bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antagonistic Interactions among Marine Pelagic Bacteria
Authors: Long Richard A. , Azam Farooq 
Published: July 2002

ABSTRACT

Recent studies suggest that bacterial abundance and species diversity in the ocean's water column are variable at the millimeter scale, apparently in response to the small-scale heterogeneity in the distribution of organic matter. We hypothesized that bacterium-bacterium antagonistic interactions may contribute to variations in community structure at the microscale. We examined each of the 86 isolates for their inhibition of growth of the remaining 85 isolates by the Burkholder agar diffusion assay. More than one-half of the isolates expressed antagonistic activity, and this trait was more common with particle-associated bacteria than with free-living bacteria. This was exemplified by members of the α subclass of the class
Proteobacteria
(α-proteobacteria), in which production of antagonistic molecules was dominated by attached bacteria. We found that γ-proteobacteria (members of the orders
Alteromonadales
and
Vibrionales
) are the most prolific producers of inhibitory materials and also the most resilient to them, while members of the
Bacteriodetes
were the organisms that were least productive and most sensitive to antagonistic interactions. Widespread interspecies growth inhibition is consistent with the role of this phenomenon in structuring bacterial communities at the microscale. Furthermore, our results suggest that bacteria from pelagic marine particles may be an underutilized source of novel antibiotics.
Two Distinct Monooxygenases for Alkane Oxidation in
Nocardioides
sp. Strain CF8
Authors: Hamamura Natsuko , Yeager Chris M. , Arp Daniel J. 
Published: July 2002

ABSTRACT

Alkane monooxygenases in
Nocardioides
sp. strain CF8 were examined at the physiological and genetic levels. Strain CF8 can utilize alkanes ranging in chain length from C
2
to C
16
. Butane degradation by butane-grown cells was strongly inhibited by allylthiourea, a copper-selective chelator, while hexane-, octane-, and decane-grown cells showed detectable butane degradation activity in the presence of allylthiourea. Growth on butane and hexane was strongly inhibited by 1-hexyne, while 1-hexyne did not affect growth on octane or decane. A specific 30-kDa acetylene-binding polypeptide was observed for butane-, hexane-, octane-, and decane-grown cells but was absent from cells grown with octane or decane in the presence of 1-hexyne. These results suggest the presence of two monooxygenases in strain CF8. Degenerate primers designed for PCR amplification of genes related to the binuclear-iron-containing alkane hydroxylase from
Pseudomonas oleovorans
were used to clone a related gene from strain CF8. Reverse transcription-PCR and Northern blot analysis showed that this gene encoding a binuclear-iron-containing alkane hydroxylase was expressed in cells grown on alkanes above C
6
. These results indicate the presence of two distinct monooxygenases for alkane oxidation in
Nocardioides
sp. strain CF8.
Quantification of Soil-to-Plant Transport of Recombinant Nucleopolyhedrovirus: Effects of Soil Type and Moisture, Air Currents, and Precipitation
Authors: Fuxa James R. , Richter Arthur R. 
Published: July 2002

