bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sugarcane Growth Promotion by the Endophytic Bacterium Pantoea agglomerans 33.1
Authors: Quecine M. C. , Araújo W. L. , Rossetto P. B. , Ferreira A. , Tsui S. , Lacava P. T. , Mondin M. , Azevedo J. L. , Pizzirani-Kleiner A. A. 
Published: August 2012

ABSTRACT

The promotion of sugarcane growth by the endophytic
Pantoea agglomerans
strain 33.1 was studied under gnotobiotic and greenhouse conditions. The green fluorescent protein (GFP)-tagged strain
P. agglomerans
33.1::pNKGFP was monitored
in vitro
in sugarcane plants by microscopy, reisolation, and quantitative PCR (qPCR). Using qPCR and reisolation 4 and 15 days after inoculation, we observed that GFP-tagged strains reached similar density levels both in the rhizosphere and inside the roots and aerial plant tissues. Microscopic analysis was performed at 5, 10, and 18 days after inoculation. Under greenhouse conditions,
P. agglomerans
33.1-inoculated sugarcane plants presented more dry mass 30 days after inoculation. Cross-colonization was confirmed by reisolation of the GFP-tagged strain. These data demonstrate that 33.1::pNKGFP is a superior colonizer of sugarcane due to its ability to colonize a number of different plant parts. The growth promotion observed in colonized plants may be related to the ability of
P. agglomerans
33.1 to synthesize indoleacetic acid and solubilize phosphate. Additionally, this strain may trigger chitinase and cellulase production by plant roots, suggesting the induction of a plant defense system. However, levels of indigenous bacterial colonization did not vary between inoculated and noninoculated sugarcane plants under greenhouse conditions, suggesting that the presence of
P. agglomerans
33.1 has no effect on these communities. In this study, different techniques were used to monitor 33.1::pNKGFP during sugarcane cross-colonization, and our results suggested that this plant growth promoter could be used with other crops. The interaction between sugarcane and
P. agglomerans
33.1 has important benefits that promote the plant's growth and fitness.
Improvement of Crystal Solubility and Increasing Toxicity against Caenorhabditis elegans by Asparagine Substitution in Block 3 of Bacillus thuringiensis Crystal Protein Cry5Ba
Authors: Wang Fenshan , Liu Yingying , Zhang Fengjuan , Chai Lujun , Ruan Lifang , Peng Donghai , Sun Ming 
Published: August 2012

ABSTRACT

The crystal proteins from
Bacillus thuringiensis
are widely used for their specific toxicity against insects and nematodes. The highly conserved sequence blocks play an important role in Cry protein stability and flexibility, the basis of toxicity. The block 3 in Cry5Ba subfamily has a shorter sequence (only 12 residues) and more asparagine residues than that of others which harbor about 48 residues but only one asparagine. Based on the theoretical structure model of Cry5Ba, all three asparagines in block 3 are closely located in the interface of putative three domains, implying their probable importance in structure and function. In this study, all three asparagines in Cry5Ba2 block 3 were individually substituted with alanine by site-directed mutagenesis. The wild-type and mutant proteins were overexpressed and crystallized in acrystalliferous
B. thuringiensis
strain BMB171. However, the crystals formed in one of the mutants, designated N586A, abnormally disappeared and dissolved into the culture supernatant once the sporulation cells lysed, whereas the Cry5Ba crystal and the other mutant crystals were stable. The mutant N586A crystal, isolated from sporulation cells by the ultrasonic process, was found to be easily dissolved at wide range of pH value (5.0 to 10.0). Moreover, the toxicity assays showed that the mutant N586A exhibited nearly 9-fold-higher activity against nematodes and damaged the host's intestine more efficiently than the native Cry5Ba2. These data support the presumption that the amide residue Asn586 at the interface of domains might adversely affect the protein flexibility, solubility and resultant toxicity of Cry5Ba.
Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing
Authors: Lee On On , Yang Jiangke , Bougouffa Salim , Wang Yong , Batang Zenon , Tian Renmao , Al-Suwailem Abdulaziz , Qian Pei-Yuan 
Published: August 2012

