE). Then, by including up to next-to-next leading order (N2LO) PT QCD corrections, which we have estimated by assuming the factorization of the four-quark spectral functions, we improve previous LO results from QCD spectral sum rules (QSSR), on the [Formula: see text]-like masses and decay constants which suffer from the ill-defined heavy quark mass. PT N3LO corrections are estimated using a geometric growth of the PT series and are included in the systematic errors. Our optimal results based on stability criteria are summarized in Tables 11–14 and compared, in Sec. 10, with experimental candidates and some LO QSSR results. We conclude that the masses of the [Formula: see text] observed states are compatible with (almost) pure [Formula: see text], [Formula: see text] molecule or/and four-quark states. The ones of the [Formula: see text], [Formula: see text] molecule/four-quark states are about 1.5 GeV above the [Formula: see text] mesons experimental candidates and hadronic thresholds. We also find that the couplings of these exotics to the associated interpolating currents are weaker than that of ordinary [Formula: see text] mesons [Formula: see text] and may behave numerically as [Formula: see text] (respectively [Formula: see text]) for the [Formula: see text], [Formula: see text] (respectively [Formula: see text], [Formula: see text]) states which can stimulate further theoretical studies of these decay constants.
Monotone homotopies and contracting discs on Riemannian surfaces
Authors: Chambers Gregory R. , Rotman Regina 
Published: December 2016

A monotone homotopy is a homotopy composed of simple closed curves which are also pairwise disjoint. In this paper, we prove a “gluing” theorem for monotone homotopies; we show that two monotone homotopies which have appropriate overlap can be replaced by a single monotone homotopy. The ideas used to prove this theorem are used in [G. R. Chambers and Y. Liokumovich, Existence of minimal hypersurfaces in complete manifolds of finite volume, arXiv:1609.04058] to prove an analogous result for cycles, which forms a critical step in their proof of the existence of minimal surfaces in complete non-compact manifolds of finite volume. We also show that, if monotone homotopies exist, then fixed point contractions through short curves exist. In particular, suppose that [Formula: see text] is a simple closed curve of a Riemannian surface, and that there exists a monotone contraction which covers a disc which [Formula: see text] bounds consisting of curves of length [Formula: see text]. If [Formula: see text] and [Formula: see text], then there exists a homotopy that contracts [Formula: see text] to [Formula: see text] over loops that are based at [Formula: see text] and have length bounded by [Formula: see text], where [Formula: see text] is the diameter of the surface. If the surface is a disc, and if [Formula: see text] is the boundary of this disc, then this bound can be improved to [Formula: see text].
Phase Ib Study of Safety and Pharmacokinetics of the PI3K Inhibitor SAR245408 with the HER3-Neutralizing Human Antibody SAR256212 in Patients with Solid Tumors
Authors: Abramson Vandana G. , Supko Jeffrey G. , Ballinger Tarah , Cleary James M. , Hilton John F. , Tolaney Sara M. , Chau Nicole G. , Cho Daniel C. , Pearlberg Joseph , Lager Joanne , Shapiro Geoffrey I. , Arteaga Carlos L. 
Published: December 2016

Abstract
Purpose: This phase Ib study was designed to determine the MTD, safety, preliminary efficacy, and pharmacokinetics of the HER3 (ErbB3) mAb SAR256212 in combination with the oral PI3K inhibitor SAR245408 for patients with metastatic or locally advanced solid tumors.
Experimental Design: Patients received the combination of intravenous SAR256212 and oral SAR245408 in a 3 + 3 dose-escalation design until occurrence of disease progression or dose-limiting toxicity. Objective response rate, pharmacokinetics, pharmacodynamics, and PIK3CA mutational status were also evaluated.
Results: Twenty-seven patients were enrolled. Thirteen of 20 patients tested (65%) had a hotspot-activating mutation in PIK3CA in their tumor. The MTD was determined to be SAR256212 at 40 mg/kg loading dose followed by 20 mg/kg weekly, plus SAR245408 200 mg daily. Dose-limiting toxicities included rash and hypotension; the most frequent treatment-related side effect was diarrhea (66.7%). Twenty-three patients were evaluable for efficacy, of which 12 patients (52.2%) had stable disease and 11 patients (47.8%) had progression of disease as best response. In this study with a limited sample size, there was no difference in best response between patients with PI3KCA-mutant versus PIK3CA wild-type tumors (P = 0.07). The concurrent administration of SAR245408 and SAR256212 did not appear to have an effect on the pharmacokinetics of either drug.
Conclusions: The combination of SAR256212 and SAR245408 resulted in stable disease as the best response. Side effects seen in combination were similar to the profiles of each individual drug. Patient outcome was the same regardless of tumor PI3KCA mutation status. Clin Cancer Res; 23(14); 3520–8. ©2016 AACR.
Let-7 Status Is Crucial for PARP1 Expression in HER2-Overexpressing Breast Tumors
Authors: Wielgos Monica E. , Rajbhandari Rajani , Cooper Tiffiny S. , Wei Shi , Nozell Susan , Yang Eddy S. 
Published: December 2016

