bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes
Authors: Pei Anna Y. , Oberdorf William E. , Nossa Carlos W. , Agarwal Ankush , Chokshi Pooja , Gerz Erika A. , Jin Zhida , Lee Peng , Yang Liying , Poles Michael , Brown Stuart M. , Sotero Steven , DeSantis Todd , Brodie Eoin , Nelson Karen , Pei Zhiheng 
Published: April 2010

ABSTRACT

Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (
http://nihroadmap.nih.gov/hmp
). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 ± 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% ± 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in
Haloarcula marismortui
(diversity, 5.63%) and
Thermoanaerobacter tengcongensis
(6.70%) were highly conserved at the 2° structure level, while the diversified gene in
B. afzelii
(20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in “
Candidatus
Protochlamydia amoebophila.” Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases.
Caenorhabditis elegans
as an Alternative Model Host for
Legionella pneumophila
, and Protective Effects of
Bifidobacterium infantis
Authors: Komura Tomomi , Yasui Chikako , Miyamoto Hiroshi , Nishikawa Yoshikazu 
Published: April 2010

ABSTRACT

The survival times of
Caenorhabditis elegans
worms infected with
Legionella pneumophila
from day 7.5 or later after hatching were shorter than those of uninfected worms. However, nematodes fed bifidobacteria prior to
Legionella
infection were resistant to
Legionella
. These nematodes may act as a unique alternative host for
Legionella
research.
Species-Specific Type II Restriction-Modification System ofXylella fastidiosaTemecula1
Authors: Matsumoto Ayumi , Igo Michele M. 
Published: April 2010

ABSTRACTThe transformation efficiency ofXylella fastidiosacan be increased by interfering with restriction by the strain-specific type II system encoded by the PD1607 and PD1608 genes. Here, we report results for two strategies:in vitromethylation using M.SssI and isolation of DNA from anEscherichia colistrain expressing the methylase PD1607.
TDP-
l
-Megosamine Biosynthesis Pathway Elucidation and Megalomicin A Production in
Escherichia coli
Authors: Useglio Mariana , Peirú Salvador , Rodríguez Eduardo , Labadie Guillermo R. , Carney John R. , Gramajo Hugo 
Published: April 2010

ABSTRACT

In vivo
reconstitution of the TDP-
l
-megosamine pathway from the megalomicin gene cluster of
Micromonospora megalomicea
was accomplished by the heterologous expression of its biosynthetic genes in
Escherichia coli.
Mass spectrometric analysis of the TDP-sugar intermediates produced from operons containing different sets of genes showed that the production of TDP-
l
-megosamine from TDP-4-keto-6-deoxy-
d
-glucose requires only five biosynthetic steps, catalyzed by MegBVI, MegDII, MegDIII, MegDIV, and MegDV. Bioconversion studies demonstrated that the sugar transferase MegDI, along with the helper protein MegDVI, catalyzes the transfer of
l
-megosamine to either erythromycin C or erythromycin D, suggesting two possible routes for the production of megalomicin A. Analysis
in vivo
of the hydroxylation step by MegK indicated that erythromycin C is the intermediate of megalomicin A biosynthesis.
Low Pore Connectivity Increases Bacterial Diversity in Soil
Authors: Carson Jennifer K. , Gonzalez-Quiñones Vanesa , Murphy Daniel V. , Hinz Christoph , Shaw Jeremy A. , Gleeson Deirdre B. 
Published: April 2010

