bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversification of Lupine
Bradyrhizobium
Strains: Evidence from Nodulation Gene Trees
Authors: Stępkowski Tomasz , Hughes Colin E. , Law Ian J. , Markiewicz Łukasz , Gurda Dorota , Chlebicka Agnieszka , Moulin Lionel 
Published: March 2007

ABSTRACT

Bradyrhizobium
strains isolated in Europe from Genisteae and serradella legumes form a distinct lineage, designated clade II, on nodulation gene trees. Clade II bradyrhizobia appear to prevail also in the soils of Western Australia and South Africa following probably accidental introduction with seeds of their lupine and serradella hosts. Given this potential for dispersal, we investigated
Bradyrhizobium
isolates originating from a range of native New World lupines, based on phylogenetic analyses of nodulation (
nodA
,
nodZ
,
noeI
) and housekeeping (
atpD
,
dnaK
,
glnII
,
recA
) genes. The housekeeping gene trees revealed considerable diversity among lupine bradyrhizobia, with most isolates placed in the
Bradyrhizobium japonicum
lineage, while some European strains were closely related to
Bradyrhizobium canariense
. The
nodA
gene tree resolved seven strongly supported groups (clades I to VII) that correlated with strain geographical origins and to some extent with major
Lupinus
clades. All European strains were placed in clade II, whereas only a minority of New World strains was placed in this clade. This work, as well as our previous studies, suggests that clade II diversified predominately in the Old World, possibly in the Mediterranean. Most New World isolates formed subclade III.2, nested in a large “pantropical” clade III, which appears to be New World in origin, although it also includes strains originating from nonlupine legumes. Trees generated using
nodZ
and
noeI
gene sequences accorded well with the
nodA
tree, but evidence is presented that the
noeI
gene may not be required for nodulation of lupine and that loss of this gene is occurring.
A Marine
Mesorhizobium
sp. Produces Structurally Novel Long-Chain
N
-Acyl-
l
-Homoserine Lactones
Authors: Krick Anja , Kehraus Stefan , Eberl Leo , Riedel Kathrin , Anke Heidrun , Kaesler Ines , Graeber Ingeborg , Szewzyk Ulrich , König Gabriele M. 
Published: March 2007

ABSTRACT

Our study focused on a
Mesorhizobium
sp. that is phylogenetically affiliated by 16S rRNA gene sequence to other marine and saline bacteria of this genus. Liquid chromatography-mass spectrometry investigations of the extract obtained from solid-phase extraction of cultures of this bacterium indicated the presence of several
N
-acyl homoserine lactones (AHLs), with chain lengths of C
10
to C
16
. Chromatographic separation of the active bacterial extract yielded extraordinarily large amounts of two unprecedented acylated homoserine lactones, 5-
cis
-3-oxo-C
12
-homoserine lactone (5-
cis
-3-oxo-C
12
-HSL) (compound 1) and 5-
cis
-C
12
-HSL (compound 2). Quorum-sensing activity of compounds 1 and 2 was shown in two different biosensor systems [
Escherichia coli
MT102(pSB403) and
Pseudomonas putida
F117(pKR-C12)]. Furthermore, it was shown that both compounds can restore protease and pyoverdin production of an AHL-deficient
Pseudomonas aeruginosa
PAO1
lasI rhlI
double mutant, suggesting that these signal molecules maybe used for intergenus signaling. In conclusion, these data indicate that the quorum-sensing activity of compounds 1 and 2 is modulated by the chain length and functional groups of the acyl moiety. Additionally, compound 1 showed antibacterial and cytotoxic activities.
Variable-Number Tandem Repeats as Molecular Markers for Biotypes of
Pasteuria ramosa
in
Daphnia
spp
Authors: Mouton Laurence , Nong Guang , Preston James F. , Ebert Dieter 
Published: March 2007

