bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimal and Contributing Sequence Determinants of the
cis
-Acting Locus of Transfer (
clt
) of Streptomycete Plasmid pIJ101 Occur within an Intrinsically Curved Plasmid Region
Authors: Ducote Matthew J. , Prakash Shubha , Pettis Gregg S. 
Published: July 2002

ABSTRACT

Efficient interbacterial transfer of streptomycete plasmid pIJ101 requires the pIJ101
tra
gene, as well as a
cis
-acting plasmid function known as
clt
. Here we show that the minimal pIJ101
clt
locus consists of a sequence no greater than 54 bp in size that includes essential inverted-repeat and direct-repeat sequences and is located in close proximity to the 3′ end of the
korB
regulatory gene. Evidence that sequences extending beyond the minimal locus and into the
korB
open reading frame influence
clt
transfer function and demonstration that
clt-korB
sequences are intrinsically curved raise the possibility that higher-order structuring of DNA and protein within this plasmid region may be an inherent feature of efficient pIJ101 transfer.
Functional Expression and Characterization of the Two Cyclic Amidohydrolase Enzymes, Allantoinase and a Novel Phenylhydantoinase, from
Escherichia coli
Authors: Kim Geun Joong , Lee Dong Eun , Kim Hak-Sung 
Published: July 2002

ABSTRACT

A superfamily of cyclic amidohydrolases, including dihydropyrimidinase, allantoinase, hydantoinase, and dihydroorotase, all of which are involved in the metabolism of purine and pyrimidine rings, was recently proposed based on the rigidly conserved structural domains in identical positions of the related enzymes. With these conserved domains, two putative cyclic amidohydrolase genes from
Escherichia coli
, flanked by related genes, were identified and characterized. From the genome sequence of
E. coli
, the
allB
gene and a putative open reading frame, tentatively designated as a
hyuA
(for hydantoin-utilizing enzyme) gene, were predicted to express hydrolases. In contrast to
allB
, high-level expression of
hyuA
in
E. coli
of a single protein was unsuccessful even under various induction conditions. We expressed HyuA as a maltose binding protein fusion protein and AllB in its native form and then purified each of them by conventional procedures.
allB
was found to encode a tetrameric allantoinase (453 amino acids) which specifically hydrolyzes the purine metabolite allantoin to allantoic acid. Another open reading frame,
hyuA
, located near 64.4 min on the physical map and known as a UUG start, coded for
d
-stereospecific phenylhydantoinase (465 amino acids) which is a homotetramer. As a novel enzyme belonging to a cyclic amidohydrolase superfamily,
E. coli
phenylhydantoinase exhibited a distinct activity toward the hydantoin derivative with an aromatic side chain at the 5′ position but did not readily hydrolyze the simple cyclic ureides. The deduced amino acid sequence of the novel phenylhydantoinase shared a significant homology (>45%) with those of allantoinase and dihydropyrimidinase, but its functional role still remains to be elucidated. Despite the unclear physiological function of HyuA, its presence, along with the allantoin-utilizing AllB, strongly suggested that the cyclic ureides might be utilized as nutrient sources in
E. coli
.
Physical Map of the Chromosome of the Apple Proliferation Phytoplasma
Authors: Lauer Ulrich , Seemüller Erich 
Published: July 2002

ABSTRACT

A physical map of the apple proliferation phytoplasma strain AT chromosome was constructed from genomic DNA extracted from diseased tobacco plants. The map was generated with single and double digestions of the chromosome with
Bss
HII,
Sma
I,
Mlu
I, and
Apa
I restriction endonucleases and resolving the fragments by pulsed-field gel electrophoresis. Partial digestion and Southern blot analysis were used to assist in the arrangement of the 14 contiguous restriction fragments obtained. From the restriction fragments generated by double digestions, the size of the circular chromosome was calculated to be approximately 645 kb. Locations of the two rRNA operons, the operon including the
fus
and
tuf
genes, and three other genes were placed on the map. Genome sizes and
Bss
HII restriction profiles of apple proliferation strain AP15 and the pear decline and European stone fruit yellows phytoplasmas were different from that of strain AT.
Multiple Alleles ofTreponema pallidumRepeat Gene D inTreponema pallidumIsolates
Authors: Centurion-Lara Arturo , Sun Eileen S. , Barrett Lynn K. , Castro Christa , Lukehart Sheila A. , Van Voorhis Wesley C. 
Published: July 2002

