bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription Antitermination by Translation Initiation Factor IF1
Authors: Phadtare Sangita , Kazakov Teymur , Bubunenko Mikhail , Court Donald L. , Pestova Tatyana , Severinov Konstantin 
Published: March 2007

ABSTRACT

Bacterial translation initiation factor IF1 is an S1 domain protein that belongs to the oligomer binding (OB) fold proteins. Cold shock domain (CSD)-containing proteins such as CspA (the major cold shock protein of
Escherichia coli
) and its homologues also belong to the OB fold protein family. The striking structural similarity between IF1 and CspA homologues suggests a functional overlap between these proteins. Certain members of the CspA family of cold shock proteins act as nucleic acid chaperones: they melt secondary structures in nucleic acids and act as transcription antiterminators. This activity may help the cell to acclimatize to low temperatures, since cold-induced stabilization of secondary structures in nascent RNA can impede transcription elongation. Here we show that the
E. coli
translation initiation factor, IF1, also has RNA chaperone activity and acts as a transcription antiterminator in vivo and in vitro. We further show that the RNA chaperone activity of IF1, although critical for transcription antitermination, is not essential for its role in supporting cell growth, which presumably functions in translation. The results thus indicate that IF1 may participate in transcription regulation and that cross talk and/or functional overlap may exist between the Csp family proteins, known to be involved in transcription regulation at cold shock, and S1 domain proteins, known to function in translation.
Mycobacterium tuberculosis
SigF Regulates Genes Encoding Cell Wall-Associated Proteins and Directly Regulates the Transcriptional Regulatory Gene
phoY1
Authors: Williams Ernest P. , Lee Jong-Hee , Bishai William R. , Colantuoni Carlo , Karakousis Petros C. 
Published: March 2007

ABSTRACT

Mycobacterium tuberculosis
SigF is homologous to stress response and sporulation sigma factors in many bacteria. Consistent with a possible role in mycobacterial survival under stress conditions,
M. tuberculosis sigF
is strongly induced within cultured human macrophages and upon nutrient starvation, and SigF has been implicated in
M. tuberculosis
entry into stationary phase. On the other hand, SigF appears to contribute to the immune pathology of tuberculosis (TB), and a
sigF
-deficient mutant has altered cell membrane properties. Using an
M. tuberculosis sigF
deletion mutant, we show here that
sigF
is not required for bacillary survival under nutrient starvation conditions and within activated murine macrophages or for extracellular persistence in an in vivo granuloma model of latent TB infection. Using a chemically inducible recombinant strain to conditionally overexpress
sigF
, we did not observe arrest or retardation of growth in exponentially growing cultures or reduced susceptibility to rifampin and isoniazid. Consistent with our hypothesis that SigF may mediate TB immunopathogenesis by altering cell membrane properties, we found that overexpression of
sigF
resulted in the differential regulation of many cell wall-associated proteins, including members of the MmpL, PE, and PPE families, several of which have been shown to influence host-pathogen interactions. The most highly upregulated gene by quantitative reverse transcription-PCR at all time points following
sigF
induction was Rv3301c (
phoY1
), which encodes a probable transcriptional regulatory protein homologous to PhoU proteins involved in regulation of phosphate uptake. Using in vitro transcription analysis, we show that SigF directly regulates
phoY1
, whose proposed promoter sequence is GGATTG-N
16
-GGGTAT.
Multidrug-ResistantSalmonella entericaSerovar Paratyphi A Harbors IncHI1 Plasmids Similar to Those Found in Serovar Typhi
Authors: Holt Kathryn E. , Thomson Nicholas R. , Wain John , Phan Minh Duy , Nair Satheesh , Hasan Rumina , Bhutta Zulfiqar A. , Quail Michael A. , Norbertczak Halina , Walker Danielle , Dougan Gordon , Parkhill Julian 
Published: March 2007

