bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alkane Hydroxylase from
Acinetobacter
sp. Strain ADP1 Is Encoded by
alkM
and Belongs to a New Family of Bacterial Integral-Membrane Hydrocarbon Hydroxylases
Authors: Ratajczak Andreas , Geißdörfer Walter , Hillen Wolfgang 
Published: December 2019

ABSTRACT

Degradation of long-chain alkanes by
Acinetobacter
sp. strain ADP1 involves rubredoxin and rubredoxin reductase. We complemented a mutant deficient in alkane utilization and sequenced four open reading frames (ORFs) on the complementing DNA. Each of these ORFs was disrupted by insertional mutagenesis on the chromosome. As determined from sequence comparisons, ORF1 and ORF4 seem to encode a rotamase of the PpiC type and an acyl coenzyme A dehydrogenase, respectively. Disruption of these ORFs does not affect alkane utilization. In contrast, the two other ORFs,
alkR
and
alkM
, are essential for growth on alkanes as sole carbon sources.
alkR
encodes a polypeptide with extensive homology to AraC-XylS-like transcriptional regulators. It is located next to
alkM
, which encodes the terminal alkane hydroxylase, but is in the opposite orientation. Sequence homologies with other bacterial integral-membrane hydrocarbon hydroxylases suggest that AlkM may be the first member of a new protein family. The genes identified here are not linked to the rubredoxin- and rubredoxin reductase-encoding genes on the
Acinetobacter
sp. strain ADP1 chromosome.
Comparison of Randomly Amplified Polymorphic DNA with Amplified Fragment Length Polymorphism To Assess Genetic Diversity and Genetic Relatedness within Genospecies III of
Pseudomonas syringae
Authors: Clerc Agathe , Manceau Charles , Nesme Xavier 
Published: December 2019

ABSTRACT

Recently, DNA pairing analyses showed that
Pseudomonas syringae
pv. tomato and related pathovars, including
P. syringae
pv. maculicola, form a genomic species (
Pseudomonas tomato
) (L. Gardan, H. L. Shafik, and P. A. D. Grimont, p. 445–448,
in
K. Rudolph, T. J. Burr, J. W. Mansfield, D. Stead, A. Vivian, and J. von Kietzell, ed.,
Pseudomonas syringae Pathovars and Related Pathogens
, 1997). The genetic diversity of 23 strains belonging to this genomic species and 4 outgroup strains was analyzed with randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphic (AFLP) techniques. Simple boiling of
P. syringae
cells was suitable for subsequent DNA amplification to obtain reliable patterns in RAPD and AFLP analyses. In general, the grouping of
P. syringae
strains by both analysis techniques corresponded well with the classification obtained from an RFLP analysis of ribosomal DNA operons, DNA pairing studies, and an analysis of pathogenicity data. However, two strains of
P. syringae
pv. maculicola produced distinct DNA patterns compared to the DNA patterns of other
P. syringae
pv. maculicola strains; these patterns led us to assume that horizontal transfer of DNA could occur between bacterial populations. Both techniques used in this study have high discriminating power because strains of
P. syringae
pv. tomato and
P. syringae
pv. maculicola which were indistinguishable by other techniques, including pathogenicity tests on tomato, were separated into two groups by both RAPD and AFLP analyses. In addition, data analysis showed that the AFLP method was more efficient for assessing intrapathovar diversity than RAPD analysis and allowed clear delineation between intraspecific and interspecific genetic distances, suggesting that it could be an alternative to DNA pairing studies. However, it was not possible to distinguish the two races of
P. syringae
pv. tomato on the basis of an analysis of the data provided by either the AFLP or RAPD technique.
Phase Variation in
Xenorhabdus nematophilus
Authors: Volgyi Antonia , Fodor Andras , Szentirmai Attila , Forst Steven 
Published: December 2019

ABSTRACT

Xenorhabdus nematophilus
is a symbiotic bacterium that inhabits the intestine of entomopathogenic nematodes. The bacterium-nematode symbiotic pair is pathogenic for larval-stage insects. The phase I cell type is the form of the bacterium normally associated with the nematode. A variant cell type, referred to as phase II, can form spontaneously under stationary-phase conditions. Phase II cells do not elaborate products normally associated with the phase I cell type. To better define phase variation in
X. nematophilus
, several strains (19061, AN6, F1, N2-4) of this bacterium were analyzed for new phenotypic traits. An analysis of pathogenicity in
Manduca sexta
larvae revealed that the phase II form of AN6 (AN6/II) was significantly less virulent than the phase I form (AN6/I). The variant form of N2-4 was also avirulent. On the other hand, F1/II and 19061/II were as virulent as the respective phase I cells. Strain 19061/II was found to be motile, and AN6/II regained motility when the bacteria were grown in low-osmolarity medium. In contrast, F1/II remained nonmotile. The phase II cells did not produce the outer membrane protein, OpnB, that is normally induced during the stationary phase. Both phase I and phase II cells were able to support nematode growth and development. These findings indicate that while certain phenotypic traits are common to all phase II cells, other characteristics, such as virulence and motility, are variable and can be influenced by environmental conditions.
Analysis of BIOLOG GN Substrate Utilization Patterns by Microbial Communities
Authors: Smalla Kornelia , Wachtendorf Ute , Heuer Holger , Liu Wen-tso , Forney Larry 
Published: December 2019

