101
|
Yusuf M, Konc J, Sy Bing C, Trykowska Konc J, Ahmad Khairudin NB, Janezic D, Wahab HA. Structurally conserved binding sites of hemagglutinin as targets for influenza drug and vaccine development. J Chem Inf Model 2013; 53:2423-36. [PMID: 23980878 DOI: 10.1021/ci400421e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ProBiS is a new method to identify the binding site of protein through local structural alignment against the nonredundant Protein Data Bank (PDB), which may result in unique findings compared to the energy-based, geometry-based, and sequence-based predictors. In this work, binding sites of Hemagglutinin (HA), which is an important target for drugs and vaccines in influenza treatment, have been revisited by ProBiS. For the first time, the identification of conserved binding sites by local structural alignment across all subtypes and strains of HA available in PDB is presented. ProBiS finds three distinctive conserved sites on HA's structure (named Site 1, Site 2, and Site 3). Compared to other predictors, ProBiS is the only one that accurately defines the receptor binding site (Site 1). Apart from that, Site 2, which is located slightly above the TBHQ binding site, is proposed as a potential novel conserved target for membrane fusion inhibitor. Lastly, Site 3, located around Helix A at the stem domain and recently targeted by cross-reactive antibodies, is predicted to be conserved in the latest H7N9 China 2013 strain as well. The further exploration of these three sites provides valuable insight in optimizing the influenza drug and vaccine development.
Collapse
Affiliation(s)
- Muhammad Yusuf
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia , 11800 Minden, Pulau Pinang, Malaysia
| | | | | | | | | | | | | |
Collapse
|
102
|
Ho YS, Saksena NK. Glycosylation in HIV-1 envelope glycoprotein and its biological implications. Future Virol 2013. [DOI: 10.2217/fvl.13.64] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Glycosylation of HIV-1 envelope proteins (Env gp120/gp41) plays a vital role in viral evasion from the host immune response, which occurs through the masking of key neutralization epitopes and the presentation of the Env glycosylation as ‘self’ to the host immune system. Env glycosylation is generally conserved, yet its continual evolution plays an important role in modulating viral infectivity and Env immunogenicity. Thus, it is believed that Env glycosylation, which is a vital part of the HIV-1 architecture, also controls intra- and inter-clade genetic variations. Discerning intra- and inter-clade glycosylation variations could therefore yield important information for understanding the molecular and biological differences between HIV clades and may assist in effectively designing Env-based immunogens and in clearly understanding HIV vaccines. This review provides an in-depth perspective of various aspects of Env glycosylation in the context of HIV-1 pathogenesis.
Collapse
Affiliation(s)
- Yung Shwen Ho
- Computational Bioscience Research Center, Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Nitin K Saksena
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Instiute & Westmead Hospital, University of Sydney, Westmead, Sydney, NSW 2145, Australia
| |
Collapse
|
103
|
Zhao N, Enns CA. N-linked glycosylation is required for transferrin-induced stabilization of transferrin receptor 2, but not for transferrin binding or trafficking to the cell surface. Biochemistry 2013; 52:3310-9. [PMID: 23556518 PMCID: PMC3656769 DOI: 10.1021/bi4000063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Transferrin receptor 2 (TfR2) is
a member of the transferrin receptor-like
family of proteins. Mutations in TfR2 can lead to a rare form of the
iron overload disease, hereditary hemochromatosis. TfR2 is proposed
to sense body iron levels and increase the level of expression of
the iron regulatory hormone, hepcidin. Human TfR2 (hTfR2) contains
four potential Asn-linked (N-linked) glycosylation sites on its ectodomain.
The importance of glycosylation in TfR2 function has not been elucidated.
In this study, by employing site-directed mutagenesis to remove glycosylation
sites of hTfR2 individually or in combination, we found that hTfR2
was glycosylated at Asn 240, 339, and 754, while the consensus sequence
for N-linked glycosylation at Asn 540 was not utilized. Cell surface
protein biotinylation and biotin-labeled Tf indicated that in the
absence of N-linked oligosaccharides, hTfR2 still moved to the plasma
membrane and bound its ligand, holo-Tf. However, without N-linked
glycosylation, hTfR2 did not form the intersubunit disulfide bonds
as efficiently as the wild type (WT). Moreover, the unglycosylated
form of hTfR2 could not be stabilized by holo-Tf. We further provide
evidence that the unglycosylated hTfR2 behaved in manner different
from that of the WT in response to holo-Tf treatment. Thus, the putative
iron-sensing function of TfR2 could not be achieved in the absence
of N-linked oligosaccharides. On the basis of our analyses, we conclude
that unlike TfR1, N-linked glycosylation is dispensable for the cell
surface expression and holo-Tf binding, but it is required for efficient
intersubunit disulfide bond formation and holo-Tf-induced stabilization
of TfR2.
Collapse
Affiliation(s)
- Ningning Zhao
- Department of Cell and Developmental Biology, Oregon Health & Science University , Portland, Oregon 97239, United States
| | | |
Collapse
|
104
|
Vandermarliere E, Martens L. Protein structure as a means to triage proposed PTM sites. Proteomics 2013; 13:1028-35. [PMID: 23172737 DOI: 10.1002/pmic.201200232] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/13/2012] [Accepted: 09/05/2012] [Indexed: 11/07/2022]
Abstract
PTMs such as phosphorylation are often important actors in protein regulation and recognition. These functions require both visibility and accessibility to other proteins; that the modification is located at the surface of the protein. Currently, many repositories provide information on PTMs but structural information is often lacking. This study, which focuses on phosphorylation sites available in UniProtKB/Swiss-Prot, illustrates that most phosphorylation sites are indeed found at the surface of the protein, but that some sites are found buried in the core of the protein. Several of these identified buried phosphorylation sites can easily become accessible upon small conformational changes while others would require the whole protein to unfold and are hence most unlikely modification sites. Subsequent analysis of phosphorylation sites available in PRIDE demonstrates that taking the structure of the protein into account would be a good guide in the identification of the actual phosphorylated positions in phophoproteomics experiments. This analysis illustrates that care must be taken when simply accepting the position of a PTM without first analyzing its position within the protein structure if the latter is available.
Collapse
Affiliation(s)
- Elien Vandermarliere
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
| | | |
Collapse
|
105
|
Lech PJ, Tobin GJ, Bushnell R, Gutschenritter E, Pham LD, Nace R, Verhoeyen E, Cosset FL, Muller CP, Russell SJ, Nara PL. Epitope dampening monotypic measles virus hemagglutinin glycoprotein results in resistance to cocktail of monoclonal antibodies. PLoS One 2013; 8:e52306. [PMID: 23300970 PMCID: PMC3536790 DOI: 10.1371/journal.pone.0052306] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 11/16/2012] [Indexed: 12/21/2022] Open
Abstract
The measles virus (MV) is serologically monotypic. Life-long immunity is conferred by a single attack of measles or following vaccination with the MV vaccine. This is contrary to viruses such as influenza, which readily develop resistance to the immune system and recur. A better understanding of factors that restrain MV to one serotype may allow us to predict if MV will remain monotypic in the future and influence the design of novel MV vaccines and therapeutics. MV hemagglutinin (H) glycoprotein, binds to cellular receptors and subsequently triggers the fusion (F) glycoprotein to fuse the virus into the cell. H is also the major target for neutralizing antibodies. To explore if MV remains monotypic due to a lack of plasticity of the H glycoprotein, we used the technology of Immune Dampening to generate viruses with rationally designed N-linked glycosylation sites and mutations in different epitopes and screened for viruses that escaped monoclonal antibodies (mAbs). We then combined rationally designed mutations with naturally selected mutations to generate a virus resistant to a cocktail of neutralizing mAbs targeting four different epitopes simultaneously. Two epitopes were protected by engineered N-linked glycosylations and two epitopes acquired escape mutations via two consecutive rounds of artificial selection in the presence of mAbs. Three of these epitopes were targeted by mAbs known to interfere with receptor binding. Results demonstrate that, within the epitopes analyzed, H can tolerate mutations in different residues and additional N-linked glycosylations to escape mAbs. Understanding the degree of change that H can tolerate is important as we follow its evolution in a host whose immunity is vaccine induced by genotype A strains instead of multiple genetically distinct wild-type MVs.
Collapse
Affiliation(s)
- Patrycja J Lech
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
106
|
Klatt S, Rohe M, Alagesan K, Kolarich D, Konthur Z, Hartl D. Production of Glycosylated Soluble Amyloid Precursor Protein Alpha (sAPPalpha) in Leishmania tarentolae. J Proteome Res 2012; 12:396-403. [DOI: 10.1021/pr300693f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stephan Klatt
- Max Planck Institute for Molecular Genetics, 14195
Berlin, Germany
- Faculty
of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Michael Rohe
- Max-Delbrueck-Center for Molecular Medicine, 13092 Berlin, Germany
| | | | - Daniel Kolarich
- Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Zoltán Konthur
- Max Planck Institute for Molecular Genetics, 14195
Berlin, Germany
| | - Daniela Hartl
- Charité, Institute for Medical
Genetics and Human Genetics, 13353 Berlin, Germany
| |
Collapse
|
107
|
Thaysen-Andersen M, Packer NH. Site-specific glycoproteomics confirms that protein structure dictates formation of N-glycan type, core fucosylation and branching. Glycobiology 2012; 22:1440-52. [DOI: 10.1093/glycob/cws110] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
108
|
N-linked glycosylation of GP5 of porcine reproductive and respiratory syndrome virus is critically important for virus replication in vivo. J Virol 2012; 86:9941-51. [PMID: 22761373 DOI: 10.1128/jvi.07067-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
It has been proposed that the N-linked glycan addition at certain sites in GP5 of porcine reproductive and respiratory syndrome virus (PRRSV) is important for production of infectious viruses and viral infectivity. However, such specific N-linked glycosylation sites do not exist in some field PRRSV isolates. This implies that the existence of GP5-associated glycan per se is not vital to the virus life cycle. In this study, we found that mutation of individual glycosylation sites at N30, N35, N44, and N51 in GP5 did not affect virus infectivity in cultured cells. However, the mutants carrying multiple mutations at N-linked glycosylation sites in GP5 had significantly reduced virus yields compared with the wild-type (wt) virus. As a result, no viremia and antibody response were detected in piglets that were injected with a mutant without all N-linked glycans in GP5. These results suggest that the N-linked glycosylation of GP5 is critically important for virus replication in vivo. The study also showed that removal of N44-linked glycan from GP5 increased the sensitivity of mutant virus to convalescent-phase serum samples but did not elicit a high-level neutralizing antibody response to wt PRRSV. The results obtained from the present study have made significant contributions to better understanding the importance of glycosylation of GP5 in the biology of PRRSV.
