The proteolytic system of lactic acid bacteria revisited: a genomic comparison

Contains fulltext : 87750.pdf (publisher's version ) (Open Access)BACKGROUND: Lactic acid bacteria (LAB) are a group of gram-positive, lactic acid producing Firmicutes. They have been extensively used in food fermentations, including the production of various dairy products. The proteolytic system of LAB converts proteins to peptides and then to amino acids, which is essential for bacterial growth and also contributes significantly to flavor compounds as end-products. Recent developments in high-throughput genome sequencing and comparative genomics hybridization arrays provide us with opportunities to explore the diversity of the proteolytic system in various LAB strains. RESULTS: We performed a genome-wide comparative genomics analysis of proteolytic system components, including cell-wall bound proteinase, peptide transporters and peptidases, in 22 sequenced LAB strains. The peptidase families PepP/PepQ/PepM, PepD and PepI/PepR/PepL are described as examples of our in silico approach to refine the distinction of subfamilies with different enzymatic activities. Comparison of protein 3D structures of proline peptidases PepI/PepR/PepL and esterase A allowed identification of a conserved core structure, which was then used to improve phylogenetic analysis and functional annotation within this protein superfamily.The diversity of proteolytic system components in 39 Lactococcus lactis strains was explored using pangenome comparative genome hybridization analysis. Variations were observed in the proteinase PrtP and its maturation protein PrtM, in one of the Opp transport systems and in several peptidases between strains from different Lactococcus subspecies or from different origin. CONCLUSIONS: The improved functional annotation of the proteolytic system components provides an excellent framework for future experimental validations of predicted enzymatic activities. The genome sequence data can be coupled to other "omics" data e.g. transcriptomics and metabolomics for prediction of proteolytic and flavor-forming potential of LAB strains. Such an integrated approach can be used to tune the strain selection process in food fermentations

LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs

Transcriptional profiling of Tongcheng and Landrace pigs using long serial analysis of gene expression provides insight into the molecular mechanism underlying differences in muscle growth

Genome-Wide Association Study Reveals Candidate Genes for Growth Relevant Traits in Pigs

Improvement of the growth rate is a challenge in the pig industry, the Average Daily Gain (ADG) and Days (AGE) to 100 kg are directly related to growth performance. We performed genome-wide association study (GWAS) and genetic parameters estimation for ADG and AGE using the genomic and phonemic from four breed (Duroc, Yorkshire, Landrace, and Pietrain) populations. All analyses were performed by a multi-loci GWAS model, FarmCPU. The GWAS results of all four breeds indicate that five genome-wide significant SNPs were associated with ADG, and the nearby genomic regions explained 4.08% of the genetic variance and 1.90% of the phenotypic variance, respectively. For AGE, six genome-wide significant SNPs were detected, and the nearby genomic regions explained 8.09% of the genetic variance and 3.52% of phenotypic variance, respectively. In total, nine candidate genes were identified to be associated with growth and metabolism. Among them, TRIB3 was reported to associate with pig growth, GRP, TTR, CNR1, GLP1R, BRD2, HCRTR2, SEC11C, and ssc-mir-122 were reported to associate with growth traits in human and mouse. The newly detected candidate genes will advance the understanding of growth related traits and the identification of the novel variants will suggest a potential use in pig genomic breeding programs

Dissociated Spatial-Arithmetic Associations in Horizontal and Vertical Dimensions

Spatial–numerical associations (small numbers—left/lower space and large numbers—right/upper space) are regularly found in elementary number processing. Recently, the interest in this phenomenon has been extended from elementary number processing to mental arithmetic. Many studies have demonstrated horizontal spatial-arithmetic associations, i.e., solving addition or subtraction problems cause spatial shifts of attention rightward or leftward, respectively. However, the role of this effect in the vertical dimension has not been addressed. This is problematic because it leaves the analogy between elementary number processing and arithmetic incomplete. In order to make a strong case for a similarity between elementary number processing and mental arithmetic, a spatial-arithmetic association should be observed in the vertical dimension too. Here, we adopted the target detection paradigm from Liu et al. (2017) to replicate the horizontal spatial-arithmetic association, and meanwhile investigate whether this effect also exists in the vertical direction. Our results confirmed that addition could induce covert movement to right side and subtraction to left side. However, such a spatial-arithmetic association was not found in the vertical dimension. The implication of these findings is discussed

In Silico Prediction of Horizontal Gene Transfer Events in Lactobacillus bulgaricus and Streptococcus thermophilus Reveals Protocooperation in Yogurt Manufacturing▿ †

Lactobacillus bulgaricus and Streptococcus thermophilus, used in yogurt starter cultures, are well known for their stability and protocooperation during their coexistence in milk. In this study, we show that a close interaction between the two species also takes place at the genetic level. We performed an in silico analysis, combining gene composition and gene transfer mechanism-associated features, and predicted horizontally transferred genes in both L. bulgaricus and S. thermophilus. Putative horizontal gene transfer (HGT) events that have occurred between the two bacterial species include the transfer of exopolysaccharide (EPS) biosynthesis genes, transferred from S. thermophilus to L. bulgaricus, and the gene cluster cbs-cblB(cglB)-cysE for the metabolism of sulfur-containing amino acids, transferred from L. bulgaricus or Lactobacillus helveticus to S. thermophilus. The HGT event for the cbs-cblB(cglB)-cysE gene cluster was analyzed in detail, with respect to both evolutionary and functional aspects. It can be concluded that during the coexistence of both yogurt starter species in a milk environment, agonistic coevolution at the genetic level has probably been involved in the optimization of their combined growth and interactions

Comparative analysis of antioxidant activities of essential oils and extracts of fennel (Foeniculum vulgare Mill.) seeds from Egypt and China

The present study was conducted to assay the antioxidant activities of essential oils and ethanol extracts of fennel (Foeniculum vulgare Mill.) seeds from Egypt and China. The major components of the Egyptian fennel essential oil were estragole (51.04%), limonene (11.45%), l-fenchone (8.19%) and trans-anethole (3.62%) by GC–MS analysis. Whereas, the major constituents of Chinese fennel essential oil were trans-anethole (54.26%), estragole (20.25%), l-fenchone (7.36%) and limonene (2.41%). The fennel seed extracts from Egypt and China contained appreciable levels of total phenolic contents (42.24 and 30.94 mg PE/g, respectively). The extracts exhibited good DPPH radical scavenging capacity with IC50 (6.34 and 7.17 mg/g), respectively. A high variation in free radical scavenging activities of essential oils was observed. The Chinese fennel essential oil showed high activity in DPPH radical scavenging with IC50 (15.66 mg/g). The Egyptian fennel essential oil showed very low activity with IC50 (141.82 mg/g). The results of the present investigation demonstrated significant variations in the antioxidant activities of fennel essential oils and extracts from Egypt and China. Keywords: Foeniculum vulgare, Essential oils, GC–MS, Total phenolic contents, Antioxidant activitie