bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selectivity of Fungal Sesquiterpene Synthases: Role of the Active Site's H-1α Loop in Catalysis
Authors: López-Gallego Fernando , Wawrzyn GraysonT. , Schmidt-Dannert Claudia 
Published: October 2010

ABSTRACT

Sesquiterpene synthases are responsible for the cyclization of farnesyl pyrophosphate into a myriad of structurally diverse compounds with various biological activities. We examine here the role of the conserved active site H-α1 loop in catalysis in three previously characterized fungal sesquiterpene synthases. The H-α1 loops of Cop3, Cop4, and Cop6 from
Coprinus cinereus
were altered by site-directed mutagenesis and the resultant product profiles were analyzed by gas chromatography-mass spectrometry and compared to the wild-type enzymes. In addition, we examine the effect of swapping the H-α1 loop from the promiscuous enzyme Cop4 with the more selective Cop6 and the effect of acidic or basic conditions on loop mutations in Cop4. Directed mutations of the H-α1 loop had a marked effect on the product profile of Cop3 and Cop4, while little to no change was shown in Cop6. Swapping of the Cop4 and Cop6 loops with one another was again shown to influence the product profile of Cop4, while the product profile of Cop6 remained identical to the wild-type enzyme. The loop mutations in Cop4 also implicate specific residues responsible for the pH sensitivity of the enzyme. These results affirm the role of the H-α1 loop in catalysis and provide a potential target to increase the product diversity of terpene synthases.
Nod1 and Nod2 Regulation of Inflammation in the
Salmonella
Colitis Model
Authors: Geddes Kaoru , Rubino Stephen , Streutker Catherine , Cho Joon Ho , Magalhaes Joao G. , Le Bourhis Lionel , Selvanantham Thirumahal , Girardin Stephen E. , Philpott Dana J. 
Published: October 2010

ABSTRACT

The pattern recognition molecules Nod1 and Nod2 play important roles in intestinal homeostasis; however, how these proteins impact on the development of inflammation during bacterial colitis has not been examined. In the streptomycin-treated mouse model of
Salmonella
colitis, we found that mice deficient for both Nod1 and Nod2 had attenuated inflammatory pathology, reduced levels of inflammatory cytokines, and increased colonization of the mucosal tissue. Nod1 and Nod2 from both hematopoietic and nonhematopoietic sources contributed to the pathology, and all phenotypes were recapitulated in mice deficient for the signaling adaptor protein Rip2. However, the influence of Rip2 was strictly dependent on infection conditions that favored expression of the
Salmonella
pathogenicity island 2 (SPI-2) type III secretion system (TTSS), as Rip2 was dispensable for inflammation when mice were infected with bacteria grown under conditions that promoted expression of the SPI-1 TTSS. Thus, Nod1 and Nod2 can modulate inflammation and mediate efficient clearance of bacteria from the mucosal tissue during
Salmonella
colitis, but their role is dependent on the expression of the SPI-2 TTSS.
Counterclockwise Circular Motion of Bacteria Swimming at the Air-Liquid Interface
Authors: Lemelle Laurence , Palierne Jean-François , Chatre Elodie , Place Christophe 
Published: October 2010

ABSTRACT

Flagellar propulsion of swimming
Escherichia coli
produces circling clockwise motions near planar solid surfaces. Counterclockwise motion was first reported near air-TN medium interfaces, showing that slip at the interface is a key parameter of bacterial swimming.
Repression of
sigK
Intervening (
skin
) Element Gene Expression by the CI-Like Protein SknR and Effect of SknR Depletion on Growth of
Bacillus subtilis
Cells
Authors: Kimura Tatsu , Amaya Yukie , Kobayashi Kazuo , Ogasawara Naotake , Sato Tsutomu 
Published: October 2010

