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The Adeno-Associated Virus Replication Protein Rep78 Contains a Strictly C-Terminal Sequence Motif Conserved Across Dependoparvoviruses.
Karlin DG. Karlin DG. Viruses. 2024 Nov 12;16(11):1760. doi: 10.3390/v16111760. Viruses. 2024. PMID: 39599875 Free PMC article.
Adeno-Associated Viruses (AAVs, genus Dependoparvovirus) are the leading gene therapy vector. Until recently, efforts to enhance their capacity for gene delivery had focused on their capsids. ...
Adeno-Associated Viruses (AAVs, genus Dependoparvovirus) are the leading gene therapy vector. Until recently, efforts to enhance thei …
Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene.
Karlin DG. Karlin DG. Viruses. 2024 Jan 26;16(2):191. doi: 10.3390/v16020191. Viruses. 2024. PMID: 38399966 Free PMC article.
Viruses frequently contain overlapping genes, which encode functionally unrelated proteins from the same DNA or RNA region but in different reading frames. Yet, overlapping genes are often overlooked during genome annotation, in particular in DNA viruses. Here we lo …
Viruses frequently contain overlapping genes, which encode functionally unrelated proteins from the same DNA or RNA region but in dif …
WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection.
Karlin DG. Karlin DG. J Gen Virol. 2024 Jan;105(1). doi: 10.1099/jgv.0.001948. J Gen Virol. 2024. PMID: 38193819
As a test case, this approach was applied to a protein without known homologues, encoded by ORF4 of Lake Sinai viruses (which infect bees). We discovered that the ORF4 protein contains a domain that has homologues in proteins from >20 taxa of viruses infecting ar …
As a test case, this approach was applied to a protein without known homologues, encoded by ORF4 of Lake Sinai viruses (which infect …
Orthoparamyxovirinae C Proteins Have a Common Origin and a Common Structural Organization.
Roy A, Chan Mine E, Gaifas L, Leyrat C, Volchkova VA, Baudin F, Martinez-Gil L, Volchkov VE, Karlin DG, Bourhis JM, Jamin M. Roy A, et al. Among authors: karlin dg. Biomolecules. 2023 Mar 1;13(3):455. doi: 10.3390/biom13030455. Biomolecules. 2023. PMID: 36979390 Free PMC article.
We solved the crystal structure of the C-terminal part of TupV C protein at a resolution of 2.4 A and found that it is structurally similar to Sendai virus C protein, suggesting that despite undetectable sequence conservation, these proteins are homologous. ...We establish …
We solved the crystal structure of the C-terminal part of TupV C protein at a resolution of 2.4 A and found that it is structurally similar …
2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bandte M, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Bigarré L, Blair CD, Blasdell KR, Bradfute SB, Briese T, Brown PA, Bruggmann R, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Candresse T, Carson J, Casas I, Chandran K, Charrel RN, Chiaki Y, Crane A, Crane M, Dacheux L, Bó ED, de la Torre JC, de Lamballerie X, de Souza WM, de Swart RL, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Feuvrier C, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, García ML, García-Sastre A, Garrison AR, Godwin SE, Gonzalez JJ, de Bellocq JG, Griffiths A, Groschup MH, Günther S, Hammond J, Hepojoki J, Hierweger MM, Hongō S, Horie M, Horikawa H, Hughes HR, Hume AJ, Hyndman TH, Jiāng D, Jonson GB, Junglen S, Kadono F, Karlin DG, Klempa B, Klingström J, Koch MC, Kondō H, Koonin EV, Krásová J, Krupovic M, Kubota K, Kuzmin IV, Laenen L, Lambert AJ, Lǐ J, Li JM, Lieffrig F, Lukashevich IS, Luo D, Maes P, Marklewitz M, Marshall SH, Marzano SL, McCauley JW, Mirazimi … See abstract for full author list ➔ Kuhn JH, et al. Among authors: karlin dg. Arch Virol. 2022 Dec;167(12):2857-2906. doi: 10.1007/s00705-022-05546-z. Arch Virol. 2022. PMID: 36437428 Free PMC article.
In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. ...
In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, t …
A novel emaravirus comprising five RNA segments is associated with ringspot disease in oak.
Rehanek M, von Bargen S, Bandte M, Karlin DG, Büttner C. Rehanek M, et al. Among authors: karlin dg. Arch Virol. 2021 Mar;166(3):987-990. doi: 10.1007/s00705-021-04955-w. Epub 2021 Jan 18. Arch Virol. 2021. PMID: 33462672 Free PMC article.