ABSTRACTSalmonella entericaserovars Typhi and Paratyphi A cause systemic infections in humans which are referred to as enteric fever. Multidrug-resistant (MDR) serovar Typhi isolates emerged in the 1980s, and in recent years MDR serovar Paratyphi A infections have become established as a significant problem across Asia. MDR in serovar Typhi is almost invariably associated with IncHI1 plasmids, but the genetic basis of MDR in serovar Paratyphi A has remained predominantly undefined. The DNA sequence of an IncHI1 plasmid, pAKU_1, encoding MDR in a serovar Paratyphi A strain has been determined. Significantly, this plasmid shares a common IncHI1-associated DNA backbone with the serovar Typhi plasmid pHCM1 and anS. entericaserovar Typhimurium plasmid pR27. Plasmids pAKU_1 and pHCM1 share 14 antibiotic resistance genes encoded within similar mobile elements, which appear to form a 24-kb composite transposon that has transferred as a single unit into different positions into their IncHI1 backbones. Thus, these plasmids have acquired similar antibiotic resistance genes independently via the horizontal transfer of mobile DNA elements. Furthermore, two IncHI1 plasmids from a Vietnamese isolate of serovar Typhi were found to contain features of the backbone sequence of pAKU_1 rather than pHCM1, with the composite transposon inserted in the same location as in the pAKU_1 sequence. Our data show that these serovar Typhi and Paratyphi A IncHI1 plasmids share highly conserved core DNA and have acquired similar mobile elements encoding antibiotic resistance genes in past decades.
Coexistence of Two Distinct Versions of O-Antigen Polymerase, Wzy-Alpha and Wzy-Beta, in
Pseudomonas aeruginosa
Serogroup O2 and Their Contributions to Cell Surface Diversity
Authors: Kaluzny Katarina , Abeyrathne Priyanka D. , Lam Joseph S. 
Published: March 2007

ABSTRACT

Assembly of B-band lipopolysaccharide (LPS) in
Pseudomonas aeruginosa
follows a Wzy-dependent pathway, requiring the O-antigen polymerase Wzy and other proteins. The peptide sequences of the
wzy
α
product from strains of serotypes O2, O5, and O16 are identical, but the O units in O5 are α-glycosidically linked, while those in O2 and O16 are β-linked. We hypothesized that a derivative of the D3 bacteriophage
wzy
β
is present in the chromosomes of O2 and O16 and that this gene is responsible for the β-linkage. By a combination of PCR and primer walking,
wzy
β
genes of both serotypes have been amplified and cloned. They are identical but share only 87.42% sequence identity with their xenolog in D3. A chromosomal knockout mutant of O16
wzy
β
was made, and it produces semirough LPS devoid of B-band O antigen. The cloned
wzy
β
is capable of complementing the O16
wzy
β
mutant, as well as cross-complementing a
wzy
α
knockout mutant. However, in the latter case, the restored O antigen was β-linked. Using reverse transcription-PCR, we showed that
wzy
α
was transcribed in O2 and O16 strains and was functional, since both of these genes could complement the
wzy
α
mutant of O5. With the coexistence of
wzy
α
and
wzy
β
in O2 and O16 and the B-band O polysaccharides in these being β-linked, we hypothesized that
iap
, an inhibitor of the alpha-polymerase gene, must be present in these serotypes. Indeed, through PCR, TOPO-cloning, and nucleotide-sequencing results, we verified the presence of
iap
in both O2 and O16 serotypes.
Roles of His-Rich Hpn and Hpn-Like Proteins in
Helicobacter pylori
Nickel Physiology
Authors: Seshadri Susmitha , Benoit Stéphane L. , Maier Robert J. 
Published: March 2007

ABSTRACT

Individual gene-targeted
hpn
and
hpn
-like mutants and a mutant with mutations in both
hpn
genes were more sensitive to nickel, cobalt, and cadmium toxicity than was the parent strain, with the
hpn
-like strain showing the most metal sensitivity of the two individual His-rich protein mutants. The mutant strains contained up to eightfold more urease activity than the parent under nickel-deficient conditions, and the parent strain was able to achieve mutant strain activity levels by nickel supplementation. The mutants contained 3- to 4-fold more and the double mutant about 10-fold more Ni associated with their total urease pools, even though all of the strains expressed similar levels of total urease protein. Hydrogenase activities in the mutants were like those in the parent strain; thus, hydrogenase is fully activated under nickel-deficient conditions. The histidine-rich proteins appear to compete with the Ni-dependent urease maturation machinery under low-nickel conditions. Upon lowering the pH of the growth medium from 7.3 to 5, the wild-type urease activity increased threefold, but the activity in the three mutant strains was relatively unaffected. This pH effect was attributed to a nickel storage role for the His-rich proteins. Under low-nickel conditions, the addition of a nickel chelator did not significantly affect the urease activity of the wild type but decreased the activity of all of the mutants, supporting a role for the His-rich proteins as Ni reservoirs. These nickel reservoirs significantly impact the active urease activities achieved. The His-rich proteins play dual roles, as Ni storage and as metal detoxification proteins, depending on the exogenous nickel levels.
Construction of Recombinant Hemagglutinin Derived from the Gingipain-Encoding Gene of
Porphyromonas gingivalis
, Identification of Its Target Protein on Erythrocytes, and Inhibition of Hemagglutination by an Interdomain Regional Peptide
Authors: Sakai Eiko , Naito Mariko , Sato Keiko , Hotokezaka Hitoshi , Kadowaki Tomoko , Kamaguchi Arihide , Yamamoto Kenji , Okamoto Kuniaki , Nakayama Koji 
Published: March 2007