ABSTRACT

The
Bacillus subtilis
phage DNA-like
sigK
intervening (
skin
) element (48 kb) is excised from the chromosome by DNA rearrangement, and a composite gene,
sigK
(
spoIIIC
and
spoIVCB
), is created on the chromosome during sporulation. In this study, we first focused on the role of
sknR
(
skin
repressor), which has homology with the gene encoding the Xre repressor of defective phage PBSX. The depletion of SknR caused overexpression of the region between
yqaF
and
yqaN
(the
yqaF-yqaN
operon) and a growth defect in
B. subtilis
. Point mutation analysis and an electrophoretic mobility shift assay (EMSA) suggested that SknR functions as a negative regulator of gene expression in the
yqaF-yqaN
operon of the
skin
element through direct interaction with operators of 2-fold symmetry located in the intergenic region between
sknR
and
yqaF
. Deletion analysis revealed that the lethal effect of depletion of SknR was related to overexpression of
yqaH
and
yqaM
, whose products were previously reported to associate with DnaA and DnaC, respectively. Furthermore, overexpression of either
yqaH
or
yqaM
caused cell filamentation and abnormal chromosome segregation, which suggested that overproduction of these proteins inhibits DNA replication. Moreover, overexpression of
yqaM
inhibited the initiation of replication. Taken together, these data demonstrate that the
B. subtilis skin
element carries lethal genes, which are induced by the depletion of
sknR
.
FliZ Regulates Expression of theSalmonellaPathogenicity Island 1 Invasion Locus by Controlling HilD Protein Activity inSalmonella entericaSerovar Typhimurium
Authors: Chubiz Jessica E. Cott , Golubeva Yekaterina A. , Lin Dongxia , Miller Lucas D. , Slauch James M. 
Published: October 2010

ABSTRACTA prerequisite forSalmonella entericato cause both intestinal and systemic disease is the direct injection of effector proteins into host intestinal epithelial cells via a type three secretion system (T3SS); the T3SS genes are carried onSalmonellapathogenicity island 1 (SPI1). These effector proteins induce inflammatory diarrhea and bacterial invasion. Expression of the SPI1 T3SS is tightly regulated in response to environmental signals through a variety of global regulatory systems. We have previously shown that three AraC-like regulators, HilD, HilC, and RtsA, act in a complex feed-forward regulatory loop to control the expression of thehilAgene, which encodes the direct regulator of the SPI1 structural genes. In this work, we characterize a major positive regulator of this system, the flagellar protein FliZ. Through genetic and biochemical analyses, we show that FliZ posttranslationally controls HilD to positively regulatehilAexpression. This mechanism is independent of other flagellar components and is not mediated through the negative regulator HilE or through FliZ-mediated RpoS regulation. We demonstrate that FliZ controls HilD protein activity and not stability. FliZ regulates HilD in the absence of Lon protease, previously shown to degrade HilD. Indeed, it appears that FliZ, rather than HilD, is the most relevant target of Lon as it relates to SPI1 expression. Mutants lacking FliZ are significantly attenuated in their ability to colonize the intestine but are unaffected during systemic infection. The intestinal attenuation is partially dependent on SPI1, but FliZ has additional pleiotropic effects.
MzrA-EnvZ Interactions in the Periplasm Influence the EnvZ/OmpR Two-Component Regulon
Authors: Gerken Henri , Misra Rajeev 
Published: October 2010

ABSTRACT

MzrA was identified as a modulator of the EnvZ/OmpR two-component signal transduction system. Previous evidence indicated that MzrA interacts with EnvZ and modulates its enzymatic activities to influence OmpR phosphate (OmpR∼P) levels. Moreover, MzrA was shown to connect the bacterial envelope stress response systems CpxA/CpxR and σ
E
to EnvZ/OmpR to widen the defensive response regulatory network. In this study, experiments were carried out to establish whether the membrane or periplasmic domain of MzrA is critical for MzrA-EnvZ interactions and to reveal MzrA residues that play an important role in these interactions. Data obtained from chimeric constructs, in which the transmembrane domain of MzrA was replaced with the unrelated transmembrane domain of NarX or signal sequence of PhoA, showed that the transmembrane domain residues of MzrA do not play a critical role in MzrA-EnvZ interactions. The importance of the periplasmic domain of MzrA in MzrA-EnvZ interactions was revealed by characterizing bifunctional, fully soluble, and periplasmically localized MalE::MzrA chimeras. This was further corroborated through the isolation of loss-of-function, single-amino-acid substitutions in the conserved periplasmic domain of MzrA that interfered with MzrA-EnvZ binding in a bacterial two-hybrid system. Together, the data suggest that the binding of MzrA to EnvZ influences the ability of EnvZ to receive and/or respond to environmental signals in the periplasm and modulate its biochemical output to OmpR.
Draft Genome Sequence of
Streptomyces clavuligerus
NRRL 3585, a Producer of Diverse Secondary Metabolites
Authors: Song Ju Yeon , Jeong Haeyoung , Yu Dong Su , Fischbach Michael A. , Park Hong-Seog , Kim Jae Jong , Seo Jeong-Sun , Jensen Susan E. , Oh Tae Kwang , Lee Kye Joon , Kim Jihyun F. 
Published: October 2010

