bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced Lysis upon Growth of
Lactococcus lactis
on Galactose Is a Consequence of Decreased Binding of the Autolysin AcmA
Authors: Steen Anton , Buist Girbe , Kramer Naomi E. , Jalving Ruud , Benus Germaine F. J. D. , Venema Gerard , Kuipers Oscar P. , Kok Jan 
Published: June 2008

ABSTRACT

When
Lactococcus lactis
subsp.
lactis
IL1403 or
L. lactis
subsp.
cremoris
MG1363 is grown in a medium with galactose as the carbon source, the culture lyses to a lesser extent in stationary phase than when the bacteria are grown in a medium containing glucose. Expression of AcmA, the major autolysin of
L. lactis
, is not influenced by the carbon source. Binding studies with a fusion protein consisting of the MSA2 protein of
Plasmodium falciparum
and the C-terminal peptidoglycan-binding domain of AcmA revealed that cell walls of cells from both subspecies grown on galactose bind less AcmA than cell walls of cells grown on glucose. Cells grown on glucose or galactose and treated with trichloroacetic acid prior to AcmA binding bind similar amounts of AcmA. Analysis of the composition of the lipoteichoic acids (LTAs) of
L. lactis
IL1403 cells grown on glucose or galactose showed that the LTA composition is influenced by the carbon source: cells grown on galactose contain LTA with less galactose than cells grown on glucose. In conclusion, growth of
L. lactis
on galactose changes the LTA composition in the cell wall in such a way that less AcmA is able to bind to the peptidoglycan, resulting in a decrease in autolysis.
Engineering of a Human Vaginal
Lactobacillus
Strain for Surface Expression of Two-Domain CD4 Molecules
Authors: Liu Xiaowen , Lagenaur Laurel A. , Lee Peter P. , Xu Qiang 
Published: June 2008

ABSTRACT

Women are at significant risk of heterosexually transmitted human immunodeficiency virus (HIV) infection, with the mucosal epithelium of the cervix and vagina serving as a major portal of entry. The cervicovaginal mucosa naturally harbors dynamic microflora composed predominantly of lactobacilli, which may be genetically modified to serve as a more efficient protective barrier against the heterosexual transmission of HIV. We selected a vaginal strain of
Lactobacillus
,
L. jensenii
1153, for genetic modification to display surface-anchored anti-HIV proteins. Genomic sequencing analyses revealed that
L. jensenii
1153 encodes several unique high-molecular-weight cell wall-anchored proteins with a C-terminal cell wall sorting LPQTG motif. In this report, we employed these proteins to express a surface-anchored two-domain CD4 (2D CD4) molecule in
L. jensenii
1153. Our studies indicated that the C-terminal cell wall sorting signal LPQTG motif alone is insufficient to drive the surface expression of heterologous proteins, and the display of surface-anchored 2D CD4 molecules required native sequences of a defined length upstream of the unique C-terminal LPQTG cell wall sorting signal and the positively charged C terminus in a
Lactobacillus
-based expression system. The modified
L. jensenii
strain displayed 2D CD4 molecules that were uniformly distributed on bacterial surfaces. The surface-anchored 2D CD4 molecule was recognized by a conformation-dependent anti-CD4 antibody, suggesting that the expressed proteins adopted a native conformation. The establishment of this
Lactobacillus
-based surface expression system, with potential broad applicability, represents a major step toward developing an inexpensive yet durable approach to topical microbicides for the mitigation of heterosexual transmission of HIV and other mucosally transmitted viral pathogens.
Influence of Shifting Positions of Ser, Thr, and Cys Residues in Prenisin on the Efficiency of Modification Reactions and on the Antimicrobial Activities of the Modified Prepeptides
Authors: Lubelski Jacek , Overkamp Wout , Kluskens Leon D. , Moll Gert N. , Kuipers Oscar P. 
Published: June 2008

ABSTRACT
Since the recent discovery that the nisin modification and transport machinery can be used to produce and modify peptides unrelated to nisin, specific questions arose concerning the specificity of the modification enzymes involved and the limits of their promiscuity with respect to the dehydration and cyclization processes. The nisin leader peptide has been postulated to fulfill a recognition and binding function required for these modifications. Here, we investigated whether the relative positions of the modifiable residues in the nisin prepeptide, with respect to the leader peptide, could influence the efficiency of their modification. We conducted a systematic study on the insertion of one to four alanines in front of either ring A or ring D to change the “reading frame” of modifiable residues, resulting in altered distance and topology of the modifiable residues relative to the leader. The insertion of N-terminal and hinge-located Ala residues had only a modest influence on the modification efficiency, demonstrating that the “phasing” of these residues relative to the leader peptide is not a critical factor in determining modification. However, in all cases, but especially with the N-terminal insertions, the antimicrobial activities of the fully modified nisin species were decreased.
Transcriptome Analysis of the
Lactococcus lactis
ArgR and AhrC Regulons
Authors: Larsen Rasmus , van Hijum Sacha A. F. T. , Martinussen Jan , Kuipers Oscar P. , Kok Jan 
Published: June 2008

