bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biogeography, Host Specificity, and Molecular Phylogeny of the Basidiomycetous Yeast
Phaffia rhodozyma
and Its Sexual Form,
Xanthophyllomyces dendrorhous
Authors: Libkind Diego , Ruffini Alejandra , van Broock Maria , Alves Leonor , Sampaio José Paulo 
Published: December 2006

ABSTRACT

Phaffia rhodozyma
(sexual form,
Xanthophyllomyces dendrorhous
) is a basidiomycetous yeast that has been found in tree exudates in the Northern Hemisphere at high altitudes and latitudes. This yeast produces astaxanthin, a carotenoid pigment with biotechnological importance because it is used in aquaculture for fish pigmentation. We isolated
X. dendrorhous
from the Southern Hemisphere (Patagonia, Argentina), where it was associated with fruiting bodies of
Cyttaria hariotii
, an ascomycetous parasite of
Nothofagus
trees. We compared internal transcribed spacer (ITS)-based phylogenies of
P. rhodozyma
and its tree host (Betulaceae, Corneaceae, Fagaceae, and Nothofagaceae) and found them to be generally concordant, suggesting that different yeast lineages colonize different trees and providing an explanation for the phylogenetic distance observed between the type strains of
P. rhodozyma
and
X. dendrorhous
. We hypothesize that the association of
Xanthophyllomyces
with
Cyttaria
derives from a previous association of the yeast with
Nothofagus
, and the sister relationship between Nothofagaceae and Betulaceae plus Fagaceae correlates with the phylogeny of
X. dendrorhous
strains originating from these three plant families. The two most basal strains of
X. dendrorhous
are those isolated from
Cornus
, an ancestral genus in the phylogenetic analysis of the host trees. Thus, we question previous conclusions that
P. rhodozyma
and
X. dendrorhous
represent different species since the polymorphisms detected in the ITS and intergenic spacer sequences can be attributed to intraspecific variation associated with host specificity. Our study provides a deeper understanding of
Phaffia
biogeography, ecology, and molecular phylogeny. Such knowledge is essential for the comprehension of many aspects of the biology of this organism and will facilitate the study of astaxanthin production within an evolutionary and ecological framework.
Transgalactosylation in a Water-Solvent Biphasic Reaction System with β-Galactosidase Displayed on the Surfaces of
Bacillus subtilis
Spores
Authors: Kwon Seok Joon , Jung Heung-Chae , Pan Jae-Gu 
Published: December 2006

ABSTRACT

The ever-increasing industrial demand for biocatalysis necessitates innovations in the preparation and stabilization of biocatalysts. In this study, we demonstrated that β-galactosidase (β-Gal) displayed on
Bacillus
spores by fusion to the spore coat proteins (CotG) may be used as a whole-cell immobilized biocatalyst for transgalactosylation in water-solvent biphasic reaction systems. The resulting spores had a specific hydrolytic activity of 5 × 10
3
U/g (dry weight) of spores. The β-Gal was tightly attached to the spore surface and was more stable in the presence of various organic solvents than its native form was. The thermostability of the spore-displayed enzyme was also increased, and the enzyme was further stabilized by chemically cross-linking it with glutaraldehyde. With spore-displayed β-Gal, octyl-β-
d
-galactopyranoside was synthesized at concentrations up to 27.7 mM (8.1 g/liter) with a conversion yield of 27.7% (wt/wt) after 24 h from 100 mM lactose and 100 mM octanol dissolved in phosphate buffer and ethyl ether, respectively. Interestingly, the spores were found to partition mainly at the interface between the water and solvent phases, and they were more available to catalysis between the two phases, as determined by light microscopy and confocal fluorescence microscopy. We propose that spore display not only offers a new and facile way to construct robust biocatalysts but also provides a novel basis for phase transfer biocatalytic processes.
Hydrogen Metabolism in
Shewanella oneidensis
MR-1
Authors: Meshulam-Simon Galit , Behrens Sebastian , Choo Alexander D. , Spormann Alfred M. 
Published: December 2006

ABSTRACT

Shewanella oneidensis
MR-1 is a facultative sediment microorganism which uses
diverse compounds, such as oxygen and fumarate, as well as insoluble
Fe(III) and Mn(IV) as electron acceptors. The electron donor spectrum
is more limited and includes metabolic end products of primary
fermenting bacteria, such as lactate, formate, and hydrogen. While the
utilization of hydrogen as an electron donor has been described
previously, we report here the formation of hydrogen from pyruvate
under anaerobic, stationary-phase conditions in the absence of an
external electron acceptor. Genes for the two
S. oneidensis
MR-1 hydrogenases,
hydA
, encoding a periplasmic [Fe-Fe]
hydrogenase, and
hyaB
, encoding a periplasmic [Ni-Fe]
hydrogenase, were found to be expressed only under anaerobic conditions
during early exponential growth and into stationary-phase growth.
Analyses of Δ
hydA
, Δ
hyaB
, andΔ
hydA
Δ
hyaB
in-frame-deletion mutants
indicated that HydA functions primarily as a hydrogen-forming
hydrogenase while HyaB has a bifunctional role and represents the
dominant hydrogenase activity under the experimental conditions tested.
Based on results from physiological and genetic experiments, we propose
that hydrogen is formed from pyruvate by multiple parallel pathways,
one pathway involving formate as an intermediate, pyruvate-formate
lyase, and formate-hydrogen lyase, comprised of HydA hydrogenase and
formate dehydrogenase, and a formate-independent pathway involving
pyruvate dehydrogenase. A reverse electron transport chain is
potentially involved in a formate-hydrogen lyase-independent pathway.
While pyruvate does not support a fermentative mode of growth in this
microorganism, pyruvate, in the absence of an electron acceptor,
increased cell viability in anaerobic, stationary-phase cultures,
suggesting a role in the survival of
S. oneidensis
MR-1 under
stationary-phase
conditions.
Biodiversity of Bacterial Ecosystems in Traditional Egyptian Domiati Cheese
Authors: El-Baradei Gaber , Delacroix-Buchet Agnès , Ogier Jean-Claude 
Published: December 2006