ABSTRACT

Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which
Gammaproteobacteria
was the most dominant group, and
Chloroflexi
,
Chlamydiae
, and the candidate phylum
WS3
were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of
Vibrio
,
Pseudoalteromonas
,
Serratia
,
Stenotrophomonas
,
Pseudomonas
, and
Achromobacter
in the corals. On the other hand, bacteria such as
Chloracidobacterium
and
Endozoicomonas
were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.
Structure-Based Engineering of Methionine Residues in the Catalytic Cores of Alkaline Amylase from Alkalimonas amylolytica for Improved Oxidative Stability
Authors: Yang Haiquan , Liu Long , Wang Mingxing , Li Jianghua , Wang Nam Sun , Du Guocheng , Chen Jian 
Published: August 2012

ABSTRACT

This work aims to improve the oxidative stability of alkaline amylase from
Alkalimonas amylolytica
through structure-based site-directed mutagenesis. Based on an analysis of the tertiary structure, five methionines (Met 145, Met 214, Met 229, Met 247, and Met 317) were selected as the mutation sites and individually replaced with leucine. In the presence of 500 mM H
2
O
2
at 35°C for 5 h, the wild-type enzyme and the M145L, M214L, M229L, M247L, and M317L mutants retained 10%, 28%, 46%, 28%, 72%, and 43% of the original activity, respectively. Concomitantly, the alkaline stability, thermal stability, and catalytic efficiency of the M247L mutant were also improved. The pH stability of the mutants (M145L, M214L, M229L, and M317L) remained unchanged compared to that of the wild-type enzyme, while the stable pH range of the M247L mutant was extended from pH 7.0 to 11.0 for the wild type to pH 6.0 to 12.0 for the mutant. The wild-type enzyme lost its activity after incubation at 50°C for 2 h, and the M145L, M214L, M229L, and M317L mutants retained less than 14% of the activity, whereas the M247L mutant retained 34% of the activity under the same conditions. Compared to the wild-type enzyme, the
k
cat
values of the M145L, M214L, M229L, and M317L mutants decreased, while that of the M247L mutant increased slightly from 5.0 × 10
4
to 5.6 × 10
4
min
−1
. The mechanism responsible for the increased oxidative stability, alkaline stability, thermal stability, and catalytic efficiency of the M247L mutant was further analyzed with a structure model. The combinational mutants were also constructed, and their biochemical properties were characterized. The resistance of the wild-type enzyme and the mutants to surfactants and detergents was also investigated. Our results indicate that the M247L mutant has great potential in the detergent and textile industries.
Vip3C, a Novel Class of Vegetative Insecticidal Proteins from Bacillus thuringiensis
Authors: Palma Leopoldo , Hernï¿½ndez-Rodrï¿½guez Carmen Sara , Maeztu Mireya , Hernï¿½ndez-Martï¿½nez Patricia , Ruiz de Escudero Iï¿½igo , Escriche Baltasar , Muï¿½oz Delia , Van Rie Jeroen , Ferrï¿½ Juan , Caballero Primitivo 
Published: August 2012

ABSTRACT

Three
vip3
genes were identified in two
Bacillus thuringiensis
Spanish collections. Sequence analysis revealed a novel Vip3 protein class (Vip3C). Preliminary bioassays of larvae from 10 different lepidopteran species indicated that Vip3Ca3 caused more than 70% mortality in four species after 10 days at 4 μg/cm
2
.
Altered Large-Ring Cyclodextrin Product Profile Due to a Mutation at Tyr-172 in the Amylomaltase of Corynebacterium glutamicum
Authors: Srisimarat Wiraya , Kaulpiboon Jarunee , Krusong Kuakarun , Zimmermann Wolfgang , Pongsawasdi Piamsook 
Published: August 2012

