bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Ratio of Bacteriochlorophyll Biosynthesis Genes to Chlorophyll Biosynthesis Genes in Bacteria of Humic Lakes
Authors: Eiler Alexander , Beier Sara , Säwström Christin , Karlsson Jan , Bertilsson Stefan 
Published: October 2009

ABSTRACT
Recent studies highlight the diversity and significance of marine phototrophic microorganisms such as picocyanobacteria, phototrophic picoeukaryotes, and bacteriochlorophyll- and rhodopsin-holding phototrophic bacteria. To assess if freshwater ecosystems also harbor similar phototroph diversity, genes involved in the biosynthesis of bacteriochlorophyll and chlorophyll were targeted to explore oxygenic and aerobic anoxygenic phototroph composition in a wide range of lakes. Partial dark-operative protochlorophyllide oxidoreductase (DPOR) and chlorophyllide oxidoreductase (COR) genes in bacteria of seven lakes with contrasting trophic statuses were PCR amplified, cloned, and sequenced. Out of 61 sequences encoding the L subunit of DPOR (L-DPOR), 22 clustered with aerobic anoxygenic photosynthetic bacteria, whereas 39 L-DPOR sequences related to oxygenic phototrophs, like cyanobacteria, were observed. Phylogenetic analysis revealed clear separation of these freshwater L-DPOR genes as well as 11 COR gene sequences from their marine counterparts. Terminal restriction fragment length analysis of L-DPOR genes was used to characterize oxygenic aerobic and anoxygenic photosynthesizing populations in 20 lakes differing in physical and chemical characteristics. Significant differences in L-DPOR community composition were observed between dystrophic lakes and all other systems, where a higher proportion of genes affiliated with aerobic anoxygenic photosynthetic bacteria was observed than in other systems. Our results reveal a significant diversity of phototrophic microorganisms in lakes and suggest niche partitioning of oxygenic and aerobic anoxygenic phototrophs in these systems in response to trophic status and coupled differences in light regime.
BchY-Based Degenerate Primers Target All Types of Anoxygenic Photosynthetic Bacteria in a Single PCR
Authors: Yutin Natalya , Suzuki Marcelino T. , Rosenberg Mira , Rotem Denisse , Madigan Michael T. , Süling Jörg , Imhoff Johannes F. , Béjà Oded 
Published: October 2009

ABSTRACT

To detect anoxygenic bacteria containing either type 1 or type 2 photosynthetic reaction centers in a single PCR, we designed a degenerate primer set based on the
bchY
gene. The new primers were validated in silico using the GenBank nucleotide database as well as by PCR on pure strains and environmental DNA.
Molecular Characterization of a Novel Peroxidase from the Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Ogola Henry Joseph Oduor , Kamiike Takaaki , Hashimoto Naoya , Ashida Hiroyuki , Ishikawa Takahiro , Shibata Hitoshi , Sawa Yoshihiro 
Published: October 2009

ABSTRACT

The open reading frame alr1585 of
Anabaena
sp. strain PCC 7120 encodes a heme-dependent peroxidase (
Anabaena
peroxidase [AnaPX]) belonging to the novel DyP-type peroxidase family (EC 1.11.1.X). We cloned and heterologously expressed the active form of the enzyme in
Escherichia coli
. The purified enzyme was a 53-kDa tetrameric protein with a pI of 3.68, a low pH optima (pH 4.0), and an optimum reaction temperature of 35°C. Biochemical characterization revealed an iron protoporphyrin-containing heme peroxidase with a broad specificity for aromatic substrates such as guaiacol, 4-aminoantipyrine and pyrogallol. The enzyme efficiently catalyzed the decolorization of anthraquinone dyes like Reactive Blue 5, Reactive Blue 4, Reactive Blue 114, Reactive Blue 119, and Acid Blue 45 with decolorization rates of 262, 167, 491, 401, and 256 μM·min
−1
, respectively. The apparent

K
m

and
k
cat
/

K
m

values for Reactive Blue 5 were 3.6 μM and 1.2 × 10
7
M
−1
s
−1
, respectively, while the apparent

K
m

and
k
cat
/

K
m

values for H
2
O
2
were 5.8 μM and 6.6 × 10
6
M
−1
s
−1
, respectively. In contrast, the decolorization activity of AnaPX toward azo dyes was relatively low but was significantly enhanced 2- to ∼50-fold in the presence of the natural redox mediator syringaldehyde. The specificity and catalytic efficiency for hydrogen donors and synthetic dyes show the potential application of AnaPX as a useful alternative of horseradish peroxidase or fungal DyPs. To our knowledge, this study represents the only extensive report in which a bacterial DyP has been tested in the biotransformation of synthetic dyes.
Prokaryotic Community Structure and Sulfate Reducer Activity in Water from High-Temperature Oil Reservoirs with and without Nitrate Treatment
Authors: Gittel Antje , Sørensen Ketil Bernt , Skovhus Torben Lund , Ingvorsen Kjeld , Schramm Andreas 
Published: October 2009

