bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coli
NsrR Regulates a Pathway for the Oxidation of 3-Nitrotyramine to 4-Hydroxy-3-Nitrophenylacetate
Authors: Rankin Linda D. , Bodenmiller Diane M. , Partridge Jonathan D. , Nishino Shirley F. , Spain Jim C. , Spiro Stephen 
Published: July 2008

ABSTRACT

Chromatin immunoprecipitation and microarray (ChIP-chip) analysis showed that the nitric oxide (NO)-sensitive repressor NsrR from
Escherichia coli
binds in vivo to the promoters of the
tynA
and
feaB
genes. These genes encode the first two enzymes of a pathway that is required for the catabolism of phenylethylamine (PEA) and its hydroxylated derivatives tyramine and dopamine. Deletion of
nsrR
caused small increases in the activities of the
tynA
and
feaB
promoters in cultures grown on PEA. Overexpression of
nsrR
severely retarded growth on PEA and caused a marked repression of the
tynA
and
feaB
promoters. Both the growth defect and the promoter repression were reversed in the presence of a source of NO. These results are consistent with NsrR mediating repression of the
tynA
and
feaB
genes by binding (in an NO-sensitive fashion) to the sites identified by ChIP-chip.
E. coli
was shown to use 3-nitrotyramine as a nitrogen source for growth, conditions which partially induce the
tynA
and
feaB
promoters. Mutation of
tynA
(but not
feaB
) prevented growth on 3-nitrotyramine. Growth yields, mutant phenotypes, and analyses of culture supernatants suggested that 3-nitrotyramine is oxidized to 4-hydroxy-3-nitrophenylacetate, with growth occurring at the expense of the amino group of 3-nitrotyramine. Accordingly, enzyme assays showed that 3-nitrotyramine and its oxidation product (4-hydroxy-3-nitrophenylacetaldehyde) could be oxidized by the enzymes encoded by
tynA
and
feaB
, respectively. The results suggest that an additional physiological role of the PEA catabolic pathway is to metabolize nitroaromatic compounds that may accumulate in cells exposed to NO.
The Helix-Loop-Helix Motif at the N Terminus of HalI Is Essential for Its Immunity Function against Halocin C8
Authors: Mei Shuangshuang , Sun Chaomin , Liu Xiaoqing , Lu Qiuhe , Cai Lei , Li Yun , Xiang Hua 
Published: July 2008

ABSTRACT
Halocin C8 (HalC8) is a stable microhalocin exhibiting strong antimicrobial activity against a wide range of haloarchaea. HalI, a 207-amino-acid peptide derived from the N terminus of the HalC8 preproprotein, is the immunity protein of HalC8. In this study, the molecular mechanism of the immunity function of HalI was investigated. Both pull-down and surface plasmon resonance assays revealed that HalI directly interacted with HalC8, and a mixture of purified HalI and HalC8 readily formed a heterocomplex, which was verified by gel filtration. Interestingly, HalC8 tended to form a self-associated complex, and one immunity protein likely sequestered multiple halocins. Significantly, the helix-loop-helix (HLH) motif containing a 4-amino-acid repeat (RELA) at the N terminus of HalI played a key role in its immunity activity. Disruption of the HLH motif or mutagenesis of the key residues of the RELA repeat resulted in loss of both the immunity function and the ability of HalI to bind to HalC8. These results demonstrated that HalI sequestered the activity of HalC8 through specific and direct binding.
Formation ofStreptococcus pneumoniaeNon-Phase-Variable Colony Variants Is Due to Increased Mutation Frequency Present under Biofilm Growth Conditions
Authors: Allegrucci Magee , Sauer Karin 
Published: July 2008

