B. Karsten Tischer

En passant mutagenesis: a two step markerless red recombination system.

Bacterial artificial chromosomes are used to maintain and modify large sequences of different origins in Escherichia coli. In addition to RecA-based shuttle mutagenesis, Red recombination is commonly used for sequence modification. Since foreign sequences, such as antibiotic resistance genes as well as frt- or loxP-sites are often unwanted in mutant BAC clones, we developed a Red-based technique that allows for the scarless generation of point mutations, deletions, and insertion of smaller and larger sequences. The method employs a sequence duplication that is inserted into the target sequence in the first recombination step and the excision of the selection marker by in vivo I-SceI cleavage and the second Red recombination. To allow for convenient and highly efficient mutagenesis without the use of additional plasmids, the E. coli strain GS1783 with a chromosomal encoded inducible Red- and I-SceI-expression was created.

Viral bacterial artificial chromosomes: generation, mutagenesis, and removal of mini-F sequences.

Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques in Escherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members of Coronaviridae and Flaviviridae could be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process.

Herpesviruses - a zoonotic threat?

Herpesviruses are highly host specific and share a long synchronous evolution with their hosts. Only in rare cases, species barriers fall and allow animal to human or human to animal transmission. Among the zoonotic herpesviruses, Cercopithecine herpesvirus 1 is the most significant and can be transmitted from macaques to human. Conversely, Human herpesvirus 1 is capable of causing severe disease in primates. Besides those two examples, there are several herpesviruses with a certainly limited or only suspected ability to cross species barriers. Those include Saimiriine herpesvirus 2, Phocid herpesvirus 2, Equid herpesvirus 1, Epstein-Barr Virus, Mareks disease virus, and Pseudorabies virus. Concerning xenotransplantations, porcine gammaherpesviruses must be considered as a zoonotic threat.

Cloning the simian varicella virus genome in E. coli as an infectious bacterial artificial chromosome

Simian varicella virus (SVV) is closely related to human varicella-zoster virus and causes varicella and zoster-like disease in nonhuman primates. In this study, a mini-F replicon was inserted into a SVV cosmid, and infectious SVV was generated by co-transfection of Vero cells with overlapping SVV cosmids. The entire SVV genome, cloned as a bacterial artificial chromosome (BAC), was stably propagated upon serial passage in E. coli. Transfection of pSVV-BAC DNA into Vero cells yielded infectious SVV (rSVV-BAC). The mini-F vector sequences flanked by loxP sites were removed by co-infection of Vero cells with rSVV-BAC and adenovirus expressing Cre-recombinase. Recombinant SVV generated using the SVV-BAC genetic system has similar molecular and in vitro replication properties as wild-type SVV. To demonstrate the utility of this approach, a SVV ORF 10 deletion mutant was created using two-step Red-mediated recombination. The results indicate that SVV ORF 10, which encodes a homolog of the HSV-1 virion VP-16 transactivator protein, is not essential for in vitro replication but is required for optimal replication in cell culture.

Red-Mediated Transposition and Final Release of the Mini-F Vector of a Cloned Infectious Herpesvirus Genome

Bacterial artificial chromosomes (BACs) are well-established cloning vehicles for functional genomics and for constructing targeting vectors and infectious viral DNA clones. Red-recombination-based mutagenesis techniques have enabled the manipulation of BACs in Escherichia coli without any remaining operational sequences. Here, we describe that the F-factor-derived vector sequences can be inserted into a novel position and seamlessly removed from the present location of the BAC-cloned DNA via synchronous Red-recombination in E. coli in an en passant mutagenesis-based procedure. Using this technique, the mini-F elements of a cloned infectious varicella zoster virus (VZV) genome were specifically transposed into novel positions distributed over the viral DNA to generate six different BAC variants. In comparison to the other constructs, a BAC variant with mini-F sequences directly inserted into the junction of the genomic termini resulted in highly efficient viral DNA replication-mediated spontaneous vector excision upon virus reconstitution in transfected VZV-permissive eukaryotic cells. Moreover, the derived vector-free recombinant progeny exhibited virtually indistinguishable genome properties and replication kinetics to the wild-type virus. Thus, a sequence-independent, efficient, and easy-to-apply mini-F vector transposition procedure eliminates the last hurdle to perform virtually any kind of imaginable targeted BAC modifications in E. coli. The herpesviral terminal genomic junction was identified as an optimal mini-F vector integration site for the construction of an infectious BAC, which allows the rapid generation of mutant virus without any unwanted secondary genome alterations. The novel mini-F transposition technique can be a valuable tool to optimize, repair or restructure other established BACs as well and may facilitate the development of gene therapy or vaccine vectors.

