bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biodegradation of 5-Nitroanthranilic Acid by
Bradyrhizobium
sp. Strain JS329
Authors: Qu Yi , Spain Jim C. 
Published: January 2010

ABSTRACT

Biodegradation of synthetic compounds has been studied extensively, but the metabolic diversity required for catabolism of many natural compounds has not been addressed. 5-Nitroanthranilic acid (5NAA), produced in soil by
Streptomyces scabies
, is also the starting material for synthetic dyes and other nitroaromatic compounds.
Bradyrhizobium
JS329 was isolated from soil by selective enrichment with 5NAA. When grown on 5NAA, the isolate released stoichiometric amounts of nitrite and half of the stoichiometric amounts of ammonia. Enzyme assays indicate that the initial step in 5NAA degradation is an unusual hydrolytic deamination for formation of 5-nitrosalicylic acid (5NSA). Cloning and heterologous expression revealed the genes that encode 5NAA deaminase (
naaA
) and the 5NSA dioxygenase (
naaB
) that cleaves the aromatic ring of 5NSA without prior removal of the nitro group. The results provide the first clear evidence for the initial steps in biodegradation of amino-nitroaromatic compounds and reveal a novel deamination reaction for aromatic amines.
Selection from Industrial Lager Yeast Strains of Variants with Improved Fermentation Performance in Very-High-Gravity Worts
Authors: Huuskonen Anne , Markkula Tuomas , Vidgren Virve , Lima Luis , Mulder Linda , Geurts Wim , Walsh Michael , Londesborough John 
Published: January 2010

ABSTRACT

There are economic and other advantages if the fermentable sugar concentration in industrial brewery fermentations can be increased from that of currently used high-gravity (ca. 14 to 17°P [degrees Plato]) worts into the very-high-gravity (VHG; 18 to 25°P) range. Many industrial strains of brewer's yeast perform poorly in VHG worts, exhibiting decreased growth, slow and incomplete fermentations, and low viability of the yeast cropped for recycling into subsequent fermentations. A new and efficient method for selecting variant cells with improved performance in VHG worts is described. In this new method, mutagenized industrial yeast was put through a VHG wort fermentation and then incubated anaerobically in the resulting beer while maintaining the α-glucoside concentration at about 10 to 20 g·liter
−1
by slowly feeding the yeast maltose or maltotriose until most of the cells had died. When survival rates fell to 1 to 10 cells per 10
6
original cells, a high proportion (up to 30%) of survivors fermented VHG worts 10 to 30% faster and more completely (residual sugars lower by 2 to 8 g·liter
−1
) than the parent strains, but the sedimentation behavior and profiles of yeast-derived flavor compounds of the survivors were similar to those of the parent strains.
Essential Role of a Trypanosome U4-Specific Sm Core Protein in Small Nuclear Ribonucleoprotein Assembly and Splicing
Authors: Jaé Nicolas , Wang Pingping , Gu Tianpeng , Hühn Martin , Palfi Zsofia , Urlaub Henning , Bindereif Albrecht 
Published: January 2010

ABSTRACTSpliceosomal small nuclear ribonucleoproteins (snRNPs) in trypanosomes contain either the canonical heptameric Sm ring or variant Sm cores with snRNA-specific Sm subunits. Here we show biochemically by a combination of RNase H cleavage and tandem affinity purification that the U4 snRNP contains a variant Sm heteroheptamer core in which only SmD3 is replaced by SSm4. This U4-specific, nuclear-localized Sm core protein is essential for growth and splicing. As shown by RNA interference (RNAi) knockdown, SSm4 is specifically required for the integrity of the U4 snRNA and the U4/U6 di-snRNP in trypanosomes. In addition, we demonstrate byin vitroreconstitution of Sm cores that under stringent conditions, the SSm4 protein suffices to specify the assembly of U4 Sm cores. Together, these data indicate that the assembly of the U4-specific Sm core provides an essential step in U4/U6 di-snRNP biogenesis and splicing in trypanosomes.
Role for Parasite Genetic Diversity in Differential Host Responses toTrypanosoma bruceiInfection
Authors: Morrison Liam J. , McLellan Sarah , Sweeney Lindsay , Chan Chi N. , MacLeod Annette , Tait Andy , Turner C. Michael R. 
Published: January 2010

