bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formate as an Auxiliary Substrate for Glucose-Limited Cultivation of
Penicillium chrysogenum
: Impact on Penicillin G Production and Biomass Yield
Authors: Harris Diana M. , van der Krogt Zita A. , van Gulik Walter M. , van Dijken Johannes P. , Pronk Jack T. 
Published: June 2007

ABSTRACT

Production of β-lactams by the filamentous fungus
Penicillium chrysogenum
requires a substantial input of ATP. During glucose-limited growth, this ATP is derived from glucose dissimilation, which reduces the product yield on glucose. The present study has investigated whether penicillin G yields on glucose can be enhanced by cofeeding of an auxiliary substrate that acts as an energy source but not as a carbon substrate. As a model system, a high-producing industrial strain of
P. chrysogenum
was grown in chemostat cultures on mixed substrates containing different molar ratios of formate and glucose. Up to a formate-to-glucose ratio of 4.5 mol·mol
−1
, an increasing rate of formate oxidation via a cytosolic NAD
+
-dependent formate dehydrogenase increasingly replaced the dissimilatory flow of glucose. This resulted in increased biomass yields on glucose. Since at these formate-to-glucose ratios the specific penicillin G production rate remained constant, the volumetric productivity increased. Metabolic modeling studies indicated that formate transport in
P. chrysogenum
does not require an input of free energy. At formate-to-glucose ratios above 4.5 mol·mol
−1
, the residual formate concentrations in the cultures increased, probably due to kinetic constraints in the formate-oxidizing system. The accumulation of formate coincided with a loss of the coupling between formate oxidation and the production of biomass and penicillin G. These results demonstrate that, in principle, mixed-substrate feeding can be used to increase the yield on a carbon source of assimilatory products such as β-lactams.
Control of
Mycosphaerella graminicola
on Wheat Seedlings by Medical Drugs Known To Modulate the Activity of ATP-Binding Cassette Transporters
Authors: Roohparvar Ramin , Huser Aurelie , Zwiers Lute-Harm , De Waard Maarten A. 
Published: June 2007

ABSTRACT

Medical drugs known to modulate the activity of human ATP-binding cassette (ABC) transporter proteins (modulators) were tested for the ability to potentiate the activity of the azole fungicide cyproconazole against in vitro growth of
Mycosphaerella graminicola
and to control disease development due to this pathogen on wheat seedlings. In vitro modulation of cyproconazole activity could be demonstrated in paper disk bioassays. Some of the active modulators (amitriptyline, flavanone, and phenothiazines) increased the accumulation of cyproconazole in
M. graminicola
, suggesting that they reversed cyproconazole efflux. However, synergism between cyproconazole and modulators against
M. graminicola
on wheat seedlings could not be shown. Despite their low in vitro toxicity to
M. graminicola
, some modulators (amitriptyline, loperamide, and promazine) did show significant intrinsic disease control activity in preventive and curative foliar spray tests with wheat seedlings. The results suggest that these compounds have indirect disease control activity based on modulation of fungal ABC transporters essential for virulence and constitute a new class of disease control agents.
Effect of Nutrient Starvation on the Cellular Composition and Metabolic Capacity of
Saccharomyces cerevisiae
Authors: Albers Eva , Larsson Christer , Andlid Thomas , Walsh Michael C. , Gustafsson Lena 
Published: June 2007

ABSTRACT

This investigation addresses the following question: what are the important factors for maintenance of a high catabolic capacity under various starvation conditions?
Saccharomyces cerevisiae
was cultured in aerobic batch cultures, and during the diauxic shift cells were transferred and subjected to 24 h of starvation. The following conditions were used: carbon starvation, nitrogen starvation in the presence of glucose or ethanol, and both carbon starvation and nitrogen starvation. During the starvation period changes in biomass composition (including protein, carbohydrate, lipid, and nucleic acid contents), metabolic activity, sugar transport kinetics, and the levels of selected enzymes were recorded. Subsequent to the starvation period the remaining catabolic capacity was measured by addition of 50 mM glucose. The results showed that the glucose transport capacity is a key factor for maintenance of high metabolic capacity in many, but not all, cases. The results for cells starved of carbon, carbon and nitrogen, or nitrogen in the presence of glucose all indicated that the metabolic capacity was indeed controlled by the glucose transport ability, perhaps with some influence of hexokinase, phosphofructokinase, aldolase, and enolase levels. However, it was also demonstrated that there was no such correlation when nitrogen starvation occurred in the presence of ethanol instead of glucose.
Phylogenetic and Metabolic Diversity of
Planctomycetes
from Anaerobic, Sulfide- and Sulfur-Rich Zodletone Spring, Oklahoma
Authors: Elshahed Mostafa S. , Youssef Noha H. , Luo Qingwei , Najar Fares Z. , Roe Bruce A. , Sisk Tracy M. , Bühring Solveig I. , Hinrichs Kai-Uwe , Krumholz Lee R. 
Published: June 2007

