bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rhodococcus erythropolis
DCL14 Contains a Novel Degradation Pathway for Limonene
Authors: van der Werf Mariët J. , Swarts Henk J. , de Bont Jan A. M. 
Published: December 2019

ABSTRACT

Strain DCL14, which is able to grow on limonene as a sole source of carbon and energy, was isolated from a freshwater sediment sample. This organism was identified as a strain of
Rhodococcus erythropolis
by chemotaxonomic and genetic studies.
R. erythropolis
DCL14 also assimilated the terpenes limonene-1,2-epoxide, limonene-1,2-diol, carveol, carvone, and (−)-menthol, while perillyl alcohol was not utilized as a carbon and energy source. Induction tests with cells grown on limonene revealed that the oxygen consumption rates with limonene-1,2-epoxide, limonene-1,2-diol, 1-hydroxy-2-oxolimonene, and carveol were high. Limonene-induced cells of
R. erythropolis
DCL14 contained the following four novel enzymatic activities involved in the limonene degradation pathway of this microorganism: a flavin adenine dinucleotide- and NADH-dependent limonene 1,2-monooxygenase activity, a cofactor-independent limonene-1,2-epoxide hydrolase activity, a dichlorophenolindophenol-dependent limonene-1,2-diol dehydrogenase activity, and an NADPH-dependent 1-hydroxy-2-oxolimonene 1,2-monooxygenase activity. Product accumulation studies showed that (1
S
,2
S
,4
R
)-limonene-1,2-diol, (1
S
,4
R
)-1-hydroxy-2-oxolimonene, and (3
R
)-3-isopropenyl-6-oxoheptanoate were intermediates in the (4
R
)-limonene degradation pathway. The opposite enantiomers [(1
R
,2
R
,4
S
)-limonene-1,2-diol, (1
R
,4
S
)-1-hydroxy-2-oxolimonene, and (3
S
)-3-isopropenyl-6-oxoheptanoate] were found in the (4
S
)-limonene degradation pathway, while accumulation of (1
R
,2
S
,4
S
)-limonene-1,2-diol from (4
S
)-limonene was also observed. These results show that
R. erythropolis
DCL14 metabolizes both enantiomers of limonene via a novel degradation pathway that starts with epoxidation at the 1,2 double bond forming limonene-1,2-epoxide. This epoxide is subsequently converted to limonene-1,2-diol, 1-hydroxy-2-oxolimonene, and 7-hydroxy-4-isopropenyl-7-methyl-2-oxo-oxepanone. This lactone spontaneously rearranges to form 3-isopropenyl-6-oxoheptanoate. In the presence of coenzyme A and ATP this acid is converted further, and this finding, together with the high levels of isocitrate lyase activity in extracts of limonene-grown cells, suggests that further degradation takes place via the β-oxidation pathway.
Evidence for Production of a New Lantibiotic (Butyrivibriocin OR79A) by the Ruminal Anaerobe
Butyrivibrio fibrisolvens
OR79: Characterization of the Structural Gene Encoding Butyrivibriocin OR79A
Authors: Kalmokoff M. L. , Lu D. , Whitford M. F. , Teather R. M. 
Published: December 2019

