bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lactococcus lactis fabH
, Encoding β-Ketoacyl-Acyl Carrier Protein Synthase, Can Be Functionally Replaced by the
Plasmodium falciparum
Congener
Authors: Du Yu , Gisselberg Jolyn E. , Johnson Jacob D. , Lee Patricia J. , Prigge Sean T. , Bachmann Brian O. 
Published: April 2010

ABSTRACT

Plasmodium falciparum
, in addition to scavenging essential fatty acids from its intra- and intercellular environments, possesses a functional complement of type II fatty acid synthase (FAS) enzymes targeted to the apicoplast organelle. Recent evidence suggests that products of the plasmodial FAS II system may be critical for the parasite's liver-to-blood cycle transition, and it has been speculated that endogenously generated fatty acids may be precursors for essential cofactors, such as lipoate, in the apicoplast. β-Ketoacyl-acyl carrier protein (ACP) synthase III (pfKASIII or FabH) is one of the key enzymes in the initiating steps of the FAS II pathway, possessing two functions in
P. falciparum
: the decarboxylative thio-Claisen condensation of malonyl-ACP and various acyl coenzymes A (acyl-CoAs; KAS activity) and the acetyl-CoA:ACP transacylase reaction (ACAT). Here, we report the generation and characterization of a hybrid
Lactococcus lactis
strain that translates pfKASIII instead of
L. lactis f
abH
to initiate fatty acid biosynthesis. The
L. lactis
expression vector pMG36e was modified for the efficient overexpression of the plasmodial gene in
L. lactis
. Transcriptional analysis indicated high-efficiency overexpression, and biochemical KAS and ACAT assays confirm these activities in cell extracts. Phenotypically, the
L. lactis
strain expressing pfKASIII has a growth rate and fatty acid profiles that are comparable to those of the strain complemented with its endogenous gene, suggesting that pfKASIII can use
L. lactis
ACP as substrate and perform near-normal function in
L. lactis
cells. This strain may have potential application as a bacterial model for pfKASIII inhibitor prescreening.
Abolition of Biofilm Formation in Urinary Tract
Escherichia coli
and
Klebsiella
Isolates by Metal Interference through Competition for Fur
Authors: Hancock Viktoria , Dahl Malin , Klemm Per 
Published: April 2010

ABSTRACT

Bacterial biofilms are associated with a large number of persistent and chronic infections. Biofilm-dwelling bacteria are particularly resistant to antibiotics and immune defenses, which makes it hard if not impossible to eradicate biofilm-associated infections. In the urinary tract, free iron is strictly limited but is critical for bacterial growth. Biofilm-associated
Escherichia coli
cells are particularly desperate for iron. An attractive way of inhibiting biofilm formation is to fool the bacterial regulatory system for iron uptake. Here, we demonstrate that biofilm formation can be impaired by the addition of divalent metal ions, such as Zn(II) and Co(II), which inhibit iron uptake by virtue of their higher-than-iron affinity for the master controller protein of iron uptake, Fur. Reduced biofilm formation of urinary tract-infectious
E. coli
strains in the presence of Zn(II) was observed in microtiter plates and flow chambers as well as on urinary catheters. These results further support that iron uptake is indeed crucial for biofilm formation, and thereby, targeting these uptake systems might be an effective way to eradicate biofilms caused by infectious strains.
Application of Multilocus Sequence Typing To Study the Genetic Structure of Megaplasmids in
Medicago
-Nodulating Rhizobia
Authors: van Berkum Peter , Elia Patrick , Eardly Bertrand D. 
Published: April 2010

ABSTRACT

A multilocus sequence typing (MLST) analysis was used to examine the genetic structure and diversity within the two large extrachromosomal replicons in
Medicago
-nodulating rhizobia (
Sinorhizobium meliloti
and
Sinorhizobium medicae
). The allelic diversity within these replicons was high compared to the reported diversity within the corresponding chromosomes of the same strains (P. van Berkum et al., J. Bacteriol. 188:5570-5577, 2006). Also, there was strong localized linkage disequilibrium (LD) between certain pSymA loci: e.g.,
nodC
and
nifD
. Although both of these observations could be explained by positive (or diversifying) selection by plant hosts, results of tests for positive selection did not provide consistent support for this hypothesis. The strong LD observed between the
nodC
and
nifD
genes could also be explained by their close proximity on the pSymA replicon. Evidence was obtained that some
nodC
alleles had a history of intragenic recombination, while other alleles of this locus had a history of intergenic recombination. Both types of recombination were associated with a decline in symbiotic competence with
Medicago sativa
as the host plant. The combined observations of LD between the
nodC
and
nifD
genes and intragenic recombination within one of these loci indicate that the symbiotic gene region on the pSymA plasmid has evolved as a clonal segment, which has been laterally transferred within the natural populations.
Analysis of the Fine-Scale Population Structure of “
Candidatus
Accumulibacter phosphatis” in Enhanced Biological Phosphorus Removal Sludge, Using Fluorescence
In Situ
Hybridization and Flow Cytometric Sorting
Authors: Kim Jeong Myeong , Lee Hyo Jung , Kim Sun Young , Song Jae Jun , Park Woojun , Jeon Che Ok 
Published: April 2010