ABSTRACT

We investigated the phylogenetic diversity and metabolic capabilities of members of the phylum
Planctomycetes
in the anaerobic, sulfide-saturated sediments of a mesophilic spring (Zodletone Spring) in southwestern Oklahoma. Culture-independent analyses of 16S rRNA gene sequences generated using
Planctomycetes
-biased primer pairs suggested that an extremely diverse community of
Planctomycetes
is present at the spring. Although sequences that are phylogenetically affiliated with cultured heterotrophic
Planctomycetes
were identified, the majority of the sequences belonged to several globally distributed, as-yet-uncultured
Planctomycetes
lineages. Using complex organic media (aqueous extracts of the spring sediments and rumen fluid), we isolated two novel strains that belonged to the
Pirellula-Rhodopirellula-Blastopirellula
clade within the
Planctomycetes
. The two strains had identical 16S rRNA gene sequences, and their closest relatives were isolates from Kiel Fjord (Germany), Keauhou Beach (HI), a marine aquarium, and tissues of marine organisms (
Aplysina
sp. sponges and postlarvae of the giant tiger prawn
Penaeus monodon
). The closest recognized cultured relative of strain Zi62 was
Blastopirellula marina
(93.9% sequence similarity). Detailed characterization of strain Zi62 revealed its ability to reduce elemental sulfur to sulfide under anaerobic conditions, as well as its ability to produce acids from sugars; both characteristics may potentially allow strain Zi62 to survive and grow in the anaerobic, sulfide- and sulfur-rich environment at the spring source. Overall, this work indicates that anaerobic metabolic abilities are widely distributed among all major
Planctomycetes
lineages and suggests carbohydrate fermentation and sulfur reduction as possible mechanisms employed by heterotrophic
Planctomycetes
for growth and survival under anaerobic conditions.
Genetic Diversity of Rhizobia Associated with
Acacia longifolia
in Two Stages of Invasion of Coastal Sand Dunes
Authors: Rodríguez-Echeverría Susana , Crisóstomo João A. , Freitas Helena 
Published: June 2007

ABSTRACT

We examined the genetic diversity of root nodule bacteria associated with the Australian legume
Acacia longifolia
in two stages of invasion of a coastal sand dune system. All isolates belonged to the genus
Bradyrhizobium.
A higher diversity was found in the long-established trees. The results suggest the introduction of exotic bradyrhizobia with the plant.
Germination of
Bacillus cereus
Spores Is Induced by Germinants from Differentiated Caco-2 Cells, a Human Cell Line Mimicking the Epithelial Cells of the Small Intestine
Authors: Wijnands L. M. , Dufrenne J. B. , van Leusden F. M. , Abee T. 
Published: June 2007

ABSTRACT

Spores of 11 enterotoxigenic strains of
Bacillus cereus
isolated from foods and humans adhered with similar efficiencies to Caco-2 cells, whereas subsequent germination triggering was observed with only 8 of these strains. Notably, Hep-2 cells did not trigger germination, while spores of all strains displayed similar germination efficiencies in brain heart infusion broth.
Mutual Dependence of
Candida albicans
Est1p and Est3p in Telomerase Assembly and Activation
Authors: Hsu Min , Yu Eun Young , Singh Sunitha M. , Lue Neal F. 
Published: June 2007

ABSTRACT

Telomerase is an RNA-protein complex responsible for extending one strand of the telomere terminal repeats. Analysis of the telomerase complex in budding yeasts has revealed the presence of one catalytic protein subunit (Est2p/TERT) and at least two noncatalytic components (Est1p and Est3p). The TERT subunit is essential for telomerase catalysis, while the functions of Est1p and Est3p have not been precisely elucidated. In an earlier study, we showed that telomerase derived from a
Candida est1
-null mutant is defective in primer utilization in vitro; it exhibits reduced initiation and processivity on primers that terminate in two regions of the telomere repeat. Here we show that telomerase derived from a
Candida est3
-null mutant has nearly identical defects in primer utilization and processivity. Further analysis revealed an unexpected mutual dependence of Est1p and Est3p in their assembly into the full telomerase complex, which accounts for the similarity between the mutant enzymes. We also developed an affinity isolation and an in vitro reconstitution protocol for the telomerase complex that will facilitate future mechanistic studies.
Identification and Characterization ofCPS1as a Hyaluronic Acid Synthase Contributing to the Pathogenesis ofCryptococcus neoformansInfection
Authors: Jong Ambrose , Wu Chun-Hua , Chen Han-Min , Luo Feng , Kwon-Chung Kyung J. , Chang Yun C. , LaMunyon Craig W. , Plaas Anna , Huang Sheng-He 
Published: June 2007