ABSTRACT

The ruminal anaerobe
Butyrivibrio fibrisolvens
OR79 produces a bacteriocin-like activity demonstrating a very broad spectrum of activity. An inhibitor was isolated from spent culture fluid by a combination of ammonium sulfate and acidic precipitations, reverse-phase chromatography, and high-resolution gel filtration. N-terminal analysis of the isolated inhibitor yielded a 15-amino-acid sequence (G-N/Q-G/P-V-I-L-X-I-X-H-E-X-S-M-N). Two different amino acid residues were detected in the second and third positions from the N terminus, indicating the presence of two distinct peptides. A gene with significant homology to one combination of the determined N-terminal sequence was cloned, and expression of the gene was confirmed by Northern blotting. The gene (
bvi79A
) encoded a prepeptide of 47 amino acids and a mature peptide, butyrivibriocin OR79A, of 25 amino acids. Significant sequence homology was found between this peptide and previously reported lantibiotics containing the double-glycine leader peptidase processing site. Immediately downstream of
bvi79A
was a second, partial open reading frame encoding a peptide with significant homology to proteins which are believed to be involved in the synthesis of lanthionine residues. These findings indicate that the isolated inhibitory peptides represent new lantibiotics. Results from both total and N-terminal amino acid sequencing indicated that the second peptide was identical to butyrivibriocin OR79A except for amino acid substitutions in positions 2 and 3 of the mature lantibiotic. Only a single coding region was detected when restriction enzyme digests of total DNA were probed either with an oligonucleotide based on the 5′ region of
bvi79A
or with degenerate oligonucleotides based on the predicted sequence of the second peptide.
Atypical Genetic Locus Associated with Constitutive Production of Enterocin B by
Enterococcus faecium
BFE 900
Authors: Franz Charles M. A. P. , Worobo Randy W. , Quadri Luis E. N. , Schillinger Ulrich , Holzapfel Wilhelm H. , Vederas John C. , Stiles Michael E. 
Published: December 2019

ABSTRACT

A purified bacteriocin produced by
Enterococcus faecium
BFE 900 isolated from black olives was shown by Edman degradation and mass spectrometric analyses to be identical to enterocin B produced by
E. faecium
T136 from meat (P. Casaus, T. Nilsen, L. M. Cintas, I. F. Nes, P. E. Hernández, and H. Holo, Microbiology 143:2287–2294, 1997). The structural gene was located on a 2.2-kb
Hin
dIII fragment and a 12.0-kb
Eco
RI chromosomal fragment. The genetic characteristics and production of EntB by
E. faecium
BFE 900 differed from that described so far by the presence of a conserved sequence like a regulatory box upstream of the EntB gene, and its production was constitutive and not regulated. The 2.2-kb chromosomal fragment contained the hitherto undetected immunity gene for EntB in an atypical orientation that is the reverse of that of the structural gene. Typical transport and other genes associated with bacteriocin production were not detected on the 12.0-kb chromosomal fragment containing the EntB structural gene. This makes the EntB genetic system different from most other bacteriocin systems, where transport and possible regulatory genes are clustered. EntB was subcloned and expressed by the dedicated secretion machinery of
Carnobacterium piscicola
LV17A. The structural gene was amplified by PCR, fused to the divergicin A signal peptide, and expressed by the general secretory pathway in
Enterococcus faecalis
ATCC 19433.
Analysis of 16S-23S rRNA Intergenic Spacer Regions of
Vibrio cholerae
and
Vibrio mimicus
Authors: Chun Jongsik , Huq Anwarul , Colwell Rita R. 
Published: December 2019

ABSTRACT

Vibrio cholerae
identification based on molecular sequence data has been hampered by a lack of sequence variation from the closely related
Vibrio mimicus
. The two species share many genes coding for proteins, such as
ctxAB
, and show almost identical 16S DNA coding for rRNA (rDNA) sequences. Primers targeting conserved sequences flanking the 3′ end of the 16S and the 5′ end of the 23S rDNAs were used to amplify the 16S-23S rRNA intergenic spacer regions of
V. cholerae
and
V. mimicus
. Two major (ca. 580 and 500 bp) and one minor (ca. 750 bp) amplicons were consistently generated for both species, and their sequences were determined. The largest fragment contains three tRNA genes (tDNAs) coding for tRNA
Glu
, tRNA
Lys
, and tRNA
Val
, which has not previously been found in bacteria examined to date. The 580-bp amplicon contained tDNA
Ile
and tDNA
Ala
, whereas the 500-bp fragment had single tDNA coding either tRNA
Glu
or tRNA
Ala
. Little variation, i.e., 0 to 0.4%, was found among
V. cholerae
O1 classical, O1 El Tor, and O139 epidemic strains. Slightly more variation was found against the non-O1/non-O139 serotypes (ca. 1% difference) and
V. mimicus
(2 to 3% difference). A pair of oligonucleotide primers were designed, based on the region differentiating all of
V. cholerae
strains from
V. mimicus
. The PCR system developed was subsequently evaluated by using representatives of
V. cholerae
from environmental and clinical sources, and of other taxa, including
V. mimicus
. This study provides the first molecular tool for identifying the species
V. cholerae
.
Biodegradation of Cyclohexylamine by
Brevibacterium oxydans
IH-35A
Authors: Iwaki Hiroaki , Shimizu Masatake , Tokuyama Tai , Hasegawa Yoshie 
Published: December 2019