Collapse
|
109
|
Dimonte S, Babakir-Mina M, Mercurio F, Di Pinto D, Ceccherini-Silberstein F, Svicher V, Perno CF. Selected amino acid changes in HIV-1 subtype-C gp41 are associated with specific gp120(V3) signatures in the regulation of co-receptor usage. Virus Res 2012; 168:73-83. [PMID: 22732432 DOI: 10.1016/j.virusres.2012.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/13/2012] [Accepted: 06/15/2012] [Indexed: 11/18/2022]
Abstract
The majority of studies have characterized the tropism of HIV-1 subtype-B isolates, but little is known about the determinants of tropism in other subtypes. So, the goal of the present study was to genetically characterize the envelope of viral proteins in terms of co-receptor usage by analyzing 356 full-length env sequences derived from HIV-1 subtype-C infected individuals. The co-receptor usage of V3 sequences was inferred by using the Geno2Pheno and PSSM algorithms, and also analyzed to the "11/25 rule". All reported env sequences were also analyzed with regard to N-linked glycosylation sites, net charge and hydrophilicity, as well as the binomial correlation phi coefficient to assess covariation among gp120(V3) and gp41 signatures and the average linkage hierarchical agglomerative clustering were also performed. Among env sequences present in Los Alamos Database, 255 and 101 sequences predicted as CCR5 and CXCR4 were selected, respectively. The classical V3 signatures at positions 11 and 25, and other specific V3 and gp41 amino acid changes were found statistically associated with different co-receptor usage. Furthermore, several statistically significant associations between V3 and gp41 signatures were also observed. The dendrogram topology showed a cluster associated with CCR5-usage composed by five gp41 mutated positions, A22V, R133M, E136G, N140L, and N166Q that clustered with T2V(V3) and G24T(V3) (bootstrap=1). Conversely, a heterogeneous cluster with CXCR4-usage, involving S11GR(V3), 13-14insIG/LG(V3), P16RQ(V3), Q18KR(V3), F20ILV(V3), D25KRQ(V3), Q32KR(V3) along with A30T(gp41), S107N(gp41), D148E(gp41), A189S(gp41) was identified (bootstrap=0.86). Our results show that as observed for HIV-1 subtype-B, also in subtype-C specific and different gp41 and gp120V3 amino acid changes are associated individually or together with CXCR4 and/or CCR5 usage. These findings strengthen previous observations that determinants of tropism may also reside in the gp41 protein.
Collapse
Affiliation(s)
- Salvatore Dimonte
- University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy.
| | | | | | | | | | | | | |
Collapse
|
110
|
Lang SL, Tao XY, Guo ZY, Tang Q, Li H, Yin CP, Li Y, Liang GD. Molecular characterization of viral G gene in emerging and re-emerging areas of rabies in China, 2007 to 2011. Virol Sin 2012; 27:194-203. [PMID: 22684474 DOI: 10.1007/s12250-012-3248-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 04/23/2012] [Indexed: 12/20/2022] Open
Abstract
In recent years (2007 to 2011), although the overall number of rabies cases in China has decreased, there is evidence of emerging or re-emerging cases in regions without previous rabies cases or with low incidence of rabies. To investigate the origin and the factors affecting the spread of rabies in China, specimens were collected from 2007 to 2011 from provinces with emerging and re-emerging cases and tested for the presence of the rabies virus. Positive specimens were combined with sequences from GenBank to perform comparisons of homology and functional sites, and to carry out phylogenetic analyses. Out of these regions, five provinces had 9 positive specimens from canine and cattle, and 34 canine or human specimens were obtained from previously high-incidence provinces. Complete sequences of G gene were obtained for these samples. Homology of the sequences of these 43 specimens was 87%-100% at the nucleotide level and 93.7%-100% at the amino acid level. These G gene sequences were combined with reference sequence from GenBank and used to construct a phylogenetic tree. The results showed that 43 specimens were all assigned to China clade I and clade II, with all specimens from emerging and re-emerging areas placed within clade I. Specimens isolated from Shanxi and Inner Mongolia in 2011 were distinct from previously-isolated local strains and had closer homology to strains from Hebei, Beijing and Tianjin whereas new isolates from Shanghai were tightly clustered with strains isolated in the 1990s. Finally, Shaanxi isolates were clustered with strains from adjacent Sichuan. Our results suggest that the rabies cases in emerging and re-emerging areas in China in the last 5 years are a consequence of the epidemic spreading from of neighboring provinces and regions experiencing a serious epidemic of rabies.
Collapse
Affiliation(s)
- Shu-Lin Lang
- College of Animal Science, Jilin Agricultural University, Changchun 130118, China
| | | | | | | | | | | | | | | |
Collapse
|
111
|
Improvement of N-glycan site occupancy of therapeutic glycoproteins produced in Pichia pastoris. Appl Microbiol Biotechnol 2012; 95:671-82. [PMID: 22569635 DOI: 10.1007/s00253-012-4067-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 03/23/2012] [Accepted: 03/27/2012] [Indexed: 10/28/2022]
Abstract
Yeast is capable of performing posttranslational modifications, such as N- or O-glycosylation. It has been demonstrated that N-glycans play critical biological roles in therapeutic glycoproteins by modulating pharmacokinetics and pharmacodynamics. However, N-glycan sites on recombinant glycoproteins produced in yeast can be underglycosylated, and hence, not completely occupied. Genomic homology analysis indicates that the Pichia pastoris oligosaccharyltransferase (OST) complex consists of multiple subunits, including OST1, OST2, OST3, OST4, OST5, OST6, STT3, SWP1, and WBP1. Monoclonal antibodies produced in P. pastoris show that N-glycan site occupancy ranges from 75-85 % and is affected mainly by the OST function, and in part, by process conditions. In this study, we demonstrate that N-glycan site occupancy of antibodies can be improved to greater than 99 %, comparable to that of antibodies produced in mammalian cells (CHO), by overexpressing Leishmania major STT3D (LmSTT3D) under the control of an inducible alcohol oxidase 1 (AOX1) promoter. N-glycan site occupancy of non-antibody glycoproteins such as recombinant human granulocyte macrophage colony-stimulating factor (rhGM-CSF) was also significantly improved, suggesting that LmSTT3D has broad substrate specificity. These results suggest that the glycosylation status of recombinant proteins can be improved by heterologous STT3 expression, which will allow for the customization of therapeutic protein profiles.
Collapse
|
112
|
Nagaoka K, Hanioka N, Ikushiro S, Yamano S, Narimatsu S. The Effects of N-Glycosylation on the Glucuronidation of Zidovudine and Morphine by UGT2B7 Expressed in HEK293 Cells. Drug Metab Pharmacokinet 2012; 27:388-97. [DOI: 10.2133/dmpk.dmpk-11-rg-135] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
113
|
Affiliation(s)
- Yuliet Mazola
- Department of Bioinformatics, Center for Genetic Engineering and Biotechnology, Havana, Cuba.
| | | | | |
Collapse
|
114
|
Miyata T, Harakuni T, Taira T, Matsuzaki G, Arakawa T. Merozoite surface protein-1 of Plasmodium yoelii fused via an oligosaccharide moiety of cholera toxin B subunit glycoprotein expressed in yeast induced protective immunity against lethal malaria infection in mice. Vaccine 2011; 30:948-58. [PMID: 22119928 DOI: 10.1016/j.vaccine.2011.11.059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 11/13/2011] [Accepted: 11/15/2011] [Indexed: 11/20/2022]
Abstract
Methylotrophic yeast (Pichia pastoris) secreted cholera toxin B subunit (CTB) predominantly as a biologically active pentamer (PpCTB) with identical ganglioside binding affinity profiles to that of choleragenoid. Unlike choleragenoid, however, the PpCTB did not induce a footpad edema response in mice. Of the two potential glycosylation sites (NIT(4-6) and NKT(90-92)) for this protein, a N-linked oligosaccharide was identified at Asn4. The oligosaccharide, presumed to extend from the lateral circumference of the CTB pentamer ring structure, was exploited as a site-specific anchoring scaffold for the C-terminal 19-kDa merozoite surface protein-1 (MSP1-19) of the rodent malaria parasite, Plasmodium yoelii. Conjugation of MSP1-19 to PpCTB via its oligosaccharide moiety induced higher protective efficacy against lethal parasite infection than conjugation directly to the PpCTB protein body in both intranasal and subcutaneous immunization regimes. Such increased protection was potentially due to the higher antigen loading capacity of CTB achieved when the antigen was linked to the extended branches of the oligosaccharide. This might have allowed the antigen to reside in more spacious molecular environment with less steric hindrance between the constituent molecules of the fusion complex.