ABSTRACT

Streptomyces clavuligerus
is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the
S. clavuligerus
NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics.
Biologically Active Isoforms of CobB Sirtuin Deacetylase in
Salmonella enterica
and
Erwinia amylovora
Authors: Tucker Alex C. , Escalante-Semerena Jorge C. 
Published: October 2010

ABSTRACT

Sirtuins are NAD
+
-dependent protein deacylases that are conserved in all domains of life and are involved in diverse cellular processes, including control of gene expression and central metabolism. Eukaryotic sirtuins have N-terminal extensions that have been linked to protein multimerization and cellular localization. Here the first evidence of sirtuin isoforms in bacteria is reported. The enterobacterium
Salmonella enterica
synthesizes two isoforms of CobB sirtuin, a shorter 236-amino-acid isoform (here CobB
S
) and a longer 273-amino-acid isoform (here CobB
L
). The N-terminal 37-amino-acid extension of CobB
L
is amphipathic, containing 18 basic amino acids (12 of which are Arg) and 13 hydrophobic ones; both isoforms were active
in vivo
and
in vitro
. Northern blot and transcription start site analyses revealed that
cobB
is primarily expressed as two monocistronic
cobB
mRNAs from two transcription start sites, one of which was mapped within the neighboring
ycfX
gene and the other of which was located within
cobB
. Additionally, a low-abundance
ycfX
-
cobB
bicistronic mRNA was observed which could encode up to three proteins (YcfX, CobB
L
, and CobB
S
). CobB
L
isoforms are common within the family
Enterobacteriaceae
, but species of the genus
Erwinia
(including the plant pathogen
Erwinia amylovora
) encode only the CobB
L
isoform. The CobB
L
isoform from
E. amylovora
restored growth of as
S. enterica cobB
mutant strain on low acetate.
The Opportunistic Human PathogenAcinetobacter baumanniiSenses and Responds to Light
Authors: Mussi María A. , Gaddy Jennifer A. , Cabruja Matías , Arivett Brock A. , Viale Alejandro M. , Rasia Rodolfo , Actis Luis A. 
Published: October 2010

ABSTRACTLight is a ubiquitous environmental signal that many organisms sense and respond to by modulating their physiological responses accordingly. While this is an expected response among phototrophic microorganisms, the ability of chemotrophic prokaryotes to sense and react to light has become a puzzling and novel issue in bacterial physiology, particularly among bacterial pathogens. In this work, we show that the opportunistic pathogenAcinetobacter baumanniisenses and responds to blue light. Motility and formation of biofilms and pellicles were observed only when bacterial cells were incubated in darkness. In contrast, the killing ofCandida albicansfilaments was enhanced when they were cocultured with bacteria under light. These bacterial responses depend on the expression of theA. baumanniiATCC 17978 A1S_2225 gene, which codes for an 18.6-kDa protein that contains an N-terminalblue-light-sensing-usingflavin (BLUF) domain and lacks a detectable output domain(s). Spectral analyses of the purified recombinant protein showed its ability to sense light by a red shift upon illumination. Therefore, the A1S_2225 gene, which is present in several members of theAcinetobactergenus, was namedblue-light-sensingA(blsA). Interestingly, temperature plays a role in the ability ofA. baumanniito sense and respond to light via the BlsA photoreceptor protein.
Characterization of a Novel Riboswitch-Regulated Lysine Transporter inAggregatibacter actinomycetemcomitans
Authors: Jorth Peter , Whiteley Marvin 
Published: October 2010