ABSTRACT

Significantly more occlusion bodies (OB) of DuPont viral construct HzSNPV-LqhIT2, expressing a scorpion toxin, were transported by artificial rainfall to cotton plants from sandy soil (70:15:15 sand-silt-clay) than from silt (15:70:15) and significantly more from silt than from clay (15:15:70). The amounts transported by 5 versus 50 mm of precipitation were the same, and transport was zero when there was no precipitation. In treatments that included precipitation, the mean number of viable OB transported to entire, 25- to 35-cm-tall cotton plants ranged from 56 (clay soil, 5 mm of rain) to 226 (sandy soil, 50 mm of rain) OB/plant. In a second experiment, viral transport increased with increasing wind velocity (0, 16, and 31 km/h) and was greater in dry (−1.0 bar of matric potential) than in moist (−0.5 bar) soil. Wind transport was greater for virus in a clay soil than in silt or sand. Only 3.3 × 10
−7
(clay soil, 5 mm rain) to 1.3 × 10
−6
(sandy soil, 50 mm rain) of the OB in surrounding soil in experiment 1 or 1.1 × 10
−7
(−0.5 bar sandy soil, 16-km/h wind) to 1.3 × 10
−6
(−1.0 bar clay soil, 31-km/h wind) in experiment 2 were transported by rainfall or wind to cotton plants. This reduces the risk of environmental release of a recombinant nucleopolyhedrovirus (NPV), because only a very small proportion of recombinant virus in the soil reservoir is transported to vegetation, where it can be ingested by and replicate in new host insects.
A Novel Regulatory Gene,
Tri10
, Controls Trichothecene Toxin Production and Gene Expression
Authors: Tag Andrew G. , Garifullina Gulnara F. , Peplow Andrew W. , Ake Charles , Phillips T. D. , Hohn Thomas M. , Beremand Marian N. 
Published: July 2002

ABSTRACT

We report here the characterization of
Tri10
, a novel regulatory gene within the trichothecene gene cluster. Comparison of
Tri10
genomic and mRNA sequences revealed that removal of a single 77-bp intron provided a 1,260-bp open reading frame, encoding a 420-amino-acid protein. Disruption of
Tri10
in
Fusarium sporotrichioides
abolished T-2 toxin production and dramatically decreased the transcript accumulation for four trichothecene genes (
Tri4
,
Tri5
,
Tri6
, and
Tri101
) and an apparent farnesyl pyrophosphate synthetase (
Fpps
) gene. Conversely, homologous integration of a disruption vector by a single upstream crossover event significantly increased T-2 toxin production and elevated the transcript accumulation of the trichothecene genes and
Fpps
. Further analysis revealed that disruption of
Tri10
, and to a greater extent the disruption of
Tri6,
increased sensitivity to T-2 toxin under certain growth conditions. Although
Tri10
is conserved in
Fusarium graminearum
and
Fusarium sambucinum
and clearly plays a central role in regulating trichothecene gene expression, it does not show any significant matches to proteins of known or predicted function or to motifs except a single transmembrane domain. We suggest a model in which
Tri10
acts upstream of the cluster-encoded transcription factor TRI6 and is necessary for full expression of both the other trichothecene genes and the genes for the primary metabolic pathway that precedes the trichothecene biosynthetic pathway, as well as for wild-type levels of trichothecene self-protection. We further suggest the presence of a regulatory loop where
Tri6
is not required for the transcription of
Tri10
but is required to limit the expression of
Tri10.
Behavior of a Recombinant Baculovirus in Lepidopteran Hosts with Different Susceptibilities
Authors: Hernández-Crespo Pedro , Sait Steven M. , Hails Rosemary S. , Cory Jenny S. 
Published: July 2002

ABSTRACT

Insect pathogens, such as baculoviruses, that are used as microbial insecticides have been genetically modified to increase their speed of action. Nontarget species will often be exposed to these pathogens, and it is important to know the consequences of infection in hosts across the whole spectrum of susceptibility. Two key parameters, speed of kill and pathogen yield, are compared here for two baculoviruses, a wild-type
Autographa californica
nucleopolyhedrovirus (AcNPV), AcNPV clone C6, and a genetically modified AcNPV which expresses an insect-selective toxin, AcNPV-ST3, for two lepidopteran hosts which differ in susceptibility. The pathogenicity of the two viruses was equal in the less-susceptible host,
Mamestra brassicae
, but the recombinant was more pathogenic than the wild-type virus in the susceptible species,
Trichoplusia ni
. Both viruses took longer to kill the larvae of
M. brassicae
than to kill those of
T. ni
. However, whereas the larvae of
T. ni
were killed more quickly by the recombinant virus, the reverse was found to be true for the larvae of
M. brassicae
. Both viruses produced a greater yield in
M. brassicae
, and the yield of the recombinant was significantly lower than that of the wild type in both species. The virus yield increased linearly with the time taken for the insects to die. However, despite the more rapid speed of kill of the wild-type AcNPV in
M. brassicae
, the yield was significantly lower for the recombinant virus at any given time to death. A lower yield for the recombinant virus could be the result of a reduction in replication rate. This was investigated by comparing determinations of the virus yield per unit of weight of insect cadaver. The response of the two species (to both viruses) was very different: the yield per unit of weight decreased over time for
M. brassicae
but increased for
T. ni
. The implications of these data for risk assessment of wild-type and genetically modified baculoviruses are discussed.
Purification, Characterization, and Overexpression of Flavin Reductase Involved in Dibenzothiophene Desulfurization by
Rhodococcus erythropolis
D-1
Authors: Matsubara Toshiyuki , Ohshiro Takashi , Nishina Yoshihiro , Izumi Yoshikazu 
Published: July 2002

