bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxygen Reactivity of Both Respiratory Oxidases in
Campylobacter jejuni
: the
cydAB
Genes Encode a Cyanide-Resistant, Low-Affinity Oxidase That Is Not of the Cytochrome
bd
Type
Authors: Jackson Rachel J. , Elvers Karen T. , Lee Lucy J. , Gidley Mark D. , Wainwright Laura M. , Lightfoot James , Park Simon F. , Poole Robert K. 
Published: December 2006

ABSTRACT

The microaerophilic bacterium
Campylobacter jejuni
is a significant food-borne pathogen and is predicted to possess two terminal respiratory oxidases with unknown properties. Inspection of the genome reveals an operon (
cydAB
) apparently encoding a cytochrome
bd
-like oxidase homologous to oxidases in
Escherichia coli
and
Azotobacter vinelandii
. However,
C. jejuni
cells lacked all spectral signals characteristic of the high-spin hemes
b
and
d
of these oxidases. Mutation of the
cydAB
operon of
C. jejuni
did not have a significant effect on growth, but the mutation reduced formate respiration and the viability of cells cultured in 5% oxygen. Since cyanide resistance of respiration was diminished in the mutant, we propose that
C. jejuni
CydAB be renamed CioAB (
c
yanide-
i
nsensitive
o
xidase), as in
Pseudomonas aeruginosa
. We measured the oxygen affinity of each oxidase, using a highly sensitive assay that exploits globin deoxygenation during respiration-catalyzed oxygen uptake. The CioAB-type oxidase exhibited a relatively low affinity for oxygen (

K
m

= 0.8 μM) and a
V
max
of >20 nmol/mg/s. Expression of
cioAB
was elevated fivefold in cells grown at higher rates of oxygen provision. The alternative,
ccoNOQP
-encoded cyanide-sensitive oxidase, expected to encode a cytochrome
cb′
-type enzyme, plays a major role in the microaerobic respiration of
C. jejuni
, since it appeared to be essential for viability and exhibited a much higher oxygen affinity, with a

K
m

value of 40 nM and a
V
max
of 6 to 9 nmol/mg/s. Low-temperature photodissociation spectrophotometry revealed that neither oxidase has ligand-binding activity typical of the heme-copper oxidase family. These data are consistent with cytochrome oxidation during photolysis at low temperatures.
Genome Sequence of Avery's Virulent Serotype 2 Strain D39 ofStreptococcus pneumoniaeand Comparison with That of Unencapsulated Laboratory Strain R6
Authors: Lanie Joel A. , Ng Wai-Leung , Kazmierczak Krystyna M. , Andrzejewski Tiffany M. , Davidsen Tanja M. , Wayne Kyle J. , Tettelin Hervé , Glass John I. , Winkler Malcolm E. 
Published: December 2006

ABSTRACTStreptococcus pneumoniae(pneumococcus) is a leading human respiratory pathogen that causes a variety of serious mucosal and invasive diseases. D39 is an historically important serotype 2 strain that was used in experiments by Avery and coworkers to demonstrate that DNA is the genetic material. Although isolated nearly a century ago, D39 remains extremely virulent in murine infection models and is perhaps the strain used most frequently in current studies of pneumococcal pathogenesis. To date, the complete genome sequences have been reported for only twoS. pneumoniaestrains: TIGR4, a recent serotype 4 clinical isolate, and laboratory strain R6, an avirulent, unencapsulated derivative of strain D39. We report here the genome sequences and new annotation of two different isolates of strain D39 and the corrected sequence of strain R6. Comparisons of these three related sequences allowed deduction of the likely sequence of the D39 progenitor and mutations that arose in each isolate. Despite its numerous repeated sequences and IS elements, the serotype 2 genome has remained remarkably stable during cultivation, and one of the D39 isolates contains only five relatively minor mutations compared to the deduced D39 progenitor. In contrast, laboratory strain R6 contains 71 single-base-pair changes, six deletions, and four insertions and has lost the cryptic pDP1 plasmid compared to the D39 progenitor strain. Many of these mutations are in or affect the expression of genes that play important roles in regulation, metabolism, and virulence. The nature of the mutations that arose spontaneously in these three strains, the relative global transcription patterns determined by microarray analyses, and the implications of the D39 genome sequences to studies of pneumococcal physiology and pathogenesis are presented and discussed.
A Gene Cluster Involved in Degradation of Substituted Salicylates viaorthoCleavage inPseudomonassp. Strain MT1 Encodes Enzymes Specifically Adapted for Transformation of 4-Methylcatechol and 3-Methylmuconate
Authors: Cámara Beatriz , Bielecki Piotr , Kaminski Filip , dos Santos Vitor Martins , Plumeier Iris , Nikodem Patricia , Pieper Dietmar H. 
Published: December 2006