Bioinformatic analysis of the HTS dataset followed by RT-PCR enabled us to determine complete sequences of four RNA genome segments of a novel virus. These sequences showed high similarity to members of the genus Emaravirus, which includes segmented negative-stranded RNA …
Bioinformatic analysis of the HTS dataset followed by RT-PCR enabled us to determine complete sequences of four RNA genome segments of a nov …
Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes.
Pavesi A, Vianelli A, Chirico N, Bao Y, Blinkova O, Belshaw R, Firth A, Karlin D. Pavesi A, et al. Among authors: karlin d. PLoS One. 2018 Oct 19;13(10):e0202513. doi: 10.1371/journal.pone.0202513. eCollection 2018. PLoS One. 2018. PMID: 30339683 Free PMC article.
They originate by a mechanism of overprinting, in which point mutations in an existing frame allow the expression (the "birth") of a completely new protein from a second frame. In viruses, in which overlapping genes are abundant, these new proteins often play a critical ro …
They originate by a mechanism of overprinting, in which point mutations in an existing frame allow the expression (the "birth") of a complet …
Bioinformatic and mutational analysis of ophiovirus movement proteins, belonging to the 30K superfamily.
Borniego MB, Karlin D, Peña EJ, Robles Luna G, García ML. Borniego MB, et al. Among authors: karlin d. Virology. 2016 Nov;498:172-180. doi: 10.1016/j.virol.2016.08.027. Epub 2016 Sep 4. Virology. 2016. PMID: 27596536 Free article.
Ophioviridae is a family of segmented, negative-sense, single-stranded RNA plant viruses. We showed that their cell-to-cell movement protein (MP) is an isolated member of the 30K MP superfamily with a unique structural organization. ...We examined its role in the MP of Cit …
Ophioviridae is a family of segmented, negative-sense, single-stranded RNA plant viruses. We showed that their cell-to-cell movement …
Sequence analysis reveals a conserved extension in the capping enzyme of the alphavirus supergroup, and a homologous domain in nodaviruses.
Ahola T, Karlin DG. Ahola T, et al. Among authors: karlin dg. Biol Direct. 2015 Apr 11;10:16. doi: 10.1186/s13062-015-0050-0. Biol Direct. 2015. PMID: 25886938 Free PMC article.
BACKGROUND: Members of the alphavirus supergroup include human pathogens such as chikungunya virus, hepatitis E virus and rubella virus. They encode a capping enzyme with methyltransferase-guanylyltransferase (MTase-GTase) activity, which is an attractive dru …
BACKGROUND: Members of the alphavirus supergroup include human pathogens such as chikungunya virus, hepatitis E virus and rube …
Evolution and structural organization of the C proteins of paramyxovirinae.
Lo MK, Søgaard TM, Karlin DG. Lo MK, et al. Among authors: karlin dg. PLoS One. 2014 Feb 25;9(2):e90003. doi: 10.1371/journal.pone.0090003. eCollection 2014. PLoS One. 2014. PMID: 24587180 Free PMC article.
The C proteins cluster in three groups, comprising measles, Nipah, and Sendai virus. We predicted that all C proteins have a similar organization: a variable, disordered N-terminus and a conserved, alpha-helical C-terminus. ...Since C is dispensable for viral replication, …
The C proteins cluster in three groups, comprising measles, Nipah, and Sendai virus. We predicted that all C proteins have a similar …
Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins.
Kuchibhatla DB, Sherman WA, Chung BY, Cook S, Schneider G, Eisenhaber B, Karlin DG. Kuchibhatla DB, et al. Among authors: karlin dg. J Virol. 2014 Jan;88(1):10-20. doi: 10.1128/JVI.02595-13. Epub 2013 Oct 23. J Virol. 2014. PMID: 24155369 Free PMC article.
The genome sequences of new viruses often contain many "orphan" or "taxon-specific" proteins apparently lacking homologs. ...We expect these methodological results to be also applicable to cellular organisms, since they generally evolve much more slowly than RNA viruses …
The genome sequences of new viruses often contain many "orphan" or "taxon-specific" proteins apparently lacking homologs. ...We expec …
Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses.
Pavesi A, Magiorkinis G, Karlin DG. Pavesi A, et al. Among authors: karlin dg. PLoS Comput Biol. 2013;9(8):e1003162. doi: 10.1371/journal.pcbi.1003162. Epub 2013 Aug 15. PLoS Comput Biol. 2013. PMID: 23966842 Free PMC article.
A well-known mechanism through which new protein-coding genes originate is by modification of pre-existing genes, e.g. by duplication or horizontal transfer. In contrast, many viruses generate protein-coding genes de novo, via the overprinting of a new reading frame onto a …
A well-known mechanism through which new protein-coding genes originate is by modification of pre-existing genes, e.g. by duplication or hor …
Experimental and bioinformatic evidence that raspberry leaf blotch emaravirus P4 is a movement protein of the 30K superfamily.
