A cross-species compendium of proteins/gene products related to cold stress identified by bioinformatic approaches

The purpose of this investigation was to construct a compendium of low temperature responsive proteins/gene products across species as identified by bioinformatics based approaches, thus allowing low temperature researchers a searchable database. Another purpose was to identify specific low temperature responsive proteins/gene products across at least two different species. We generated a database containing 2030 low temperature responsive protein/gene product entries, of which 1353 were up-regulated and 549 were down-regulated in response to various cold exposures across 34 different species; including bacteria (9 species), yeast (1 species), animals (including nematodes (1 species), collembola (2 species), insects (5 species), fish (1 species), amphibians (1 species), reptiles (1 species), mammals (2 species)), and plants (moss (1 species), gymnosperms (1 species) and angiosperms (9 species)). There were 39 studies using 12 different cold treatments; 20 used proteomics and 18 used transcriptomics. Concerning our purpose of identifying specific temperature responsive proteins/gene products across species, we found 113 shared proteins/gene products groups, each of which was found in at least two species. Of these shared proteins/gene products groups, 58 proteins/gene products (including protein/gene product families) that were consistently regulated, meaning always either up- or down-regulated, across species. Another 23 proteins/gene products were inconsistently regulated, meaning that the proteins/gene products were up-regulated in some species and treatments while being down-regulated in other species and treatments. An additional 32 proteins/gene products that are part of larger family headings and are difficult to separate from related member proteins (such the ribosomal proteins, 30S, 50S, and others) were inconsistently regulated. This work is an attempt to create a centralized database and repository for low temperature responsive proteins/gene products in all species.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► First attempt to construct a cold responsive protein database. ► By focusing on bioinformatic based publications investigating cold treatments of any organism (bacteria, plants, animals, and more), we identified 2030 cold responsive proteins. ► We used the constructed database to examine shared, cold responsive proteins between species, as well as those that were consistently or inconsistently up- or down-regulated.