bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining the Bacteroides Ribosomal Binding Site
Authors: Wegmann Udo , Horn Nikki , Carding Simon R. 
Published: January 2013

ABSTRACT

The human gastrointestinal tract, in particular the colon, hosts a vast number of commensal microorganisms. Representatives of the genus
Bacteroides
are among the most abundant bacterial species in the human colon.
Bacteroidetes
diverged from the common line of eubacterial descent before other eubacterial groups. As a result, they employ unique transcription initiation signals and, because of this uniqueness, they require specific genetic tools. Although some tools exist, they are not optimal for studying the roles and functions of these bacteria in the human gastrointestinal tract. Focusing on translation initiation signals in
Bacteroides
, we created a series of expression vectors allowing for different levels of protein expression in this genus, and we describe the use of
pepI
from
Lactobacillus delbrueckii
subsp.
lactis
as a novel reporter gene for
Bacteroides
. Furthermore, we report the identification of the 3′ end of the 16S rRNA of
Bacteroides ovatus
and analyze in detail its ribosomal binding site, thus defining a core region necessary for efficient translation, which we have incorporated into the design of our expression vectors. Based on the sequence logo information from the 5′ untranslated region of other
Bacteroidales
ribosomal protein genes, we conclude that our findings are relevant to all members of this order.
Involvement of Intermediate Sulfur Species in Biological Reduction of Elemental Sulfur under Acidic, Hydrothermal Conditions
Authors: Boyd Eric S. , Druschel Gregory K. 
Published: January 2013

ABSTRACT

The thermoacidophile and obligate elemental sulfur (S
8
0
)-reducing anaerobe
Acidilobus sulfurireducens
18D70 does not associate with bulk solid-phase sulfur during S
8
0
-dependent batch culture growth. Cyclic voltammetry indicated the production of hydrogen sulfide (H
2
S) as well as polysulfides after 1 day of batch growth of the organism at pH 3.0 and 81ï¿½C. The production of polysulfide is likely due to the abiotic reaction between S
8
0
and the biologically produced H
2
S, as evinced by a rapid cessation of polysulfide formation when the growth temperature was decreased, inhibiting the biological production of sulfide. After an additional 5 days of growth, nanoparticulate S
8
0
was detected in the cultivation medium, a result of the hydrolysis of polysulfides in acidic medium. To examine whether soluble polysulfides and/or nanoparticulate S
8
0
can serve as terminal electron acceptors (TEA) supporting the growth of
A. sulfurireducens
, total sulfide concentration and cell density were monitored in batch cultures with S
8
0
provided as a solid phase in the medium or with S
8
0
sequestered in dialysis tubing. The rates of sulfide production in 7-day-old cultures with S
8
0
sequestered in dialysis tubing with pore sizes of 12 to 14 kDa and 6 to 8 kDa were 55% and 22%, respectively, of that of cultures with S
8
0
provided as a solid phase in the medium. These results indicate that the TEA existed in a range of particle sizes that affected its ability to diffuse through dialysis tubing of different pore sizes. Dynamic light scattering revealed that S
8
0
particles generated through polysulfide rapidly grew in size, a rate which was influenced by the pH of the medium and the presence of organic carbon. Thus, S
8
0
particles formed through abiological hydrolysis of polysulfide under acidic conditions appeared to serve as a growth-promoting TEA for
A. sulfurireducens
.
Thaumarchaeotal Signature Gene Distribution in Sediments of the Northern South China Sea: an Indicator of the Metabolic Intersection of the Marine Carbon, Nitrogen, and Phosphorus Cycles?
Authors: Dang Hongyue , Zhou Haixia , Yang Jinying , Ge Huangmin , Jiao Nianzhi , Luan Xiwu , Zhang Chuanlun , Klotz Martin G. 
Published: January 2013

