BACTIBASE: a new web-accessible database for bacteriocin characterization

<p>Abstract</p> <p>Background</p> <p>Bacteriocins are very diverse group of antimicrobial peptides produced by a wide range of bacteria and known for their inhibitory activity against various human and animal pathogens. Although many bacteriocins are now well characterized, much information is still missing or is unavailable to potential users. The assembly of such information in one central resource such as a database would therefore be of great benefit to the exploitation of these bioactive molecules in the present context of increasing antibiotic resistance and natural bio-preservation need.</p> <p>Description</p> <p>In the present paper, we present the development of a new and original database BACTIBASE that contains calculated or predicted physicochemical properties of 123 bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships structure/function and target organisms of these peptides and therefore better exploitation of their biological activity in both the medical and food sectors.</p> <p>Conclusion</p> <p>The BACTIBASE database is freely available at <url>http://bactibase.pfba-lab.org</url>, web-based platform enabling easy retrieval, via various filters, of sets of bacteriocins that will enable detailed analysis of a number of microbiological and physicochemical data.</p

BACTIBASE second release: a database and tool platform for bacteriocin characterization

<p>Abstract</p> <p>Background</p> <p>BACTIBASE is an integrated open-access database designed for the characterization of bacterial antimicrobial peptides, commonly known as bacteriocins.</p> <p>Description</p> <p>For its second release, BACTIBASE has been expanded and equipped with additional functions aimed at both casual and power users. The number of entries has been increased by 44% and includes data collected from published literature as well as high-throughput datasets. The database provides a manually curated annotation of bacteriocin sequences. Improvements brought to BACTIBASE include incorporation of various tools for bacteriocin analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modelling and retrieval through our taxonomy Browser.</p> <p>Conclusion</p> <p>The provided features should make BACTIBASE a useful tool in food preservation or food safety applications and could have implications for the development of new drugs for medical use. BACTIBASE is available at <url>http://bactibase.pfba-lab-tun.org</url>.</p

Cloning, Sequence Analysis and Expression Patterns during Seed Germination of a Rapeseed (Brassica napus L.) G-x-S-x-G-motif Lipase Gene

[EN] Lipases catalyze the hydrolysis of ester bonds in triacylglycerides, generating glycerol and free fatty acids. These enzymes are encoded by extremely complex gene families, and appear to fulfil many different biological functions. Although they are present in all types of organisms, available information on plant lipases is still very limited, as compared to their bacterial and animal counterparts. A full-length clone, BnLIP, encoding a putative lipase, has been isolated by PCR amplification of Brassica napus genomic DNA, with oligonucleotide primers derived from the sequence of an Arabidopsis thaliana homologue. The clone included an open reading frame of 1581 bp encoding a polypeptide of 526 amino acids, with a calculated molecular mass of 59.5 kDa. Analysis of the deduced protein sequence, sequence alignment with homologous proteins from related plant species, and a phylogenetic analysis revealed that the BnLIP protein belongs to the classical GxSxG-motif lipase family. RTPCR assays indicated that the BnLIP gene is expressed specifically, but only transiently, during seed germination: the lipase mRNA was not present at detectable levels in ungerminated seeds, was detected only three days after seed imbibition, but its levels decreased rapidly afterwards. No expression was observed in roots, stems or leaves of adult plants. This expression pattern suggests that BnLIP is one of the lipases involved in the hydrolysis of triacylglycerides stored in rapeseed seeds, ultimately providing nutrients and energy to sustain seedling growth until photosynthesis is activatedGlaied Ghram, I.; Belguith, H.; Ben Mustapha, M.; Himila, I.; Bouhaouala, B.; Vicente, O.; Ben Hamida, J. (2016). Cloning, Sequence Analysis and Expression Patterns during Seed Germination of a Rapeseed (Brassica napus L.) G-x-S-x-G-motif Lipase Gene. Notulae Botanicae Horti Agrobotanici Cluj-Napoca. 44(2):437-444. doi:10.15835/nbha4421047243744444

Amplification of the active site of BnLIP3 gene of Brassica napus L. during germination

