Bibliographies: 'Initiative multipartite'

1

Vega-Arreguín, Julio C., Tatiana Timchenko, Bruno Gronenborn, and Bertha Cecilia Ramírez. "A Functional Histidine-Tagged Replication Initiator Protein: Implications for the Study of Single-Stranded DNA Virus Replication In Planta." Journal of Virology 79, no. 13 (July 1, 2005): 8422–30. http://dx.doi.org/10.1128/jvi.79.13.8422-8430.2005.

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ABSTRACT Replication initiation of nanoviruses, plant viruses with a multipartite circular single-stranded DNA genome, is triggered by the master Rep (M-Rep) protein. To enable the study of interactions between M-Rep and viral or host factors involved in replication, we designed oligohistidine-tagged variants of the nanovirus Faba bean necrotic yellows virus (FBNYV) M-Rep protein that allow affinity purification of enzymatically active M-Rep from plant tissue. The tagged M-Rep protein was able to initiate replication of its cognate and other FBNYV DNAs in Nicotiana benthamiana leaf disks and plants. The replicon encoding the tagged M-Rep protein multiplied and moved systemically in FBNYV-infected Vicia faba plants and was transmitted by the aphid vector of the virus. Using the tagged M-Rep protein, we demonstrated the in planta interaction between wild-type M-Rep and its tagged counterpart. Such a tagged and fully functional replication initiator protein will have bearings on the isolation of protein complexes from plants.

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Maurya, Ganesh K., Reema Chaudhary, Neha Pandey, and Hari S. Misra. "Molecular insights into replication initiation in a multipartite genome harboring bacterium Deinococcus radiodurans." Journal of Biological Chemistry 296 (January 2021): 100451. http://dx.doi.org/10.1016/j.jbc.2021.100451.

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Mailand, Mikkel. "Social partnership as an approach to CSR: ‘traditional’ and ‘new’ actors, their roles and relations." Transfer: European Review of Labour and Research 10, no. 3 (August 2004): 416–32. http://dx.doi.org/10.1177/102425890401000308.

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This article reports on research into social partnerships aiming at labour market inclusion that developed during the 1990s in Denmark, the UK and Spain. Some of these partnerships are directly related to corporate social responsibility (CSR initiatives in individual firms), whereas others are only indirectly related (for instance, active labour market policy initiatives at local, regional and national level). Developments such as new target groups for such policies, the weakening of the social partners, ideological change, policy transfer and budget constraints of the state have led to more partnerships taking a multipartite form, meaning that not only the public authorities and the social partners, but also new actors such as business networks, commercial operators and NGOs, participate. The involvement of new actors poses a challenge for the traditional actors – among them the trade unions. Whether the relations between traditional and new actors are best described by conflict or by cooperation cannot be explained by regime theories. The decisive factor seems to be the extent to which the new actors challenge the privileged positions of the traditional actors.

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4

Pal, Debasish, Tatiana Venkova-Canova, Preeti Srivastava, and Dhruba K. Chattoraj. "Multipartite Regulation of rctB, the Replication Initiator Gene of Vibrio cholerae Chromosome II." Journal of Bacteriology 187, no. 21 (November 1, 2005): 7167–75. http://dx.doi.org/10.1128/jb.187.21.7167-7175.2005.

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ABSTRACT Replication initiator proteins in bacteria not only allow DNA replication but also often regulate the rate of replication initiation as well. The regulation is mediated by limiting the synthesis or availability of initiator proteins. The applicability of this principle is demonstrated here for RctB, the replication initiator for the smaller of the two chromosomes of Vibrio cholerae. A strong promoter for the rctB gene named rctBp was identified and found to be autoregulated in Escherichia coli. Promoter activity was lower in V. cholerae than in E. coli, and a part of this reduction is likely to be due to autorepression. Sequences upstream of rctBp, implicated earlier in replication control, enhanced the repression. The action of the upstream sequences required that they be present in cis, implying long-range interactions in the control of the promoter activity. A second gene specific for chromosome II replication, rctA, reduced rctB translation, most likely by antisense RNA control. Finally, optimal rctBp activity was found to be dependent on Dam. Increasing RctB in trans increased the copy number of a miniplasmid carrying oriCIIVC , implying that RctB can be rate limiting for chromosome II replication. The multiple modes of control on RctB are expected to reduce fluctuations in the initiator concentration and thereby help maintain chromosome copy number homeostasis.

