16 research outputs found
The Genome of a Thermo Tolerant, Pathogenic Albino Aspergillus fumigatus
Biotechnologists are interested in thermo tolerant fungi to manufacture enzymes active and stable at high temperatures, because they provide improved catalytic efficiency, strengthen enzyme substrate interactions, accelerate substrate enzyme conversion rates, enhance mass transfer, lower substrate viscosity, lessen contamination risk and offer the potential for enzyme recycling. Members of the genus Aspergillus live a wide variety of lifestyles, some embrace GRAS status routinely employed in food processing while others such as Aspergillus fumigatus are human pathogens. A. fumigatus produces melanins, pyomelanin protects the fungus against reactive oxygen species and DHN melanin produced by the pksP gene cluster confers the gray-greenish color. pksP mutants are attenuated in virulence. Here we report on the genomic DNA sequence of a thermo tolerant albino Aspergillus isolated from rain forest composted floors. Unexpectedly, the nucleotide sequence was 95.7% identical to the reported by Aspergillus fumigatus Af293. Genome size and predicted gene models were also highly similar, however differences in DNA content and conservation were observed. The albino strain, classified as Aspergillus fumigatus var. niveus, had 160 gene models not present in A. fumigatus Af293 and A. fumigatus Af293 had 647 not found in the albino strain. Furthermore, the major pigment generating gene cluster pksP appeared to have undergone genomic rearrangements and a key tyrosinase present in many aspergilli was missing from the genome. Remarkably however, despite the lack of pigmentation A. fumigatus var. niveus killed neutropenic mice and survived macrophage engulfment at similar rates as A. fumigatus Af293
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Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes.
The anaerobic gut fungi (AGF), or Neocallimastigomycota, inhabit the rumen and alimentary tract of herbivorous mammals, where they play important roles in the degradation of plant fiber. Comparative genomic and phylogenomic analyses of the AGF have long been hampered by their fastidious growth condition, as well as their large (up to 200 Mb) and AT-biased (78 to 84%) genomes. We sequenced 21 AGF transcriptomes and combined them with 5 available AGF genome sequences to explore their evolutionary relationships, time their divergence, and characterize gene gain/loss patterns associated with their evolution. We estimate that the most recent common ancestor of the AGF diverged 66 (±10) million years ago, a time frame that coincides with the evolution of grasses (Poaceae), as well as the mammalian transition from insectivory to herbivory. The concordance of independent estimations suggests that AGF have been important in shaping the success of mammalian herbivory transition by improving the efficiency of energy acquisition from recalcitrant plant materials. Comparative genomics identified multiple lineage-specific genes in the AGF, two of which were acquired from rumen gut bacteria and animal hosts via horizontal gene transfer (HGT). A third AGF domain, plant-like polysaccharide lyase, represents a novel gene in fungi that potentially aids AGF to degrade pectin. Analysis of genomic and transcriptomic sequences confirmed both the presence and expression of these lineage-specific genes in nearly all AGF clades. These genetic elements may contribute to the exceptional abilities of AGF to degrade plant biomass and enable metabolism of the rumen microbes and animal hosts.IMPORTANCE Anaerobic fungi living in the rumen of herbivorous mammals possess an extraordinary ability to degrade plant biomass. We examined the origin and genomic composition of these poorly characterized anaerobic gut fungi using both transcriptome and genomic data. Phylogenomics and molecular dating analyses found remarkable concurrence of the divergence times of the rumen fungi, the forage grasses, and the dietary shift of ancestral mammals from primarily insectivory to herbivory. Comparative genomics identified unique machinery in these fungi to utilize plant polysaccharides. The rumen fungi were also identified with the ability to code for three protein domains with putative functions in plant pectin degradation and microbial defense, which were absent from all other fungal organisms (examined over 1,000 fungal genomes). Two of these domains were likely acquired from rumen gut bacteria and animal hosts separately via horizontal gene transfer. The third one is a plant-like polysaccharide lyase, representing a unique fungal enzyme with potential pectin breakdown abilities
Genome Analysis of Staphylococcus agnetis, an Agent of Lameness in Broiler Chickens.
