Paul Hooley

Demystified . . . Human endogenous retroviruses

Human endogenous retroviruses (HERVs) are a family of viruses within our genome with similarities to present day exogenous retroviruses. HERVs have been inherited by successive generations and it is possible that some have conferred biological benefits. However, several HERVs have been implicated in certain cancers and autoimmune diseases. This article demystifies these retroviruses by providing an insight into HERVs, their means of classification, and a synopsis of HERVs implicated in cancer and autoimmunity. Furthermore, the biological roles of HERVs are explored.

Salinity induced differences in growth, ion distribution and partitioning in barley between the cultivar Maythorpe and its derived mutant Golden Promise

Dry matter changes and ion partitioning in two near isogenic barley cultivars Maythorpe (relatively salt sensitive) and Golden Promise (relatively salt tolerant) were studied in response to increasing salinity. Although the growth of both cultivars was significantly reduced by exposure to NaCl, the effect was greater in Maythorpe, whilst Golden Promise maintained an increased ratio of young to old leaf blade. Golden Promise maintained significantly lower Na+ concentrations in young expanding tissues compared with Maythorpe. Partitioning of Cl− was evident in that both varieties maintained lower Cl− concentrations in mesophyll than in epidermal cells. Golden Promise maintained higher K+/Na+ and Ca2+/Na+ ratios in young leaf blade and young sheath tissues than Maythorpe when exposed to salt. Differences in ion partitioning and the maintenance of higher K+ and Ca2+ to Na+ ratios, especially in young growing and recently expanded tissues, would appear to be important mechanisms contributing to the improved salt tolerance of Golden Promise.

Human endogenous retroviruses: transposable elements with potential?

Human endogenous retroviruses (HERVs) are a significant component of a wider family of retroelements that constitute part of the human genome. These viruses, perhaps representative of previous exogenous retroviral infection, have been integrated and passed through successive generations within the germ line. The retention of HERVs and isolated elements, such as long‐terminal repeats, could have the potential to harm. In this review we describe HERVs within the context of the family of known transposable elements and survey these viruses in terms of superantigens and molecular mimics. It is entirely possible that these mechanisms provide the potential for undesired immune responses.

A role for human endogenous retrovirus‐K (HML‐2) in rheumatoid arthritis: investigating mechanisms of pathogenesis

Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections within the human genome. These molecular fossils draw parallels with present‐day exogenous retroviruses and have been linked previously with immunopathology within rheumatoid arthritis (RA). Mechanisms of pathogenesis for HERV‐K in RA such as molecular mimicry were investigated. To clarify a role for HERVs in RA, potential autoantigens implicated in autoimmunity were scanned for sequence identity with retroviral epitopes. Short retroviral peptides modelling shared epitopes were synthesized, to survey anti‐serum of RA patients and disease controls. A novel real‐time polymerase chain reaction (PCR) assay was also developed to quantify accurately levels of HERV‐K (HML‐2) gag expression, relative to normalized housekeeping gene expression. Both serological and molecular assays showed significant increases in HERV‐K (HML‐2) gag activity in RA patients, compared to disease controls. The real‐time PCR assay identified significant up‐regulation in HERV‐K mRNA levels in RA patients compared to inflammatory and healthy controls. Exogenous viral protein expression and proinflammatory cytokines were also shown to exert modulatory effects over HERV‐K (HML‐2) transcription. From our data, it can be concluded that RA patients exhibited significantly elevated levels of HERV‐K (HML‐2) gag activity compared to controls. Additional factors influencing HERV activity within the synovium were also identified. The significant variation in RA patients, both serologically and transcriptionally, may be an indication that RA is an umbrella term for a number of separate disease entities, of which particular HERV polymorphisms may play a role in development.

Cloning of a novel gene encoding a C2H2 zinc finger protein that alleviates sensitivity to abiotic stresses in Aspergillus nidulans

We report the cloning and sequencing of a DNA fragment encoding a putative C 2 H 2 zinc finger protein from Aspergillus nidulans. The gene was isolated by complementation cloning of a salt sensitive phenotype of the A. nidulans sltAl mutant. A 3.8 kb Pst I fragment that restored wild type salt tolerance contained one large open reading frame of 2202 bp. The predicted protein (StzA) from this reading frame comprises 698 amino acids and has three Zinc fingers along with a putative transcriptional activation domain rich in acidic amino acids. The corresponding sequence from a sltAl mutant contains a premature STOP codon resulting in loss of the putative transcriptional activator in the C-terminal region. The Zinc fingers show conserved motifs with a number of transcription factors including CreA from A. nidulans and the human Wilms tumour susceptibility protein WT-1.

