bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Basis of Tetracycline Resistance in
Bifidobacterium animalis
subsp.
lactis
Authors: Gueimonde Miguel , Flórez Ana Belén , van Hoek Angela H. A. M. , Stuer-Lauridsen Birgitte , Strøman Per , de los Reyes-Gavilán Clara G. , Margolles Abelardo 
Published: March 2010

ABSTRACT

All strains of
Bifidobacterium animalis
subsp.
lactis
described to date show medium level resistance to tetracycline. Screening of 26 strains from a variety of sources revealed the presence of
tet
(W) in all isolates. A transposase gene upstream of
tet
(W) was found in all strains, and both genes were cotranscribed in strain IPLAIC4. Mutants with increased tetracycline resistance as well as tetracycline-sensitive mutants of IPLAIC4 were isolated and genetically characterized. The native
tet
(W) gene was able to restore the resistance phenotype to a mutant with an alteration in
tet
(W) by functional complementation, indicating that
tet
(W) is necessary and sufficient for the tetracycline resistance seen in
B. animalis
subsp.
lactis
.
Constitutive Secretion in Tetrahymena thermophila
Authors: Madinger Catherine L. , Collins Kathleen , Fields Lauren G. , Taron Christopher H. , Benner Jack S. 
Published: March 2010

ABSTRACT

The growth, survival, and life cycle progression of the freshwater ciliated protozoan
Tetrahymena thermophila
are responsive to protein signals thought to be released by constitutive secretion. In addition to providing insights about ciliate communication, studies of constitutive secretion are of interest for evaluating the utility of
T. thermophila
as a platform for the expression of secreted protein therapeutics. For these reasons, we undertook an unbiased investigation of
T. thermophila
secreted proteins using wild-type and secretion mutant strains. Extensive tandem mass spectrometry analyses of secretome samples were performed. We identified a total of 207 secretome proteins, most of which were not detected in a set of abundant whole-cell protein identifications. Numerous proteases and other hydrolases were secreted from cells grown in rich medium but not cells transferred to a nutrient starvation condition. On the other hand, we detected the starvation-enhanced secretion of a small number of cytosolic proteins, suggestive of an exosome-like pathway in
T. thermophila
. Subsets of proteins from the
T. thermophila
regulated secretion pathway were detected with differential representation across strains and culture conditions. Finally, many secretome proteins had a predicted N-terminal signal sequence but no other annotated characteristic or functional classification. Our work provides the first comprehensive analysis of secreted proteins in
T. thermophila
and establishes the groundwork for future studies of constitutive protein secretion biology and biotechnology in ciliates.
Interaction of the Aspergillus nidulans Microtubule-Organizing Center (MTOC) Component ApsB with Gamma-Tubulin and Evidence for a Role of a Subclass of Peroxisomes in the Formation of Septal MTOCs
Authors: Zekert Nadine , Veith Daniel , Fischer Reinhard 
Published: March 2010

ABSTRACT

Peroxisomes are a diverse class of organelles involved in different physiological processes in eukaryotic cells. Although proteins imported into peroxisomes carry a peroxisomal targeting sequence at the C terminus (PTS1) or an alternative one close to the N terminus (PTS2), the protein content of peroxisomes varies drastically. Here we suggest a new class of peroxisomes involved in microtubule (MT) formation. Eukaryotic cells assemble MTs from distinct points in the cell. In the fungus
Aspergillus nidulans
, septum-associated microtubule-organizing centers (sMTOCs) are very active in addition to the spindle pole bodies (SPBs). Previously, we identified a novel MTOC-associated protein, ApsB (
Schizosaccharomyces pombe
mto1), whose absence affected MT formation from sMTOCs more than from SPBs, suggesting that the two protein complexes are organized differently. We show here that sMTOCs share at least two further components, gamma-tubulin and GcpC (
S. pombe
Alp6) with SPBs and found that ApsB interacts with gamma-tubulin. In addition, we discovered that ApsB interacts with the Woronin body protein HexA and is targeted to a subclass of peroxisomes via a PTS2 peroxisomal targeting sequence. The PTS2 motif was necessary for function but could be replaced with a PTS1 motif at the C terminus of ApsB. These results suggest a novel function for a subclass of peroxisomes in cytoskeletal organization.
Analysis of the High-Affinity Iron Uptake System at the Chlamydomonas reinhardtii Plasma Membrane
Authors: Terzulli Alaina , Kosman Daniel J. 
Published: March 2010