ABSTRACT

The dibenzothiophene (DBT)-desulfurizing bacterium,
Rhodococcus erythropolis
D-1, removes sulfur from DBT to form 2-hydroxybiphenyl using four enzymes, DszC, DszA, DszB, and flavin reductase. In this study, we purified and characterized the flavin reductase from
R. erythropolis
D-1 grown in a medium containing DBT as the sole source of sulfur. It is conceivable that the enzyme is essential for two monooxygenase (DszC and DszA) reactions in vivo. The purified flavin reductase contains no chromogenic cofactors and was found to have a molecular mass of 86 kDa and four identical 22-kDa subunits. The enzyme catalyzed NADH-dependent reduction of flavin mononucleotide (FMN), and the

K
m

values for NADH and FMN were 208 and 10.8 μM, respectively. Flavin adenine dinucleotide was a poor substrate, and NADPH was inert. The enzyme did not catalyze reduction of any nitroaromatic compound. The optimal temperature and optimal pH for enzyme activity were 35°C and 6.0, respectively, and the enzyme retained 30% of its activity after heat treatment at 80°C for 30 min. The N-terminal amino acid sequence of the purified flavin reductase was identical to that of DszD of
R. erythropolis
IGTS8 (K. A. Gray, O. S. Pogrebinsky, G. T. Mrachko, L. Xi, D. J. Monticello, and C. H. Squires, Nat. Biotechnol. 14:1705–1709, 1996). The flavin reductase gene was amplified with primers designed by using
dszD
of
R. erythropolis
IGTS8, and the enzyme was overexpressed in
Escherichia coli
. The specific activity in crude extracts of the overexpressed strain was about 275-fold that of the wild-type strain.
Seasonal Variation and Indirect Monitoring of Microcystin Concentrations in Daechung Reservoir, Korea
Authors: Oh Hee-Mock , Lee Seog June , Kim Jee-Hwan , Kim Hee-Sik , Yoon Byung-Dae 
Published: July 2002

