bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Tetralin Biodegradation and Identification of Genes Essential for Expression of
thn
Operons
Authors: Martínez-Pérez O. , Moreno-Ruiz E. , Floriano B. , Santero E. 
Published: September 2004

ABSTRACT

The tetralin biodegradation genes of
Sphingomonas macrogolitabida
strain TFA are clustered in two closely linked and divergent operons. To analyze expression of both operons under different growth conditions, transcriptional and translational gene fusions of the first genes of each operon to
lacZ
have been constructed in plasmids unable to replicate in
Sphingomonas
and integrated by recombination into the genome of strain TFA. Expression analysis indicated that the transcription of both genes is induced in similar ways by the presence of tetralin. Gene expression in both operons is also subjected to overimposed catabolic repression. Two additional genes named
thnR
and
thnY
have been identified downstream of
thnCA3A4
genes. ThnR is similar to LysR-type regulators, and mutational analysis indicated that ThnR is strictly required for expression of the
thn
operons. Unlike other LysR-type regulators, ThnR does not repress its own synthesis. In fact, ThnR activates its own expression, since
thnR
is cotranscribed with the
thnCA3A4
genes. ThnY is similar to the ferredoxin reductase components of dioxygenase systems and shows the fer2 domain, binding a Cys
4
[2Fe-2S] iron sulfur center, and the FAD-binding domain, common to those reductases. However, it lacks the NAD-binding domain. Intriguingly, ThnY has a regulatory role, since it is also strictly required for expression of the
thn
operons. Given the similarity of ThnY to reductases and the possibility of its being present in the two redox states, it is tempting to speculate that ThnY is a regulatory component connecting expression of the
thn
operons to the physiological status of the cell.
Reversible Phase Variation in the
phnE
Gene, Which Is Required for Phosphonate Metabolism in
Escherichia coli
K-12
Authors: Iqbal Samina , Parker George , Davidson Helen , Moslehi-Rahmani Elham , Robson Robert L. 
Published: September 2004

ABSTRACT

It is known that
Escherichia coli
K-12 is cryptic (Phn
−
) for utilization of methyl phosphonate (MePn) and that Phn
+
variants can be selected for growth on MePn as the sole P source. Variants arise from deletion via a possible slip strand mechanism of one of three direct 8-bp repeat sequences in
phnE
, which restores function to a component of a putative ABC type transporter. Here we show that Phn
+
variants are present at the surprisingly high frequency of >10
−2
in K-12 strains. Amplified-fragment length polymorphism analysis was used to monitor instability in
phnE
in various strains growing under different conditions. This revealed that, once selection for growth on MePn is removed,
Phn
+
revertants reappear and accumulate at high levels through reinsertion of the 8-bp repeat element sequence. It appears that, in K-12,
phnE
contains a high-frequency reversible gene switch, producing phase variation which either allows (“on” form) or blocks (“off” form) MePn utilization. The switch can also block usage of other metabolizable alkyl phosphonates, including the naturally occurring 2-aminoethylphosphonate. All K-12 strains, obtained from collections, appear in the “off” form even when bearing mutations in
mutS
,
mutD
, or
dnaQ
which are known to enhance slip strand events between repetitive sequences. The ability to inactivate the
phnE
gene appears to be unique to K-12 strains since the B strain is naturally Phn
+
and lacks the inactivating 8-bp insertion in
phnE
, as do important pathogenic strains for which genome sequences are known and also strains isolated recently from environmental sources.
Arginine Biosynthesis inThermotoga maritima: Characterization of the Arginine-SensitiveN-Acetyl-l-Glutamate Kinase
Authors: Fernández-Murga M. Leonor , Gil-Ortiz Fernando , Llácer José L. , Rubio Vicente 
Published: September 2004