ABSTRACTThe postgenomic era has revolutionized approaches to defining host-pathogen interactions and the investigation of the influence of genetic variation in either protagonist upon infection outcome. We analyzed pathology induced by infection with two genetically distinctTrypanosoma bruceistrains and found that pathogenesis is partly strain specific, involving distinct host mechanisms. Infections of BALB/c mice with one strain (927) resulted in more severe anemia and greater erythropoietin production compared to infections with the second strain (247), which, contrastingly, produced greater splenomegaly and reticulocytosis. Plasma interleukin-10 (IL-10) and gamma interferon levels were significantly higher in strain 927-infected mice, whereas IL-12 was higher in strain 247-infected mice. To define mechanisms underlying these differences, expression microarray analysis of host genes in the spleen at day 10 postinfection was undertaken. Rank product analysis (RPA) showed that 40% of the significantly differentially expressed genes were specific to infection with one or the other trypanosome strain. RPA and pathway analysis identified LXR/RXR signaling, IL-10 signaling, and alternative macrophage activation as the most significantly differentially activated host processes. These data suggest that innate immune response modulation is a key determinant in trypanosome infections, the pattern of which can vary, dependent upon the trypanosome strain. This strongly suggests that a parasite genetic component is responsible for causing disease in the host. Our understanding of trypanosome infections is largely based on studies involving single parasite strains, and our results suggest that an integrated host-parasite approach is required for future studies on trypanosome pathogenesis. Furthermore, it is necessary to incorporate parasite variation into both experimental systems and models of pathogenesis.
F Plasmid TraF and TraH Are Components of an Outer Membrane Complex Involved in Conjugation
Authors: Arutyunov Denis , Arenson Barbara , Manchak Jan , Frost Laura S. 
Published: January 2010

ABSTRACTF plasmid TraF and TraH are required for F pilus assembly and F plasmid transfer. Using flotation sucrose density gradients, we found that TraF and TraH (as well as TraU and TraW) localized to the outer membrane in the presence of the complete F transfer region, especially TraV, the putative anchor. Mutational analysis of TraH revealed two domains that are important for its function and possible interaction with TrbI, which in turn has a role in stabilizing TraH.
The Receiver Domain of Hybrid Histidine Kinase VirA: an Enhancing Factor for
vir
Gene Expression in
Agrobacterium tumefaciens
Authors: Wise Arlene A. , Fang Fang , Lin Yi-Han , He Fanglian , Lynn David G. , Binns Andrew N. 
Published: January 2010

ABSTRACT

The plant pathogen
Agrobacterium tumefaciens
expresses virulence (
vir
) genes in response to chemical signals found at the site of a plant wound. VirA, a hybrid histidine kinase, and its cognate response regulator, VirG, regulate
vir
gene expression. The receiver domain at the carboxyl end of VirA has been described as an inhibitory element because its removal increased
vir
gene expression relative to that of full-length VirA. However, experiments that characterized the receiver region as an inhibitory element were performed in the presence of constitutively expressed
virG
. We show here that VirA's receiver domain is an activating factor if
virG
is expressed from its native promoter on the Ti plasmid. When
virA
ΔR was expressed from a multicopy plasmid, both sugar and the phenolic inducer were essential for
vir
gene expression. Replacement of wild-type
virA
on pTi with
virA
ΔR precluded
vir
gene induction, and the cells did not accumulate VirG or induce transcription of a
virG
-
lacZ
fusion in response to acetosyringone. These phenotypes were corrected if the
virG
copy number was increased. In addition, we show that the VirA receiver domain can interact with the VirG DNA-binding domain.
Identification of Tail Genes in the Temperate Phage
16
-
3
of
Sinorhizobium meliloti
41
Authors: Deák Veronika , Lukács Rita , Buzás Zsuzsanna , Pálvölgyi Adrienn , Papp Péter P. , Orosz László , Putnoky Péter 
Published: January 2010

