bluuebunny/crossref_metadata_2025_split huggingface dataset:
CheX Is a Phosphorylated CheY Phosphatase Essential forBorrelia burgdorferiChemotaxis
Authors: Motaleb M. A. , Miller Michael R. , Li Chunhao , Bakker Richard G. , Goldstein Stuart F. , Silversmith Ruth E. , Bourret Robert B. , Charon Nyles W. 
Published: November 2005

ABSTRACTMotility and chemotaxis are believed to be important in the pathogenesis of Lyme disease caused by the spirocheteBorrelia burgdorferi. Controlling the phosphorylation state of CheY, a response regulator protein, is essential for regulating bacterial chemotaxis and motility. Rapid dephosphorylation of phosphorylated CheY (CheY-P) is crucial for cells to respond to environmental changes. CheY-P dephosphorylation is accomplished by one or more phosphatases in different species, including CheZ, CheC, CheX, FliY, and/or FliY/N. Only acheXphosphatase homolog has been identified in theB. burgdorferigenome. However, a role forcheXin chemotaxis has not been established in any bacterial species. InactivatingB. burgdorferi cheXby inserting aflgB-kancassette resulted in cells (cheXmutant cells) with a distinct motility phenotype. While wild-type cells ran, paused (stopped or flexed), and reversed, thecheXmutant cells continuously flexed and were not able to run or reverse. Furthermore, swarm plate and capillary tube chemotaxis assays demonstrated thatcheXmutant cells were deficient in chemotaxis. Wild-type chemotaxis and motility were restored whencheXmutant cells were complemented with a shuttle vector expressing CheX. Furthermore, CheX dephosphorylated CheY3-P in vitro and eluted as a homodimer in gel filtration chromatography. These findings demonstrated thatB. burgdorferiCheX is a CheY-P phosphatase that is essential for chemotaxis and motility, which is consistent with CheX being the only CheY-P phosphatase in theB. burgdorferichemotaxis signal transduction pathway.
The
plmS
2
-Encoded Cytochrome P450 Monooxygenase Mediates Hydroxylation of Phoslactomycin B in
Streptomyces
sp. Strain HK803
Authors: Ghatge Mohini S. , Reynolds Kevin A. 
Published: November 2005

ABSTRACT

Streptomyces
sp. strain HK803 produces six analogues of phoslactomycin (Plm A through Plm F). With the exception of Plm B, these analogues contain a C-18 hydroxyl substituent esterified with a range of short-alkyl-chain carboxylic acids. Deletion of the
plmS
2
open reading frame (ORF), showing high sequence similarity to bacterial cytochrome P450 monooxygenases (CYPs), from the Plm biosynthetic gene cluster has previously resulted in an NP1 mutant producing only Plm B (N. Palaniappan, B. S. Kim, Y. Sekiyama, H. Osada, and K. A. Reynolds, J. Biol. Chem.
278:
35552-35557, 2003). Herein, we report that a complementation experiment with an NP1 derivative (NP2), using a recombinant conjugative plasmid carrying the
plmS
2
ORF downstream of the
ermE*
constitutive promoter (pMSG1), restored production of Plm A and Plm C through Plm F. The 1.2-kbp
plmS
2
ORF was also expressed efficiently as an N-terminal polyhistidine-tagged protein in
Streptomyces coelicolor
. The recombinant PlmS
2
converted Plm B to C-18-hydroxy Plm B (Plm G). PlmS
2
was highly specific for Plm B and unable to process a series of derivatives in which either the lactone ring was hydrolyzed or the C-9 phosphate ester was converted to C-9/C-11 phosphorinane. This biochemical analysis and complementation experiment are consistent with a proposed Plm biosynthetic pathway in which the penultimate step is hydroxylation of the cyclohexanecarboxylic acid-derived side chain of Plm B by PlmS
2
(the resulting Plm G is then esterified to provide Plm A and Plm C through Plm F). Kinetic parameters for Plm B hydroxylation by PlmS
2
(

K
m

of 45.3 ± 9.0 μM and
k
cat
of 0.27 ± 0.04 s
−1
) are consistent with this step being a rate-limiting step in the biosynthetic pathway. The penultimate pathway intermediate Plm G has less antifungal activity than Plm A through Plm F and is not observed in fermentations of either the wild-type strain or NP2/pMSG1.
Demonstration of Cotranscription and 1-Methyl-3-Nitroso-Nitroguanidine Induction of a 30-Gene Operon ofBorrelia burgdorferi: Evidence that the 32-Kilobase Circular Plasmids Are Prophages
Authors: Zhang Hongming , Marconi Richard T. 
Published: November 2005