ABSTRACT

Variable-number tandem repeats (VNTRs) have been identified in populations of
Pasteuria ramosa
, a castrating endobacterium of
Daphnia
species. The allelic polymorphisms at 14 loci in laboratory and geographically diverse soil samples showed that VNTRs may serve as biomarkers for the genetic characterization of
P. ramosa
isolates.
PsrA, the
Pseudomonas
Sigma Regulator, Controls Regulators of Epiphytic Fitness, Quorum-Sensing Signals, and Plant Interactions in
Pseudomonas syringae
pv. tomato Strain DC3000
Authors: Chatterjee Asita , Cui Yaya , Hasegawa Hiroaki , Chatterjee Arun K. 
Published: March 2007

ABSTRACT

Pseudomonas syringae
pv. tomato strain DC3000, a pathogen of tomato and
Arabidopsis
, occurs as an epiphyte. It produces
N
-acyl homoserine lactones (AHLs) which apparently function as quorum-sensing signals. A Tn
5
insertion mutant of DC3000, designated PsrA
−
(Psr is for
Pseudomonas
sigma regulator), overexpresses
psyR
(a LuxR-type regulator of
psyI
) and
psyI
(the gene for AHL synthase), and it produces a ca. 8-fold-higher level of AHL than does DC3000. The mutant is impaired in its ability to elicit the hypersensitive reaction and is attenuated in its virulence in tomato. These phenotypes correlate with reduced expression of
hrpL
, the gene for an alternate sigma factor, as well as several
hrp
and
hop
genes during early stages of incubation in a Hrp-inducing medium. PsrA also positively controls
rpoS
, the gene for an alternate sigma factor known to control various stress responses. By contrast, PsrA negatively regulates
rsmA1
, an RNA-binding protein gene known to function as negative regulator, and
aefR
, a
tetR
-like gene known to control AHL production and epiphytic fitness in
P. syringae
pv. syringae. Gel mobility shift assays and other lines of evidence demonstrate a direct interaction of PsrA protein with
rpoS
promoter DNA and
aefR
operator DNA. In addition, PsrA negatively autoregulates and binds the
psrA
operator. In an AefR
−
mutant, the expression of
psyR
and
psyI
and AHL production are lower than those in DC3000, the AefR
+
parent. In an RpoS
−
mutant, on the other hand, the levels of AHL and transcripts of
psyR
and
psyI
are much higher than those in the RpoS
+
parent, DC3000. We present evidence, albeit indirect, that the RpoS effect occurs via
psyR
. Thus, AefR positively regulates AHL production, whereas RpoS has a strong negative effect. We show that AefR and RpoS do not regulate PsrA and that the PsrA effect on AHL production is exerted via its cumulative, but independent, effects on both AefR and RpoS.
Seasonal Variations in the Contributions of Different Bacterial Groups to the Uptake of Low-Molecular-Weight Compounds in Northwestern Mediterranean Coastal Waters
Authors: Alonso-Sáez Laura , Gasol Josep M. 
Published: March 2007

ABSTRACTWe analyzed the contributions of different heterotrophic bacterial groups to the uptake of several low-molecular weight compounds during a seasonal cycle on the northwestern Mediterranean coast (Blanes Bay Microbial Observatory). The bacterial assemblage structure had been shown to change substantially year-round for this site, but whether changes in the activities of the different bacterial groups also occurred on the seasonal scale was unknown. Microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization was used to analyze the patterns of glucose, amino acid, and ATP uptake by different bacterial groups.GammaproteobacteriaandBacteroideteswere not very active in the uptake of glucose at any time of the year (<10% of cells were active) compared toAlphaproteobacteria(generally >20% of cells were active). Dissolved free amino acids were taken up considerably byAlphaproteobacteriaandGammaproteobacteriabut not byBacteroidetes. Relatively high percentages of cells of the three broad phylogenetic groups actively took up ATP, which could be related to the important phosphorous limitation of bacterial production during most of the year in Blanes Bay. The contribution of SAR11 to the uptake of the monomers was variable year-round, generally with fewer than 30% of the cells being active. By contrast,Roseobacterwere highly overrepresented in the uptake of all the substrates throughout all the year, with more than 50% of cells being active in all the samples and for all substrates. Our results suggest that substantial changes in the activity of some phylogenetic groups of bacteria occur throughout the year.
Use of PCR-Targeted Mutagenesis To Disrupt Production of Fusaricidin-Type Antifungal Antibiotics in
Paenibacillus polymyxa
Authors: Li Jingru , Beatty Perrin K. , Shah Saleh , Jensen Susan E. 
Published: March 2007

