bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Genome of the Novel Phage Rtp, with a Rosette-Like Tail Tip, IsHomologous to the Genome of Phage T1
Authors: Wietzorrek Andreas , Schwarz Heinz , Herrmann Christina , Braun Volkmar 
Published: February 2006

ABSTRACTAnewEscherichia coliphage, named Rtp, was isolated and shown to be closely related to phage T1. Electron microscopy revealed that phage Rtp has a morphologically unique tail tip consisting of four leaf-like structures arranged in a rosette, whereas phage T1 has thinner, flexible leaves that thicken toward the ends. In contrast to T1, Rtp did not require FhuA and TonB for infection. The 46.2-kb genome of phage Rtp encodes 75 open reading frames, 47 of which are homologous to phage T1 genes. Like phage T1, phage Rtp encodes a large number of small genes at the genome termini that exhibit no sequence similarity to known genes. Six predicted genes larger than 300 nucleotides in the highly homologous region of Rtp are not found in T1. Two predicted HNH endonucleases are encoded at positions different from those in phage T1. The sequence similarity ofrtp37, -38, -39, -41, -42, and -43to equally arranged genes of lambdoid phages suggests a common tail assembly initiation complex. Protein Rtp43 is homologous to the λ J protein, which determines λ host specificity. Since the two proteins differ most in the C-proximal area, where the binding site to the LamB receptor resides in the J protein, we propose that Rtp43 contributes to Rtp host specificity. Lipoproteins similar to the predicted lipoprotein Rtp45 are found in a number of phages (encoded bycorgenes) in which they prevent superinfection by inactivating the receptors. We propose that, similar to the proposed function of the phage T5 lipoprotein, Rtp45 prevents inactivation of Rtp by adsorption to its receptor during cells lysis. Rtp52 is a putative transcriptional regulator, for which 10 conserved inverted repeats were identified upstream of genes in the Rtp genome. In contrast, the much largerE. coligenome has only one such repeat sequence.
Lethal Mutations in the Isoprenoid Pathway of
Salmonella enterica
Authors: Cornish Rita M. , Roth John R. , Poulter C. Dale 
Published: February 2006

ABSTRACT

Essential isoprenoid compounds are synthesized using the 2-
C
-methyl-
d
-erythritol 4-phosphate (MEP) pathway in many gram-negative bacteria, some gram-positive bacteria, some apicomplexan parasites, and plant chloroplasts. The alternative mevalonate pathway is found in archaea and eukaryotes, including cytosolic biosynthesis in plants. The existence of orthogonal essential pathways in eukaryotes and bacteria makes the MEP pathway an attractive target for the development of antimicrobial agents. A system is described for identifying mutations in the MEP pathway of
Salmonella enterica
serovar Typhimurium. Using this system, point mutations induced by diethyl sulfate were found in the all genes of the essential MEP pathway and also in genes involved in uptake of methylerythritol. Curiously, none of the MEP pathway genes could be identified in the same parent strain by transposon mutagenesis, despite extensive searches. The results complement the biochemical and bioinformatic approaches to the elucidation of the genes involved in the MEP pathway and also identify key residues for activity in the enzymes of the pathway.
Quorum Sensing inYersinia enterocoliticaControls Swimming and Swarming Motility
Authors: Atkinson Steve , Chang Chien-Yi , Sockett R. Elizabeth , Cámara Miguel , Williams Paul 
Published: February 2006

