The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research

Abstract

Autophagy is a process of self-digestion generally observed in eukaryotes and has been shown to play crucial roles for survival under starvation and removal of deleterious substances. Despite great advances that have been made, many problems in mechanisms of autophagy remain unsolved. As a large number of autophagy-related proteins are identified in each species, a database that collects data, identifies their homologs in other species and makes them available will contribute to research advancement. As no such resources exist, we built the Autophagy database (http://tp-apg.genes.nig.ac.jp/autophagy) to provide basics, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in 41 eukaryotes. From the database, the user can search for proteins by keywords or sequences to obtain a wealth of data including functional and structural information and find possible functional homologs of proteins whose functions have been demonstrated in other species. As proteins that bind the phospholipid, phosphatidyl inositol 3-phosphate (PI3P) are essential for autophagy to proceed, we carried out an original analysis to identify probable PI3P-binding proteins, and made the list available from the database. The database is expected to give impetus to further research on autophagy by providing basic and specialized data on the subject.

Proteomic analysis of the mitochondria from embryonic and postnatal rat brains reveals response to developmental changes in energy demands

“…Lists of proteins were generated from databases for mitochondrial proteins (MitoMiner, http://mitominer.mrc-mbu.cam.ac.uk/release-3.1/begin.do) [16], autophagy proteins (Autophagy Database; http://www.tanpaku.org/autophagy) [17], lysosomal proteins [18], mt-UPR proteins [19], and synaptic proteins (SynDB; http://syndb.cbi.pku.edu.cn) [20]. Heap maps of protein expression were built with Multi Experiment Viewer (Version 4.8.1, http://www.tm4.org/mev.html) [21].…”

Regulation of autophagy by the Rab GTPase network

“…Each complex has a different role in autophagy; the Atg9 Á Atg2-Atg18 complex is required for the initial step in autophagosome formation, [18][19][20] the Vps34-Atg6/beclin1 class III PI3-kinase complex produces PI3P that contributes to the localization of Atg proteins on the autophagic membrane, [21][22][23] and the Atg12 and the Atg8/LC3 conjugation systems are responsible for the lipidation process of LC3-I to LC3-II that is localized to the autophagosome until its fusion with lysosomes and is thus a well-known marker of autophagosomes. [24][25][26] It is known that Rab proteins constitute the largest family in the Ras-like GTPase superfamily and shuttle between an active state (GTP-bound) and an inactive state (GDP-bound) to have a key role in diverse vesicular trafficking events.…”

Conversation between apoptosis and autophagy: “Is it your turn or mine?”

“…Indeed, the actual body of evidence obtained by different research groups points out that autophagy is a very complex pathway, as it emerges also from a recent proteomic survey defining various functional modules within the process [62]. To enhance the availability of the many data so far collected, Homma et al [63] provided the scientific community with the Autophagy Database (http://tp-apg.genes.nig.ac.jp/autophagy) that is an invaluable tool for classifying autophagy-related proteins and updating the specific literature, which increased dramatically in the last 10 years [63].…”