ABSTRACTCorynebacterium glutamicumamylomaltase (CgAM) catalyzes the formation of large-ring cyclodextrins (LR-CDs) with a degree of polymerization of 19 and higher. The clonedCgAMgene was ligated into the pET-17b vector and used to transformEscherichia coliBL21(DE3). Site-directed mutagenesis of Tyr-172 inCgAM to alanine (Y172A) was performed to determine its role in the control of LR-CD production. Both the recombinant wild-type (WT) and Y172A enzymes were purified to apparent homogeneity and characterized. The Y172A enzyme exhibited lower disproportionation, cyclization, and hydrolysis activities than the WT. Thekcat/Kmof the disproportionation reaction of the Y172A enzyme was 2.8-fold lower than that of the WT enzyme. The LR-CD product profile from enzyme catalysis depended on the incubation time and the enzyme concentration. Interestingly, the Y172A enzyme showed a product pattern different from that of the WTCgAM at a long incubation time. The principal LR-CD products of the Y172A mutated enzyme were a cycloamylose mixture with a degree of polymerization of 28 or 29 (CD28 or CD29), while the principal LR-CD product of the WT enzyme was CD25 at 0.05 U of amylomaltase. These results suggest that Tyr-172 plays an important role in determining the LR-CD product profile of this novelCgAM.
Increased Penicillin Production in Penicillium chrysogenum Production Strains via Balanced Overexpression of Isopenicillin N Acyltransferase
Authors: Weber Stefan S. , Polli Fabiola , Boer Rï¿½mon , Bovenberg Roel A. L. , Driessen Arnold J. M. 
Published: August 2012

ABSTRACT

Intense classical strain improvement has yielded industrial
Penicillium chrysogenum
strains that produce high titers of penicillin. These strains contain multiple copies of the penicillin biosynthesis cluster encoding the three key enzymes: δ-(l-α-aminoadipyl)-
l
-cysteinyl-
d
-valine synthetase (ACVS), isopenicillin N synthase (IPNS), and isopenicillin N acyltransferase (IAT). The phenylacetic acid coenzyme A (CoA) ligase (PCL) gene encoding the enzyme responsible for the activation of the side chain precursor phenylacetic acid is localized elsewhere in the genome in a single copy. Since the protein level of IAT already saturates at low cluster copy numbers, IAT might catalyze a limiting step in high-yielding strains. Here, we show that penicillin production in high-yielding strains can be further improved by the overexpression of IAT while at very high levels of IAT the precursor 6-aminopenicillic acid (6-APA) accumulates. Overproduction of PCL only marginally stimulates penicillin production. These data demonstrate that in high-yielding strains IAT is the limiting factor and that this limitation can be alleviated by a balanced overproduction of this enzyme.
Identification and Regulation offusA, the Polyketide Synthase Gene Responsible for Fusarin Production in Fusarium fujikuroi
Authors: Díaz-Sánchez Violeta , Avalos Javier , Limón M. Carmen 
Published: August 2012

ABSTRACTFusarins are a class of mycotoxins of the polyketide family produced by differentFusariumspecies, including the gibberellin-producing fungusFusarium fujikuroi. Based on sequence comparisons between polyketide synthase (PKS) enzymes for fusarin production in otherFusariumstrains, we have identified theF. fujikuroiorthologue, calledfusA. The participation offusAin fusarin biosynthesis was demonstrated by targeted mutagenesis. Fusarin production is transiently stimulated by nitrogen availability in this fungus, a regulation paralleled by thefusAmRNA levels in the cell. Illumination of the cultures results in a reduction of the fusarin content, an effect partially explained by a high sensitivity of these compounds to light. Mutants of thefusAgene exhibit no external phenotypic alterations, including morphology and conidiation, except for a lack of the characteristic yellow and/or orange pigmentation of fusarins. Moreover, thefusAmutants are less efficient than the wild type at degrading cellophane on agar cultures, a trait associated with pathogenesis functions inFusarium oxysporum. ThefusAmutants, however, are not affected in their capacities to grow on plant tissues.
Engineering a Cyanobacterial Cell Factory for Production of Lactic Acid
Authors: Angermayr S. Andreas , Paszota Michal , Hellingwerf Klaas J. 
Published: August 2012