ABSTRACT

A bacterial strain capable of growing on cyclohexylamine (CHAM) was isolated by using enrichment and isolation techniques. The strain isolated, strain IH-35A, was classified as a member of the genus
Brevibacterium
. The results of growth and enzyme studies are consistent with degradation of CHAM via cyclohexanone (CHnone), 6-hexanolactone, 6-hydroxyhexanoate, and adipate. Cell extracts obtained from this strain grown on CHAM contained CHAM oxidase, and the model for CHAM oxidation by this enzyme was similar to the model for deamino oxidation of amine by amine oxidase.
A Sandwiched-Culture Technique for Evaluation of Heterologous Protein Production in a Filamentous Fungus
Authors: Ásgeirsdóttir Sigrídur A. , Scholtmeijer Karin , Wessels Joseph G. H. 
Published: December 2019

ABSTRACT

Aspergillus niger
is known for its efficient excretion machinery. However, problems have often arisen in obtaining high amounts of heterologous proteins in the culture medium. Here we present a quick method using sandwiched colonies to evaluate transgenic strains for secretion of heterologous proteins. Expressing the ABH1 hydrophobin of
Agaricus bisporus
in
A. niger
, we showed that low production levels of the heterologous protein are probably due to extracellular proteolytic degradation of the protein.
Examination of Physiological and Molecular Factors Involved in Enhanced Solvent Production by
Clostridium beijerinckii
BA101
Authors: Chen Chih-Kuang , Blaschek Hans P. 
Published: December 2019

ABSTRACT

The specific activities and the mRNA expression levels associated with coenzyme A transferase, acetoacetate decarboxylase, and butyraldehyde dehydrogenase were elevated in hyper-solvent-producing
Clostridium beijerinckii
BA101 during the exponential growth phase. The increase in expression of the
sol
operon and associated enzyme activities may be responsible for enhanced solvent production by
C. beijerinckii
BA101.
The Pediocin AcH Precursor Is Biologically Active
Authors: Ray Bibek , Schamber Robin , Miller Kurt W. 
Published: December 2019

ABSTRACT

The properties of the pediocin AcH precursor, prepediocin AcH, have been studied to gain insight into how producer cells may protect themselves from the activity of intracellular prebacteriocins. The native 62-amino-acid precursor and the 44-amino-acid mature species were expressed in
Escherichia coli
host strains that lack the leader peptide processing enzyme, PapD. Both forms inhibited the growth of the test bacterium
Listeria innocua
Lin11, indicating that the native precursor is biologically active. The two species also were synthesized in the context of maltose-binding protein chimeric proteins to facilitate the measurement of their relative specific activities. The chimeric form of the precursor was ∼80% as active as the chimeric mature species. Of relevance to cell protection and pediocin AcH production, it was determined that the precursor is strongly susceptible to inactivation by reducing agents and to degradation by chymotrypsin and endogenous
E. coli
proteases. Taken together, the results indicate that the activity of prepediocin AcH may have to be controlled prior to secretion to prevent toxicity to the host. Perhaps producer cells avoid membrane damage by maintaining the precursor in a reduced inactive state or by degrading molecules whose secretion is delayed.
Relationship between Acid Tolerance, Cytoplasmic pH, and ATP and H
+
-ATPase Levels in Chemostat Cultures of
Lactococcus lactis
Authors: O’Sullivan Eilís , Condon Séamus 
Published: December 2019