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Hema, M., K. Gopinath, and C. Kao. "Repair of the tRNA-Like CCA Sequence in a Multipartite Positive-Strand RNA Virus." Journal of Virology 79, no. 3 (February 1, 2005): 1417–27. http://dx.doi.org/10.1128/jvi.79.3.1417-1427.2005.

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ABSTRACT The 3′ portions of plus-strand brome mosaic virus (BMV) RNAs mimic cellular tRNAs. Nucleotide substitutions or deletions in the 3′ CCA of the tRNA-like sequence (TLS) affect minus-strand initiation unless repaired. We observed that 2-nucleotide deletions involving the CCA 3′ sequence in one or all BMV RNAs still allowed RNA accumulation in barley protoplasts at significant levels. Alterations of CCA to GGA in only BMV RNA3 also allowed RNA accumulation at wild-type levels. However, substitutions in all three BMV RNAs severely reduced RNA accumulation, demonstrating that substitutions have different repair requirements than do small deletions. Furthermore, wild-type BMV RNA1 was required for the repair and replication of RNAs with nucleotide substitutions. Results from sequencing of progeny viral RNA from mutant input RNAs demonstrated that RNA1 did not contribute its sequence to the mutant RNAs. Instead, the repaired ends were heterogeneous, with one-third having a restored CCA and others having sequences with the only commonality being the restoration of one cytidylate. The role of BMV RNA1 in increased repair was examined.

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Strobel, Eric J., and Jeffrey W. Roberts. "Two transcription pause elements underlie a σ70-dependent pause cycle." Proceedings of the National Academy of Sciences 112, no. 32 (July 27, 2015): E4374—E4380. http://dx.doi.org/10.1073/pnas.1512986112.

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The movement of RNA polymerase (RNAP) during transcription elongation is modulated by DNA-encoded elements that cause the elongation complex to pause. One of the best-characterized pause sequences is a binding site for the σ70 initiation factor that induces pausing at a site near lambdoid phage late-gene promoters. An essential component of this σ70-dependent pause is the elemental pause site (EPS), a sequence that itself induces transcription pausing throughout the Escherichia coli genome and underlies other complex regulatory pause elements, such as the ops and his operon pauses. Here, we identify and provide a detailed kinetic analysis of a transcription cycle analogous to abortive cycling that underlies the σ70-dependent pause. We show that, in σ70-dependent pausing, the elemental pause acts primarily to modulate the rate at which complexes attempt to disengage the σ70:DNA interaction. Our findings establish the σ70-dependent pause-encoding region as a multipartite element in which several pause-inducing components make distinct mechanistic contributions to the induction and maintenance of a regulatory transcription pause.

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7

Betancourt, Mónica, Alberto Fereres, Aurora Fraile, and Fernando García-Arenal. "Estimation of the Effective Number of Founders That Initiate an Infection after Aphid Transmission of a Multipartite Plant Virus." Journal of Virology 82, no. 24 (October 8, 2008): 12416–21. http://dx.doi.org/10.1128/jvi.01542-08.

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ABSTRACT The fecundity of RNA viruses can be very high. Thus, it is often assumed that viruses have large populations, and RNA virus evolution has been mostly explained using purely deterministic models. However, population bottlenecks during the virus life cycle could result in effective population numbers being much smaller than reported censuses, and random genetic drift could be important in virus evolution. A step at which population bottlenecks may be severe is host-to-host transmission. We report here an estimate of the size of the population that starts a new infection when Cucumber mosaic virus (CMV) is transmitted by the aphid Aphis gossypii, based on the segregation of two CMV genotypes in plants infected by aphids that acquired the virus from plants infected by both genotypes. Results show very small effective numbers of founders, between one and two, both in experiments in which the three-partite genome of CMV was aphid transmitted and in experiments in which a fourth RNA, CMV satellite RNA, was also transmitted. These numbers are very similar to those published for Potato virus Y, which has a monopartite genome and is transmitted by aphids according to a different mechanism than CMV. Thus, the number of genomic segments seems not to be a major determinant of the effective number of founders. Also, our results suggest that the occurrence of severe bottlenecks during horizontal transmission is general for viruses nonpersistently transmitted by aphids, indicating that random genetic drift should be considered when modeling virus evolution.

