Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes

Until relatively recently, DNA primases were viewed simply as a class of proteins that synthesize short RNA primers requisite for the initiation of DNA replication. However, recent studies have shown that this perception of the limited activities associated with these diverse enzymes can no longer be justified. Numerous examples can now be cited demonstrating how the term 'DNA primase' only describes a very narrow subset of these nucleotidyltransferases, with the vast majority fulfilling multifunctional roles from DNA replication to damage tolerance and repair. This article focuses on the archaeo-eukaryotic primase (AEP) superfamily, drawing on recently characterized examples from all domains of life to highlight the functionally diverse pathways in which these enzymes are employed. The broad origins, functionalities and enzymatic capabilities of AEPs emphasizes their previous functional misannotation and supports the necessity for a reclassification of these enzymes under a category called primase-polymerases within the wider functional grouping of polymerases. Importantly, the repositioning of AEPs in this way better recognizes their broader roles in DNA metabolism and encourages the discovery of additional functions for these enzymes, aside from those highlighted here

Cloning and Characterization of Subunits of the T-Cell Receptor and Murine Leukemia Virus Enhancer Core-Binding Factor.

Moloney murine leukemia virus causes thymic leukemias when injected into newborn mice. A major determinant of the thymic disease specificity of Moloney virus genetically maps to the conserved viral core motif in the Moloney virus enhancer. Point mutations introduced into the core site significantly shifted the disease specificity of the Moloney virus from thymic leukemia to erythroid leukemia (N.A. Speck, B. Renjifo, E. Golemis, T.N. Fredrickson, J.W. Hartley, and N. Hopkins, Genes Dev. 4:233-242, 1990). We previously reported the purification of core-binding factors (CBF) from calf thymus nuclei (S. Wang and N.A. Speck, Mol. Cell. Biol. 12:89-102, 1992). CBF binds to core sites in murine leukemia virus and T-cell receptor enhancers. Affinity-purified CBF contains multiple polypeptides. In this study, we sequenced five tryptic peptides from two of the bovine CBF proteins and isolated three cDNA clones from a mouse thymus cDNA library encoding three of the tryptic peptides from the bovine proteins. The cDNA clones, which we call CBF beta p22.0, CBF beta p21.5, and CBF beta p17.6, encode three highly related but distinct proteins with deduced molecular sizes of 22.0, 21.5, and 17.6 kDa that appear to be translated from multiply spliced mRNAs transcribed from the same gene. CBF beta p22.0, CBF beta p21.5, and CBF beta p17.6 do not by themselves bind the core site. However, CBF beta p22.0 and CBF beta p21.5 form a complex with DNA-binding CBF alpha subunits and as a result decrease the rate of dissociation of the CBF protein-DNA complex. Association of the CBF beta subunits does not extend the phosphate contacts in the binding site. We propose that CBF beta is a non-DNA-binding subunit of CBF and does not contact DNA directly

The future of the global food system

Although food prices in major world markets are at or near a historical low, there is increasing concern about food security—the ability of the world to provide healthy and environmentally sustainable diets for all its peoples. This article is an introduction to a collection of reviews whose authors were asked to explore the major drivers affecting the food system between now and 2050. A first set of papers explores the main factors affecting the demand for food (population growth, changes in consumption patterns, the effects on the food system of urbanization and the importance of understanding income distributions) with a second examining trends in future food supply (crops, livestock, fisheries and aquaculture, and ‘wild food’). A third set explores exogenous factors affecting the food system (climate change, competition for water, energy and land, and how agriculture depends on and provides ecosystem services), while the final set explores cross-cutting themes (food system economics, food wastage and links with health). Two of the clearest conclusions that emerge from the collected papers are that major advances in sustainable food production and availability can be achieved with the concerted application of current technologies (given sufficient political will), and the importance of investing in research sooner rather than later to enable the food system to cope with both known and unknown challenges in the coming decades

Towards a broad-based and holistic framework of sustainable intensification indicators

The concept of 'Sustainable Intensification' (SI) has been promoted as a potential solution to the many contemporary challenges facing agriculture, but has also received widespread criticism for being too narrow in scope and failing to address all aspects of sustainability. Despite this, there are few suggestions in the literature as to what a holistic, broad-based approach to SI should comprise and what issues and trade-offs are likely to arise in the adoption and operation of such a broadly-based approach. We report a suit of SI indicators suggested by UK stakeholders, evaluate the plausibility of these in terms of the commonly established principles of sustainability, and identify the critical issues that may arise in the adoption and operation of these indicators. The purpose of this paper is not to recommend a specific blueprint for SI but to raise issues and questions for dialogue amongst stakeholders. Data were collected via semi-structured interviews with 32 stakeholders from throughout the UK agrifood system. The data were analysed thematically and organised using a Social-Ecological Systems (SESs) framework. The interviewees suggested a total of 110 SI indicators, of which the most frequently suggested related to agricultural production and ecological considerations. There was less emphasis placed on social and cultural dimensions of agricultural systems. A number of the indicators suggested were poorly-defined and it was difficult to determine what particular aspects of sustainability they addressed. Many potential trade-offs between the indicators were also evident. The findings raise a number of questions. Is it appropriate to continue referring to SI as Sustainable Intensification when it fails to give equal consideration to all accepted aspects of sustainability? Would it be more appropriate to refer to the SI concept as 'Ecological Intensification'? Is a broad-based and all-encompassing definition of 'sustainability' always desirable, or should 'sustainability' be considered as context specific, with the weighting of the different dimensions varying according to operational circumstances? We argue that these questions need to be resolved through stakeholder dialogues in order for the concept of SI to become more widely accepted and implementable in practice

Pathotypic diversity of Hyaloperonospora brassicae collected from Brassica oleracea

Downy mildew caused by Hyaloperonospora brassicae is an economically destructive disease of brassica crops in many growing regions throughout the world. Specialised pathogenicity of downy mildews from different Brassica species and closely related ornamental or wild relatives has been described from host range studies. Pathotypic variation amongst Hyaloperonospora brassicae isolates from Brassica oleracea has also been described; however, a standard set of B. oleracea lines that could enable reproducible classification of H. brassicae pathotypes was poorly developed. For this purpose, we examined the use of eight genetically refined host lines derived from our previous collaborative work on downy mildew resistance as a differential set to characterise pathotypes in the European population of H. brassicae. Interaction phenotypes for each combination of isolate and host line were assessed following drop inoculation of cotyledons and a spectrum of seven phenotypes was observed based on the level of sporulation on cotyledons and visible host responses. Two host lines were resistant or moderately resistant to the entire collection of isolates, and another was universally susceptible. Five lines showed differential responses to the H. brassicae isolates. A minimum of six pathotypes and five major effect resistance genes are proposed to explain all of the observed interaction phenotypes. The B. oleracea lines from this study can be useful for monitoring pathotype frequencies in H. brassicae populations in the same or other vegetable growing regions, and to assess the potential durability of disease control from different combinations of the predicted downy mildew resistance genes