ABSTRACT

Multicopper ferroxidases play a vital role in iron metabolism in bacteria, fungi, algae, and mammals.
Saccharomyces cerevisiae
utilizes a channeling mechanism to couple the ferroxidase activity of Fet3p to Fe
3+
transport into the cell by Ftr1p. In contrast, the mechanisms by which mammals couple the ferroxidase reaction to iron trafficking is unclear. The human ferroxidases ceruloplasmin and hephaestin are twice the size of Fet3p and interact with proteins that are not expressed in fungi.
Chlamydomonas
FOX1 is a homolog of the human ferroxidases but likely supports iron uptake in a manner similar to that of yeast, since
Chlamydomonas reinhardtii
expresses a ferric iron permease homolog, FTR1. The results presented support this hypothesis. We show that FOX1 is trafficked to the plasma membrane and is oriented with its multicopper oxidase/ferroxidase domain in the exocytoplasmic space. Our analysis of FTR1 indicates its topology is similar to that of
S. cerevisiae
Ftr1p, with a potential exocytoplasmic iron channeling motif and two potential iron permeation motifs in membrane-spanning regions. We demonstrate that high-affinity iron uptake is dependent on FOX1 and the copper status of the cell. Kinetic inhibition of high-affinity iron uptake by a ferric iron chelator does not reflect the strength of the chelator, supporting a ferric iron channeling mechanism for high-affinity iron uptake in
Chlamydomonas
. Last, recombinant FOX1 (rFOX1) has been isolated in a partially holo form that exhibits the UV-visible absorbance spectrum of a multicopper oxidase and the catalytic activity of a ferroxidase.
Marker Fusion Tagging, a New Method for Production of Chromosomally Encoded Fusion Proteins
Authors: Lai Julian , Ng Seng Kah , Liu Fang Fang , Patkar Rajesh Narhari , Lu Yanfen , Chan Jing Ru , Suresh Angayarkanni , Naqvi Naweed , Jedd Gregory 
Published: March 2010

ABSTRACT

A new gene-tagging method (marker fusion tagging [MFT]) is demonstrated for
Neurospora crassa
and
Magnaporthe oryzae
. Translational fusions between the hygromycin B resistance gene and various markers are inserted into genes of interest by homologous recombination to produce chromosomally encoded fusion proteins. This method can produce tags at any position and create deletion alleles that maintain N- and C-terminal sequences. We show the utility of MFT by producing enhanced green fluorescent protein (EGFP) tags in proteins localized to nuclei, spindle pole bodies, septal pore plugs, Woronin bodies, developing septa, and the endoplasmic reticulum.
Growth Phase-Dependent Activation of the DccRS Regulon of
Campylobacter jejuni
Authors: Wösten Marc M. S. M. , van Dijk Linda , Parker Craig T. , Guilhabert Magalie R. , van der Meer-Janssen Ynske P. M. , Wagenaar Jaap A. , van Putten Jos P. M. 
Published: March 2010