ABSTRACTTo help clarify the control of arginine synthesis inThermotoga maritima, the putative gene (argB) forN-acetyl-l-glutamate kinase (NAGK) from this microorganism was cloned and overexpressed, and the resulting protein was purified and shown to be a highly thermostable and specific NAGK that is potently and selectively inhibited by arginine. Therefore, NAGK is inT. maritimathe feedback control point of arginine synthesis, a process that in this organism involves acetyl group recycling and appears not to involve classical acetylglutamate synthase. The inhibition of NAGK by arginine was found to be pH independent and to depend sigmoidally on the concentration of arginine, with a Hill coefficient (N) of ∼4, and the 50% inhibitory arginine concentration (I0.5) was shown to increase with temperature, approaching above 65°C the I0.50observed at 37°C with the mesophilic NAGK ofPseudomonas aeruginosa(the best-studied arginine-inhibitable NAGK). At 75°C, the inhibition by arginine ofT. maritimaNAGK was due to a large increase in theKmfor acetylglutamate triggered by the inhibitor, but at 37°C arginine also substantially decreased theVmaxof the enzyme. The NAGKs ofT. maritimaandP. aeruginosabehaved in gel filtration as hexamers, justifying the sigmoidicity and high Hill coefficient of arginine inhibition, and arginine or the substrates failed to disaggregate these enzymes. In contrast,Escherichia coliNAGK is not inhibited by arginine and is dimeric, and thus the hexameric architecture may be an important determinant of arginine sensitivity. Potential thermostability determinants ofT. maritimaNAGK are also discussed.
Characterization of Heme Uptake Cluster Genes in the Fish PathogenVibrio anguillarum
Authors: Mouriño Susana , Osorio Carlos R. , Lemos Manuel L. 
Published: September 2004

ABSTRACTVibrio anguillarumcan utilize hemin and hemoglobin as sole iron sources. In previous work we identified HuvA, theV. anguillarumouter membrane heme receptor by complementation of a heme utilization mutant with a cosmid clone (pML1) isolated from a genomic library ofV. anguillarum. In the present study, we describe a gene cluster contained in cosmid pML1, coding for nine potential heme uptake and utilization proteins: HuvA, the heme receptor; HuvZ and HuvX; TonB, ExbB, and ExbD; HuvB, the putative periplasmic binding protein; HuvC, the putative inner membrane permease; and HuvD, the putative ABC transporter ATPase. AV. anguillarumstrain with an in-frame chromosomal deletion of the nine-gene cluster was impaired for growth with heme or hemoglobin as the sole iron source. Single-gene in-frame deletions were constructed, demonstrating that each of thehuvAZBCDgenes are essential for utilization of heme as an iron source inV. anguillarum, whereashuvXis not. When expressed inEscherichia coli hemA(strain EB53), a plasmid carrying the gene for the heme receptor, HuvA, was sufficient to allow the use of heme as the porphyrin source. For utilization of heme as an iron source inE. coli ent(strain 101ESD), thetonB exbBDandhuvBCDgenes were required in addition tohuvA. TheV. anguillarumheme uptake cluster shows some differences in gene arrangement when compared to homologous clusters described for otherVibriospecies.
AglZ Is a Filament-Forming Coiled-Coil Protein Required for Adventurous Gliding Motility ofMyxococcus xanthus
Authors: Yang Ruifeng , Bartle Sarah , Otto Rebecca , Stassinopoulos Angela , Rogers Matthew , Plamann Lynda , Hartzell Patricia 
Published: September 2004

ABSTRACTTheaglZgene ofMyxococcus xanthuswas identified from a yeast two-hybrid assay in which MglA was used as bait. MglA is a 22-kDa cytoplasmic GTPase required for both adventurous and social gliding motility and sporulation. Genetic studies showed thataglZis part of the A motility system, because disruption or deletion ofaglZabolished movement of isolated cells andaglZ sglKdouble mutants were nonmotile. TheaglZgene encodes a 153-kDa protein that interacts with purified MglA in vitro. The N terminus of AglZ shows similarity to the receiver domain of two-component response regulator proteins, while the C terminus contains heptad repeats characteristic of coiled-coil proteins, such as myosin. Consistent with this motif, expression of AglZ inEscherichia coliresulted in production of striated lattice structures. Similar to the myosin heavy chain, the purified C-terminal coiled-coil domain of AglZ forms filament structures in vitro.
Inactivations of
rsbU
and
sarA
by IS
256
Represent Novel Mechanisms of Biofilm Phenotypic Variation in
Staphylococcus epidermidis
Authors: Conlon Kevin M. , Humphreys Hilary , O'Gara James P. 
Published: September 2004