ABSTRACT

Sulfate-reducing prokaryotes (SRP) cause severe problems like microbial corrosion and reservoir souring in seawater-injected oil production systems. One strategy to control SRP activity is the addition of nitrate to the injection water. Production waters from two adjacent, hot (80°C) oil reservoirs, one with and one without nitrate treatment, were compared for prokaryotic community structure and activity of SRP. Bacterial and archaeal 16S rRNA gene analyses revealed higher prokaryotic abundance but lower diversity for the nitrate-treated field. The 16S rRNA gene clone libraries from both fields were dominated by sequences affiliated with
Firmicutes
(
Bacteria
) and
Thermococcales
(
Archaea
). Potential heterotrophic nitrate reducers (
Deferribacterales
) were exclusively found at the nitrate-treated field, possibly stimulated by nitrate addition. Quantitative PCR of
dsrAB
genes revealed that archaeal SRP (
Archaeoglobus
) dominated the SRP communities, but with lower relative abundance at the nitrate-treated site. Bacterial SRP were found in only low abundance at both sites and were nearly exclusively affiliated with thermophilic genera (
Desulfacinum
and
Desulfotomaculum
). Despite the high abundance of archaeal SRP, no archaeal SRP activity was detected in [
35
S]sulfate incubations at 80°C. Sulfate reduction was found at 60°C in samples from the untreated field and accompanied by the growth of thermophilic bacterial SRP in batch cultures. Samples from the nitrate-treated field generally lacked SRP activity. These results indicate that (i)
Archaeoglobus
can be a major player in hot oil reservoirs, and (ii) nitrate may act in souring control—not only by inhibiting SRP, but also by changing the overall community structure, including the stimulation of competitive nitrate reducers.
Generation of Amylosucrase Variants That Terminate Catalysis of Acceptor Elongation at the Di- or Trisaccharide Stage
Authors: Schneider Jens , Fricke Christin , Overwin Heike , Hofmann Birgit , Hofer Bernd 
Published: October 2009

ABSTRACTAn amylosucrase gene was subjected to high-rate segmental random mutagenesis, which was directed toward a segment encoding amino acids that influence the interaction with substrate molecules in subsites −1 to +3. A screen was used to identify enzyme variants with compromised glucan chain elongation. With an average mutation rate of about one mutation per targeted codon, a considerable fraction (82%) of the clones that retained catalytic activity were deficient in this trait. A detailed characterization of selected variants revealed that elongation terminated when chains reached lengths of only two or three glucose moieties. Sequencing showed that the amylosucrase derivatives had an average of no more than two amino acid substitutions and suggested that predominantly exchanges of Asp394 or Gly396 were crucial for the novel properties. Structural models of the variants indicated that steric interference between the amino acids introduced at these sites and the growing oligosaccharide chain are mainly responsible for the limitation of glucosyl transfers. The variants generated may serve as biocatalysts for limited addition of glucose moieties to acceptor molecules, using sucrose as a readily available donor substrate.
Metabolic Engineering of
Saccharomyces cerevisiae
for Astaxanthin Production and Oxidative Stress Tolerance
Authors: Ukibe Ken , Hashida Keisuke , Yoshida Nobuyuki , Takagi Hiroshi 
Published: October 2009