ABSTRACTIn this report, we show that biofilm formation byStreptococcus pneumoniaeserotype 19 gives rise to variants (the small mucoid variant [SMV] and the acapsular small-colony variant [SCV]) differing in capsule production, attachment, and biofilm formation compared to wild-type strains. All biofilm-derived variants harbored SNPs incps19F. SCVs reverted to SMV, but no reversion to the wild-type phenotype was noted, indicating that these variants were distinct from opaque- and transparent-phase variants. The SCV-SMV reversion frequency was dependent on growth conditions and treatment with tetracycline. Increased reversion rates were coincident with antibiotic treatment, implicating oxidative stress as a trigger for the SCV-SMV switch. We, therefore, evaluated the role played by hydrogen peroxide, the oxidizing chemical, in the reversion and emergence of variants. Biofilms ofS. pneumoniaeTIGR4-ΔspxB, defective in hydrogen peroxide production, showed a significant reduction in variant formation. Similarly, supplementing the medium with catalase or sodium thiosulfate yielded a significant reduction in variants formed by wild-type biofilms. Resistance to rifampin, an indicator for mutation frequency, was found to increase approximately 55-fold in biofilms compared to planktonic cells for each of the three wild-type strains examined. In contrast, TIGR4-ΔspxBgrown as a biofilm showed no increase in rifampin resistance compared to the same cells grown planktonically. Furthermore, addition of 2.5 and 10 mM hydrogen peroxide to planktonic cells resulted in a 12- and 160-fold increase in mutation frequency, respectively, and gave rise to variants similar in appearance, biofilm-related phenotypes, and distribution of biofilm-derived variants. The results suggest that hydrogen peroxide and environmental conditions specific to biofilms are responsible for the development of non-phase-variable colony variants.
Identification of Functional Tat Signal Sequences in
Mycobacterium tuberculosis
Proteins
Authors: McDonough Justin A. , McCann Jessica R. , Tekippe Erin McElvania , Silverman Jason S. , Rigel Nathan W. , Braunstein Miriam 
Published: July 2008

ABSTRACT

The twin-arginine translocation (Tat) pathway is a system used by some bacteria to export proteins out from the cytosol to the cell surface or extracellular environment. A functional Tat pathway exists in the important human pathogen
Mycobacterium tuberculosis
. Identification of the substrates exported by the Tat pathway can help define the role that this pathway plays in the physiology and pathogenesis of
M. tuberculosis
. Here we used a reporter of Tat export, a truncated β-lactamase, ′BlaC, to experimentally identify
M. tuberculosis
proteins with functional Tat signal sequences. Of the 13 proteins identified, one lacks the hallmark of a Tat-exported substrate, the twin-arginine dipeptide, and another is not predicted by in silico analysis of the annotated
M. tuberculosis
genome. Full-length versions of a subset of these proteins were tested to determine if the native proteins are Tat exported. For three proteins, expression in a Δ
tat
mutant of
Mycobacterium smegmatis
revealed a defect in precursor processing compared to expression in the wild type, indicating Tat export of the full-length proteins. Conversely, two proteins showed no obvious Tat export in
M. smegmatis
. One of this latter group of proteins was the
M. tuberculosis
virulence factor phospholipase C (PlcB). Importantly, when tested in
M. tuberculosis
a different result was obtained and PlcB was exported in a twin-arginine-dependent manner. This suggests the existence of an
M. tuberculosis
-specific factor(s) for Tat export of a proven virulence protein. It also emphasizes the importance of domains beyond the Tat signal sequence and bacterium-specific factors in determining if a given protein is Tat exported.
Formate-Dependent Autotrophic Growth in
Sinorhizobium meliloti
Authors: Pickering Brad S. , Oresnik Ivan J. 
Published: July 2008

ABSTRACT

It was found that
S. meliloti
strain SmA818, which is cured of pSymA, could not grow on defined medium containing only formate and bicarbonate as carbon sources. Growth experiments showed that Rm1021 was capable of formate/bicarbonate-dependent growth, suggesting that it was capable of autotrophic-type growth. The annotated genome of
S. meliloti
Rm1021 contains three formate dehydrogenase genes. A systematic disruption of each of the three formate dehydrogenase genes, as well as the genes encoding determinants of the Calvin-Benson-Bassham, cycle was carried out to determine which of these determinants played a role in growth on this defined medium. The results showed that
S. meliloti
is capable of formate-dependent autotrophic growth. Formate-dependent autotrophic growth is dependent on the presence of the chromosomally located
fdsABCDG
operon, as well as the
cbb
operon carried by pSymB. Growth was also dependent on the presence of either of the two triose-phosphate isomerase genes (
tpiA
or
tpiB
) that are found in the genome. In addition, it was found that
fdoGHI
carried by pSymA encodes a formate dehydrogenase that allows Rm1021 to carry out formate-dependent respiration. Taken together, the data allow us to present a model of how
S. meliloti
can grow on defined medium containing only formate and bicarbonate as carbon sources.
Identification of Sesquiterpene Synthases fromNostoc punctiformePCC 73102 andNostocsp. Strain PCC 7120
Authors: Agger Sean A. , Lopez-Gallego Fernando , Hoye Thomas R. , Schmidt-Dannert Claudia 
Published: July 2008