ABSTRACT

Porphyromonas gingivalis
, an anaerobic gram-negative bacterium associated with chronic periodontitis, can agglutinate human erythrocytes. In general, hemagglutination can be considered the ability to adhere to host cells; however,
P. gingivalis
-mediated hemagglutination has special significance because heme markedly accelerates growth of this bacterium. Although a number of studies have indicated that a major hemagglutinin of
P. gingivalis
is intragenically encoded by
rgpA
,
kgp
, and
hagA
, direct evidence has not been obtained. We demonstrated in this study that recombinant HGP44
720-1081
, a fully processed HGP44 domain protein, had hemagglutinating activity but that an unprocessed form, HGP44
720-1138
, did not. A peptide corresponding to residues 1083 to 1102, which was included in HGP44
720-1138
but not in HGP44
720-1081
, could bind HGP44
720-1081
in a dose-dependent manner and effectively inhibited HGP44
720-1081
-mediated hemagglutination, indicating that the interdomain regional amino acid sequence may function as an intramolecular suppressor of hemagglutinating activity. Analyses by solid-phase binding and chemical cross-linking suggested that HGP44 interacted with glycophorin A on the erythrocyte membrane. Glycophorin A and, more effectively, asialoglycophorin, which were added exogenously, inhibited HGP44
720-1081
-mediated hemagglutination. Treatment of erythrocytes with RgpB proteinase resulted in degradation of glycophorin A on the membrane and a decrease in HGP44
720-1081
-mediated hemagglutination. Surface plasmon resonance detection analysis revealed that HGP44
720-1081
could bind to asialoglycophorin with a dissociation constant of 3.0 × 10
−7
M. These results indicate that the target of HGP44 on the erythrocyte membrane appears to be glycophorin A.
Mutations in
rsmG
, Encoding a 16S rRNA Methyltransferase, Result in Low-Level Streptomycin Resistance and Antibiotic Overproduction in
Streptomyces coelicolor
A3(2)
Authors: Nishimura Kenji , Hosaka Takeshi , Tokuyama Shinji , Okamoto Susumu , Ochi Kozo 
Published: March 2007

ABSTRACT

Certain
str
mutations that confer high- or low-level streptomycin resistance result in the overproduction of antibiotics by
Streptomyces
spp. The
str
mutations that confer the high-level resistance occur within
rpsL
, which encodes the ribosomal protein S12, while those that cause low-level resistance are not as well known. We have used comparative genome sequencing to determine that low-level resistance is caused by mutations of
rsmG
, which encodes an
S
-adenosylmethionine (SAM)-dependent 16S rRNA methyltransferase containing a SAM binding motif. Deletion of
rsmG
from wild-type
Streptomyces coelicolor
resulted in the acquisition of streptomycin resistance and the overproduction of the antibiotic actinorhodin. Introduction of wild-type
rsmG
into the deletion mutant completely abrogated the effects of the
rsmG
deletion, confirming that
rsmG
mutation underlies the observed phenotype. Consistent with earlier work using a spontaneous
rsmG
mutant, the strain carrying
ΔrsmG
exhibited increased SAM synthetase activity, which mediated the overproduction of antibiotic. Moreover, high-performance liquid chromatography analysis showed that the
ΔrsmG
mutant lacked a 7-methylguanosine modification in the 16S rRNA (possibly at position G518, which corresponds to G527 of
Escherichia coli
). Like certain
rpsL
mutants, the
ΔrsmG
mutant exhibited enhanced protein synthetic activity during the late growth phase. Unlike
rpsL
mutants, however, the
ΔrsmG
mutant showed neither greater stability of the 70S ribosomal complex nor increased expression of ribosome recycling factor, suggesting that the mechanism underlying increased protein synthesis differs in the
rsmG
and the
rpsL
mutants. Finally, spontaneous
rsmG
mutations arose at a 1,000-fold-higher frequency than
rpsL
mutations. These findings provide new insight into the role of rRNA modification in activating secondary metabolism in
Streptomyces
.
Transcriptomic Analysis Identifies Growth Rate Modulation as a Component of the Adaptation of Mycobacteria to Survival inside the Macrophage
Authors: Beste D. J. V. , Laing E. , Bonde B. , Avignone-Rossa C. , Bushell M. E. , McFadden J. J. 
Published: March 2007