Recovery of infectious virus from full-length cowpox virus (CPXV) DNA cloned as a bacterial artificial chromosome (BAC)

Transmission from pet rats and cats to humans as well as severe infection in felids and other animal species have recently drawn increasing attention to cowpox virus (CPXV). We report the cloning of the entire genome of cowpox virus strain Brighton Red (BR) as a bacterial artificial chromosome (BAC) in Escherichia coli and the recovery of infectious virus from cloned DNA. Generation of a full-length CPXV DNA clone was achieved by first introducing a mini-F vector, which allows maintenance of large circular DNA in E. coli, into the thymidine kinase locus of CPXV by homologous recombination. Circular replication intermediates were then electroporated into E. coli DH10B cells. Upon successful establishment of the infectious BR clone, we modified the full-length clone such that recombination-mediated excision of bacterial sequences can occur upon transfection in eukaryotic cells. This self-excision of the bacterial replicon is made possible by a sequence duplication within mini-F sequences and allows recovery of recombinant virus progeny without remaining marker or vector sequences. The in vitro growth properties of viruses derived from both BAC clones were determined and found to be virtually indistinguishable from those of parental, wild-type BR. Finally, the complete genomic sequence of the infectious clone was determined and the cloned viral genome was shown to be identical to that of the parental virus. In summary, the generated infectious clone will greatly facilitate studies on individual genes and pathogenesis of CPXV. Moreover, the vector potential of CPXV can now be more systematically explored using this newly generated tool.

Identification of 10 cowpox virus proteins that are necessary for induction of hemorrhagic lesions (red pocks) on chorioallantoic membranes

ABSTRACT Cowpox viruses (CPXV) cause hemorrhagic lesions (“red pocks”) on infected chorioallantoic membranes (CAM) of embryonated chicken eggs, while most other members of the genus Orthopoxvirus produce nonhemorrhagic lesions (“white pocks”). Cytokine response modifier A (CrmA) of CPXV strain Brighton Red (BR) is necessary but not sufficient for the induction of red pocks. To identify additional viral proteins involved in the induction of hemorrhagic lesions, a library of single-gene CPXV knockout mutants was screened. We identified 10 proteins that are required for the formation of hemorrhagic lesions, which are encoded by CPXV060, CPXV064, CPXV068, CPXV069, CPXV074, CPXV136, CPXV168, CPXV169, CPXV172, and CPXV199. The genes are the homologues of F12L, F15L, E2L, E3L, E8R, A4L, A33R, A34R, A36R, and B5R of vaccinia virus (VACV). Mutants with deletions in CPXV060, CPXV168, CPXV169, CPXV172, or CPXV199 induced white pocks with a comet-like shape on the CAM. The homologues of these five genes in VACV encode proteins that are involved in the production of extracellular enveloped viruses (EEV) and the repulsion of superinfecting virions by actin tails. The homologue of CPXV068 in VACV is also involved in EEV production but is not related to actin tail induction. The other genes encode immunomodulatory proteins (CPXV069 and crmA) and viral core proteins (CPXV074 and CPXV136), and the function of the product of CPXV064 is unknown. IMPORTANCE It has been known for a long time that cowpox virus induces hemorrhagic lesions on chicken CAM, while most of the other orthopoxviruses produce nonhemorrhagic lesions. Although cowpox virus CrmA has been proved to be responsible for the hemorrhagic phenotype, other proteins causing this phenotype remain unknown. Recently, we generated a complete single-gene knockout bacterial artificial chromosome (BAC) library of cowpox virus Brighton strain. Out of 183 knockout BAC clones, 109 knockout viruses were reconstituted. The knockout library makes possible high-throughput screening for studying poxvirus replication and pathogenesis. In this study, we screened all 109 single-gene knockout viruses and identified 10 proteins necessary for inducing hemorrhagic lesions. The identification of these genes gives a new perspective for studying the hemorrhagic phenotype and may give a better understanding of poxvirus virulence.

