A Computational Module Assembled from Different Protease Family Motifs Identifies PI PLC from Bacillus cereus as a Putative Prolyl Peptidase with a Serine Protease Scaffold

Proteolytic enzymes have evolved several mechanisms to cleave peptide bonds. These distinct types have been systematically categorized in the MEROPS database. While a BLAST search on these proteases identifies homologous proteins, sequence alignment methods often fail to identify relationships arising from convergent evolution, exon shuffling, and modular reuse of catalytic units. We have previously established a computational method to detect functions in proteins based on the spatial and electrostatic properties of the catalytic residues (CLASP). CLASP identified a promiscuous serine protease scaffold in alkaline phosphatases (AP) and a scaffold recognizing a beta-lactam (imipenem) in a cold-active Vibrio AP. Subsequently, we defined a methodology to quantify promiscuous activities in a wide range of proteins. Here, we assemble a module which encapsulates the multifarious motifs used by protease families listed in the MEROPS database. Since APs and proteases are an integral component of outer membrane vesicles (OMV), we sought to query other OMV proteins, like phospholipase C (PLC), using this search module. Our analysis indicated that phosphoinositide-specific PLC from Bacillus cereus is a serine protease. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). Edman degradation analysis linked the specificity of the protease activity to a proline in the amino terminal, suggesting that the PI-PLC is a prolyl peptidase. Thus, we propose a computational method of extending protein families based on the spatial and electrostatic congruence of active site residues.

Annotation of orthologous genes in Tunnus thynnus and T.albacore species

Albacore and Atlantic Bluefin tuna are two pelagic fish. Atlantic Bluefin tuna is included in the IUCN red list of threatened species and albacore is considered to be near threatened, so conservation plans are needed. However, no genomic resources are available for any of them. In this study, to better understand their transcriptome we functionally annotated orthologous genes. In all, 159 SNPs distributed in 120 contigs of the muscle transcriptome were analyzed. Genes were predicted for 98 contigs (81.2%) using the bioinformatics tool BLAST. In addition, another bioinformatics tool, BLAST2GO was used in order to achieve GO terms for the genes, in which 41 sequences were given a biological process, and 39 sequences were given a molecular process. The most repeated biological process was metabolism and it is important that no cellular process was given in any of the sequences. The most abundant molecular process was binding and very few catalytic activity processes were given. From the initial 159 SNPs, 40 were aligned with a sequence in the database after BLAST2GO was run, and were polymorphic in Atlantic Bluefin tuna and monomorphic in albacore. From these 40 SNPs, 24 were located in an open reading frame of which four were non-synonymous and 20 were synonymous and 16 were not located in a known open reading frame,. This study provides information for better understanding the ecology and evolution of these species and this is important in order to establish a proper conservation plan and an appropriate management.

Reutilización de escoria negra de acería como soporte en biofiltros para la eliminación de H2S del biogás.

[EN]Due to the limitations associated with fossil fuels it is necessary to promote energy sources that are renewable as well as eco-friendly, such as biogas generated in anaerobic digesters. The biogas, composed principally of methane and CO2, is the result of the biodegradation of organic matter under anaerobic conditions. Its use as fuel is limited by the presence of minority compounds such as hydrogen sulphide (H2S); therefore, its pre-treatment is necessary. Currently there are various technologies for the removal of H2S from a gas stream, but most of them are based on physic-chemical treatments which have a number of drawbacks as reactive consumption, generation of secondary flows, etc. Biofiltration has been used as an efficient and low cost alternative to conventional purification processes, and excellent results for the degradation of H2S have been obtained. However process can be limited due to the progressive ageing of the support material, along with the loss of nutrients and other specific characteristics necessary for the good development of biomass. The purpose of this project is to develop a mixed support consisting of a mixture of an organic material and an inorganic support for its application in the removal of the H2S from biogas. This support material helps to optimize the characteristics of the bed and extend its lifespan. The development of such material will contribute to the implementation of biofiltration for treating biogas from anaerobic digesters for its use as biofuel. The inorganic material used is electric arc furnace (EAF) black slag, a by-product generated in large quantities in the production of steel in the Basque Country. Although traditionally the slag has been used in civil engineering, its physicochemical characteristics make it suitable for reuse as a filter medium in biofiltration. The main conclusion drawn from the experimental results is that EAF black slag is a suitable co-packing material in organic biofilters treating H2S-polluted gaseous streams. High pollutant removal rates have been achieved during the whole experimental period. The removal capacity recorded in biofilters with less inorganic material was higher than in those with higher slag portion. Nevertheless, all the biofilters have shown a satisfactory response even at high inlet loads (48 g·m-3·h-1), where the RE has not decreased over 82%.