ABSTRACTTheYersinia enterocoliticaLuxI homologue YenI directs the synthesis ofN-3-(oxohexanoyl)homoserine lactone (3-oxo-C6-HSL) andN-hexanoylhomoserine lactone (C6-HSL). In aY. enterocolitica yenImutant, swimming motility is temporally delayed while swarming motility is abolished. Since both swimming and swarming are flagellum dependent, we purified the flagellin protein from the parent andyenImutant. Electrophoresis revealed that in contrast to the parent strain, theyenImutant grown for 17 h at 26°C lacked the 45-kDa flagellin protein FleB. Reverse transcription-PCR indicated that while mutation ofyenIhad no effect onyenR,flhDC(the motility master regulator) orfliA(the flagellar sigma factor) expression,fleB(the flagellin structural gene) was down-regulated. Since 3-oxo-C6-HSL and C6-HSL did not restore swimming or swarming in theyenImutant, we reexamined theN-acylhomoserine lactone (AHL) profile ofY. enterocolitica. Using AHL biosensors and mass spectrometry, we identified three additional AHLs synthesized via YenI:N-(3-oxodecanoyl)homoserine lactone,N-(3-oxododecanoyl)homoserine lactone (3-oxo-C12-HSL), andN-(3-oxotetradecanoyl)homoserine lactone. However, none of the long-chain AHLs either alone or in combination with the short-chain AHLs restored swarming or swimming in theyenImutant. By investigating the transport of radiolabeled 3-oxo-C12-HSL and by introducing an AHL biosensor into theyenImutant we demonstrate that the inability of exogenous AHLs to restore motility to theyenImutant is not related to a lack of AHL uptake. However, both AHL synthesis and motility were restored by complementation of theyenImutant with a plasmid-borne copy ofyenI.
Genetic Diversity inMycobacterium ulceransIsolates from Ghana Revealed by a Newly Identified Locus Containing a Variable Number of Tandem Repeats
Authors: Hilty Markus , Yeboah-Manu Dorothy , Boakye Daniel , Mensah-Quainoo Ernestina , Rondini Simona , Schelling Esther , Ofori-Adjei David , Portaels Françoise , Zinsstag Jakob , Pluschke Gerd 
Published: February 2006

ABSTRACTThe molecular typing methods used so far forMycobacterium ulceransisolates have not been able to identify genetic differences among isolates from Africa. This apparent lack of genetic diversity amongM. ulceransisolates is indicative of a clonal population structure. We analyzed the genetic diversity of 72 African isolates, including 57 strains from Ghana, by variable number of tandem repeat (VNTR) typing based on a newly identified polymorphic locus designated ST1 and the previously described locus MIRU 1. Three different genotypes were found in Ghana, demonstrating for the first time the genetic diversity ofM. ulceransin an African country. While the ST1/MIRU 1 allele combination BD/BAA seems to dominate in Africa, it was only rarely found in isolates from Ghana, where the combination BD/B was dominant and observed in all districts studied. A third variant genotype (C/BAA) was found only in the Amansie-West district. The results indicate that new genetic variants ofM. ulceransemerged and spread within Ghana and support the potential of VNTR-based typing for genotyping ofM. ulcerans.
Roles of Charged Residues of Rotor and Stator in Flagellar Rotation: Comparative Study using H
+
-Driven and Na
+
-Driven Motors in
Escherichia coli
Authors: Yakushi Toshiharu , Yang Junghoon , Fukuoka Hajime , Homma Michio , Blair David F. 
Published: February 2006

ABSTRACT

In
Escherichia coli
, rotation of the flagellar motor has been shown to depend upon electrostatic interactions between charged residues of the stator protein MotA and the rotor protein FliG. These charged residues are conserved in the Na
+
-driven polar flagellum of
Vibrio alginolyticus
, but mutational studies in
V. alginolyticus
suggested that they are relatively unimportant for motor rotation. The electrostatic interactions detected in
E. coli
therefore might not be a general feature of flagellar motors, or, alternatively, the
V. alginolyticus
motor might rely on similar interactions but incorporate additional features that make it more robust against mutation. Here, we have carried out a comparative study of chimeric motors that were resident in
E. coli
but engineered to use
V. alginolyticus
stator components, rotor components, or both. Charged residues in the
V. alginolyticus
rotor and stator proteins were found to be essential for motor rotation when the proteins functioned in the setting of the
E. coli
motor. Patterns of synergism and suppression in rotor/stator double mutants indicate that the
V. alginolyticus
proteins interact in essentially the same way as their counterparts in
E. coli
. The robustness of the rotor-stator interface in
V. alginolyticus
is in part due to the presence of additional charged residues in PomA but appears mainly due to other factors, because an
E. coli
motor using both rotor and stator components from
V. alginolyticus
remained sensitive to mutation. Motor function in
V. alginolyticus
may be enhanced by the proteins MotX and MotY.
The Genome Sequence of the Obligately Chemolithoautotrophic, Facultatively Anaerobic Bacterium
Thiobacillus denitrificans
Authors: Beller Harry R. , Chain Patrick S. G. , Letain Tracy E. , Chakicherla Anu , Larimer Frank W. , Richardson Paul M. , Coleman Matthew A. , Wood Ann P. , Kelly Donovan P. 
Published: February 2006