ABSTRACT

Thaumarchaeota are abundant and active in marine waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in marine sediments, however, has rarely been investigated, even though marine sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA and
amoA
genes in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial genes. This finding correlates with high levels of
hcd
genes, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in marine sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotal
amoA
genes. When the pore water PO
4
3−
concentration was controlled for via partial-correlation analysis, thaumarchaeotal
amoA
gene abundance significantly correlated with the sediment pore water NO
2
−
concentration, suggesting that the
amoA
-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in marine sediments.
Distinct Actions by Paenibacillus sp. Strain E18 α-
l
-Arabinofuranosidases and Xylanase in Xylan Degradation
Authors: Shi Pengjun , Chen Xiaoyan , Meng Kun , Huang Huoqing , Bai Yingguo , Luo Huiying , Yang Peilong , Yao Bin 
Published: January 2013

ABSTRACT

We cloned a
Paenibacillus
sp. strain E18 5.3-kb xylanolytic gene cluster that contains three open reading frames encoding two family 43 α-
l
-arabinofuranosidases (Abf43A and Abf43B) and one family 10 xylanase (XynBE18). The deduced amino acid sequences of Abf43A and Abf43B were at most 68% and 63% identical to those of two putative family 43 proteins from
Clostridium
sp. strain DL-VIII (EHI98634.1 and EHI98635.1), respectively, but were only 11% identical to each other. Recombinant Abf43A and Abf43B had similar activities at 45ï¿½C and pH 6.0 but varied in thermostabilities and substrate specificities. Abf43B was active against only 4-nitrophenyl α-
l
-arabinofuranoside, whereas Abf43A acted on 4-nitrophenyl α-
l
-arabinofuranoside, wheat arabinoxylan, 4-nitrophenyl α-
d
-xylopyranoside, and sugar beet arabinan. The sequential and combined effects on xylan degradation by XynBE18, Abf43A, and Abf43B were characterized. For beechwood, birchwood, and oat spelt xylans as the substrates, synergistic effects were found when XynBE18 and Abf43A or Abf43B were incubated together and when the substrates were first incubated with Abf43A or Abf43B and then with XynBE18. Further high-performance liquid chromatography (HPLC) analysis showed that the amounts of xylobiose and xylose increased sharply in the aforementioned reactions. For water-soluble wheat arabinoxylan as the substrate, Abf43A not only released arabinose but also had a synergistic effect with XynBE18. Synergy may arise as the result of removal of arabinose residues from xylans by α-
l
-arabinofuranosidases, which eliminates steric hindrance caused by the arabinose side chains and which allows xylanases to then degrade the xylan backbone, producing short xylooligosaccharides.
Evolutionary Acquisition and Loss of Saxitoxin Biosynthesis in Dinoflagellates: the Second “Core” Gene,
sxtG
Authors: Orr Russell J. S. , Stï¿½ken Anke , Murray Shauna A. , Jakobsen Kjetill S. 
Published: January 2013

ABSTRACT

Saxitoxin and its derivatives are potent neurotoxins produced by several cyanobacteria and dinoflagellate species. SxtA is the initial enzyme in the biosynthesis of saxitoxin. The dinoflagellate full mRNA and partial genomic sequences have previously been characterized, and it appears that
sxtA
originated in dinoflagellates through a horizontal gene transfer from a bacterium. So far, little is known about the remaining genes involved in this pathway in dinoflagellates. Here we characterize
sxtG
, an amidinotransferase enzyme gene that putatively encodes the second step in saxitoxin biosynthesis. In this study, the entire
sxtG
transcripts from
Alexandrium fundyense
CCMP1719 and
Alexandrium minutum
CCMP113 were amplified and sequenced. The transcripts contained typical dinoflagellate spliced leader sequences and eukaryotic poly(A) tails. In addition, partial
sxtG
transcript fragments were amplified from four additional
Alexandrium
species and
Gymnodinium catenatum
. The phylogenetic inference of dinoflagellate
sxtG
, congruent with
sxtA
, revealed a bacterial origin. However, it is not known if
sxtG
was acquired independently of
sxtA
. Amplification and sequencing of the corresponding genomic
sxtG
region revealed noncanonical introns. These introns show a high interspecies and low intraspecies variance, suggesting multiple independent acquisitions and losses. Unlike
sxtA
,
sxtG
was also amplified from
Alexandrium
species not known to synthesize saxitoxin. However, amplification was not observed for 22 non-saxitoxin-producing dinoflagellate species other than those of the genus
Alexandrium
or
G. catenatum
. This result strengthens our hypothesis that saxitoxin synthesis has been secondarily lost in conjunction with
sxtA
for some descendant species.
CO-Dependent H
2
Production by Genetically Engineered Thermococcus onnurineus NA1
Authors: Kim Min-Sik , Bae Seung Seob , Kim Yun Jae , Kim Tae Wan , Lim Jae Kyu , Lee Seong Hyuk , Choi Ae Ran , Jeon Jeong Ho , Lee Jung-Hyun , Lee Hyun Sook , Kang Sung Gyun 
Published: January 2013