ABSTRACT

One of soil microbiology's most intriguing puzzles is how so many different bacterial species can coexist in small volumes of soil when competition theory predicts that less competitive species should decline and eventually disappear. We provide evidence supporting the theory that low pore connectivity caused by low water potential (and therefore low water content) increases the diversity of a complex bacterial community in soil. We altered the pore connectivity of a soil by decreasing water potential and increasing the content of silt- and clay-sized particles. Two textures were created, without altering the chemical properties or mineral composition of the soil, by adding silt- and clay-sized particles of quartz to a quartz-based sandy soil at rates of 0% (sand) or 10% (silt+clay). Both textures were incubated at several water potentials, and the effect on the active bacterial communities was measured using terminal restriction fragment length polymorphism (TRFLP) of bacterial 16S rRNA. Bacterial richness and diversity increased as water potential decreased and soil became drier (
P
< 0.012), but they were not affected by texture (
P
> 0.553). Bacterial diversity increased at water potentials of ≤2.5 kPa in sand and ≤4.0 kPa in silt+clay, equivalent to ≤56% water-filled pore space (WFPS) in both textures. The bacterial community structure in soil was affected by both water potential and texture (
P
< 0.001) and was correlated with WFPS (sum of squared correlations [δ
2
] = 0.88,
P
< 0.001). These findings suggest that low pore connectivity is commonly experienced by soil bacteria under field conditions and that the theory of pore connectivity may provide a fundamental principle to explain the high diversity of bacteria in soil.
TbPRMT6 Is a Type I Protein Arginine Methyltransferase That Contributes to Cytokinesis in Trypanosoma brucei
Authors: Fisk John C. , Zurita-Lopez Cecilia , Sayegh Joyce , Tomasello Danielle L. , Clarke Steven G. , Read Laurie K. 
Published: April 2010

ABSTRACT

Arginine methylation is a widespread posttranslational modification of proteins catalyzed by a family of protein arginine methyltransferases (PRMTs). In
Saccharomyces cerevisiae
and mammals, this modification affects multiple cellular processes, such as chromatin remodeling leading to transcriptional regulation, RNA processing, DNA repair, and cell signaling. The protozoan parasite
Trypanosoma brucei
possesses five putative PRMTs in its genome. This is a large number of PRMTs relative to other unicellular eukaryotes, suggesting an important role for arginine methylation in trypanosomes. Here, we present the
in vitro
and
in vivo
characterization of a
T. brucei
enzyme homologous to human PRMT6, which we term TbPRMT6. Like human PRMT6, TbPRMT6 is a type I PRMT, catalyzing the production of monomethylarginine and asymmetric dimethylarginine residues. In
in vitro
methylation assays, TbPRMT6 utilizes bovine histones as a substrate, but it does not methylate several
T. brucei
glycine/arginine-rich proteins. As such, it exhibits a relatively narrow substrate specificity compared to other
T. brucei
PRMTs. Knockdown of TbPRMT6 in both procyclic form and bloodstream form
T. brucei
leads to a modest but reproducible effect on parasite growth in culture. Moreover, upon TbPRMT6 depletion, both PF and BF exhibit aberrant morphologies indicating defects in cell division, and these defects differ in the two life cycle stages. Mass spectrometry of TbPRMT6-associated proteins reveals histones, components of the nuclear pore complex, and flagellar proteins that may represent TbPRMT6 substrates contributing to the observed growth and morphological defects.
Transcriptional Response to Hypoxia in the Aquatic Fungus Blastocladiella emersonii
Authors: Camilo César M. , Gomes Suely L. 
Published: April 2010

ABSTRACT

Global gene expression analysis was carried out with
Blastocladiella emersonii
cells subjected to oxygen deprivation (hypoxia) using cDNA microarrays. In experiments of gradual hypoxia (gradual decrease in dissolved oxygen) and direct hypoxia (direct decrease in dissolved oxygen), about 650 differentially expressed genes were observed. A total of 534 genes were affected directly or indirectly by oxygen availability, as they showed recovery to normal expression levels or a tendency to recover when cells were reoxygenated. In addition to modulating many genes with no putative assigned function,
B. emersonii
cells respond to hypoxia by readjusting the expression levels of genes responsible for energy production and consumption. At least transcriptionally, this fungus seems to favor anaerobic metabolism through the upregulation of genes encoding glycolytic enzymes and lactate dehydrogenase and the downregulation of most genes coding for tricarboxylic acid (TCA) cycle enzymes. Furthermore, genes involved in energy-costly processes, like protein synthesis, amino acid biosynthesis, protein folding, and transport, had their expression profiles predominantly downregulated during oxygen deprivation, indicating an energy-saving effort. Data also revealed similarities between the transcriptional profiles of cells under hypoxia and under iron(II) deprivation, suggesting that Fe
2+
ion could have a role in oxygen sensing and/or response to hypoxia in
B. emersonii
. Additionally, treatment of fungal cells prior to hypoxia with the antibiotic geldanamycin, which negatively affects the stability of mammalian hypoxia transcription factor HIF-1α, caused a significant decrease in the levels of certain upregulated hypoxic genes.
Detailed
In Vivo
Analysis of the Role of
Helicobacter pylori
Fur in Colonization and Disease
Authors: Miles Shana , Piazuelo M. Blanca , Semino-Mora Cristina , Washington Mary Kay , Dubois Andre , Peek Richard M. , Correa Pelayo , Merrell D. Scott 
Published: April 2010