Abstract
HER2+ breast tumors have been shown to express elevated levels of PARP1 protein. Yet, the mechanism by which PARP1 is upregulated in HER2+ breast cancer is unknown. Here, knockdown of HER2 (ERBB2) in HER2+ breast cancer cells resulted in a reduction in PARP1 protein. Conversely, ectopic overexpression of HER2 in a non-HER2–overexpressing cell line resulted in increased PARP1 protein levels. Alterations in HER2 expression had no significant effect on PARP1 transcript levels. Instead, HER2 mRNA status was inversely correlated with let-7a miRNA levels in breast cancer cells. Ectopic expression of let-7a miRNA resulted in downregulation of PARP1 protein, whereas expression of the let-7a anti-miRNA increased PARP1 protein. Furthermore, luciferase assays demonstrate that let-7a regulates PARP1 via its 3′UTR. Importantly, let-7a was significantly lower in human HER2+ breast tumors compared with HER2− breast tumors and inversely correlated with PARP1 protein levels. Finally, HER2+ breast cancer cells exhibited similar cytotoxicity to ectopic let-7a expression as the PARP inhibitor veliparib (ABT-888). Collectively, these results reveal that increased PARP1 expression in HER2+ breast cancers is regulated by the let-7a miRNA, and that let-7a is a potential strategy to suppress PARP1 activity.
Implications: This study reports the novel findings that HER2 increases PARP1 protein via suppression of the let-7a miRNA, which regulates the PARP1 3′-UTR. Moreover, HER2 status correlates with high PARP1 and low let-7a in breast cancer clinical specimens. Mol Cancer Res; 15(3); 340–7. ©2016 AACR.
Nuclear Import of JAK1 Is Mediated by a Classical NLS and Is Required for Survival of Diffuse Large B-cell Lymphoma
Authors: Zhu Fen , Hwang Byounghoon , Miyamoto Shigeki , Rui Lixin 
Published: December 2016

Abstract
JAKs are non-receptor tyrosine kinases that are generally found in association with cytokine receptors. In the canonical pathway, roles of JAKs have well been established in activating STATs in response to cytokine stimulation to modulate gene transcription. In contrast, a noncanonical role of JAK2 has recently been discovered, in which JAK2 in the nucleus imparts the epigenetic regulation of gene transcription through phosphorylation of tyrosine 41 on the histone protein H3. Recent work further demonstrated that this noncanonical mechanism is conserved with JAK1, which is activated by the autocrine cytokines IL6 and IL10 in activated B-cell–like diffuse large B-cell lymphoma (ABC DLBCL), a cancer type that is particularly difficult to treat and has poor prognosis. However, how JAK1 gains access to the nucleus to enable epigenetic regulation remains undefined. Here, we investigated this question and revealed that JAK1 has a classical nuclear localization signal toward the N-terminal region, which can be recognized by multiple importin α isoforms. Moreover, the nuclear import of JAK1 is independent of its kinase activity but is required for the optimal expansion of ABC DLBCL cells in vitro.
Implications: This study demonstrates that the nuclear import of JAK1 is essential for the optimal fitness of ABC DLBCL cells, and targeting JAK1 nuclear localization is a potential therapeutic strategy for ABC DLBCL. Mol Cancer Res; 15(3); 348–57. ©2016 AACR.