ABSTRACT

BIOLOG GN plates are increasingly used to characterize microbial communities by determining the ability of the communities to oxidize various carbon sources. Studies were done to determine whether the BIOLOG GN plate assay accurately reflects the catabolic potential of the inoculum used. To gain insight into which populations of microbial communities contribute to the BIOLOG patterns, denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis (TGGE) were used to assess the diversity of ribotypes in the inocula and individual wells of BIOLOG plates following incubation. These studies were done with microbial communities from the rhizosphere of potatoes and an activated sludge reactor fed with glucose and peptone. TGGE analyses of BIOLOG wells inoculated with cell suspensions from the potato rhizosphere revealed that, compared with the inoculum, there was a decrease in the number of 16S rRNA gene fragments obtained from various wells, as well as a concomitant loss of populations that had been numerically dominant in the inoculum. The dominant fragments in TGGE gels could be assigned to the γ subclass of the class
Proteobacteria
, suggesting that fast-growing bacteria adapted to high substrate concentrations were numerically dominant in the wells and may have been primarily responsible for the patterns of substrate use that were observed. Similarly, the community structure changed in wells inoculated with cells from activated sludge; one or more populations were enriched, but all dominant populations of the inoculum could be detected in at least one well. This study showed that carbon source utilization profiles obtained with BIOLOG GN plates do not necessarily reflect the functional potential of the numerically dominant members of the microbial community used as the inoculum.
Development of a Laboratory-Scale Leaching Plant for Metal Extraction from Fly Ash by
Thiobacillus
Strains
Authors: Brombacher Christoph , Bachofen Reinhard , Brandl Helmut 
Published: December 2019

ABSTRACT

Semicontinuous biohydrometallurgical processing of fly ash from municipal waste incineration was performed in a laboratory-scale leaching plant (LSLP) by using a mixed culture of
Thiobacillus thiooxidans
and
Thiobacillus ferrooxidans
. The LSLP consisted of three serially connected reaction vessels, reservoirs for a fly ash suspension and a bacterial stock culture, and a vacuum filter unit. The LSLP was operated with an ash concentration of 50 g liter
−1
, and the mean residence time was 6 days (2 days in each reaction vessel). The leaching efficiencies (expressed as percentages of the amounts applied) obtained for the economically most interesting metal, Zn, were up to 81%, and the leaching efficiencies for Al were up to 52%. Highly toxic Cd was completely solubilized (100%), and the leaching efficiencies for Cu, Ni, and Cr were 89, 64, and 12%, respectively. The role of
T. ferrooxidans
in metal mobilization was examined in a series of shake flask experiments. The release of copper present in the fly ash as chalcocite (Cu
2
S) or cuprite (Cu
2
O) was dependent on the metabolic activity of
T. ferrooxidans
, whereas other metals, such as Al, Cd, Cr, Ni, and Zn, were solubilized by biotically formed sulfuric acid. Chemical leaching with 5 N H
2
SO
4
resulted in significantly increased solubilization only for Zn. The LSLP developed in this study is a promising first step toward a pilot plant with a high capacity to detoxify fly ash for reuse for construction purposes and economical recovery of valuable metals.
19
F Nuclear Magnetic Resonance as a Tool To Investigate Microbial Degradation of Fluorophenols to Fluorocatechols and Fluoromuconates
Authors: Boersma Marelle G. , Dinarieva Tatiana Y. , Middelhoven Wouter J. , van Berkel Willem J. H. , Doran Joel , Vervoort Jacques , Rietjens Ivonne M. C. M. 
Published: December 2019