ABSTRACT

Genes encoding the tail proteins of the temperate phage
16
-
3
of the symbiotic nitrogen-fixing bacterium
Sinorhizobium meliloti
41 have been identified. First, a new host range gene, designated
hII
, was localized by using missense mutations. The corresponding protein was shown to be identical to the 85-kDa tail protein by determining its N-terminal sequence. Electron microscopic analysis showed that phage
16
-
3
possesses an icosahedral head and a long, noncontractile tail characteristic of the
Siphoviridae
. By using a lysogenic
S. meliloti
41 strain, mutants with insertions in the putative tail region of the genome were constructed and virion morphology was examined after induction of the lytic cycle. Insertions in
ORF017
,
ORF018a
,
ORF020
,
ORF021
, the previously described
h
gene, and
hII
resulted in uninfectious head particles lacking tail structures, suggesting that the majority of the genes in this region are essential for tail formation. By using different bacterial mutants, it was also shown that not only the RkpM and RkpY proteins but also the RkpZ protein of the host takes part in the formation of the phage receptor. Results for the host range phage mutants and the receptor mutant bacteria suggest that the H
II
tail protein interacts with the capsular polysaccharide of the host and that the tail protein encoded by the original
h
gene recognizes a proteinaceous receptor.
PcaO Positively Regulates
pcaHG
of the β-Ketoadipate Pathway in
Corynebacterium glutamicum
Authors: Zhao Ke-Xin , Huang Yan , Chen Xi , Wang Nan-Xi , Liu Shuang-Jiang 
Published: January 2010

ABSTRACT

We identified a new regulator, PcaO, which is involved in regulation of the protocatechuate (PCA) branch of the β-ketoadipate pathway in
Corynebacterium glutamicum
. PcaO is an atypical
l
arge
A
TP-binding
L
uxR family (LAL)-type regulator and does not have a Walker A motif. A mutant of
C. glutamicum
in which
pcaO
was disrupted (RES167Δ
pcaO
) was unable to grow on PCA, and growth on PCA was restored by complementation with
pcaO
. Both an enzymatic assay of PCA 3,4-dioxygenase activity (encoded by
pcaHG
) and transcriptional analysis of
pcaHG
by reverse transcription-PCR revealed that PcaO positively regulated
pcaHG
. A promoter-LacZ transcriptional fusion assay suggested that PcaO interacted with the sequence upstream of
pcaHG
. Electrophoretic mobility shift assay (EMSA) analysis indicated that an imperfect palindromic sequence (
−78
AACCCCTGACCTTCGGGGTT
−59
) that was located upstream of the −35 region of the
pcaHG
promoter was essential for PcaO regulation. DNase I footprinting showed that this imperfect palindrome was protected from DNase I digestion. Site-directed mutation and EMSA tests revealed that this palindrome sequence was essential for PcaO binding to the DNA fragment.
In vitro
EMSA results showed that ATP weakened the binding between PcaO and its target sequence but ADP strengthened this binding, while the effect of protocatechuate on PcaO binding was dependent on the protocatechuate concentration.
Identification and Regulation of the
N
-Acetylglucosamine Utilization Pathway of the Plant Pathogenic Bacterium
Xanthomonas campestris
pv. campestris
Authors: Boulanger Alice , Déjean Guillaume , Lautier Martine , Glories Marie , Zischek Claudine , Arlat Matthieu , Lauber Emmanuelle 
Published: January 2010