ABSTRACT

Helicobacter pylori
persistently colonizes the harsh and dynamic environment of the stomach in over one-half of the world's population and has been identified as a causal agent in a spectrum of pathologies that range from gastritis to invasive adenocarcinoma. The ferric uptake regulator (Fur) is one of the few regulatory proteins that has been identified in
H. pylori
. Fur regulates genes important for acid acclimation and oxidative stress and has been shown to be important for colonization of
H. pylori
in both murine and Mongolian gerbil models of infection. To more thoroughly define the role of Fur
in vivo
, we conducted an extensive temporal analysis of the location of, competitive ability of, and resultant pathology induced by a Δ
fur
strain in the Mongolian gerbil model of infection and compared the results to results for its wild-type parent. We found that at the earliest time points postinfection, significantly more Δ
fur
bacteria than wild-type bacteria were recovered. However, this trend was reversed by day 3, when there was significantly increased recovery of the wild-type strain. The increased recovery of the Δ
fur
strain at 1 day postinfection reflected increased recovery from both the corpus and the antrum of the stomach. When the wild-type strain was allowed to colonize first, the Δ
fur
strain was unable to compete for colonization at any time postinfection. However, when the Δ
fur
strain was allowed to colonize first, the wild type efficiently outcompeted the Δ
fur
strain only at early times postinfection. Finally, we demonstrated that there was a delay in the development and severity of inflammation and pathology of the Δ
fur
strain in the gastric mucosa even after comparable levels of colonization occurred. Together, these data indicate that
H. pylori
Fur is most important at early stages of infection and illustrate the importance of the ability of
H. pylori
to adapt to its constantly fluctuating environment when it is establishing infection, inflammation, and disease.
Three Paralogous LysR-Type Transcriptional Regulators Control Sulfur Amino Acid Supply in
Streptococcus mutans
Authors: Sperandio Brice , Gautier Céline , Pons Nicolas , Ehrlich Dusko S. , Renault Pierre , Guédon Eric 
Published: April 2010

ABSTRACT

The genome of
Streptococcus mutans
encodes 4 LysR-type transcriptional regulators (LTTRs), three of which, MetR, CysR (
cys
teine synthesis
r
egulator), and HomR (
hom
ocysteine synthesis
r
egulator), are phylogenetically related. MetR was previously shown to control methionine metabolic gene expression. Functional analysis of CysR and HomR was carried out by phenotypical studies and transcriptional analysis. CysR is required to activate the transcription of
cysK
encoding the cysteine biosynthesis enzyme,
tcyABC
and
gshT
genes encoding cysteine and glutathione transporter systems, and
homR
. HomR activates the transcription of
metBC
encoding methionine biosynthesis enzymes,
tcyDEFGH
involved in cysteine transport, and still uncharacterized thiosulfate assimilation genes. Control of HomR by CysR provides evidence of a cascade regulation for sulfur amino acid metabolism in
S. mutans
. Two conserved motifs were found in the promoter regions of CysR and HomR target genes, suggesting their role in the regulator binding recognition site. Both CysR and HomR require
O
-acetylserine to activate transcription. A global sulfur amino acid supply gene regulatory pathway is proposed for
S. mutans
, including the cascade regulation consequent to transcriptional activation of HomR by CysR. Phylogenetic study of MetR, CysR, and HomR homologues and comparison of their potential regulatory patterns among the
Streptococcaceae
suggest their rapid evolution.
The Virulence of aDickeya dadantii3937 Mutant Devoid of Osmoregulated Periplasmic Glucans Is Restored by Inactivation of the RcsCD-RcsB Phosphorelay
Authors: Bouchart Franck , Boussemart Gilles , Prouvost Anne-France , Cogez Virginie , Madec Edwige , Vidal Olivier , Delrue Brigitte , Bohin Jean-Pierre , Lacroix Jean-Marie 
Published: April 2010

