bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Ultramicrobacterium “
Elusimicrobium minutum
” gen. nov., sp. nov., the First Cultivated Representative of the Termite Group 1 Phylum
Authors: Geissinger Oliver , Herlemann Daniel P. R. , Mörschel Erhard , Maier Uwe G. , Brune Andreas 
Published: March 2009

ABSTRACT

Insect intestinal tracts harbor several novel, deep-rooting clades of as-yet-uncultivated bacteria whose biology is typically completely unknown. Here, we report the isolation of the first representative of the termite group 1 (TG1) phylum from sterile-filtered gut homogenates of a humivorous scarab beetle larva. Strain Pei191
T
is a mesophilic, obligately anaerobic ultramicrobacterium with a gram-negative cell envelope. Cells are typically rod shaped, but cultures are pleomorphic in all growth phases (0.3 to 2.5 μm long and 0.17 to 0.3 μm wide). The isolate grows heterotrophically on sugars and ferments
d
-galactose,
d
-glucose,
d
-fructose,
d
-glucosamine, and
N
-acetyl-
d
-glucosamine to acetate, ethanol, hydrogen, and alanine as major products but only if amino acids are present in the medium. PCR-based screening and comparative 16S rRNA gene sequence analysis revealed that strain Pei191
T
belongs to the “intestinal cluster,” a lineage of hitherto uncultivated bacteria present in arthropod and mammalian gut systems. It is only distantly related to the previously described so-called “endomicrobia” lineage, which comprises mainly uncultivated endosymbionts of termite gut flagellates. We propose the name “
Elusimicrobium minutum
” gen. nov., sp. nov. (type strain, Pei191
T
= ATCC BAA-1559
T
= JCM 14958
T
) for the first isolate of this deep-branching lineage and the name “
Elusimicrobia
” phyl. nov. for the former TG1 phylum.
Genomic Analysis of “
Elusimicrobium minutum
,” the First Cultivated Representative of the Phylum “
Elusimicrobia
” (Formerly Termite Group 1)
Authors: Herlemann D. P. R. , Geissinger O. , Ikeda-Ohtsubo W. , Kunin V. , Sun H. , Lapidus A. , Hugenholtz P. , Brune A. 
Published: March 2009

ABSTRACT

Organisms of the candidate phylum termite group 1 (TG1) are regularly encountered in termite hindguts but are present also in many other habitats. Here, we report the complete genome sequence (1.64 Mbp) of “
Elusimicrobium minutum
” strain Pei191
T
, the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut, and we discuss the findings in light of physiological data.
E. minutum
has all genes required for uptake and fermentation of sugars via the Embden-Meyerhof pathway, including several hydrogenases, and an unusual peptide degradation pathway comprising transamination reactions and leading to the formation of alanine, which is excreted in substantial amounts. The presence of genes encoding lipopolysaccharide biosynthesis and the presence of a pathway for peptidoglycan formation are consistent with ultrastructural evidence of a gram-negative cell envelope. Even though electron micrographs showed no cell appendages, the genome encodes many genes putatively involved in pilus assembly. We assigned some to a type II secretion system, but the function of 60
pilE
-like genes remains unknown. Numerous genes with hypothetical functions, e.g., polyketide synthesis, nonribosomal peptide synthesis, antibiotic transport, and oxygen stress protection, indicate the presence of hitherto undiscovered physiological traits. Comparative analysis of 22 concatenated single-copy marker genes corroborated the status of “
Elusimicrobia
” (formerly TG1) as a separate phylum in the bacterial domain, which was so far based only on 16S rRNA sequence analysis.
Establishment of Oxidative
d
-Xylose Metabolism in
Pseudomonas putida
S12
Authors: Meijnen Jean-Paul , de Winde Johannes H. , Ruijssenaars Harald J. 
Published: March 2009