ABSTRACT

Xanthomonas campestris
pv. campestris, the causal agent of black rot disease of brassicas, is known for its ability to catabolize a wide range of plant compounds. This ability is correlated with the presence of specific
c
arbohydrate
u
tilization loci containing
T
onB-dependent transporters (CUT loci) devoted to scavenging specific carbohydrates. In this study, we demonstrate that there is an
X. campestris
pv. campestris CUT system involved in the import and catabolism of
N
-acetylglucosamine (GlcNAc). Expression of genes belonging to this GlcNAc CUT system is under the control of GlcNAc via the LacI family NagR and GntR family NagQ regulators. Analysis of the NagR and NagQ regulons confirmed that GlcNAc utilization involves NagA and NagB-II enzymes responsible for the conversion of GlcNAc-6-phosphate to fructose-6-phosphate. Mutants with mutations in the corresponding genes are sensitive to GlcNAc, as previously reported for
Escherichia coli
. This GlcNAc sensitivity and analysis of the NagQ and NagR regulons were used to dissect the
X. campestris
pv. campestris GlcNAc utilization pathway. This analysis revealed specific features, including the fact that uptake of GlcNAc through the inner membrane occurs via a major facilitator superfamily transporter and the fact that this amino sugar is phosphorylated by two proteins belonging to the glucokinase family, NagK-IIA and NagK-IIB. However, NagK-IIA seems to play a more important role in GlcNAc utilization than NagK-IIB under our experimental conditions. The
X. campestris
pv. campestris GlcNAc NagR regulon includes four genes encoding TonB-dependent active transporters (TBDTs). However, the results of transport experiments suggest that GlcNAc passively diffuses through the bacterial envelope, an observation that calls into question whether GlcNAc is a natural substrate for these TBDTs and consequently is the source of GlcNAc for this nonchitinolytic plant-associated bacterium.
The
Sinorhizobium meliloti
RNA Chaperone Hfq Mediates Symbiosis of
S. meliloti
and Alfalfa
Authors: Barra-Bily Lise , Pandey Shree P. , Trautwetter Annie , Blanco Carlos , Walker Graham C. 
Published: January 2010

ABSTRACT

There exist commonalities between symbiotic
Sinorhizobium meliloti
and pathogenic
Brucella
bacteria in terms of extensive gene synteny and the requirements for intracellular survival in their respective hosts. The RNA chaperone Hfq is essential for virulence for several bacterial groups, including
Brucella
; however, its role in
S. meliloti
has not been investigated. Our studies of an
S. meliloti
loss-of-function
hfq
mutant have revealed that Hfq plays a key role in the establishment of the symbiosis between
S. meliloti
and its host
Medicago sativa. S. meliloti
Hfq is involved in controlling the population density under a free-living state and affects the growth parameters and nodulation. An
hfq
mutant poorly colonizes the infection threads that are necessary for the bacteria to invade the developing nodule. An
hfq
mutant is severely impaired in its ability to invade plant cells within the nodule, which leads to the formation of small, ineffective nodules unable to fix nitrogen. In culture, the
hfq
mutant did not accumulate transcripts of
nifA
, which encodes a key regulator necessary for nitrogen fixation. Hfq may be involved in regulation of several proteins relevant to
hfq
mutant phenotypes. The crucial role of Hfq in symbiosis suggests that small regulatory RNAs are important for its interactions with its plant host.
Proteomic Alterations Explain Phenotypic Changes in
Sinorhizobium meliloti
Lacking the RNA Chaperone Hfq
Authors: Barra-Bily Lise , Fontenelle Catherine , Jan Gwenael , Flechard Maud , Trautwetter Annie , Pandey Shree P. , Walker Graham C. , Blanco Carlos 
Published: January 2010

ABSTRACT

The ubiquitous bacterial RNA-binding protein Hfq is involved in stress resistance and pathogenicity. In
Sinorhizobium meliloti
, Hfq is essential for the establishment of symbiosis with
Medicago sativa
and for nitrogen fixation. A proteomic analysis identifies 55 proteins with significantly affected expression in the
hfq
mutant; most of them are involved in cell metabolism or stress resistance. Important determinants of oxidative stress resistance, such as CysK, Gsh, Bfr, SodC, KatB, KatC, and a putative peroxiredoxine (SMc00072), are downregulated in the
hfq
mutant. The
hfq
mutant is affected for H
2
O
2
, menadione, and heat stress resistance. Part of these defects could result from the reductions of
rpoE1
,
rpoE2
,
rpoE3
, and
rpoE4
expression levels in the
hfq
mutant. Some proteins required for efficient symbiosis are reduced in the
hfq
mutant, contributing to the drastic defect in nodulation observed in this mutant.
Systematic Domain Deletion Analysis of the Major Sporulation Kinase in
Bacillus subtilis
Authors: Eswaramoorthy Prahathees , Fujita Masaya 
Published: January 2010