ABSTRACTTheBorreliagenome is comprised of linear and circular elements, including a group of 32-kb circular plasmids (cp32s). Earlier analyses identified a bacteriophage, φBB-1, that may package cp32s, suggesting that these plasmids are prophages. cp32-8, cp32-9, and cp32-1 (plasmids L, N, and P, respectively) encode virulence factors such as the factor H binding, OspE proteins (BBL39, BBN38, and BBP38). Here the expression patterns of cp32-8 open reading frames (ORFs) in in vitro-cultivated 1-methyl-3-nitroso-nitroguanidine (MNNG)-treated and untreated spirochetes and during infection were assessed. ORFs BBL42 through BBL28, which encode several bacteriophage protein homologs, were found to be cotranscribed and expression was upregulated by MNNG. Immunoblotting revealed that MNNG-induced transcription led to increased protein production. The expression of several genes that reside outside of the BBL42-BBL28 operon was not affected by MNNG. Some of these genes, including OspE (BBL39), appear to represent morons. Real-time reverse transcription-PCR of spirochetes in mouse tissue revealed that although the phage operon was not induced during infection, transcription of BBL23 (previously designated BlyA), a putative holin, was upregulated. This observation indicates that some genes within the operon can be independently transcribed from internal promoters. Additional transcriptional analyses of the operon identified multiple transcriptional start sites and provided evidence for the expression of a homologous operon from other cp32s. The data support the hypothesis put forth by C. Eggers and D. S. Samuels (J. Bacteriol. 181:7308-7313, 1999) that the cp32s are prophages, a finding with broad implications for our understanding ofBorreliapathogenesis andBorreliagenome evolution.
Growth Substrate- and Phase-Specific Expression of Biphenyl, Benzoate, and C
1
Metabolic Pathways in
Burkholderia xenovorans
LB400
Authors: Denef V. J. , Patrauchan M. A. , Florizone C. , Park J. , Tsoi T. V. , Verstraete W. , Tiedje J. M. , Eltis L. D. 
Published: November 2005

ABSTRACT

Recent microarray experiments suggested that
Burkholderia xenovorans
LB400, a potent polychlorinated biphenyl (PCB)-degrading bacterium, utilizes up to three apparently redundant benzoate pathways and a C
1
metabolic pathway during biphenyl and benzoate metabolism. To better characterize the roles of these pathways, we performed quantitative proteome profiling of cells grown on succinate, benzoate, or biphenyl and harvested during either mid-logarithmic growth or the transition between the logarithmic and stationary growth phases. The Bph enzymes, catabolizing biphenyl, were ∼16-fold more abundant in biphenyl- versus succinate-grown cells. Moreover, the upper and lower
bph
pathways were independently regulated. Expression of each benzoate pathway depended on growth substrate and phase. Proteins specifying catabolism via benzoate dihydroxylation and catechol
ortho
-cleavage (
ben
-
cat
pathway) were approximately an order of magnitude more abundant in benzoate- versus biphenyl-grown cells at the same growth phase. The chromosomal copy of the benzoyl-coenzyme A (CoA) (
box
C
) pathway was also expressed during growth on biphenyl: Box
C
proteins were approximately twice as abundant as Ben and Cat proteins under these conditions. By contrast, proteins of the megaplasmid copy of the benzoyl-CoA (
box
M
) pathway were only detected in transition-phase benzoate-grown cells. Other proteins detected at increased levels in benzoate- and biphenyl-grown cells included general stress response proteins potentially induced by reactive oxygen species formed during aerobic aromatic catabolism. Finally, C
1
metabolic enzymes were present in biphenyl-grown cells during transition phase. This study provides insights into the physiological roles and integration of apparently redundant catabolic pathways in large-genome bacteria and establishes a basis for investigating the PCB-degrading abilities of this strain.
Decaprenylphosphoryl Arabinofuranose, the Donor of the
d
-Arabinofuranosyl Residues of Mycobacterial Arabinan, Is Formed via a Two-Step Epimerization of Decaprenylphosphoryl Ribose
Authors: Mikušová Katarína , Huang Hairong , Yagi Tetsuya , Holsters Marcelle , Vereecke Danny , D'Haeze Wim , Scherman Michael S. , Brennan Patrick J. , McNeil Michael R. , Crick Dean C. 
Published: November 2005