Horizontal transfer of bacterial polyphosphate kinases to eukaryotes: implications for the ice age and land colonisation

BackgroundStudies of online database(s) showed that convincing examples of eukaryote PPKs derived from bacteria type PPK1 and PPK2 enzymes are rare and currently confined to a few simple eukaryotes. These enzymes probably represent several separate horizontal transfer events. Retention of such sequences may be an advantage for tolerance to stresses such as desiccation or nutrient depletion for simple eukaryotes that lack more sophisticated adaptations available to multicellular organisms. We propose that the acquisition of encoding sequences for these enzymes by horizontal transfer enhanced the ability of early plants to colonise the land. The improved ability to sequester and release inorganic phosphate for carbon fixation by photosynthetic algae in the ocean may have accelerated or even triggered global glaciation events. There is some evidence for DNA sequences encoding PPKs in a wider range of eukaryotes, notably some invertebrates, though it is unclear that these represent functional genes.Polyphosphate (poly P) is found in all cells, carrying out a wide range of essential roles. Studied mainly in prokaryotes, the enzymes responsible for synthesis of poly P in eukaryotes (polyphosphate kinases PPKs) are not well understood. The best characterised enzyme from bacteria known to catalyse the formation of high molecular weight polyphosphate from ATP is PPK1 which shows some structural similarity to phospholipase D. A second bacterial PPK (PPK2) resembles thymidylate kinase. Recent reports have suggested a widespread distribution of these bacteria type enzymes in eukaryotes.ResultsOn – line databases show evidence for the presence of genes encoding PPK1 in only a limited number of eukaryotes. These include the photosynthetic eukaryotes Ostreococcus tauri, O. lucimarinus, Porphyra yezoensis, Cyanidioschyzon merolae and the moss Physcomitrella patens, as well as the amoeboid symbiont Capsaspora owczarzaki and the non-photosynthetic eukaryotes Dictyostelium (3 species), Polysphondylium pallidum and Thecamonas trahens. A second bacterial PPK (PPK2) is found in just two eukaryotes (O. tauri and the sea anemone Nematostella vectensis). There is some evidence for PPK1 and PPK2 encoding sequences in other eukaryotes but some of these may be artefacts of bacterial contamination of gene libraries.ConclusionsEvidence for the possible origins of these eukaryote PPK1s and PPK2s and potential prokaryote donors via horizontal gene transfer is presented. The selective advantage of acquiring and maintaining a prokaryote PPK in a eukaryote is proposed to enhance stress tolerance in a changing environment related to the capture and metabolism of inorganic phosphate compounds. Bacterial PPKs may also have enhanced the abilities of marine phytoplankton to sequester phosphate, hence accelerating global carbon fixation.

Evidence for sltA1 as a salt-sensitive allele of the arginase gene (agaA) in the ascomycete Aspergillus nidulans

Abstract Strains of Aspergillus nidulans carrying the sltA1 mutation, conferring sensitivity to KCl and NaCl, also showed an arginine-sensitive phenotype whereby concentrations of the L-amino acid at or above 10 mM were toxic to growth. Sexual progeny of a cross between a sltA1 mutant and a wild-type strain showed a co-segregation of salt and arginine sensitivity. Similarly, revertants to salt tolerance showed a loss of arginine sensitivity as did sltA1 strains that were transformed with a cosmid carrying the putative sltA1+ wild-type allele. In addition, arginine sensitivity could be relieved by L-ornithine. It is suggested that sltA1 is a salt-sensitive allele of the arginase gene (agaA).

Complementation cloning of salt tolerance determinants from the marine hyphomycete Dendryphiella salina in Aspergillus nidulans

A preliminary physiological characterization of osmoregulation in an Aspergillus nidulans salt sensitive mutant carrying cotransformed DNA sequences from the marine hyphomycete Dendryphiella salina is described. A genomic DNA library made in lambda EMBL3 was cotransformed with the plasmid pDJB3 into an A. nidulans host carrying a selectable marker for transformation (pyrG89) and a salt sensitivity mutation (sltA1). In some cases D. salina clones appeared to directly complement the salt sensitivity mutation by restoring salt and arginine insensitivity. Other clones gave marked increases in salt tolerance and yet the hosts remained arginine sensitive. Improvements in salt tolerance correlated with an enhanced ability to induce polyol biosynthesis during salt challenge.

A comparative physiological and morphological study of Dendryphiella salina and D. arenaria in relation to adaptation to life in the sea

A series of comparative physiological and morphological analyses are described for eighteen Dendryphiella isolates. Conidial characteristics of ten isolates showed relatively little variation as a result of different incubation conditions. Isolates were markedly tolerant to NaCl and KCl, although some variation between isolates was noted. A variety of nitrogen compounds could be utilized by most isolates although some grew poorly with certain nitrogen sources. Most isolates showed a wide pH growth range, particularly at alkaline values, and broad temperature growth profiles. The relevance of these physiological characteristics to the survival and fitness of Dendryphiella species in the marine environment is discussed.

Fungal gene sequences make excellent models for teaching data mining

A brief introductory exercise in the use of on-line databases to examine fungal genes and their products is described. Fungal genes make particularly good teaching models owing to their relatively simple eukaryotic structure and wide range of homologues in higher organisms including humans. An evaluation of students’ reactions to the exercise is included.