ABSTRACT

To investigate the fine-scale diversity of the polyphosphate-accumulating organisms (PAO) “
Candidatus
Accumulibacter phosphatis” (henceforth referred to as “
Ca.
Accumulibacter”), two laboratory-scale sequencing batch reactors (SBRs) for enhanced biological phosphorus removal (EBPR) were operated with sodium acetate as the sole carbon source. During SBR operations, activated sludge always contained morphologically different “
Ca
. Accumulibacter” strains showing typical EBPR performances, as confirmed by the combined technique of fluorescence
in situ
hybridization (FISH) and microautoradiography (MAR). Fragments of “
Ca.
Accumulibacter” 16S rRNA genes were retrieved from the sludge. Phylogenetic analyses together with sequences from the GenBank database showed that “
Ca.
Accumulibacter” 16S rRNA genes of the EBPR sludge were clearly differentiated into four “
Ca.
Accumulibacter” clades, Acc-SG1, Acc-SG2, Acc-SG3, and Acc-SG4. The specific FISH probes Acc444, Acc184, Acc72, and Acc119 targeting these clades and some helpers and competitors were designed by using the ARB program. Microbial characterization by FISH analysis using specific FISH probes also clearly indicated the presence of different “
Ca.
Accumulibacter” cell morphotypes. Especially, members of Acc-SG3, targeted by probe Acc72, were coccobacillus-shaped cells with a size of approximately 2 to 3 μm, while members of Acc-SG1, Acc-SG2, and Acc-SG4, targeted by Acc444, Acc184, and Acc119, respectively, were coccus-shaped cells approximately 1 μm in size. Subsequently, cells targeted by each FISH probe were sorted by use of a flow cytometer, and their polyphosphate kinase 1 (
ppk1
) gene homologs were amplified by using a
ppk1
-specific PCR primer set for “
Ca.
Accumulibacter.” The phylogenetic tree based on sequences of the
ppk1
gene homologs was basically congruent with that of the 16S rRNA genes, but members of Acc-SG3 with a distinct morphology comprised two different
ppk1
genes. These results suggest that “
Ca.
Accumulibacter” strains may be diverse physiologically and ecologically and represent distinct populations with genetically determined adaptations in EBPR systems.
Chromosome Stability and Gene Loss in Cockroach Endosymbionts
Authors: Sabree Zakee L. , Degnan Patrick H. , Moran Nancy A. 
Published: April 2010

ABSTRACT

Insect endosymbiont genomes reflect massive gene loss. Two
Blattabacterium
genomes display colinearity and similar gene contents, despite high orthologous gene divergence, reflecting over 140 million years of independent evolution in separate cockroach lineages. We speculate that distant homologs may replace the functions of some eliminated genes through broadened substrate specificity.
Killing of Bacteria by Copper Surfaces Involves Dissolved Copper
Authors: Molteni Cristina , Abicht Helge K. , Solioz Marc 
Published: April 2010

ABSTRACT

Bacteria are rapidly killed on copper surfaces. However, the mechanism of this process remains unclear. Using
Enterococcus hirae
, the effect of inactivation of copper homeostatic genes and of medium compositions on survival and copper dissolution was tested. The results support a role for dissolved copper ions in killing.
Structure, Function, and Insights into the Biosynthesis of a Head-to-Head Hydrocarbon in
Shewanella oneidensis
Strain MR-1
Authors: Sukovich David J. , Seffernick Jennifer L. , Richman Jack E. , Hunt Kristopher A. , Gralnick Jeffrey A. , Wackett Lawrence P. 
Published: April 2010