ABSTRACT

The oxidative
d
-xylose catabolic pathway of
Caulobacter crescentus
, encoded by the
xylXABCD
operon, was expressed in the gram-negative bacterium
Pseudomonas putida
S12. This engineered transformant strain was able to grow on
d
-xylose as a sole carbon source with a biomass yield of 53% (based on g [dry weight] g
d
-xylose
−1
) and a maximum growth rate of 0.21 h
−1
. Remarkably, most of the genes of the
xylXABCD
operon appeared to be dispensable for growth on
d
-xylose. Only the
xylD
gene, encoding
d
-xylonate dehydratase, proved to be essential for establishing an oxidative
d
-xylose catabolic pathway in
P. putida
S12. The growth performance on
d
-xylose was, however, greatly improved by coexpression of
xylXA
, encoding 2-keto-3-deoxy-
d
-xylonate dehydratase and α-ketoglutaric semialdehyde dehydrogenase, respectively. The endogenous periplasmic glucose dehydrogenase (Gcd) of
P. putida
S12 was found to play a key role in efficient oxidative
d
-xylose utilization. Gcd activity not only contributes to
d
-xylose oxidation but also prevents the intracellular accumulation of toxic catabolic intermediates which delays or even eliminates growth on
d
-xylose.
Effect of Iron Concentration on the Growth Rate of
Pseudomonas syringae
and the Expression of Virulence Factors in
hrp
-Inducing Minimal Medium
Authors: Kim Beum Jun , Park Joon Ho , Park Tai Hyun , Bronstein Philip A. , Schneider David J. , Cartinhour Samuel W. , Shuler Michael L. 
Published: March 2009

ABSTRACT

Although chemically defined media have been developed and widely used to study the expression of virulence factors in the model plant pathogen
Pseudomonas syringae
, it has been difficult to link specific medium components to the induction response. Using a chemostat system, we found that iron is the limiting nutrient for growth in the standard
hrp
-inducing minimal medium and plays an important role in inducing several virulence-related genes in
Pseudomonas syringae
pv.
tomato
DC3000. With various concentrations of iron oxalate, growth was found to follow Monod-type kinetics for low to moderate iron concentrations. Observable toxicity due to iron began at 400 μM Fe
3+
. The kinetics of virulence factor gene induction can be expressed mathematically in terms of supplemented-iron concentration. We conclude that studies of induction of virulence-related genes in
P. syringae
should control iron levels carefully to reduce variations in the availability of this essential nutrient.
FvtA Is the Receptor for the Siderophore Vanchrobactin inVibrio anguillarum: Utility as a Route of Entry for Vanchrobactin Analogues
Authors: Balado Miguel , Osorio Carlos R. , Lemos Manuel L. 
Published: March 2009

ABSTRACTSome strains ofVibrio anguillarum, the causative agent of vibriosis in a variety of marine animals, produce a catechol-type siderophore named vanchrobactin. The biosynthetic pathway and regulation of vanchrobactin are quite well understood. However, aspects concerning its entry into the cell have remained uncharacterized. In the present study we characterized two genes,fvtAandorf13, encoding potential TonB-dependent ferric-vanchrobactin receptors in serotype O2V. anguillarumstrain RV22. We found that anfvtAmutant was defective for growth under iron limitation conditions and for utilization of vanchrobactin, suggesting thatfvtAencodes the vanchrobactin receptor ofV. anguillarum. Interestingly, anorf13mutant was not significantly affected, and results of reverse transcriptase PCR, as well as analysis of outer membrane proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, suggested that this gene is not expressed. Furthermore,fatA, a plasmid gene coding for the anguibactin receptor in plasmid pJM1-harboring strains, is also present in the chromosome of RV22, although it is inactivated by insertion of transposases. In addition, we found that FvtA is the route of entry for vanchrobactin analogues, and there is evidence that it recognizes primarily the catechol-iron center. These analogues are potential candidate vectors for a Trojan horse strategy aimed at generating antimicrobial compounds exploiting the same route of entry for native siderophores. We found thatfvtAand vanchrobactin biosynthesis genes are ubiquitous in both vanchrobactin- and anguibactin-producingV. anguillarumstrains, which reinforces the utility of the vanchrobactin route of entry for the design of future strategies for the control of vibriosis.
Depletion of the Cullin Cdc53p Induces Morphogenetic Changes in
Candida albicans
Authors: Trunk Katharina , Gendron Patrick , Nantel André , Lemieux Sébastien , Roemer Terry , Raymond Martine 
Published: March 2009