ABSTRACT

Hydrogenogenic CO oxidation (CO + H
2
O → CO
2
+ H
2
) has the potential for H
2
production as a clean renewable fuel.
Thermococcus onnurineus
NA1, which grows on CO and produces H
2
, has a unique gene cluster encoding the carbon monoxide dehydrogenase (CODH) and the hydrogenase. The gene cluster was identified as essential for carboxydotrophic hydrogenogenic metabolism by gene disruption and transcriptional analysis. To develop a strain producing high levels of H
2
, the gene cluster was placed under the control of a strong promoter. The resulting mutant, MC01, showed 30-fold-higher transcription of the mRNA encoding CODH, hydrogenase, and Na
+
/H
+
antiporter and a 1.8-fold-higher specific activity for CO-dependent H
2
production than did the wild-type strain. The H
2
production potential of the MC01 mutant in a bioreactor culture was 3.8-fold higher than that of the wild-type strain. The H
2
production rate of the engineered strain was severalfold higher than those of any other CO-dependent H
2
-producing prokaryotes studied to date. The engineered strain also possessed high activity for the bioconversion of industrial waste gases created as a by-product during steel production. This work represents the first demonstration of H
2
production from steel mill waste gas using a carboxydotrophic hydrogenogenic microbe.
Catabolism of
N
-Acetylneuraminic Acid, a Fitness Function of the Food-Borne Lactic Acid Bacterium Lactobacillus sakei, Involves Two Newly Characterized Proteins
Authors: Anba-Mondoloni Jamila , Chaillou Stï¿½phane , Zagorec Monique , Champomier-Vergï¿½s Marie-Christine 
Published: January 2013

ABSTRACT

In silico
analysis of the genome sequence of the meat-borne lactic acid bacterium (LAB)
Lactobacillus sakei
23K has revealed a repertoire of potential functions related to the adaptation of this bacterium to the meat environment. Among these functions, the ability to use
N
-acetyl-neuraminic acid (NANA) as a carbon source could provide a competitive advantage for growth on meat in which this amino sugar is present. In this work, we proposed to analyze the functionality of a gene cluster encompassing
nanTEAR
and
nanK
(
nanTEAR-nanK
). We established that this cluster encoded a pathway allowing transport and early steps of the catabolism of NANA in this genome. We also demonstrated that this cluster was absent from the genome of other
L. sakei
strains that were shown to be unable to grow on NANA. Moreover,
L. sakei
23K
nanA
,
nanT
,
nanK
, and
nanE
genes were able to complement
Escherichia coli
mutants. Construction of different mutants in
L. sakei
23K Δ
nanR
, Δ
nanT
, and Δ
nanK
and the double mutant
L. sakei
23K Δ(
nanA-nanE
) made it possible to show that all were impaired for growth on NANA. In addition, two genes located downstream from
nanK
,
lsa1644
and
lsa1645
, are involved in the catabolism of sialic acid in
L. sakei
23K, as a
L. sakei
23K Δ
lsa1645
mutant was no longer able to grow on NANA. All these results demonstrate that the gene cluster
nanTEAR-nanK-lsa1644-lsa1645
is indeed involved in the use of NANA as an energy source by
L. sakei
.
Selection for Loss of RpoS in Cronobacter sakazakii by Growth in the Presence of Acetate as a Carbon Source
Authors: ï¿½lvarez-Ordï¿½ï¿½ez Avelino , Begley Mï¿½ire , Hill Colin 
Published: January 2013

