PSI:Biology-materials repository: a biologist’s resource for protein expression plasmids

Abstract

The Protein Structure Initiative:Biology-Materials Repository (PSI:Biology-MR; MR; http://psimr.asu.edu) sequence-verifies, annotates, stores, and distributes the protein expression plasmids and vectors created by the Protein Structure Initiative (PSI). The MR has developed an informatics and sample processing pipeline that manages this process for thousands of samples per month from nearly a dozen PSI centers. DNASU (http://dnasu.asu.edu), a freely searchable database, stores the plasmid annotations, which include the full-length sequence, vector information, and associated publications for over 130,000 plasmids created by our laboratory, by the PSI and other consortia, and by individual laboratories for distribution to researchers worldwide. Each plasmid links to external resources, including the PSI Structural Biology Knowledgebase (http://sbkb.org), which facilitates cross-referencing of a particular plasmid to additional protein annotations and experimental data. To expedite and simplify plasmid requests, the MR uses an expedited material transfer agreement (EP-MTA) network, where researchers from network institutions can order and receive PSI plasmids without institutional delays. Currently over 39,000 protein expression plasmids and 78 empty vectors from the PSI are available upon request from DNASU. Overall, the MR’s repository of expression-ready plasmids, its automated pipeline, and the rapid process for receiving and distributing these plasmids more effectively allows the research community to dissect the biological function of proteins whose structures have been studied by the PSI.

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

“…Assuming current trends, ∼55% coverage will be achieved within 15 y, a level considered sufficient to fully characterize the metabolic network of an organism. These efforts are complemented by nine centers focused on membrane protein structure determination, as well as additional resources for data tracking and dissemination (www.sbkb.org) (13) and a materials repository (14).…”

Structure and Function of a Novel ld -Carboxypeptidase A Involved in Peptidoglycan Recycling

“…The gene encoding NaLdcA was amplified by PCR from N. aromaticivorans DSM 12444 genomic DNA by using Pfu Turbo DNA polymerase (Stratagene) and I-PIPE (insert) primers that included sequences for the predicted 5= and 3= ends. The Joint Center for Structural Genomics (JCSG) NaLdcA expression plasmid was deposited in the PSI Biology Materials Repository (DNASU ID NaCD00087837) (21). The expression vector pSpeedET, which encodes an amino-terminal tobacco etch virus (TEV) protease-cleavable expression and purification tag (MGSDKIHH HHHHENLYFQ/G), was PCR amplified with V-PIPE (vector) primers (forward primer, 5=-TAACGCGACTTAATTAACTCGTTTAAACGGTC TCCAGC-3=; and reverse primer, 5=-GCCCTGGAAGTACAGGTTTTCG TGATGATGATGATGATG-3=).…”

Sustainability in a Hospital-Based Biobank and University-Based DNA Biorepository: Strategic Roadmaps

“…Originally established at the Harvard Institute of Proteomics in 2006 as the PlasmID Repository, the repository moved and re-established itself at ASU in 2009 as DNASU. [7][8][9] The overall goal and mission of DNASU (https://dnasu.org) is to facilitate research by providing high quality, annotated plasmids and resources to the research community and to support research scientists by functioning as a centralized facility to distribute plasmids that they create as part of their research. 9 Plasmids are circular pieces of DNA, each of which contains one or multiple genes, and serve as a useful experimental resource to have stored in and distributed by a centralized repository.…”

“…For example, the National Institute of General Medical Sciences (NIGMS) funded DNASU for 10 years to function at the PSI-MR. [7][8][9] Within this collaboration, DNASU evaluated the full-length DNA sequence of the gene inserts for over 90,000 plasmids from PSI researchers and significantly improved the DNASU website and database to support the distribution of these plasmids. In addition, DNASU was awarded an American Recovery and Reinvestment Act (ARRA) grant to enable the purchase of a Brooks automated freezer storage system.…”