ABSTRACT

Candida albicans
is an important opportunistic human fungal pathogen that can cause both mucosal and systemic infections in immunocompromised patients. Critical for the virulence of
C. albicans
is its ability to undergo a morphological transition from yeast to hyphal growth mode. Proper induction of filamentation is dependent on the ubiquitination pathway, which targets proteins for proteasome-mediated protein degradation or activates them for signaling events. In the present study, we evaluated the role of ubiquitination in
C. albicans
by impairing the function of the major ubiquitin-ligase complex SCF. This was done by depleting its backbone, the cullin Cdc53p (orf19.1674), using a tetracycline downregulatable promoter system. Cdc53p-depleted cells displayed an invasive phenotype and constitutive filamentation under conditions favoring yeast growth mode, both on solid and in liquid media. In addition, these cells exhibited an early onset of cell death, as judged from propidium iodide staining, suggesting that
CDC53
is an essential gene in
C. albicans
. To identify Cdc53p-dependent pathways in
C. albicans
, a genome-wide expression analysis was carried out that revealed a total of 425 differentially expressed genes (fold change, ≥2;
P
≤ 0.05) with 192 up- and 233 downregulated genes in the
CDC53
-repressed mutant compared to the control strain. GO term analysis identified biological processes significantly affected by Cdc53p depletion, including amino acid starvation response, with 14 genes being targets of the transcriptional regulator Gcn4p, and reductive iron transport. These results indicate that Cdc53p enables
C. albicans
to adequately respond to environmental signals.
Surface-Expressed Enolase Contributes to the Pathogenesis of Clinical Isolate SSU ofAeromonas hydrophila
Authors: Sha Jian , Erova Tatiana E. , Alyea Rebecca A. , Wang Shaofei , Olano Juan P. , Pancholi Vijay , Chopra Ashok K. 
Published: March 2009

ABSTRACTIn this study, we demonstrated that the surface-expressed enolase from diarrheal isolate SSU ofAeromonas hydrophilabound to human plasminogen and facilitated the latter's tissue-type plasminogen activator-mediated activation to plasmin. The bacterial surface-bound plasmin was more resistant to the action of its specific physiological inhibitor, the antiprotease α2-antiplasmin. We found that immunization of mice with purified recombinant enolase significantly protected the animals against a lethal challenge dose of wild-type (WT)A. hydrophila. Minimal histological changes were noted in organs from mice immunized with enolase and then challenged with WT bacteria compared to severe pathological changes found in the infected and nonimmunized group of animals. This correlated with the smaller bacterial load of WT bacteria in the livers and spleens of enolase-immunized mice than that found in the nonimmunized controls. We also showed that the enolase gene could potentially be important for the viability ofA. hydrophilaSSU as we could delete the chromosomal copy of the enolase gene only when another copy of the targeted gene was supplied intrans. By site-directed mutagenesis, we altered five lysine residues located at positions 343, 394, 420, 427, and 430 of enolase inA. hydrophilaSSU; the mutated forms of enolase were hyperexpressed inEscherichia coli, and the proteins were purified. Our results indicated that lysine residues at positions 420 and 427 of enolase were crucial in plasminogen-binding activity. We also identified a stretch of amino acid residues (252FYDAEKKEY260) in theA. hydrophilaSSU enolase involved in plasminogen binding. To our knowledge, this is the first report of the direct involvement of surface-expressed enolase in the pathogenesis ofA. hydrophilaSSU infections and of any gram-negative bacteria in general.
Genetic Variation and Evolution of the Pathogenicity Island of
Enterococcus faecalis
Authors: McBride Shonna M. , Coburn Phillip S. , Baghdayan Arto S. , Willems Rob J. L. , Grande Maria J. , Shankar Nathan , Gilmore Michael S. 
Published: March 2009

ABSTRACT

Enterococcus faecalis
is a leading cause of nosocomial infections and is known for its ability to acquire and transfer virulence and antibiotic resistance determinants from other organisms. A 150-kb pathogenicity island (PAI) encoding several genes that contribute to pathogenesis was identified among antibiotic-resistant clinical isolates. In the current study, we examined the structure of the PAI in a collection of isolates from diverse sources in order to gain insight into its genesis and dynamics. Using multilocus sequence typing to assess relatedness at the level of strain background and microarray analysis to identify variations in the PAI, we determined the extent to which structural variations occur within the PAI and also the extent to which these variations occur independently of the chromosome. Our findings provide evidence for a modular gain of defined gene clusters by the PAI. These results support horizontal transfer as the mechanism for accretion of genes into the PAI and highlight a likely role for mobile elements in the evolution of the
E. faecalis
PAI.
Potassium Transport in
Corynebacterium glutamicum
Is Facilitated by the Putative Channel Protein CglK, Which Is Essential for pH Homeostasis and Growth at Acidic pH
Authors: Follmann Martin , Becker Markus , Ochrombel Ines , Ott Vera , Krämer Reinhard , Marin Kay 
Published: March 2009

