bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iridescence of a Marine Bacterium and Classification of Prokaryotic Structural Colors
Authors: Kientz Betty , Vukusic Peter , Luke Stephen , Rosenfeld Eric 
Published: January 2012

ABSTRACT

Iridescence is a property of structural color that is occasionally encountered in higher eukaryotes but that has been poorly documented in the prokaryotic kingdom. In the present work, we describe a marine bacterium, identified as
Cellulophaga lytica
, isolated from the surface of an anemone, that exhibits bright green iridescent colonies under direct epi-illumination. This phenomenon has not previously been investigated in detail. In this study, color changes of
C. lytica
colonies were observed at various angles of direct illumination or observation. Its iridescent green appearance was dominant on various growth media. Red and violet colors were also discerned on colony edges. Remarkable
C. lytica
bacterial iridescence was revealed and characterized using high-resolution optical spectrometry. In addition to this, by culturing other bacterial strains to which various forms of faintly iridescent traits have previously been attributed, we identify four principal appearance characteristics of structural color in prokaryotes. A new general classification of bacterial iridescence is therefore proposed in this study. Furthermore, a specific separate class is described for iridescent
C. lytica
strains because they exhibit what is so far a unique intense glitter-like iridescence in reflection.
C. lytica
is the first prokaryote discovered to produce the same sort of intense iridescence under direct illumination as that associated with higher eukaryotes, like some insects and birds. Due to the nature of bacterial biology, cultivation, and ubiquity, this discovery may be of significant interest for both ecological and nanoscience endeavors.
Quantitative Trait Locus Mapping of Yield-Related Components and Oligogenic Control of the Cap Color of the Button Mushroom, Agaricus bisporus
Authors: Foulongne-Oriol Marie , Rodier Anne , Rousseau Thierry , Savoie Jean-Michel 
Published: January 2012

ABSTRACT

As in other crops, yield is an important trait to be selected for in edible mushrooms, but its inheritance is poorly understood. Therefore, we have investigated the complex genetic architecture of yield-related traits in
Agaricus bisporus
through the mapping of quantitative trait loci (QTL), using second-generation hybrid progeny derived from a cross between a wild strain and a commercial cultivar. Yield, average weight per mushroom, number of fruiting bodies per m
2
, earliness, and cap color were evaluated in two independent experiments. A total of 23 QTL were detected for 7 yield-related traits. These QTL together explained between 21% (two-flushes yield) and 59% (earliness) of the phenotypic variation. Fifteen QTL (65%) were consistent between the two experiments. Four regions underlying significant QTL controlling yield, average weight, and number were detected on linkage groups II, III, IV, and X, suggesting a pleiotropic effect or tight linkage. Up to six QTL were identified for earliness. The
PPC1
locus, together with two additional genomic regions, explained up to 90% of the phenotypic variation of the cap color. Alleles from the wild parent showed beneficial effects for some yield traits, suggesting that the wild germ plasm is a valuable source of variation for several agronomic traits. Our results constitute a key step toward marker-assisted selection and provide a solid foundation to go further into the biological mechanisms controlling productive traits in the button mushroom.
Link between Culture Zeta Potential Homogeneity and Ebp in Enterococcus faecalis
Authors: Tariq Muhammad , Bruijs Chissa , Kok Jan , Krom Bastiaan P. 
Published: January 2012

ABSTRACT

Enterococcus faecalis
, a commensal of the gastrointestinal tract and an opportunistic pathogen, has the ability to adhere to surfaces and form biofilms. It has been shown earlier that only 10 to 20% of an
E. faecalis
OG1RF culture expresses endocarditis- and biofilm-associated pili (Ebp), which are involved in biofilm formation. Another study revealed that
E. faecalis
clinical isolates, as well as OG1RF, are heterogeneous with respect to their apparent zeta potential, which was also correlated with increased ability to form biofilm. The aim of this study was to demonstrate that the heterogeneity in the presence of Ebp is correlated to that in apparent zeta potential. Heterogeneous cultures of OG1RF showed two distinct subpopulations with the most (−38 mV) and least (−26 mV) negative zeta potential. Deletion of EbpR, the activator of the
ebp
operon, or the structural genes
ebpABC
resulted in homogeneous culture with the most negative zeta potential. Conversely, overexpression of EbpR or the structural genes
ebpABC
resulted in homogeneous culture with the least negative zeta potential. The results show that
ebp
operon expression in
E. faecalis
, as measured by using P

ebp

-
gfp
promoter fusion, is the cause of heterogeneity in zeta potential and that pilus production causes the cells to behave as the least negative particle in an electric field.
Enhanced Staphylolytic Activity of the Staphylococcus aureus Bacteriophage vB_SauS-phiIPLA88 HydH5 Virion-Associated Peptidoglycan Hydrolase: Fusions, Deletions, and Synergy with LysH5
Authors: Rodríguez-Rubio Lorena , Martínez Beatriz , Rodríguez Ana , Donovan David M. , García Pilar 
Published: January 2012