ABSTRACT

Two-component systems are widespread prokaryotic signal transduction devices which allow the regulation of cellular functions in response to changing environmental conditions. The two-component system DccRS (Cj1223c-Cj1222c) of
Campylobacter jejuni
is important for the colonization of chickens. Here, we dissect the DccRS system in more detail and provide evidence that the sensor DccS selectively phosphorylates the cognate effector, DccR. Microarray expression profiling, real-time reverse transcription-PCR (RT-PCR), electrophoretic mobility shift assay, and primer extension analyses revealed that the DccRS regulon of strain 81116 consists of five promoter elements, all containing the consensus direct repeat sequence WTTCAC-N6-TTCACW covering the putative −35 promoter regions. One of these promoters is located in front of an operon encoding a putative macrolide efflux pump while the others are in front of genes coding for putative periplasmic or membrane proteins. The DccRS-regulated genes in
C. jejuni
strain 81116 are needed to enhance early
in vivo
growth of
C. jejuni
in 7-day-old chickens. The DccRS system is activated in the late stationary bacterial growth phase, probably by released metabolic products. Whole-genome mRNA profiling and real-time RT-PCR analysis under these conditions demonstrated that the system has no influence on the transcription of genes outside the DccRS regulon.
Genome Sequence of Hybrid
V
ibrio cholerae
O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with
V. cholerae
Authors: Grim Christopher J. , Hasan Nur A. , Taviani Elisa , Haley Bradd , Chun Jongsik , Brettin Thomas S. , Bruce David C. , Detter J. Chris , Han Cliff S. , Chertkov Olga , Challacombe Jean , Huq Anwar , Nair G. Balakrish , Colwell Rita R. 
Published: March 2010

ABSTRACT

The genomes of
V
ibrio cholerae
O1 Matlab variant MJ-1236, Mozambique O1 El Tor variant B33, and altered O1 El Tor CIRS101 were sequenced. All three strains were found to belong to the phylocore group 1 clade of
V. cholerae
, which includes the 7th-pandemic O1 El Tor and serogroup O139 isolates, despite displaying certain characteristics of the classical biotype. All three strains were found to harbor a hybrid variant of CTXΦ and an integrative conjugative element (ICE), leading to their establishment as successful clinical clones and the displacement of prototypical O1 El Tor. The absence of strain- and group-specific genomic islands, some of which appear to be prophages and phage-like elements, seems to be the most likely factor in the recent establishment of dominance of
V. cholerae
CIRS101 over the other two hybrid strains.
Complete Genome Sequence of the Probiotic
Lactobacillus casei
Strain BL23
Authors: Mazé Alain , Boël Grégory , Zúñiga Manuel , Bourand Alexa , Loux Valentin , Yebra Maria Jesus , Monedero Vicente , Correia Karine , Jacques Noémie , Beaufils Sophie , Poncet Sandrine , Joyet Philippe , Milohanic Eliane , Casarégola Serge , Auffray Yanick , Pérez-Martínez Gaspar , Gibrat Jean-François , Zagorec Monique , Francke Christof , Hartke Axel , Deutscher Josef 
Published: March 2010

ABSTRACT

The entire genome of
Lactobacillus casei
BL23, a strain with probiotic properties, has been sequenced. The genomes of BL23 and the industrially used probiotic strain Shirota YIT 9029 (Yakult) seem to be very similar.
Complete Genome Sequence of the Thermophilic, Obligately Chemolithoautotrophic Hydrogen-Oxidizing Bacterium
Hydrogenobacter thermophilus
TK-6
Authors: Arai Hiroyuki , Kanbe Haruna , Ishii Masaharu , Igarashi Yasuo 
Published: March 2010

ABSTRACT

Hydrogenobacter thermophilus
is a thermophilic, obligately chemolithoautotrophic and aerobic hydrogen-oxidizing bacterium. It is unique in its ability to fix carbon dioxide via the reductive tricarboxylic acid cycle under aerobic conditions. It utilizes molecular hydrogen, elemental sulfur, or thiosulfate as the sole energy source. Here, we report the complete genome sequence of
H. thermophilus
TK-6.
Complete Genome Sequence and Annotation of the
Treponema pallidum
subsp.
pallidum
Chicago Strain
Authors: Giacani Lorenzo , Jeffrey Brendan M. , Molini Barbara J. , Le HoaVan T. , Lukehart Sheila A. , Centurion-Lara Arturo , Rockey Daniel D. 
Published: March 2010

