Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research this field we have updated our mining web server. BAGEL4 faster than its predecessor now fully independent from ORF-calling. Gene clusters of interest are discovered using core-peptide database and/or through HMM motifs that present associated context genes. The databases used for been extended with literature references links...

Enterococci are considered mainly responsible for the undesirable accumulation of biogenic amines tyramine and putrescine in cheeses. The biosynthesis has been described as a species trait Enterococcus faecalis. Tyramine is formed by decarboxylation amino acid tyrosine, tyrosine decarboxylase (TDC) route encoded tdc cluster. Putrescine from agmatine deiminase (AGDI) pathway agdi These routes have independently studied, transcriptionally regulate clusters. objective present work to study...

Identifying genes encoding bacteriocins and ribosomally synthesized posttranslationally modified peptides (RiPPs) can be a challenging task.Especially those that do not have strong homology to previously identified easily overlooked.Extensive use of BAGEL2 user feedback has led us develop BAGEL3.BAGEL3 features genome mining prokaryotes, which is largely independent open reading frame (ORF) predictions been extended cover more (novel) classes peptides.BAGEL3 uses an identification approach...

Lactococcus lactis is of great importance for the nutrition hundreds millions people worldwide. This paper describes genome sequence subsp. cremoris MG1363, lactococcal strain most intensively studied throughout world. The 2,529,478-bp contains 81 pseudogenes and encodes 2,436 proteins. Of 530 unique proteins, 47 belong to COG (clusters orthologous groups) functional category "carbohydrate metabolism transport," by far largest novel proteins in comparison with L. IL1403. Nearly one-fifth 71...

The cryptic Streptococcus cremoris Wg2 plasmid pWV01 (1.5 megadaltons) was genetically marked with the chloramphenicol resistance (Cmr) gene from pC194. recombinant (pGK1, 2.4 replicated and expressed Cmr in Bacillus subtilis. From this an insertion-inactivation vector constructed by inserting erythromycin (Emr) pE194 cop-6. This (pGK12, 2.9 contained a unique BclI site Emr ClaI HpaII sites outside both genes. It stably maintained B. subtilis at copy number of approximately 5. pGK12 also...

Significance More than 70 years ago, Monod described the phenomenon of diauxic growth bacteria, observation that in presence two alternative sugars, cells first use one them and then, after a short lag phase, switch to other. Until now it had been assumed all population engage outgrowth on second sugar major metabolic adaptation enzymatic composition has occurred, which takes time (hence phase growth). Here, we show actually only subpopulation is fit enough partake present an evolutionary...

A system for generating chromosomal insertions in lactococci is described. It based on the conditional replication of lactococcal pWV01-derived Ori+ RepA- vector pORI19, containing lacZ alpha and multiple cloning site pUC19. Chromosomal AluI fragments Lactococcus lactis were cloned pORI19 RepA+ helper strain Escherichia coli EC101. The frequency Campbell-type recombinants, following introduction this plasmid bank into L. (RepA-), was increased by combining with temperature-sensitive pWV01...

A pair of vectors for expression heterologous genes in Lactococcus lactis was constructed. In addition to an origin replication that has a broad host range, these contain multiple cloning site flanked by gene signals originating from L. subsp. cremoris Wg2. The two vectors, about 3.7 kilobase pairs size, differ only the type antibiotic resistance they confer their hosts. pMG36 carries kanamycin marker, which replaced erythromycin marker pMG36e. As example use hen egg white lysozyme-coding...

A common problem in the annotation of open reading frames (ORFs) is identification genes that are functionally similar but have limited or no sequence homology. This particularly case for bacteriocins, a very diverse group antimicrobial peptides produced by bacteria and usually encoded small, poorly conserved ORFs. ORFs surrounding bacteriocin often biosynthetic genes. information can be used to locate putative structural Here, we describe BAGEL, web server identifies DNA using novel,...

ABSTRACT A bile salt hydrolase (BSH) was isolated from Bifidobacterium longum SBT2928, purified, and characterized. Furthermore, we describe for the first time cloning analysis of gene encoding BSH ( bsh ) in a member genus . The enzyme has native molecular weight 125,000 to 130,000 subunit 35,024, as determined deduced amino acid sequence, indicating that is tetramer. pH optimum B. between 5 7, temperature 40°C. strongly inhibited by thiol inhibitors, Cys residue likely be involved...