ABSTRACTDickeya dadantiiis a pectinolytic phytopathogen enterobacterium that causes soft rot disease on a wide range of plant species. The virulence ofD. dadantiiinvolves several factors, including the osmoregulated periplasmic glucans (OPGs) that are general constituents of the envelope of proteobacteria. In addition to the loss of virulence,opg-negative mutants display a pleiotropic phenotype, including decreased motility and increased exopolysaccharide synthesis. A nitrosoguanidine-induced mutagenesis was performed on theopgGstrain, and restoration of motility was used as a screen. The phenotype of theopgmutant echoes that of the Rcs system: high level activation of the RcsCD-RcsB phosphorelay is needed to activate exopolysaccharide synthesis and to repress motility, while low level activation is required for virulence in enterobacteria. Here, we show that mutations in the RcsCDB phosphorelay system restored virulence and motility in aD. dadantii opg-negative strain, indicating a relationship between the Rcs phosphorelay and OPGs.
Methanococci Use the Diaminopimelate Aminotransferase (DapL) Pathway for Lysine Biosynthesis
Authors: Liu Yuchen , White Robert H. , Whitman William B. 
Published: April 2010

ABSTRACT

The pathway of lysine biosynthesis in the methanococci has not been identified previously. A variant of the diaminopimelic acid (DAP) pathway uses diaminopimelate aminotransferase (DapL) to catalyze the direct conversion of tetrahydrodipicolinate (THDPA) to
ll
-DAP. Recently, the enzyme DapL (MTH52) was identified in
Methanothermobacter thermautotrophicus
and shown to belong to the DapL1 group. Although the
Methanococcus maripaludis
genome lacks a gene that can be unambiguously assigned a DapL function based on sequence similarity, the open reading frame MMP1527 product shares 30% amino acid sequence identity with MTH52. A Δ
mmp1527
deletion mutant was constructed and found to be a lysine auxotroph, suggesting that this DapL homolog in methanococci is required for lysine biosynthesis. In cell extracts of the
M. maripaludis
wild-type strain, the specific activity of DapL using
ll
-DAP and α-ketoglutarate as substrates was 24.3 ± 2.0 nmol min
−1
mg of protein
−1
. The gene encoding the DapL homolog in
Methanocaldococcus jannaschii
(MJ1391) was cloned and expressed in
Escherichia coli
, and the protein was purified. The maximum activity of MJ1391 was observed at 70°C and pH 8.0 to 9.0. The apparent

K
m

s of MJ1391 for
ll
-DAP and α-ketoglutarate were 82.8 ± 10 μM and 0.42 ± 0.02 mM, respectively. MJ1391 was not able to use succinyl-DAP or acetyl-DAP as a substrate. Phylogenetic analyses suggested that two lateral gene transfers occurred in the DapL genes, one from the archaea to the bacteria in the DapL2 group and one from the bacteria to the archaea in the DapL1 group. These results demonstrated that the DapL pathway is present in marine methanogens belonging to the
Methanococcales
.
Repression of
recA
Induction by RecX Is Independent of the RecA Protein in
Deinococcus radiodurans
Authors: Sheng Duohong , Li Mingfeng , Jiao Jiandong , Sheng Xiehuang , Deng Wenqiang , Hua Yuejin 
Published: April 2010

ABSTRACT

Besides inhibiting RecA activity at the protein level,
Deinococcus radiodurans
RecX can suppress RecA induction at the transcriptional level. The regulation of RecX on
recA
induction is independent of RecA activity, and its N terminus is involved in this process.
Multiple Signals Direct the Assembly and Function of a Type 1 Secretion System
Authors: Masi Muriel , Wandersman Cécile 
Published: April 2010

ABSTRACT

Type 1 secretion systems (T1SS) are present in a wide range of Gram-negative bacteria and are involved in the secretion of diverse substrates such as proteases, lipases, and hemophores. T1SS consist of three proteins: an inner membrane ABC (ATP binding cassette) protein, a periplasmic adaptor, and an outer membrane channel of the TolC family. Assembly of the tripartite complex is transient and induced upon binding of the substrate to the ABC protein. It is generally accepted that T1SS-secreted proteins have a C-terminal secretion signal required for secretion and that this signal interacts with the ABC protein. However, we have previously shown that for the
Serratia marcescens
hemophore HasA, interactions with the ABC protein and subsequent T1SS assembly require additional regions. In this work, we characterize these regions and demonstrate that they are numerous, distributed throughout the HasA polypeptide, and most likely linear. Together with the C-terminal signal, these elements maximize the secretion of HasA. The data also show that the C-terminal signal of HasA triggers HasD-driven ATP hydrolysis, leading to disassembly of the complex. These data support a model of type 1 secretion involving a multistep interaction between the substrate and the ABC protein that stabilizes the assembled secretion system until the C terminus is presented. This model also supports tight coupling between synthesis and secretion.
Initiation of Decay of
Bacillus subtilis rpsO
mRNA by Endoribonuclease RNase Y
Authors: Yao Shiyi , Bechhofer David H. 
Published: April 2010