ABSTRACT

The complete genome sequence of
Thiobacillus denitrificans
ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, β-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding
c
-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for
T. denitrificans
and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including
sox
genes,
dsr
genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of
T. denitrificans
will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by β-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.
ParABS Systems of the Four Replicons ofBurkholderia cenocepacia: New Chromosome Centromeres Confer Partition Specificity
Authors: Dubarry Nelly , Pasta Franck , Lane David 
Published: February 2006

ABSTRACTMost bacterial chromosomes carry an analogue of theparABSsystems that govern plasmid partition, but their role in chromosome partition is ambiguous.parABSsystems might be particularly important for orderly segregation of multipartite genomes, where their role may thus be easier to evaluate. We have characterizedparABSsystems inBurkholderia cenocepacia, whose genome comprises three chromosomes and one low-copy-number plasmid. A singleparABlocus and a set of ParB-binding (parS) centromere sites are located near the origin of each replicon. ParA and ParB of the longest chromosome are phylogenetically similar to analogues in other multichromosome and monochromosome bacteria but are distinct from those of smaller chromosomes. The latter form subgroups that correspond to the taxa of their hosts, indicating evolution from plasmids. TheparSsites on the smaller chromosomes and the plasmid are similar to the “universal”parSof the main chromosome but with a sequence specific to their replicon. In anEscherichia coliplasmid stabilization test, eachparABexhibits partition activity only with theparSof its own replicon. Hence,parABSfunction is based on the independent partition of individual chromosomes rather than on a single communal system or network of interacting systems. Stabilization by the smaller chromosome and plasmid systems was enhanced by mutation ofparSsites and a promoter internal to theirparABoperons, suggesting autoregulatory mechanisms. The small chromosome ParBs were found to silence transcription, a property relevant to autoregulation.
The Bifunctional FtsK Protein Mediates Chromosome Partitioning and Cell Division in
Caulobacter
Authors: Wang Sherry C. E. , West Lisandra , Shapiro Lucy 
Published: February 2006

ABSTRACT

Bacterial chromosome partitioning and cell division are tightly connected cellular processes. We show here that the
Caulobacter crescentus
FtsK protein localizes to the division plane, where it mediates multiple functions involved in chromosome segregation and cytokinesis. The first 258 amino acids of the N terminus are necessary and sufficient for targeting the protein to the division plane. Furthermore, the FtsK N terminus is required to either assemble or maintain FtsZ rings at the division plane. The FtsK C terminus is essential in
Caulobacter
and is involved in maintaining accurate chromosome partitioning. In addition, the C-terminal region of FtsK is required for the localization of the topoisomerase IV ParC subunit to the replisome to facilitate chromosomal decatenation prior to cell division. These results suggest that the interdependence between chromosome partitioning and cell division in
Caulobacte
r is mediated, in part, by the FtsK protein.
Solution Structure of a Low-Molecular-Weight Protein Tyrosine Phosphatase from
Bacillus subtilis
Authors: Xu Huimin , Xia Bin , Jin Changwen 
Published: February 2006

ABSTRACT

The low-molecular-weight (LMW) protein tyrosine phosphatases (PTPs) exist ubiquitously in prokaryotes and eukaryotes and play important roles in cellular processes. We report here the solution structure of YwlE, an LMW PTP identified from the gram-positive bacteria
Bacillus subtilis.
YwlE consists of a twisted central four-stranded parallel β-sheet with seven α-helices packing on both sides. Similar to LMW PTPs from other organisms, the conformation of the YwlE active site is favorable for phosphotyrosine binding, indicating that it may share a common catalytic mechanism in the hydrolysis of phosphate on tyrosine residue in proteins. Though the overall structure resembles that of the eukaryotic LMW PTPs, significant differences were observed around the active site. Residue Asp115 is likely interacting with residue Arg13 through electrostatic interaction or hydrogen bond interaction to stabilize the conformation of the active cavity, which may be a unique character of bacterial LMW PTPs. Residues in the loop region from Phe40 to Thr48 forming a wall of the active cavity are more flexible than those in other regions. Ala41 and Gly45 are located near the active cavity and form a noncharged surface around it. These unique properties demonstrate that this loop may be involved in interaction with specific substrates. In addition, the results from spin relaxation experiments elucidate further insights into the mobility of the active site. The solution structure in combination with the backbone dynamics provides insights into the mechanism of substrate specificity of bacterial LMW PTPs.
A Mobile Quorum-Sensing System inSerratia marcescens
Authors: Wei Jun-Rong , Tsai Yu-Huan , Horng Yu-Tze , Soo Po-Chi , Hsieh Shang-Chen , Hsueh Po-Ren , Horng Jim-Tong , Williams Paul , Lai Hsin-Chih 
Published: February 2006

