Mycobacteriophage Mindy is a newly isolated phage of Mycobacterium smegmatis, recovered from a soil sample in Pittsburgh, Pennsylvania, USA. Mindy has a genome length of 75,796 bp, encodes 147 predicted proteins and two tRNAs, and is closely related to mycobacteriophages in cluster E.
Gordonia phages BaxterFox, Kita, Nymphadora, and Yeezy are newly characterized phages of Gordonia terrae, isolated from soil samples in Pittsburgh, Pennsylvania. These phages have genome lengths between 50,346 and 53,717 bp, and encode on average 84 predicted proteins. All have G+C content of 66.6%.
Emalyn is a newly isolated bacteriophage of Gordonia terrae 3612 and has a double-stranded DNA genome 43,982 bp long with 67 predicted protein-encoding genes, 32 of which we can assign putative functions. Emalyn has a prolate capsid and has extensive nucleotide similarity with several previously sequenced phages.
Endoplasmic Reticulum Associated Degradation (ERAD) clears misfolded or incorrectly processed proteins from the ER. One family of ER resident proteins that are involved in ERAD and exhibit disulfide redox, isomerization, and chaperone activity is the Protein Disulfide Isomerase (PDI) family. In humans there are twenty PDI homologs, whereas in Saccharomyces cerevisiase there are five. To address substrate specificity among the PDI family members and their mechanisms of action during ERAD, we investigated the contributions of distinct yeast PDIs on the ERAD of model substrates that either contain disulfide bonds or lack cysteines. Through the use of a yeast expression system for Apolipoprotein B (ApoB), which is disulfide‐rich, we discovered that Pdi1 interacts with ApoB and facilitates degradation through its chaperone activity. In contrast, Pdi1's redox activity was required for the ERAD of CPY*, an ERAD substrate containing five disulfide bonds. Distinct effects of mammalian PDI homologues on ApoB degradation were then observed in hepatic cells. These data indicate that PDIs contribute to ERAD through different mechanisms.
Endoplasmic-reticulum-associated protein degradation
ABSTRACT BetterKatz is a bacteriophage isolated from a soil sample collected in Pittsburgh, Pennsylvania using the host Gordonia terrae 3612. BetterKatz's genome is 50,636 bp long and contains 75 predicted protein-coding genes, 35 of which have been assigned putative functions. BetterKatz is not closely related to other sequenced Gordonia phages.
Luchador and Nerujay are two newly isolated mycobacteriophages recovered from soil samples using Mycobacterium smegmatis. Their genomes are 53,387 bp and 53,455 bp long and have 96 and 97 predicted open reading frames, respectively. Nerujay is related to subcluster A1 phages, and Luchador represents a new subcluster, A14.
Bacteriophages Katyusha and Benczkowski14 are newly isolated phages that infect Gordonia terrae 3612. Both have siphoviral morphologies with isometric heads and long tails (500 nm). The genomes are 75,380 bp long and closely related, and the tape measure genes (9 kbp) are among the largest to be identified.
ABSTRACT Hotorobo, Woes, and Monty are newly isolated bacteriophages of Gordonia terrae 3612. The three phages are related, and their genomes are similarly sized (76,972 bp, 73,752 bp, and 75,680 bp for Hotorobo, Woes, and Monty, respectively) and organized. They have extremely long tails and among the longest tape measure protein genes described to date.
Bacteriophages Phinally and Vivi2 were isolated from soil from Pittsburgh, Pennsylvania, USA, using host Gordonia terrae 3612. The Phinally and Vivi2 genomes are 59,265 bp and 59,337 bp, respectively, and share sequence similarity with each other and with GTE6. Fewer than 25% of the 87 to 89 putative genes have predictable functions.
Apolipoprotein B (ApoB) is a lipoprotein that transports cholesterol and triglycerides through the bloodstream. High plasma levels of ApoB are one of the strongest risk factors for the development of Coronary Artery Disease. Using a yeast expression system for ApoB, I focused my research on identifying new therapeutic targets to reduce the amount of ApoB secreted into the bloodstream. One way that ApoB levels are regulated is through Endoplasmic Reticulum-Associated Degradation (ERAD), a quality control mechanism that rids the secretory pathway of misfolded proteins. Due to ApoB’s hydrophobic character and high number of disulfide bonds, one class of proteins that I hypothesized may contribute to ApoB ERAD was the Protein
Disulfide Isomerase (PDI) family. PDI’s catalyze the oxidation, reduction, and isomerization of disulfide bonds and some also have chaperone-like activity. I found that in yeast, Pdi1 contributes to ApoB ERAD through its chaperone like domain. I identified mammalian PDI candidates that may similarly affect ApoB biogenesis based on my yeast data. I found that in hepatic cells, two PDI family members, ERp57 and ERp72, contribute to ApoB ERAD, while another family member, PDI, promoted ApoB secretion. A unique aspect of ApoB ERAD is that the protein is co-translationally retrotranslocated and degraded. I hypothesized that proteins that regulate the Sec61 translocon, a proteinacious channel that allows ApoB entrance to the ER as well as an exit to the cytoplasm for degradation, would contribute to ApoB retrotranslocation and degradation. I discovered that two conserved ER-membrane proteins that are candidates for Sec61 regulators, Yet2 and Yet3, facilitate the ERAD of ApoB in yeast. To determine whether my results are relevant in mammalian cells, I am currently working to determine if the mammalian homologs of Yet2 and Yet3, BAP29 and BAP31 facilitate ApoB ERAD in hepatic cells.
Endoplasmic-reticulum-associated protein degradation