ABSTRACT

The adaptation of the tubercle bacillus to the host environment is likely to involve a complex set of gene regulatory events and physiological switches in response to environmental signals. In order to deconstruct the physiological state of
Mycobacterium tuberculosis
in vivo, we used a chemostat model to study a single aspect of the organism's in vivo state, slow growth.
Mycobacterium bovis
BCG was cultivated at high and low growth rates in a carbon-limited chemostat, and transcriptomic analysis was performed to identify the gene regulation events associated with slow growth. The results demonstrated that slow growth was associated with the induction of expression of several genes of the dormancy survival regulon. There was also a striking overlap between the transcriptomic profile of BCG in the chemostat model and the response of
M. tuberculosis
to growth in the macrophage, implying that a significant component of the response of the pathogen to the macrophage environment is the response to slow growth in carbon-limited conditions. This demonstrated the importance of adaptation to a low growth rate to the virulence strategy of
M. tuberculosis
and also the value of the chemostat model for deconstructing components of the in vivo state of this important pathogen.
Transcription of All
amoC
Copies Is Associated with Recovery of
Nitrosomonas europaea
from Ammonia Starvation
Authors: Berube Paul M. , Samudrala Ram , Stahl David A. 
Published: March 2007

ABSTRACT

The chemolithotrophic ammonia-oxidizing bacterium
Nitrosomonas europaea
is known to be highly resistant to starvation conditions. The transcriptional response of
N. europaea
to ammonia addition following short- and long-term starvation was examined by primer extension and S1 nuclease protection analyses of genes encoding enzymes for ammonia oxidation (
amoCAB
operons) and CO
2
fixation (
cbbLS
), a third, lone copy of
amoC
(
amoC

3

), and two representative housekeeping genes (
glyA
and
rpsJ
). Primer extension analysis of RNA isolated from growing, starved, and recovering cells revealed two differentially regulated promoters upstream of the two
amoCAB
operons. The distal σ
70
type
amoCAB
promoter was constitutively active in the presence of ammonia, but the proximal promoter was only active when cells were recovering from ammonia starvation. The lone, divergent copy of
amoC
(
amoC

3

) was expressed only during recovery. Both the proximal
amoC

1
,
2

promoter and the
amoC

3

promoter are similar to gram-negative σ
E
promoters, thus implicating σ
E
in the regulation of the recovery response. Although modeling of subunit interactions suggested that a nonconservative proline substitution in AmoC
3
may modify the activity of the holoenzyme, characterization of a Δ
amoC

3

strain showed no significant difference in starvation recovery under conditions evaluated. In contrast to the
amo
transcripts, a delayed appearance of transcripts for a gene required for CO
2
fixation (
cbbL
) suggested that its transcription is retarded until sufficient energy is available. Overall, these data revealed a programmed exit from starvation likely involving regulation by σ
E
and the coordinated regulation of catabolic and anabolic genes.
Descriptive Profile of Hip Rotation Range of Motion in Elite Tennis Players and Professional Baseball Pitchers
Authors: Ellenbecker Todd S. , Ellenbecker Gail A. , Roetert E. Paul , Silva Rogerio Teixeira , Keuter Greg , Sperling Fabio 
Published: March 2007