ABSTRACT

Paenibacillus polymyxa
(formerly
Bacillus polymyxa
) PKB1 has been identified as a potential agent for biocontrol of blackleg disease of canola, caused by the pathogenic fungus
Leptosphaeria maculans
. The factors presumed to contribute to disease suppression by strain PKB1 include the production of fusaricidin-type antifungal metabolites that appear around the onset of bacterial sporulation. The fusaricidins are a family of lipopeptide antibiotics consisting of a β-hydroxy fatty acid linked to a cyclic hexapeptide. Using a reverse genetic approach based on conserved motifs of nonribosomal peptide synthetases, a DNA fragment that appears to encode the first two modules of the putative fusaricidin synthetase (
fusA
) was isolated from PKB1. To confirm the involvement of
fusA
in production of fusaricidins, a modified PCR targeting mutagenesis protocol was developed to create a
fusA
mutation in PKB1. A DNA fragment internal to
fusA
was replaced by a gene disruption cassette containing two antibiotic resistance genes for independent selection of apramycin resistance in
Escherichia coli
and chloramphenicol resistance in
P. polymyxa
. Inclusion of an
oriT
site in the disruption cassette allowed efficient transfer of the inactivated
fusA
allele to
P. polymyxa
by intergeneric conjugation. Targeted disruption of
fusA
led to the complete loss of antifungal activity against
L. maculans
, suggesting that
fusA
plays an essential role in the nonribosomal synthesis of fusaricidins.
Identification of Unconventional Intestinal Pathogenic
Escherichia coli
Isolates Expressing Intermediate Virulence Factor Profiles by Using a Novel Single-Step Multiplex PCR
Authors: Müller Daniel , Greune Lilo , Heusipp Gerhard , Karch Helge , Fruth Angelika , Tschäpe Helmut , Schmidt M. Alexander 
Published: March 2007

ABSTRACT

Intestinal pathogenic
Escherichia coli
represents a global health problem for mammals, including humans. At present, diarrheagenic
E. coli
bacteria are grouped into seven major pathotypes that differ in their virulence factor profiles, severity of clinical manifestations, and prognosis. In this study, we developed and evaluated a one-step multiplex PCR (MPCR) for the straightforward differential identification of intestinal pathotypes of
E. coli
. The specificity of this novel MPCR was validated by using a subset of reference strains and further confirmed by PCR-independent pheno- and genotypic characterization. Moreover, we tested 246 clinical
E. coli
isolates derived from diarrhea patients from several distinct geographic regions. Interestingly, besides strains belonging to the defined and well-described pathotypes, we identified five unconventional strains expressing intermediate virulence factor profiles. These strains have been further characterized and appear to represent intermediate strains carrying genes and expressing factors associated with enteropathogenic
E. coli
, Shiga toxin-producing
E. coli
, enterotoxigenic
E. coli
, and enteroaggregative
E. coli
alike. These strains represent further examples of the extraordinary plasticity of the
E. coli
genome. Moreover, this implies that the important identification of specific pathotypes has to be based on a broad matrix of indicator genes. In addition, the presence of intermediate strains needs to be accounted for.
Shiga Toxin Gene Loss and Transfer In Vitro and In Vivo during Enterohemorrhagic
Escherichia coli
O26 Infection in Humans
Authors: Bielaszewska Martina , Prager Rita , Köck Robin , Mellmann Alexander , Zhang Wenlan , Tschäpe Helmut , Tarr Phillip I. , Karch Helge 
Published: March 2007