Collapse
MESH Headings
- Administration, Intranasal
- Animals
- Cholera Toxin/genetics
- Cholera Toxin/immunology
- Disease Models, Animal
- Female
- Glycoproteins/genetics
- Glycoproteins/immunology
- Injections, Subcutaneous
- Malaria/immunology
- Malaria/prevention & control
- Malaria Vaccines/administration & dosage
- Malaria Vaccines/genetics
- Malaria Vaccines/immunology
- Merozoite Surface Protein 1/genetics
- Merozoite Surface Protein 1/immunology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Pichia/genetics
- Pichia/metabolism
- Plasmodium yoelii/genetics
- Plasmodium yoelii/immunology
- Survival Analysis
- Vaccines, Conjugate/administration & dosage
- Vaccines, Conjugate/genetics
- Vaccines, Conjugate/immunology
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
Collapse
Affiliation(s)
- Takeshi Miyata
- Molecular Microbiology Group, Department of Tropical Infectious Diseases, COMB, Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | | | | | | | | |
Collapse
|
115
|
Characterization of human endogenous retroviral elements in the blood of HIV-1-infected individuals. J Virol 2011; 86:262-76. [PMID: 22031938 DOI: 10.1128/jvi.00602-11] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We previously reported finding the RNA of a type K human endogenous retrovirus, HERV-K (HML-2), at high titers in the plasma of HIV-1-infected and cancer patients (R. Contreras-Galindo et al., J. Virol. 82:9329-9236, 2008.). The extent to which the HERV-K (HML-2) proviruses become activated and the nature of their activated viral RNAs remain important questions. Therefore, we amplified and sequenced the full-length RNA of the env gene of the type 1 and 2 HERV-K (HML-2) viruses collected from the plasma of seven HIV-1-infected patients over a period of 1 to 3 years and from five breast cancer patients in order to reconstruct the genetic evolution of these viruses. HERV-K (HML-2) RNA was found in plasma fractions of HIV-1 patients at a density of ∼1.16 g/ml that contained both immature and correctly processed HERV-K (HML-2) proteins and virus-like particles that were recognized by anti-HERV-K (HML-2) antibodies. RNA sequences from novel HERV-K (HML-2) proviruses were discovered, including K111, which is specifically active during HIV-1 infection. Viral RNA arose from complete proviruses and proviruses devoid of a 5' long terminal repeat, suggesting that the expression of HERV-K (HML-2) RNA in these patients may involve sense and antisense transcription. In HIV-1-infected individuals, the HERV-K (HML-2) viral RNA showed evidence of frequent recombination, accumulation of synonymous rather than nonsynonymous mutations, and conserved N-glycosylation sites, suggesting that some of the HERV-K (HML-2) viral RNAs have undergone reverse transcription and are under purifying selection. In contrast, HERV-K (HML-2) RNA sequences found in the blood of breast cancer patients showed no evidence of recombination and exhibited only sporadic viral mutations. This study suggests that HERV-K (HML-2) is active in HIV-1-infected patients, and the resulting RNA message reveals previously undiscovered HERV-K (HML-2) genomic sequences.
Collapse
|
116
|
Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, DeCamp AC, Magaret CA, Schief WR, Ban YEA, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog 2011; 7:e1002209. [PMID: 21980282 PMCID: PMC3182927 DOI: 10.1371/journal.ppat.1002209] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 06/26/2011] [Indexed: 12/15/2022] Open
Abstract
Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413-415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.
Collapse
Affiliation(s)
- S. Gnanakaran
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Marcus Daniels
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Brandon F. Keele
- SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Peter T. Hraber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Lapedes
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tongye Shen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Molecular Biophysics and Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Brian Gaschen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Mohan Krishnamoorthy
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hui Li
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Julie M. Decker
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jesus F. Salazar-Gonzalez
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Shuyi Wang
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chunlai Jiang
- National Engineering Laboratory of AIDS Vaccine School of Life Science, Jilin University, Changchun, China
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Feng Gao
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffrey A. Anderson
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Li-Hua Ping
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Myron S. Cohen
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, an affiliate of the Rockefeller University, New York, New York, United States of America
| | - Paul A. Goepfert
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael S. Saag
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joseph J. Eron
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Charles B. Hicks
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - William A. Blattner
- Institute of Human Virology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Georgia D. Tomaras
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Mohammed Asmal
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Norman L. Letvin
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Division of Viral Pathogenesis, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter B. Gilbert
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Allan C. DeCamp
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Craig A. Magaret
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Yih-En Andrew Ban
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Arzeda Corporation, Seattle, Washington, United States of America
| | - Ming Zhang
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia, United States of America
| | - Kelly A. Soderberg
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Joseph G. Sodroski
- Dana-Farber Cancer Institute, Department of Cancer Immunology and AIDS, Boston, Massachusetts, United States of America
| | - Barton F. Haynes
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - George M. Shaw
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Bette Korber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
| |
Collapse
|
117
|
Matsui T, Takita E, Sato T, Kinjo S, Aizawa M, Sugiura Y, Hamabata T, Sawada K, Kato K. N-glycosylation at noncanonical Asn-X-Cys sequences in plant cells. Glycobiology 2011; 21:994-9. [PMID: 21123369 DOI: 10.1093/glycob/cwq198] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The vesicular transport pathway in plant cells is often used for higher accumulation of recombinant proteins. In the endoplasmic reticulum, which acts as a gateway to the vesicular transport pathway, N-glycosylation occurs on specific Asn residues. This N-glycosylation in recombinant proteins must be carefully regulated as it can impact their enzymatic activity, half lives in serum when injected, structural stability, etc. In eukaryotic cells, including plant cells, N-glycans were found to be attached to Asn residues in Asn-X-Ser/Thr (X ≠ Pro) sequences. However, recently, N-glycosylations at noncanonical Asn-X-Cys sequences have been found in mammals and yeast. Our laboratory has discovered that N-glycans are attached to Asn residues at Asn-Thr-Cys sequences of double-repeated B subunit of Shiga toxin 2e produced in plant cells, the first reported case of N-glycosylation at a noncanonical Asn-X-Cys sequence in plant cells.
Collapse
Affiliation(s)
- Takeshi Matsui
- Advanced Technology Research Laboratories, Idemitsu Kosan Co., Ltd., 1280 Kamiizumi, Sodegaura-shi, Chiba 299-0293, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
118
|
Song W, Henquet MG, Mentink RA, van Dijk AJ, Cordewener JH, Bosch D, America AH, van der Krol AR. N-glycoproteomics in plants: Perspectives and challenges. J Proteomics 2011; 74:1463-74. [DOI: 10.1016/j.jprot.2011.05.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 04/27/2011] [Accepted: 05/02/2011] [Indexed: 12/20/2022]
|
119
|
Margraf-Schönfeld S, Böhm C, Watzl C. Glycosylation affects ligand binding and function of the activating natural killer cell receptor 2B4 (CD244) protein. J Biol Chem 2011; 286:24142-9. [PMID: 21606496 DOI: 10.1074/jbc.m111.225334] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
2B4 (CD244) is an important activating receptor for the regulation of natural killer (NK) cell responses. Here we show that 2B4 is heavily and differentially glycosylated in primary human NK cells and NK cell lines. The differential glycosylation could be attributed to sialic acid residues on N- and O-linked carbohydrates. Using a recombinant fusion protein of the extracellular domain of 2B4, we demonstrate that N-linked glycosylation of 2B4 is essential for the binding to its ligand CD48. In contrast, sialylation of 2B4 has a negative impact on ligand binding, as the interaction between 2B4 and CD48 is increased after the removal of sialic acids. This was confirmed in a functional assay system, where the desialylation of NK cells or the inhibition of O-linked glycosylation resulted in increased 2B4-mediated lysis of CD48-expressing tumor target cells. These data demonstrate that glycosylation has an important impact on 2B4-mediated NK cell function and suggest that regulated changes in glycosylation during NK cell development and activation might be involved in the regulation of NK cell responses.
Collapse
|
120
|
Bañó-Polo M, Baldin F, Tamborero S, Marti-Renom MA, Mingarro I. N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon. Protein Sci 2011; 20:179-86. [PMID: 21082725 DOI: 10.1002/pro.551] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
N-glycosylation is the most common and versatile protein modification. In eukaryotic cells, this modification is catalyzed cotranslationally by the enzyme oligosaccharyltransferase, which targets the β-amide of the asparagine in an Asn-Xaa-Ser/Thr consensus sequon (where Xaa is any amino acid but proline) in nascent proteins as they enter the endoplasmic reticulum. Because modification of the glycosylation acceptor site on membrane proteins occurs in a compartment-specific manner, the presence of glycosylation is used to indicate membrane protein topology. Moreover, glycosylation sites can be added to gain topological information. In this study, we explored the determinants of N-glycosylation with the in vitro transcription/translation of a truncated model protein in the presence of microsomes and surveyed 25,488 glycoproteins, of which 2,533 glycosylation sites had been experimentally validated. We found that glycosylation efficiency was dependent on both the distance to the C-terminus and the nature of the amino acid that preceded the consensus sequon. These findings establish a broadly applicable method for membrane protein tagging in topological studies.