ABSTRACT

The red carotenoid astaxanthin possesses higher antioxidant activity than other carotenoids and has great commercial potential for use in the aquaculture, pharmaceutical, and food industries. In this study, we produced astaxanthin in the budding yeast
Saccharomyces cerevisiae
by introducing the genes involved in astaxanthin biosynthesis of carotenogenic microorganisms. In particular, expression of genes of the red yeast
Xanthophyllomyces dendrorhous
encoding phytoene desaturase (
crtI
product) and bifunctional phytoene synthase/lycopene cyclase (
crtYB
product) resulted in the accumulation of a small amount of β-carotene in
S. cerevisiae
. Overexpression of geranylgeranyl pyrophosphate (GGPP) synthase from
S. cerevisiae
(the
BTS1
gene product) increased the intracellular β-carotene levels due to the accelerated conversion of farnesyl pyrophosphate to GGPP. Introduction of the
X. dendrorhous crtS
gene, encoding astaxanthin synthase, assumed to be the cytochrome P450 enzyme, did not lead to astaxanthin production. However, coexpression of CrtS with
X. dendrorhous
CrtR, a cytochrome P450 reductase, resulted in the accumulation of a small amount of astaxanthin. In addition, the β-carotene-producing yeast cells transformed by the bacterial genes
crtW
and
crtZ
, encoding β-carotene ketolase and hydroxylase, respectively, also accumulated astaxanthin and its intermediates, echinenone, canthaxanthin, and zeaxanthin. Interestingly, we found that these ketocarotenoids conferred oxidative stress tolerance on
S. cerevisiae
cells. This metabolic engineering has potential for overproduction of astaxanthin and breeding of novel oxidative stress-tolerant yeast strains.
CO Dehydrogenase Genes Found in Metagenomic Fosmid Clones from the Deep Mediterranean Sea
Authors: Martin-Cuadrado Ana-Belen , Ghai Rohit , Gonzaga Aitor , Rodriguez-Valera Francisco 
Published: October 2009

ABSTRACT

The use of carbon monoxide (CO) as a biological energy source is widespread in microbes. In recent years, the role of CO oxidation in superficial ocean waters has been shown to be an important energy supplement for heterotrophs (carboxydovores). The key enzyme CO dehydrogenase was found in both isolates and metagenomes from the ocean's photic zone, where CO is continuously generated by organic matter photolysis. We have also found genes that code for both forms I (low affinity) and II (high affinity) in fosmids from a metagenomic library generated from a 3,000-m depth in the Mediterranean Sea. Analysis of other metagenomic databases indicates that similar genes are also found in the mesopelagic and bathypelagic North Pacific and on the surfaces of this and other oceanic locations (in lower proportions and similarities). The frequency with which this gene was found indicates that this energy-generating metabolism would be at least as important in the bathypelagic habitat as it is in the photic zone. Although there are no data about CO concentrations or origins deep in the ocean, it could have a geothermal origin or be associated with anaerobic metabolism of organic matter. The identities of the microbes that carry out these processes were not established, but they seem to be representatives of either
Bacteroidetes
or
Chloroflexi
.
Mechanically Ventilated Broiler Sheds: a Possible Source of AerosolizedSalmonella,Campylobacter, andEscherichia coli
Authors: Chinivasagam H. N. , Tran T. , Maddock L. , Gale A. , Blackall P. J. 
Published: October 2009

ABSTRACTThis study assessed the levels of two key pathogens,SalmonellaandCampylobacter, along with the indicator organismEscherichia coliin aerosols within and outside poultry sheds. The study ranged over a 3-year period on four poultry farms and consisted of six trials across the boiler production cycle of around 55 days. Weekly testing of litter and aerosols was carried out through the cycle. A key point that emerged is that the levels of airborne bacteria are linked to the levels of these bacteria in litter. This hypothesis was demonstrated byE. coli. The typical levels ofE. coliin litter were ∼108CFU g−1and, as a consequence, were in the range of 102to 104CFU m−3in aerosols, both inside and outside the shed. The external levels were always lower than the internal levels.Salmonellawas only present intermittently in litter and at lower levels (103to 105most probable number [MPN] g−1) and consequently present only intermittently and at low levels in air inside (range of 0.65 to 4.4 MPN m−3) and once outside (2.3 MPN m−3). TheSalmonellaserovars isolated in litter were generally also isolated from aerosols and dust, with theSalmonellaserovars Chester and Sofia being the dominant serovars across these interfaces.Campylobacterwas detected late in the production cycle, in litter at levels of around 107MPN g−1.Campylobacterwas detected only once inside the shed and then at low levels of 2.2 MPN m−3. Thus, the public health risk from these organisms in poultry environments via the aerosol pathway is minimal.
Strain-Specific Genotyping ofBifidobacterium animalissubsp.lactisby Using Single-Nucleotide Polymorphisms, Insertions, and Deletions
Authors: Briczinski Elizabeth P. , Loquasto Joseph R. , Barrangou Rodolphe , Dudley Edward G. , Roberts Anastasia M. , Roberts Robert F. 
Published: October 2009