ABSTRACT

We studied the requirement for potassium and for potassium transport activity for the biotechnologically important bacterium
Corynebacterium glutamicum
, which is used for large-scale production of amino acids. Different from many other bacteria, at alkaline or neutral pH,
C. glutamicum
is able to grow without the addition of potassium, resulting in very low cytoplasmic potassium concentrations. In contrast, at acidic pH, the ability for growth was found to depend on the presence of K
+
. For the first time, we provide experimental evidence that a potential potassium channel (CglK) acts as the major potassium uptake system in a bacterium and proved CglK's function directly in its natural membrane environment. A full-length CglK protein and a separate soluble protein harboring the RCK domain can be translated from the
cglK
gene, and both are essential for full CglK functionality. As a reason for potassium-dependent growth limitation at acidic pH, we identified the impaired capacity for internal pH homeostasis, which depends on the availability and internal accumulation of potassium. Potassium uptake via CglK was found to be relevant for major physiological processes, like the activity of the respiratory chain, and to be crucial for maintenance of the internal pH, as well as for the adjustment of the membrane potential in
C. glutamicum
.
Regulation of
Corynebacterium glutamicum
Heat Shock Response by the Extracytoplasmic-Function Sigma Factor SigH and Transcriptional Regulators HspR and HrcA
Authors: Ehira Shigeki , Teramoto Haruhiko , Inui Masayuki , Yukawa Hideaki 
Published: March 2009

ABSTRACT

Heat shock response in
Corynebacterium glutamicum
was characterized by whole-genome expression analysis using a DNA microarray. It was indicated that heat shock response of
C. glutamicum
included not only upregulation of heat shock protein (HSP) genes encoding molecular chaperones and ATP-dependent proteases, but it also increased and decreased expression of more than 300 genes related to disparate physiological functions. An extracytoplasmic-function sigma factor, SigH, was upregulated by heat shock. The SigH regulon was defined by gene expression profiling using
sigH
-disrupted and overexpressing strains in conjunction with mapping of transcription initiation sites. A total of 45 genes, including HSP genes and genes involved in oxidative stress response, were identified as the SigH regulon. Expression of some HSP genes was also upregulated by deletion of the transcriptional regulators HspR and HrcA. HspR represses expression of the
clpB
and
dnaK
operons, and HrcA represses expression of
groESL1
and
groEL2
. SigH was shown to play an important role in regulation of heat shock response in concert with HspR and HrcA, but its role is likely restricted to only a part of the regulation of
C. glutamicum
heat shock response. Upregulation of 18 genes encoding transcriptional regulators by heat shock suggests a complex regulatory network of heat shock response in
C. glutamicum
.
Plasmid pAMS1-Encoded, Bacteriocin-Related “Siblicide” in
Enterococcus faecalis
Authors: Sedgley Christine M. , Clewell Don B. , Flannagan Susan E. 
Published: March 2009

ABSTRACT

The
Enterococcus faecalis
class IIa bacteriocin MC4-1 encoded by the sex pheromone-responding, multiple-antibiotic resistance plasmid pAMS1 exhibits “siblicidal” (sibling-killing) activity under certain conditions. Stabs of plasmid-containing cells on solid medium containing lawns of bacteria of the same (plasmid-containing) strain give rise to zones of inhibition. If the plasmid-containing host also produces gelatinase, bacteriocin cannot be detected.
Pseudomonas aeruginosaAlgR Controls Cyanide Production in an AlgZ-Dependent Manner
Authors: Cody William L. , Pritchett Christopher L. , Jones Adriana K. , Carterson Alexander J. , Jackson Debra , Frisk Anders , Wolfgang Matthew C. , Schurr Michael J. 
Published: March 2009