ABSTRACTPseudomonassp. strain MT1 has recently been reported to degrade 4- and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. Genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. One of the gene clusters characterized (sal) showed a novel gene arrangement, withsalA, encoding a salicylate 1-hydroxylase, being clustered withsalCDgenes, encoding muconate cycloisomerase and catechol 1,2-dioxygenase, respectively, and was expressed during growth on salicylate and chlorosalicylate. A second gene cluster (cat), exhibiting the typicalcatRBCAarrangement of genes of the catechol branch of the 3-oxoadipate pathway inPseudomonasstrains, was expressed during growth on salicylate. Despite their high sequence similarities with isoenzymes encoded by thecatgene cluster, the catechol 1,2-dioxygenase and muconate cycloisomerase encoded by thesalcluster showed unusual kinetic properties. Enzymes were adapted for turnover of 4-chlorocatechol and 3-chloromuconate; however, 4-methylcatechol and 3-methylmuconate were identified as the preferred substrates. Investigation of the substrate spectrum identified 4- and 5-methylsalicylate as growth substrates, which were effectively converted by enzymes of thesalcluster into 4-methylmuconolactone, followed by isomerization to 3-methylmuconolactone. The function of thesalgene cluster is therefore to channel both chlorosubstituted and methylsubstituted salicylates into a catecholorthocleavage pathway, followed by dismantling of the formed substituted muconolactones through specific pathways.
Loss of a Universal tRNA Feature
Authors: Wang Chunxia , Sobral Bruno W. , Williams Kelly P. 
Published: December 2006

ABSTRACT

tRNA
His
has thus far always been found with one of the most distinctive of tRNA
features, an extra 5′ nucleotide that is usually a guanylate.
tRNA
His
genes in a disjoint alphaproteobacterial group
comprising the
Rhizobiales
,
Rhodobacterales
,
Caulobacterales
,
Parvularculales
, and
Pelagibacter
generally fail to encode this extra guanylate,
unlike those of other alphaproteobacteria and bacteria in general.
Rather than adding an extra 5′ guanylate posttranscriptionally
as eukaryotes do, evidence is presented here that two of these species,
Sinorhizobium meliloti
and
Caulobacter crescentus
,
simply lack any extra nucleotide on tRNA
His
. This loss
correlates with changes at the 3′ end sequence of
tRNA
His
and at many sites in histidyl-tRNA synthetase that
might be expected to affect tRNA
His
recognition, in the
flipping loop, the insertion domain, the anticodon-binding domain, and
the motif 2 loop. The altered tRNA charging system may have affected
other tRNA charging systems in these bacteria; for example, a site in
tRNA
Glu
sequences was found to covary with
tRNA
His
among
alphaproteobacteria.
Influence of Wall Teichoic Acid on Lysozyme Resistance inStaphylococcus aureus
Authors: Bera Agnieszka , Biswas Raja , Herbert Silvia , Kulauzovic Emir , Weidenmaier Christopher , Peschel Andreas , Götz Friedrich 
Published: December 2006

ABSTRACTStaphylococcus aureuspeptidoglycan (PG) is completely resistant to the hydrolytic activity of lysozyme. Here we show that modifications in PG by O acetylation, wall teichoic acid, and a high degree of cross-linking contribute to this resistance.
Role of FtsEX in Cell Division of
Escherichia coli
: Viability of
ftsEX
Mutants Is Dependent on Functional SufI or High Osmotic Strength
Authors: Reddy Manjula 
Published: December 2006

ABSTRACT

In
Escherichia coli
, at least 12 proteins, FtsZ, ZipA, FtsA, FtsE/X, FtsK, FtsQ, FtsL, FtsB, FtsW, FtsI, FtsN, and AmiC, are known to localize to the septal ring in an interdependent and sequential pathway to coordinate the septum formation at the midcell. The FtsEX complex is the latest recruit of this pathway, and unlike other division proteins, it is shown to be essential only on low-salt media. In this study, it is shown that
ftsEX
null mutations are not only salt remedial but also osmoremedial, which suggests that FtsEX may not be involved in salt transport as previously thought. Increased coexpression of cell division proteins FtsQ-FtsA-FtsZ or FtsN alone restored the growth defects of
ftsEX
mutants.
ftsEX
deletion exacerbated the defects of most of the mutants affected in Z ring localization and septal assembly; however, the
ftsZ84
allele was a weak suppressor of
ftsEX
. The viability of
ftsEX
mutants in high-osmolarity conditions was shown to be dependent on the presence of a periplasmic protein, SufI, a substrate of twin-arginine translocase. In addition, SufI in multiple copies could substitute for the functions of FtsEX. Taken together, these results suggest that FtsE and FtsX are absolutely required for the process of cell division in conditions of low osmotic strength for the stability of the septal ring assembly and that, during high-osmolarity conditions, the FtsEX and SufI functions are redundant for this essential process.
Identification of IspC, an 86-Kilodalton Protein Target of Humoral Immune Response to Infection with
Listeria monocytogenes
Serotype 4b, as a Novel Surface Autolysin
Authors: Wang Linru , Lin Min 
Published: December 2006