Collapse
Affiliation(s)
- Manuel Bañó-Polo
- Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot E-46100, València, Spain
| | | | | | | | | |
Collapse
|
121
|
Iavarone C, Ramsauer K, Kubarenko AV, Debasitis JC, Leykin I, Weber ANR, Siggs OM, Beutler B, Zhang P, Otten G, D'Oro U, Valiante NM, Mbow ML, Visintin A. A point mutation in the amino terminus of TLR7 abolishes signaling without affecting ligand binding. THE JOURNAL OF IMMUNOLOGY 2011; 186:4213-22. [PMID: 21383246 DOI: 10.4049/jimmunol.1003585] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
TLR7 is the mammalian receptor for ssRNA and some nucleotide-like small molecules. We have generated a mouse by N-nitrose-N'-ethyl urea mutagenesis in which threonine 68 of TLR7 was substituted with isoleucine. Cells bearing this mutant TLR7 lost the sensitivity to the small-molecule TLR7 agonist resiquimod, hence the name TLR7(rsq1). In this work, we report the characterization of this mutant protein. Similar to the wild-type counterpart, TLR7(rsq1) localizes to the endoplasmic reticulum and is expressed at normal levels in both primary cells and reconstituted 293T cells. In addition to small-molecule TLR7 agonists, TLR7(rsq1) fails to be activated by ssRNA. Whole-transcriptome analysis demonstrates that TLR7 is the exclusive and indispensable receptor for both classes of ligands, consistent with the fact that both ligands induce highly similar transcriptional signatures in TLR7(wt/wt) splenocytes. Thus, TLR7(rsq1) is a bona fide phenocopy of the TLR7 null mouse. Because TLR7(rsq1) binds to ssRNA, our studies imply that the N-terminal portion of TLR7 triggers a yet to be identified event on TLR7. TLR7(rsq1) mice might represent a valuable tool to help elucidate novel aspects of TLR7 biology.
Collapse
Affiliation(s)
- Carlo Iavarone
- Immunology US, Novartis Vaccines and Diagnostics, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
122
|
Igura M, Kohda D. Selective control of oligosaccharide transfer efficiency for the N-glycosylation sequon by a point mutation in oligosaccharyltransferase. J Biol Chem 2011; 286:13255-60. [PMID: 21357684 DOI: 10.1074/jbc.m110.213900] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asn-linked glycosylation is the most ubiquitous posttranslational protein modification in eukaryotes and archaea, and in some eubacteria. Oligosaccharyltransferase (OST) catalyzes the transfer of preassembled oligosaccharides on lipid carriers onto asparagine residues in polypeptide chains. Inefficient oligosaccharide transfer results in glycoprotein heterogeneity, which is particularly bothersome in pharmaceutical glycoprotein production. Amino acid variation at the X position of the Asn-X-Ser/Thr sequon is known to modulate the glycosylation efficiency. The best amino acid at X is valine, for an archaeal Pyrococcus furiosus OST. We performed a systematic alanine mutagenesis study of the archaeal OST to identify the essential and dispensable amino acid residues in the three catalytic motifs. We then investigated the effects of the dispensable mutations on the amino acid preference in the N-glycosylation sequon. One residue position was found to selectively affect the amino acid preference at the X position. This residue is located within the recently identified DXXKXXX(M/I) motif, suggesting the involvement of this motif in N-glycosylation sequon recognition. In applications, mutations at this position may facilitate the design of OST variants adapted to particular N-glycosylation sites to reduce the heterogeneity of glycan occupancy. In fact, a mutation at this position led to 9-fold higher activity relative to the wild-type enzyme, toward a peptide containing arginine at X in place of valine. This mutational approach is potentially applicable to eukaryotic and eubacterial OSTs for the production of homogenous glycoproteins in engineered mammalian and Escherichia coli cells.
Collapse
Affiliation(s)
- Mayumi Igura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | | |
Collapse
|
123
|
Tomczak A, Pisabarro MT. Identification of CCR2-binding features in Cytl1 by a CCL2-like chemokine model. Proteins 2011; 79:1277-92. [DOI: 10.1002/prot.22963] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 12/01/2010] [Accepted: 12/03/2010] [Indexed: 11/05/2022]
|
124
|
Igura M, Kohda D. Quantitative assessment of the preferences for the amino acid residues flanking archaeal N-linked glycosylation sites. Glycobiology 2010; 21:575-83. [PMID: 21115605 DOI: 10.1093/glycob/cwq196] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oligosaccharyltransferase (OST) catalyzes the transfer of an oligosaccharide to an asparagine residue in polypeptide chains. Using positional scanning peptide libraries, we assessed the effects of amino acid variations on the in vitro glycosylation efficiency within and adjacent to an N-glycosylation consensus, Asn-X-Ser/Thr, with an archaeal OST from Pyrococcus furiosus. The amino acid variations at the X(-2), X(-1) and X(+1) positions in the sequence X(-2)-X(-1)-Asn-X-Ser/Thr-X(+1) strongly influenced the glycosylation efficiency to a similar extent at position X. The rank orders of the amino acid preferences were unique at each site. We experimentally confirmed that the archaeal OST does not require an acidic residue at the -2 position, unlike the eubacterial OSTs. Pro was disfavored at the -1 and +1 positions, although the exclusion was not as strict as that at X, whereas Pro was the most favored amino acid residue among those studied at the -2 position. The overall amino acid preferences are correlated with a conformational propensity to extend around the sequon. The results of the library experiments revealed that the optimal acceptor sequence was PYNVTK, with a K(m) of 10 µM. The heat-stable, single-subunit OST of P. furiosus is a potential candidate enzyme for the production of recombinant glycoproteins in bacterial cells. Quantitative assessment of the amino acid preferences of the OST enzyme will facilitate the proper design of a production system.
Collapse
Affiliation(s)
- Mayumi Igura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | | |
Collapse
|
125
|
Heeregrave EJ, Ampofo WK, Tetteh JKA, Ofori M, Ofori SB, Shah AS, Pollakis G, Paxton WA. Generation of HIV-1 primary isolates representative of plasma variants using the U87.CD4 cell line. J Virol Methods 2010; 169:341-50. [PMID: 20705104 DOI: 10.1016/j.jviromet.2010.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/28/2010] [Accepted: 08/03/2010] [Indexed: 11/26/2022]
Abstract
In order to obtain HIV-1 primary isolates in settings with limited access to donor PBMCs, a culture method was developed where patient PBMCs infected with HIV-1 were cultured together with U87.CD4 cells. Using this non-laborious method, it is possible to harvest virus solely on the basis of syncytia formation and circumventing monitoring of viral replication by CA-p24 ELISA. Primary isolates from 23 out of 33 patients (70%) were isolated successfully. From PCR amplification and sequencing of the V1V5 region of the viral gp120 envelope gene, primary isolates were compared with variants obtained from plasma and PBMCs of 13 patients. The primary isolates of seven patients (54%) resembled closely the plasma viral quasispecies, whereas different variants were isolated from the other patients (46%). Three patients harboured a dual infection, while this remained unnoticed from sequencing the plasma or PBMC compartment. The primary isolates were highly infectious for TZM-bl cells and could infect CD4-enriched lymphocytes. This study demonstrates that it is possible to grow viral isolates using a non-laborious and simple method. These isolates may be used in the field for studies on antiretroviral therapy or for vaccine trials.
Collapse
Affiliation(s)
- Edwin J Heeregrave
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
126
|
Lo WY, Lagrange AH, Hernandez CC, Harrison R, Dell A, Haslam SM, Sheehan JH, Macdonald RL. Glycosylation of {beta}2 subunits regulates GABAA receptor biogenesis and channel gating. J Biol Chem 2010; 285:31348-61. [PMID: 20639197 DOI: 10.1074/jbc.m110.151449] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
γ-aminobutyric acid type A (GABA(A)) receptors are heteropentameric glycoproteins. Based on consensus sequences, the GABA(A) receptor β2 subunit contains three potential N-linked glycosylation sites, Asn-32, Asn-104, and Asn-173. Homology modeling indicates that Asn-32 and Asn-104 are located before the α1 helix and in loop L3, respectively, near the top of the subunit-subunit interface on the minus side, and that Asn-173 is located in the Cys-loop near the bottom of the subunit N-terminal domain. Using site-directed mutagenesis, we demonstrated that all predicted β2 subunit glycosylation sites were glycosylated in transfected HEK293T cells. Glycosylation of each site, however, produced specific changes in α1β2 receptor surface expression and function. Although glycosylation of Asn-173 in the Cys-loop was important for stability of β2 subunits when expressed alone, results obtained with flow cytometry, brefeldin A treatment, and endo-β-N-acetylglucosaminidase H digestion suggested that glycosylation of Asn-104 was required for efficient α1β2 receptor assembly and/or stability in the endoplasmic reticulum. Patch clamp recording revealed that mutation of each site to prevent glycosylation decreased peak α1β2 receptor current amplitudes and altered the gating properties of α1β2 receptor channels by reducing mean open time due to a reduction in the proportion of long open states. In addition to functional heterogeneity, endo-β-N-acetylglucosaminidase H digestion and glycomic profiling revealed that surface β2 subunit N-glycans at Asn-173 were high mannose forms that were different from those of Asn-32 and N104. Using a homology model of the pentameric extracellular domain of α1β2 channel, we propose mechanisms for regulation of GABA(A) receptors by glycosylation.