ABSTRACT

In previous studies, we have shown that direct protein-protein interaction between the two regulators ArgR and AhrC in
Lactococcus lactis
is required for arginine-dependent repression of the biosynthetic
argC
promoter and the activation of the catabolic
arcA
promoter. Here, we establish the global ArgR and AhrC regulons by transcriptome analyses and show that both regulators are dedicated to the control of arginine metabolism in
L. lactis
.
Morphology, Genome Sequence, and Structural Proteome of Type Phage P335 from
Lactococcus lactis
Authors: Labrie Simon J. , Josephsen Jytte , Neve Horst , Vogensen Finn K. , Moineau Sylvain 
Published: June 2008

ABSTRACT

Lactococcus lactis
phage P335 is a virulent type phage for the species that bears its name and belongs to the
Siphoviridae
family. Morphologically, P335 resembled the
L. lactis
phages TP901-1 and Tuc2009, except for a shorter tail and a different collar/whisker structure. Its 33,613-bp double-stranded DNA genome had 50 open reading frames. Putative functions were assigned to 29 of them. Unlike other sequenced genomes from lactococcal phages belonging to this species, P335 did not have a lysogeny module. However, it did carry a dUTPase gene, the most conserved gene among this phage species. Comparative genomic analyses revealed a high level of identity between the morphogenesis modules of the phages P335, ul36, TP901-1, and Tuc2009 and two putative prophages of
L. lactis
SK11. Differences were noted in genes coding for receptor-binding proteins, in agreement with their distinct host ranges. Sixteen structural proteins of phage P335 were identified by liquid chromatography-tandem mass spectrometry. A 2.8-kb insertion was recognized between the putative genes coding for the activator of late transcription (Alt) and the small terminase subunit (TerS). Four genes within this region were autonomously late transcribed and possibly under the control of Alt. Three of the four deduced proteins had similarities with proteins from
Streptococcus pyogenes
prophages, suggesting that P335 acquired this module from another phage genome. The genetic diversity of the P335 species indicates that they are exceptional models for studying the modular theory of phage evolution.
Differential Transcriptional Response of
Bifidobacterium longum
to Human Milk, Formula Milk, and Galactooligosaccharide
Authors: González Rina , Klaassens Eline S. , Malinen Erja , de Vos Willem M. , Vaughan Elaine E. 
Published: June 2008

ABSTRACT

In order to gain insight into the effects of human breast milk on the development of the intestinal bifidobacteria and associated health effects, the transcriptome of
Bifidobacterium longum
LMG 13197 grown in breast milk and formula milk containing galactooligosaccharides (GOS) and long-chain fructooligosaccharides was compared to that obtained in a semisynthetic medium with glucose. Total RNA was isolated from exponentially growing cells and hybridized to a clone library-based microarray. Inserts of clones with significant hybridization signals were sequenced and identified. The
B. longum
transcriptomes obtained during growth on human and formula milk were more similar to each other than to that obtained from growth in semisynthetic medium with glucose. Remarkably, there were only a few genes implicated in carbohydrate metabolism that were similarly upregulated during growth in both human and formula milk although oligosaccharides were added to the formula. Common highly upregulated genes notably included putative genes for cell surface type 2 glycoprotein-binding fimbriae that are implicated in attachment and colonization in the intestine. Genes involved in carbohydrate metabolism formed the dominant group specifically upregulated in breast milk and included putative genes for
N
-acetylglucosamine degradation and for metabolism of mucin and human milk oligosaccharides via the galactose/lacto-
N
-biose gene cluster. This supports the notion that the bifidogenic effect of human milk is to a great extent based on its oligosaccharides. The transcriptional effect of semisynthetic medium containing GOS, which, like human milk, contains a large amount of lactose and galactose, on the
B. longum
transcriptome was also studied and revealed substantial similarity with carbohydrate-utilization genes upregulated during growth in human milk. This knowledge provides leads to optimizing formula milk to better simulate the observed bifidogenic effects of human breast milk.
Streptococcus thermophilus
Core Genome: Comparative Genome Hybridization Study of 47 Strains
Authors: Rasmussen Thomas Bovbjerg , Danielsen Morten , Valina Ondrej , Garrigues Christel , Johansen Eric , Pedersen Martin Bastian 
Published: June 2008