ABSTRACTCyanobacteria are a rich source of natural products and are known to produce terpenoids. These bacteria are the major source of the musty-smelling terpenes geosmin and 2-methylisoborneol, which are found in many natural water supplies; however, no terpene synthases have been characterized from these organisms to date. Here, we describe the characterization of three sesquiterpene synthases identified inNostocsp. strain PCC 7120 (terpene synthase NS1) andNostoc punctiformePCC 73102 (terpene synthases NP1 and NP2). The second terpene synthase inN. punctiforme(NP2) is homologous to fusion-type sesquiterpene synthases fromStreptomycesspp. shown to produce geosmin via an intermediate germacradienol. The enzymes were functionally expressed inEscherichia coli, and their terpene products were structurally identified as germacrene A (from NS1), the eudesmadiene 8a-epi-α-selinene (from NP1), and germacradienol (from NP2). The product of NP1, 8a-epi-α-selinene, so far has been isolated only from termites, in which it functions as a defense compound. Terpene synthases NP1 and NS1 are part of an apparent minicluster that includes a P450 and a putative hybrid two-component protein located downstream of the terpene synthases. Coexpression of P450 genes with their adjacent located terpene synthase genes inE. colidemonstrates that the P450 fromNostocsp. can be functionally expressed inE. coliwhen coexpressed with a ferredoxin gene and a ferredoxin reductase gene fromNostocand that the enzyme oxygenates the NS1 terpene product germacrene A. This represents to the best of our knowledge the first example of functional expression of a cyanobacterial P450 inE. coli.
Identification and Characterization of the Dicarboxylate Uptake System DccT inCorynebacterium glutamicum
Authors: Youn Jung-Won , Jolkver Elena , Krämer Reinhard , Marin Kay , Wendisch Volker F. 
Published: July 2008

ABSTRACTMany bacteria can utilize C4-carboxylates as carbon and energy sources. However,Corynebacterium glutamicumATCC 13032 is not able to use tricarboxylic acid cycle intermediates such as succinate, fumarate, andl-malate as sole carbon sources. Upon prolonged incubation, spontaneous mutants which had gained the ability to grow on succinate, fumarate, andl-malate could be isolated. DNA microarray analysis showed higher mRNA levels of cg0277, which subsequently was nameddccT, in the mutants than in the wild type, and transcriptional fusion analysis revealed that a point mutation in the promoter region ofdccTwas responsible for increased expression. The overexpression ofdccTwas sufficient to enable theC. glutamicumwild type to grow on succinate, fumarate, andl-malate as the sole carbon sources. Biochemical analyses revealed that DccT, which is a member of the divalent anion/Na+symporter family, catalyzes the effective uptake of dicarboxylates like succinate, fumarate,l-malate, and likely also oxaloacetate in a sodium-dependent manner.
Transcription Activation by NtcA and 2-Oxoglutarate of Three Genes Involved in Heterocyst Differentiation in the Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Valladares Ana , Flores Enrique , Herrero Antonia 
Published: July 2008

ABSTRACT

In
Anabaena
sp. strain PCC 7120, differentiation of heterocysts takes place in response to the external cue of combined nitrogen deprivation, allowing the organism to fix atmospheric nitrogen in oxic environments. NtcA, a global transcriptional regulator of cyanobacteria, is required for activation of the expression of multiple genes involved in heterocyst differentiation, including key regulators that are specific to the process. We have set up a fully defined in vitro system, which includes the purified
Anabaena
RNA polymerase, and have studied the effects of NtcA and its signaling effector 2-oxoglutarate on RNA polymerase binding, open complex formation, and transcript production from promoters of the
hetC
,
nrrA
, and
devB
genes that are activated by NtcA at different stages of heterocyst differentiation. Both RNA polymerase and NtcA could specifically bind to the target DNA in the absence of any effector. 2-Oxoglutarate had a moderate positive effect on NtcA binding, and NtcA had a limited positive effect on RNA polymerase recruitment at the promoters. However, a stringent requirement of both NtcA and 2-oxoglutarate was observed for the detection of open complexes and transcript production at the three investigated promoters. These results support a key role for 2-oxoglutarate in transcription activation in the developing heterocyst.
Purification and Characterization of Active-Site Components of the Putative
p
-Cresol Methylhydroxylase Membrane Complex from
Geobacter metallireducens
Authors: Johannes Jörg , Bluschke Alexander , Jehmlich Nico , von Bergen Martin , Boll Matthias 
Published: July 2008