ABSTRACT

rpsO
mRNA, a small monocistronic mRNA that encodes ribosomal protein S15, was used to study aspects of mRNA decay initiation in
Bacillus subtilis
. Decay of
rpsO
mRNA in a panel of 3′-to-5′ exoribonuclease mutants was analyzed using a 5′-proximal oligonucleotide probe and a series of oligonucleotide probes that were complementary to overlapping sequences starting at the 3′ end. The results provided strong evidence that endonuclease cleavage in the body of the message, rather than degradation from the native 3′ end, is the rate-determining step for mRNA decay. Subsequent to endonuclease cleavage, the upstream products were degraded by polynucleotide phosphorylase (PNPase), and the downstream products were degraded by the 5′ exonuclease activity of RNase J1. The
rpsO
mRNA half-life was unchanged in a strain that had decreased RNase J1 activity and no RNase J2 activity, but it was 2.3-fold higher in a strain with decreased activity of RNase Y, a recently discovered RNase of
B. subtilis
encoded by the
ymdA
gene. Accumulation of full-length
rpsO
mRNA and its decay intermediates was analyzed using a construct in which the
rpsO
transcription unit was under control of a bacitracin-inducible promoter. The results were consistent with RNase Y-mediated initiation of decay. This is the first report of a specific mRNA whose stability is determined by RNase Y.
Complete Genome Sequence of the Photosynthetic Purple Nonsulfur Bacterium
Rhodobacter capsulatus
SB 1003
Authors: Strnad Hynek , Lapidus Alla , Paces Jan , Ulbrich Pavel , Vlcek Cestmir , Paces Vaclav , Haselkorn Robert 
Published: April 2010

ABSTRACT

Rhodobacter capsulatus
SB 1003 belongs to the group of purple nonsulfur bacteria. Its genome consists of a 3.7-Mb chromosome and a 133-kb plasmid. The genome encodes genes for photosynthesis, nitrogen fixation, utilization of xenobiotic organic substrates, and synthesis of polyhydroxyalkanoates. These features made it a favorite research tool for studying these processes. Here we report its complete genome sequence.
Genome Sequences of
Oceanicola granulosus
HTCC2516
T
and
O
ceanicola batsensis
HTCC2597
T
Authors: Thrash J. Cameron , Cho Jang-Cheon , Vergin Kevin L. , Giovannoni Stephen J. 
Published: April 2010

ABSTRACT

Genome sequences from the prolific
Roseobacter
clade in the
Alphaproteobacteria
are beginning to reveal the genetic basis for the diverse lifestyles of these organisms. Here we present the genome sequences of
Oceanicola granulosus
HTCC2516
T
and
O
ceanicola batsensis
HTCC2597
T
, two marine
Roseobacter
species isolated from the Sargasso Sea using dilution-to-extinction culturing, whose genomes encode for significant differences in metabolic potential.
YieJ (CbrC) Mediates CreBC-Dependent Colicin E2 Tolerance in
Escherichia coli
Authors: Cariss S. James L. , Constantinidou Chrystala , Patel Mala D. , Takebayashi Yuiko , Hobman Jon L. , Penn Charles W. , Avison Matthew B. 
Published: April 2010

ABSTRACT

Colicin E2-tolerant (known as Cet2)
Escherichia coli
K-12 mutants overproduce an inner membrane protein, CreD, which is believed to cause the Cet2 phenotype. Here, we show that overproduction of CreD in a Cet2 strain results from hyperactivation of the CreBC two-component regulator, but CreD overproduction is not responsible for the Cet2 phenotype. Through microarray analysis and gene knockout and overexpression studies, we show that overexpression of another CreBC-regulated gene,
yieJ
(also known as
cbrC
), causes the Cet2 phenotype.