ABSTRACT

A DNA microarray platform based on 2,200 genes from publicly available sequences was designed for
Streptococcus thermophilus
. We determined how single-nucleotide polymorphisms in the 65- to 75-mer oligonucleotide probe sequences affect the hybridization signals. The microarrays were then used for comparative genome hybridization (CGH) of 47 dairy
S. thermophilus
strains. An analysis of the exopolysaccharide genes in each strain confirmed previous findings that this class of genes is indeed highly variable. A phylogenetic tree based on the CGH data showed similar distances for most strains, indicating frequent recombination or gene transfer within
S. thermophilus
. By comparing genome sizes estimated from the microarrays and pulsed-field gel electrophoresis, the amount of unknown DNA in each strain was estimated. A core genome comprised of 1,271 genes detected in all 47 strains was identified. Likewise, a set of noncore genes detected in only some strains was identified. The concept of an industrial core genome is proposed. This is comprised of the genes in the core genome plus genes that are necessary in an applied industrial context.
Impact of
luxS
and Suppressor Mutations on the Gastrointestinal Transit of
Lactobacillus rhamnosus
GG
Authors: Lebeer Sarah , Claes Ingmar J. J. , Verhoeven Tine L. A. , Shen Chong , Lambrichts Ivo , Ceuppens Jan L. , Vanderleyden Jos , De Keersmaecker Sigrid C. J. 
Published: June 2008

ABSTRACT

It is generally believed that probiotic bacteria need to survive gastrointestinal transit to exert a health-promoting effect. In this study, a genuine
luxS
mutant and a
luxS
mutant containing unknown suppressor mutations of the probiotic strain
Lactobacillus rhamnosus
GG were compared to the wild type for survival and persistence in the murine gastrointestinal tract. The LuxS enzyme, catalyzing the production of the autoinducer-2 signaling molecule, also forms an integral part of the activated methyl cycle and the metabolism of methionine and cysteine. The genuine
luxS
mutant CMPG5412 showed drastically reduced persistence in mice, which was related to less survival in simulated gastric juice, indicating that LuxS metabolism is crucial for the gastric stress resistance of
L. rhamnosus
GG. The suppressor mutations in the other
luxS
mutant, CMPG5413, appear to compensate for the metabolic defects of the
luxS
mutation and to restore the resistance to gastric juice but cause a defect in adherence, biofilm formation, and exopolysaccharide production. The shorter residence time of this suppressor mutant in the murine gastrointestinal tract indicates a role for biofilm formation and exopolysaccharides in the persistence capacity of
L. rhamnosus
GG.
Plasmid pCS1966, a New Selection/Counterselection Tool for Lactic Acid Bacterium Strain Construction Based on the
oroP
Gene, Encoding an Orotate Transporter from
Lactococcus lactis
Authors: Solem Christian , Defoor Els , Jensen Peter Ruhdal , Martinussen Jan 
Published: June 2008

ABSTRACT

In this paper we describe the new selection/counterselection vector pCS1966, which is suitable for both sequence-specific integration based on homologous recombination and integration in a bacteriophage attachment site. This plasmid harbors
oroP
, which encodes a dedicated orotate transporter, and can replicate only in
Escherichia coli
. Selection for integration is performed primarily by resistance to erythromycin; alternatively, the ability to utilize orotate as a pyrimidine source in a pyrimidine auxotrophic mutant could be utilized. Besides allowing the cell to utilize orotate, the transporter renders the cell sensitive to 5-fluoroorotate. This sensitivity is used to select for loss of the plasmid. When expressed from its own promoter,
oroP
was toxic to
E. coli
, whereas in
Lactococcus lactis
the level of expression of
oroP
from a chromosomal copy was too low to confer 5-fluoroorotate sensitivity. In order to obtain a plasmid that confers 5-fluoroorotate sensitivity when it is integrated into the chromosome of
L. lactis
and at the same time can be stably maintained in
E. coli
, the expression of the
oroP
gene was controlled from a synthetic promoter conferring these traits. To demonstrate its use, a number of
L. lactis
strains expressing triosephosphate isomerase (
tpiA
) at different levels were constructed.
Improvement of
Lactobacillus plantarum
Aerobic Growth as Directed by Comprehensive Transcriptome Analysis
Authors: Stevens Marc J. A. , Wiersma Anne , de Vos Willem M. , Kuipers Oscar P. , Smid Eddy J. , Molenaar Douwe , Kleerebezem Michiel 
Published: June 2008