ABSTRACT

Escherichia coli
serogroup O26 consists of enterohemorrhagic
E. coli
(EHEC) and atypical enteropathogenic
E. coli
(aEPEC). The former produces Shiga toxins (Stx), major determinants of EHEC pathogenicity, encoded by bacteriophages; the latter is Stx negative. We have isolated EHEC O26 from patient stools early in illness and aEPEC O26 from stools later in illness, and vice versa. Intrapatient EHEC and aEPEC isolates had quite similar pulsed-field gel electrophoresis (PFGE) patterns, suggesting that they might have arisen by conversion between the EHEC and aEPEC pathotypes during infection. To test this hypothesis, we asked whether EHEC O26 can lose
stx
genes and whether aEPEC O26 can be lysogenized with Stx-encoding phages from EHEC O26 in vitro. The
stx
2
loss associated with the loss of Stx2-encoding phages occurred in 10% to 14% of colonies tested. Conversely, Stx2- and, to a lesser extent, Stx1-encoding bacteriophages from EHEC O26 lysogenized aEPEC O26 isolates, converting them to EHEC strains. In the lysogens and EHEC O26 donors, Stx2-converting bacteriophages integrated in
yecE
or
wrbA
. The loss and gain of Stx-converting bacteriophages diversifies PFGE patterns; this parallels findings of similar but not identical PFGE patterns in the intrapatient EHEC and aEPEC O26 isolates. EHEC O26 and aEPEC O26 thus exist as a dynamic system whose members undergo ephemeral interconversions via loss and gain of Stx-encoding phages to yield different pathotypes. The suggested occurrence of this process in the human intestine has diagnostic, clinical, epidemiological, and evolutionary implications.
Chitosan, the Deacetylated Form of Chitin, Is Necessary for Cell Wall Integrity in
Cryptococcus neoformans
Authors: Baker Lorina G. , Specht Charles A. , Donlin Maureen J. , Lodge Jennifer K. 
Published: March 2007

ABSTRACT

Cryptococcus neoformans
is an opportunistic fungal pathogen that causes cryptococcal meningoencephalitis, particularly in immunocompromised patients. The fungal cell wall is an excellent target for antifungal therapies as it is an essential organelle that provides cell structure and integrity, it is needed for the localization or attachment of known virulence factors, including the polysaccharide capsule, melanin, and phospholipase, and it is critical for host-pathogen interactions. In
C. neoformans
, chitosan produced by the enzymatic removal of acetyl groups from nascent chitin polymers has been implicated as an important component of the vegetative cell wall. In this study, we identify four putative chitin/polysaccharide deacetylases in
C. neoformans
. We have demonstrated that three of these deacetylases, Cda1, Cda2, and Cda3, can account for all of the chitosan produced during vegetative growth in culture, but the function for one, Fpd1, remains undetermined. The data suggest a model for chitosan production in vegetatively growing
C. neoformans
where the three chitin deacetylases convert chitin generated by the chitin synthase Chs3 into chitosan. Utilizing a collection of chitin/polysaccharide deacetylase deletion strains, we determined that during vegetative growth, chitosan helps to maintain cell integrity and aids in bud separation. Additionally, chitosan is necessary for maintaining normal capsule width and the lack of chitosan results in a “leaky melanin” phenotype. Our analysis indicates that chitin deacetylases and the chitosan made by them may prove to be excellent antifungal targets.
Insights into the Autotrophic CO
2
Fixation Pathway of the Archaeon
Ignicoccus hospitalis
: Comprehensive Analysis of the Central Carbon Metabolism
Authors: Jahn Ulrike , Huber Harald , Eisenreich Wolfgang , Hügler Michael , Fuchs Georg 
Published: March 2007

