High Cooperativity of the SV40 Major Capsid Protein VP1 in Virus Assembly

SV40 is a small, non enveloped DNA virus with an icosahedral capsid of 45 nm. The outer shell is composed of pentamers of the major capsid protein, VP1, linked via their flexible carboxy-terminal arms. Its morphogenesis occurs by assembly of capsomers around the viral minichromosome. However the steps leading to the formation of mature virus are poorly understood. Intermediates of the assembly reaction could not be isolated from cells infected with wt SV40. Here we have used recombinant VP1 produced in insect cells for in vitro assembly studies around supercoiled heterologous plasmid DNA carrying a reporter gene. This strategy yields infective nanoparticles, affording a simple quantitative transduction assay. We show that VP1 assembles under physiological conditions into uniform nanoparticles of the same shape, size and CsCl density as the wild type virus. The stoichiometry is one DNA molecule per capsid. VP1 deleted in the C-arm, which is unable to assemble but can bind DNA, was inactive indicating genuine assembly rather than non-specific DNA-binding. The reaction requires host enzymatic activities, consistent with the participation of chaperones, as recently shown. Our results demonstrate dramatic cooperativity of VP1, with a Hill coefficient of ∼6. These findings suggest that assembly may be a concerted reaction. We propose that concerted assembly is facilitated by simultaneous binding of multiple capsomers to a single DNA molecule, as we have recently reported, thus increasing their local concentration. Emerging principles of SV40 assembly may help understanding assembly of other complex systems. In addition, the SV40-based nanoparticles described here are potential gene therapy vectors that combine efficient gene delivery with safety and flexibility

A CI-Independent Form of Replicative Inhibition: Turn Off of Early Replication of Bacteriophage Lambda

Several earlier studies have described an unusual exclusion phenotype exhibited by cells with plasmids carrying a portion of the replication region of phage lambda. Cells exhibiting this inhibition phenotype (IP) prevent the plating of homo-immune and hybrid hetero-immune lambdoid phages. We have attempted to define aspects of IP, and show that it is directed to repλ phages. IP was observed in cells with plasmids containing a λ DNA fragment including oop, encoding a short OOP micro RNA, and part of the lambda origin of replication, oriλ, defined by iteron sequences ITN1-4 and an adjacent high AT-rich sequence. Transcription of the intact oop sequence from its promoter, pO is required for IP, as are iterons ITN3–4, but not the high AT-rich portion of oriλ. The results suggest that IP silencing is directed to theta mode replication initiation from an infecting repλ genome, or an induced repλ prophage. Phage mutations suppressing IP, i.e., Sip, map within, or adjacent to cro or in O, or both. Our results for plasmid based IP suggest the hypothesis that there is a natural mechanism for silencing early theta-mode replication initiation, i.e. the buildup of λ genomes with oop+ oriλ+ sequence

Explaining state development: Indonesia from its pre-independence origins to contemporary democracy.

Explaining State Development: Indonesia from Pre-Independence Origins to Contemporary Democracy. This thesis uses the Indonesian case to present a new paradigm for explaining the state development of new or relatively new (post-World War II) states. The first chapter describes this paradigm of organic and mechanical types of state development, argues that the development of the Indonesian state from the 1950s to 1990s is a good example of the mechanical type of development and shows how this can be confirmed by assessing and comparing the capabilities of the four different versions of a modern state developed by Indonesia since independence. The next chapter examines Indonesia’s pre-independence debates about the form of state to be adopted, which led to Indonesia accepting a Western model of the state that has since undergone a development process involving four different versions of a ‘modern’ state. These four versions of the state are defined according to their type of regime and policymaking institutions: I) parliamentary democracy, II) Sukarno’s civilian presidential monarchy, III) Suharto’s military presidential monarchy and IV) presidential democracy. Chapters Three to Six assess and compare these four versions’ capability in three key areas: 1) achieving legal legitimacy, 2) control of the military and 3) dealing with political disorder – a crucial area of state capability that requires two chapters. Then Chapter Seven examines and explains the pre-democratic origins of the present version of the Indonesian state, the presidential democracy of Version IV. The Conclusion collates the findings of Chapters Three to Six on capabilities and summarises the arguments of Chapters Two and Seven regarding the 1940s acceptance of the Western model of the state and the late 1990s opportunity for democratisation. Finally, there is a concluding assessment of the potential of the organic/mechanical typology as a new paradigm for studying state development in other countries, regions and eras