Yu C, Karlin DG, Lu Y, Wright K, Chen J, MacFarlane S. Yu C, et al. Among authors: karlin dg. J Gen Virol. 2013 Sep;94(Pt 9):2117-2128. doi: 10.1099/vir.0.053256-0. Epub 2013 Jun 12. J Gen Virol. 2013. PMID: 23761405
Emaravirus is a recently described genus of negative-strand RNA plant viruses. Emaravirus P4 protein localizes to plasmodesmata, suggesting that it could be a viral movement protein (MP). In the current study, we showed that the P4 protein of raspberry leaf blotch emaravir …
Emaravirus is a recently described genus of negative-strand RNA plant viruses. Emaravirus P4 protein localizes to plasmodesmata, sugg …
Evolution of viral proteins originated de novo by overprinting.
Sabath N, Wagner A, Karlin D. Sabath N, et al. Among authors: karlin d. Mol Biol Evol. 2012 Dec;29(12):3767-80. doi: 10.1093/molbev/mss179. Epub 2012 Jul 19. Mol Biol Evol. 2012. PMID: 22821011 Free PMC article.
Recently, the importance of de novo origination has been recognized in eukaryotes, although eukaryotic genes originated de novo are relatively rare and difficult to identify. In contrast, viruses contain many de novo genes, namely those in which an existing gene has been " …
Recently, the importance of de novo origination has been recognized in eukaryotes, although eukaryotic genes originated de novo are relative …
Detecting remote sequence homology in disordered proteins: discovery of conserved motifs in the N-termini of Mononegavirales phosphoproteins.
Karlin D, Belshaw R. Karlin D, et al. PLoS One. 2012;7(3):e31719. doi: 10.1371/journal.pone.0031719. Epub 2012 Mar 5. PLoS One. 2012. PMID: 22403617 Free PMC article.
Paramyxovirinae are a large group of viruses that includes measles virus and parainfluenza viruses. The viral Phosphoprotein (P) plays a central role in viral replication. ...
Paramyxovirinae are a large group of viruses that includes measles virus and parainfluenza viruses. The viral Phosphopr …
Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation.
Rancurel C, Khosravi M, Dunker AK, Romero PR, Karlin D. Rancurel C, et al. Among authors: karlin d. J Virol. 2009 Oct;83(20):10719-36. doi: 10.1128/JVI.00595-09. Epub 2009 Jul 29. J Virol. 2009. PMID: 19640978 Free PMC article.
To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition globally biased toward disorder-promot …
To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera o …
Structural disorder and modular organization in Paramyxovirinae N and P.
Karlin D, Ferron F, Canard B, Longhi S. Karlin D, et al. J Gen Virol. 2003 Dec;84(Pt 12):3239-3252. doi: 10.1099/vir.0.19451-0. J Gen Virol. 2003. PMID: 14645906
The existence and extent of disorder within the replicative complex (N, P and the polymerase, L) of Paramyxovirinae were investigated, drawing on the discovery that the N-terminal moiety of the phosphoprotein (P) and the C-terminal moiety of the nucleoprotein (N) of measles vi …
The existence and extent of disorder within the replicative complex (N, P and the polymerase, L) of Paramyxovirinae were investigated, drawi …
The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphoprotein.
Longhi S, Receveur-Bréchot V, Karlin D, Johansson K, Darbon H, Bhella D, Yeo R, Finet S, Canard B. Longhi S, et al. Among authors: karlin d. J Biol Chem. 2003 May 16;278(20):18638-48. doi: 10.1074/jbc.M300518200. Epub 2003 Mar 5. J Biol Chem. 2003. PMID: 12621042 Free article.
The nucleoprotein of measles virus consists of an N-terminal moiety, N(CORE), resistant to proteolysis and a C-terminal moiety, N(TAIL), hypersensitive to proteolysis and not visible as a distinct domain by electron microscopy. We report the bacterial expression, purificat …
The nucleoprotein of measles virus consists of an N-terminal moiety, N(CORE), resistant to proteolysis and a C-terminal moiety, N(TAI …
Substitution of two residues in the measles virus nucleoprotein results in an impaired self-association.
Karlin D, Longhi S, Canard B. Karlin D, et al. Virology. 2002 Oct 25;302(2):420-32. doi: 10.1006/viro.2002.1634. Virology. 2002. PMID: 12441086 Free article.
The nucleoprotein (N) of measles virus encapsidates viral genomic RNA to form a helical nucleocapsid. Its strong self-association is a major hurdle in determining its high-resolution structure using X-ray crystallography. ...
The nucleoprotein (N) of measles virus encapsidates viral genomic RNA to form a helical nucleocapsid. Its strong self-association is …
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