ABSTRACTSeveral probiotic strains ofBifidobacterium animalissubsp.lactisare widely supplemented into food products and dietary supplements due to their documented health benefits and ability to survive within the mammalian gastrointestinal tract and acidified dairy products. The strain specificity of these characteristics demands techniques with high discriminatory power to differentiate among strains. However, to date, molecular approaches, such as pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR, have been ineffective at achieving strain separation due to the monomorphic nature of this subspecies. Previously, sequencing and comparison of twoB. animalissubsp.lactisgenomes (DSMZ 10140 and Bl-04) confirmed this high level of sequence similarity, identifying only 47 single-nucleotide polymorphisms (SNPs) and four insertions and/or deletions (INDELs) between them. In this study, we hypothesized that a sequence-based typing method targeting these loci would permit greater discrimination between strains than previously attempted methods. Sequencing 50 of these loci in 24 strains ofB. animalissubsp.lactisrevealed that a combination of nine SNPs/INDELs could be used to differentiate strains into 14 distinct genotypic groups. In addition, the presence of a nonsynonymous SNP within the gene encoding a putative glucose uptake protein was found to correlate with the ability of certain strains to transport glucose and to grow rapidly in a medium containing glucose as the sole carbon source. The method reported here can be used in clinical, regulatory, and commercial applications requiring identification ofB. animalissubsp.lactisat the strain level.
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Authors: Schloss Patrick D. , Westcott Sarah L. , Ryabin Thomas , Hall Justine R. , Hartmann Martin , Hollister Emily B. , Lesniewski Ryan A. , Oakley Brian B. , Parks Donovan H. , Robinson Courtney J. , Sahl Jason W. , Stres Blaz , Thallinger Gerhard G. , Van Horn David J. , Weber Carolyn F. 
Published: October 2009

ABSTRACT
mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
Cadherin Fragments from
Anopheles gambiae
Synergize
Bacillus thuringiensis
Cry4Ba's Toxicity against
Aedes aegypti
Larvae
Authors: Park Youngjin , Hua Gang , Abdullah Mohd Amir F. , Rahman Khalidur , Adang Michael J. 
Published: October 2009

ABSTRACT

A peptide from cadherin AgCad1 of
Anopheles gambiae
larvae was reported as a synergist of
Bacillus thuringiensis
subsp.
israelensis
Cry4Ba's toxicity to the
Anopheles
mosquito (G. Hua, R. Zhang, M. A. Abdullah, and M. J. Adang, Biochemistry 47:5101-5110, 2008). We report that CR11 to the membrane proximal extracellular domain (MPED) (CR11-MPED) and a longer peptide, CR9 to CR11 (CR9-11), from AgCad1 act as synergists of Cry4Ba's toxicity to
Aedes aegypti
larvae, but a
Diabrotica virgifera virgifera
cadherin-based synergist of Cry3 (Y. Park, M. A. F. Abdullah, M. D. Taylor, K. Rahman, and M. J. Adang, Appl. Environ. Microbiol. 75:3086-3092, 2009) did not affect Cry4Ba's toxicity. Peptides CR9-11 and CR11-MPED bound Cry4Ba with high affinity (13 nM and 23 nM, respectively) and inhibited Cry4Ba binding to the larval
A. aegypti
brush border membrane. The longer CR9-11 fragment was more potent than CR11-MPED in enhancing Cry4Ba against
A. aegypti
.
Influence of Environmental Gradients on the Abundance and Distribution of
Mycobacterium
spp. in a Coastal Lagoon Estuary
Authors: Jacobs John , Rhodes Matt , Sturgis Brian , Wood Bob 
Published: October 2009

ABSTRACT

Environmental mycobacteria are of increasing concern in terms of the diseases they cause in both humans and animals. Although they are considered to be ubiquitous in aquatic environments, few studies have examined their ecology, and no ecological studies of coastal marine systems have been conducted. This study uses indirect gradient analysis to illustrate the strong relationships that exists between coastal water quality and the abundance of
Mycobacterium
spp. within a U.S. mid-Atlantic embayment.
Mycobacterium
species abundance and water quality conditions (based on 16 physical and chemical variables) were examined simultaneously in monthly samples obtained at 18 Maryland and Virginia coastal bay stations from August 2005 to November 2006 (
n
= 212). A quantitative molecular assay for
Mycobacterium
spp. was evaluated and applied, allowing for rapid, direct enumeration. By using indirect gradient analysis (environmental principal-components analysis), a strong linkage between eutrophic conditions, characterized by low dissolved-oxygen levels and elevated nutrient concentrations, and mycobacteria was determined. More specifically, a strong nutrient response was noted, with all nitrogen components and turbidity measurements correlating positively with abundance (
r
values of >0.30;
P
values of <0.001), while dissolved oxygen showed a strong negative relationship (
r
= −0.38;
P
= 0.01). Logistic regression models developed using salinity, dissolved oxygen, and total nitrogen showed a high degree of concordance (83%). These results suggest that coastal restoration and management strategies designed to reduce eutrophication may also reduce total mycobacteria in coastal waters.
Identification of Two Aflatrem Biosynthesis Gene Loci inAspergillus flavusand Metabolic Engineering ofPenicillium paxilliTo Elucidate Their Function
Authors: Nicholson Matthew J. , Koulman Albert , Monahan Brendon J. , Pritchard Beth L. , Payne Gary A. , Scott Barry 
Published: October 2009