Collapse
Affiliation(s)
- Wen-Yi Lo
- Department of Neurology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | | | | | | | | | | | | | | |
Collapse
|
127
|
Liu ZH, Yang CP, Qi XT, Xiu LL, Wang YC. Cloning, heterologous expression, and functional characterization of a chitinase gene, Lbchi32, from Limonium bicolor. Biochem Genet 2010; 48:669-79. [PMID: 20512617 DOI: 10.1007/s10528-010-9348-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 02/12/2010] [Indexed: 11/29/2022]
Abstract
In the present study, an endochitinase gene, Lbchi32, was cloned from Limonium bicolor. The cDNA sequence of Lbchi32 was 1,443 bp in length and encoded 319 amino acid residues. The DNA sequence of Lbchi32 was 2,512 bp in length and contained three exons and two introns. The Lbchi32 gene was inserted into a pPIC9 vector and transferred into Pichia pastoris strains GS115 and KM71 for heterologous expression. SDS-PAGE analyses indicated that LbCHI32 was expressed in both GS115 and KM71 and that it was secreted extracellularly. The optimal reaction conditions for LbCHI32 activity are 45 degrees C, pH 5.0, and 5 mM Ba(2+). The LbCHI32 enzyme can efficiently degrade chitin, chitin derivatives, and the cell walls of different pathogenic fungi, including phytopathogenic Rhizoctonia solani, Fusarium oxysporum, Sclerotinia sclerotiorum, Valsa sordida, Septoria tritici, and Phytophthora sojae. These findings suggest that Lbchi32 has potential use in the degradation of chitin and chitin derivatives.
Collapse
Affiliation(s)
- Zhi Hua Liu
- Northeast Forestry University, Ministry of Education, Harbin, China
| | | | | | | | | |
Collapse
|
128
|
Raska M, Novak J. Involvement of Envelope-Glycoprotein Glycans in HIV-1 Biology and Infection. Arch Immunol Ther Exp (Warsz) 2010; 58:191-208. [DOI: 10.1007/s00005-010-0072-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 11/30/2009] [Indexed: 01/24/2023]
|
129
|
Valliere-Douglass JF, Eakin CM, Wallace A, Ketchem RR, Wang W, Treuheit MJ, Balland A. Glutamine-linked and non-consensus asparagine-linked oligosaccharides present in human recombinant antibodies define novel protein glycosylation motifs. J Biol Chem 2010; 285:16012-22. [PMID: 20233717 DOI: 10.1074/jbc.m109.096412] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We report the presence of oligosaccharide structures on a glutamine residue present in the V(L) domain sequence of a recombinant human IgG2 molecule. Residue Gln-106, present in the QGT sequence following the rule of an asparagine-linked consensus motif, was modified with biantennary fucosylated oligosaccharide structures. In addition to the glycosylated glutamine, analysis of a lectin-enriched antibody population showed that 4 asparagine residues: heavy chain Asn-162, Asn-360, and light chain Asn-164, both of which are present in the IgG1 and IgG2 constant domain sequences, and Asn-35, which was present in CDR(L)1, were also modified with oligosaccharide structures at low levels. The primary sequences around these modified residues do not adhere to the N-linked consensus sequon, NX(S/T). Modeling of these residues from known antibody crystal structures and sequence homology comparison indicates that non-consensus glycosylation occurs on Asn residues in the context of a reverse consensus motif (S/T)XN located on highly flexile turns within 3 residues of a conformational change. Taken together our results indicate that protein glycosylation is governed by more diversified requirements than previously appreciated.
Collapse
|
130
|
Wu C, Zhang X, Tian Y, Song J, Yang D, Roggendorf M, Lu M, Chen X. Biological significance of amino acid substitutions in hepatitis B surface antigen (HBsAg) for glycosylation, secretion, antigenicity and immunogenicity of HBsAg and hepatitis B virus replication. J Gen Virol 2009; 91:483-92. [PMID: 19812261 DOI: 10.1099/vir.0.012740-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Amino acid substitutions of hepatitis B surface antigen (HBsAg) may affect the antigenicity and immunogenicity of HBsAg, leading to immune escape and diagnostic failure. The amino acid positions 122 and 160 are known as determinants for HBsAg subtypes d/y and w/r, respectively. The substitution K122I has been shown to strongly affect HBsAg antigenicity. In this study, we investigated the significance of naturally occurring amino acid substitutions K122I, T123N, A159G and K160N. Both T123N and K160N substitutions resulted in additional N-glycosylated forms of HBsAg, while the other mutations produced more glycosylated HBsAg compared with the wild type (wt). Detection of HBsAg by ELISA and immunofluorescence staining indicated that variant HBsAg (vtHBsAg) with K122I was not recognized by HBsAg immunoassays, while vtHBsAg with T123N, A159G, K160N and A159G/K160N had reduced antigenicity. DNA immunization in BALB/c mice revealed that wtHBsAg and vtHBsAg with T123N and K160N are able to induce antibodies to HBsAg (anti-HBs), whereas K122I and A159G greatly impair the ability of HBsAg to trigger anti-HBs responses. The cellular immune response to the HBsAg aa 29-38 epitope was enhanced by the K160N substitution. Using replication competent clones of hepatitis B virus (HBV), T123N and A159G substitutions were shown to strongly reduce virion assembly. The amino acid substitution K160N appeared to compensate for the negative effect of A159G on virion production. These results reveal complex effects of amino acid substitutions on biochemical properties of HBsAg, on antigenicity and immunogenicity, and on the replication of HBV.
Collapse
Affiliation(s)
- Chunchen Wu
- State Key Lab of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | | | | | | | | | | | | | | |
Collapse
|
131
|
Valliere-Douglass JF, Kodama P, Mujacic M, Brady LJ, Wang W, Wallace A, Yan B, Reddy P, Treuheit MJ, Balland A. Asparagine-linked oligosaccharides present on a non-consensus amino acid sequence in the CH1 domain of human antibodies. J Biol Chem 2009; 284:32493-506. [PMID: 19767389 DOI: 10.1074/jbc.m109.014803] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report that N-linked oligosaccharide structures can be present on an asparagine residue not adhering to the consensus site motif NX(S/T), where X is not proline, described in the literature. We have observed oligosaccharides on a non-consensus asparaginyl residue in the C(H)1 constant domain of IgG1 and IgG2 antibodies. The initial findings were obtained from characterization of charge variant populations evident in a recombinant human antibody of the IgG2 subclass. HPLC-MS results indicated that cation-exchange chromatography acidic variant populations were enriched in antibody with a second glycosylation site, in addition to the well documented canonical glycosylation site located in the C(H)2 domain. Subsequent tryptic and chymotryptic peptide map data indicated that the second glycosylation site was associated with the amino acid sequence TVSWN(162)SGAL in the C(H)1 domain of the antibody. This highly atypical modification is present at levels of 0.5-2.0% on most of the recombinant antibodies that have been tested and has also been observed in IgG1 antibodies derived from human donors. Site-directed mutagenesis of the C(H)1 domain sequence in a recombinant-human IgG1 antibody resulted in an increase in non-consensus glycosylation to 3.15%, a greater than 4-fold increase over the level observed in the wild type, by changing the -1 and +1 amino acids relative to the asparagine residue at position 162. We believe that further understanding of the phenomenon of non-consensus glycosylation can be used to gain fundamental insights into the fidelity of the cellular glycosylation machinery.
Collapse
|
132
|
Fahrenkrug J, Falktoft B, Georg B, Rask L. N-linked deglycosylated melanopsin retains its responsiveness to light. Biochemistry 2009; 48:5142-8. [PMID: 19413349 DOI: 10.1021/bi900249n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Melanopsin is an opsin expressed in the plasma membrane of retinal ganglion cells that mainly project to the circadian clock and thus is important for nonvisual responses to light. Rat melanopsin contains two potential sites (Asn31 and Asn35) for N-linked glycosylation in the N-terminal extracellular part. To investigate if melanopsin is N-linked glycosylated and whether N-bound glycans influence the response of melanopsin to light as evidenced by Fos mRNA induction, we transfected PC12 cells to stably express rat wild-type melanopsin or mutant melanopsin lacking both N-linked glycosylation sites. Immunoblotting for membrane-bound melanopsin from the PC12 cells transfected to express wild-type melanopsin disclosed two immunoreactive bands of 62 and 49 kDa. Removal of N-linked glycosylation by tunicamycin or PNGase F changed the 62 kDa band to a 55 kDa band, while the 49 kDa band corresponding to the core melanopsin protein was unaffected. Likewise, mutation of the two extracellular N-linked glycosylation sites gave a melanopsin size comparable to that of PNGase F or tunicamycin treatment (55 kDa). Further in vitro O-linked deglycosylation of wild-type or mutant melanopsin with O-glycosidase and neuraminidase converted the 55 kDa band to a 49 kDa band. Finally, neither in vivo N-linked deglycosylation nor mutations of the two N-linked glycosylation sites significantly affected melanopsin function measured by Fos induction after light stimulation. In conclusion, we have shown that heterologously expressed rat melanopsin is both N-linked and O-linked glycosylated and that N-linked glycosylation is not crucial for the melanopsin response to light.