ABSTRACT

A method was developed to study the biodegradation and oxidative biodehalogenation of fluorinated phenols by
19
F nuclear magnetic resonance (NMR). Characterization of the
19
F NMR spectra of metabolite profiles of a series of fluorophenols, converted by purified phenol hydroxylase, catechol 1,2-dioxygenase, and/or by the yeast-like fungus
Exophiala jeanselmei
, provided possibilities for identification of the
19
F NMR chemical shift values of fluorinated catechol and muconate metabolites. As an example, the
19
F NMR method thus defined was used to characterize the time-dependent metabolite profiles of various halophenols in either cell extracts or in incubations with whole cells of
E. jeanselmei
. The results obtained for these two systems are similar, except for the level of muconates observed. Altogether, the results of the present study describe a
19
F NMR method which provides an efficient tool for elucidating the metabolic pathways for conversion of fluorine-containing phenols by microorganisms, with special emphasis on possibilities for biodehalogenation and detection of the type of fluorocatechols and fluoromuconates involved. In addition, the method provides possibilities for studying metabolic pathways in vivo in whole cells.
Reductive Dechlorination of Tetrachloroethene to Ethene by a Two-Component Enzyme Pathway
Authors: Magnuson Jon K. , Stern Robert V. , Gossett James M. , Zinder Stephen H. , Burris David R. 
Published: December 2019

ABSTRACT

Two membrane-bound, reductive dehalogenases that constitute a novel pathway for complete dechlorination of tetrachloroethene (perchloroethylene [PCE]) to ethene were partially purified from an anaerobic microbial enrichment culture containing
Dehalococcoides ethenogenes
195. When titanium(III) citrate and methyl viologen were used as reductants, PCE-reductive dehalogenase (PCE-RDase) (51 kDa) dechlorinated PCE to trichloroethene (TCE) at a rate of 20 μmol/min/mg of protein. TCE-reductive dehalogenase (TCE-RDase) (61 kDa) dechlorinated TCE to ethene. TCE,
cis
-1,2-dichloroethene, and 1,1-dichloroethene were dechlorinated at similar rates, 8 to 12 μmol/min/mg of protein. Vinyl chloride and
trans
-1,2-dichloroethene were degraded at rates which were approximately 2 orders of magnitude lower. The light-reversible inhibition of TCE-RDase by iodopropane and the light-reversible inhibition of PCE-RDase by iodoethane suggest that both of these dehalogenases contain Co(I) corrinoid cofactors. Isolation and characterization of these novel bacterial enzymes provided further insight into the catalytic mechanisms of biological reductive dehalogenation.
Oxygen-Dependent Regulation of the Expression of the Catalase Gene
katA
of
Lactobacillus sakei
LTH677
Authors: Hertel Christian , Schmidt Gudrun , Fischer Marc , Oellers Katja , Hammes Walter P. 
Published: December 2019

ABSTRACT

The catalase gene
katA
of
Lactobacillus sakei
LTH677 was cloned and expressed in
Escherichia coli
UM2,
Lactobacillus casei
LK1, and
Lactobacillus curvatus
LTH1432. The last host is a catalase-deficient plasmid-cured derivative of a starter organism used in meat fermentation. The regulation of
katA
expression was found to be the same in
L. sakei
LTH677 and the recombinant strains. The addition of H
2
O
2
to anaerobic cultures, as well as a switch to aerobic conditions, resulted in a strong increase in KatA activity. The expression was investigated in more detail with
L. sakei
LTH677 and
L. curvatus
LTH4002. The recombinant strain LTH4002 did not accumulate H
2
O
2
under glucose-limited aerobic conditions and remained viable in the stationary phase. Under inductive conditions, the
katA
-specific mRNA and the apoenzyme were synthesized de novo. Deletion derivatives of the
katA
promoter were produced, and the regulatory response was investigated by fusion to the β-glucuronidase reporter gene
gusA
and expression in
L. sakei
LTH677. The fact that gene expression was subject to induction was confirmed at the level of transcription and protein synthesis. A small putative regulatory sequence of at least 25 bp was identified located upstream of the −35 site. Competition experiments performed with
L. sakei
LTH677 harboring the fusion constructs consisting of the
katA
promoter and
gusA
revealed that an activator protein is involved in the transcriptional induction of
katA.
Differential Effects of Dimethylsulfoniopropionate, Dimethylsulfonioacetate, and Other S-Methylated Compounds on the Growth of
Sinorhizobium meliloti
at Low and High Osmolarities
Authors: Pichereau Vianney , Pocard Jean-Alain , Hamelin Jack , Blanco Carlos , Bernard Théophile 
Published: December 2019