ABSTRACT

Virion-associated peptidoglycan hydrolases have potential as antimicrobial agents due to their ability to lyse Gram-positive bacteria on contact. In this work, our aim was to improve the lytic activity of HydH5, a virion-associated peptidoglycan hydrolase from the
Staphylococcus aureus
bacteriophage vB_SauS-phiIPLA88. Full-length HydH5 and two truncated derivatives containing only the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) domain exhibited high lytic activity against live
S. aureus
cells. In addition, three different fusion proteins were created between lysostaphin and HydH5, each of which showed higher staphylolytic activity than the parental enzyme or its deletion construct. Both parental and fusion proteins lysed
S. aureus
cells in zymograms and plate lysis and turbidity reduction assays. In plate lysis assays, HydH5 and its derivative fusions lysed bovine and human
S. aureus
strains, the methicillin-resistant
S. aureus
(MRSA) strain N315, and human
Staphylococcus epidermidis
strains. Several nonstaphylococcal bacteria were not affected. HydH5 and its derivative fusion proteins displayed antimicrobial synergy with the endolysin LysH5
in vitro
, suggesting that the two enzymes have distinct cut sites and, thus, may be more efficient in combination for the elimination of staphylococcal infections.
Cloning, Baeyer-Villiger Biooxidations, and Structures of the Camphor Pathway 2-Oxo-Δ
3
-4,5,5-Trimethylcyclopentenylacetyl-Coenzyme A Monooxygenase of Pseudomonas putida ATCC 17453
Authors: Leisch Hannes , Shi Rong , Grosse Stephan , Morley Krista , Bergeron Hélène , Cygler Miroslaw , Iwaki Hiroaki , Hasegawa Yoshie , Lau Peter C. K. 
Published: January 2012

ABSTRACT

A dimeric Baeyer-Villiger monooxygenase (BVMO) catalyzing the lactonization of 2-oxo-Δ
3
-4,5,5-trimethylcyclopentenylacetyl-coenzyme A (CoA), a key intermediate in the metabolism of camphor by
Pseudomonas putida
ATCC 17453, had been initially characterized in 1983 by Ougham and coworkers (H. J. Ougham, D. G. Taylor, and P. W. Trudgill, J. Bacteriol. 153:140–152, 1983). Here we cloned and overexpressed the 2-oxo-Δ
3
-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase (OTEMO) in
Escherichia coli
and determined its three-dimensional structure with bound flavin adenine dinucleotide (FAD) at a 1.95-Å resolution as well as with bound FAD and NADP
+
at a 2.0-Å resolution. OTEMO represents the first homodimeric type 1 BVMO structure bound to FAD/NADP
+
. A comparison of several crystal forms of OTEMO bound to FAD and NADP
+
revealed a conformational plasticity of several loop regions, some of which have been implicated in contributing to the substrate specificity profile of structurally related BVMOs. Substrate specificity studies confirmed that the 2-oxo-Δ
3
-4,5,5-trimethylcyclopentenylacetic acid coenzyme A ester is preferred over the free acid. However, the catalytic efficiency (
k
cat
/

K
m

) favors 2-
n
-hexyl cyclopentanone (4.3 × 10
5
M
−1
s
−1
) as a substrate, although its affinity (

K
m

= 32 μM) was lower than that of the CoA-activated substrate (

K
m

= 18 μM). In whole-cell biotransformation experiments, OTEMO showed a unique enantiocomplementarity to the action of the prototypical cyclohexanone monooxygenase (CHMO) and appeared to be particularly useful for the oxidation of 4-substituted cyclohexanones. Overall, this work extends our understanding of the molecular structure and mechanistic complexity of the type 1 family of BVMOs and expands the catalytic repertoire of one of its original members.
Increased Furan Tolerance in Escherichia coli Due to a Cryptic
ucpA
Gene
Authors: Wang Xuan , Miller Elliot N. , Yomano Lorraine P. , Shanmugam K. T. , Ingram Lonnie O. 
Published: January 2012

