Patterns of recombination in HIV-1M are influenced by selection disfavouring the survival of recombinants with disrupted genomic RNA and protein structures

Genetic recombination is a major contributor to the ongoing diversification of HIV. It is clearly apparent that across the HIV-genome there are defined recombination hot and cold spots which tend to co-localise both with genomic secondary structures and with either inter-gene boundaries or intra-gene domain boundaries. There is also good evidence that most recombination breakpoints that are detectable within the genes of natural HIV recombinants are likely to be minimally disruptive of intra-protein amino acid contacts and that these breakpoints should therefore have little impact on protein folding. Here we further investigate the impact on patterns of genetic recombination in HIV of selection favouring the maintenance of functional RNA and protein structures. We confirm that chimaeric Gag p24, reverse transcriptase, integrase, gp120 and Nef proteins that are expressed by natural HIV-1 recombinants have significantly lower degrees of predicted folding disruption than randomly generated recombinants. Similarly, we use a novel single-stranded RNA folding disruption test to show that there is significant, albeit weak, evidence that natural HIV recombinants tend to have genomic secondary structures that more closely resemble parental structures than do randomly generated recombinants. These results are consistent with the hypothesis that natural selection has acted both in the short term to purge recombinants with disrupted RNA and protein folds, and in the longer term to modify the genome architecture of HIV to ensure that recombination prone sites correspond with those where recombination will be minimally deleterious

Recombinant Goose Circoviruses Circulating in Domesticated and Wild Geese in Poland

Circoviruses are circular single-stranded DNA (ssDNA) viruses that infect a variety of animals, both domestic and wild. Circovirus infection in birds is associated with immunosuppression and this in turn predisposes the infected animals to secondary infections that can lead to mortality. Farmed geese (Anser anser) in many parts of the world are infected with circoviruses. The majority of the current genomic information for goose circoviruses (GoCVs) (n = 40) are from birds sampled in China and Taiwan, and only two genome sequences are available from Europe (Germany and Poland). In this study, we sampled 23 wild and 19 domestic geese from the Gopło Lake area in Poland. We determined the genomes of GoCV from 21 geese; 14 domestic Greylag geese (Anser anser), three wild Greylag geese (A. anser), three bean geese (A. fabalis), and one white fronted goose (A. albifrons). These genomes share 83–95% nucleotide pairwise identities with previously identified GoCV genomes, most are recombinants with exchanged fragment sizes up to 50% of the genome. Higher diversity levels can be seen within the genomes from domestic geese compared with those from wild geese. In the GoCV capsid protein (cp) and replication associated protein (rep) gene sequences we found that episodic positive selection appears to largely mirror those of beak and feather disease virus and pigeon circovirus. Analysis of the secondary structure of the ssDNA genome revealed a conserved stem-loop structure with the G-C rich stem having a high degree of negative selection on these nucleotides

Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of beak and feather disease viruses

Pigeon circovirus (PiCV) has a ~2 kb genome circular ssDNA genome. All but one of the known PiCV isolates have been found infecting pigeons in various parts of the world. In this study, we screened 324 swab and tissue samples from Polish pigeons and recovered 30 complete genomes, 16 of which came from birds displaying no obvious pathology. Together with 17 other publicly available PiCV complete genomes sampled throughout the Northern Hemisphere and Australia, we find that PiCV displays a similar degree of genetic diversity to that of the related psittacine-infecting circovirus species, beak and feather disease virus (BFDV). We show that, as is the case with its pathology and epidemiology, PiCV also displays patterns of recombination, genomic secondary structure and natural selection that are generally very similar to those of BFDV. It is likely that breeding facilities play a significant role in the emergence of new recombinant PiCV variants and given that ~50 % of the domestic pigeon population is infected subclinically, all pigeon breeding stocks should be screened routinely for this virus

PGE2 alters chromatin through H2A.Z-variant enhancer nucleosome modification to promote hematopoietic stem cell fate

Prostaglandin E2 (PGE2) and 16,16-dimethyl-PGE2 (dmPGE2) are important regulators of hematopoietic stem and progenitor cell (HSPC) fate and offer potential to enhance stem cell therapies [C. Cutler et al. Blood 122, 3074–3081(2013); W. Goessling et al. Cell Stem Cell 8, 445–458 (2011); W. Goessling et al. Cell 136, 1136–1147 (2009)]. Here, we report that PGE2-induced changes in chromatin at enhancer regions through histone-variant H2A.Z permit acute inflammatory gene induction to promote HSPC fate. We found that dmPGE2-inducible enhancers retain MNase-accessible, H2A.Z-variant nucleosomes permissive of CREB transcription factor (TF) binding. CREB binding to enhancer nucleosomes following dmPGE2 stimulation is concomitant with deposition of histone acetyltransferases p300 and Tip60 on chromatin. Subsequent H2A.Z acetylation improves chromatin accessibility at stimuli-responsive enhancers. Our findings support a model where histone-variant nucleosomes retained within inducible enhancers facilitate TF binding. Histone-variant acetylation by TF-associated nucleosome remodelers creates the accessible nucleosome landscape required for immediate enhancer activation and gene induction. Our work provides a mechanism through which inflammatory mediators, such as dmPGE2, lead to acute transcriptional changes and modify HSPC behavior to improve stem cell transplantation

List of PDB structure files used in the chimaeric protein-fold disruption tests.