ABSTRACT

The major cell wall polysaccharide of mycobacteria is a branched-chain arabinogalactan in which arabinan chains are attached to the 5 carbon of some of the 6-linked galactofuranose residues; these arabinan chains are composed exclusively of
d
-arabinofuranose (Ara
f
) residues. The immediate precursor of the polymerized Ara
f
is decaprenylphosphoryl-
d
-Ara
f
, which is derived from 5-phosphoribose 1-diphosphate (pRpp) in an undefined manner. On the basis of time course, feedback, and chemical reduction experiment results we propose that decaprenylphosphoryl-Ara
f
is synthesized by the following sequence of events. (i) pRpp is transferred to a decaprenyl-phosphate molecule to form decaprenylphosphoryl-β-
d
-5-phosphoribose. (ii) Decaprenylphosphoryl-β-
d
-5-phosphoribose is dephosphorylated to form decaprenylphosphoryl-β-
d
-ribose. (iii) The hydroxyl group at the 2 position of the ribose is oxidized and is likely to form decaprenylphosphoryl-2-keto-β-
d
-
erythro
-pentofuranose. (iv) Decaprenylphosphoryl-2-keto-β-
d
-
erythro
-pentofuranose is reduced to form decaprenylphosphoryl-β-
d
-Ara
f
. Thus, the epimerization of the ribosyl to an arabinosyl residue occurs at the lipid-linked level; this is the first report of an epimerase that utilizes a lipid-linked sugar as a substrate. On the basis of similarity to proteins implicated in the arabinosylation of the
Azorhizobium caulidans
nodulation factor, two genes were cloned from the
Mycobacterium tuberculosis
genome and expressed in a heterologous host, and the protein was purified. Together, these proteins (Rv3790 and Rv3791) are able to catalyze the epimerization, although neither protein individually is sufficient to support the activity.
Characterization of
Bacillus anthracis
Germinant Receptors In Vitro
Authors: Fisher Nathan , Hanna Philip 
Published: November 2005

ABSTRACT

Bacillus anthracis
begins its infectious cycle as a metabolically dormant cell type, the endospore. Upon entry into a host, endospores rapidly differentiate into vegetative bacilli through the process of germination, thus initiating anthrax. Elucidation of the signals that trigger germination and the receptors that recognize them is critical to understanding the pathogenesis of
B. anthracis
. Individual mutants deficient in each of the seven putative germinant receptor-encoding loci were constructed via temperature-dependent, plasmid insertion mutagenesis and used to correlate these receptors with known germinant molecules. These analyses showed that the GerK and GerL receptors are jointly required for the alanine germination pathway and also are individually required for recognition of either proline and methionine (GerK) or serine and valine (GerL) as cogerminants in combination with inosine. The germinant specificity of GerS was refined from a previous study in a nonisogenic background since it was required only for germination in response to aromatic amino acid cogerminants. The
gerA
and
gerY
loci were found to be dispensable for recognition of all known germinant molecules. In addition, we show that the promoter of each putative germinant receptor operon, except that of the
gerA
locus, is active during sporulation. A current model of
B. anthracis
endospore germination is presented.
Involvement of SenC in Assembly of Cytochrome
c
Oxidase in
Rhodobacter capsulatus
Authors: Swem Danielle L. , Swem Lee R. , Setterdahl Aaron , Bauer Carl E. 
Published: November 2005

ABSTRACT

SenC, a Sco1 homolog found in the purple photosynthetic bacteria, has been implicated in affecting photosynthesis and respiratory gene expression, as well as assembly of cytochrome
c
oxidase. In this study, we show that SenC from
Rhodobacter capsulatus
is involved in the assembly of a fully functional
cbb
3
-type cytochrome
c
oxidase, as revealed by decreased cytochrome
c
oxidase activity in a
senC
mutant. We also show that a putative copper-binding site in SenC is required for activity and that a SenC deletion phenotype can be rescued by the addition of exogenous copper to the growth medium. In addition, we demonstrate that a SenC mutation has an indirect effect on gene expression caused by a reduction in cytochrome
c
oxidase activity. A model is proposed whereby a reduction in cytochrome
c
oxidase activity impedes the flow of electrons through the respiratory pathway, thereby affecting the oxidation/reduction state of the ubiquinone pool, leading to alterations of photosystem and respiratory gene expression.
Identification of
Erwinia amylovora
Genes Induced during Infection of Immature Pear Tissue
Authors: Zhao Youfu , Blumer Sara E. , Sundin George W. 
Published: November 2005

