The evolutionary history of calreticulin and calnexin genes in green plants

Calreticulin and calnexin are Ca2+-binding chaperones localized in the endoplasmic reticulum of eukaryotes acting in glycoprotein folding quality control and Ca2+ homeostasis. The evolutionary histories of calreticulin and calnexin gene families were inferred by comprehensive phylogenetic analyses using 18 completed genomes and ESTs covering the major green plants groups, from green algae to angiosperms. Calreticulin and calnexin possibly share a common origin, and both proteins are present along all green plants lineages. The calreticulin founder gene within green plants duplicated in early tracheophytes leading to two possible groups of orthologs with specialized functions, followed by lineage-specific gene duplications in spermatophytes. Calnexin founder gene in land plants was inherited from basal green algae during evolution in a very conservative copy number. A comprehensive classification in possible groups of orthologs and a catalog of calreticulin and calnexin genes from green plants are provided.139225525

Proteome analysis of castor bean seeds

Castor bean (Ricinus communis L.) seeds serve as raw material for the production of nonedible oil used in medicine and industry, whereas the presence of allergenic and toxic proteins in the residue left after oil extraction precludes the use of this protein-rich by-product in animal feeding. To better understand the enzymes involved in the biosynthesis and deuradation of fatty acids and to identify proteins with toxic/anti-nutritional properties, exZ, extracts of developing and germinating seeds were prepared and prefractionated according to solubility properties of the proteins. An enriched plastid organelle fraction embracing mostly plastids and rnitochondria was also prepared. Two-dimensional electrophoresis (2DE) reference map,, of these fractions were obtained from which nearly 400 proteins were identified by matrix-assisted laser desorption ionization-time of flight-time of flight (MALDI-TOF-TOF) mass spectrometry after a search in a National Center for Biotechnology Information (NCBI) database and in an expressed sequence tag (EST) primary bank prepared from a cDNA library of developing seeds. These proteomics techniques resulted in the identification Of several classes of seed reserve proteins such as 2S albumins, legumin-like and seed storage proteins, as well as other proteins of' plastidial or mitochondrial functions and proteins involved in plant defense against biotic and abiotic stresses. It is expected that the collected data will facilitate the application of genetic techniques to improve the quality/profile of castor seed fatty acids, and pave the way for a rational approach to inactivate allergenic and toxic proteins, allowing the use of castor bean meal in animal feeding 1182125926

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

Kamke J, Sczyrba A, Ivanova N, et al. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. The ISME journal. 2013;7(12):2287-2300.Many marine sponges are hosts to dense and phylogenetically diverse microbial communities that are located in the extracellular matrix of the animal. The candidate phylum Poribacteria is a predominant member of the sponge microbiome and its representatives are nearly exclusively found in sponges. Here we used single-cell genomics to obtain comprehensive insights into the metabolic potential of individual poribacterial cells representing three distinct phylogenetic groups within Poribacteria. Genome sizes were up to 5.4 Mbp and genome coverage was as high as 98.5%. Common features of the poribacterial genomes indicated that heterotrophy is likely to be of importance for this bacterial candidate phylum. Carbohydrate-active enzyme database screening and further detailed analysis of carbohydrate metabolism suggested the ability to degrade diverse carbohydrate sources likely originating from seawater and from the host itself. The presence of uronic acid degradation pathways as well as several specific sulfatases provides strong support that Poribacteria degrade glycosaminoglycan chains of proteoglycans, which are important components of the sponge host matrix. Dominant glycoside hydrolase families further suggest degradation of other glycoproteins in the host matrix. We therefore propose that Poribacteria are well adapted to an existence in the sponge extracellular matrix. Poribacteria may be viewed as efficient scavengers and recyclers of a particular suite of carbon compounds that are unique to sponges as microbial ecosystems