ABSTRACT

p
-Cresol methylhydroxylases (PCMH) from aerobic and facultatively anaerobic bacteria are soluble, periplasmic flavocytochromes that catalyze the first step in biological
p
-cresol degradation, the hydroxylation of the substrate with water. Recent results suggested that
p
-cresol degradation in the strictly anaerobic
Geobacter metallireducens
involves a tightly membrane-bound PCMH complex. In this work, the soluble components of this complex were purified and characterized. The data obtained suggest a molecular mass of 124 ± 15 kDa and a unique αα′β
2
subunit composition, with α and α′ representing isoforms of the flavin adenine dinucleotide (FAD)-containing subunit and β representing a
c
-type cytochrome. Fluorescence and mass spectrometric analysis suggested that one FAD was covalently linked to Tyr
394
of the α subunit. In contrast, the α′ subunit did not contain any FAD cofactor and is therefore considered to be catalytically inactive. The UV/visible spectrum was typical for a flavocytochrome with two heme
c
cofactors and one FAD cofactor.
p
-Cresol reduced the FAD but only one of the two heme cofactors. PCMH catalyzed both the hydroxylation of
p
-cresol to
p
-hydroxybenzyl alcohol and the subsequent oxidation of the latter to
p
-hydroxybenzaldehyde in the presence of artificial electron acceptors. The very low

K
m

values (1.7 and 2.7 μM, respectively) suggest that the in vivo function of PCMH is to oxidize both
p
-cresol and
p
-hydroxybenzyl alcohol. The latter was a mixed inhibitor of
p
-cresol oxidation, with inhibition constants of a
K
ic
(competitive inhibition) value of 18 ± 9 μM and a
K
iu
(uncompetitive inhibition) value of 235 ± 20 μM. A putative functional model for an unusual PCMH enzyme is presented.
Designation of the Provisional New
Enterococcus
Species CDC PNS-E2 as
Enterococcus sanguinicola
sp. nov., Isolated from Human Blood, and Identification of a Strain Previously Named
Enterococcus
CDC PNS-E1 as
Enterococcus italicus
Fortina, Ricci, Mora, and Manachini 2004
Authors: Carvalho Maria da Glória S. , Steigerwalt Arnold G. , Morey Roger E. , Shewmaker Patricia Lynn , Falsen Enevold , Facklam Richard R. , Teixeira Lucia M. 
Published: July 2008

ABSTRACT

We have previously characterized two new enterococcal species (provisionally designated CDC PNS-E1 and CDC PNS-E2) recovered from clinically significant specimens associated with invasive infections in humans. In the present report we provide additional data and propose formal denominations for isolates of these two species of
Enterococcus
. Results of 16S rRNA gene sequencing, sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of whole-cell protein profiles, and DNA-DNA reassociation experiments indicated that the blood isolate ATCC BAA-780 (SS 1728; CDC PNS-E1) corresponds to
Enterococcus italicus
, whose species epithet was proposed to designate isolates from artisanal Italian cheese. Strain ATCC BAA-781 (CCUG 47861; SS 1729; CDC PNS-E2), a vancomycin-resistant isolate recovered from the blood of a patient in the United States, was found to be highly related at the species level to another blood isolate (SS 1743; CCUG 47884) from Sweden, and for these we propose the designation
Enterococcus sanguinicola
sp. nov.
Lymphoid-Related CD11c+CD8α+Dendritic Cells Are Involved in Enhancing Herpes Simplex Virus Type 1 Latency
Authors: Mott Kevin R. , UnderHill David , Wechsler Steven L. , Ghiasi Homayon 
Published: July 2008