ABSTRACT

The enterobacterium
Erwinia amylovora
is a devastating plant pathogen causing necrotrophic fire blight disease of apple, pear, and other rosaceous plants. In this study, we used a modified in vivo expression technology system to identify
E. amylovora
genes that are activated during infection of immature pear tissue, a process that requires the major pathogenicity factors of this organism. We identified 394 unique pear fruit-induced (
pfi
) genes on the basis of sequence similarity to known genes and separated them into nine putative function groups including host-microbe interactions (3.8%), stress response (5.3%), regulation (11.9%), cell surface (8.9%), transport (13.5%), mobile elements (1.0%), metabolism (20.3%), nutrient acquisition and synthesis (15.5%), and unknown or hypothetical proteins (19.8%). Known virulence genes, including
hrp/hrc
components of the type III secretion system, the major effector gene
dspE
, type II secretion, levansucrase (
lsc
), and regulators of levansucrase and amylovoran biosynthesis, were upregulated during pear tissue infection. Known virulence factors previously identified in
E
. (
Pectobacterium
)
carotovora
and
Pseudomonas syringae
were identified for the first time in
E. amylovora
and included HecA hemagglutinin family adhesion, Peh polygalacturonase, new effector HopPtoC
EA
, and membrane-bound lytic murein transglycosylase MltE
EA
. An insertional mutation within
hopPtoC
EA
did not result in reduced virulence; however, an
mltE
EA
knockout mutant was reduced in virulence and growth in immature pears. This study suggests that
E. amylovora
utilizes a variety of strategies during plant infection and to overcome the stressful and poor nutritional environment of its plant hosts.
Genetic and Biochemical Analysis of the Twin-Arginine Translocation Pathway in Halophilic Archaea
Authors: Dilks Kieran , Giménez María Inés , Pohlschröder Mechthild 
Published: November 2005

ABSTRACT

The twin-arginine translocation (Tat) pathway is present in a wide variety of prokaryotes and is capable of exporting partially or fully folded proteins from the cytoplasm. Although diverse classes of proteins are transported via the Tat pathway, in most organisms it facilitates the secretion of a relatively small number of substrates compared to the Sec pathway. However, computational evidence suggests that haloarchaea route nearly all secreted proteins to the Tat pathway. We have expanded previous computational analyses of the haloarchaeal Tat pathway and initiated in vivo characterization of the Tat machinery in a model haloarchaeon,
Haloferax volcanii
. Consistent with the predicted usage of the this pathway in the haloarchaea, we determined that three of the four identified
tat
genes in
Haloferax volcanii
are essential for viability when grown aerobically in complex medium. This represents the first report of an organism that requires the Tat pathway for viability when grown under such conditions. Deletion of the nonessential gene had no effect on the secretion of a verified substrate of the Tat pathway. The two TatA paralogs TatAo and TatAt were detected in both the membrane and cytoplasm and could be copurified from the latter fraction. Using size exclusion chromatography to further characterize cytoplasmic and membrane TatA proteins, we find these proteins present in high-molecular-weight complexes in both cellular fractions.
Biosynthesis of Hexahydroxyperylenequinone Melanin via Oxidative Aryl Coupling by Cytochrome P-450 in
Streptomyces griseus
Authors: Funa Nobutaka , Funabashi Masanori , Ohnishi Yasuo , Horinouchi Sueharu 
Published: November 2005

ABSTRACT

Dihydroxyphenylalanine (DOPA) melanins formed from tyrosine by tyrosinases are found in microorganisms, plants, and animals. Most species in the soil-dwelling, gram-positive bacterial genus
Streptomyces
produce DOPA melanins and melanogenesis is one of the characteristics used for taxonomy. Here we report a novel melanin biosynthetic pathway involving a type III polyketide synthase (PKS), RppA, and a cytochrome P-450 enzyme, P-450mel, in
Streptomyces griseus
. In vitro reconstitution of the P-450mel catalyst with spinach ferredoxin-NADP
+
reductase/ferredoxin revealed that it catalyzed oxidative biaryl coupling of 1,3,6,8-tetrahydroxynaphthalene (THN), which was formed from five molecules of malonyl-coenzyme A by the action of RppA to yield 1,4,6,7,9,12-hexahydroxyperylene-3,10-quinone (HPQ). HPQ readily autopolymerized to generate HPQ melanin. Disruption of either the chromosomal
rppA
or
P-450mel
gene resulted in abolishment of the HPQ melanin synthesis in
S. griseus
and a decrease in the resistance of spores to UV-light irradiation. These findings show that THN-derived melanins are not exclusive in eukaryotic fungal genera but an analogous pathway is conserved in prokaryotic streptomycete species as well. A vivid contrast in THN melanin biosynthesis between streptomycetes and fungi is that the THN synthesized by the action of a type III PKS is used directly for condensation in the former, while the THN synthesized by the action of type I PKSs is first reduced and the resultant 1,8-dihydroxynaphthalene is then condensed in the latter.
Proteomic Characterization ofYersinia pestisVirulence
Authors: Chromy Brett A. , Choi Megan W. , Murphy Gloria A. , Gonzales Arlene D. , Corzett Chris H. , Chang Brian C. , Fitch J. Patrick , McCutchen-Maloney Sandra L. 
Published: November 2005

