What Makes a Prion: Infectious Proteins From Animals to Yeast

While philosophers in ancient times had many ideas for the cause of contagion, the modern study of infective agents began with Fracastoro\u27s 1546 proposal that invisible “spores” spread infectious disease. However, firm categorization of the pathogens of the natural world would need to await a mature germ theory that would not arise for 300 years. In the 19th century, the earliest pathogens described were bacteria and other cellular microbes. By the close of that century, the work of Ivanovsky and Beijerinck introduced the concept of a virus, an infective particle smaller than any known cell. Extending into the early–mid-20th century there was an explosive growth in pathogenic microbiology, with a cellular or viral cause identified for nearly every transmissible disease. A few occult pathogens remained to be discovered, including the infectious proteins (prions) proposed by Prusiner in 1982. This review discusses the prions identified in mammals, yeasts, and other organisms, focusing on the amyloid-based prions. I discuss the essential biochemical properties of these agents and the application of this knowledge to diseases of protein misfolding and aggregation, as well as the utility of yeast as a model organism to study prion and amyloid proteins that affect human and animal health. Further, I summarize the ideas emerging out of these studies that the prion concept may go beyond proteinaceous infectious particles and that prions may be a subset of proteins having general nucleating or seeding functions involved in noninfectious as well as infectious pathogenic protein aggregation

Genome Sequence of Kurthia Type Species Kurthia zopfii Strain ATCC 33403T

The genome of the type strain of the Kurthia genus, Kurthia zopfii ATCC 33403, was sequenced. Nonpathogenic K. zopfii has been isolated from intestinal contents, fecal material, meats, meat products, milk, water, and air, including air at high altitudes. The predicted genome size is 2,878,279 bp, with 37.05% G+C content

Complete Genome Sequence of Staphylococcus epidermidis ATCC 12228 Chromosome and Plasmids Generated by Long-Read Sequencing

Staphylococcus epidermidis ATCC 12228 was sequenced using a long-read method to generate a complete genome sequence, including some plasmid sequences. Some differences from the previously generated short-read sequence of this nonpathogenic and non-biofilm-forming strain were noted. The assembly size was 2,570,371 bp with a total G+C% content of 32.08%

Genome Sequence of the Deep-Sea Bacterium Idiomarina abyssalis KMM 227T

diomarina abyssalis KMM 227T is an aerobic flagellar gammaproteobacterium found at a depth of 4,000 to 5,000 m below sea level in the Pacific Ocean. This paper presents a draft genome sequence for I. abyssalis KMM 227T, with a predicted composition of 2,684,812 bp (47.15% G+C content) and 2,611 genes, of which 2,508 were predicted coding sequences

Draft Whole-Genome Sequence of the Marine Bacterium Idiomarina zobellii KMM 231T

Idiomarina zobellii was isolated from the northwest Pacific Ocean at a depth of 4,000 to 5,000 m in 1985. The draft whole-genome shotgun sequence of I. zobellii KMM 231T described in this paper has a predicted length of 2,602,160 bp, containing 2,570 total genes, 52 tRNAs, and a G+C content of 47.10%

Genome Sequence of the Halophilic Bacterium Kangiella spongicola ATCC BAA-2076T

The Gram-negative genus Kangiella contains a number of halophilic species that display high levels of iso-branched fatty acids. Kangiella spongicola was isolated from a marine sponge, Chondrilla nucula, from the Florida Keys in the United States. A genome assembly of 2,825,399 bp with a 44.31% G+C content was generated from strain A79T (=ATCC BAA-2076T)

Genome Sequences for Three Strains of Kocuria rosea, Including the Type Strain

Genomes from three strains of Kocuria rosea were sequenced. K. rosea ATCC 186, the type strain, was 3,958,612 bp in length with a total G+C content of 72.70%. When assembled, K. rosea ATCC 516 was 3,862,128 bp with a 72.82% G+C content. K. rosea ATCC 49321 was 4,018,783 bp in size with a 72.49% G+C content

Genome Sequence of the Moderately Halophilic Yellow Sea Bacterium Lentibacillus salicampi ATCC BAA-719T

Lentibacillus salicampi SF-20T (=ATCC BAA-719T) was first isolated from a Yellow Sea salt field in Korea in 2002. Here, we report that the L. salicampi ATCC BAA-719T genome sequence has a predicted length of 3,897,716 bp, containing 3,945 total genes and a CRISPR array, with a G+C content of 43.0%

Genome Sequence of the Radiation-Resistant Bacterium Deinococcus radiophilus ATCC 27603

The pigmented bacterium Deinococcus radiophilus, which is highly resistant to radiation exposure, was first isolated from irradiated lizardfish. We report a genome assembly of D. radiophilus UWO 1055T (=ATCC 27603T), with a predicted genome size of 2.7 Mbp (62.66% G+C content). A number of CRISPR-associated proteins and two CRISPR arrays were identified

Mechanistic target of rapamycin (mTOR) signaling genes in decapod crustaceans: cloning and tissue expression of mTOR, Akt, Rheb, and S6 kinase in the green crab, Carcinus maenas, and blackback land crab, Gecarcinus lateralis

Mechanistic target of rapamycin (mTOR) controls global translation of mRNA into protein by phosphorylating p70 S6 kinase (S6K) and eIF4E-binding protein-1. Akt and Rheb, a GTP-binding protein, regulate mTOR protein kinase activity. Molting in crustaceans is regulated by ecdysteroids synthesized by a pair of molting glands, or Y-organs (YOs), located in the cephalothorax. During premolt, the YOs hypertrophy and increase production of ecdysteroids. Rapamycin (1 μM) inhibited ecdysteroid secretion in Carcinus maenas and Gecarcinus lateralis YOs in vitro, indicating that ecdysteroidogenesis requires mTOR-dependent protein synthesis. The effects of molting on the expression of four key mTOR signaling genes (mTOR, Akt, Rheb, and S6K) in the YO was investigated. Partial cDNAs encoding green crab (C. maenas) mTOR (4031 bp), Akt (855 bp), and S6K (918 bp) were obtained from expressed sequence tags. Identity/similarity of the deduced amino acid sequence of the C. maenas cDNAs to human orthologs were 72%/81% for Cm-mTOR, 58%/73% for Cm-Akt, and 77%/88% for Cm-S6K. mTOR, Akt, S6K, and elongation factor 2 (EF2) in C. maenas and blackback land crab (G. lateralis) were expressed in all tissues examined. The two species differed in the effects of molting on gene expression in the YO. In G. lateralis, Gl-mTOR, Gl-Akt, and Gl-EF2 mRNA levels were increased during premolt. By contrast, molting had no effect on the expression of Cm-mTOR, Cm-Akt, Cm-S6K, Cm-Rheb, and Cm-EF2. These data suggest that YO activation during premolt involves up regulation of mTOR signaling genes in G. lateralis, but is not required in C. maenas