ABSTRACT

Ignicoccus hospitalis
is an autotrophic hyperthermophilic archaeon that serves as a host for another parasitic/symbiotic archaeon,
Nanoarchaeum equitans
. In this study, the biosynthetic pathways of
I. hospitalis
were investigated by in vitro enzymatic analyses, in vivo
13
C-labeling experiments, and genomic analyses. Our results suggest the operation of a so far unknown pathway of autotrophic CO
2
fixation that starts from acetyl-coenzyme A (CoA). The cyclic regeneration of acetyl-CoA, the primary CO
2
acceptor molecule, has not been clarified yet. In essence, acetyl-CoA is converted into pyruvate via reductive carboxylation by pyruvate-ferredoxin oxidoreductase. Pyruvate-water dikinase converts pyruvate into phosphoenolpyruvate (PEP), which is carboxylated to oxaloacetate by PEP carboxylase. An incomplete citric acid cycle is operating: citrate is synthesized from oxaloacetate and acetyl-CoA by a (re)-specific citrate synthase, whereas a 2-oxoglutarate-oxidizing enzyme is lacking. Further investigations revealed that several special biosynthetic pathways that have recently been described for various archaea are operating. Isoleucine is synthesized via the uncommon citramalate pathway and lysine via the α-aminoadipate pathway. Gluconeogenesis is achieved via a reverse Embden-Meyerhof pathway using a novel type of fructose 1,6-bisphosphate aldolase. Pentosephosphates are formed from hexosephosphates via the suggested ribulose-monophosphate pathway, whereby formaldehyde is released from C-1 of hexose. The organism may not contain any sugar-metabolizing pathway. This comprehensive analysis of the central carbon metabolism of
I. hospitalis
revealed further evidence for the unexpected and unexplored diversity of metabolic pathways within the (hyperthermophilic) archaea.
Growth Rate Toxicity Phenotypes and Homeostatic Supercoil Control Differentiate
Escherichia coli
from
Salmonella enterica
Serovar Typhimurium
Authors: Champion Keith , Higgins N. Patrick 
Published: March 2007

ABSTRACT

Escherichia coli
and
Salmonella enterica
serovar Typhimurium share high degrees of DNA and amino acid identity for 65% of the homologous genes shared by the two genomes. Yet, there are different phenotypes for null mutants in several genes that contribute to DNA condensation and nucleoid formation. The mutant R436-S form of the GyrB protein has a temperature-sensitive phenotype in
Salmonella
, showing disruption of supercoiling near the terminus and replicon failure at 42°C. But this mutation in
E. coli
is lethal at the permissive temperature. A unifying hypothesis for why the same mutation in highly conserved homologous genes of different species leads to different physiologies focuses on homeotic supercoil control. During rapid growth in mid-log phase,
E. coli
generates 15% more negative supercoils in pBR322 DNA than
Salmonella
. Differences in compaction and torsional strain on chromosomal DNA explain a complex set of single-gene phenotypes and provide insight into how supercoiling may modulate epigenetic effects on chromosome structure and function and on prophage behavior in vivo.
SpontaneoustrpYMutants and Mutational Analysis of the TrpY Archaeal Transcription Regulator
Authors: Čuboňová L'ubomíra , Sandman Kathleen , Karr Elizabeth A. , Cochran Andrew J. , Reeve John N. 
Published: March 2007

ABSTRACTOver 90% ofMethanothermobacter thermautotrophicusmutants isolated as spontaneously resistant to 5-methyl tryptophan had mutations intrpY. Most were single-base-pair substitutions that identified separate DNA- and tryptophan-binding regions in TrpY. In vivo and in vitro studies revealed that DNA binding was sufficient for TrpY repression oftrpYtranscription but that TrpY must bind DNA and tryptophan to assemble a complex that repressestrpEGCFBAD.
Microcin J25 Has Dual and Independent Mechanisms of Action inEscherichia coli: RNA Polymerase Inhibition and Increased Superoxide Production
Authors: Bellomio Augusto , Vincent Paula A. , de Arcuri Beatriz F. , Farías Ricardo N. , Morero Roberto D. 
Published: March 2007