ABSTRACT

Expression of
ica
operon-mediated biofilm formation in
Staphylococcus epidermidis
RP62A is subject to phase variable regulation. Reversible transposition of IS
256
into
icaADBC
or downregulation of
icaADBC
expression are two important mechanisms of biofilm phenotypic variation. Interestingly, the presence of IS
256
was generally associated with a more rapid rate of phenotypic variation, suggesting that IS
256
insertions outside the
ica
locus may affect
ica
transcription. Consistent with this, we identified variants with diminished
ica
expression, which were associated with IS
256
insertions in the σ
B
activator
rsbU
or
sarA
. Biofilm development and
ica
expression were activated only by ethanol and not NaCl in
rsbU
::IS
256
insertion variants, which were present in ∼11% of all variants. σ
B
activity was impaired in
rsbU
::IS
256
variants, as evidenced by reduced expression of the σ
B
-regulated genes
asp23
,
csb9
, and
rsbV
. Moreover, expression of
sarA
, which is σ
B
regulated, and SarA-regulated RNAIII were also suppressed. A biofilm-forming phenotype was restored to
rsbU
::IS
256
variants only after repeated passage and was not associated with IS
256
excision from
rsbU
. Only one
sarA
::IS
256
insertion mutant was identified among 43 biofilm-negative variants. Both NaCl and ethanol-activated
ica
expression in this
sarA
::IS
256
variant, but only ethanol increased biofilm development. Unlike
rsbU
::IS
256
variants, reversion of the
sarA
::IS
256
variant to a biofilm-positive phenotype was accompanied by precise excision of IS
256
from
sarA
and restoration of normal
ica
expression. These data identify new roles for IS
256
in
ica
and biofilm phenotypic variation and demonstrate the capacity of this element to influence the global regulation of transcription in
S. epidermidis
.
Bacillus subtilisStoA Is a Thiol-Disulfide Oxidoreductase Important for Spore Cortex Synthesis
Authors: Erlendsson Lýður S. , Möller Mirja , Hederstedt Lars 
Published: September 2004

ABSTRACTBacillus subtilisis an endospore-forming bacterium. There are indications that protein disulfide linkages occur in spores, but the role of thiol-disulfide chemistry in spore synthesis is not understood. Thiol-disulfide oxidoreductases catalyze formation or breakage of disulfide bonds in proteins. CcdA is the onlyB. subtilisthiol-disulfide oxidoreductase that has previously been shown to play some role in endospore biogenesis. In this work we show that lack of the StoA (YkvV) protein results in spores sensitive to heat, lysozyme, and chloroform. Compared to CcdA deficiency, StoA deficiency results in a 100-fold-stronger negative effect on sporulation efficiency. StoA is a membrane-bound protein with a predicted thioredoxin-like domain probably localized in the intermembrane space of the forespore. Electron microscopy of spores of CcdA- and StoA-deficient strains showed that the spore cortex is absent in both cases. The BdbD protein catalyzes formation of disulfide bonds in proteins on the outer side of the cytoplasmic membrane but is not required for sporulation. Inactivation ofbdbDwas found to suppress the sporulation defect of a strain deficient in StoA. Our results indicate that StoA is a thiol-disulfide oxidoreductase that is involved in breaking disulfide bonds in cortex components or in proteins important for cortex synthesis.
The Paralogous Pairs of Genes Involved in Clavulanic Acid and Clavam Metabolite Biosynthesis Are Differently Regulated in
Streptomyces clavuligerus
Authors: Tahlan Kapil , Anders Cecilia , Jensen Susan E. 
Published: September 2004

ABSTRACT

Carboxyethylarginine synthase, encoded by the paralogous
ceaS1
and
ceaS2
genes, catalyzes the first reaction in the shared biosynthetic pathway leading to clavulanic acid and the other clavam metabolites in
Streptomyces clavuligerus
. The nutritional regulation of
ceaS1
and
ceaS2
expression was analyzed by reverse transcriptase PCR and by the use of the enhanced green fluorescent protein-encoding gene (e
gfp
) as a reporter.
ceaS1
was transcribed in complex soy medium only, whereas
ceaS2
was transcribed in both soy and defined starch-asparagine (SA) media. The transcriptional start points of the two genes were also mapped to a C residue 98 bp upstream of
ceaS1
and a G residue 51 bp upstream of the
ceaS2
start codon by S1 nuclease protection and primer extension analyses. Furthermore, transcriptional mapping of the genes encoding the beta-lactam synthetase (
bls1
) and proclavaminate amidinohydrolase (
pah1
) isoenzymes from the paralogue gene cluster indicated that a single polycistronic transcript of ∼4.9 kb includes
ceaS1
,
bls1
, and
pah1
. The expression of
ceaS1
and
ceaS2
in a mutant strain defective in the regulatory protein CcaR was also examined.
ceaS1
transcription was not affected in the
ccaR
mutant, whereas that of
ceaS2
was greatly reduced compared to the wild-type strain. Overall, our results suggest that different mechanisms are involved in regulating the expression of
ceaS1
and
ceaS2
, and presumably also of other paralogous genes that encode proteins involved in the early stages of clavulanic acid and clavam metabolite biosynthesis.
Temporal Global Changes in Gene Expression during Temperature Transition in
Yersinia pestis
Authors: Motin Vladimir L. , Georgescu Anca M. , Fitch Joseph P. , Gu Pauline P. , Nelson David O. , Mabery Shalini L. , Garnham Janine B. , Sokhansanj Bahrad A. , Ott Linda L. , Coleman Matthew A. , Elliott Jeffrey M. , Kegelmeyer Laura M. , Wyrobek Andrew J. , Slezak Thomas R. , Brubaker Robert R. , Garcia Emilio 
Published: September 2004