ABSTRACTPhysicochemical and biological water quality, including the microcystin concentration, was investigated from spring to autumn 1999 in the Daechung Reservoir, Korea. The dominant genus in the cyanobacterial blooming season wasMicrocystis. The microcystin concentration in particulate form increased dramatically from August up to a level of 200 ng liter−1in early October and thereafter tended to decrease. The microcystin concentration in dissolved form was about 28% of that of the particulate form. The microcystins detected using a protein phosphatase (PP) inhibition assay were highly correlated with those microcystins detected by a high-performance liquid chromatograph (r= 0.973;P< 0.01). Therefore, the effectiveness of a PP inhibition assay for microcystin detection in a high number of water samples was confirmed as easy, quick, and convenient. The microcystin concentration was highly correlated with the phytoplankton number (r= 0.650;P< 0.01) and chlorophyll-aconcentration (r= 0.591;P< 0.01). When the microcystin concentration exceeded about 100 ng liter−1, the ratio of particulate to dissolved total nitrogen (TN) or total phosphorus (TP) converged at a value of 0.6. Furthermore, the microcystin concentration was lower than 50 ng liter−1at a particulate N/P ratio below 8, whereas the microcystin concentration varied quite substantially from 50 to 240 ng liter−1at a particulate N/P ratio of >8. Therefore, it seems that the microcystin concentration in water can be estimated and indirectly monitored by analyzing the following: the phytoplankton number and chlorophyll-aconcentration, the ratio of the particulate and the dissolved forms of N and P, and the particulate N/P ratio when the dominant genus is toxigenicMicrocystis.
Characterization of a Novel Type II Restriction-Modification System,
Sth
368I, Encoded by the Integrative Element ICE
St1
of
Streptococcus thermophilus
CNRZ368
Authors: Burrus Vincent , Bontemps Cyril , Decaris Bernard , Guédon Gérard 
Published: July 2002

ABSTRACT

A novel type II restriction and modification (R-M) system,
Sth
368I, which confers resistance to φST84, was found in
Streptococcus thermophilus
CNRZ368 but not in the very closely related strain A054. Partial sequencing of the integrative conjugative element ICE
St1,
carried by
S. thermophilus
CNRZ368 but not by A054, revealed a divergent cluster of two genes,
sth368IR
and
sth368IM
. The protein sequence encoded by
sth368IR
is related to the type II endonucleases R.
Lla
KR2I and R.
Sau
3AI, which recognize and cleave the sequence 5′-GATC-3′. The protein sequence encoded by
sth368IM
is very similar to numerous type II 5-methylcytosine methyltransferases, including M.
Lla
KR2I and M.
Sau
3AI. Cell extracts of CNRZ368 but not A054 were found to cleave at the GATC site. Furthermore, the C residue of the sequence 5′-GATC-3′ was found to be methylated in CNRZ368 but not in A054. Cloning and integration of a copy of
sth368IR
and
sth368IM
in the A054 chromosome confers on this strain phenotypes similar to those of CNRZ368, i.e., phage resistance, endonuclease activity of cell extracts, and methylation of the sequence 5′-GATC-3′. Disruption of
sth368IR
removes resistance and restriction activity. We conclude that ICE
St1
encodes an R-M system,
Sth
368I, which recognizes the sequence 5′-GATC-3′ and is related to the
Sau
3AI and
Lla
KR2I restriction systems.
Genomic Interspecies Microarray Hybridization: Rapid Discovery of Three Thousand Genes in the Maize Endophyte,
Klebsiella pneumoniae
342, by Microarray Hybridization with
Escherichia coli
K-12 Open Reading Frames
Authors: Dong Yuemei , Glasner Jeremy D. , Blattner Frederick R. , Triplett Eric W. 
Published: July 2002

ABSTRACT

In an effort to efficiently discover genes in the diazotrophic endophyte of maize,
Klebsiella pneumoniae
342, DNA from strain 342 was hybridized to a microarray containing 96% (
n
= 4,098) of the annotated open reading frames from
Escherichia coli
K-12. Using a criterion of 55% identity or greater, 3,000 (70%) of the
E. coli
K-12 open reading frames were also found to be present in strain 342. Approximately 24% (
n
= 1,030) of the
E. coli
K-12 open reading frames are absent in strain 342. For 1.6% (
n
= 68) of the open reading frames, the signal was too low to make a determination regarding the presence or absence of the gene. Genes with high identity between the two organisms are those involved in energy metabolism, amino acid metabolism, fatty acid metabolism, cofactor synthesis, cell division, DNA replication, transcription, translation, transport, and regulatory proteins. Functions that were less highly conserved included carbon compound metabolism, membrane proteins, structural proteins, putative transport proteins, cell processes such as adaptation and protection, and central intermediary metabolism. Open reading frames of
E. coli
K-12 with little or no identity in strain 342 included putative regulatory proteins, putative chaperones, surface structure proteins, mobility proteins, putative enzymes, hypothetical proteins, and proteins of unknown function, as well as genes presumed to have been acquired by lateral transfer from sources such as phage, plasmids, or transposons. The results were in agreement with the physiological properties of the two strains. Whole genome comparisons by genomic interspecies microarray hybridization are shown to rapidly identify thousands of genes in a previously uncharacterized bacterial genome provided that the genome of a close relative has been fully sequenced. This approach will become increasingly more useful as more full genome sequences become available.
Characterization of the 450-kb Linear Plasmid in a Polychlorinated Biphenyl Degrader,
Rhodococcus
sp. Strain RHA1
Authors: Shimizu Satoru , Kobayashi Hiroyuki , Masai Eiji , Fukuda Masao 
Published: July 2002