Collapse
Affiliation(s)
- Jan Fahrenkrug
- Department of Clinical Biochemistry, Bispebjerg Hospital, Faculty of Health Sciences, University of Copenhagen, DK-2400 Copenhagen NV, Denmark.
| | | | | | | |
Collapse
|
133
|
Mild M, Kvist A, Esbjörnsson J, Karlsson I, Fenyö EM, Medstrand P. Differences in molecular evolution between switch (R5 to R5X4/X4-tropic) and non-switch (R5-tropic only) HIV-1 populations during infection. INFECTION GENETICS AND EVOLUTION 2009; 10:356-64. [PMID: 19446658 DOI: 10.1016/j.meegid.2009.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Revised: 05/01/2009] [Accepted: 05/07/2009] [Indexed: 01/02/2023]
Abstract
The recent introduction of entry inhibitors in the clinic as components of antiretroviral treatment has heightened the interest in coreceptor use of human immunodeficiency virus type 1 (HIV-1). Viruses using CCR5 as coreceptor (R5 viruses) are generally present over the entire course of infection whereas viruses using the CXCR4 coreceptor (R5X4/X4 viruses) emerge in about 50% of infected individuals during later stages of infection. The CCR5-to-CXCR4 switch represents a concern because CCR5 inhibitors, while suppressing R5 viruses, may allow the emergence of CXCR4-tropic viruses. In this study, HIV-1 populations that maintained CCR5 usage during infection were compared with populations that switched coreceptor usage to include CXCR4 later during infection, with the aim to find molecular properties of the virus populations associated with the CCR5-to-CXCR4 switch. We amplified and molecularly cloned the V1-V3 region of the HIV-1 envelope from 51 sequential HIV-1 isolates derived from 4 to 10 serial samples for each of the patients. Four of the patients had virus populations that switched coreceptor usage to include CXCR4 (switch populations: SP) during infection and four patients had viral populations that maintained exclusive CCR5 usage (non-switch populations: nSP). Coreceptor usage was determined experimentally on individual clones from dualtropic R5X4 isolates. In nSP we found that the number of potential N-linked glycosylation sites (PNGS) increased over time, whereas no pattern of change was observed in SP. We also found differences in V2 length and V3 charge between R5 viruses of nSP and R5 viruses of SP before the switch. The V2 region was significantly longer in R5 viruses of SP compared to viruses of nSP throughout the course of infection, and the V3 charge increased with time in R5 populations from SP, while it remained unchanged or decreased in nSP. These molecular properties could prove important for understanding the evolution of coreceptor usage in HIV-1 populations, and maybe even for predicting an upcoming coreceptor switch at early stages after primary infection.
Collapse
Affiliation(s)
- Mattias Mild
- Department of Experimental Medical Science, Lund University, Sweden
| | | | | | | | | | | |
Collapse
|
134
|
Belair M, Dovat M, Foley B, Mayerat C, Pantaleo G, Graziosi C. The polymorphic nature of HIV type 1 env V4 affects the patterns of potential N-glycosylation sites in proviral DNA at the intrahost level. AIDS Res Hum Retroviruses 2009; 25:199-206. [PMID: 19239359 DOI: 10.1089/aid.2008.0162] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have previously shown that env V4 from HIV-1 plasma RNA is highly heterogeneous within a single patient, due to indel-associated polymorphism. In this study, we have analyzed the variability of V4 in proviral DNA from unfractionated PBMC and sorted T and non-T cell populations within individual patients. Our data show that the degree of sequence variability and length polymorphism in V4 from HIV provirus is even higher than we previously reported in plasma. The data also show that the sequence of V4 depends largely on the experimental approach chosen. We could observe no clear trend for compartmentalization of V4 variants in specific cell types. Of interest is the fact that some variants that had been found to be predominant in plasma were not detected in any of the cell subsets analyzed. Consistently with our observations in plasma, V3 was found to be relatively conserved at both interpatient and intrapatient level. Our data show that V4 polymorphism involving insertions and deletions in addition to point mutations results in changes in the patterns of sequons in HIV-1 proviral DNA as well as in plasma RNA. These rearrangements may result in the coexistence, within the same individual, of a swarm of different V4 regions, each characterized by a different carbohydrate surface shield. Further studies are needed to investigate the mechanism responsible for the variability observed in V4 and its role in HIV pathogenesis.
Collapse
Affiliation(s)
| | - Magali Dovat
- Institut Universitaire de Médecine Légale, CHUV, Lausanne, Switzerland
| | - Brian Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratories, Los Alamos, New Mexico 87544
| | - Claude Mayerat
- Laboratory of AIDS Immunopathogenesis, CHUV, Lausanne, Switzerland
| | | | - Cecilia Graziosi
- Laboratory of AIDS Immunopathogenesis, CHUV, Lausanne, Switzerland
| |
Collapse
|
135
|
Schulz BL, Aebi M. Analysis of glycosylation site occupancy reveals a role for Ost3p and Ost6p in site-specific N-glycosylation efficiency. Mol Cell Proteomics 2008; 8:357-64. [PMID: 18854577 DOI: 10.1074/mcp.m800219-mcp200] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Asparagine-linked glycosylation is the most common post-translational modification of proteins catalyzed in eukaryotes by the multiprotein complex oligosaccharyltransferase. Apart from the catalytic Stt3p, the roles of the subunits are ill defined. Here we describe functional investigations of the Ost3/6p components of the yeast enzyme. We developed novel analytical tools to quantify glycosylation site occupancy by enriching glycoproteins bound to the yeast polysaccharide cell wall, tagging glycosylated asparagines using endoglycosidase H glycan release, and detecting peptides and glycopeptides with LC-ESI-MS/MS. We found that the paralogues Ost3p and Ost6p were required for efficient glycosylation of distinct defined glycosylation sites. Our results describe a novel method for relative quantification of glycosylation occupancy in the genetically tractable yeast system and show that eukaryotic oligosaccharyltransferase isoforms have different activities toward protein substrates at the level of individual glycosylation sites.
Collapse
Affiliation(s)
- Benjamin L Schulz
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | | |
Collapse
|
136
|
Markkanen PMH, Petäjä-Repo UE. N-glycan-mediated quality control in the endoplasmic reticulum is required for the expression of correctly folded delta-opioid receptors at the cell surface. J Biol Chem 2008; 283:29086-98. [PMID: 18703511 DOI: 10.1074/jbc.m801880200] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A great majority of G protein-coupled receptors are modified by N-glycosylation, but the functional significance of this modification for receptor folding and intracellular transport has remained elusive. Here we studied these phenomena by mutating the two N-terminal N-glycosylation sites (Asn(18) and Asn(33)) of the human delta-opioid receptor, and expressing the mutants from the same chromosomal integration site in stably transfected inducible HEK293 cells. Both N-glycosylation sites were used, and their abolishment decreased the steady-state level of receptors at the cell surface. However, pulse-chase labeling, cell surface biotinylation, and immunofluorescence microscopy revealed that this was not because of intracellular accumulation. Instead, the non-N-glycosylated receptors were exported from the endoplasmic reticulum with enhanced kinetics. The results also revealed differences in the significance of the individual N-glycans, as the one attached to Asn(33) was found to be more important for endoplasmic reticulum retention of the receptor. The non-N-glycosylated receptors did not show gross functional impairment, but flow cytometry revealed that a fraction of them was incapable of ligand binding at the cell surface. In addition, the receptors that were devoid of N-glycans showed accelerated turnover and internalization and were targeted for lysosomal degradation. The results accentuate the importance of protein conformation-based screening before export from the endoplasmic reticulum, and demonstrate how the system is compromised when N-glycosylation is disrupted. We conclude that N-glycosylation of the delta-opioid receptor is needed to maintain the expression of fully functional and stable receptor molecules at the cell surface.
Collapse
Affiliation(s)
- Piia M H Markkanen
- Department of Anatomy and Cell Biology, Institute of Biomedicine, University of Oulu, FI-90014, Oulu, Finland
| | | |
Collapse
|
137
|
Go EP, Irungu J, Zhang Y, Dalpathado DS, Liao HX, Sutherland LL, Alam SM, Haynes BF, Desaire H. Glycosylation site-specific analysis of HIV envelope proteins (JR-FL and CON-S) reveals major differences in glycosylation site occupancy, glycoform profiles, and antigenic epitopes' accessibility. J Proteome Res 2008; 7:1660-74. [PMID: 18330979 DOI: 10.1021/pr7006957] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The HIV-1 envelope (Env) is a key determinant in mediating viral entry and fusion to host cells and is a major target for HIV vaccine development. While Env is typically about 50% glycan by mass, glycosylation sites are known to evolve, with some glycosylation profiles presumably being more effective at facilitating neutralization escape than others. Thus, characterizing glycosylation patterns of Env and native virions and correlating glycosylation profiles with infectivity and Env immunogenicity are necessary first steps in designing effective immunogens. Herein, we describe a mass spectrometry-based strategy to determine HIV-1 Env glycosylation patterns and have compared two mammalian cell expressed recombinant Env immunogens, one a limited immunogen and one that induces cross-clade neutralizing antibodies. We have used a glycopeptide-based mass mapping approach to identify and characterize Env's glycosylation patterns by elucidating which sites are utilized and what type of glycan motif is present at each glycosylation site. Our results show that the immunogens displayed different degrees of glycosylation as well as a different characteristic set of glycan motifs. Thus, these techniques can be used to (1) define glycosylation profiles of recombinant Env proteins and Env on mature virions, (2) define specific carbohydrate moieties at each glycosylation site, and (3) determine the role of certain carbohydrates in HIV-1 infectivity and in modulation of Env immunogenicity.
Collapse
Affiliation(s)
- Eden P Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
138
|
Nagaya H, Tamura T, Higa-Nishiyama A, Ohashi K, Takeuchi M, Hashimoto H, Hatsuzawa K, Kinjo M, Okada T, Wada I. Regulated motion of glycoproteins revealed by direct visualization of a single cargo in the endoplasmic reticulum. ACTA ACUST UNITED AC 2008; 180:129-43. [PMID: 18195104 PMCID: PMC2213621 DOI: 10.1083/jcb.200704078] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The quality of cargo proteins in the endoplasmic reticulum (ER) is affected by their motion during folding. To understand how the diffusion of secretory cargo proteins is regulated in the ER, we directly analyze the motion of a single cargo molecule using fluorescence imaging/fluctuation analyses. We find that the addition of two N-glycans onto the cargo dramatically alters their diffusion by transient binding to membrane components that are confined by hyperosmolarity. Via simultaneous observation of a single cargo and ER exit sites (ERESs), we could exclude ERESs as the binding sites. Remarkably, actin cytoskeleton was required for the transient binding. These results provide a molecular basis for hypertonicity-induced immobilization of cargo, which is dependent on glycosylation at multiple sites but not the completion of proper folding. We propose that diffusion of secretory glycoproteins in the ER lumen is controlled from the cytoplasm to reduce the chances of aggregation.