ABSTRACT

We identified and biochemically characterized a novel surface-localized autolysin from
Listeria monocytogenes
serotype 4b, an 86-kDa protein consisting of 774 amino acids and known from our previous studies as the target (designated IspC) of the humoral immune response to listerial infection. Recombinant IspC, expressed in
Escherichia coli
, was purified and used to raise specific rabbit polyclonal antibodies for protein characterization. The native IspC was detected in all growth phases at a relatively stable low level during a 22-h in vitro culture, although its gene was transiently transcribed only in the early exponential growth phase. This and our previous findings suggest that IspC is upregulated in vivo during infection. The protein was unevenly distributed in clusters on the cell surface, as shown by immunofluorescence and immunogold electron microscopy. The recombinant IspC was capable of hydrolyzing not only the cell walls of the gram-positive bacterium
Micrococcus lysodeikticus
and the gram-negative bacterium
E. coli
but also that of the IspC-producing strain of
L. monocytogenes
serotype 4b, indicating that it was an autolysin. The IspC autolysin exhibited peptidoglycan hydrolase activity over a broad pH range of between 3 and 9, with a pH optimum of 7.5 to 9. Analysis of various truncated forms of IspC for cell wall-hydrolyzing or -binding activity has defined two separate functional domains: the N-terminal catalytic domain (amino acids [aa] 1 to 197) responsible for the hydrolytic activity and the C-terminal domain (aa 198 to 774) made up of seven GW modules responsible for anchoring the protein to the cell wall. In contrast to the full-length IspC, the N-terminal catalytic domain showed hydrolytic activity at acidic pHs, with a pH optimum of between 4 and 6 and negligible activity at alkaline pHs. This suggests that the cell wall binding domain may be of importance in modulating the activity of the N-terminal hydrolase domain. Elucidation of the biochemical properties of IspC may have provided new insights into its biological function(s) and its role in pathogenesis.
SRP19 Is a Dispensable Component of the Signal Recognition Particle in
Archaea
Authors: Yurist Sophie , Dahan Idit , Eichler Jerry 
Published: December 2006

ABSTRACT

In vitro, archaeal SRP54 binds SRP RNA in the absence of SRP19, suggesting the latter to be expendable in
Archaea
. Accordingly, the
Haloferax volcanii SRP19
gene was deleted. Although normally transcribed at a level comparable to that of the essential
SRP54
gene,
SRP19
deletion had no effect on cell growth, membrane protein insertion, protein secretion, or ribosome levels. The absence of SRP19 did, however, increase membrane bacterioruberin levels.
Complete Genome Sequence of
Haemophilus somnus
(
Histophilus somni
) Strain 129Pt and Comparison to
Haemophilus ducreyi
35000HP and
Haemophilus influenzae
Rd
Authors: Challacombe Jean F. , Duncan A. J. , Brettin Thomas S. , Bruce David , Chertkov Olga , Detter J. Chris , Han Cliff S. , Misra Monica , Richardson Paul , Tapia Roxanne , Thayer Nina , Xie Gary , Inzana Thomas J. 
Published: December 2006