The C-terminal region (cA) of the major autolysin AcmA <i>Lactococcus lactis</i> contains three highly similar repeated regions 45 amino acid residues (LysM domains), which are separated by nonhomologous sequences. cA domain could be deleted without destroying cell wall-hydrolyzing activity enzyme <i>in vitro</i>. This derivative was capable neither binding to lactococcal cells nor lysing these while separation producer incomplete. and a chimeric protein consisting fused C terminus MSA2,...

The nucleotide sequence of a chromosomal DNA fragment Lactococcus lactis subsp. SSL135, previously implicated in peptide utilization, has been determined. genes oppDFBCA, encoding the oligopeptide transport system (Opp), and that endopeptidase PepO were located on this 8.9-kb fragment. oppDFBCA pepO are probably organized an operon. Analysis deduced amino acid sequences indicated consists two ATP-binding proteins OppD OppF, integral membrane OppB OppC, substrate-binding protein OppA. On...

A 6.5-kilobase HindIII fragment that specifies the proteolytic activity of Streptococcus cremoris Wg2 was sequenced entirely. The nucleotide sequence revealed two open reading frames (ORFs), a small ORF1 with 295 codons and large ORF2 containing 1,772 codons. For both ORFs, there no stop codon on fragment. partially overlapping PstI used to locate translation ORF2. entire contained 1,902 coding triplets, followed by an apparently rho-independent terminator sequence. inferred amino acid would...

Lactococcin A is a bacteriocin produced by Lactococcus lactis. Its structural gene has recently been cloned and sequenced (M. J. van Belkum, B. Hayema, R. E. Jeeninga, Kok, G. Venema, Appl. Environ. Microbiol. 57:492-498, 1991). Purified lactococcin increased the permeability of cytoplasmic membrane L. lactis dissipated potential. significantly higher concentration was needed to dissipate potential in an immune strain at low concentrations (0.029 microgram/mg protein) inhibited secondary...

CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression several genes encoding proteins proteolytic system. DNA microarray analysis, comparing profiles L. and an isogenic strain in which codY was mutated, used to determine regulon. In peptide-rich medium exponentially growing cells, where exerts strong repressing activity, over 30 significantly increased upon removal codY. The differentially expressed included those predominantly involved amino acid...

Mining bacterial genomes for bacteriocins is a challenging task due to the substantial structure and sequence diversity, generally small sizes, of these antimicrobial peptides. Major progress in research peptides ever-increasing quantities genomic data, varying from (un)finished meta-genomic led us develop significantly improved genome mining software BAGEL2, as follow-up our previous BAGEL software. BAGEL2 identifies putative on basis conserved domains, physical properties presence...

A novel display system is described that allows highly efficient immobilization of heterologous proteins on bacterial surfaces in applications for which the use genetically modified bacteria less desirable. This based nonliving and non-genetically gram-positive cells, designated enhancer matrix (GEM) particles, are used as substrates to bind externally added by means a high-affinity binding domain. domain, protein anchor (PA), was derived from Lactococcus lactis peptidoglycan hydrolase AcmA....

Abstract Background Accurate prediction of DNA motifs that are targets RNA polymerases, sigma factors and transcription (TFs) in prokaryotes is a difficult mission mainly due to as yet undiscovered features sequences or structures promoter regions. Improved comparison algorithms currently available for identifying factor binding sites (TFBSs) their accompanying TFs regulon members. Results We here extend the current databases TFs, TFBSs regulons with our knowledge on Lactococcus lactis...

Carbon catabolite control protein A (CcpA) is the main regulator involved in carbon repression gram-positive bacteria. Time series gene expression analyses of Lactococcus lactis MG1363 and L. MG1363DeltaccpA using DNA microarrays were used to define CcpA regulon lactis. Based on a comparison transcriptome data with putative binding motifs (cre sites) promoter sequences genome lactis, 82 direct targets predicted. The differences time-dependent CcpA-regulated genes between exponential...