ABSTRACT

Expression arrays were used to identify 4 putative oxidoreductases that were upregulated (>3-fold) by furfural (15 mM, 15 min). Plasmid expression of one (
ucpA
) increased furan tolerance in ethanologenic strain LY180 and wild-type strain W. Deleting
ucpA
decreased furfural tolerance. Although the mechanism remains unknown, the cryptic
ucpA
gene is now associated with a phenotype: furan resistance.
Genome-Based Reconstruction of the Protein Import Machinery in the Secondary Plastid of a Chlorarachniophyte Alga
Authors: Hirakawa Yoshihisa , Burki Fabien , Keeling Patrick J. 
Published: January 2012

ABSTRACT

Most plastid proteins are encoded by their nuclear genomes and need to be targeted across multiple envelope membranes. In vascular plants, the translocons at the outer and inner envelope membranes of chloroplasts (TOC and TIC, respectively) facilitate transport across the two plastid membranes. In contrast, several algal groups harbor more complex plastids, the so-called secondary plastids, which are surrounded by three or four membranes, but the plastid protein import machinery (in particular, how proteins cross the membrane corresponding to the secondary endosymbiont plasma membrane) remains unexplored in many of these algae. To reconstruct the putative protein import machinery of a secondary plastid, we used the chlorarachniophyte alga
Bigelowiella natans
, whose plastid is bounded by four membranes and still possesses a relict nucleus of a green algal endosymbiont (the nucleomorph) in the intermembrane space. We identified nine homologs of plant-like TOC/TIC components in the recently sequenced
B. natans
nuclear genome, adding to the two that remain in the nucleomorph genome (
B. natans
TOC75 [BnTOC75] and BnTIC20). All of these proteins were predicted to be localized to the plastid and might function in the inner two membranes. We also show that the homologs of a protein, Der1, that is known to mediate transport across the second membrane in the several lineages with secondary plastids of red algal origin is not associated with plastid protein targeting in
B. natans
. How plastid proteins cross this membrane remains a mystery, but it is clear that the protein transport machinery of chlorarachniophyte plastids differs from that of red algal secondary plastids.
Insights into the Gene Expression Profile of Uncultivable Hemotrophic Mycoplasma suis during Acute Infection, Obtained Using Proteome Analysis
Authors: Felder Kathrin M. , Carranza Paula M. , Gehrig Peter M. , Roschitzki Bernd , Barkow-Oesterreicher Simon , Hoelzle Katharina , Riedel Katharina , Kube Michael , Hoelzle Ludwig E. 
Published: January 2012

ABSTRACTHemotrophic mycoplasmas, bacteria without cell walls whose niche is the erythrocytes of their hosts, have never been cultivatedin vitro. Therefore, knowledge of their pathogenesis is fundamental.Mycoplasma suisinfects pigs, causing either acute fatal hemolytic anemia or chronic low-grade anemia, growth retardation, and immune suppression. Recently, the complete genomes of two hemotrophic mycoplasma species,M. suisandM. haemofelis, were sequenced, offering new strategies for the analysis of their pathogenesis. In this study we implemented a proteomic approach to identifyM. suisproteins during acute infection by using tandem mass spectrometry. Twenty-two percent of the predicted proteins encoded inM. suisstrain KI_3806 were identified. These included nearly all encoded proteins of glycolysis and nucleotide metabolism. The proteins for lipid metabolism, however, were underrepresented. A high proportion of the detected proteins are involved in information storage and processing (72.6%). In addition, several proteins of different functionalities, i.e., posttranslational modification, membrane genesis, signal transduction, intracellular trafficking, inorganic ion transport, and defense mechanisms, were identified. In its reduced genome,M. suisharbors 65.3% (strain Illinois) and 65.9% (strain KI_3806) of the genes encode hypothetical proteins. Of these, only 6.3% were identified at the proteome level. All proteins identified in this study are present in bothM. suisstrains and are encoded in more highly conserved regions of the genome sequence. In conclusion, our proteome approach is a further step toward the elucidation of the pathogenesis and life cycle ofM. suisas well as the establishment of anin vitrocultivation system.
Perturbation of the Oxidizing Environment of the Periplasm Stimulates the PhoQ/PhoP System in Escherichia coli
Authors: Lippa Andrew M. , Goulian Mark 
Published: January 2012

