bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modes of Overinitiation,dnaAGene Expression, and Inhibition of Cell Division in a Novel Cold-SensitivehdaMutant ofEscherichia coli
Authors: Fujimitsu Kazuyuki , Su'etsugu Masayuki , Yamaguchi Yoko , Mazda Kensaku , Fu Nisi , Kawakami Hironori , Katayama Tsutomu 
Published: May 2008

ABSTRACTThe chromosomal replication cycle is strictly coordinated with cell cycle progression inEscherichia coli. ATP-DnaA initiates replication, leading to loading of the DNA polymerase III holoenzyme. The DNA-loaded form of the β clamp subunit of the polymerase binds the Hda protein, which promotes ATP-DnaA hydrolysis, yielding inactive ADP-DnaA. This regulation is required to repress overinitiation. In this study, we have isolated a novel cold-sensitivehdamutant, thehda-185mutant. Thehda-185mutant caused overinitiation of chromosomal replication at 25°C, which most likely led to blockage of replication fork progress. Consistently, the inhibition of colony formation at 25°C was suppressed by disruption of thediaAgene, an initiation stimulator. Disruption of theseqAgene, an initiation inhibitor, showed synthetic lethality withhda-185even at 42°C. The cellular ATP-DnaA level was increased in anhda-185-dependent manner. The cellular concentrations of DnaA protein anddnaAmRNA were comparable at 25°C to those in a wild-typehdastrain. We also found that multiple copies of the ribonucleotide reductase genes (nrdABornrdEF) ordnaBgene repressed overinitiation. The cellular levels of dATP and dCTP were elevated in cells bearing multiple copies ofnrdAB. The catalytic site within NrdA was required for multicopy suppression, suggesting the importance of an active form of NrdA or elevated levels of deoxyribonucleotides in inhibition of overinitiation in thehda-185cells. Cell division in thehda-185mutant was inhibited at 25°C in a LexA regulon-independent manner, suggesting that overinitiation in thehda-185mutant induced a unique division inhibition pathway.
Glycerol Metabolism and PrfA Activity inListeria monocytogenes
Authors: Joseph Biju , Mertins Sonja , Stoll Regina , Schär Jennifer , Umesha Kanasinakatte Rudrappa , Luo Qin , Müller-Altrock Stefanie , Goebel Werner 
Published: May 2008

ABSTRACTListeria monocytogenesis able to efficiently utilize glycerol as a carbon source. In a defined minimal medium, the growth rate (during balanced growth) in the presence of glycerol is similar to that in the presence of glucose or cellobiose. Comparative transcriptome analyses ofL. monocytogenesshowed high-level transcriptional upregulation of the genes known to be involved in glycerol uptake and metabolism (glpFKandglpD) in the presence of glycerol (compared to that in the presence of glucose and/or cellobiose). Levels of expression of the genes encoding a second putative glycerol uptake facilitator (GlpF2) and a second putative glycerol kinase (GlpK2) were less enhanced under these conditions. GlpK1but not GlpK2was essential for glycerol catabolism inL. monocytogenesunder extracellular conditions, while the loss of GlpK1affected replication in Caco-2 cells less than did the loss of GlpK2and GlpD. Additional genes whose transcription levels were higher in the presence of glycerol than in the presence of glucose and cellobiose included those for two dihydroxyacetone (Dha) kinases and many genes that are under carbon catabolite repression control. Transcriptional downregulation in the presence of glycerol (compared to those in the presence glucose and cellobiose) was observed for several genes and operons that are positively regulated by glucose, including genes involved in glycolysis, N metabolism, and the biosynthesis of branched-chain amino acids. The highest level of transcriptional upregulation was observed for all PrfA-dependent genes during early and late logarithmic growth in glycerol. Under these conditions, a low level of HPr-Ser-P and a high level of HPr-His-P were present in the cells, suggesting that all enzyme IIA (EIIA) (or EIIB) components of the phosphotransferase system (PTS) permeases expressed will be phosphorylated. These and other data suggest that the phosphorylation state of PTS permeases correlates with PrfA activity.
Involvement of Nitrogen Regulation in
Bacillus subtilis degU
Expression
Authors: Yasumura Ayako , Abe Sadanobu , Tanaka Teruo 
Published: May 2008