Lipases are useful enzymes that are responsible for the hydrolysis of triacylglycerides and play an important role in plant growth. In this study, we report a rapid molecular method to amplify a partial sequence of the lipase class 3 family designated BnLIP3 gene of Brassica napus L. in order to follow its expression and analyze its role during seed germination. Therefore, we conceived PCR homologous primers to amplify the active site encoding region of the BnLIP3 family genes. Subsequently, to sequence determination of the 582 bp fragment, we deduced BnLIP3 specific primers for a nested RTPCR application. The deduced 194 amino acid sequence (Genbank 1160264) was found to share 85% of identity with lipase from Arabidopsis thaliana class 3 family. The GxSxG consensus motif near the catalytic triad at the active serine site was also identified. The peptidic sequence showed little homology with mammalian and microbial lipases. RT-PCR analysis indicated that BnLIP3 gene was expressed during B. napus seed germination.Keywords: Brassica napus L., GxSxG lipase, germination, BnLIP3, RT-PCR.African Journal of Biotechnology Vol. 12(25), pp. 3905-391

PEPTIDES EXTRACTED FROM ARTEMISIA HERBA ALBA HAVE ANTIMICROBIAL ACTIVITY AGAINST FOODBORNE PATHOGENIC GRAM-POSITIVE BACTERIA

Background: Artemisia herba alba, classified into the family of Asteraceae, is an aromatic herb that is traditionally used as a purgative and anti-pyretic folk medicine by rural people of south Tunisia. This study reports the first identification of antimicrobial peptides from this medicinal plant that inhibited the growth of several food-borne pathogenic bacteria. Materials and methods: The extraction and purification of peptidic agents from Artemisia herba alba, have been performed using precipitation by ammonium sulfate of a phosphate buffer crude extract obtained from the plant leaves, followed by reverse-phase HPLC on a C18 column. The mass of the peptides was estimated by SDS-PAGE electrophoresis, followed by a gel overlay assay and ultra-filtration through a 5 kDa cut-off membrane. Fractions from every purification steps were sampled and assayed for activity towards different food-borne bacterial strains pathogenic and non pathogenic to humans. Results: The phosphate buffer crude extract, as well as its ammonium sulfate precipitate, designated AS-P, inhibited the growth of Listeria monocytogenes, Staphylococcus aureus, Bacillus cereus sensu stricto and the new approved species Bacillus cytotoxicus. AS-P MICs (minimum inhibitory concentrations) ranged from 0.241 to 3.8 mg/ml proteins for L. monocytogenes and B. cereus sensu stricto (strains ATCC10987 and IP5832), respectively. The bioactive AS-P molecules were stable up to 10 minutes heating at 120°C and they resisted organic solvent effects. Antimicrobial activity of A. herba alba AS-P decreased to 40 and 60% after proteolytic treatment with trypsin and proteinase K, respectively, suggesting peptides being responsible for the A. herba alba AS-P activity. The mass of antibacterial A. herba alba peptides was estimated below 5 kDa. Two AS-P fractions, eluted at 40 and 37% acetonitrile, showed antibacterial activity when assayed against L. monocytogenes. Conclusion: A. herba alba could make a new source of novel natural anti-infective agents that could be used in food bio-preservation as natural additives or in human infectious disease treatments against multi-drug resistant pathogens

Amplification of the active site of BnLIP3 gene of Brassica napus L. during germination

Lipases are useful enzymes that are responsible for the hydrolysis of triacylglycerides and play an important role in plant growth. In this study, we report a rapid molecular method to amplify a partial sequence of the lipase class 3 family designated BnLIP3 gene of Brassica napus L. in order to follow its expression and analyze its role during seed germination. Therefore, we conceived PCR homologous primers to amplify the active site encoding region of the BnLIP3 family genes. Subsequently, to sequence determination of the 582 bp fragment, we deduced BnLIP3 specific primers for a nested RTPCR application. The deduced 194 amino acid sequence (Genbank 1160264) was found to share 85% of identity with lipase from Arabidopsis thaliana class 3 family. The GxSxG consensus motif near the catalytic triad at the active serine site was also identified. The peptidic sequence showed little homology with mammalian and microbial lipases. RT-PCR analysis indicated that BnLIP3 gene was expressed during B. napus seed germination.Glaied Ghram, I.; Belguith, H.; Messaoudi, A.; Fattouch, S.; Vicente Meana, Ó.; Ben Hamida, J. (2013). Amplification of the active site of BnLIP3 gene of Brassica napus L. during germination. African Journal of Biotechnology. 12(25):3905-3913. doi:10.5897/AJB12.2861S39053913122