Tertiary structure of SaGNAT in cartoon format, with α-helices, β-strands, and loops colored in red, yellow, and green respectively.

<p>Tertiary structure of SaGNAT in cartoon format, with α-helices, β-strands, and loops colored in red, yellow, and green respectively.</p

Quaternary structure of SaGNAT showing interacting residues at the dimer interface.

<p>Quaternary structure of SaGNAT showing interacting residues at the dimer interface.</p

Structure based alignment of the <i>Sa</i>GNAT (green) with 3 acyl-transferases and RMSD less than 1 Å. 1YR0 (orange), 1BL1 (blue), and 2JLM (magenta) are crystal structure of phosphinothricin acetyltransferase from <i>Agrobacterium tumefaciens</i>, <i>Pseudomonas aeruginosa</i>, and <i>Acinetobacter baylyi</i> respectively.

<p>Blue and red boxes depict conserved CoA binding and active site residues respectively, yellow box indicate residues involved in dimer formation, and unfilled boxes represent strictly conserved residues.</p

Protein purification profile of <i>Sa</i>GNAT.

<p>(A) FPLC profile of the affinity purification, with SDS-PAGE insert showing lane 1 - whole bacterial cell lysate; lane 2 - soluble protein fraction of the bacterial cell lysate; lane 3 – flow-through from the affinity column; lane 4 – affinity elution. (B) Size exclusion purification indicating the theoretical elution volumes for monomer, dimer, and trimer, and an SDS PAGE insert lane 5 – showing the final purity of the protein.</p

Data collection and refinement statistics.

<p>Statistics for the highest-resolution shell are shown in parentheses.</p

Mutability Dynamics of an Emergent Single Stranded DNA Virus in a Naïve Host

<div><p>Quasispecies variants and recombination were studied longitudinally in an emergent outbreak of <i>beak and feather disease virus</i> (BFDV) infection in the orange-bellied parrot (<i>Neophema chrysogaster</i>). Detailed health monitoring and the small population size (<300 individuals) of this critically endangered bird provided an opportunity to longitudinally track viral replication and mutation events occurring in a circular, single-stranded DNA virus over a period of four years within a novel bottleneck population. Optimized PCR was used with different combinations of primers, primer walking, direct amplicon sequencing and sequencing of cloned amplicons to analyze BFDV genome variants. Analysis of complete viral genomes (n = 16) and <i>Rep</i> gene sequences (n = 35) revealed that the outbreak was associated with mutations in functionally important regions of the normally conserved <i>Rep</i> gene and immunogenic capsid (<i>Cap</i>) gene with a high evolutionary rate (3.41×10⁻³ subs/site/year) approaching that for RNA viruses; simultaneously we observed significant evidence of recombination hotspots between two distinct progenitor genotypes within orange-bellied parrots indicating early cross-transmission of BFDV in the population. Multiple quasispecies variants were also demonstrated with at least 13 genotypic variants identified in four different individual birds, with one containing up to seven genetic variants. Preferential PCR amplification of variants was also detected. Our findings suggest that the high degree of genetic variation within the BFDV species as a whole is reflected in evolutionary dynamics within individually infected birds as quasispecies variation, particularly when BFDV jumps from one host species to another.</p></div

Positively selected sites in BFDV from orange-bellied parrots inferred by different methods.

<p>Estimates of ω represents the selection parameter and <i>P^a</i> the posterior probability, and <i>P</i>^b,c,d the level of significance from the posterior probability of ω>1 at a site derived from the approximate codon model.</p

Details of primer used in this study in different combinations to amplify the full genome of BFDV DNA^*.

<p>Combinations attempted were 2 and BFDV-B-R; 1 and BFDV-C-R; 2 and BFDV-J-R; BFDV-I-F and BFDV-C-R.</p

Bayesian phylogenetic inference of evolutionary relationship among <i>Rep</i> gene sequences from orange-bellied parrots.

<p>Maximum clade credibility tree automatically rooted by using relaxed molecular clock model in Beast v1.7.5. Labels at branch tips refer to GenBank accession number, and with country code, original sample ID, collection site and year of isolation in parentheses. Nodes with posterior probability of ≥0.9 are indicated with asterisks and with a hash for <i>P</i>≥0.6. Inferred nonsynonymous substitutions (blue colour) at codons are indicated at the appropriate lineages where the majority of genomes in a clade possess a particular substitution then the ancestral node has been labeled.</p

Bayesian phylogenetic tree inferred evolutionary relationships among BFDV full genome sequences from orange-bellied parrots.

<p>Maximum clade credibility tree automatically rooted by using relaxed molecular clock model in Beast v1.7.5. Labels at branch tips refer to GenBank accession number, and with country code, original sample ID, collection site and year of isolation in parentheses. Nodes with posterior probability of ≥0.95 are indicated with asterisks and with a hash for <i>P</i>≥0.7. Inferred nonsynonymous substitutions at codons are indicated at the appropriate lineages where the majority of genomes in a clade possess a particular substitution then the ancestral node has been labeled.</p