ABSTRACT

Bacillus subtilis
DegS-DegU belongs to a bacterial two-component system that controls many processes, including the production of exocellular proteases and competence development. It was found that when the glutamine synthetase gene
glnA
, which is involved in nitrogen regulation, was disrupted, the expression of the response regulator
degU
gene was increased. Deletion analysis and 5′-end mapping of the
degU
transcripts showed that the increase was caused by induction of a promoter (P2) located before the
degU
gene. Disruption of
tnrA
, a global regulator of nitrogen regulation, eliminated the P2 promoter induction by the
glnA
mutation. The fact that the P2 promoter is under nitrogen regulation was demonstrated by an increase in P2 expression with nitrogen-limited growth. It was also found by primer extension analysis that
degU
was transcribed by another promoter, P3, that is located downstream of P2. Efficient expression of P3 was dependent on phosphorylated DegU, as inactivation of the sensor kinase gene,
degS
, resulted in the loss of
degU
expression, although less efficient stimulation of
degU
expression was also observed with an enhanced level of DegU in a
degS
-deficient mutant. The promoter located upstream of the
degSU
operon, designated the P1 promoter here, was insensitive to
glnA
and
degU
mutations. These results suggest that
degU
expression is controlled by the three promoters under different growth conditions.
Transient Shielding of Intimin and the Type III Secretion System of Enterohemorrhagic and Enteropathogenic
Escherichia coli
by a Group 4 Capsule
Authors: Shifrin Yulia , Peleg Adi , Ilan Ophir , Nadler Chen , Kobi Simi , Baruch Kobi , Yerushalmi Gal , Berdichevsky Tatiana , Altuvia Shoshy , Elgrably-Weiss Maya , Abe Cecilia , Knutton Stuart , Sasakawa Chihiro , Ritchie Jennifer M. , Waldor Matthew K. , Rosenshine Ilan 
Published: May 2008

ABSTRACT

Enterohemorrhagic and enteropathogenic
Escherichia coli
(EHEC and EPEC, respectively) strains represent a major global health problem. Their virulence is mediated by the concerted activity of an array of virulence factors including toxins, a type III protein secretion system (TTSS), pili, and others. We previously showed that EPEC O127 forms a group 4 capsule (G4C), and in this report we show that EHEC O157 also produces a G4C, whose assembly is dependent on the
etp
,
etk
, and
wzy
genes. We further show that at early time points postinfection, these G4Cs appear to mask surface structures including intimin and the TTSS. This masking inhibited the attachment of EPEC and EHEC to tissue-cultured epithelial cells, diminished their capacity to induce the formation of actin pedestals, and attenuated TTSS-mediated protein translocation into host cells. Importantly, we found that Ler, a positive regulator of intimin and TTSS genes, represses the expression of the capsule-related genes, including
etp
and
etk
. Thus, the expression of TTSS and G4C is conversely regulated and capsule production is diminished upon TTSS expression. Indeed, at later time points postinfection, the diminishing capsule no longer interferes with the activities of intimin and the TTSS. Notably, by using the rabbit infant model, we found that the EHEC G4C is required for efficient colonization of the rabbit large intestine. Taken together, our results suggest that temporal expression of the capsule, which is coordinated with that of the TTSS, is required for optimal EHEC colonization of the host intestine.
Direct Involvement of Type II Secretion System in Extracellular Translocation of
Shewanella oneidensis
Outer Membrane Cytochromes MtrC and OmcA
Authors: Shi Liang , Deng Shuang , Marshall Matthew J. , Wang Zheming , Kennedy David W. , Dohnalkova Alice C. , Mottaz Heather M. , Hill Eric A. , Gorby Yuri A. , Beliaev Alexander S. , Richardson David J. , Zachara John M. , Fredrickson James K. 
Published: May 2008

ABSTRACT
MtrC and OmcA are cell surface-exposed lipoproteins important for reducing solid metal oxides. Deletions of type II secretion system (T2SS) genes reduced their extracellular release and their accessibility to the proteinase K treatment, demonstrating the direct involvement of T2SS in translocation of MtrC and OmcA to the bacterial cell surface.
Hydroquinone Dioxygenase from
Pseudomonas fluorescens
ACB: a Novel Member of the Family of Nonheme-Iron(II)-Dependent Dioxygenases
Authors: Moonen Mariëlle J. H. , Synowsky Silvia A. , van den Berg Willy A. M. , Westphal Adrie H. , Heck Albert J. R. , van den Heuvel Robert H. H. , Fraaije Marco W. , van Berkel Willem J. H. 
Published: May 2008