Background Repetitive loading to the hip joint in athletes has been reported as a factor in the development of degenerative joint disease and intra-articular injury. Little information is available on the bilateral symmetry of hip rotational measures in unilaterally dominant upper extremity athletes. Hypothesis Side-to-side differences in hip joint range of motion may be present because of asymmetrical loading in the lower extremities of elite tennis players and professional baseball pitchers. Study Design Cohort (cross-sectional) study (prevalence); Level of evidence, 1. Methods Descriptive measures of hip internal and external rotation active range of motion were taken in the prone position of 64 male and 83 female elite tennis players and 101 male professional baseball pitchers using digital photos and computerized angle calculation software. Bilateral differences in active range of motion between the dominant and nondominant hip were compared using paired t tests and Bonferroni correction for hip internal, external, and total rotation range of motion. A Pearson correlation test was used to test the relationship between years of competition and hip rotation active range of motion. Results No significant bilateral difference (P > .005) was measured for mean hip internal or external rotation for the elite tennis players or the professional baseball pitchers. An analysis of the number of subjects in each group with a bilateral difference in hip rotation greater than 10° identified 17% of the professional baseball pitchers with internal rotation differences and 42% with external rotation differences. Differences in the elite male tennis players occurred in only 15% of the players for internal rotation and 9% in external rotation. Female subjects had differences in 8% and 12% of the players for internal and external rotation, respectively. Statistical differences were found between the mean total arc of hip range of internal and external rotation in the elite tennis players with the dominant side being greater by a clinically insignificant mean value of 2.5°. Significantly less (P < .005) dominant hip internal rotation and less dominant and nondominant hip total rotation range of motion were found in the professional baseball pitchers compared with the elite male tennis players. Conclusion This study established typical range of motion patterns and identified bilaterally symmetric hip active range of motion rotation values in elite tennis players and professional baseball pitchers. Asymmetric hip joint rotational active range of motion encountered during clinical examination and screening may indicate abnormalities and would indicate the application of flexibility training, rehabilitation, and further evaluation.
JS-K, a GST-activated nitric oxide generator, induces DNA double-strand breaks, activates DNA damage response pathways, and induces apoptosis in vitro and in vivo in human multiple myeloma cells
Authors: Kiziltepe Tanyel , Hideshima Teru , Ishitsuka Kenji , Ocio Enrique M. , Raje Noopur , Catley Laurence , Li Chun-Qi , Trudel Laura J. , Yasui Hiroshi , Vallet Sonia , Kutok Jeffery L. , Chauhan Dharminder , Mitsiades Constantine S. , Saavedra Joseph E. , Wogan Gerald N. , Keefer Larry K. , Shami Paul J. , Anderson Kenneth C. 
Published: March 2007

AbstractHere we investigated the cytotoxicity of JS-K, a prodrug designed to release nitric oxide (NO•) following reaction with glutathione S-transferases, in multiple myeloma (MM). JS-K showed significant cytotoxicity in both conventional therapy-sensitive and -resistant MM cell lines, as well as patient-derived MM cells. JS-K induced apoptosis in MM cells, which was associated with PARP, caspase-8, and caspase-9 cleavage; increased Fas/CD95 expression; Mcl-1 cleavage; and Bcl-2 phosphorylation, as well as cytochrome c, apoptosis-inducing factor (AIF), and endonuclease G (EndoG) release. Moreover, JS-K overcame the survival advantages conferred by interleukin-6 (IL-6) and insulin-like growth factor 1 (IGF-1), or by adherence of MM cells to bone marrow stromal cells. Mechanistic studies revealed that JS-K–induced cytotoxicity was mediated via NO• in MM cells. Furthermore, JS-K induced DNA double-strand breaks (DSBs) and activated DNA damage responses, as evidenced by neutral comet assay, as well as H2AX, Chk2 and p53 phosphorylation. JS-K also activated c-Jun NH2-terminal kinase (JNK) in MM cells; conversely, inhibition of JNK markedly decreased JS-K–induced cytotoxicity. Importantly, bortezomib significantly enhanced JS-K–induced cytotoxicity. Finally, JS-K is well tolerated, inhibits tumor growth, and prolongs survival in a human MM xenograft mouse model. Taken together, these data provide the preclinical rationale for the clinical evaluation of JS-K to improve patient outcome in MM.