ABSTRACT

An extract from the marine alga
Ulva lactuca
was highly osmoprotective in salt-stressed cultures of
Sinorhizobium meliloti
102F34. This beneficial activity was due to algal 3-dimethylsulfoniopropionate (DMSP), which was accumulated as a dominant compatible solute and strongly reduced the accumulation of endogenous osmolytes in stressed cells. Synthetic DMSP also acted as a powerful osmoprotectant and was accumulated as a nonmetabolizable cytosolic osmolyte (up to a concentration of 1,400 nmol/mg of protein) throughout the growth cycles of the stressed cultures. In contrast, 2-dimethylsulfonioacetate (DMSA), the sulfonium analog of the universal osmoprotectant glycine betaine (GB), was highly toxic to unstressed cells and was not osmoprotective in stressed cells of wild-type strains of
S. meliloti
. Nonetheless, the transport and accumulation of DMSA, like the transport and accumulation of DMSP and GB, were osmoregulated and increased fourfold in stressed cells of strain 102F34. Strikingly, DMSA was not toxic and became highly osmoprotective in mutants that are impaired in their ability to demethylate GB and DMSA. Furthermore, 2-methylthioacetate and thioglycolic acid (TGA), the demethylation products of DMSA, were excreted, apparently as a mechanism of cellular detoxification. Also, exogenous TGA and DMSA displayed similar inhibitory effects in strain 102F34. Thus, on the basis of these findings and other physiological and biochemical evidence, we infer that the toxicity of DMSA in wild-type strains of
S. meliloti
stems from its catabolism via the GB demethylation pathway. This is the first report describing the toxicity of DMSA in any organism and a metabolically stable osmoprotectant (DMSP) in
S. meliloti.
Detection of Infectious Tobamoviruses in Forest Soils
Authors: Fillhart Ronald C. , Bachand George D. , Castello John D. 
Published: December 2019

ABSTRACT

Our objectives were to evaluate elution and bait plant methods to detect infectious tobamoviruses in forest soils in New York State. Soils were collected from two forest sites: Whiteface Mountain (WF) and Heiberg Forest (HF). The effectiveness of four buffers to elute tomato mosaic tobamovirus (ToMV) from organic and mineral fractions of WF soil amended with ToMV was tested, and virus content was assessed by enzyme-linked immunosorbent assay (ELISA). The effectiveness of
Chenopodium quinoa
(Willd.) bait plants to detect the virus also was tested. Both methods then were utilized to detect tobamoviruses in 11 WF and 2 HF soil samples. A phosphate buffer (100 mM, pH 7.0) eluted more ToMV from soil than the other buffers tested. Mineral soil bound more virus than organic soil. Virus recoveries from virus-amended organic and mineral soils were 3 and 10%, respectively, and the detection sensitivity was 10 to 20 ng/g of soil. Roots of bait plants grown in all virus-amended soils tested positive by ELISA, and virus concentrations averaged 10 ng/g. Both ToMV and tobacco mosaic tobamovirus (TMV) were transmitted to
C. quinoa
by elution from one of two HF soil samples but not from the WF soil samples. A tobamovirus was detected by bait planting in 12 of 73 (16%) root extracts representing 5 of 13 soil samples (38%). Tobamovirus-like particles were seen by transmission electron microscopy in 6 of 12 infected root extracts. Tobamoviruses occur in forest soils in New York State. Abiotic soil transmission to trees may permit localized spread and persistence of these viruses in forest ecosystems.
A Small-Scale Method for Screening of Lignin-Degrading Microorganisms
Authors: Temp Ulrike , Eggert Claudia , Eriksson Karl-Erik L. 
Published: December 2019

ABSTRACT

A new method to facilitate rapid screening of lignin-degrading microorganisms was developed. Fungal strains are cultivated in tissue culture plates containing
14
C-ring-labeled dehydrogenation polymerizate (DHP) (synthetic lignin). Evolved
14
CO
2
is trapped in barium-saturated filter paper and is detected by exposing the paper to X-ray film. Analysis of the autoradiograms, carried out by density measurement with an image analysis program, allows for a semiquantitative estimation of the amount of
14
CO
2
evolved. The method is especially useful for screening for new, powerful lignin-degrading strains in both man-made and natural environments. It eliminates the need for special equipment for their cultivation and trapping of
14
CO
2
as well as laborious sample analysis. The method has in this study been used to test three novel fungal isolates and a laccaseless mutant of the basidiomycete
Pycnoporus cinnabarinus
. Their ligninolytic capacities were compared with those of the potent lignin degrader
Ceriporiopsis subvermispora.
Effect of
Leuconostoc mesenteroides
NRRL B-512F Dextransucrase Carboxy-Terminal Deletions on Dextran and Oligosaccharide Synthesis
Authors: Monchois Vincent , Reverte Augustin , Remaud-Simeon Magali , Monsan Pierre , Willemot René-Marc 
Published: December 2019