ABSTRACTQuorum-sensing systems that have been widely identified in bacteria play important roles in the regulation of bacterial multicellular behavior by which bacteria sense population density to control various biological functions, including virulence. One characteristic of theluxIRquorum-sensing genes is their diverse and discontinuous distribution among proteobacteria. Here we report that thespnIRquorum-sensing system identified in the enterobacteriumSerratia marcescensstrain SS-1 is carried in a transposon, TnTIR, which has common characteristics of Tn3family transposons and is mobile between chromosomes and plasmids of different enterobacterial hosts. SpnIR functions in the new host and was shown to negatively regulate the TnTIRtransposition frequency. This finding may help reveal the horizontal transfer and evolutionary mechanism of quorum-sensing genes and alter the way that we perceive regulation of bacterial multicellular behavior.
Assembly of Distinct Pilus Structures on the Surface of
Corynebacterium diphtheriae
Authors: Gaspar Andrew H. , Ton-That Hung 
Published: February 2006

ABSTRACT

Different surface organelles contribute to specific interactions of a pathogen with host tissues or infectious partners. Multiple pilus gene clusters potentially encoding different surface structures have been identified in several gram-positive bacterial genomes sequenced to date, including actinomycetales, clostridia, corynebacteria, and streptococci.
Corynebacterium diphtheriae
has been shown to assemble a pilus structure, with sortase SrtA essential for the assembly of a major subunit SpaA and two minor proteins, SpaB and SpaC. We report here the characterization of a second pilus consisting of SpaD, SpaE, and SpaF, of which SpaD and SpaE form the pilus shaft and SpaF may be located at the pilus tip. The structure of the SpaDEF pilus contains no SpaABC pilins as detected by immunoelectron microscopy. Neither deletion of
spaA
nor sortase
srtA
abolishes SpaDEF pilus formation. The assembly of the SpaDEF pilus requires specific sortases located within the SpaDEF pilus gene cluster. Although either sortase SrtB or SrtC is sufficient to polymerize SpaDF, the incorporation of SpaE into the SpaD pili requires sortase SrtB. In addition, an alanine in place of the lysine of the SpaD pilin motif abrogates pilus polymerization. Thus, SpaD, SpaE, and SpaF constitute a different pilus structure that is independently assembled and morphologically distinct from the SpaABC pili and possibly other pili of
C. diphtheriae
.
In the
Bacillus stearothermophilus
DnaB-DnaG Complex, the Activities of the Two Proteins Are Modulated by Distinct but Overlapping Networks of Residues
Authors: Thirlway Jenny , Soultanas Panos 
Published: February 2006

ABSTRACT

We demonstrate the primase activity of
Bacillus stearothermophilus
DnaG and show that it initiates at 3′-ATC-5′ and 3′-ATT-5′ sites synthesizing primers that are 22 or 23 nucleotides long. In the presence of the helicase DnaB the size distribution of primers is different, and a range of additional smaller primers are also synthesized. Nine residues from the N- and C-terminal domains of DnaB, as well as its linker region, have been reported previously to affect this interaction. In
Bacillus stearothermophilus
only three residues from the linker region (I119 and I125) and the N-terminal domain (Y88) of DnaB have been shown previously to have direct structural importance, and I119 and I125 mediate DnaG-induced effects on DnaB activity. The functions of the other residues (L138, T191, E192, R195, and M196) are still a mystery. Here we show that the E15A, Y88A, and E15A Y88A mutants bind DnaG but are not able to modulate primer size, whereas the R195A M196A mutant inhibited the primase activity. Therefore, four of these residues, E15 and Y88 (N-terminal domain) and R195 and M196 (C-terminal domain), mediate DnaB-induced effects on DnaG activity. Overall, the data suggest that the effects of DnaB on DnaG activity and vice versa are mediated by distinct but overlapping networks of residues.
Influence of CrgA on Assembly of the Cell Division Protein FtsZ during Development of
Streptomyces coelicolor
Authors: Del Sol Ricardo , Mullins Jonathan G. L. , Grantcharova Nina , Flärdh Klas , Dyson Paul 
Published: February 2006