ABSTRACT

DNA microarrays encompassing the entire genome of
Yersinia pestis
were used to characterize global regulatory changes during steady-state vegetative growth occurring after shift from 26 to 37°C in the presence and absence of Ca
2+
. Transcriptional profiles revealed that 51, 4, and 13 respective genes and open reading frames (ORFs) on pCD, pPCP, and pMT were thermoinduced and that the majority of these genes carried by pCD were downregulated by Ca
2+
. In contrast, Ca
2+
had little effect on chromosomal genes and ORFs, of which 235 were thermally upregulated and 274 were thermally downregulated. The primary consequence of these regulatory events is profligate catabolism of numerous metabolites available in the mammalian host.
The Secretion Signal of YopN, a Regulatory Protein of the
Yersinia enterocolitica
Type III Secretion Pathway
Authors: Goss John W. , Sorg Joseph A. , Ramamurthi Kumaran S. , Ton-That Hung , Schneewind Olaf 
Published: September 2004

ABSTRACT

The type III secretion signal of
Yersinia enterocolitica
YopN was mapped using a gene fusion approach.
yopN
codons 1 to 12 were identified as critical for signal function. Several synonymous mutations that abolish secretion of hybrid proteins without altering the codon specificity of
yopN
mRNA were identified.
THE MESH WITH BINARY TREE NETWORKS: AN ENHANCED MESH WITH LOW BUS-LOADING
Authors: DHARMASENA HETTIHE P. , VAIDYANATHAN RAMACHANDRAN 
Published: September 2004

The literature abounds with enhanced mesh models and numerous results for them. These models employ buses connecting a large (usually a polynomial) number of processors resulting in high bus loading and a very low bus data rate. In this paper we propose an enhanced mesh model called the mesh with binary-tree (multiple bus) network (MBTN) with low bus loading. We measure the cost of the model in terms of its loading, degree (connections per processor), number of buses and layout area. We also devise an algorithm to perform prefix computations on the MBTN. The MBTN's parameters can be selected to provide a wide range of tradeoffs between its cost and performance. Most importantly, for every major existing enhanced mesh model, there is a choice of parameters that makes the MBTN superior to the existing model. Key to the MBTN is a novel implementation of a binary-tree algorithm on a multiple bus network (MBN). We propose two constant loading MBNs that can run binary tree algorithms optimally. We also show that any network (such as the MBTN) that is capable of running binary tree algorithms efficiently can also solve linear recurrences efficiently. These results may be of independent interest.
An Electronic Cash Scheme and its Management
Authors: Wang Hua , Zhang Yanchun , Cao Jinli 
Published: September 2004

A secure electronic cash scheme and its role-based access control (RBAC) management are proposed in this paper. The scheme uses electronic cash for payment transactions. In this protocol, from the viewpoint of banks, consumers can improve anonymity if they are worried about disclosure of their identities. A new role called anonymity provider agent (AP) provides a highly anonymous certificate for consumers during a payment processing. The role AP certifies re-encrypted data after verifying the validity of the content from consumers, but with no private information of the consumers required. Each consumer can get a required anonymity level through this new method, depending on the available time, computation and cost. Consumers can also use different banks (cross-payment) and anonymity provider agents (multiple APs) without double-spending problems. Role-based access control is widely used in system management and products since its advantages such as reducing administration cost and complexity. However, conflicting problems may arise between roles when RBAC is applied for system management. For example, mutually exclusive roles may be granted to a user with RBAC and the user may have or derive a high level of authority. To solve these problems, we analyze the duty separation constraints of the roles and role hierarchies in the scheme, then discuss how to grant a role to a user.
Retinoids and myelomonocytic growth factors cooperatively activate RARΑ and induce human myeloid leukemia cell differentiation via MAP kinase pathways
Authors: Glasow Annegret , Prodromou Natalia , Xu Ke , von Lindern Marieke , Zelent Arthur 
Published: September 2004