Collapse
Affiliation(s)
- Hisao Nagaya
- Department of Cell Science, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
139
|
Dubois M, Fenaille F, Clement G, Lechmann M, Tabet JC, Ezan E, Becher F. Immunopurification and Mass Spectrometric Quantification of the Active Form of a Chimeric Therapeutic Antibody in Human Serum. Anal Chem 2008; 80:1737-45. [DOI: 10.1021/ac7021234] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mathieu Dubois
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - François Fenaille
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Gilles Clement
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Martin Lechmann
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Jean-Claude Tabet
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Eric Ezan
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - François Becher
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| |
Collapse
|
140
|
Castro E, Bélair M, Rizzardi GP, Bart PA, Pantaleo G, Graziosi C. Independent evolution of hypervariable regions of HIV-1 gp120: V4 as a swarm of N-Linked glycosylation variants. AIDS Res Hum Retroviruses 2008; 24:106-13. [PMID: 18275355 DOI: 10.1089/aid.2007.0139] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In this study we have characterized intra-patient length polymorphism in V4 by cloning and sequencing a C2-C4 fragment from HIV plasma RNA in patients at different stages of HIV disease. Clonal analysis of clade B, G, and CRF02 isolates during early infection shows extensive intra-patient V4 variability, due to the presence of indel-associated polymorphism. Indels, coupled to amino acid substitution events, affect the number and distribution of potential N-glycosylation sites, resulting in the coexistence, within the same patient, of V4 subsets, each characterized by different sizes, amino acid sequences, and potential N-glycosylation patterns. In contrast, V3 appears to be relatively homogeneous, with similar V3 associated to significantly different V4 within the same clinical specimen. Based on these data, we propose that during early chronic infection V4 is present as a highly divergent quasispecies, enabling the virus to adopt different conformational structures according to immune constrains and other selective pressures.
Collapse
Affiliation(s)
- Erika Castro
- Laboratory of AIDS Immunopathogenesis, CHUV, Lausanne, Switzerland
| | | | | | - Pierre A. Bart
- Laboratory of AIDS Immunopathogenesis, CHUV, Lausanne, Switzerland
| | | | - Cecilia Graziosi
- Laboratory of AIDS Immunopathogenesis, CHUV, Lausanne, Switzerland
| |
Collapse
|
141
|
Milstein ML, McFarland TP, Marsh JD, Cala SE. Inefficient glycosylation leads to high steady-state levels of actively degrading cardiac triadin-1. J Biol Chem 2007; 283:1929-35. [PMID: 18025088 DOI: 10.1074/jbc.m704623200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In junctional sarcoplasmic reticulum, binding to cardiac triadin-1 provides a mechanism by which the Ca(2+)-release channel/ryanodine receptor may link with calsequestrin to regulate Ca(2+) release. Calsequestrin and triadin-1 both contain N-linked glycans, but about half of triadin-1 in the heart remains unglycosylated. To investigate mechanisms for this incomplete glycosylation, we overexpressed triadin-1 as a series of glycoform variants in non-muscle cell lines and neonatal heart cells using plasmid and adenoviral vectors. We showed that the characteristic incomplete glycosylation stemmed from properties of the glycosylation sequence that are conserved among triadin splice variants, including the close proximity of Asn(75) to the sarcoplasmic reticulum inner membrane. Although triadin-1 appeared by SDS-PAGE analysis as a 35/40-kDa doublet in all cells, variations occurred in the relative levels of the two glycoforms depending on the cell type and whether overexpression involved a plasmid or adenoviral vector. Treatment of triadin-1 with the proteasome inhibitor MG-132 led to striking changes in the relative levels of triadin-1 that indicated active breakdown of unglycosylated, but not glycosylated, triadin-1. Besides substantial increases in the relative levels of unglycosylated triadin-1, proteasome inhibition led to an accumulation of two new modified forms of triadin-1 that were seen with triadin-1 only when it is not glycosylated on Asn(75). Effects of tunicamycin and endoglycosidase H confirmed that these novel isoforms represent two alternative N-linked glycosylation sites, indicating that an alternative topology occurs infrequently leading to yet other glycoforms with short half-lives.
Collapse
Affiliation(s)
- Michelle L Milstein
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
| | | | | | | |
Collapse
|
142
|
Kupfer B, Sing T, Schüffler P, Hall R, Kurz R, McKeown A, Schneweis KE, Eberl W, Oldenburg J, Brackmann HH, Rockstroh JK, Spengler U, Däumer MP, Kaiser R, Lengauer T, Matz B. Fifteen years of env C2V3C3 evolution in six individuals infected clonally with human immunodeficiency virus type 1. J Med Virol 2007; 79:1629-39. [PMID: 17854039 DOI: 10.1002/jmv.20976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The study of the evolution of human immunodeficiency virus type 1 (HIV-1) requires blood samples collected longitudinally and data on the approximate time point of infection. Although these requirements were fulfilled in several previous studies, the infectious sources were either unknown or heterogeneous genetically. In the present study, HIV-1 env C2V3C3 (nt 7029-7315) evolution was examined retrospectively in a cohort of hemophiliacs. Compared to other cohorts, the area of interest here was the infection of six hemophiliacs by the same virus strain, that is, the infecting viruses shared an identical genome. As expected, divergence from the founder sequence as well as interpatient divergence of the predominant virus strains increased significantly over time. Based on the V3 nucleotide sequences, CCR5 usage was predicted exclusively throughout the whole period of infection in all patients. Interestingly, common patterns of viral evolution were detected in the patients of the cohort. Four amino acid substitutions within the V3 loop emerged and persisted subsequently in five (positions 305 and 308 of the HXB2 gp120 reference sequence) and six patients (positions 325 and 328 in HXB2 gp120), respectively. These common changes within the V3 loop are likely to be enforced by HIV-1 specific immune response.
Collapse
Affiliation(s)
- Bernd Kupfer
- Institute for Medical Microbiology, Immunology, and Parasitology, University of Bonn, Bonn, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
143
|
Reading PC, Tate MD, Pickett DL, Brooks AG. Glycosylation as a target for recognition of influenza viruses by the innate immune system. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 598:279-92. [PMID: 17892219 DOI: 10.1007/978-0-387-71767-8_20] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Glycosylation clearly plays an important role in the life cycle of influenza viruses and certain glycosylation sites are required for the structural integrity and stability of the HA and NA glycoproteins during biosynthesis and formation of intact virions. Furthermore, glycosylation has been shown to modulate the functions of influenza glycoproteins, in particular the recognition of host cell receptors and in shielding antigenic epitopes on the viral HA. The addition of oligosaccharide moieties to the globular head of the HA does, however, correlate with an increased sensitivity to the antiviral activities of SP-D and to recognition and destruction of virus via the MMR on murine macrophages. Consequently, the degree of glycosylation appears to be an important factor in determining sensitivity to lectin-mediated defences, and therefore in determining the ability of a particular virus strain to replicate in the respiratory tract of mice following intranasal infection. The mouse-adapted PR8 strain which lacks mannose-containing glycans from the head of its HA molecule was largely resistant to the antiviral activities of SP-D and the MMR in vitro and induced severed clinical disease following intranasal infection of mice. The finding that mannan treatment of BJx109-infected mice facilitated an early and dramatic enhancement of disease severity is also consistent with a major role for mannose-specific lectins in limiting influenza virus growth and spread in the respiratory tract.
Collapse
MESH Headings
- Animals
- Antigens, Viral/immunology
- Collectins/metabolism
- Glycosylation
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Humans
- Immunity, Innate/physiology
- Influenza A virus/immunology
- Influenza, Human/immunology
- Lectins, C-Type/metabolism
- Macrophages/metabolism
- Mannose/metabolism
- Mannose Receptor
- Mannose-Binding Lectins/metabolism
- Models, Molecular
- Polysaccharides/chemistry
- Protein Structure, Tertiary
- Receptors, Cell Surface/metabolism
- Receptors, Immunologic/metabolism
Collapse
Affiliation(s)
- Patrick C Reading
- The University of Melbourne, Department of Microbiology and Immunology, Victoria, Australia 3010
| | | | | | | |
Collapse
|
144
|
Abu-Qarn M, Eichler J. An analysis of amino acid sequences surrounding archaeal glycoprotein sequons. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2007; 2:73-81. [PMID: 17350928 PMCID: PMC2686383 DOI: 10.1155/2006/510578] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Despite having provided the first example of a prokaryal glycoprotein, little is known of the rules governing the N-glycosylation process in Archaea. As in Eukarya and Bacteria, archaeal N-glycosylation takes place at the Asn residues of Asn-X-Ser/Thr sequons. Since not all sequons are utilized, it is clear that other factors, including the context in which a sequon exists, affect glycosylation efficiency. As yet, the contribution to N-glycosylation made by sequon-bordering residues and other related factors in Archaea remains unaddressed. In the following, the surroundings of Asn residues confirmed by experiment as modified were analyzed in an attempt to define sequence rules and requirements for archaeal N-glycosylation.