ABSTRACT

Hydroquinone 1,2-dioxygenase (HQDO), an enzyme involved in the catabolism of 4-hydroxyacetophenone in
Pseudomonas fluorescens
ACB, was purified to apparent homogeneity. Ligandation with 4-hydroxybenzoate prevented the enzyme from irreversible inactivation. HQDO was activated by iron(II) ions and catalyzed the ring fission of a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes. HQDO was inactivated by 2,2′-dipyridyl,
o
-phenanthroline, and hydrogen peroxide and inhibited by phenolic compounds. The inhibition with 4-hydroxybenzoate (
K

i

= 14 μM) was competitive with hydroquinone. Online size-exclusion chromatography-mass spectrometry revealed that HQDO is an α2β2 heterotetramer of 112.4 kDa, which is composed of an α-subunit of 17.8 kDa and a β-subunit of 38.3 kDa. Each β-subunit binds one molecule of 4-hydroxybenzoate and one iron(II) ion. N-terminal sequencing and peptide mapping and sequencing based on matrix-assisted laser desorption ionization—two-stage time of flight analysis established that the HQDO subunits are encoded by neighboring open reading frames (
hapC
and
hapD
) of a gene cluster, implicated to be involved in 4-hydroxyacetophenone degradation. HQDO is a novel member of the family of nonheme-iron(II)-dependent dioxygenases. The enzyme shows insignificant sequence identity with known dioxygenases.
Role of Cell Surface Signaling in Proteolysis of an Alternative Sigma Factor inPseudomonas aeruginosa
Authors: Spencer Matthew R. , Beare Paul A. , Lamont Iain L. 
Published: May 2008

ABSTRACTAlternative sigma factor proteins enable transcription of specific sets of genes in bacterial cells. Their activities can be controlled by posttranslational mechanisms including inhibition by antisigma proteins and proteolytic degradation. PvdS is an alternative sigma factor that is required for expression of genes involved in synthesis of a siderophore, pyoverdine, byPseudomonas aeruginosa. In the absence of pyoverdine, the activity of PvdS is inhibited by a membrane-spanning antisigma factor, FpvR. Inhibition is relieved by a cell surface signaling pathway. In this pathway, a combination of pyoverdine and a cell surface receptor protein, FpvA, suppresses the antisigma activity of FpvR, enabling transcription of PvdS-dependent genes. In this research, we investigated proteolytic degradation of PvdS in response to the signaling pathway. Proteolysis of PvdS was observed in strains ofP. aeruginosain which FpvR had anti-sigma factor activity due to the absence of pyoverdine or the FpvA receptor protein or overproduction of FpvR. Suppression of antisigma activity by addition of pyoverdine or through the absence of FpvR prevented detectable proteolysis of PvdS. The amounts of PvdS were less in bacteria in which proteolysis was observed, and reporter gene assays showed that this reduction was not due to decreased expression of PvdS. In wild-type bacteria, there was an average of 730 molecules of PvdS per cell in late exponential growth phase. Our results show that proteolysis and amounts of PvdS are affected by the antisigma factor FpvR and that this activity of FpvR is controlled by the cell surface signaling pathway.
Are Variable-Number Tandem Repeats Appropriate for GenotypingMycobacterium leprae?
Authors: Monot Marc , Honoré Nadine , Balière Charlotte , Ji Baohong , Sow Samba , Brennan Patrick J. , Cole Stewart T. 
Published: May 2008

ABSTRACTComparative genomics analysis of the Tamil Nadu strain ofMycobacterium lepraehas uncovered several polymorphic sites with potential as epidemiological tools. In this study we compared the stability of two different markers of genomic biodiversity ofM. lepraein several biopsy samples isolated from the same leprosy patient. The first type comprises five different variable-number tandem repeats (VNTR), while the second is composed of three single nucleotide polymorphisms (SNP). Contrasting results were obtained, since no variation was seen in the SNP profiles ofM. lepraefrom 42 patients from 7 different locations in Mali whereas the VNTR profiles varied considerably. Furthermore, since variation in the VNTR pattern was seen not only between different isolates ofM. lepraebut also between biopsy samples from the same patient, these VNTR may be too dynamic for use as epidemiological markers for leprosy.
Practical Method for Detection and Identification of
Candida, Aspergillus
, and
Scedosporium
spp. by Use of Rolling-Circle Amplification
Authors: Zhou Xiaoyong , Kong Fanrong , Sorrell Tania C. , Wang Hui , Duan Yiqun , Chen Sharon C. A. 
Published: May 2008

ABSTRACT

A sensitive rolling-circle amplification (RCA)-based method utilizing species-specific padlock probes targeted to the internal transcribed spacer 2 region of the fungal ribosomal DNA gene complex was developed. The assay was rapid (2 hours) and specific. Of 28 fungal isolates (16 of
Candida
, six of
Aspergillus
, and six of
Scedosporium
spp.), all were all identified correctly.
Primary Human Hepatocytes Are Susceptible to Infection by Hepatitis Delta Virus Assembled with Envelope Proteins of Woodchuck Hepatitis Virus
Authors: Gudima Severin , He Yiping , Chai Ning , Bruss Volker , Urban Stephan , Mason William , Taylor John 
Published: May 2008