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8

Sharp, S. J., and A. D. Garcia. "Transcription of the Drosophila melanogaster 5S RNA gene requires an upstream promoter and four intragenic sequence elements." Molecular and Cellular Biology 8, no. 3 (March 1988): 1266–74. http://dx.doi.org/10.1128/mcb.8.3.1266.

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Linker-scanning (LS) mutations were constructed spanning the length of the Drosophila melanogaster 5S RNA gene. In vitro transcription analysis of the LS 5S DNAs revealed five transcription control regions. One control region essential for transcription initiation was identified in the 5'-flanking sequence. The major sequence determinants of this upstream promoter region were located between coordinates -39 and -26 (-30 region), but important sequences extended to the transcription start site at position 1. Since mutations in the upstream promoter did not alter the ability of 5S DNA to sequester transcription factors into a stable transcription complex, it appears that this control region involved the interaction of RNA polymerase III. Active 5S DNA transcription additionally required the four intragenic control regions (ICRs) located between coordinates 3 and 18 (ICR I), 37 and 44 (ICR II), 48 and 61 (ICR III), and 78 and 98 (ICR IV). LS mutations in each ICR decreased the ability of 5S DNA to sequester transcription factors. ICR III, ICR IV, and the spacer sequence between were similar in sequence and position to the determinant elements of the multipartite ICR of Xenopus 5S DNA. The importance of ICR III and ICR IV in transcription initiation and in sequestering transcription factors suggests the presence of an activity in D. melanogaster similar to transcription factor TFIIIA of Xenopus laevis and HeLa cells. Transcription initiation of Drosophila 5S DNA was not eliminated by LS mutations in the spacer region even though these mutations reduced the ability of the TFIIIA-like activity to bind. The previously unidentified control regions ICR I and ICR II appear to be important for the interaction of a transcription factor activity, or multiple-factor activities, distinct from the TFIIIA-like activity. The interaction of this activity with ICR I directed the selection of the transcription start site.

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9

Sharp, S. J., and A. D. Garcia. "Transcription of the Drosophila melanogaster 5S RNA gene requires an upstream promoter and four intragenic sequence elements." Molecular and Cellular Biology 8, no. 3 (March 1988): 1266–74. http://dx.doi.org/10.1128/mcb.8.3.1266-1274.1988.

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Abstract:

Linker-scanning (LS) mutations were constructed spanning the length of the Drosophila melanogaster 5S RNA gene. In vitro transcription analysis of the LS 5S DNAs revealed five transcription control regions. One control region essential for transcription initiation was identified in the 5'-flanking sequence. The major sequence determinants of this upstream promoter region were located between coordinates -39 and -26 (-30 region), but important sequences extended to the transcription start site at position 1. Since mutations in the upstream promoter did not alter the ability of 5S DNA to sequester transcription factors into a stable transcription complex, it appears that this control region involved the interaction of RNA polymerase III. Active 5S DNA transcription additionally required the four intragenic control regions (ICRs) located between coordinates 3 and 18 (ICR I), 37 and 44 (ICR II), 48 and 61 (ICR III), and 78 and 98 (ICR IV). LS mutations in each ICR decreased the ability of 5S DNA to sequester transcription factors. ICR III, ICR IV, and the spacer sequence between were similar in sequence and position to the determinant elements of the multipartite ICR of Xenopus 5S DNA. The importance of ICR III and ICR IV in transcription initiation and in sequestering transcription factors suggests the presence of an activity in D. melanogaster similar to transcription factor TFIIIA of Xenopus laevis and HeLa cells. Transcription initiation of Drosophila 5S DNA was not eliminated by LS mutations in the spacer region even though these mutations reduced the ability of the TFIIIA-like activity to bind. The previously unidentified control regions ICR I and ICR II appear to be important for the interaction of a transcription factor activity, or multiple-factor activities, distinct from the TFIIIA-like activity. The interaction of this activity with ICR I directed the selection of the transcription start site.

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10

Waterworth, Samantha C., Laura V. Flórez, Evan R. Rees, Christian Hertweck, Martin Kaltenpoth, and Jason C. Kwan. "Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome." mBio 11, no. 1 (February 25, 2020). http://dx.doi.org/10.1128/mbio.02430-19.

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ABSTRACT Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont’s genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction. IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation—bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation.

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