ABSTRACT

Haemophilus somnus
can be either a commensal of bovine mucosal surfaces or an opportunistic pathogen. Pathogenic strains of
H. somnus
are a significant cause of systemic disease in cattle. We report the genome sequence of
H. somnus
129Pt, a nonpathogenic commensal preputial isolate, and the results of a genome-wide comparative analysis of
H. somnus
129Pt,
Haemophilus influenzae
Rd, and
Haemophilus ducreyi
35000HP. We found unique genes in
H. somnus
129Pt involved in lipooligosaccharide biosynthesis, carbohydrate uptake and metabolism, cation transport, amino acid metabolism, ubiquinone and menaquinone biosynthesis, cell surface adhesion, biosynthesis of cofactors, energy metabolism, and electron transport. There were also many genes in common among the three organisms. Our comparative analyses of
H. somnus
129Pt,
H. influenzae
Rd, and
H. ducreyi
35000HP revealed similarities and differences in the numbers and compositions of genes involved in metabolism, host colonization, and persistence. These results lay a foundation for research on the host specificities and niche preferences of these organisms. Future comparisons between
H. somnus
129Pt and virulent strains will aid in the development of protective strategies and vaccines to protect cattle against
H. somnus
disease.
The Crystal Structure of Rv0813c from
Mycobacterium tuberculosis
Reveals a New Family of Fatty Acid-Binding Protein-Like Proteins in Bacteria
Authors: Shepard William , Haouz Ahmed , Graña Martin , Buschiazzo Alejandro , Betton Jean-Michel , Cole Stewart T. , Alzari Pedro M. 
Published: December 2006

ABSTRACT

The gene Rv0813c from
Mycobacterium tuberculosis
, which codes for a hypothetical protein of unknown function, is conserved within the order
Actinomycetales
but absent elsewhere. The crystal structure of Rv0813c reveals a new family of proteins that resemble the fatty acid-binding proteins (FABPs) found in eukaryotes. Rv0813c adopts the 10-stranded β-barrel fold typical of FABPs but lacks the double-helix insert that covers the entry to the binding site in the eukaryotic proteins. The barrel encloses a deep cavity, at the bottom of which a small cyclic ligand was found to bind to the hydroxyl group of Tyr192. This residue is part of a conserved Arg-X-Tyr motif much like the triad that binds the carboxylate group of fatty acids in FABPs. Most of the residues forming the internal surface of the cavity are conserved in homologous protein sequences found in CG-rich prokaryotes, strongly suggesting that Rv0813c is a member of a new family of bacterial FABP-like proteins that may have roles in the recognition, transport, and/or storage of small molecules in the bacterial cytosol.
The
Sphingomonas
Plasmid pCAR3 Is Involved in Complete Mineralization of Carbazole
Authors: Shintani Masaki , Urata Masaaki , Inoue Kengo , Eto Kaori , Habe Hiroshi , Omori Toshio , Yamane Hisakazu , Nojiri Hideaki 
Published: December 2006

ABSTRACT

We determined the complete 254,797-bp nucleotide sequence of the plasmid pCAR3, a carbazole-degradative plasmid from
Sphingomonas
sp. strain KA1. A region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pNL1 isolated from the aromatic-degrading
Novosphingobium aromaticivorans
strain F199. The presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. Although pCAR3 is thought to carry clustered genes for conjugative transfer, a filter-mating assay between KA1 and a pCAR3-cured strain (KA1W) was unsuccessful, indicating that pCAR3 might be deficient in conjugative transfer. Several degradative genes were found on pCAR3, including two kinds of carbazole-degradative gene clusters (
car
-I and
car
-II), and genes for electron transfer components of initial oxygenase for carbazole (
fdxI
,
fdrI
, and
fdrII
). Putative genes were identified for the degradation of anthranilate (
and
), catechol (
cat
), 2-hydroxypenta-2,4-dienoate (
carDFE
), dibenzofuran/fluorene (
dbf/fln
), protocatechuate (
lig
), and phthalate (
oph
). It appears that pCAR3 may carry clustered genes (
car
-I,
car
-II,
fdxI
,
fdrI
,
fdrII
,
and
, and
cat
) for the degradation of carbazole into tricarboxylic acid cycle intermediates; KA1W completely lost the ability to grow on carbazole, and the carbazole-degradative genes listed above were all expressed when KA1 was grown on carbazole. Reverse transcription-PCR analysis also revealed that the transcription of
car
-I,
car
-II, and
cat
genes was induced by carbazole or its metabolic intermediate. Southern hybridization analyses with probes prepared from
car
-I,
car-
II,
repA
,
parA
,
traI
, and
traD
genes indicated that several
Sphingomonas
carbazole degraders have DNA regions similar to parts of pCAR3.
A Suppressor of Cell Death Caused by the Loss of σ
E
Downregulates Extracytoplasmic Stress Responses and Outer Membrane Vesicle Production in
Escherichia coli
Authors: Button Julie E. , Silhavy Thomas J. , Ruiz Natividad 
Published: December 2006