ABSTRACTAggregatibacter actinomycetemcomitansis an opportunistic pathogen that resides primarily in the mammalian oral cavity. In this environment,A. actinomycetemcomitansfaces numerous host- and microbe-derived stresses, including intense competition for nutrients and exposure to the host immune system. While it is clear thatA. actinomycetemcomitansresponds to precise cues that allow it to adapt and proliferate in the presence of these stresses, little is currently known about the regulatory mechanisms that underlie these responses. Many bacteria use noncoding regulatory RNAs (ncRNAs) to rapidly alter gene expression in response to environmental stresses. Although no ncRNAs have been reported inA. actinomycetemcomitans, we propose that they are likely important for colonization and persistence in the oral cavity. Using a bioinformatic and experimental approach, we identified three putative metabolite-sensing riboswitches and nine small regulatory RNAs (sRNAs) inA. actinomycetemcomitansduring planktonic and biofilm growth. Molecular characterization of one of the riboswitches revealed that it is a lysine riboswitch and that its target gene,lysT, encodes a novel lysine-specific transporter. Finally, we demonstrated thatlysTand thelysTlysine riboswitch are conserved in over 40 bacterial species, including the phylogenetically related pathogenHaemophilus influenzae.
Sequencing of Multiple Clostridial Genomes Related to Biomass Conversion and Biofuel Production
Authors: Hemme Christopher L. , Mouttaki Housna , Lee Yong-Jin , Zhang Gengxin , Goodwin Lynne , Lucas Susan , Copeland Alex , Lapidus Alla , Glavina del Rio Tijana , Tice Hope , Saunders Elizabeth , Brettin Thomas , Detter John C. , Han Cliff S. , Pitluck Sam , Land Miriam L. , Hauser Loren J. , Kyrpides Nikos , Mikhailova Natalia , He Zhili , Wu Liyou , Van Nostrand Joy D. , Henrissat Bernard , He Qiang , Lawson Paul A. , Tanner Ralph S. , Lynd Lee R. , Wiegel Juergen , Fields Matthew W. , Arkin Adam P. , Schadt Christopher W. , Stevenson Bradley S. , McInerney Michael J. , Yang Yunfeng , Dong Hailiang , Xing Defeng , Ren Nanqi , Wang Aijie , Huhnke Raymond L. , Mielenz Jonathan R. , Ding Shi-You , Himmel Michael E. , Taghavi Safiyh , van der Lelie Daniël , Rubin Edward M. , Zhou Jizhong 
Published: October 2010

ABSTRACT

Modern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidates for processes involving biomass conversion and production of various biofuels and other industrial products. To expand the knowledge base for clostridial species relevant to current biofuel production efforts, we have sequenced the genomes of 20 species spanning multiple genera. The majority of species sequenced fall within the class III cellulosome-encoding
Clostridium
and the class V saccharolytic
Thermoanaerobacteraceae
. Species were chosen based on representation in the experimental literature as model organisms, ability to degrade cellulosic biomass either by free enzymes or by cellulosomes, ability to rapidly ferment hexose and pentose sugars to ethanol, and ability to ferment synthesis gas to ethanol. The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology.
Repeated oestrus synchrony and fixed‐time artificial insemination in beef cows
Authors: Penny C. D. , Lowman B. G. , Scott N. A. , Scott P. R. 
Published: October 2010

The feasibility of breeding spring‐calving, single‐suckled beef cows without the use of natural service was investigated over two breeding seasons by using repeated oestrus synchrony and fixed‐time artificial insemination (AI). Initially, cows were oestrus‐synchronised with subcutaneous norgestomet implants inserted for 10 days, with an injection of prostaglandin before the implants were removed. The cows were inseminated once 56 hours after the implants were removed, and 12 days later they were re‐treated with norgestomet implants to allow a second synchronised service. Twenty‐one days after the first synchronised AI, milk samples were taken for progesterone assay and the norgestomet implants were removed. The cows received a second service 56 hours later if the 21‐day milk progesterone assay suggested that they were not pregnant. All the cows receiving a second service were retreated with norgestomet implants to allow a third synchronised service as necessary. Pregnancy was later confirmed by rectal palpation. In the first year, 48 cows entered the programme and the pregnancy rates to the first, second and third synchronised services were 56, 69 and 40 per cent, respectively, with 17 per cent of cows barren at the end of the breeding period. In the second year, 69 cows entered the programme and the pregnancy rates were 58, 48 and 33 per cent to the successive services with 20 per cent of cows barren at the end of the breeding period. The accuracy of milk progesterone assay for pregnancy diagnosis was 84 per cent and 87 per cent in the first and second years, respectively.
Infectivity assays of foot‐and‐mouth disease virus: contact transmission between cattle and buffalo (Bubalus bubalis) in the early stages of infection
Authors: Gomes I. , Ramalho A. K. , Augé de Mello P. 
Published: October 2010