AbstractUse of all-trans-retinoic acid (ATRA) in combinatorial differentiation therapy of acute promyelocytic leukemia (APL) results in exceptional cure rates. However, potent cell differentiation effects of ATRA are so far largely restricted to this disease and long-term survival rates in non-APL acute myelogeneous leukemia (AML) remain unacceptably poor, requiring development of novel therapeutic strategies. We demonstrate here that myelomonocytic growth factors (granulocyte colony-stimulating factor [G-CSF] and/or granulocyte macrophage colony-stimulating factor [GM-CSF]) potentiate differentiation effects of ATRA in different AML cell lines and primary cells from patients with myeloid leukemia. The ligand-dependent activities of endogenous and transiently expressed retinoic acid receptor alpha (RARα) isoforms can be potentiated by G/GM-CSF in U-937 cells and correlate with increased expression of ATRA-inducible RARα2 isoform. Specific inhibitors of mitogen mitogen-activated protein kinase (MAPK) (MEK)-1/-2 or p38 extracellular signal-related kinase (ERK) kinase diminish the ATRA as well as ATRA and G/GM-CSF-induced activation of the RARα proteins and decreased the differentiation-induced decline in cell numbers. Our data demonstrate that acting, at least in part, via the MAP kinase pathways, myelomonocytic growth factors enhance ATRA-dependent activation of the RARα isoforms and maturation of myeloid leukemia cells. These results suggest that combinatorial use of these agents may be effective in differentiation therapy of AML. (Blood. 2005;105:341-349)
Combined effects of As4S4 and imatinib on chronic myeloid leukemia cells and BCR-ABL oncoprotein
Authors: Yin Tong , Wu Ying-Li , Sun Hui-Ping , Sun Guan-Lin , Du Yan-Zhi , Wang Kan-Kan , Zhang Ji , Chen Guo-Qiang , Chen Sai-Juan , Chen Zhu 
Published: September 2004

AbstractImatinib (STI571, Gleevec) is a tailored drug for chronic myelogenous leukemia (CML), whereas arsenic compounds were used as ancient remedies for CML with certain efficacy. The aim of this study was to investigate the potential benefit of combination therapy with imatinib and arsenic sulfide (As4S4). Analysis of cell proliferation and clonogenic ability showed that As4S4 and imatinib exerted synergistic effects on both K562 cells and fresh CML cells. The effective concentrations on fresh CML cells were pharmacokinetically available in vivo but had much less inhibitory effect on CD34+ cells from the nonleukemic donors. Examination of cell cycles showed that As4S4 induced G2/M arrest whereas imatinib induced G1 arrest. Using a number of parameters such as morphology, annexin V/propidium iodide (PI), mitochondrial transmembrane potential, caspase-3 activity, and Fas/Fas-L, the synergistic effects were revealed on induction of cell apoptosis, largely through the mitochondrial pathway. The 2 drugs also exhibited a synergistic effect in targeting BCR-ABL protein. While As4S4 triggered its degradation and imatinib inhibited its tyrosine kinase activity, combined use of the 2 led to lower protein/enzymatic activity levels of BCR-ABL. Our in vitro data thus strongly suggest a potential clinical application of imatinib and As4S4 combination on CML.
Rod mutations associated with MYH9-related disorders disrupt nonmuscle myosin-IIA assembly
Authors: Franke Josef D. , Dong Fan , Rickoll Wayne L. , Kelley Michael J. , Kiehart Daniel P. 
Published: September 2004

AbstractMYH9-related disorders are autosomal dominant syndromes, variably affecting platelet formation, hearing, and kidney function, and result from mutations in the human nonmuscle myosin-IIA heavy chain gene. To understand the mechanisms by which mutations in the rod region disrupt nonmuscle myosin-IIA function, we examined the in vitro behavior of 4 common mutant forms of the rod (R1165C, D1424N, E1841K, and R1933Stop) compared with wild type. We used negative-stain electron microscopy to analyze paracrystal morphology, a model system for the assembly of individual myosin-II molecules into bipolar filaments. Wild-type tail fragments formed ordered paracrystal arrays, whereas mutants formed aberrant aggregates. In mixing experiments, the mutants act dominantly to interfere with the proper assembly of wild type. Using circular dichroism, we find that 2 mutants affect the α-helical coiled-coil structure of individual molecules, and 2 mutants disrupt the lateral associations among individual molecules necessary to form higher-order assemblies, helping explain the dominant effects of these mutants. These results demonstrate that the most common mutations in MYH9, lesions in the rod, cause defects in nonmuscle myosin-IIA assembly. Further, the application of these methods to biochemically characterize rod mutations could be extended to other myosins responsible for disease.