ABSTRACT

The acid tolerance response (ATR) of chemostat cultures of
Lactococcus lactis
subsp.
cremoris
NCDO 712 was dependent on the dilution rate and on the extracellular pH (pH
o
). A decrease in either the dilution rate or the pH
o
led to a decrease in the cytoplasmic pH (pH
i
) of the cells, and similar levels of acid tolerance were observed at any specific pH
i
irrespective of whether the pH
i
resulted from manipulation of the growth rate, manipulation of the pH
o
, or both. Acid tolerance was also induced by sudden additions of acid to chemostat cultures growing at a pH
o
of 7.0, and this induction was completely inhibited by chloramphenicol. The end products of glucose fermentation depended on the growth rate and the environmental pH
o
of the cultures, but neither the spectrum of end products nor the total rate of acid production correlated with a specific pH
i
. The rate of ATP formation was not correlated with pH
i
, but a good correlation between the cellular level of H
+
-ATPase and pH
i
was observed. Moreover, an inverse correlation between the cytoplasmic levels of ATP and pH
i
was established. Each pH
i
below 6.6 was characterized by unique levels of ATR, H
+
-ATPase, and ATP. High levels of H
+
-ATPase also coincided with high levels of acid tolerance of cells in batch cultures induced with sublethal levels of acid. We concluded that H
+
-ATPase is one of the ATR proteins induced by acid pH
i
through growth at an acid pH
o
or a slow growth rate.
Two-Component Transcriptional Regulation of N -Acyl-Homoserine Lactone Production in
Pseudomonas aureofaciens
Authors: Chancey S. T. , Wood D. W. , Pierson L. S. 
Published: December 2019

ABSTRACT

Production of phenazine antibiotics by the biological control bacterium
Pseudomonas aureofaciens
30-84 is regulated in part by the PhzI/PhzR
N
-acyl-homoserine lactone (AHL) response system (L. S. Pierson III, V. D. Keppenne, and D. W. Wood, J. Bacteriol. 176:3966–3974, 1994; D. W. Wood and L. S. Pierson III, Gene 168:49–53, 1996). Two mutants, 30-84W and 30-84.A2, were isolated and were found to be deficient in the production of phenazine, protease, hydrogen cyanide (HCN), and the AHL signal
N
-hexanoyl-homoserine lactone. These mutants were not complemented by
phzI
,
phzR
, or the phenazine biosynthetic genes (
phzFABCD
) (L. S. Pierson III, T. Gaffney, S. Lam, and F. Gong, FEMS Microbiol. Lett. 134:299–307, 1995). A 2.2-kb region of the 30-84 chromosome which fully restored production of all of these compounds in strain 30-84W was identified. Nucleotide sequence analysis of this region revealed a single open reading frame encoding a predicted 213-amino-acid protein which is very similar to the global response regulator GacA. Strain 30-84.A2 was not complemented by
gacA
or any cosmid from a genomic library of strain 30-84 but was complemented by
gacS
(formerly
lemA
) homologs from
Pseudomonas fluorescens
Pf-5 (N. Corbel and J. E. Loper, J. Bacteriol. 177:6230–6236, 1995) and
Pseudomonas syringae
pv. syringae B728a (E. M. Hrabek and D. K. Willis, J. Bacteriol. 174:3011–3020, 1992). Transcription of
phzR
was not altered in either mutant; however,
phzI
transcription was eliminated in strains 30-84W and 30-84.A2. These results indicated that the GacS/GacA two-component signal transduction system of
P. aureofaciens
30-84 controls the production of AHL required for phenazine production by mediating the transcription of
phzI
. Addition of exogenous AHL did not complement either mutant for phenazine production, indicating that the GacS/GacA global regulatory system controls phenazine production at multiple levels. Our results reveal for the first time a mechanism by which a two-component regulatory system and an AHL-mediated regulatory system interact.
Measurement of Monosaccharides and Conversion of Glucose to Acetate in Anoxic Rice Field Soil
Authors: Chidthaisong Amnat , Rosenstock Bernd , Conrad Ralf 
Published: December 2019