<p>List of PDB structure files used in the chimaeric protein-fold disruption tests.</p

Degrees of protein fold disruption in natural and simulated HIV-1 recombinants.

1<p>The p-value is the probability that mimic recombination breakpoints do not tend to avoid disrupting protein folding to a greater degree than S-recombinants.</p>2<p>Covarying contact model of coevolution. Amino acids within van der Waals contact in the 3D structure were considered to be potentially covarying. The p-value is determined from a comparison of observed numbers of coevolving residues that are segregated by recombination with numbers predicted under random recombination.</p>3<p>Mutual information model of coevolution. Amino acids in contact in the 3D structure with associated mutual information values >0.25 were considered to be potentially covarying. P-values were determined as in ².</p>4<p>Not determined.</p

Diagrammatic representation of how simulated recombinants were generated.

<p>For a particular recombination event specifying a major parent, a minor parent, and a pair of recombination breakpoint locations delineating a fragment of sequence derived from the minor parent (containing in this particular case two nucleotides that vary between the major and minor parents), an <i>in silico</i> mimic of the real recombinant sequence is created using the minor and the major parent sequences. Following that, a set of N simulated recombinants is generated in a similar way to the mimic recombinant, but using random starting and ending positions, whilst maintaining the same number of either variable nucleotides (for the RNA folding tests) or non-synonymous codon sites (for the protein folding tests) between the randomized breakpoint sites as occur in the mimic recombinant. In this example the mimic and simulated recombinants all have two such “informative” sites between the 3′ and 5′ breakpoints that are not identical between the parental sequences.</p

The predicted sensitivity of HIV-1M proteins to recombinational disruption.

<p>(<b>A</b>) Depicted are the means (black lines) and ranges (gray backgrounds) of predicted degrees of recombination-induced folding disruption in various HIV-1 proteins (those for which suitable atomic resolution three dimensional structures are available). The white areas interspersed between the gray areas are positions where there was no protein structure data available or where there were extra amino acids inserted into the alignment that were not present in the protein structure used. For all genome regions that had associated protein structure data, all conceivable single breakpoint recombinants were simulated using parental sequences that resembled as closely as possible the parental sequences of actual recombinant viruses with single detectable recombination breakpoints in these genome regions. Amino acid substitution rates and breakpoint positions occurring in these actual HIV-1 recombinants are displayed at the top of the figure. (<b>B</b>) Recombination breakpoint density plot illustrating breakpoint positions detected across 434 detectable HIV-1M recombination events (After <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100400#pone.0100400-SimonLoriere2" target="_blank">[14]</a>). Light and dark grey areas respectively indicate the 95% and 99% confidence intervals of breakpoint numbers that would have been detectable in different genome locations under random recombination. The grey areas undulate with degrees of sequence conservation because recombination events are more easily detectable in genome regions that are genetically diverse. Note firstly that the peaks of the plots in <b>A</b> indicate recombination breakpoint positions that are predicted to have the greatest disruptive effects on protein folding, and secondly that in actual recombinant HIV-1M genomes sampled from nature these “disruptive breakpoint positions” tend to correspond in plot <b>B</b> with regions of low recombination breakpoint densities.</p

Recombinant Goose Circoviruses Circulating in Domesticated and Wild Geese in Poland

Circoviruses are circular single-stranded DNA (ssDNA) viruses that infect a variety of animals, both domestic and wild. Circovirus infection in birds is associated with immunosuppression and this in turn predisposes the infected animals to secondary infections that can lead to mortality. Farmed geese (Anser anser) in many parts of the world are infected with circoviruses. The majority of the current genomic information for goose circoviruses (GoCVs) (n = 40) are from birds sampled in China and Taiwan, and only two genome sequences are available from Europe (Germany and Poland). In this study, we sampled 23 wild and 19 domestic geese from the Gopło Lake area in Poland. We determined the genomes of GoCV from 21 geese; 14 domestic Greylag geese (Anser anser), three wild Greylag geese (A. anser), three bean geese (A. fabalis), and one white fronted goose (A. albifrons). These genomes share 83–95% nucleotide pairwise identities with previously identified GoCV genomes, most are recombinants with exchanged fragment sizes up to 50% of the genome. Higher diversity levels can be seen within the genomes from domestic geese compared with those from wild geese. In the GoCV capsid protein (cp) and replication associated protein (rep) gene sequences we found that episodic positive selection appears to largely mirror those of beak and feather disease virus and pigeon circovirus. Analysis of the secondary structure of the ssDNA genome revealed a conserved stem-loop structure with the G-C rich stem having a high degree of negative selection on these nucleotides

Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains

In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ~73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species