Lameness in broiler chickens is a significant animal welfare and financial issue. Lameness can be enhanced by rearing young broilers on wire flooring. We have identified Staphylococcus agnetis as significantly involved in bacterial chondronecrosis with osteomyelitis (BCO) in proximal tibia and femorae, leading to lameness in broiler chickens in the wire floor system. Administration of S. agnetis in water induces lameness. Previously reported in some cases of cattle mastitis, this is the first report of this poorly described pathogen in chickens. We used long and short read next generation sequencing to assemble single finished contigs for the genome and a large plasmid from the chicken pathogen. Comparison of the S. agnetis genome to those of other pathogenic Staphylococci shows that S.agnetis contains a distinct repertoire of virulence determinants. Additionally, the S. agnetis genome has several regions that differ substantially from the genomes of other pathogenic Staphylococci. Comparison of our finished genome to a recent draft genome for a cattle mastitis isolate suggests that future investigations focus on the evolutionary epidemiology of this emerging pathogen of domestic animals
Phylogenetic trees of toxin virulence factors.
<p>Trees were constructed using the closest homologs to <i>S</i>. <i>agnetis</i> toxin proteins from BLASTp searches of refseq proteins from <i>S</i>. <i>hyicus</i>, S.chromgenes, <i>S</i>. <i>pseudintermedius</i> and <i>S</i>. <i>aureus</i>. Tress are for Superantigen-like protein homologs (Panel A), beta hemolysin (Panel B), and exfoliative toxin A (Panel C). The <i>S</i>. <i>agnetis</i> ortholog are prefixed with the ORF number from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143336#pone.0143336.s001" target="_blank">S1 Table</a>. Details of the alignment strategy are in Materials and Methods.</p
Representative BCO lesions for proximal femora.
<p>Severity of the lesions are scored by macroscopic examination: Femoral Head Separation, FHS (Panel A), Femoral Head Transitional degeneration, FHT (Panel B), Femoral Head Necrosis, FHN (Panels C and D) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143336#pone.0143336.ref001" target="_blank">1</a>].</p
Phylogenetic tree of fibronectin binding proteins from <i>S</i>. <i>agnetis</i> with homologs from <i>S</i>. <i>hyicus</i>.
<p>The protein sequences predicted for the seven ORFs from <i>S</i>. <i>agnetis</i> (see text) were aligned using Clustal W to the five predicted fibronectin proteins for the <i>S</i>. <i>hyicus</i> ATCC11294 genome (AJC entries are accession numbers) representing the closest orthologs in NCBI for the proteins from <i>S</i>. <i>agnetis</i>. The phylogenetic tree includes bootstrap significance for 2500 iterations.</p
Bacterial species from lame birds based on bone lesion.
<p>Lesion designations were <b>Normal-</b> no macroscopic abnormalities of the proximal femur or tibia; <b>FHS</b>- proximal femoral head separation; <b>FHT-</b>proximal femoral head transitional degeneration; <b>FHN-</b>proximal femoral head necrosis; <b>THN-</b> mild proximal tibial head necrosis; <b>THNs</b>-"severe" THN in which the growth plate was imminently threatened or damaged; and, <b>THNc</b>- "caseous" THN in which caseous exudates or bacterial sequestrae were macroscopically evident [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143336#pone.0143336.ref001" target="_blank">1</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143336#pone.0143336.ref029" target="_blank">29</a>]. Species identification and Total number of infections diagnosed was as for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143336#pone.0143336.t001" target="_blank">Table 1</a>.</p><p>Bacterial species from lame birds based on bone lesion.</p
Bacterial species from lame birds based on site sampled.
<p>A total of 24 lame birds were sampled from all five locations and bacterial colonies diagnosed by PCR-sequencing of a portion of the 16S rDNA. The number of infection sites diagnosed excludes sampled that either did not show bacterial growth, failed in the PCR, or yielded poor sequence data.</p><p>Bacterial species from lame birds based on site sampled.</p