ABSTRACTCryptococcus neoformansis a pathogenic yeast that often causes devastating meningoencephalitis in immunocompromised individuals. We have previously identified theC. neoformans CPS1gene, which is required for a capsular layer on the outer cell wall. In this report, we investigate the function of theCPS1gene and its pathogenesis. We demonstrated that treatment of yeast with either 4-methylumbelliferone or hyaluronidase resulted in a reduction of the level ofC. neoformansbinding to human brain microvascular endothelial cells (HBMEC). Yeast extracellular structures were also altered accordingly in hyaluronidase-treated cells. Furthermore, observation of yeast strains with different hyaluronic acid contents showed that the ability to bind to HBMEC is proportional to the hyaluronic acid content. A killing assay withCaenorhabditis elegansdemonstrated that theCPS1wild-type strain is more virulent than thecps1Δ strain. WhenCPS1is expressed inSaccharomyces cerevisiaeandEscherichia coli, hyaluronic acid can be detected in the cells. Additionally, we determined by fluorophore-assisted carbohydrate electrophoretic analysis that hyaluronic acid is a component of theC. neoformanscapsule. The size of hyaluronic acid molecules is evaluated by gel filtration and transmission electron microscopy studies. Together, our results support thatC. neoformans CPS1encodes hyaluronic acid synthase and that its product, hyaluronic acid, plays a role as an adhesion molecule during the association of endothelial cells with yeast.
Trichoderma atroviride
PHR1, a Fungal Photolyase Responsible for DNA Repair, Autoregulates Its Own Photoinduction
Authors: Berrocal-Tito Gloria M. , Esquivel-Naranjo Edgardo U. , Horwitz Benjamin A. , Herrera-Estrella Alfredo 
Published: June 2007

ABSTRACT

The photolyases, DNA repair enzymes that use visible and long-wavelength UV light to repair cyclobutane pyrimidine dimers (CPDs) created by short-wavelength UV, belong to the larger photolyase-cryptochrome gene family. Cryptochromes (UVA-blue light photoreceptors) lack repair activity, and sensory and regulatory roles have been defined for them in plants and animals. Evolutionary considerations indicate that cryptochromes diverged from CPD photolyases before the emergence of eukaryotes. In prokaryotes and lower eukaryotes, some photolyases might have photosensory functions.
phr1
codes for a class I CPD photolyase in
Trichoderma atroviride. phr1
is rapidly induced by blue and UVA light, and its photoinduction requires functional blue light regulator (BLR) proteins, which are White Collar homologs in
Trichoderma
. Here we show that deletion of
phr1
abolished photoreactivation of UVC (200 to 280 nm)-inhibited spores and thus that PHR1 is the main component of the photorepair system. The 2-kb 5′ upstream region of
phr1
, with putative light-regulated elements, confers blue light regulation on a reporter gene. To assess
phr1
photosensory function, fluence response curves of this light-regulated promoter were tested in null mutant (Δ
phr1
) strains. Photoinduction of the
phr1
promoter in Δ
phr1
strains was >5-fold more sensitive to light than that in the wild type, whereas in PHR1-overexpressing lines the sensitivity to light increased about 2-fold. Our data suggest that PHR1 may regulate its expression in a light-dependent manner, perhaps through negative modulation of the BLR proteins. This is the first evidence for a regulatory role of photolyase, a role usually attributed to cryptochromes.
Crystal Structures of the Receiver Domain of the Response Regulator PhoP from
Escherichia coli
in the Absence and Presence of the Phosphoryl Analog Beryllofluoride
Authors: Bachhawat Priti , Stock Ann M. 
Published: June 2007