ABSTRACT

A polyolefinic hydrocarbon was found in nonpolar extracts of
Shewanella oneidensis
MR-1 and identified as 3,6,9,12,15,19,22,25,28-hentriacontanonaene (compound I) by mass spectrometry, chemical modification, and nuclear magnetic resonance spectroscopy. Compound I was shown to be the product of a head-to-head fatty acid condensation biosynthetic pathway dependent on genes denoted as
ole
(for
ole
fin biosynthesis). Four
ole
genes were present in
S. oneidensis
MR-1. Deletion of the entire
oleABCD
gene cluster led to the complete absence of nonpolar extractable products. Deletion of the
oleC
gene alone generated a strain that lacked compound I but produced a structurally analogous ketone. Complementation of the
oleC
gene eliminated formation of the ketone and restored the biosynthesis of compound I. A recombinant
S. oneidensis
strain containing
oleA
from
Stenotrophomonas maltophilia
strain R551-3 produced at least 17 related long-chain compounds in addition to compound I, 13 of which were identified as ketones. A potential role for OleA in head-to-head condensation was proposed. It was further proposed that long-chain polyunsaturated compounds aid in adapting cells to a rapid drop in temperature, based on three observations. In
S. oneidensis
wild-type cells, the cellular concentration of polyunsaturated compounds increased significantly with decreasing growth temperature. Second, the
oleABCD
deletion strain showed a significantly longer lag phase than the wild-type strain when shifted to a lower temperature. Lastly, compound I has been identified in a significant number of bacteria isolated from cold environments.
Widespread Head-to-Head Hydrocarbon Biosynthesis in Bacteria and Role of OleA
Authors: Sukovich David J. , Seffernick Jennifer L. , Richman Jack E. , Gralnick Jeffrey A. , Wackett Lawrence P. 
Published: April 2010

ABSTRACTPrevious studies identified theoleABCDgenes involved in head-to-head olefinic hydrocarbon biosynthesis. The present study more fully defined the OleABCD protein families within the thiolase, α/β-hydrolase, AMP-dependent ligase/synthase, and short-chain dehydrogenase superfamilies, respectively. Only 0.1 to 1% of each superfamily represents likely Ole proteins. Sequence analysis based on structural alignments and gene context was used to identify highly likelyolegenes. Selected microorganisms from the phylaVerucomicrobia,Planctomyces,Chloroflexi,Proteobacteria, andActinobacteriawere tested experimentally and shown to produce long-chain olefinic hydrocarbons. However, different species from the same genera sometimes lack theolegenes and fail to produce olefinic hydrocarbons. Overall, only 1.9% of 3,558 genomes analyzed showed clear evidence for containingolegenes. The type of olefins produced by different bacteria differed greatly with respect to the number of carbon-carbon double bonds. The greatest number of organisms surveyed biosynthesized a single long-chain olefin, 3,6,9,12,15,19,22,25,28-hentriacontanonaene, that contains nine double bonds.Xanthomonas campestrisproduced the greatest number of distinct olefin products, 15 compounds ranging in length from C28to C31and containing one to three double bonds. The type of long-chain product formed was shown to be dependent on theoleAgene in experiments withShewanella oneidensisMR-1olegene deletion mutants containing native or heterologousoleAgenes expressed intrans. A strain deleted inoleABCDand containingoleAintransproduced only ketones. Based on these observations, it was proposed that OleA catalyzes a nondecarboxylative thiolytic condensation of fatty acyl chains to generate a β-ketoacyl intermediate that can decarboxylate spontaneously to generate ketones.
Molecular Detection and Characterization of Aichi Viruses in Sewage-Polluted Waters of Venezuela
Authors: Alcalá Ana , Vizzi Esmeralda , Rodríguez-Díaz Jesús , Zambrano José L. , Betancourt Walter , Liprandi Ferdinando 
Published: April 2010

ABSTRACT
The circulation of Aichi virus in a major urban area was demonstrated using molecular detection with samples recovered from a major river polluted with sewage discharges in Caracas, Venezuela. Five out of 11 water samples studied were positive, being classified by phylogenetic analysis as genotype B. Analysis of sewage waters appears to be a useful methodology to uncover the presence of a hitherto undetected fecal pathogen in a given geographical area.
The Aminolysis Reaction of
Streptomyces
S9 Aminopeptidase Promotes the Synthesis of Diverse Prolyl Dipeptides
Authors: Arima Jiro , Morimoto Masazumi , Usuki Hirokazu , Mori Nobuhiro , Hatanaka Tadashi 
Published: April 2010