No differences were observed between cattle and Indian buffalo (Bubalus bubalis) in terms of temperature, viraemia or virus replication in the pharyngeal area, during the acute phase of foot‐and‐mouth disease. Like cattle, the Indian buffalo became infected and excreted virus before any clinical signs of foot‐and‐mouth disease developed. The disease was transmitted from cattle to buffalo and vice versa, during the acute stage of infection, as if the animals had been of the same species, presumably because of their close phylogenetic relationship. There were more tongue lesions in the cattle than in the buffalo. Foot lesions in the buffalo at first had a scaley appearance, but later became vesicular. Anti‐virus infection associated antigen and neutralising antibodies were synthesised at the same time in both species and reached similar titres in the same period. Persistent infection in the buffalo during the first 35 days after infection was similar to that in the cattle.
Field efficacy of injectable doramectin against Chorioptes bovis in naturally infected cattle
Authors: Losson B. J. , Mignon B. , Bossaert K. , Leclipteux T. , Lonneux J.‐F. 
Published: October 2010

A single subcutaneous injection of doramectin at a dose rate of 200 μg/kg bodyweight was effective in controlling an infection of Chorioptes bovis mites in naturally infected cattle. From 14 days after treatment, the geometric mean number of live mites was significantly lower (P<0.001) in the doramectin‐treated cattle than in the control group at each sampling until day 35. The percentage efficacy (treated versus controls) of doramectin against C bovis at day 35 was 99.9 per cent and the percentage reduction (day 35 versus day 0) in the treated animals was 99.3 per cent. At day 35, all seven controls were still positive for C bovis whereas five of the eight doramectin‐treated animals were free of live mites.
Evaluation of false ultrasonographic diagnoses in cows by measuring plasma levels of bovine pregnancy‐associated glycoprotein 1
Authors: Szenci O. , Taverne M.A.M. , Beckers J.F. , Sulon J. , Varga J. , Börzsönyi L. , Hanzen Ch. , Schekk Gy. 
Published: October 2010

Between days 27 and 59 after artificial insemination (AI), 189 ultrasonographic pregnancy diagnoses were made in 56 dairy cows using a 7.5 MHz linear‐array rectal transducer. Blood samples were withdrawn from a jugular vein on the day of Al, on day 21, and after each ultrasonographic examination between days 27 and 31, days 34 and 38, days 41 and 45 and days 55 and 59 after AI. Plasma concentrations of bovine pregnancy‐ associated glycoprotein 1 (bPAG‐1) were measured by radioimmunoassay. The results showed that before day 31, ultrasonographic scanning was not very sensitive because six of the 30 calving cows were incorrectly diagnosed as non‐pregnant. In five of these animals, the uterus was located far cranial to the pelvic inlet. Five of the cows examined between days 27 and 31 were pregnant on the basis of plasma bPAG‐1 levels on the same day, using 0.5 ng/ml as the cut‐off point. Plasma levels of bPAG‐1 and progesterone proved that four of the cows which had early positive ultrasonographic diagnoses but did not produce a calf, were pregnant when they were examined.
Tonsillar biopsy and PrPSc detection in the preclinical diagnosis of scrapie
Authors: Schreuder B. E. C. , van Keulen L. J. M. , Vromans M. E. W. , Langeveld J. P. M. , Smits M. A. 
Published: October 2010

Preliminary findings have indicated that in naturally infected sheep, fully susceptible to scrapie (vRQ‐homozygous), PrPSc can be detected in the tonsils approximately one year before the expected onset of clinical disease, whereas no immunostaining can be detected in animals with a semi‐resistant genotype. This paper describes the technique for taking tonsillar biopsies from sheep and gives the results of the completed experiment. In another experiment PrPSc was detected even earlier in comparable vRQ‐homozygous sheep born and raised in different surroundings. At three‐and‐a‐half months of age no PrPSc could be detected in three homozygous susceptible sheep (VRQ/VRQ), but PrpSc was detected at four months in one similar sheep. At eight months of age all seven sampled VRQ/VRQ sheep showed positive immunostaining in the biopsies, but none of the biopsies from three VRQ/ARQ heterozygotes showed any immunostaining; they were positive when sampled at 14 to 15 months of age. Biopsies from VRQ/ARR sheep were negative throughout this period. On the basis of the established or expected incubation period, PrPSc could thus be detected in the tonsils of live susceptible animals at between one‐third and a half of the incubation period, more than oneand‐a‐half years before clinical signs normally appear in both these genotypes.