ABSTRACT

An aerobic
Lactobacillus plantarum
culture displayed growth stagnation during early growth. Transcriptome analysis revealed that resumption of growth after stagnation correlated with activation of CO
2
-producing pathways, suggesting that a limiting CO
2
concentration induced the stagnation. Analogously, increasing the CO
2
gas partial pressure during aerobic fermentation prevented the temporal growth stagnation.
Functional Analysis of Four Bile Salt Hydrolase and Penicillin Acylase Family Members in
Lactobacillus plantarum
WCFS1
Authors: Lambert Jolanda M. , Bongers Roger S. , de Vos Willem M. , Kleerebezem Michiel 
Published: June 2008

ABSTRACT

Bile salts play an important role in the digestion of lipids in vertebrates and are synthesized and conjugated to either glycine or taurine in the liver. Following secretion of bile salts into the small intestine, intestinal microbes are capable of deconjugating the glycine or taurine from the bile salts, using an enzyme called bile salt hydrolase (Bsh). Intestinal lactobacilli are regarded as major contributors to bile salt hydrolysis in vivo. Since the bile salt-hydrolyzing strain
Lactobacillus plantarum
WCFS1 was predicted to carry four
bsh
genes (
bsh1, bsh2, bsh3
, and
bsh4
), the functionality of these
bsh
genes was explored using
Lactococcus lactis
heterologous overexpression and multiple
bsh
deletion strains. Thus, Bsh1 was shown to be responsible for the majority of Bsh activity in
L. plantarum
WCFS1. In addition,
bsh1
of
L. plantarum
WCFS1 was shown to be involved in conferring tolerance to specific bile salts (i.e., glycocholic acid). Northern blot analysis established that
bsh1, bsh2, bsh3
, and
bsh4
are all expressed in
L. plantarum
WCFS1 during the exponential growth phase. Following biodiversity analysis,
bsh1
appeared to be the only
bsh
homologue that was variable among
L. plantarum
strains; furthermore, the presence of
bsh1
correlated with the presence of Bsh activity, suggesting that Bsh1 is commonly responsible for Bsh activity in
L. plantarum
strains. The fact that
bsh2, bsh3
, and
bsh4
genes appeared to be conserved among
L. plantarum
strains suggests an important role of these genes in the physiology and lifestyle of the species
L. plantarum
. Analysis of these additional
bsh
-like genes in
L. plantarum
WCFS1 suggests that they might encode penicillin acylase rather than Bsh activity, indicating their implication in the conversion of substrates other than bile acids in the natural habitat.
Evaluation of Reuterin Production in Urogenital Probiotic
Lactobacillus reuteri
RC-14
Authors: Cadieux Peter , Wind Anette , Sommer Philip , Schaefer Laura , Crowley Kate , Britton Robert A. , Reid Gregor 
Published: June 2008

ABSTRACT

Classified as a distinct species in 1980,
Lactobacillus reuteri
strains have been used in probiotic formulations for intestinal and urogenital applications. In the former, the primary mechanism of action of
L. reuteri
SD2112 (ATCC 55730) has been purported to be its ability to produce the antibiotic 3-hydroxypropionaldehyde (3-HPA), also known as reuterin. In the vagina, it has been postulated that probiotic
Lactobacillus reuteri
RC-14 does not require reuterin production but mediates a restoration of the normal microbiota via hydrogen peroxide, biosurfactant, lactic acid production, and immune modulation. The aim of the present study was to determine whether strain RC-14 produced reuterin. Using PCR and DNA dot blot analyses, numerous
Lactobacillus
species, including RC-14, were screened for the presence of the gene encoding the large subunit of glycerol dehydratase (
gldC
), the enzyme responsible for reuterin production. In addition, lactobacilli were grown in glycerol-based media and both high-performance liquid chromatography and a colorimetric assay were used to test for the presence of reuterin.
L. reuteri
RC-14 was determined to be negative for
gldC
sequences, as well as for the production of reuterin when cultured in the presence of glycerol. These findings support that the probiotic effects of
L. reuteri
RC-14, repeatedly demonstrated during numerous studies of the intestine and vagina, are independent of reuterin production.
Detection of a Lysozyme Inhibitor in
Proteus mirabilis
by a New Reverse Zymogram Method
Authors: Callewaert Lien , Vanderkelen Lise , Deckers Daphne , Aertsen Abram , Robben Johan , Michiels Chris W. 
Published: June 2008