ABSTRACT

Metabolic engineering of microorganisms has become a versatile tool to facilitate production of bulk chemicals, fuels, etc. Accordingly, CO
2
has been exploited via cyanobacterial metabolism as a sustainable carbon source of biofuel and bioplastic precursors. Here we extended these observations by showing that integration of an
ldh
gene from
Bacillus subtilis
(encoding an
l
-lactate dehydrogenase) into the genome of
Synechocystis
sp. strain PCC6803 leads to
l
-lactic acid production, a phenotype which is shown to be stable for prolonged batch culturing. Coexpression of a heterologous soluble transhydrogenase leads to an even higher lactate production rate and yield (lactic acid accumulating up to a several-millimolar concentration in the extracellular medium) than those for the single
ldh
mutant. The expression of a transhydrogenase alone, however, appears to be harmful to the cells, and a mutant carrying such a gene is rapidly outcompeted by a revertant(s) with a wild-type growth phenotype. Furthermore, our results indicate that the introduction of a lactate dehydrogenase rescues this phenotype by preventing the reversion.
Cloning and Expression Analysis of Genes Encoding Lytic Endopeptidases L1 and L5 from Lysobacter sp. Strain XL1
Authors: Lapteva Y. S. , Zolova O. E. , Shlyapnikov M. G. , Tsfasman I. M. , Muranova T. A. , Stepnaya O. A. , Kulaev I. S. , Granovsky I. E. 
Published: August 2012

ABSTRACT

Lytic enzymes are the group of hydrolases that break down structural polymers of the cell walls of various microorganisms. In this work, we determined the nucleotide sequences of the
Lysobacter
sp. strain XL1
alpA
and
alpB
genes, which code for, respectively, secreted lytic endopeptidases L1 (AlpA) and L5 (AlpB).
In silico
analysis of their amino acid sequences showed these endopeptidases to be homologous proteins synthesized as precursors similar in structural organization: the mature enzyme sequence is preceded by an N-terminal signal peptide and a pro region. On the basis of phylogenetic analysis, endopeptidases AlpA and AlpB were assigned to the S1E family [clan PA(S)] of serine peptidases. Expression of the
alpA
and
alpB
open reading frames (ORFs) in
Escherichia coli
confirmed that they code for functionally active lytic enzymes. Each ORF was predicted to have the Shine-Dalgarno sequence located at a canonical distance from the start codon and a potential Rho-independent transcription terminator immediately after the stop codon. The
alpA
and
alpB
mRNAs were experimentally found to be monocistronic; transcription start points were determined for both mRNAs. The synthesis of the
alpA
and
alpB
mRNAs was shown to occur predominantly in the late logarithmic growth phase. The amount of
alpA
mRNA in cells of
Lysobacter
sp. strain XL1 was much higher, which correlates with greater production of endopeptidase L1 than of L5.
Genotyping of Present-Day and Historical Geobacillus Species Isolates from Milk Powders by High-Resolution Melt Analysis of Multiple Variable-Number Tandem-Repeat Loci
Authors: Seale R. Brent , Dhakal Rajat , Chauhan Kanika , Craven Heather M. , Deeth Hilton C. , Pillidge Christopher J. , Powell Ian B. , Turner Mark S. 
Published: August 2012

ABSTRACT

Spores of thermophilic
Geobacillus
species are a common contaminant of milk powder worldwide due to their ability to form biofilms within processing plants. Genotyping methods can provide information regarding the source and monitoring of contamination. A new genotyping method was developed based on multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) in conjunction with high-resolution melt analysis (MLV-HRMA) and compared to the currently used method, randomized amplified polymorphic DNA PCR (RAPD-PCR). Four VNTR loci were identified and used to genotype 46
Geobacillus
isolates obtained from retailed powder and samples from 2 different milk powder processing plants. These 46 isolates were differentiated into 16 different groups using MLV-HRMA (
D
= 0.89). In contrast, only 13 RAPD-PCR genotypes were identified among the 46 isolates (
D
= 0.79). This new method was then used to analyze 35 isolates obtained from powders with high spore counts (>10
4
spores ï¿½ g
−1
) from a single processing plant together with 27 historical isolates obtained from powder samples processed in the same region of Australia 17 years ago. Results showed that three genotypes can coexist in a single processing run, while the same genotypes observed 17 years ago are present today. While certain genotypes could be responsible for powders with high spore counts, there was no correlation to specific genotypes being present in powder plants and retailed samples. In conclusion, the MLV-HRMA method is useful for genotyping
Geobacillus
spp. to provide insight into the prevalence and persistence of certain genotypes within milk powder processing plants.
Protection of Wood from Microorganisms by Laccase-Catalyzed Iodination
Authors: Schubert M. , Engel J. , Thöny-Meyer L. , Schwarze F. W. M. R. , Ihssen J. 
Published: August 2012