ABSTRACT

In syphilis research, the Nichols strain of
Treponema pallidum
, isolated in 1912, has been the most widely studied. Recently, important differences among
T. pallidum
strains emerged; therefore, we sequenced and annotated the Chicago strain genome to facilitate and encourage the use of this strain in studying the pathogenesis of syphilis.
In V
itro
and
In V
ivo
Characterization of the
Pseudomonas aeruginosa
Cyclic AMP (cAMP) Phosphodiesterase CpdA, Required for cAMP Homeostasis and Virulence Factor Regulation
Authors: Fuchs Erin L. , Brutinel Evan D. , Klem Erich R. , Fehr Anthony R. , Yahr Timothy L. , Wolfgang Matthew C. 
Published: March 2010

ABSTRACT

Cyclic AMP (cAMP) is an important second messenger signaling molecule that controls a wide variety of eukaryotic and prokaryotic responses to extracellular cues. For cAMP-dependent signaling pathways to be effective, the intracellular cAMP concentration is tightly controlled at the level of synthesis and degradation. In the opportunistic human pathogen
Pseudomonas aeruginosa
, cAMP is a key regulator of virulence gene expression. To better understand the role of cAMP homeostasis in this organism, we identified and characterized the enzyme CpdA, a putative cAMP phosphodiesterase. We demonstrate that CpdA possesses 3′,5′-cAMP phosphodiesterase activity
in vitro
and that it utilizes an iron-dependent catalytic mechanism. Deletion of
cpdA
results in the accumulation of intracellular cAMP and altered regulation of
P. aeruginosa
virulence traits. Further, we demonstrate that the cAMP-dependent transcription factor Vfr directly regulates
cpdA
expression in response to intracellular cAMP accumulation, thus providing a feedback mechanism for controlling cAMP levels and fine-tuning virulence factor expression.
Expanded Role for the Nitrogen Assimilation Control Protein in the Response of
Klebsiella pneumoniae
to Nitrogen Stress
Authors: Frisch Ryan L. , Bender Robert A. 
Published: March 2010

ABSTRACT

Klebsiella pneumoniae
is able to utilize many nitrogen sources, and the utilization of some of these nitrogen sources is dependent on the nitrogen assimilation control (NAC) protein. Seven NAC-regulated promoters have been characterized in
K. pneumoniae
, and nine NAC-regulated promoters have been found by microarray analysis in
Escherichia coli
. So far, all characterized NAC-regulated promoters have been directly related to nitrogen metabolism. We have used a genome-wide analysis of NAC binding under nitrogen limitation to identify the regions of the chromosome associated with NAC in
K. pneumoniae
. We found NAC associated with 99 unique regions of the chromosome under nitrogen limitation.
In vitro
, 84 of the 99 regions associate strongly enough with purified NAC to produce a shifted band by electrophoretic mobility shift assay. Primer extension analysis of the mRNA from genes associated with 17 of the fragments demonstrated that at least one gene associated with each fragment was NAC regulated under nitrogen limitation. The large size of the NAC regulon in
K. pneumoniae
indicates that NAC plays a larger role in the nitrogen stress response than it does in
E. coli
. Although a majority of the genes with identifiable functions that associated with NAC under nitrogen limitation are involved in nitrogen metabolism, smaller subsets are associated with carbon and energy acquisition (18 genes), and growth rate control (10 genes). This suggests an expanded role for NAC regulation during the nitrogen stress response, where NAC not only regulates genes involved in nitrogen metabolism but also regulates genes involved in balancing carbon and nitrogen pools and growth rate.
Agrobacterium tumefaciensType IV Secretion Protein VirB3 Is an Inner Membrane Protein and Requires VirB4, VirB7, and VirB8 for Stabilization
Authors: Mossey Pamela , Hudacek Andrew , Das Anath 
Published: March 2010