ABSTRACTPseudomonas aeruginosais an opportunistic pathogen that causes chronic infections in individuals suffering from the genetic disorder cystic fibrosis. InP. aeruginosa, the transcriptional regulator AlgR controls a variety of virulence factors, including alginate production, twitching motility, biofilm formation, quorum sensing, and hydrogen cyanide (HCN) production. In this study, the regulation of HCN production was examined. Strains lacking AlgR or the putative AlgR sensor AlgZ produced significantly less HCN than did a nonmucoid isogenic parent. In contrast,algRandalgZmutants showed increased HCN production in an alginate-producing (mucoid) background. HCN production was optimal in a 5% O2environment. In addition, cyanide production was elevated in bacteria grown on an agar surface compared to bacteria grown in planktonic culture. A conserved AlgR phosphorylation site (aspartate at amino acid position 54), which is required for surface-dependent twitching motility but not alginate production, was found to be critical for cyanide production. Nuclease protection mapping of thehcnApromoter identified a new transcriptional start site required for HCN production. A subset of clinical isolates that lack this start site produced small amounts of cyanide. Taken together, these data show that theP. aeruginosa hcnApromoter contains three transcriptional start sites and that HCN production is regulated by AlgZ and AlgR and is maximal under microaerobic conditions when the organism is surface attached.
Influences of Capsule on Cell Shape and Chain Formation of Wild-Type andpcsBMutants of Serotype 2Streptococcus pneumoniae
Authors: Barendt Skye M. , Land Adrian D. , Sham Lok-To , Ng Wai-Leung , Tsui Ho-Ching T. , Arnold Randy J. , Winkler Malcolm E. 
Published: March 2009

ABSTRACTPcsB is a protein of unknown function that plays a critical role in cell division inStreptococcus pneumoniaeand other ovococcus species ofStreptococcus. We constructed isogenic sets of mutants expressing different amounts of PcsB in laboratory strain R6 and virulent serotype 2 strain D39 to evaluate its cellular roles. Insertion mutagenesis in parent andpcsB+merodiploid strains indicated thatpcsBis essential in serotype 2S. pneumoniae.Quantitative Western blotting of wild-type and epitope-tagged PcsB showed that all PcsB was processed into cell-associated and secreted forms of the same molecular mass and that cell-associated PcsB was moderately abundant and present at ≈4,900 monomers per cell. Controlled expression and complementation experiments indicated that there was a causative relationship between the severity of defects in cell division and decreasing PcsB amount. These experiments also showed that perturbations of expression of the upstreammreCDgenes did not contribute to the cell division defects ofpcsBmutants and thatmreCDcould be deleted. Unexpectedly, capsule influenced the cell shape and chain formation phenotypes of the wild-type D39 strain and mutants underexpressing PcsB or deleted for other genes involved in peptidoglycan biosynthesis, such asdacA. Underexpression of PcsB did not result in changes in the amounts or composition of lactoyl-peptides, which were markedly different in the R6 and D39 strains, and there was no correlation between decreased PcsB amount and sensitivity to penicillin. Finally, microarray analyses indicated that underexpression of PcsB may generate a signal that increases expression of the VicRK regulon, which includespcsB.
Isolation and Characterization of
Azotobacter vinelandii
Mutants Impaired in Alkylresorcinol Synthesis: Alkylresorcinols Are Not Essential for Cyst Desiccation Resistance
Authors: Segura Daniel , Vite Odon , Romero Yanet , Moreno Soledad , Castañeda Miguel , Espín Guadalupe 
Published: March 2009

ABSTRACT

During encystment of
Azotobacter vinelandii
, a family of alkylresorcinols (ARs) and alkylpyrones (APs) are synthesized. In the mature cyst, these lipids replace the membrane phospholipids and are also components of the layers covering the cyst. In this study,
A. vinelandii
strains unable to synthesize ARs were isolated after mini-Tn
5
mutagenesis. Cloning and nucleotide sequencing of the affected loci revealed the presence of the transposons within the
arsA
gene of the previously reported
arsABCD
gene cluster, which encodes a type I fatty acid synthase. A mutant strain (SW-A) carrying an
arsA
mutation allowing transcription of
arsBCD
was constructed and shown to be unable to produce ARs, indicating that the ArsA protein is essential for the synthesis of these phenolic lipids. Transcription of
arsA
was induced 200-fold in cells undergoing encystment, but only 14-fold in aged cultures of
A. vinelandii
, in accordance with AR synthesis and cyst formation percentages under the two conditions. Although it was previously reported that the inactivation of
arsB
abolishes AR synthesis and results in a failure in encystment, the
arsA
mutants were able to form cysts resistant to desiccation. These data indicate that ARs play a structural role in the exine layer of the cysts, but they are not essential for either cyst formation or for desiccation resistance.