ABSTRACT

Dextransucrase (DSR-S) from
Leuconostoc mesenteroides
NRRL B-512F is a glucosyltransferase that catalyzes synthesis of soluble dextran from sucrose. In the presence of efficient acceptor molecules, such as maltose, the reaction pathway is shifted toward glucooligosaccharide synthesis. Like glucosyltransferases from oral streptococci, DSR-S possesses a C-terminal glucan-binding domain composed of a series of tandem repeats. In order to determine the role of the C-terminal region of DSR-S in dextran or oligosaccharide synthesis, four DSR-S genes with deletions at the 3′ end were constructed. The results showed that the C-terminal region modulated the initial velocity of dextran synthesis but that the

K
m

for sucrose, the optimum pH, and the activation energy were all unaffected by the deletions. The C-terminal domain modulated the rate of oligosaccharide synthesis whatever acceptor molecule was used (a good acceptor molecule such as maltose or a poor acceptor molecule such as fructose). The C-terminal domain seemed to play no role in the catalytic process in dextran and oligosaccharide synthesis. In fact, it seems that the role of the C-terminal domain of DSR-S may be to facilitate the translation of dextran and oligosaccharides from the catalytic site.
Distribution of
Xanthomonas oryzae
pv. oryzae DNA Modification Systems in Asia
Authors: Choi Seong Ho , Vera Cruz Casiana M. , Leach Jan E. 
Published: December 2019

ABSTRACT

The presence or absence of two DNA modification systems,
Xor
I and
Xor
II, in 195 strains of
Xanthomonas oryzae
pv. oryzae collected from different major rice-growing countries of Asia was assessed. All four possible phenotypes (
Xor
I
+
Xor
II
+
,
Xor
I
+
Xor
II
−
,
Xor
I
−
Xor
II
+
and
Xor
I
−
Xor
II
−
) were detected in the population at a ratio of approximately 1:2:2:2. The
Xor
I
+
Xor
II
+
and
Xor
I
−
Xor
II
+
phenotypes were observed predominantly in strains from southeast Asia (Philippines, Malaysia, and Indonesia), whereas strains with the phenotypes
Xor
I
−
Xor
II
−
and
Xor
I
+
Xor
II
−
were distributed in south Asia (India and Nepal) and northeast Asia (China, Korea, and Japan), respectively. Based on the prevalence and geographic distribution of the
Xor
I and
Xor
II systems, we suggest that the
Xor
I modification system originated in northeast Asia and was later introduced to southeast Asia, while the
Xor
II system originated in southeast Asia and moved to northeast Asia and south Asia. Genomic DNA from all tested strains of
X. oryzae
pv. oryzae that were resistant to digestion by endonuclease
Xor
II or its isoschizomer
Pvu
I also hybridized with a 7.0-kb clone that contained the
Xor
II modification system, whereas strains that were digested by
Xor
II or
Pvu
I lacked DNA that hybridized with the clone. Size polymorphisms were observed in fragments that hybridized with the 7.0-kb clone. However, a single hybridization pattern generally was found in
Xor
II
+
strains within a country, indicating clonal maintenance of the
Xor
II methyltransferase gene locus. The locus was monomorphic for
X. oryzae
pv. oryzae strains from the Philippines and all strains from Indonesia and Korea.
Molecular Analysis of a Laccase Gene from the White Rot Fungus
Pycnoporus cinnabarinus
Authors: Eggert Claudia , LaFayette Peter R. , Temp Ulrike , Eriksson Karl-Erik L. , Dean Jeffrey F. D. 
Published: December 2019

ABSTRACT

It was recently shown that the white rot basidiomycete
Pycnoporus cinnabarinus
secretes an unusual set of phenoloxidases when it is grown under conditions that stimulate ligninolysis (C. Eggert, U. Temp, and K.-E. L. Eriksson, Appl. Environ. Microbiol. 62:1151–1158, 1996). In this report we describe the results of a cloning and structural analysis of the laccase-encoding gene (
lcc3-1
) expressed by
P. cinnabarinus
during growth under xylidine-induced conditions. The coding region of the genomic laccase sequence, which is preceded by the eukaryotic promoter elements TATA and CAATA, spans more than 2,390 bp. The corresponding laccase cDNA was identical to the genomic sequence except for 10 introns that were 50 to 60 bp long. A sequence analysis indicated that the
P. cinnabarinus lcc3-1
product has a Phe residue at a position likely to influence the reduction-oxidation potential of the enzyme’s type 1 copper center. The
P. cinnabarinus lcc3-1
sequence was most similar to the sequence encoding a laccase from
Coriolus hirsutus
(level of similarity, 84%).