ABSTRACT

We demonstrate that growth of
Cronobacter sakazakii
in the presence of acetate as a carbon source promotes loss of RpoS, with a consequent reduction in stress tolerance. This suggests that
C. sakazakii
is capable of regulating cell fitness through mutation of the
rpoS
gene.
Characterization of the Biosynthetic Genes for 10,11-Dehydrocurvularin, a Heat Shock Response-Modulating Anticancer Fungal Polyketide from Aspergillus terreus
Authors: Xu Yuquan , Espinosa-Artiles Patricia , Schubert Vivien , Xu Ya-ming , Zhang Wei , Lin Min , Gunatilaka A. A. Leslie , Sï¿½ssmuth Roderich , Molnï¿½r Istvï¿½n 
Published: January 2013

ABSTRACT

10,11-Dehydrocurvularin is a prevalent fungal phytotoxin with heat shock response and immune-modulatory activities. It features a dihydroxyphenylacetic acid lactone polyketide framework with structural similarities to resorcylic acid lactones like radicicol or zearalenone. A genomic locus was identified from the dehydrocurvularin producer strain
Aspergillus terreus
AH-02-30-F7 to reveal genes encoding a pair of iterative polyketide synthases (
A. terreus
CURS1 [AtCURS1] and AtCURS2) that are predicted to collaborate in the biosynthesis of 10,11-dehydrocurvularin. Additional genes in this locus encode putative proteins that may be involved in the export of the compound from the cell and in the transcriptional regulation of the cluster. 10,11-Dehydrocurvularin biosynthesis was reconstituted in
Saccharomyces cerevisiae
by heterologous expression of the polyketide synthases. Bioinformatic analysis of the highly reducing polyketide synthase AtCURS1 and the nonreducing polyketide synthase AtCURS2 highlights crucial biosynthetic programming differences compared to similar synthases involved in resorcylic acid lactone biosynthesis. These differences lead to the synthesis of a predicted tetraketide starter unit that forms part of the 12-membered lactone ring of dehydrocurvularin, as opposed to the penta- or hexaketide starters in the 14-membered rings of resorcylic acid lactones. Tetraketide
N
-acetylcysteamine thioester analogues of the starter unit were shown to support the biosynthesis of dehydrocurvularin and its analogues, with yeast expressing AtCURS2 alone. Differential programming of the product template domain of the nonreducing polyketide synthase AtCURS2 results in an aldol condensation with a different regiospecificity than that of resorcylic acid lactones, yielding the dihydroxyphenylacetic acid scaffold characterized by an S-type cyclization pattern atypical for fungal polyketides.
RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage
Authors: Guo Xue , Yin Huaqun , Cong Jing , Dai Zhimin , Liang Yili , Liu Xueduan 
Published: January 2013

ABSTRACT

The enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (
cbbL
). Forty-six
cbbL
-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities of
cbbL
and the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.
Interactions of Nitrifying Bacteria and Heterotrophs: Identification of a Micavibrio-Like Putative Predator of Nitrospira spp
Authors: Dolinšek Jan , Lagkouvardos Ilias , Wanek Wolfgang , Wagner Michael , Daims Holger 
Published: January 2013

ABSTRACT

Chemolithoautotrophic nitrifying bacteria release soluble organic compounds, which can be substrates for heterotrophic microorganisms. The identities of these heterotrophs and the specificities of their interactions with nitrifiers are largely unknown. In this study, we incubated nitrifying activated sludge with
13
C-labeled bicarbonate and used stable isotope probing of 16S rRNA to monitor the flow of carbon from uncultured nitrifiers to heterotrophs. To facilitate the identification of heterotrophs, the abundant 16S rRNA molecules from nitrifiers were depleted by catalytic oligonucleotides containing locked nucleic acids (LNAzymes), which specifically cut the 16S rRNA of defined target organisms. Among the
13
C-labeled heterotrophs were organisms remotely related to
Micavibrio
, a microbial predator of Gram-negative bacteria. Fluorescence
in situ
hybridization revealed a close spatial association of these organisms with microcolonies of nitrite-oxidizing sublineage I
Nitrospira
in sludge flocs. The high specificity of this interaction was confirmed by confocal microscopy and a novel image analysis method to quantify the localization patterns of biofilm microorganisms in three-dimensional (3-D) space. Other isotope-labeled bacteria, which were affiliated with
Thermomonas
, colocalized less frequently with nitrifiers and thus were commensals or saprophytes rather than specific symbionts or predators. These results suggest that
Nitrospira
spp. are subject to bacterial predation, which may influence the abundance and diversity of these nitrite oxidizers and the stability of nitrification in engineered and natural ecosystems.
In silico
screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured
Micavibrio
-like lineage.
Characterization of the Denitrification-Associated Phosphorus Uptake Properties of “Candidatus Accumulibacter phosphatis” Clades in Sludge Subjected to Enhanced Biological Phosphorus Removal
Authors: Kim Jeong Myeong , Lee Hyo Jung , Lee Dae Sung , Jeon Che Ok 
Published: January 2013