Collapse
Affiliation(s)
- Mehtap Abu-Qarn
- Department of Life Sciences, Ben Gurion University, Beersheva 84105, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University, Beersheva 84105, Israel
- Corresponding author ()
| |
Collapse
|
145
|
Wang H, Julenius K, Hryhorenko J, Hagen FK. Systematic Analysis of proteoglycan modification sites in Caenorhabditis elegans by scanning mutagenesis. J Biol Chem 2007; 282:14586-97. [PMID: 17369258 DOI: 10.1074/jbc.m609193200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteoglycan modification is essential for development and early cell division in Caenorhabditis elegans. The specification of proteoglycan attachment sites is defined by the Golgi enzyme polypeptide xylosyltransferase. Here we evaluate the substrate specificity of this xylosyltransferase for its downstream targets by using reporter proteins containing proteoglycan modification sites from C. elegans syndecan/SDN-1. The N terminus of the SDN-1 contains a Ser-Gly proteoglycan site at Ser(71), flanked by potential mucin and N-glycosylation sites. However, Ser(71) was exclusively used as a proteoglycan site in vivo, based on mapping studies with a Ser(71) reporter protein, glycosyltransferase RNA interference, and co-expression of worm polypeptide xylosyltransferase. To elucidate the substrate requirements of this enzyme, a library of 42 point mutants of the Ser(71) reporter was expressed in tissue culture. The nematode proteoglycan modification site in SDN-1 required serine (not threonine), two flanking glycine residues (positions -1 and +1), and either one proximal acidic N-terminal amino acid (positions -4, -3, and -2) or a pair of distal N-terminal acidic amino acids (positions -6 and -5). C-terminal acidic amino acids, although present in many proteoglycan modification sites, had minimal impact on xylosylation at Ser(71). Proline inhibited glycosylation when present at -1, +1, or +2. The position of glycine, proline, and acidic amino acids allows the glycosylation machinery to discriminate between mucin and proteoglycan modification sites. The key residues that define proteoglycan modification sites also function with the Drosophila polypeptide xylosyltransferase, indicating that the specificity in the glycosylation process is evolutionarily conserved. Using a neural network method, a preliminary proteoglycan predictor has been developed.
Collapse
Affiliation(s)
- Huan Wang
- Department of Biochemistry and Biophysics, Center for Oral Biology, Aab Institute of Biomedical Sciences, University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | | | | |
Collapse
|
146
|
Lehle L, Strahl S, Tanner W. Proteinglycosylierung, konserviert von der Bäckerhefe bis zum Menschen: Ein Modellorganismus hilft bei der Aufklärung menschlicher Erbkrankheiten. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200601645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
147
|
Lehle L, Strahl S, Tanner W. Protein Glycosylation, Conserved from Yeast to Man: A Model Organism Helps Elucidate Congenital Human Diseases. Angew Chem Int Ed Engl 2006; 45:6802-18. [PMID: 17024709 DOI: 10.1002/anie.200601645] [Citation(s) in RCA: 204] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Proteins can be modified by a large variety of covalently linked saccharides. The present review concentrates on two types, protein N-glycosylation and protein O-mannosylation, which, with only a few exceptions, are evolutionary conserved from yeast to man. They are also distinguished by some special features: The corresponding glycosylation processes start in the endoplasmatic reticulum, are continued in the Golgi apparatus, and require dolichol-activated precursors for the initial biosynthetic steps. With respect to the molecular biology of both types of protein glycosylation, the pathways and the genetic background of the reactions have most successfully been studied with the genetically easy-to-handle baker's yeast, Saccharomyces cerevisae. Many of the severe developmental disturbances in children are related to protein glycosylation, for example, the CDG syndrome (congenital disorders of glycosylation) as well as congenital muscular dystrophies with neuronal-cell-migration defects have been elucidated with the help of yeast.
Collapse
Affiliation(s)
- Ludwig Lehle
- Lehrstuhl für Zellbiologie und Pflanzenphysiologie, Universität Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany.
| | | | | |
Collapse
|
148
|
Kowarik M, Young NM, Numao S, Schulz BL, Hug I, Callewaert N, Mills DC, Watson DC, Hernandez M, Kelly JF, Wacker M, Aebi M. Definition of the bacterial N-glycosylation site consensus sequence. EMBO J 2006; 25:1957-66. [PMID: 16619027 PMCID: PMC1456941 DOI: 10.1038/sj.emboj.7601087] [Citation(s) in RCA: 266] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2005] [Accepted: 03/21/2006] [Indexed: 11/09/2022] Open
Abstract
The Campylobacter jejuni pgl locus encodes an N-linked protein glycosylation machinery that can be functionally transferred into Escherichia coli. In this system, we analyzed the elements in the C. jejuni N-glycoprotein AcrA required for accepting an N-glycan. We found that the eukaryotic primary consensus sequence for N-glycosylation is N terminally extended to D/E-Y-N-X-S/T (Y, X not equalP) for recognition by the bacterial oligosaccharyltransferase (OST) PglB. However, not all consensus sequences were N-glycosylated when they were either artificially introduced or when they were present in non-C. jejuni proteins. We were able to produce recombinant glycoproteins with engineered N-glycosylation sites and confirmed the requirement for a negatively charged side chain at position -2 in C. jejuni N-glycoproteins. N-glycosylation of AcrA by the eukaryotic OST in Saccharomyces cerevisiae occurred independent of the acidic residue at the -2 position. Thus, bacterial N-glycosylation site selection is more specific than the eukaryotic equivalent with respect to the polypeptide acceptor sequence.
Collapse
Affiliation(s)
- Michael Kowarik
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
| | - N Martin Young
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Shin Numao
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
| | - Benjamin L Schulz
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
| | - Isabelle Hug
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
| | - Nico Callewaert
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
- The Zürich Glycomics Initiative (GlycoInit), Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
| | - Dominic C Mills
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
| | - David C Watson
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Marcela Hernandez
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
| | - John F Kelly
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Michael Wacker
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, Zürich, Switzerland
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg, 8093 Zürich, Switzerland. Tel.: +41 1 632 6413; Fax: +41 1 632 1375; E-mail:
| |
Collapse
|
149
|
Clevestig P, Pramanik L, Leitner T, Ehrnst A. CCR5 use by human immunodeficiency virus type 1 is associated closely with the gp120 V3 loop N-linked glycosylation site. J Gen Virol 2006; 87:607-612. [PMID: 16476981 DOI: 10.1099/vir.0.81510-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) enters cells through the chemokine receptors CCR5 (R5 virus) and/or CXCR4 (X4 virus). Loss of N-linked glycans and increased net charge of the third variable loop (V3) of the gp120 envelope glycoprotein have been observed to be important steps towards CXCR4 use. All reported sequences using CCR5 or CXCR4 exclusively, or using both, were gathered from the Los Alamos HIV Database and analysed with regard to the V3 N-linked glycosylation motifs (sequons) and charge. The V3 loop glycan had a sensitivity of 0.98 and a 0.92 positive predictive value in the context of CCR5 use. The difference from X4 was remarkable (P<10(-12)). Especially, the sequon motif NNT within the V3 loop was conserved in 99.2 % of the major clades. The results suggest a close association between the V3 loop glycan and CCR5 use and may provide new insight into HIV-1 tropism and help to improve phenotype-prediction models.
Collapse
Affiliation(s)
- Peter Clevestig
- Microbiology and Tumor Biology Center, Karolinska Institutet, Box 280, SE-171 77 Stockholm, Sweden
| | - Lotta Pramanik
- Microbiology and Tumor Biology Center, Karolinska Institutet, Box 280, SE-171 77 Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Anneka Ehrnst
- Department of Laboratory Medicine, Division of Clinical Virology, Karolinska University Hospital Huddinge, Karolinska Institutet, Box 280, SE-171 77 Stockholm, Sweden
- Microbiology and Tumor Biology Center, Karolinska Institutet, Box 280, SE-171 77 Stockholm, Sweden
| |
Collapse
|
150
|
Mann K, Siedler F. Amino acid sequences and phosphorylation sites of emu and rhea eggshell C-type lectin-like proteins. Comp Biochem Physiol B Biochem Mol Biol 2006; 143:160-70. [PMID: 16403478 DOI: 10.1016/j.cbpb.2005.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Revised: 11/05/2005] [Accepted: 11/06/2005] [Indexed: 11/30/2022]
Abstract
Avian calcified eggshell layers contain in their organic matrix one or two C-type lectin-like proteins. Previously characterized eggshell proteins of this family are chicken ovocleidin-17 (OC-17), goose ansocalcin and ostrich struthiocalcins 1 and 2 (SCA-1, SCA-2). In this report we present the amino acid sequences of two emu (Dromaius novaehollandiae) (dromaiocalcin-1 and -2; DCA-1, DCA-2) and of two rhea (Rhea americana) (rheacalcin-1 and -2; RCA-1, RCA-2) C-type lectin-like eggshell proteins, thus doubling the data set for comparison of these major specific eggshell proteins. The ratite proteins can be divided into two groups. Group 1, comprising SCA-1, DCA-1 and RCA-1, shows by 70--77% identity of sequences, the lack of phosphorylation, and a variable number (7--9) of cysteines. Group 2, consisting of SCA-2, DCA-2 and RCA-2, shows 78--85% identical sequences, 2--3 phosphorylated serines located at almost identical sites, and contains only the common set of six conserved cysteins characteristic for this family of proteins. While goose ansocalcin fits perfectly into group 1 with a sequence identity of 63--70% to the other members, no phosphorylation, and seven cysteines, chicken OC-17 was assigned to group 2 in spite of only 42--47% sequence identity (and 37--39% to group 1) because of its two phosphorylated serines and its regular set of six cysteines. At present it remains unknown why ratites, but not goose or chicken, require two different types of C-type lectin-like proteins to construct their eggshells.
Collapse
Affiliation(s)
- Karlheinz Mann
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany.
| | | |
Collapse
|