ABSTRACT

When envelope biogenesis is compromised or damage to envelope components occurs, bacteria trigger signaling cascades, which lead to the production of proteins that combat such extracytoplasmic stresses. In
Escherichia coli
, there are three pathways known to deal with envelope stresses: the Bae, Cpx, and σ
E
responses. Although the effectors of the Bae and Cpx responses are not essential in
E. coli
, the effector of the σ
E
response, the sigma factor RpoE (σ
E
), is essential for viability. However, mutations that suppress the lethality of an
rpoE
-null allele can be easily obtained, and here we describe how we have isolated at least four classes of these suppressors. We present the first description of one such suppressor class, loss-of-function mutations in
ydcQ
, a gene encoding a putative DNA-binding protein. In wild-type
rpoE

+

strains,
ydcQ
mutants have two distinct phenotypes: extracytoplasmic stress responses are significantly downregulated, and the production of outer membrane vesicles is severely reduced. We present a model in which σ
E
is not essential per se but, rather, we propose that
rpoE
mutant cells die, possibly because they overreact to the absence of this σ factor by triggering a cell death signal.
Porin Activity of
Anaplasma phagocytophilum
Outer Membrane Fraction and Purified P44
Authors: Huang Haibin , Wang Xueqi , Kikuchi Takane , Kumagai Yumi , Rikihisa Yasuko 
Published: December 2006

ABSTRACT

Anaplasma phagocytophilum
, an obligatory intracellular bacterium that causes human granulocytic anaplasmosis, has significantly less coding capacity for biosynthesis and central intermediary metabolism than do free-living bacteria. Thus,
A. phagocytophilum
needs to usurp and acquire various compounds from its host. Here we demonstrate that the isolated outer membrane of
A. phagocytophilum
has porin activity, as measured by a liposome swelling assay. The activity allows the diffusion of
l
-glutamine, the monosaccharides arabinose and glucose, the disaccharide sucrose, and even the tetrasaccharide stachyose, and this diffusion could be inhibited with an anti-P44 monoclonal antibody. P44s are the most abundant outer membrane proteins and neutralizing targets of
A. phagocytophilum
. The P44 protein demonstrates characteristics consistent with porins of gram-negative bacteria, including detergent solubility, heat modifiability, a predicted structure of amphipathic and antiparallel β-strands, an abundance of polar residues, and a C-terminal phenylalanine. We purified native P44s under two different nondenaturing conditions. When reconstituted into proteoliposomes, both purified P44s exhibited porin activity. P44s are encoded by approximately 100
p44
paralogs and go through extensive antigenic variation. The 16-transmembrane-domain β-strands consist of conserved P44 N- and C-terminal regions. By looping out the hypervariable region, the porin structure is conserved among diverse P44 proteins yet enables antigenic variation for immunoevasion. The tricarboxylic acid (TCA) cycle of
A. phagocytophilum
is incomplete and requires the exogenous acquisition of
l
-glutamine or
l
-glutamate for function. Efficient diffusion of
l
-glutamine across the outer membrane suggests that the porin feeds the
Anaplasma
TCA cycle and that the relatively large pore size provides
Anaplasma
with the necessary metabolic intermediates from the host cytoplasm.
The
Pseudomonas
Quorum-Sensing Regulator RsaL Belongs to the Tetrahelical Superclass of H-T-H Proteins
Authors: Rampioni Giordano , Polticelli Fabio , Bertani Iris , Righetti Karima , Venturi Vittorio , Zennaro Elisabetta , Leoni Livia 
Published: December 2006

ABSTRACT

In the opportunistic human pathogen
Pseudomonas aeruginosa
, quorum sensing (QS) is crucial for virulence. The RsaL protein directly represses the transcription of
lasI
, the synthase gene of the main QS signal molecule. On the basis of sequence homology, RsaL cannot be predicted to belong to any class of characterized DNA-binding proteins. In this study, an in silico model of the RsaL structure was inferred showing that RsaL belongs to the tetrahelical superclass of helix-turn-helix proteins. The overall structure of RsaL is very similar to the
N
-terminal domain of the lambda
c
I repressor and to the POU-specific domain of the mammalian transcription factor Oct-1 (Oct-1 POUs). Moreover, residues of Oct-1 POUs important for structural stability and/or DNA binding are conserved in the same positions in RsaL and in its homologs found in GenBank. These residues were independently replaced with Ala, and the activities of the mutated variants of RsaL were compared to that of the wild-type counterpart in vivo by complementation assays and in vitro by electrophoretic mobility shift assays. The results validated the RsaL in silico model and showed that residues Arg 20, Gln 38, Ser 42, Arg 43, and Glu 45 are important for RsaL function. Our data indicate that RsaL could be the founding member of a new protein family within the tetrahelical superclass of helix-turn-helix proteins. Finally, the minimum DNA sequence required for RsaL binding on the
lasI
promoter was determined, and our data support the hypothesis that RsaL binds DNA as a dimer.