ABSTRACT

Degradation of glucose has been implicated in acetate production in rice field soil, but the abundance of glucose, the temporal change of glucose turnover, and the relationship between glucose and acetate catabolism are not well understood. We therefore measured the pool sizes of glucose and acetate in rice field soil and investigated the turnover of [U-
14
C]glucose and [2-
14
C]acetate. Acetate accumulated up to about 2 mM during days 5 to 10 after flooding of the soil. Subsequently, methanogenesis started and the acetate concentration decreased to about 100 to 200 μM. Glucose always made up >50% of the total monosaccharides detected. Glucose concentrations decreased during the first 10 days from 90 μM initially to about 3 μM after 40 days of incubation. With the exception at day 0 when glucose consumption was slow, the glucose turnover time was in the range of minutes, while the acetate turnover time was in the range of hours. Anaerobic degradation of [U-
14
C]glucose released [
14
C]acetate and
14
CO
2
as the main products, with [
14
C]acetate being released faster than
14
CO
2
. The products of [2-
14
C]acetate metabolism, on the other hand, were
14
CO
2
during the reduction phase of soil incubation (days 0 to 15) and
14
CH
4
during the methanogenic phase (after day 15). Except during the accumulation period of acetate (days 5 to 10), approximately 50 to 80% of the acetate consumed was produced from glucose catabolism. However, during the accumulation period of acetate, the rate of acetate production from glucose greatly exceeded that of acetate consumption. Under steady-state conditions, up to 67% of the CH
4
was produced from acetate, of which up to 56% was produced from glucose degradation.
Multiple Epoxide Hydrolases in
Alternaria alternata
f. sp.
lycopersici
and Their Relationship to Medium Composition and Host-Specific Toxin Production
Authors: Morisseau Christophe , Ward Barney L. , Gilchrist David G. , Hammock Bruce D. 
Published: December 2019

ABSTRACT

The production of
Alternaria alternata
f. sp.
lycopersici
host-specific toxins (AAL toxins) and epoxide hydrolase (EH) activity were studied during the growth of this plant-pathogenic fungus in stationary liquid cultures. Media containing pectin as the primary carbon source displayed peaks of EH activity at day 4 and at day 12. When pectin was replaced by glucose, there was a single peak of EH activity at day 6. Partial characterization of the EH activities suggests the presence of three biochemically distinguishable EH activities. Two of them have a molecular mass of 25 kDa and a pI of 4.9, while the other has a molecular mass of 20 kDa and a pI of 4.7. Each of the EH activities can be distinguished by substrate preference and sensitivity to inhibitors. The EH activities present at day 6 (glucose) or day 12 (pectin) are concomitant with AAL toxin production.
Occurrence of Nontuberculous Mycobacteria in Environmental Samples
Authors: Covert Terry C. , Rodgers Mark R. , Reyes Antolin L. , Stelma Gerard N. 
Published: December 2019

ABSTRACT

Nontuberculous mycobacteria (NTM) are a major cause of opportunistic infection in immunocompromised hosts. Because there is no evidence of person-to-person transmission and NTM have been found in drinking water, the environment is considered a likely source of infection. In this study the widespread occurrence of NTM was examined in drinking water, bottled water, and ice samples. A total of 139 samples were examined for NTM by a membrane filtration culture technique followed by PCR amplification and 16S rRNA sequence determination to identify the isolates. NTM were not detected in bottled water or cisterns but were detected in 54% of the ice samples and 35% of the public drinking-water samples from 21 states. The most frequently occurring isolate was
M. mucogenicum
(formerly referred to as an
M. chelonae
-like organism).
Role of
pfkA
and General Carbohydrate Catabolism in Seed Colonization by
Enterobacter cloacae
Authors: Roberts D. P. , Dery P. D. , Yucel I. , Buyer J. , Holtman M. A. , Kobayashi D. Y. 
Published: December 2019