ABSTRACT

To characterize the role of the three PAS domains in KinA, the major sporulation kinase in
Bacillus subtilis
, we constructed a series of systematic PAS domain deletion mutants and analyzed their activities using an IPTG (isopropyl-β-
d
-thiogalactopyranoside)-inducible artificial sporulation induction system, which we have developed recently. The results showed that any one of the three PAS domains is sufficient to maintain the kinase activity and trigger sporulation, if not fully then at least partially, when the protein levels increase beyond a certain level.
RamA, a Member of the AraC/XylS Family, Influences Both Virulence and Efflux inSalmonella entericaSerovar Typhimurium
Authors: Bailey Andrew M. , Ivens Al , Kingsley Rob , Cottell Jennifer L. , Wain John , Piddock Laura J. V. 
Published: January 2010

ABSTRACTThe transcriptomes ofSalmonella entericaserovar Typhimurium SL1344 lacking a functionalramAorramRor with plasmid-mediated high-level overexpression oframAwere compared to those of the wild-type parental strain. Inactivation oframAled to increased expression of 14 SPI-1 genes and decreased expression of three SPI-2 genes, and it altered expression of ribosomal biosynthetic genes and several amino acid biosynthetic pathways. Furthermore, disruption oframAled to decreased survival within RAW 264.7 mouse macrophages and attenuation within the BALB/c ByJ mouse model. Highly overexpressedramAled to increased expression of genes encoding multidrug resistance (MDR) efflux pumps, includingacrAB,acrEF, andtolC. Decreased expression of 34Salmonellapathogenicity island (SPI) 1 and 2 genes, decreased SipC production, decreased adhesion to and survival within macrophages, and decreased colonization ofCaenorhabditis eleganswere also seen. Disruption oframRled to the increased expression oframA,acrAB, andtolC, but not to the same level as whenramAwas overexpressed on a plasmid. Inactivation oframRhad a more limited effect on pathogenicity gene expression.In silicoanalysis of a suggested RamA-binding consensus sequence identified target genes, includingramR,acrA,tolC,sipABC, andssrA. This study demonstrates that the regulation of a mechanism of MDR and expression of virulence genes show considerable overlap, and we postulate that such a mechanism is dependent on transcriptional activator concentration and promoter sensitivity. However, we have no evidence to support the hypothesis that increased MDR via RamA regulation of AcrAB-TolC gives rise to a hypervirulent strain.
The Role of Knowledge Management in Innovation
Authors: Dasgupta Meeta , Sahay A. , Gupta R. K. 
Published: January 2010

Research on innovation practices reinforces the notion that majority of innovation projects fail systematically due to being managed as raw technology projects. Open forms of innovation where internal and external ideas are leveraged across the organisation are gaining importance over the internal and centralised approach to R&D. India, during the last 15 years, has been spiralling ahead towards ultimate economic success based on its 'knowledge-based talent pool'. Innovation has become a top strategic focus for most Indian companies. Seeing the growing importance of innovation and knowledge management, a need was felt to understand how organisations manage their knowledge capital so as to promote innovation.This paper aims to provide insights into how an organisation manages knowledge through culture, structure, technology and leadership, so as to promote acquisition and application of knowledge which leads to innovation. The study brings out the importance of tacit knowledge embedded in the firm's culture, structure and leadership as a complement to the explicit knowledge embedded in the firm's technology and documents.
Effective Information Flow in the Internal Supply Chain: Results from a Snowball Method to Map Information Flows
Authors: Chibba Aron , Rundquist Jonas 
Published: January 2010

Information sharing is an important factor for effectiveness within the internal supply chain. In this paper we use a methodology for mapping information flows in an internal supply chain, and case studies of two Swedish multinational organisations. Eight retrospective cases were used to map, describe and analyse the information flow that supports the physical material flow from the receipt of an order to point of delivery. Every involved person was interviewed on at least one occasion each. The interviews were conducted to map and describe the information and physical material flow. The aim was to identify factors that could improve and rationalise information flows and generate a better flow within the organisation.The study shows the importance of an integrated information system, but also clearly indicates the importance of a collaborative culture and an awareness of the human–technology interface. The study also shows that three factors of interface distortions are most frequent in the cases: (1) changes registered in the database trigger no action among the staff, (2) new knowledge to staff is stored only orally and not in the database, and (3) interface between the paper system and the database, and between the old and the new information storage culture.