ABSTRACTTwo newtprDalleles have been identified inTreponema pallidum:tprD2is found in 7 of 12T. pallidumsubsp.pallidumisolates and 7 of 8 non-pallidumisolates, andtprD3is found in oneT. pallidumsubsp.pertenueisolate. Antibodies against TprD2 are found in persons with syphilis, demonstrating thattprD2is expressed during infection.
NadN and
e
(P4) Are Essential for Utilization of NAD and Nicotinamide Mononucleotide but Not Nicotinamide Riboside in
Haemophilus influenzae
Authors: Kemmer Gabriele , Reilly Thomas J. , Schmidt-Brauns Joachim , Zlotnik Gary W. , Green Bruce A. , Fiske Michael J. , Herbert Mark , Kraiß Anita , Schlör Stefan , Smith Arnold , Reidl Joachim 
Published: July 2002

ABSTRACT

Haemophilus influenzae
has an absolute requirement for NAD (factor V) because it lacks almost all the biosynthetic enzymes necessary for the de novo synthesis of that cofactor. Factor V can be provided as either nicotinamide adenosine dinucleotide (NAD), nicotinamide mononucleotide (NMN), or nicotinamide riboside (NR) in vitro, but little is known about the source or the mechanism of uptake of these substrates in vivo. As shown by us earlier, at least two gene products are involved in the uptake of NAD, the outer membrane lipoprotein
e
(P4), which has phosphatase activity and is encoded by
hel
, and a periplasmic NAD nucleotidase, encoded by
nadN
. It has also been observed that the latter gene product is essential for
H. influenzae
growth on media supplemented with NAD. In this report, we describe the functions and substrates of these two proteins as they act together in an NAD utilization pathway. Data are provided which indicate that NadN harbors not only NAD pyrophosphatase but also NMN 5′-nucleotidase activity. The
e
(P4) protein is also shown to have NMN 5′-nucleotidase activity, recognizing NMN as a substrate and releasing NR as its product. Insertion mutants of
nadN
or deletion and site-directed mutants of
hel
had attenuated growth and a reduced uptake phenotype when NMN served as substrate. A
hel
and
nadN
double mutant was only able to grow in the presence of NR, whereas no uptake of NMN was observed.
Autotrophic CO2Fixation byChloroflexus aurantiacus: Study of Glyoxylate Formation and Assimilation via the 3-Hydroxypropionate Cycle
Authors: Herter Sylvia , Farfsing Jan , Gad'On Nasser , Rieder Christoph , Eisenreich Wolfgang , Bacher Adelbert , Fuchs Georg 
Published: July 2002

ABSTRACTIn the facultative autotrophic organismChloroflexus aurantiacus, a phototrophic green nonsulfur bacterium, the Calvin cycle does not appear to be operative in autotrophic carbon assimilation. An alternative cyclic pathway, the 3-hydroxypropionate cycle, has been proposed. In this pathway, acetyl coenzyme A (acetyl-CoA) is assumed to be converted to malate, and two CO2molecules are thereby fixed. Malyl-CoA is supposed to be cleaved to acetyl-CoA, the starting molecule, and glyoxylate, the carbon fixation product. Malyl-CoA cleavage is shown here to be catalyzed by malyl-CoA lyase; this enzyme activity is induced severalfold in autotrophically grown cells. Malate is converted to malyl-CoA via an inducible CoA transferase with succinyl-CoA as a CoA donor. Some enzyme activities involved in the conversion of malonyl-CoA via 3-hydroxypropionate to propionyl-CoA are also induced under autotrophic growth conditions. So far, no clue as to the first step in glyoxylate assimilation has been obtained. One possibility for the assimilation of glyoxylate involves the conversion of glyoxylate to glycine and the subsequent assimilation of glycine. However, such a pathway does not occur, as shown by labeling of whole cells with [1,2-13C2]glycine. Glycine carbon was incorporated only into glycine, serine, and compounds that contained C1units derived therefrom and not into other cell compounds.
In Vivo Synthesis of the Periplasmic Domain of TonB Inhibits Transport through the FecA and FhuA Iron Siderophore Transporters of
Escherichia coli
Authors: Howard S. Peter , Herrmann Christina , Stratilo Chad W. , Braun V. 
Published: July 2002