ABSTRACT
Hepatitis B virus (HBV) and hepatitis delta virus (HDV) share the HBV envelope proteins. When woodchucks chronically infected with woodchuck hepatitis virus (WHV) are superinfected with HDV, they produce HDV with a WHV envelope, wHDV. Several lines of evidence are provided that wHDV infects not only cultured primary woodchuck hepatocytes (PWH) but also primary human hepatocytes (PHH). Surprisingly, HBV-enveloped HDV (hHDV) and wHDV infected PHH with comparable efficiencies; however, hHDV did not infect PWH. The basis for these host range specificities was investigated using as inhibitors peptides bearing species-specific pre-S (where S is the small envelope protein) sequences. It was found that pre-S1 contributed to the ability of wHDV to infect both PHH and PWH. In addition, the inability of hHDV to infect PWH was not overcome using a chimeric form of hHDV containing WHV S protein, again supporting the essential role of pre-S1 in infection of target cells. One interpretation of these data is that host range specificity of HDV is determined entirely by pre-S1 and that the WHV and HBV pre-S1 proteins recognize different receptors on PHH.
Dimerization of the Papillomavirus E2 Protein Is Required for Efficient Mitotic Chromosome Association and Brd4 Binding
Authors: Cardenas-Mora Juan , Spindler Jonathan E. , Jang Moon Kyoo , McBride Alison A. 
Published: May 2008

ABSTRACT
The E2 proteins of several papillomaviruses link the viral genome to mitotic chromosomes to ensure retention and the efficient partitioning of genomes into daughter cells following cell division. Bovine papillomavirus type 1 E2 binds to chromosomes in a complex with Brd4, a cellular bromodomain protein. Interaction with Brd4 is also important for E2-mediated transcriptional regulation. The transactivation domain of E2 is crucial for interaction with the Brd4 protein; proteins lacking or mutated in this domain do not interact with Brd4. However, we found that the C-terminal DNA binding/dimerization domain of E2 is also required for efficient binding to Brd4. Mutations that eliminated the DNA binding function of E2 had no effect on the ability of E2 to interact with Brd4, but an E2 protein with a mutation that disrupted C-terminal dimerization bound Brd4 with greatly reduced efficiency. Furthermore, E2 proteins in which the C-terminal domains were replaced with the dimeric DNA binding domain of EBNA-1 or Gal4 bound efficiently to the Brd4 protein, but the replacement of the E2 C-terminal domain with a monomeric red fluorescent protein did not rescue efficient Brd4 binding. Thus, E2 bound to Brd4 most efficiently as a dimer. To prove this finding further, the E2 DNA binding domain was replaced with an FKBP12-derived domain in which dimerization was regulated by a bivalent ligand. This fusion protein bound Brd4 efficiently only in the presence of the ligand, confirming that a dimer of E2 was required. Correspondingly, E2 proteins that could dimerize were able to bind to mitotic chromosomes much more efficiently than monomeric E2 polypeptides.
Vpx Is Critical for Reverse Transcription of the Human Immunodeficiency Virus Type 2 Genome in Macrophages
Authors: Fujita Mikako , Otsuka Masami , Miyoshi Masami , Khamsri Boonruang , Nomaguchi Masako , Adachi Akio 
Published: May 2008

ABSTRACT

The abilities of wild-type and
vpx
-defective human immunodeficiency virus type 2 (HIV-2) clones to synthesize viral DNA in human monocyte-derived macrophages (MDMs) and lymphocytic cells were comparatively and quantitatively evaluated. While the
vpx
-defective mutant directed the synthesis of viral DNA comparably to the wild-type virus and normally in lymphocytic cells, no appreciable viral DNA was detected in MDMs infected with the mutant. To substantiate this finding and to determine whether there is some specific region(s) in Vpx crucial for viral DNA synthesis in MDMs, we generated a series of site-specific point mutants of
vpx
and examined their phenotypes. The resultant five mutants, with no infectivity for MDMs, showed, without exception, the same defect as the
vpx
-defective mutant. Our results here clearly demonstrated that the entire Vpx protein is critical for reverse transcription of the HIV-2 genome in human MDMs.
Cystidial structure in two genera of the Russulales
Authors: McLaughlin David J. , Celio Gail J. , Padamsee Mahajabeen , Dentinger Bryn T.M. 
Published: May 2008