ABSTRACT

To characterize the denitrifying phosphorus (P) uptake properties of “
Candidatus
Accumulibacter phosphatis,” a sequencing batch reactor (SBR) was operated with acetate. The SBR operation was gradually acclimated from anaerobic-oxic (AO) to anaerobic-anoxic-oxic (A2O) conditions by stepwise increases of nitrate concentration and the anoxic time. The communities of “
Ca
. Accumulibacter” and associated bacteria at the initial (AO) and final (A2O) stages were compared using 16S rRNA and polyphosphate kinase genes and using fluorescence
in situ
hybridization (FISH). The acclimation process led to a clear shift in the relative abundances of recognized “
Ca
. Accumulibacter” subpopulations from clades IIA > IA > IIF to clades IIC > IA > IIF, as well as to increases in the abundance of other associated bacteria (
Dechloromonas
[from 1.2% to 19.2%] and “
Candidatus
Competibacter phosphatis” [from 16.4% to 20.0%]), while the overall “
Ca
. Accumulibacter” abundance decreased (from 55.1% to 29.2%). A series of batch experiments combined with FISH/microautoradiography (MAR) analyses was performed to characterize the denitrifying P uptake properties of the “
Ca
. Accumulibacter” clades. In FISH/MAR experiments using slightly diluted sludge (∼0.5 g/liter), all “
Ca
. Accumulibacter” clades successfully took up phosphorus in the presence of nitrate. However, the “
Ca
. Accumulibacter” clades showed no P uptake in the presence of nitrate when the sludge was highly diluted (∼0.005 g/liter); under these conditions, reduction of nitrate to nitrite did not occur, whereas P uptake by “
Ca
. Accumulibacter” clades occurred when nitrite was added. These results suggest that the “
Ca
. Accumulibacter” cells lack nitrate reduction capabilities and that P uptake by “
Ca
. Accumulibacter” is dependent upon nitrite generated by associated nitrate-reducing bacteria such as
Dechloromonas
and “
Ca
. Competibacter.”
Arabinose Induces Pellicle Formation by Vibrio fischeri
Authors: Visick Karen L. , Quirke Kevin P. , McEwen Sheila M. 
Published: January 2013

ABSTRACT

Biofilms are multicellular communities of bacteria attached to a surface and embedded in a protective matrix. In many cases, the signals that induce biofilm formation are unknown. Here, we report that biofilm formation by the marine bacterium
Vibrio fischeri
can be induced by the addition of arabinose to LBS (Luria-Bertani-salt), a tryptone-based medium. Growth of cells in the presence of 0.2% arabinose, but not other sugars, induced the production of a pellicle at the air/liquid interfaces of static cultures.
V. fischeri
failed to grow on arabinose as the sole carbon source, suggesting that pellicle production did not occur as a result of increased growth, but experiments using the acid/base indicator phenol red suggested that
V. fischeri
may partially metabolize arabinose. Pellicle production was independent of the
syp
polysaccharide locus but was altered upon disruption of the
bcs
cellulose locus. Through a screen for mutants defective for pellicle production, we found that loss of motility disrupted the formation of the arabinose-induced pellicle. Among the ∼20 mutants that retained motility were strains with insertions in a putative
msh
pilus locus and a strain with a defect in
yidK
, which is involved in galactose catabolism. Mutants with the
msh
gene disrupted grew poorly in the presence of arabinose, while the
yidK
mutant appeared to be “blind” to the presence of arabinose. Finally, arabinose impaired symbiotic colonization by
V. fischeri
. This work thus identifies a novel signal and new pathways involved in control of biofilm formation by
V. fischeri
.