ABSTRACT

A strong polychlorinated biphenyl (PCB) degrader,
Rhodococcus
sp. strain RHA1, has diverse biphenyl/PCB degradative genes and harbors huge linear plasmids, including pRHL1 (1,100 kb), pRHL2 (450 kb), and pRHL3 (330 kb). The diverse degradative genes are distributed mainly on the pRHL1 and pRHL2 plasmids. In this study, the structural and functional characteristics of pRHL2 were determined. We constructed a physical map of pRHL2, and the degradative enzyme genes, including
bphB2, etbD2, etbC, bphDEF, bphC2
, and
bphC4
, were localized in three regions. Conjugal transfer of pRHL2 between RHA1 mutant derivatives was observed at a frequency of 7.5 × 10
−5
transconjugant per recipient. These results suggested that the linear plasmid is a possible determinant of propagation of the diverse degradative genes in rhodococci. The termini of pRHL2 were cloned and sequenced. The left and right termini of pRHL2 had 3-bp perfect terminal inverted repeats and were not as similar to each other (64% identity) as the known actinomycete linear replicons are. Southern hybridization analysis with pRHL2 terminal probes suggested that the right terminus of pRHL2 is similar to pRHL1 and pRHL3 termini. Retardation of both terminal fragments in the gel shift assay indicated that each terminus of pRHL2 is linked to a protein. We suggest that pRHL2 has invertron termini, as has been reported previously for
Streptomyces
linear replicons.
Purification ofSynechocystissp. Strain PCC6308 Cyanophycin Synthetase and Its Characterization with Respect to Substrate and Primer Specificity
Authors: Aboulmagd Elsayed , Oppermann-Sanio Fred B. , Steinbüchel Alexander 
Published: July 2002