ABSTRACT

The product of the
crgA
gene of
Streptomyces coelicolor
represents a novel family of small proteins. A single orthologous gene is located close to the origin of replication of all fully sequenced actinomycete genomes and borders a conserved gene cluster implicated in cell growth and division. In
S. coelicolor
, CrgA is important for coordinating growth and cell division in sporogenic hyphae. In this study, we demonstrate that CrgA is an integral membrane protein whose peak expression is coordinated with the onset of development of aerial hyphae. The protein localizes to discrete foci away from growing hyphal tips. Upon overexpression, CrgA localizes to apical syncytial cells of aerial hyphae and inhibits the formation of productive cytokinetic rings of the bacterial tubulin homolog FtsZ, leading to proteolytic turnover of this major cell division determinant. In the absence of known prokaryotic cell division inhibitors in actinomycetes, CrgA may have an important conserved function influencing Z-ring formation in these bacteria.
Genetic and Transcriptional Analysis of the Siderophore Malleobactin Biosynthesis and Transport Genes in the Human Pathogen
Burkholderia pseudomallei
K96243
Authors: Alice Alejandro F. , López Claudia S. , Lowe Carolyn A. , Ledesma Maria A. , Crosa Jorge H. 
Published: February 2006

ABSTRACT

Burkholderia pseudomallei
is a gram-negative facultative intracellular pathogen that causes melioidosis, an invasive disease of humans and animals. To address the response of this bacterium to iron-limiting conditions, we first performed a global transcriptional analysis of RNA extracted from bacteria grown under iron-limiting and iron-rich conditions by microarrays. We focused our study on those open reading frames (ORFs) induced under iron limitation, which encoded predicted proteins that could be involved in the biosynthesis and uptake of the siderophore malleobactin. We purified this siderophore and determined that it consisted of at least three compounds with different molecular weights. We demonstrated that ORFs BPSL1776 and BPSL1774, designated
mbaA
and
mbaF
, respectively, are involved in the biosynthesis of malleobactin, while BPSL1775, named
fmtA
, is involved in its transport. These genes are in an operon with two other ORFs (
mbaJ
and
mbaI
) whose transcription is under the control of MbaS, a protein that belongs to the extracytoplasmic function sigma factors. Interestingly, the transcription of the
mbaA
,
fmtA
, and
mbaS
genes is not controlled by the availability of the siderophore malleobactin.
Tetrapyrrole Biosynthesis in
Rhodobacter capsulatus
Is Transcriptionally Regulated by the Heme-Binding Regulatory Protein, HbrL
Authors: Smart James L. , Bauer Carl E. 
Published: February 2006

ABSTRACT

We demonstrate that the expression of
hem
genes in
Rhodobacter capsulatus
is transcriptionally repressed in response to the exogenous addition of heme. A high-copy suppressor screen for regulators of
hem
gene expression resulted in the identification of an LysR-type transcriptional regulator, called HbrL, that regulates
hem
promoters in response to the availability of heme. HbrL is shown to activate the expression of
hemA
and
hemZ
in the absence of exogenous hemin and repress
hemB
expression in the presence of exogenous hemin. Heterologously expressed HbrL apoprotein binds heme
b
and is purified with bound heme
b
when expressed in the presence of 5-aminolevulinic acid. Electrophoretic gel shift analysis demonstrated that HbrL binds the promoter region of
hemA
,
hemB
, and
hemZ
as well as its own promoter and that the presence of heme increases the binding affinity of HbrL to
hemB.