As a part of a broader study to determine whether the subcellular structure of cystidia can provide synapomorphies for clades of Agaricomycetes, cystidia of Auriscalpium vulgare Gray and Russula emetica (Schaeff.) Pers. were examined ultrastructurally, after freeze substitution. Vesicles with tubular invaginations occurred in immature hymenial cystidia of both species, and microbodies were also present. Gloeohyphae of A. vulgare also contained these organelles. The tubular invaginations disappeared from the vesicles in maturing cystidia of A. vulgare and were replaced by electron-dense deposits. These patterns of cellular organization may be synapomorphic for the Russulales. The data will be incorporated into the “Assembling the Fungal Tree of Life” (AFTOL) Structural and Biochemical Database to facilitate the use of morphological characters in phylogenetic analyses.
Influence of water chemistry and migratory distance on ability to distinguish progeny of sympatric resident and anadromous rainbow trout (Oncorhynchus mykiss)
Authors: Donohoe Christopher J. , Adams Peter B. , Royer Chantell F. 
Published: May 2008

Otolith Sr:Ca ratios near primordia (Sr:CaCore) have been used to distinguish progeny of resident and anadromous Oncorhynchus mykiss and to estimate rates of exchange between the two forms; however, the influences of confounding variables on Sr:CaCore have not been quantified. We analyzed Sr:CaCore in juvenile O. mykiss produced at 13 California hatcheries that spawn primarily resident or anadromous broodstock. Mean Sr:CaCore of progeny of resident females increased with increasing Sr:Ca ratio of the stream (Sr:CaWater) in which the mother spawned (r2 = 0.71). Mean Sr:CaCore of progeny of anadromous females averaged 1.0 × 10–3 higher, also increased with Sr:CaWater, and decreased with increasing migratory difficulty (distance × elevation) of the mother (r2 = 0.96). Model results predict that discrimination of sympatric progeny is equally good among streams where Sr:CaWater is less than 5 mmol·mol–1, but limited at higher Sr:CaWater or when anadromous females return to freshwater 6 months or more before spawning (e.g., summer steelhead). The models also provide an alternative method of interpreting Sr:CaCore data that can improve discrimination between sympatric progeny. Analysis of adults from one stream and eight hatchery sites suggested that resident females made little or no contribution to populations of anadromous adults, but anadromous females contributed to populations of resident adults.
The role of temperature in controlling diel activity in upstream migrant sea lampreys (Petromyzon marinus)
Authors: Binder Thomas R. , McDonald D. Gordon 
Published: May 2008

This study used controlled laboratory conditions to directly assess the role of temperature in controlling diel activity in sexually immature, upstream migrant sea lampreys ( Petromyzon marinus ). Our results identified three separate temperature-induced changes to the normal nocturnal activity pattern of lampreys: (i) at low temperature (7 °C), lampreys became inactive; (ii) at high temperatures (≥20 °C), the normal nocturnal peak in activity was reduced and lampreys became active during the day; and (iii) rapid increases in temperature (7 or 8 °C over 4 h) stimulated transient daytime activity that subsided once temperature stabilized. In addition, we found evidence that temperature directly influences other aspects of sea lampreys behaviour, specifically light avoidance and rheotaxis. We propose that temperature-induced changes in diel activity represent adaptive behaviour, increasing the probability of lampreys reaching the spawning grounds within the narrow thermal range for successful embryonic development.
Biblical Feminisms: Knowledge, Theory and Politics in the Study of Women in the Hebrew Bible
Authors: Fuchs Esther 
Published: May 2008

AbstractThe proliferation of biblical feminist interpretations and readings in the last two decades suggests that we may witness the emergence of an autonomous field of studies. In this essay I suggest that in order for such a field to emerge as an autonomous and thriving area of academic inquiry we must begin to think theoretically and critically about the work that has been done, the objectives of this work and the relationships between and among various approaches to the field. In this essay I call for a rigorous and critical biblical feminist epistemology that seeks to address on every turn the question of knowledge production as power; on the other hand I call for a radical democratization of the field and the questioning of any and all orthodoxies and hierarchies that may have already emerged in the field. The first "centripetal" approach insists on clarifying the foundations of the field, establishing genealogies of knowledge and an evolutionary trajectory, crediting and acknowledging theoretical points of origination. Respect for precedence and antecedence is required so as to avoid repetition, imitation and dilution. The second "centrifugal" approach emphasizes the need for interrogating, displacing and destabilizing foundational paradigms in Biblical Studies at large and for the continued questioning of stable identities of "women" as subjects and objects of inquiry. A vigorous field of Feminist Biblical Studies ought to deploy both approaches opening the way to both debate and contestation between various feminist approaches to the Bible on the one hand and to dialogue and alliance between methodologically, theoretically, politically and culturally different approaches on the other.