ABSTRACTMicrocin J25 (MccJ25) uptake byEscherichia colirequires the outer membrane receptor FhuA and the inner membrane proteins TonB, ExbD, ExbB, and SbmA. MccJ25 appears to have two intracellular targets: (i) RNA polymerase (RNAP), which has been described inE. coliandSalmonella entericaserovars, and (ii) the respiratory chain, reported only inS. entericaserovars. In the current study, it is shown that the observed difference between the actions of microcin on the respiratory chain inE. coliandS. entericais due to the relatively low microcin uptake via the chromosomally encoded FhuA. Higher expression by a plasmid-encoded FhuA allowed greater uptake of MccJ25 byE. colistrains and the consequent inhibition of oxygen consumption. The two mechanisms, inhibition of RNAP and oxygen consumption, are independent of each other. Further analysis revealed for the first time that MccJ25 stimulates the production of reactive oxygen species (O2·−) in bacterial cells, which could be the main reason for the damage produced on the membrane respiratory chain.
The Anaerobic Regulatory Network Required for
Pseudomonas aeruginosa
Nitrate Respiration
Authors: Schreiber Kerstin , Krieger Robert , Benkert Beatrice , Eschbach Martin , Arai Hiroyuki , Schobert Max , Jahn Dieter 
Published: March 2007

ABSTRACT

In
Pseudomonas aeruginosa
, the
narK
1
K
2
GHJI
operon encodes two nitrate/nitrite transporters and the dissimilatory nitrate reductase. The
narK
1
promoter is anaerobically induced in the presence of nitrate by the dual activity of the oxygen regulator Anr and the N-oxide regulator Dnr in cooperation with the nitrate-responsive two-component regulatory system NarXL. The DNA bending protein IHF is essential for this process. Similarly,
narXL
gene transcription is enhanced under anaerobic conditions by Anr and Dnr. Furthermore, Anr and NarXL induce expression of the N-oxide regulator gene
dnr
. Finally, NarXL in cooperation with Dnr is required for anaerobic nitrite reductase regulatory gene
nirQ
transcription. A cascade regulatory model for the fine-tuned genetic response of
P. aeruginosa
to anaerobic growth conditions in the presence of nitrate was deduced.
Analysis of LuxR Regulon Gene Expression during Quorum Sensing inVibrio fischeri
Authors: Qin Nan , Callahan Sean M. , Dunlap Paul V. , Stevens Ann M. 
Published: March 2007

ABSTRACTThe regulation of theluxoperon (luxICDABEG) ofVibrio fischerihas been intensively studied as a model for quorum sensing in proteobacteria. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis previously identified several non-Lux proteins inV. fischeriMJ-100 whose expression was dependent on LuxR and 3-oxo-hexanoyl-l-homoserine lactone (3-oxo-C6-HSL). To determine if the LuxR-dependent regulation of the genes encoding these proteins was due to direct transcriptional control by LuxR and 3-oxo-C6-HSL or instead was due to indirect control via an unidentified regulatory element, promoters of interest were cloned into alacZreporter and tested for their LuxR and 3-oxo-C6-HSL dependence in recombinantEscherichia coli. The promoters forqsrP,acfA, andribBwere found to be directly activated via LuxR-3-oxo-C6-HSL. The sites of transcription initiation were established via primer extension analysis. Based on this information and the position of theluxbox-binding site near position −40, all three promoters appear to have a class II-type promoter structure. In order to more fully characterize the LuxR regulon inV. fischeriMJ-100, real-time reverse transcription-PCR was used to study the temporal expression ofqsrP,acfA, andribBduring the exponential and stationary phases of growth, and electrophoretic mobility shift assays were used to compare the binding affinities of LuxR to the promoters under investigation. Taken together, the results demonstrate that regulation of the production of QsrP, RibB, and AcfA is controlled directly by LuxR at the level of transcription, thereby establishing that there is a LuxR regulon inV. fischeriMJ-100 whose genes are coordinately expressed during mid-exponential growth.