ABSTRACT

The siderophore transport activities of the two outer membrane proteins FhuA and FecA of
Escherichia coli
require the proton motive force of the cytoplasmic membrane. The energy of the proton motive force is postulated to be transduced to the transport proteins by a protein complex that consists of the TonB, ExbB, and ExbD proteins. In the present study, TonB fragments lacking the cytoplasmic membrane anchor were exported to the periplasm by fusing them to the cleavable signal sequence of FecA. Overexpressed TonB(33-239), TonB(103-239), and TonB(122-239) fragments inhibited transport of ferrichrome by FhuA and of ferric citrate by FecA, transcriptional induction of the
fecABCDE
transport genes by FecA, infection by phage φ80, and killing of cells by colicin M via FhuA. Transport of ferrichrome by FhuAΔ5-160 was also inhibited by TonB(33-239), although FhuAΔ5-160 lacks the TonB box which is involved in TonB binding. The results show that TonB fragments as small as the last 118 amino acids of the protein interfere with the function of wild-type TonB, presumably by competing for binding sites at the transporters or by forming mixed dimers with TonB that are nonfunctional. In addition, the interactions that are inhibited by the TonB fragments must include more than the TonB box, since transport through corkless FhuA was also inhibited. Since the periplasmic TonB fragments cannot assume an energized conformation, these in vivo studies also agree with previous cross-linking and in vitro results, suggesting that neither recognition nor binding to loaded siderophore receptors is the energy-requiring step in the TonB-receptor interactions.
Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes
Authors: Klein Michael , Friedrich Michael , Roger Andrew J. , Hugenholtz Philip , Fishbain Susan , Abicht Heike , Blackall Linda L. , Stahl David A. , Wagner Michael 
Published: July 2002

ABSTRACT

A large fragment of the dissimilatory sulfite reductase genes (
dsrAB
) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of the
dsrAB
gene homologs of the sulfite reducer
Desulfitobacterium dehalogenans
was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of several
Desulfotomaculum
species (low G+C gram-positive division) and two members of the genus
Thermodesulfobacterium
(a separate bacterial division) were monophyletic with δ-proteobacterial DsrAB sequences. The most parsimonious interpretation of these data is that
dsrAB
genes from ancestors of as-yet-unrecognized sulfate reducers within the δ-
Proteobacteria
were laterally transferred across divisions. A number of insertions and deletions in the DsrAB alignment independently support these inferred lateral acquisitions of
dsrAB
genes. Evidence for a
dsrAB
lateral gene transfer event also was found within the δ-
Proteobacteria,
affecting
Desulfobacula toluolica
. The root of the
dsr
tree was inferred to be within the
Thermodesulfovibrio
lineage by paralogous rooting of the alpha and beta subunits. This rooting suggests that the
dsrAB
genes in
Archaeoglobus
species also are the result of an ancient lateral transfer from a bacterial donor. Although these findings complicate the use of
dsrAB
genes to infer phylogenetic relationships among sulfate reducers in molecular diversity studies, they establish a framework to resolve the origins and diversification of this ancient respiratory lifestyle among organisms mediating a key step in the biogeochemical cycling of sulfur.
SseBCD Proteins Are Secreted by the Type III Secretion System of
Salmonella
Pathogenicity Island 2 and Function as a Translocon
Authors: Nikolaus Thomas , Deiwick Jörg , Rappl Catherine , Freeman Jeremy A. , Schröder Werner , Miller Samuel I. , Hensel Michael 
Published: July 2002