ABSTRACTThe mechanism(s) by which herpes simplex virus type 1 (HSV-1) latency is established in neurons is not known. In this study, we examined the effect of dendritic cells (DCs) on the level of HSV-1 latency in trigeminal ganglia (TGs) of ocularly infected BALB/c and C57BL/6 mice. We found that immunization of wild-type mice with FMS-like tyrosine kinase 3 ligand (Flt3L) DNA, which increases the number of DCs, increased the amount of latency in infected mice. Conversely, depletion of DCs was associated with reduced latency. Latency was also significantly reduced in Flt3L−/−and CD8−/−mice. Interestingly, immunization of Flt3L−/−but not CD8−/−mice with Flt3L DNA increased latency. Transfer experiments using DCs expanded ex vivo with Flt3L or granulocyte-macrophage colony-stimulating factor suggested that increased latency was associated with the presence of lymphoid-related (CD11c+CD8α+) DCs, while reduced latency was associated with myeloid-related (CD11c+CD8α−) DCs. Modulation of DC numbers by Flt3L DNA immunization or depletion did not alter acute virus replication in the eye or TG or eye disease in ocularly infected mice. Our results suggest that CD11c+CD8α+DCs directly or indirectly increase the amount of HSV-1 latency in mouse TGs.
Targeting Tat Inhibitors in the Assembly of Human Immunodeficiency Virus Type 1 Transcription Complexes
Authors: D'Orso Iván , Grunwell Jocelyn R. , Nakamura Robert L. , Das Chandreyee , Frankel Alan D. 
Published: July 2008

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1) transcription is regulated by the viral Tat protein, which relieves a block to elongation by recruiting an elongation factor, P-TEFb, to the viral promoter. Here, we report the discovery of potent Tat inhibitors that utilize a localization signal to target a dominant negative protein to its site of action. Fusing the Tat activation domain to some splicing factors, particularly to the Arg-Ser (RS) domain of U2AF65, creates Tat inhibitors that localize to subnuclear speckles, sites where pre-mRNA processing factors are stored for assembly into transcription complexes. A U2AF65 fusion named T-RS interacts with the nonphosphorylated C-terminal domain of RNA polymerase II (RNAP II) via its RS domain and is loaded into RNAP II holoenzyme complexes. T-RS is recruited efficiently to the HIV-1 promoter in a TAR-independent manner before RNAP II hyperphosphorylation but not to cellular promoters. The “preloading” of T-RS into HIV-1 preinitiation complexes prevents the entry of active Tat molecules, leaving the complexes in an elongation-incompetent state and effectively suppressing HIV-1 replication. The ability to deliver inhibitors to transcription complexes through the use of targeting/localization signals may provide new avenues for designing viral and transcription inhibitors.
Temporal trends in adults’ sports participation patterns in England between 1997 and 2006: the Health Survey for England
Authors: Stamatakis E , Chaudhury M 
Published: July 2008

Objective:To examine temporal trends in participation in sport and exercise activities in England between 1997 and 2006 while taking into account wider societal changes.Design:A series of annual cross-sectional surveys.Setting and participants:Nationally representative samples of men (n = 27 217) and women (n = 33 721) aged ⩾16 years.Main outcome measures:Any (more than once every 4 weeks) and regular (more than once a week) participation in overall sport and exercise and a number of sport and exercise groupings (eg cycling, swimming, gym and fitness club-based activities (G/FC), racquet sports). Time point (1997/98, 2003/04, 2006) was the main dependent variable.Results:Age-standardised overall regular participation changed from 40.8% in 1997/98 to 41.2% in 2006 for men (multivariable-adjusted participation OR = 1.11 in 2006, 95% CI 1.03 to 1.19, p<0.001) and from 31.2% to 33.9% for women (1.21, 1.13 to 1.29, p<0.001). Regular G/FC increased from 17.0% to 19.2% for men (1.19, 1.09 to 1.30) and from 15.9% to 18.7% for women (1.23, 1.14 to 1.33) and regular running increased from 2.4% to 4.0% for women only (1.84, 1.56 to 2.18). Overall increases were apparent only in older adults (⩾45 years) (1.25, 1.16 to 1.35, p<0.001). Young men (16–29 years) had reduced ORs for cycling (0.72, 0.58 to 0.88, p = 0.008), dancing (0.60, 0.45 to 0.82, p = 0.001), running (0.78, 0.64 to 0.94, p<0.001) and racquet sports (0.60, 0.42 to 0.86, p = 0.003). In men, increases were pronounced only among men from non-manual social classes, higher income households and white ethnic backgrounds.Conclusions:Sports and exercise participation in England has changed between 1997 and 2006 as the result of increases among middle-aged and older adults and decreases among young men. There are no signs that the participation gap between less and more advantaged population groups is narrowing.