ABSTRACT

Prolyl dipeptide synthesis by S9 aminopeptidase from
Streptomyces thermocyaneoviolaceus
(S9AP-St) has been demonstrated. In the synthesis, S9AP-St preferentially used
l
-Pro-OBzl as the acyl donor, yielding synthesized dipeptides having an
l
-Pro-Xaa structure. In addition, S9AP-St showed broad specificity toward the acyl acceptor. Furthermore, S9AP-St produced cyclo (
l
-Pro-
l
-His) with a conversion ratio of substrate to cyclo (
l
-Pro-
l
-His) higher than 40%.
Enterocin X, a Novel Two-Peptide Bacteriocin from
Enterococcus faecium
KU-B5, Has an Antibacterial Spectrum Entirely Different from Those of Its Component Peptides
Authors: Hu Chih-Bo , Malaphan Wanna , Zendo Takeshi , Nakayama Jiro , Sonomoto Kenji 
Published: April 2010

ABSTRACT

Enterocin X, composed of two antibacterial peptides (Xα and Xβ), is a novel class IIb bacteriocin from
Enterococcus faecium
KU-B5. When combined, Xα and Xβ display variably enhanced or reduced antibacterial activity toward a panel of indicators compared to each peptide individually. In
E. faecium
strains that produce enterocins A and B, such as KU-B5, only one additional bacteriocin had previously been known.
Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing
Authors: Harris J. Kirk , Sahl Jason W. , Castoe Todd A. , Wagner Brandie D. , Pollock David D. , Spear John R. 
Published: April 2010

ABSTRACT
Constructing mixtures of tagged or bar-coded DNAs for sequencing is an important requirement for the efficient use of next-generation sequencers in applications where limited sequence data are required per sample. There are many applications in which next-generation sequencing can be used effectively to sequence large mixed samples; an example is the characterization of microbial communities where ≤1,000 sequences per samples are adequate to address research questions. Thus, it is possible to examine hundreds to thousands of samples per run on massively parallel next-generation sequencers. However, the cost savings for efficient utilization of sequence capacity is realized only if the production and management costs associated with construction of multiplex pools are also scalable. One critical step in multiplex pool construction is the normalization process, whereby equimolar amounts of each amplicon are mixed. Here we compare three approaches (spectroscopy, size-restricted spectroscopy, and quantitative binding) for normalization of large, multiplex amplicon pools for performance and efficiency. We found that the quantitative binding approach was superior and represents an efficient scalable process for construction of very large, multiplex pools with hundreds and perhaps thousands of individual amplicons included. We demonstrate the increased sequence diversity identified with higher throughput. Massively parallel sequencing can dramatically accelerate microbial ecology studies by allowing appropriate replication of sequence acquisition to account for temporal and spatial variations. Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel.
Formation and Attachment of the Deoxysugar Moiety and Assembly of the Gene Cluster for Caprazamycin Biosynthesis
Authors: Kaysser Leonard , Wemakor Emmanuel , Siebenberg Stefanie , Salas Jose A. , Sohng Jae Kyung , Kammerer Bernd , Gust Bertolt 
Published: April 2010

ABSTRACT

Caprazamycins are antimycobacterials produced by
Streptomyces
sp. MK730-62F2. Previously, cosmid cpzLK09 was shown to direct the biosynthesis of caprazamycin aglycones, but not of intact caprazamycins. Sequence analysis of cpzLK09 identified 23 genes involved in the formation of the caprazamycin aglycones and the transfer and methylation of the sugar moiety, together with genes for resistance, transport, and regulation. In this study, coexpression of cpzLK09 in
Streptomyces coelicolor
M512 with pRHAM, containing all the required genes for dTDP-
l
-rhamnose biosynthesis, led to the production of intact caprazamycins.
In vitro
studies showed that Cpz31 is responsible for the attachment of the
l
-rhamnose to the caprazamycin aglycones, generating a rare acylated deoxyhexose. An
l
-rhamnose gene cluster was identified elsewhere on the
Streptomyces
sp. MK730-62F2 genome, and its involvement in caprazamycin formation was demonstrated by insertional inactivation of
cpzDIII
. The
l
-rhamnose subcluster was assembled with cpzLK09 using Red/ET-mediated recombination. Heterologous expression of the resulting cosmid, cpzEW07, led to the production of caprazamycins, demonstrating that both sets of genes are required for caprazamycin biosynthesis. Knockouts of
cpzDI
and
cpzDV
in the
l
-rhamnose subcluster confirmed that four genes,
cpzDII
,
cpzDIII
,
cpzDIV
, and
cpzDVI
, are sufficient for the biosynthesis of the deoxysugar moiety. The presented recombineering strategy may provide a useful tool for the assembly of biosynthetic building blocks for heterologous production of microbial compounds.
Genetic Detection of Extended-Spectrum β-Lactamase-Containing
Escherichia coli
Isolates from Birds of Prey from Serra da Estrela Natural Reserve in Portugal
Authors: Pinto Luís , Radhouani Hajer , Coelho Céline , Martins da Costa Paulo , Simões Roméo , Brandão Ricardo M. L. , Torres Carmen , Igrejas Gilberto , Poeta Patrícia 
Published: April 2010