ABSTRACT

The type III secretion system encoded by
Salmonella
pathogenicity island 2 (SPI2) is required for systemic infections and intracellular accumulation of
Salmonella enterica
. This system is induced by intracellular
Salmonella
and subsequently transfers effector proteins into the host cell. Growth conditions either inducing expression of the type III secretion system or the secretion of substrate proteins were defined. Here we report the identification of a set of substrate proteins consisting of SseB, SseC, and SseD that are secreted by the SPI2 system in vitro. Secretion was observed if bacterial cells were exposed to acidic pH after growth in minimal medium with limitation of Mg
2+
or phosphate. SseB, -C, and -D were isolated in a fraction detached from the bacterial cell surface by mechanical shearing, indicating that these proteins are predominantly assembled into complexes on the bacterial cell surface. The three proteins were required for the translocation of SPI2 effector proteins SspH1 and SspH2 into infected host cells. Thus, SseB, SseC, and SseD function as the translocon for effector proteins by intracellular
Salmonella
.
TspO as a Modulator of the Repressor/Antirepressor (PpsR/AppA) Regulatory System in
Rhodobacter sphaeroides
2.4.1
Authors: Zeng Xiaohua , Kaplan Samuel 
Published: July 2002

ABSTRACT

The TspO outer membrane protein of
Rhodobacter sphaeroides
has been shown to be involved in controlling the transcription of a number of genes which encode enzymes involved in photopigment biosynthesis and the
puc
operon. The display of regulated genes appears identical to those genes encompassing the PpsR/AppA repressor/antirepressor regulon, although the effect of TspO is modest relative to that of PpsR/AppA. To directly address the hypothesis that TspO is effective through the PpsR/AppA system, we constructed mutant strains with mutations in both
tspO
and
appA
. In all cases, the phenotypes examined resembled those of the
appA
lesion by itself, leading us to conclude that TspO works through or modulates the PpsR/AppA system and acts upstream of the site of action of these regulatory proteins. In earlier publications, we had suggested that TspO is involved in the efflux of a certain intermediate(s) of the porphyrin biosynthesis pathway and that transcriptional regulation of target gene expression could be explained by the accumulation of a coactivator of AppA function. Although the data reported here do not precisely identify this coactivator, they lend support to this hypothesis. We discuss the importance of this form of gene control as the result of the recent extension of the TspO system to
Sinorhizobium meliloti
, as described by Davey and de Bruijn (M. E. Davey and F. J. de Bruijn, Appl. Environ. Microbiol. 66:5353–5359, 2000). It is therefore possible that this system constitutes a more widely, although not universally, demonstrated form of gene regulation.
Localization of Cold Shock Proteins to Cytosolic Spaces Surrounding Nucleoids in
Bacillus subtilis
Depends on Active Transcription
Authors: Weber Michael H. W. , Volkov Arsen V. , Fricke Ingo , Marahiel Mohamed A. , Graumann Peter L. 
Published: July 2002

ABSTRACT

Using immunofluorescence microscopy and a fusion of a cold shock protein (CSP), CspB, to green fluorescent protein (GFP), we showed that in growing cells
Bacillus subtilis
CSPs specifically localize to cytosolic regions surrounding the nucleoid. The subcellular localization of CSPs is influenced by the structure of the nucleoid. Decondensed chromosomes in
smc
mutant cells reduced the sizes of the regions in which CSPs localized, while cold shock-induced chromosome compaction was accompanied by an expansion of the space in which CSPs were present. As a control, histone-like protein HBsu localized to the nucleoids, while β-galactosidase and GFP were detectable throughout the cell. After inhibition of translation, CspB-GFP was still present around the nucleoids in a manner similar to that in cold-shocked cells. However, in stationary-phase cells and after inhibition of transcription, CspB was distributed throughout the cell, indicating that specific localization of CspB depends on active transcription and is not due to simple exclusion from the nucleoid. Furthermore, we observed that nucleoids are more condensed and frequently abnormal in
cspB cspC
and
cspB cspD
double-mutant cells. This suggests that the function of CSPs affects chromosome structure, probably through coupling of transcription to translation, which is thought to decondense nucleoids. In addition, we found that
cspB cspD
and
cspB cspC
double mutants are defective in sporulation, with a block at or before stage 0. Interestingly, CspB and CspC are depleted from the forespore compartment but not from the mother cell. In toto, our findings suggest that CSPs localize to zones of newly synthesized RNA, coupling transcription with initiation of translation.
DNA Microarray Analysis of the Hyperthermophilic Archaeon
Pyrococcus furiosus
: Evidence for a New Type of Sulfur-Reducing Enzyme Complex
Authors: Schut Gerrit J. , Zhou Jizhong , Adams Michael W. W. 
Published: July 2002