ABSTRACT

The response regulator PhoP is part of the PhoQ/PhoP two-component system involved in responses to depletion of extracellular Mg
2+
. Here, we report the crystal structures of the receiver domain of
Escherichia coli
PhoP determined in the absence and presence of the phosphoryl analog beryllofluoride. In the presence of beryllofluoride, the active receiver domain forms a twofold symmetric dimer similar to that seen in structures of other regulatory domains from the OmpR/PhoB family, providing further evidence that members of this family utilize a common mode of dimerization in the active state. In the absence of activating agents, the PhoP receiver domain crystallizes with a similar structure, consistent with the previous observation that high concentrations can promote an active state of PhoP independent of phosphorylation.
Cell-Wide Responses to Low-Oxygen Exposure inDesulfovibrio vulgarisHildenborough
Authors: Mukhopadhyay Aindrila , Redding Alyssa M. , Joachimiak Marcin P. , Arkin Adam P. , Borglin Sharon E. , Dehal Paramvir S. , Chakraborty Romy , Geller Jil T. , Hazen Terry C. , He Qiang , Joyner Dominique C. , Martin Vincent J. J. , Wall Judy D. , Yang Zamin Koo , Zhou Jizhong , Keasling Jay D. 
Published: June 2007

ABSTRACTThe responses of the anaerobic, sulfate-reducing organismDesulfovibrio vulgarisHildenborough to low-oxygen exposure (0.1% O2) were monitored via transcriptomics and proteomics. Exposure to 0.1% O2caused a decrease in the growth rate without affecting viability. Concerted upregulation of the predicted peroxide stress response regulon (PerR) genes was observed in response to the 0.1% O2exposure. Several of the candidates also showed increases in protein abundance. Among the remaining small number of transcript changes was the upregulation of the predicted transmembrane tetraheme cytochromec3complex. Other known oxidative stress response candidates remained unchanged during the low-O2exposure. To fully understand the results of the 0.1% O2exposure, transcriptomics and proteomics data were collected for exposure to air using a similar experimental protocol. In contrast to the 0.1% O2exposure, air exposure was detrimental to both the growth rate and viability and caused dramatic changes at both the transcriptome and proteome levels. Interestingly, the transcripts of the predicted PerR regulon genes were downregulated during air exposure. Our results highlight the differences in the cell-wide responses to low and high O2levels inD. vulgarisand suggest that while exposure to air is highly detrimental toD. vulgaris, this bacterium can successfully cope with periodic exposure to low O2levels in its environment.
Deletion of theparA(soj) Homologue inPseudomonas aeruginosaCauses ParB Instability and Affects Growth Rate, Chromosome Segregation, and Motility
Authors: Lasocki Krzysztof , Bartosik Aneta A. , Mierzejewska Jolanta , Thomas Christopher M. , Jagura-Burdzy Grazyna 
Published: June 2007

ABSTRACTTheparAandparBgenes ofPseudomonas aeruginosaare located approximately 8 kb anticlockwise fromoriC. ParA is a cytosolic protein present at a level of around 600 molecules per cell in exponential phase, but the level drops about fivefold in stationary phase. Overproduction of full-length ParA or the N-terminal 85 amino acids severely inhibits growth ofP. aeruginosaandP. putida. Both inactivation ofparAand overexpression ofparAintransinP. aeruginosaalso lead to accumulation of anucleate cells and changes in motility. Inactivation ofparAalso increases the turnover rate (degradation) of ParB. This may provide a mechanism for controlling the level of ParB in response to the growth rate and expression of theparABoperon.
Oxidative DNA Damage Defense Systems in Avoidance of Stationary-Phase Mutagenesis in
Pseudomonas putida
Authors: Saumaa Signe , Tover Andres , Tark Mariliis , Tegova Radi , Kivisaar Maia 
Published: June 2007