ABSTRACTTheYersinia pestisproteome was studied as a function of temperature and calcium by two-dimensional differential gel electrophoresis. Over 4,100 individual protein spots were detected, of which hundreds were differentially expressed. A total of 43 differentially expressed protein spots, representing 24 unique proteins, were identified by mass spectrometry. Differences in expression were observed for several virulence-associated factors, including catalase-peroxidase (KatY), murine toxin (Ymt), plasminogen activator (Pla), and F1 capsule antigen (Caf1), as well as several putative virulence factors and membrane-bound and metabolic proteins. Differentially expressed proteins not previously reported to contribute to virulence are candidates for more detailed mechanistic studies, representing potential new virulence determinants.
CspA Regulates Pigment Production in
Staphylococcus aureus
through a SigB-Dependent Mechanism
Authors: Katzif Samuel , Lee Eun-Hee , Law Anthony B. , Tzeng Yih-Ling , Shafer William M. 
Published: November 2005

ABSTRACT

We report that the cold shock protein CspA of
Staphylococcus aureus
is required for maximal production of pigment. Results from transcriptional studies revealed that loss of CspA resulted in decreased expression of genes needed for the biosynthesis of 4,4′-diaponeurosporene and the alternative sigma factor SigB.
New Class of Competitive Inhibitor of Bacterial Histidine Kinases
Authors: Gilmour Raymond , Foster J. Estelle , Sheng Qin , McClain Jonathan R. , Riley Anna , Sun Pei-Ming , Ng Wai-Leung , Yan Dalai , Nicas Thalia I. , Henry Kenneth , Winkler Malcolm E. 
Published: November 2005

ABSTRACTBacterial histidine kinases have been proposed as targets for the discovery of new antibiotics, yet few specific inhibitors of bacterial histidine kinases have been reported. We report here a novel thienopyridine (TEP) compound that inhibits bacterial histidine kinases competitively with respect to ATP but does not comparably inhibit mammalian serine/threonine kinases. Although it partitions into membranes and does not inhibit the growth of bacterial or mammalian cells, TEP could serve as a starting compound for a new class of histidine kinase inhibitors with antibacterial activity.
A Second Case of −1 Ribosomal Frameshifting Affecting a Major Virion Protein of the
Lactobacillus
Bacteriophage A2
Authors: Rodríguez Isabel , García Pilar , Suárez Juan E. 
Published: November 2005

ABSTRACT
The bacteriophage A2 major tail protein gene utilizes a −1 translational frameshift to generate two structural polypeptides. Frameshifting is promoted by a slippery sequence and an RNA pseudoknot located 3′ of the gene. The major head gene presents a similar recoding ability. A2 is the only phage described with two −1 frameshifts.
Identification of Regions Involved in Enzymatic Stability of Peptide Deformylase ofMycobacterium tuberculosis
Authors: Saxena Rahul , Chakraborti Pradip K. 
Published: November 2005

ABSTRACTSequence analysis of peptide deformylase ofMycobacterium tuberculosisrevealed the presence of insertions (residues 74 to 85) and an unusually long carboxy-terminal end (residues 182 to 197). Our results with deletion mutants indicated the contribution of these regions in maintaining enzymatic stability. Furthermore, we showed that the region spanning the insertions was responsible for maintaining resistance to oxidizing agents, like H2O2.
A device independent computer plotting system
Authors: Gujar Uday G. 
Published: November 2005

This paper describes a computer plotting system which is completely device independent. The user can switch from one plotting device to another without any programming changes. The interface for adding new plotting devices is formalized and discussed. The addition of a new plotting device is completely transparent to the user; in fact, the old programs may be used to produce plots on the new device without any programming changes whatsoever.
The system was designed and implemented by the author in late 1971 and has been in use ever since (see Ref. 1). Several new plotting devices, real as well as pseudo, have been added successfully without affecting the users of the system.
Interactive computer graphics and macromolecular structures
Authors: Bond Peter J. 
Published: November 2005

In 1964 on Project MAC at MIT, Levinthal and Langridge first applied interactive computer graphics to molecular model building (1, 2). Since then a number of laboratories have developed computer graphics systems to suit their particular needs (3, 4, 5, 6).
I shall begin by describing the system that we have developed in the Princeton University Computer Graphics Laboratory during the past year to investigate macromolecular structures.