ABSTRACT

Extended-spectrum β-lactamase-containing
Escherichia coli
isolates were detected in 32 of 119 fecal samples (26.9%) from birds of prey at Serra da Estrela, and these isolates contained the following β-lactamases: CTX-M-1 (
n
= 13), CTX-M-1 plus TEM-1 (
n
= 14), CTX-M-1 plus TEM-20 (
n
= 1), SHV-5 (
n
= 1), SHV-5 plus TEM-1 (
n
= 2), and TEM-20 (
n
= 1).
Multiplex Identification of Microbes
Authors: Hyman Richard W. , St.Onge Robert P. , Allen Edward A. , Miranda Molly , Aparicio Ana Maria , Fukushima Marilyn , Davis Ronald W. 
Published: April 2010

ABSTRACT
We have adapted molecular inversion probe technology to identify microbes in a highly multiplexed procedure. This procedure does not require growth of the microbes. Rather, the technology employs DNA homology twice: once for the molecular probe to hybridize to its homologous DNA and again for the 20-mer oligonucleotide barcode on the molecular probe to hybridize to a commercially available molecular barcode array. As proof of concept, we have designed, tested, and employed 192 molecular probes for 40 microbes. While these particular molecular probes are aimed at our interest in the microbes in the human vagina, this molecular probe method could be employed to identify the microbes in any ecological niche.
Characterization of a Thermostable Short-Chain Alcohol Dehydrogenase from the Hyperthermophilic Archaeon
Thermococcus sibiricus
Authors: Stekhanova Tatiana N. , Mardanov Andrey V. , Bezsudnova Ekaterina Y. , Gumerov Vadim M. , Ravin Nikolai V. , Skryabin Konstantin G. , Popov Vladimir O. 
Published: April 2010

ABSTRACT

Short-chain alcohol dehydrogenase, encoded by the gene Tsib_0319 from the hyperthermophilic archaeon
Thermococcus sibiricus
, was expressed in
Escherichia coli
, purified and characterized as an NADPH-dependent enantioselective oxidoreductase with broad substrate specificity. The enzyme exhibits extremely high thermophilicity, thermostability, and tolerance to organic solvents and salts.
TaqMan Real-Time PCR Assays To Assess Arbuscular Mycorrhizal Responses to Field Manipulation of Grassland Biodiversity: Effects of Soil Characteristics, Plant Species Richness, and Functional Traits
Authors: König Stephan , Wubet Tesfaye , Dormann Carsten F. , Hempel Stefan , Renker Carsten , Buscot François 
Published: April 2010

ABSTRACT

Large-scale (temporal and/or spatial) molecular investigations of the diversity and distribution of arbuscular mycorrhizal fungi (AMF) require considerable sampling efforts and high-throughput analysis. To facilitate such efforts, we have developed a TaqMan real-time PCR assay to detect and identify AMF in environmental samples. First, we screened the diversity in clone libraries, generated by nested PCR, of the nuclear ribosomal DNA internal transcribed spacer (ITS) of AMF in environmental samples. We then generated probes and forward primers based on the detected sequences, enabling AMF sequence type-specific detection in TaqMan multiplex real-time PCR assays. In comparisons to conventional clone library screening and Sanger sequencing, the TaqMan assay approach provided similar accuracy but higher sensitivity with cost and time savings. The TaqMan assays were applied to analyze the AMF community composition within plots of a large-scale plant biodiversity manipulation experiment, the Jena Experiment, primarily designed to investigate the interactive effects of plant biodiversity on element cycling and trophic interactions. The results show that environmental variables hierarchically shape AMF communities and that the sequence type spectrum is strongly affected by previous land use and disturbance, which appears to favor disturbance-tolerant members of the genus
Glomus
. The AMF species richness of disturbance-associated communities can be largely explained by richness of plant species and plant functional groups, while plant productivity and soil parameters appear to have only weak effects on the AMF community.