ABSTRACT

Oxidative damage of DNA is a source of mutation in living cells. Although all organisms have evolved mechanisms of defense against oxidative damage, little is known about these mechanisms in nonenteric bacteria, including pseudomonads. Here we have studied the involvement of oxidized guanine (GO) repair enzymes and DNA-protecting enzyme Dps in the avoidance of mutations in starving
Pseudomonas putida
. Additionally, we examined possible connections between the oxidative damage of DNA and involvement of the error-prone DNA polymerase (Pol)V homologue RulAB in stationary-phase mutagenesis in
P. putida
. Our results demonstrated that the GO repair enzymes MutY, MutM, and MutT are involved in the prevention of base substitution mutations in carbon-starved
P. putida
. Interestingly, the antimutator effect of MutT was dependent on the growth phase of bacteria. Although the lack of MutT caused a strong mutator phenotype under carbon starvation conditions for bacteria, only a twofold increased effect on the frequency of mutations was observed for growing bacteria. This indicates that MutT has a backup system which efficiently complements the absence of this enzyme in actively growing cells. The knockout of MutM affected only the spectrum of mutations but did not change mutation frequency. Dps is known to protect DNA from oxidative damage. We found that
dps
-defective
P. putida
cells were more sensitive to sudden exposure to hydrogen peroxide than wild-type cells. At the same time, the absence of Dps did not affect the accumulation of mutations in populations of starved bacteria. Thus, it is possible that the protective role of Dps becomes essential for genome integrity only when bacteria are exposed to exogenous agents that lead to oxidative DNA damage but not under physiological conditions. Introduction of the Y family DNA polymerase PolV homologue
rulAB
into
P. putida
increased the proportion of A-to-C and A-to-G base substitutions among mutations, which occurred under starvation conditions. Since PolV is known to perform translesion synthesis past damaged bases in DNA (e.g., some oxidized forms of adenine), our results may imply that adenine oxidation products are also an important source of mutation in starving bacteria.
The Oligomeric State of c Rings from Cyanobacterial F-ATP Synthases Varies from 13 to 15
Authors: Pogoryelov Denys , Reichen Christian , Klyszejko Adriana L. , Brunisholz René , Muller Daniel J. , Dimroth Peter , Meier Thomas 
Published: June 2007

ABSTRACT

We isolated the c rings of F-ATP synthases from eight cyanobacterial strains belonging to four different taxonomic classes (
Chroococcales
,
Nostocales
,
Oscillatoriales
, and
Gloeobacteria
). These c rings showed different mobilities on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), probably reflecting their molecular masses. This supposition was validated with the previously characterized c
11
, c
14
, and c
15
rings, which migrated on SDS-PAGE in proportion to their molecular masses. Hence, the masses of the cyanobacterial c rings can conveniently be deduced from their electrophoretic mobilities and, together with the masses of the c monomers, allow the calculation of the c ring stoichiometries. The method is a simple and fast way to determine stoichiometries of SDS-stable c rings and hence a convenient means to unambiguously determine the ion-to-ATP ratio, a parameter reflecting the bioenergetic efficacy of F-ATP synthases. AFM imaging was used to prove the accuracy of the method and confirmed that the c ring of
Synechococcus elongatus
SAG 89.79 is a tridecameric oligomer. Despite the high conservation of the c-subunit sequences from cyanobacterial strains from various environmental groups, the stoichiometries of their c rings varied between c
13
and c
15
. This systematic study of the c-ring stoichiometries suggests that variability of c-ring sizes might represent an adaptation of the individual cyanobacterial species to their particular environmental and physiological conditions. Furthermore, the two new examples of c
15
rings underline once more that an F
1
/F
o
symmetry mismatch is not an obligatory feature of all F-ATP synthases.
pH of the Cytoplasm and Periplasm of
Escherichia coli
: Rapid Measurement by Green Fluorescent Protein Fluorimetry
Authors: Wilks Jessica C. , Slonczewski Joan L. 
Published: June 2007

ABSTRACT

Cytoplasmic pH and periplasmic pH of
Escherichia coli
cells in suspension were observed with 4-s time resolution using fluorimetry of TorA-green fluorescent protein mutant 3* (TorA-GFPmut3*) and TetR-yellow fluorescent protein. Fluorescence intensity was correlated with pH using cell suspensions containing 20 mM benzoate, which equalizes the cytoplasmic pH with the external pH. When the external pH was lowered from pH 7.5 to 5.5, the cytoplasmic pH fell within 10 to 20 s to pH 5.6 to 6.5. Rapid recovery occurred until about 30 s after HCl addition and was followed by slower recovery over the next 5 min. As a control, KCl addition had no effect on fluorescence. In the presence of 5 to 10 mM acetate or benzoate, recovery from external acidification was diminished. Addition of benzoate at pH 7.0 resulted in cytoplasmic acidification with only slow recovery. Periplasmic pH was observed using TorA-GFPmut3* exported to the periplasm through the Tat system. The periplasmic location of the fusion protein was confirmed by the observation that osmotic shock greatly decreased the periplasmic fluorescence signal by loss of the protein but had no effect on the fluorescence of the cytoplasmic protein. Based on GFPmut3* fluorescence, the pH of the periplasm equaled the external pH under all conditions tested, including rapid acid shift. Benzoate addition had no effect on periplasmic pH. The cytoplasmic pH of
E. coli
was measured with 4-s time resolution using a method that can be applied to any strain construct, and the periplasmic pH was measured directly for the first time.