ABSTRACTAgrobacterium tumefaciensVirB proteins assemble a type IV secretion apparatus and a T-pilus for secretion of DNA and proteins into plant cells. The pilin-like protein VirB3, a membrane protein of unknown topology, is required for the assembly of the T-pilus and for T-DNA secretion. Using PhoA and green fluorescent protein (GFP) as periplasmic and cytoplasmic reporters, respectively, we demonstrate that VirB3 contains two membrane-spanning domains and that both the N and C termini of the protein reside in the cytoplasm. Fusion proteins with GFP at the N or C terminus of VirB3 were fluorescent and, like VirB3, localized to a cell pole. Biochemical fractionation studies demonstrated that VirB3 proteins encoded by three Ti plasmids, the octopine Ti plasmid pTiA6NC, the supervirulent plasmid pTiBo542, and the nopaline Ti plasmid pTiC58, are inner membrane proteins and that VirB4 has no effect on membrane localization of pTiA6NC-encoded VirB3 (pTiA6NC VirB3). The pTiA6NC and pTiBo542 VirB2 pilins, like VirB3, localized to the inner membrane. The pTiC58 VirB4 protein was earlier found to be essential for stabilization of VirB3. Stabilization of pTiA6NC VirB3 requires not only VirB4 but also two additional VirB proteins, VirB7 and VirB8. A binary interaction between VirB3 and VirB4/VirB7/VirB8 is not sufficient for VirB3 stabilization. We hypothesize that bacteria use selective proteolysis as a mechanism to prevent assembly of unproductive precursor complexes under conditions that do not favor assembly of large macromolecular structures.
Structure and Protein-Protein Interaction Studies on
Chlamydia trachomatis
Protein CT670 (YscO Homolog)
Authors: Lorenzini Emily , Singer Alexander , Singh Bhag , Lam Robert , Skarina Tatiana , Chirgadze Nickolay Y. , Savchenko Alexei , Gupta Radhey S. 
Published: March 2010

ABSTRACT

Comparative genomic studies have identified many proteins that are found only in various
Chlamydiae
species and exhibit no significant sequence similarity to any protein in organisms that do not belong to this group. The CT670 protein of
Chlamydia trachomatis
is one of the proteins whose genes are in one of the type III secretion gene clusters but whose cellular functions are not known. CT670 shares several characteristics with the YscO protein of
Yersinia pestis
, including the neighboring genes, size, charge, and secondary structure, but the structures and/or functions of these proteins remain to be determined. Although a BLAST search with CT670 did not identify YscO as a related protein, our analysis indicated that these two proteins exhibit significant sequence similarity. In this paper, we report that the CT670 crystal, solved at a resolution of 2 Å, consists of a single coiled coil containing just two long helices. Gel filtration and analytical ultracentrifugation studies showed that in solution CT670 exists in both monomeric and dimeric forms and that the monomer predominates at lower protein concentrations. We examined the interaction of CT670 with many type III secretion system-related proteins (viz., CT091, CT665, CT666, CT667, CT668, CT669, CT671, CT672, and CT673) by performing bacterial two-hybrid assays. In these experiments, CT670 was found to interact only with the CT671 protein (YscP homolog), whose gene is immediately downstream of
ct670
. A specific interaction between CT670 and CT671 was also observed when affinity chromatography pull-down experiments were performed. These results suggest that CT670 and CT671 are putative homologs of the YcoO and YscP proteins, respectively, and that they likely form a chaperone-effector pair.
Two Distantly Homologous DnaG Primases from
Thermoanaerobacter tengcongensis
Exhibit Distinct Initiation Specificities and Priming Activities
Authors: Li Jie , Liu Jingfang , Zhou Ligang , Pei Huadong , Zhou Jian , Xiang Hua 
Published: March 2010