ABSTRACT

A reverse zymogram method for the detection of bacterial lysozyme inhibitors was developed. This method was validated by using a periplasmic protein extract of
Escherichia coli
containing a known inhibitor and subsequently led to the detection of a new proteinaceous hen egg white lysozyme inhibitor in
Proteus mirabilis
.
Expression of Green Fluorescent Protein Fused to Magnetosome Proteins in Microaerophilic Magnetotactic Bacteria
Authors: Lang Claus , Schüler Dirk 
Published: June 2008

ABSTRACT

The magnetosomes of magnetotactic bacteria are prokaryotic organelles consisting of a magnetite crystal bounded by a phospholipid bilayer that contains a distinct set of proteins with various functions. Because of their unique magnetic and crystalline properties, magnetosome particles are potentially useful as magnetic nanoparticles in a number of applications, which in many cases requires the coupling of functional moieties to the magnetosome membrane. In this work, we studied the use of green fluorescent protein (GFP) as a reporter for the magnetosomal localization and expression of fusion proteins in the microaerophilic
Magnetospirillum gryphiswaldense
by flow cytometry, fluorescence microscopy, and biochemical analysis. Although optimum conditions for high fluorescence and magnetite synthesis were mutually exclusive, we established oxygen-limited growth conditions, which supported growth, magnetite biomineralization, and GFP fluorophore formation at reasonable rates. Under these optimized conditions, we studied the subcellular localization and expression of the GFP-tagged magnetosome proteins MamC, MamF, and MamG by fluorescence microscopy and immunoblotting. While all fusions specifically localized at the magnetosome membrane, MamC-GFP displayed the strongest expression and fluorescence. MamC-GFP-tagged magnetosomes purified from cells displayed strong fluorescence, which was sensitive to detergents but stable under a wide range of temperature and salt concentrations. In summary, our data demonstrate the use of GFP as a reporter for protein localization under magnetite-forming conditions and the utility of MamC as an anchor for magnetosome-specific display of heterologous gene fusions.
Molecular Characterization of the Diversity and Distribution of a Thermal Spring Microbial Community by Using rRNA and Metabolic Genes
Authors: Hall Justine R. , Mitchell Kendra R. , Jackson-Weaver Olan , Kooser Ara S. , Cron Brandi R. , Crossey Laura J. , Takacs-Vesbach Cristina D. 
Published: June 2008

ABSTRACTThe diversity and distribution of a bacterial community from Coffee Pots Hot Spring, a thermal spring in Yellowstone National Park with a temperature range of 39.3 to 74.1°C and pH range of 5.75 to 6.91, were investigated by sequencing cloned PCR products and quantitative PCR (qPCR) of 16S rRNA and metabolic genes. The spring was inhabited by threeAquificaegenera—Thermocrinis, Hydrogenobaculum, andSulfurihydrogenibium—and members of theAlpha-,Beta-, andGammaproteobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, and candidate division OP5. The in situ chemical affinities were calculated for 41 potential metabolic reactions using measured environmental parameters and a range of hydrogen and oxygen concentrations. Reactions that use oxygen, ferric iron, sulfur, and nitrate as electron acceptors were predicted to be the most energetically favorable, while reactions using sulfate were expected to be less favorable. Samples were screened for genes used in ammonia oxidation (amoA, bacterial gene only), the reductive tricarboxylic acid (rTCA) cycle (aclB), the Calvin cycle (cbbM), sulfate reduction (dsrAB), nitrogen fixation (nifH), nitrite reduction (nirK), and sulfide oxidation (soxEF1) by PCR. Genes for carbon fixation by the rTCA cycle and nitrogen fixation were detected. AllaclBsequences were phylogenetically related and spatially correlated toSulfurihydrogenibium16S rRNA gene sequences using qPCR (R2= 0.99). This result supports the recent finding of citrate cleavage by enzymes other than ATP citrate lyase in the rTCA cycle of theAquificaceaefamily. We briefly consider potential biochemical mechanisms that may allowSulfurihydrogenibiumandThermocrinisto codominate some hydrothermal environments.
Multiplex Fast Real-Time PCR for Quantitative Detection and Identification of
cos
- and
pac
-Type
Streptococcus thermophilus
Bacteriophages
Authors: del Rio Beatriz , Martín María Cruz , Martínez Noelia , Magadán Alfonso H. , Alvarez Miguel A. 
Published: June 2008

ABSTRACT

The fermentation of milk by
Streptococcus thermophilus
is a widespread industrial process that is susceptible to bacteriophage attack. In this work, a preventive fast real-time PCR method for the detection, quantification, and identification of types of
S. thermophilus
phages in 30 min is described.