ABSTRACT

Enterobacter cloacae
A-11 is a transposon mutant of strain 501R3 that was deficient in cucumber spermosphere colonization and in the utilization of certain carbohydrates (D. P. Roberts, C. J. Sheets, and J. S. Hartung, Can. J. Microbiol. 38:1128–1134, 1992). In vitro growth of strain A-11 was reduced or deficient on most carbohydrates that supported growth of strain 501R3 but was unaffected on fructose, glycerol, and all amino acids and organic acids tested. Colonization by strain A-11 was significantly reduced (
P
≤ 0.05) for cucumber and radish seeds compared to that of strain 501R3, but colonization of pea, soybean, sunflower, and sweet corn seeds was not reduced. Pea seeds released several orders of magnitude more total carbohydrates and amino acids than cucumber and radish seeds and approximately 4,000-fold more fructose. Fructose was the only carbohydrate detected in the seed exudates which supported wild-type levels of in vitro growth of strain A-11. Soybean, sunflower, and sweet corn seeds also released significantly greater amounts of fructose and total carbohydrates and amino acids than cucumber or radish seeds. The exogenous addition of fructose to cucumber and radish seeds at quantities similar to the total quantity of carbohydrates released from pea seeds over 96 h increased the populations of strain A-11 to levels comparable to those of strain 501R3 in sterile sand. Molecular characterization of strain A-11 indicated that the mini-Tn
5
kanamycin transposon was inserted in a region of the genome with significant homology to
pfkA
, which encodes phosphofructo kinase. A comparison of strain A-11 with
Escherichia coli
DF456, a known
pfkA
mutant, indicated that the nutritional loss phenotypes were identical. Furthermore, the
pfkA
homolog cloned from
E. cloacae
501R3 complemented the nutritional loss phenotypes of both
E. coli
DF456 and
E. cloacae
A-11 and restored colonization by strain A-11 to near wild-type levels. These genetic and biochemical restoration experiments provide strong evidence that the quantities of reduced carbon sources found in seed exudates and the ability of microbes to use these compounds play important roles in the colonization of the spermosphere.
Generation of a Superoxide Dismutase (SOD)-Deficient Mutant of
Campylobacter coli
: Evidence for the Significance of SOD in Campylobacter Survival and Colonization
Authors: Purdy Desmond , Cawthraw Sean , Dickinson Joanne H. , Newell Diane G. , Park Simon F. 
Published: December 2019

ABSTRACT

The microaerophilic nature of
Campylobacter
species implies an inherent sensitivity towards oxygen and its reduction products, particularly the superoxide anion. The deleterious effects of exposure to superoxide radicals are counteracted by the activity of superoxide dismutase (SOD). We have shown previously that
Campylobacter coli
possesses an iron cofactored SOD. The
sodB
gene of
C. coli
UA585 was insertionally inactivated by the site-specific insertion of a
tetO
cassette. Organisms harboring the inactivated gene failed to produce a biologically functional form of the enzyme. While the ability of this mutant to grow in aerobic conditions was unchanged relative to the parental strain, its survival was severely compromised when nongrowing cells were exposed to air. Accordingly, the SOD-deficient mutant was unable to survive for prolonged periods in model foods. Furthermore, inactivation of the
sodB
gene decreased the colonization potential in an experimental infection of 1-day-old chicks. In contrast, strain CK100, which is deficient in catalase activity, showed the same survival and colonization characteristics as the parental strain. These results indicate that SOD, but not catalase, is an important determinant in the ability of
C. coli
to survive aerobically and for optimal colonization within the chicken gut.