ABSTRACT

Primase, encoded by
dnaG
in bacteria, is a specialized DNA-dependent RNA polymerase that synthesizes RNA primers
de novo
for elongation by DNA polymerase. Genome sequence analysis has revealed two distantly related
dnaG
genes,
TtdnaG
and
TtdnaG
2
, in the thermophilic bacterium
Thermoanaerobacter tengcongensis
. Both TtDnaG (600 amino acids) and TtDnaG2 (358 amino acids) exhibit primase activities
in vitro
at a wide range of temperatures. Interestingly, the template recognition specificities of these two primases are quite distinctive. When trinucleotide-specific templates were tested, TtDnaG initiated RNA primer synthesis efficiently only on templates containing the trinucleotide 5′-CCC-3′, not on the other 63 possible trinucleotides. When the 5′-CCC-3′ sequence was flanked by additional cytosines or guanines, the initiation efficiency of TtDnaG increased remarkably. Significantly, TtDnaG could specifically and efficiently initiate RNA primer synthesis on a limited set of tetranucleotides composed entirely of cytosines and guanines, indicating that TtDnaG initiated RNA primer synthesis more preferably on GC-containing tetranucleotides. In contrast, it seemed that TtDnaG2 had no specific initiation nucleotides, as it could efficiently initiate RNA primer synthesis on all templates tested. The DNA binding affinity of TtDnaG2 was usually 10-fold higher than that of TtDnaG, which might correlate with its high activity but low template specificity. These distinct priming activities and specificities of TtDnaG and TtDnaG2 might shed new light on the diversity in the structure and function of the primases.
Biochemical Characterization of a Novel Indole Prenyltransferase from
Streptomyces
sp. SN-593
Authors: Takahashi Shunji , Takagi Hiroshi , Toyoda Atsushi , Uramoto Masakazu , Nogawa Toshihiko , Ueki Masashi , Sakaki Yoshiyuki , Osada Hiroyuki 
Published: March 2010

ABSTRACT

Genome sequencing of
Streptomyces
species has highlighted numerous potential genes of secondary metabolite biosynthesis. The mining of cryptic genes is important for exploring chemical diversity. Here we report the metabolite-guided genome mining and functional characterization of a cryptic gene by biochemical studies. Based on systematic purification of metabolites from
Streptomyces
sp. SN-593, we isolated a novel compound, 6-dimethylallylindole (DMAI)-3-carbaldehyde. Although many 6-DMAI compounds have been isolated from a variety of organisms, an enzyme catalyzing the transfer of a dimethylallyl group to the C-6 indole ring has not been reported so far. A homology search using known prenyltransferase sequences against the draft sequence of the
Streptomyces
sp. SN-593 genome revealed the
iptA
gene. The IptA protein showed 27% amino acid identity to cyanobacterial LtxC, which catalyzes the transfer of a geranyl group to (−)-indolactam V. A BLAST search against IptA revealed much-more-similar homologs at the amino acid level than LtxC, namely, SAML0654 (60%) from
Streptomyces ambofaciens
ATCC 23877 and SCO7467 (58%) from
S. coelicolor
A3(2). Phylogenetic analysis showed that IptA was distinct from bacterial aromatic prenyltransferases and fungal indole prenyltransferases. Detailed kinetic analyses of IptA showed the highest catalytic efficiency (6.13 min
−1
μM
−1
) for
l
-Trp in the presence of dimethylallyl pyrophosphate (DMAPP), suggesting that the enzyme is a 6-dimethylallyl-
l
-Trp synthase (6-DMATS). Substrate specificity analyses of IptA revealed promiscuity for indole derivatives, and its reaction products were identified as novel 6-DMAI compounds. Moreover, Δ
iptA
mutants abolished the production of 6-DMAI-3-carbaldehyde as well as 6-dimethylallyl-
l
-Trp, suggesting that the
iptA
gene is involved in the production of 6-DMAI-3-carbaldehyde.