ABSTRACT

The PhoQ/PhoP two-component system is repressed by divalent cations, such as Mg
2+
and Ca
2+
, in the growth medium and stimulated by low pH and certain cationic antimicrobial peptides. In
Escherichia coli
, it was recently shown that the histidine kinase PhoQ is also modulated by at least two additional factors, the small membrane proteins SafA and MgrB. This raises the possibility that the PhoQ/PhoP circuit has additional regulatory components and integrates additional input signals. We screened
E. coli
transposon insertion mutants to look for proteins that modulate the activity of the PhoQ/PhoP system, and we uncovered a role for DsbA, a periplasmic oxidant that facilitates the formation of disulfide bonds. Deletion of
dsbA
or
dsbB
, which maintains a pool of oxidized DsbA, leads to increased transcription of at least two PhoP-regulated genes. Addition of the reducing agent dithiothreitol to wild-type cells had a similar effect, and treatment of a
dsbA
null strain with the oxidant Cu
2+
rescued the reporter gene expression phenotype. We also demonstrated that expression of an MgrB mutant that lacked cysteines blocked the effect of a
dsbA
null mutation on PhoQ/PhoP activity, suggesting that MgrB acts downstream of DsbA in this pathway. Taken together, these results demonstrate that a decrease in the oxidizing activity of the periplasm stimulates PhoQ/PhoP and may reveal a new input stimulus for this important two-component system.
Francisella tularensis RipA Protein Topology and Identification of Functional Domains
Authors: Mortensen Brittany L. , Fuller James R. , Taft-Benz Sharon , Collins Edward J. , Kawula Thomas H. 
Published: January 2012

ABSTRACT

Francisella tularensis
is a Gram-negative coccobacillus and is the etiological agent of the disease tularemia. Expression of the cytoplasmic membrane protein RipA is required for
Francisella
replication within macrophages and other cell types; however, the function of this protein remains unknown. RipA is conserved among all sequenced
Francisella
species, and RipA-like proteins are present in a number of individual strains of a wide variety of species scattered throughout the prokaryotic kingdom. Cross-linking studies revealed that RipA forms homoligomers. Using a panel of RipA-green fluorescent protein and RipA-PhoA fusion constructs, we determined that RipA has a unique topology within the cytoplasmic membrane, with the N and C termini in the cytoplasm and periplasm, respectively. RipA has two significant cytoplasmic domains, one composed roughly of amino acids 1 to 50 and the second flanked by the second and third transmembrane domains and comprising amino acids 104 to 152. RipA functional domains were identified by measuring the effects of deletion mutations, amino acid substitution mutations, and spontaneously arising intragenic suppressor mutations on intracellular replication, induction of interleukin-1β (IL-1β) secretion by infected macrophages, and oligomer formation. Results from these experiments demonstrated that each of the cytoplasmic domains and specific amino acids within these domains are required for RipA function.
OnpA, an Unusual Flavin-Dependent Monooxygenase Containing a Cytochrome
b
5
Domain
Authors: Xiao Yi , Liu Ting-Ting , Dai Hui , Zhang Jun-Jie , Liu Hong , Tang Huiru , Leak David J. , Zhou Ning-Yi 
Published: January 2012

ABSTRACT

ortho
-Nitrophenol 2-monooxygenase (EC 1.14.13.31) from
Alcaligenes
sp. strain NyZ215 catalyzes monooxygenation of
ortho
-nitrophenol to form catechol via
ortho
-benzoquinone. Sequence analysis of this
onpA
-encoded enzyme revealed that it contained a flavin-binding monooxygenase domain and a heme-binding cytochrome
b
5
domain. OnpA was purified to homogeneity as a His-tagged protein and was considered a monomer, as determined by gel filtration. FAD and heme were identified by high-performance liquid chromatography (HPLC) and HPLC-mass spectrometry (HPLC-MS) as cofactors in this enzyme, and quantitative analysis indicated that 1 mol of the purified recombinant OnpA contained 0.66 mol of FAD and 0.20 mol of heme. However, the enzyme activity of OnpA was increased by 60% and 450% after addition of FAD and hemin, respectively, suggesting that the optimal stoichiometry was 1:1:1. In addition, site-directed mutagenesis experiments confirmed that two highly conserved histidines located in the cytochrome
b
5
domain were associated with binding of the heme, and the cytochrome
b
5
domain was involved in the OnpA activity. These results indicate that OnpA is an unusual FAD-dependent monooxygenase containing a fused cytochrome
b
5
domain that is essential for its activity. Therefore, we here demonstrate a link between cytochrome
b
5
and flavin-dependent monooxygenases.
Expression of Multidrug Resistance Efflux Pump Gene
norA
Is Iron Responsive in Staphylococcus aureus
Authors: Deng Xin , Sun Fei , Ji Quanjiang , Liang Haihua , Missiakas Dominique , Lan Lefu , He Chuan 
Published: January 2012