ABSTRACT

In the present work, Norway spruce wood (
Picea abies
L.) was reacted with a commercial
Trametes versicolor
laccase in the presence of potassium iodide salt or the phenolic compounds thymol and isoeugenol to impart an antimicrobial property to the wood surface. In order to assess the efficacy of the wood treatment, a leaching of the iodinated and polymerized wood and two biotests including bacteria, a yeast, blue stain fungi, and wood decay fungi were performed. After laccase-catalyzed oxidation of the phenols, the antimicrobial effect was significantly reduced. In contrast, the enzymatic oxidation of iodide (I
−
) to iodine (I
2
) in the presence of wood led to an enhanced resistance of the wood surface against all microorganisms, even after exposure to leaching. The efficiency of the enzymatic wood iodination was comparable to that of a chemical wood preservative, VP 7/260a. The modification of the lignocellulose by the laccase-catalyzed iodination was assessed by the Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR) technique. The intensities of the selected lignin-associated bands and carbohydrate reference bands were analyzed, and the results indicated a structural change in the lignin matrix. The results suggest that the laccase-catalyzed iodination of the wood surface presents an efficient and ecofriendly method for wood protection.
Insight into the Evolution of Magnetotaxis in Magnetospirillum spp., Based on
mam
Gene Phylogeny
Authors: Lefèvre Christopher T. , Schmidt Marian L. , Viloria Nathan , Trubitsyn Denis , Schüler Dirk , Bazylinski Dennis A. 
Published: August 2012

ABSTRACT

Vibrioid- to helical-shaped magnetotactic bacteria phylogenetically related to the genus
Magnetospirillum
were isolated in axenic cultures from a number of freshwater and brackish environments located in the southwestern United States. Based on 16S rRNA gene sequences, most of the new isolates represent new
Magnetospirillum
species or new strains of known
Magnetospirillum
species, while one isolate appears to represent a new genus basal to
Magnetospirillum
. Partial sequences of conserved
mam
genes, genes reported to be involved in the magnetosome and magnetosome chain formation, and form II of the ribulose-1,5-bisphosphate carboxylase/oxygenase gene (
cbbM
) were determined in the new isolates and compared. The
cbbM
gene was chosen for comparison because it is not involved in magnetosome synthesis; it is highly conserved and is present in all but possibly one of the genomes of the magnetospirilla and the new isolates. Phylogenies based on 16S rRNA,
cbbM
, and
mam
gene sequences were reasonably congruent, indicating that the genes involved in magnetotaxis were acquired by a common ancestor of the
Magnetospirillum
clade. However, in one case, magnetosome genes might have been acquired through horizontal gene transfer. Our results also extend the known diversity of the
Magnetospirillum
group and show that they are widespread in freshwater environments.
Regulation of the Cell Division Cycle in Trypanosoma brucei
Authors: Li Ziyin 
Published: August 2012

ABSTRACT

The cell division cycle is tightly regulated by the activation and inactivation of a series of proteins that control the replication and segregation of organelles to the daughter cells. During the past decade, we have witnessed significant advances in our understanding of the cell cycle in
Trypanosoma brucei
and how the cycle is regulated by various regulatory proteins. However, many other regulators, especially those unique to trypanosomes, remain to be identified, and we are just beginning to delineate the signaling pathways that drive the transitions through different cell cycle stages, such as the G
1
/S transition, G
2
/M transition, and mitosis-cytokinesis transition. Trypanosomes appear to employ both evolutionarily conserved and trypanosome-specific molecules to regulate the various stages of its cell cycle, including DNA replication initiation, spindle assembly, chromosome segregation, and cytokinesis initiation and completion. Strikingly, trypanosomes lack some crucial regulators that are well conserved across evolution, such as Cdc6 and Cdt1, which are involved in DNA replication licensing, the spindle motor kinesin-5, which is required for spindle assembly, the central spindlin complex, which has been implicated in cytokinesis initiation, and the actomyosin contractile ring, which is located at the cleavage furrow. Conversely, trypanosomes possess certain regulators, such as cyclins, cyclin-dependent kinases, and mitotic centromere-associated kinesins, that are greatly expanded and likely play diverse cellular functions. Overall, trypanosomes apparently have integrated unique regulators into the evolutionarily conserved pathways to compensate for the absence of those conserved molecules and, additionally, have evolved certain cell cycle regulatory pathways that are either different from its human host or distinct between its own life cycle forms.