ABSTRACT

DNA microarrays were constructed by using 271 open reading frame (ORFs) from the genome of the archaeon
Pyrococcus furiosus.
They were used to investigate the effects of elemental sulfur (S°) on the levels of gene expression in cells grown at 95°C with maltose as the carbon source. The ORFs included those that are proposed to encode proteins mainly involved in the pathways of sugar and peptide catabolism, in the metabolism of metals, and in the biosynthesis of various cofactors, amino acids, and nucleotides. The expression of 21 ORFs decreased by more than fivefold when cells were grown with S° and, of these, 18 encode subunits associated with three different hydrogenase systems. The remaining three ORFs encode homologs of ornithine carbamoyltransferase and HypF, both of which appear to be involved in hydrogenase biosynthesis, as well as a conserved hypothetical protein. The expression of two previously uncharacterized ORFs increased by more than 25-fold when cells were grown with S°. Their products, termed SipA and SipB (for sulfur-induced proteins), are proposed to be part of a novel S°-reducing, membrane-associated, iron-sulfur cluster-containing complex. Two other previously uncharacterized ORFs encoding a putative flavoprotein and a second FeS protein were upregulated more than sixfold in S°-grown cells, and these are also thought be involved in S° reduction. Four ORFs that encode homologs of proteins involved in amino acid metabolism were similarly upregulated in S°-grown cells, a finding consistent with the fact that growth on peptides is a S°-dependent process. An ORF encoding a homolog of the eukaryotic rRNA processing protein, fibrillarin, was also upregulated sixfold in the presence of S°, although the reason for this is as yet unknown. Of the 20 S°-independent ORFs that are the most highly expressed (at more than 20 times the detection limit), 12 of them represent enzymes purified from
P. furiosus,
but none of the products of the 34 S°-independent ORFs that are not expressed above the detection limit have been characterized. These results represent the first derived from the application of DNA microarrays to either an archaeon or a hyperthermophile.
The Initiation Codon Affects Ribosome Binding and Translational Efficiency in
Escherichia coli
of
c
I mRNA with or without the 5′ Untranslated Leader
Authors: O'Donnell Sean M. , Janssen Gary R. 
Published: July 2002

ABSTRACT

Translational efficiency of an AUG, CUG, GUG, or UUG initiation codon was measured for the naturally leaderless
c
I mRNA from bacteriophage λ. In a
c
I-
lacZ
translational fusion, only AUG supported a high level of expression; GUG supported a low level of expression, while UUG and CUG expression was barely above background levels. Addition of an untranslated
lac
leader and Shine-Dalgarno sequence to
c
I increased expression but still showed a dependence on an AUG for maximum expression.
c
I-
lacZ
mRNA with an AUG initiation codon showed a greater in vitro ribosome binding strength and a higher level of full-length in vivo mRNA, suggesting that the initiation codon is an important determinant of ribosome binding strength and translational efficiency for mRNA with or without the 5′ untranslated leader.
Control of
hemA
Expression in
Rhodobacter sphaeroides
2.4.1: Effect of a Transposon Insertion in the
hbdA
Gene
Authors: Fales Linda , Kryszak Luiza , Zeilstra-Ryalls Jill 
Published: July 2002

ABSTRACT

The common precursor to all tetrapyrroles is 5-aminolevulinic acid (ALA), and in
Rhodobacter sphaeroides
its formation occurs via the Shemin pathway. ALA synthase activity is encoded by two differentially regulated genes in
R. sphaeroides
2.4.1:
hemA
and
hemT
. In our investigations of
hemA
regulation, we applied transposon mutagenesis under aerobic conditions, followed by a selection that identified transposon insertion mutants in which
hemA
expression is elevated. One of these mutants has been characterized previously (J. Zeilstra-Ryalls and S. Kaplan, J. Bacteriol. 178:985–993, 1996), and here we describe our analysis of a second mutant strain. The transposon inserted into the coding sequences of
hbdA
, coding for
S
-(+)-β-hydroxybutyryl–coenzyme A dehydrogenase and catalyzing an NAD-dependent reaction. We provide evidence that the
hbdA
gene product participates in polyhydroxybutyrate (PHB) metabolism and, based on our findings, we discuss possibilities as to how defective PHB metabolism might alter the level of
hemA
expression.