ABSTRACTAflatrem is a potent tremorgenic toxin produced by the soil fungusAspergillus flavus, and a member of a structurally diverse group of fungal secondary metabolites known as indole-diterpenes. Gene clusters for indole-diterpene biosynthesis have recently been described in several species of filamentous fungi. A search ofAspergilluscomplete genome sequence data identified putative aflatrem gene clusters in the genomes ofA. flavusandAspergillus oryzae. In both species the genes for aflatrem biosynthesis cluster at two discrete loci; the first,ATM1, is telomere proximal on chromosome 5 and contains a cluster of three genes,atmG,atmC, andatmM, and the second,ATM2, is telomere distal on chromosome 7 and contains five genes,atmD,atmQ,atmB,atmA, andatmP. Reverse transcriptase PCR inA. flavusdemonstrated that aflatrem biosynthesis transcript levels increased with the onset of aflatrem production. Transfer ofatmPandatmQintoPenicillium paxilli paxPandpaxQdeletion mutants, known to accumulate paxilline intermediates paspaline and 13-desoxypaxilline, respectively, showed that AtmP is a functional homolog of PaxP and that AtmQ utilizes 13-desoxypaxilline as a substrate to synthesize aflatrem pathway-specific intermediates, paspalicine and paspalinine. We propose a scheme for aflatrem biosynthesis inA. flavusbased on these reconstitution experiments inP. paxilliand identification of putative intermediates in wild-type cultures ofA. flavus.
Leishmania majorMPK7 Protein Kinase Activity Inhibits Intracellular Growth of the Pathogenic Amastigote Stage
Authors: Morales Miguel A. , Pescher Pascale , Späth Gerald F. 
Published: October 2009

ABSTRACTDuring the infectious cycle, protozoan parasites of the genusLeishmaniaundergo several adaptive differentiation steps that are induced by environmental factors and crucial for parasite infectivity. Genetic analyses of signaling proteins underlyingLeishmaniastage differentiation are often rendered difficult due to lethal null mutant phenotypes. Here we used a transgenic strategy to gain insight into the functions of the mitogen-activatedLeishmania majorprotein kinases LmaMPK7 and LmaMPK10 in parasite virulence. We establishedL. majorandLeishmania donovanilines expressing episomal green fluorescent protein (GFP)-LmaMPK7 and GFP-LmaMPK10 fusion proteins. The transgenic lines were normal in promastigote morphology, growth, and the ability to differentiate into metacyclic and amastigote stages. While parasites expressing GFP-LmaMPK10 showed normal infectivity by mouse footpad analysis and macrophage infection assays, GFP-LmaMPK7 transgenic parasites displayed a strong delay in lesion formation and reduced intracellular parasite growth. Significantly, the effects of GFP-LmaMPK7 on virulence and proliferation were due exclusively to protein kinase activity, as the overexpression of two kinase-dead mutants had no effect on parasite infectivity. GFP-LmaMPK7 transgenicL. donovanicells revealed a reversible, stage-specific growth defect in axenic amastigotes that was independent of cell death but linked to nonsynchronous growth arrest and a significant reduction of de novo protein biosynthesis. Our data suggest that LmaMPK7 protein kinase activity may be implicated in parasite growth control and thus relevant for the development of nonproliferating stages during the infectious cycle.
Role of Intracellular Polysaccharide in Persistence of
Streptococcus mutans
Authors: Busuioc Monica , Mackiewicz Katarzyna , Buttaro Bettina A. , Piggot Patrick J. 
Published: October 2009

ABSTRACT

Intracellular polysaccharide (IPS) is accumulated by
Streptococcus mutans
when the bacteria are grown in excess sugar and can contribute toward the cariogenicity of
S. mutans
. Here we show that inactivation of the
glgA
gene (SMU1536), encoding a putative glycogen synthase, prevented accumulation of IPS. IPS is important for the persistence of
S. mutans
grown in batch culture with excess glucose and then starved of glucose. The IPS was largely used up within 1 day of glucose starvation, and yet survival of the parental strain was extended by at least 15 days beyond that of a
glgA
mutant; potentially, some feature of IPS metabolism distinct from providing nutrients is important for persistence. IPS was not needed for persistence when sucrose was the carbon source or when mucin was present.