Cowpox virus serpin CrmA is necessary but not sufficient for the red pock phenotype on chicken chorioallantoic membranes

It was previously reported that cowpox virus (CPXV) strain Brighton Red (BR) causes red pocks upon inoculation of chorioallantoic membranes (CAMs) of embryonated chicken eggs. Red pocks are characterized by hemorrhage and reduced numbers of inflammatory cells while white pocks induced by other members of the genus Orthopoxvirus lack hemorrhage and have higher numbers of infiltrating heterophils. Analyses of CPXV BR white pock variants identified the cytokine response modifier A (CrmA) as the factor responsible for the differences in pock phenotype through induction of hemorrhage and inhibition of chemotaxis. In the present study CPXV crmA deletion mutants were generated based on a full-length bacterial artificial chromosome clone of CPXV BR (pBR). Deletion of the first crmA start codon was sufficient to abolish protein expression, whereas modification of a potential second start codon had no impact on CrmA production as shown by Western blot analysis. Immunohistochemistry of CAMs inoculated with crmA-positive BR viruses showed accumulation of viral antigen in endothelial cells, which was consistent with the red pock phenotype. On the other hand, crmA-negative mutants were characterized by the induction of white pocks and the absence of CPXV antigen in endothelia. The introduction of the complete CPXV BR crmA gene into the homologous genome region of the attenuated vaccinia virus strain MVA (modified vaccinia virus Ankara), however, resulted in CrmA production but not the red pock phenotype. We therefore conclude that (i) CPXV CrmA is associated with increased accumulation of virus in endothelial cells and (ii) the poxvirus-encoded serpin is necessary but not sufficient for the red pock phenotype and the anti-chemotactic capabilities on CAMs.

Phocine herpesvirus 1 (PhHV-1) in harbor seals from Svalbard, Norway

Phocine herpesvirus 1 (PhHV-1) infections in seals are associated with disease and sometimes high mortality, primarily in young animals. PhHV-1 has been detected in seals from European waters as well as in waters on both coasts of North America. Serological surveys of various pinniped species have indicated a wide geographical distribution of PhHV-1. A quantitative and sensitive real-time PCR assay targeting the gene encoding glycoprotein B of PhHV-1 was developed for detection of PhHV-1 in ocular and nasal swab samples from wild harbor seals (Phoca vitulina) from Svalbard (Norway). PhHV-1 DNA was detected in samples from 6 (8%) seals collected in 2009 and 2 (3%) in 2010; all had herpesvirus DNA in the ocular swab sample, whereas only one of these animals also had herpesvirus DNA in the nasal swab sample. Four PCR positive animals were approximately 1 year of age and four were pups of the year. Serum samples obtained in 1998 (n=59), 1999 (n=74), 2000 (n=81), 2009 (n=69) and 2010 (n=83) were tested for anti-PhHV-1 antibodies in an indirect ELISA. The PhHV-1 seroprevalence in the population remained high throughout this period, varying from 77 to 100% between years. No eye disease was observed in this harbor seal population, but the ELISA and PCR findings reported here suggest that PhHV-1 is endemic in this globally northernmost harbor seal colony, and that the virus is shed on the mucosa of the eye and nose.

Generation and characterization of a Cowpox virus mutant lacking host range factor CP77

Cowpox virus (CPXV) host range factor CP77 was identified to be required for virus replication in Chinese hamster ovary (CHO) cells, but the underlying molecular mechanism by which CP77 modulates host range has remained unclear. Therefore, a CPXVΔCP77 deletion mutant was constructed by applying bacterial artificial chromosome (BAC) technology. Integrity of BAC-derived viral DNA was confirmed by whole genome sequencing. In vitro growth characteristics of CPXV wild type (WT), BAC-derived vCPXV WT and vCPXVΔCP77 were virtually indistinguishable in HEK293T cells, whereas in CHO-K1 cells replication of virus lacking CP77 was unambiguously attenuated. This block of viral replication was confirmed by lack of late viral protein expression. The replication defect of various Orthopoxviruses lacking CP77 in CHO cells could be restored by recombinant expression of CP77. Thus, for the first time, the described CP77-dependent host range effect in CHO cells was shown in the background of CPXV as well as Camelpox virus. To further characterize the mutant virus, cells of several different species were comparably infected with vCPXV WT and vCPXVΔCP77, respectively. Interestingly, except for CHO-K1 cells, vCPXV WT and vCPXVΔCP77 showed no significant difference in terms of morphology of cytopathic effects, expression of a late transcribed virus-encoded green fluorescent protein and virus reproduction, even in other hamster-derived cells. Additionally, in ovo inoculation with either virus revealed the same red-pock phenotype on chicken egg chorioallantoic membranes. Since the data presented indicate a CP77-dependent host range effect only for CHO cells, we conclude that the protein might mediate additional functions not identified yet. The vCPXVΔCP77 deletion mutant generated can now be applied as a useful tool to investigate the function of the putative host range protein CP77.