ABSTRACT

Staphylococcus aureus
utilizes efflux transporter NorA to pump out a wide range of structurally dissimilar drugs, conferring low-level multidrug resistance. The regulation of
norA
expression has yet to be fully understood although past studies have revealed that this gene is under the control of the global transcriptional regulator MgrA and the two-component system ArlRS. To identify additional regulators of
norA
, we screened a transposon library in strain Newman expressing the transcriptional fusion
norA-lacZ
for altered β-galactosidase activity. We identify a transposon insertion in
fhuB
, a gene that encodes a ferric hydroxamate uptake system permease, and propose that the
norA
transcription is iron responsive. In agreement with this observation, addition of FeCl
3
repressed the induction of
norA-lacZ
, suggesting that bacterial iron uptake plays an important role in regulating
norA
transcription. In addition, a
fur
(ferric uptake regulator) deletion exhibited compromised
norA
transcription and reduced resistance to quinolone compared to the wild-type strain, indicating that
fur
functions as a positive regulator of
norA
. A putative Fur box identified in the promoter region of
norA
was confirmed by electrophoretic mobility shift and DNase I footprint assays. Finally, by employing a siderophore secretion assay, we reveal that NorA may contribute to the export of siderophores. Collectively, our experiments uncover some novel interactions between cellular iron level and
norA
regulation in
S. aureus
.
Group X Aldehyde Dehydrogenases of Pseudomonas aeruginosa PAO1 Degrade Hydrazones
Authors: Taniyama Kosuke , Itoh Hideomi , Takuwa Atsushi , Sasaki Yasuyuki , Yajima Shunsuke , Toyofuku Masanori , Nomura Nobuhiko , Takaya Naoki 
Published: January 2012

ABSTRACT

Hydrazones are natural and synthetic compounds containing a C=N-N moiety. Here we found that the opportunistic pathogen
Pseudomonas aeruginosa
PAO1 produced NAD
+
- or NADP
+
-dependent hydrazone dehydrogenase (HDH), which converts hydrazones to the corresponding hydrazides and acids rather than to the simple hydrolytic product aldehydes. Gene cloning indicated that the HDH is part of the group X aldehyde dehydrogenase (ALDH) family, which is distributed among bacteria, although the physiological roles of the ALDH family remain unknown. The PAO1 strain upregulated HDH in the presence of the hydrazone adipic acid bis(ethylidene hydrazide) (AEH). Gene disruption of the HDH-encoding
hdhA
(PA4022) decreased growth rates in culture medium containing AEH as the sole carbon source, and this effect was more obvious in the double gene disruption of
hdhA
and its orthologous
exaC
(PA1984), indicating that these genes are responsible for hydrazone utilization. Recombinant proteins of group X ALDHs from
Escherichia coli
,
Paracoccus denitrificans
, and
Ochrobactrum anthropi
also acted as HDHs in that they produced HDH activity in the cells and degraded hydrazones. These findings indicated the physiological roles of group X ALDHs in bacteria and showed that they comprise a distinct ALDH subfamily.
Dynamics ofspeBmRNA Transcripts in Streptococcus pyogenes
Authors: Chen Zhiyun , Itzek Andreas , Malke Horst , Ferretti Joseph J. , Kreth Jens 
Published: January 2012

ABSTRACTStreptococcus pyogenes(group A streptococcus [GAS]) is a human-specific pathogen that causes a variety of diseases ranging from superficial infections to life-threatening diseases. SpeB, a potent extracellular cysteine proteinase, plays an important role in the pathogenesis of GAS infections. Previous studies show that SpeB expression and activity are controlled at the transcriptional and posttranslational levels, though it had been unclear whetherspeBwas also regulated at the posttranscriptional level. In this study, we examined the growth phase-dependentspeBmRNA level and decay using quantitative reverse transcription-PCR (qRT-PCR) and Northern blot analyses. We observed thatspeBmRNA accumulated rapidly during exponential growth, which occurred concomitantly with an increase inspeBmRNA stability. A closer observation revealed that the increasedspeBmRNA stability was mainly due to progressive acidification. Inactivation of RNase Y, a recently identified endoribonuclease, revealed a role in processing and degradation ofspeBmRNA. We conclude that the increasedspeBmRNA stability contributes to the rapid accumulation ofspeBtranscript during growth.