20 research outputs found
A Catalog of Reference Genomes from the Human Microbiome
The human microbiome refers to the community of microorganisms including prokaryotes, viruses
and microbial eukaryotes that populate the human body. The National Institutes of Health launched
an initiative that focuses describing the diversity of microbial species associated with health and
disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference
genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results
from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted
polypeptides that correspond to the gene complement of these strains “novel” polypeptides that had
both unmasked sequence length > 100 amino acids and no BLASTP match to any non-reference
entry in the nr subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which
29,987 (~97%) were unique. In addition, this set of microbial genomes allows for ~ 40% of random
sequences from the microbiome of the gastrointestinal tract to be associated with organisms based
on the match criteria used. Insights into pan-genome analysis suggest that we are still far from
saturating microbial species genetic datasets. In addition, the associated metrics and standards used
by the group for quality assurance are presented
Effects of a defective ERAD pathway on growth and heterologous protein production in Aspergillus niger
Endoplasmic reticulum associated degradation (ERAD) is a conserved mechanism to remove misfolded proteins from the ER by targeting them to the proteasome for degradation. To assess the role of ERAD in filamentous fungi, we have examined the consequences of disrupting putative ERAD components in the filamentous fungus Aspergillus niger. Deletion of derA, doaA, hrdC, mifA, or mnsA in A. niger yields viable strains, and with the exception of doaA, no significant growth phenotype is observed when compared to the parental strain. The gene deletion mutants were also made in A. niger strains containing single- or multicopies of a glucoamylase–glucuronidase (GlaGus) gene fusion. The induction of the unfolded protein response (UPR) target genes (bipA and pdiA) was dependent on the copy number of the heterologous gene and the ERAD gene deleted. The highest induction of UPR target genes was observed in ERAD mutants containing multiple copies of the GlaGus gene. Western blot analysis revealed that deletion of the derA gene in the multicopy GlaGus overexpressing strain resulted in a 6-fold increase in the intracellular amount of GlaGus protein detected. Our results suggest that impairing some components of the ERAD pathway in combination with high expression levels of the heterologous protein results in higher intracellular protein levels, indicating a delay in protein degradation