ABSTRACTSynechocystissp. strain PCC6308 cyanophycin synthetase was purified 72-fold in three steps by anion exchange chromatography on Q Sepharose, affinity chromatography on the triazine dye matrix Procion Blue HE-RD Sepharose, and gel filtration on Superdex 200 HR from recombinant cells ofEscherichia coli.The native enzyme, which catalyzed the incorporation of arginine and aspartic acid into cyanophycin, has an apparent molecular mass of 240 ± 30 kDa and consists of identical subunits of 85 ± 5 kDa. TheKmvalues for arginine (49 μM), aspartic acid (0.45 mM), and ATP (0.20 mM) indicated that the enzyme had a high affinity towards these substrates. During in vitro cyanophycin synthesis, 1.3 ± 0.1 mol of ATP per mol of incorporated amino acid was converted to ADP. The optima for the enzyme-catalyzed reactions were pH 8.2 and 50°C, respectively. Arginine methyl ester (99.5 and 97% inhibition), argininamide (99 and 96%), S-(2-aminoethyl) cysteine (43 and 42%), β-hydroxy aspartic acid (35 and 37%), aspartic acid β-methyl ester (38 and 40%), norvaline (0 and 3%), citrulline (9 and 7%), and asparagine (2 and 0%) exhibited an almost equal inhibitory effect on the incorporation of both arginine and aspartic acid, respectively, when these compounds were added to the complete reaction mixture. In contrast, the incorporation of arginine was diminished to a greater extent than that of aspartic acid, respectively, with canavanine (82 and 53%), lysine (36 and 19%), agmatine (33 and 25%),d-aspartic acid (37 and 30%),l-glutamic acid (13 and 5%), and ornithine (23 and 11%). On the other hand, canavanine (45% of maximum activity) and lysine (13%) stimulated the incorporation of aspartic acid, whereas aspartic acid β-methyl ester (53%) and asparagine (9%) stimulated the incorporation of arginine. [3H]lysine (15% of maximum activity) and [3H]canavanine (13%) were incorporated into the polymer, when they were either used instead of arginine or added to the complete reaction mixture, whereasl-glutamic acid was not incorporated. No effect on arginine incorporation was obtained by the addition of other amino acids (i.e., alanine, histidine, leucine, proline, tryptophan, and glycine). Various samples of chemically synthesized poly-α,β-d,l-aspartic acid served as primers for in vitro synthesis of cyanophycin, whereas poly-α-l-aspartic acid was almost inactive.
Changes in Activity and Community Structure of Methane-Oxidizing Bacteria over the Growth Period of Rice
Authors: Eller Gundula , Frenzel Peter 
Published: July 2002

ABSTRACT

The activity and community structure of methanotrophs in compartmented microcosms were investigated over the growth period of rice plants. In situ methane oxidation was important only during the vegetative growth phase of the plants and later became negligible. The in situ activity was not directly correlated with methanotrophic cell counts, which increased even after the decrease in in situ activity, possibly due to the presence of both vegetative cells and resting stages. By dividing the microcosms into two soil and two root compartments it was possible to locate methanotrophic growth and activity, which was greatest in the rhizoplane of the rice plants. Molecular analysis by denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH) with family-specific probes revealed the presence of both families of methanotrophs in soil and root compartments over the whole season. Changes in community structure were detected only for members of the
Methylococcaceae
and could be associated only with changes in the genus
Methylobacter
and not with changes in the dominance of different genera in the family
Methylococcaceae
. For the family
Methylocystaceae
stable communities in all compartments for the whole season were observed. FISH analysis revealed evidence of in situ dominance of the
Methylocystaceae
in all compartments. The numbers of
Methylococcaceae
cells were relatively high only in the rhizoplane, demonstrating the importance of rice roots for growth and maintenance of methanotrophic diversity in the soil.
Metabolic Behavior of
Lactococcus lactis
MG1363 in Microaerobic Continuous Cultivation at a Low Dilution Rate
Authors: Jensen Niels Bang Siemsen , Melchiorsen Claus Rix , Jokumsen Kirsten Væver , Villadsen John 
Published: July 2002

ABSTRACT

Minute amounts of oxygen were supplied to a continuous cultivation of
Lactococcus lactis
subsp.
cremoris
MG1363 grown on a defined glucose-limited medium at a dilution rate of 0.1 h
−1
. More than 80% of the carbon supplied with glucose ended up in fermentation products other than lactate. Addition of even minute amounts of oxygen increased the yield of biomass on glucose by more than 10% compared to that obtained under anaerobic conditions and had a dramatic impact on catabolic enzyme activities and hence on the distribution of carbon at the pyruvate branch point. Increasing aeration caused carbon dioxide and acetate to replace formate and ethanol as catabolic end products while hardly affecting the production of either acetoin or lactate. The negative impact of oxygen on the synthesis of pyruvate formate lyase was confirmed. Moreover, oxygen was shown to down regulate the protein level of alcohol dehydrogenase while increasing the enzyme activity levels of the pyruvate dehydrogenase complex, α-acetolactate synthase, and the NADH oxidases. Lactate dehydrogenase and glyceraldehyde dehydrogenase enzyme activity levels were unaffected by aeration.