ABSTRACT

Bacterial biodiversity occurring in traditional Egyptian soft Domiati cheese was studied by PCR-temporal temperature gel electrophoresis (TTGE) and PCR-denaturing gradient gel electrophoresis (DGGE). Bands were identified using a reference species database (J.-C. Ogier et al., Appl. Environ. Microbiol. 70:5628-5643, 2004); de novo bands having nonidentified migration patterns were identified by DNA sequencing. Results reveal a novel bacterial profile and extensive bacterial biodiversity in Domiati cheeses, as reflected by the numerous bands present in TTGE and DGGE patterns. The dominant lactic acid bacteria (LAB) identified were as follows:
Leuconostoc mesenteroides
,
Lactococcus garvieae
,
Aerococcus viridans
,
Lactobacillus versmoldensis
,
Pediococcus inopinatus
, and
Lactococcus lactis
. Frequent non-LAB species included numerous coagulase-negative staphylococci,
Vibrio
spp.,
Kocuria rhizophila
,
Kocuria kristinae
,
Kocuria halotolerans
,
Arthrobacter
spp.
/Brachybacterium tyrofermentans
. This is the first time that the majority of these species has been identified in Domiati cheese. Nearly all the dominant and frequent bacterial species are salt tolerant, and several correspond to known marine bacteria. As Domiati cheese contains 5.4 to 9.5% NaCl, we suggest that these bacteria are likely to have an important role in the ripening process. This first systematic study of the microbial composition of Domiati cheeses reveals great biodiversity and evokes a role for marine bacteria in determining cheese type.
Global Effect of Indole-3-Acetic Acid Biosynthesis on Multiple Virulence Factors of
Erwinia chrysanthemi
3937
Authors: Yang Shihui , Zhang Qiu , Guo Jianhua , Charkowski Amy O. , Glick Bernard R. , Ibekwe A. Mark , Cooksey Donald A. , Yang Ching-Hong 
Published: December 2006

ABSTRACT

Production of the plant hormone indole-3-acetic acid (IAA) is widespread among plant-associated microorganisms. The non-gall-forming phytopathogen
Erwinia chrysanthemi
3937 (strain Ech3937) possesses
iaaM
(ASAP16562) and
iaaH
(ASAP16563) gene homologues. In this work, the null knockout
iaaM
mutant strain Ech138 was constructed. The IAA production by Ech138 was reduced in M9 minimal medium supplemented with
l
-tryptophan. Compared with wild-type Ech3937, Ech138 exhibited reduced ability to produce local maceration, but its multiplication in
Saintpaulia ionantha
was unaffected. The pectate lyase production of Ech138 was diminished. Compared with wild-type Ech3937, the expression levels of an oligogalacturonate lyase gene,
ogl
, and three endopectate lyase genes,
pelD
,
pelI
, and
pelL
, were reduced in Ech138 as determined by a green fluorescent protein-based fluorescence-activated cell sorting promoter activity assay. In addition, the transcription of type III secretion system (T3SS) genes,
dspE
(a putative T3SS effector) and
hrpN
(T3SS harpin), was found to be diminished in the
iaaM
mutant Ech138. Compared with Ech3937, reduced expression of
hrpL
(a T3SS alternative sigma factor) and
gacA
but increased expression of
rsmA
in Ech138 was also observed, suggesting that the regulation of T3SS and pectate lyase genes by IAA biosynthesis might be partially due to the posttranscriptional regulation of the Gac-Rsm regulatory pathway.
The Absence of Intervening Sequences in 23S rRNA Genes of
Campylobacter coli
Isolates from Turkeys Is a Unique Attribute of a Cluster of Related Strains Which Also Lack Resistance to Erythromycin
Authors: Chan Kamfai , Miller William G. , Mandrell Robert E. , Kathariou Sophia 
Published: December 2006

ABSTRACT

Certain
Campylobacter
strains harbor a transcribed intervening sequence (IVS) in their 23S rRNA genes. Following transcription, the IVS is excised, leading to fragmentation of the 23S rRNA. The origin and possible functions of the IVS are unknown. Furthermore, the distribution of IVS-harboring strains within
Campylobacter
populations is poorly understood. In this study, 104 strains of
Campylobacter coli
from turkeys, representing 27 different multilocus sequence typing-based sequence types (STs), were characterized in terms of IVS content and erythromycin susceptibility. Sixty-nine strains harbored IVSs in all three 23S rRNA genes, whereas the other 35 strains lacked IVSs from at least one of the genes. The STs of the latter strains belonged to an unusual cluster of
C. coli
STs (cluster II), earlier found primarily in turkey strains and characterized by the presence of the
C. jejuni aspA103
allele. The majority (66/69) of strains harboring IVSs in all three 23S rRNA genes were resistant to erythromycin, whereas none of the 35 strains with at least one IVS-free 23S rRNA gene were resistant. Cluster II strains could be transformed to erythromycin resistance with genomic DNA from
C. coli
that harbored IVS and the A2075G transition in the 23S rRNA gene, associated with resistance to erythromycin in
Campylobacter
. Erythromycin-resistant transformants harbored both the A2075 transition and IVS. The findings suggest that the absence of IVS in
C. coli
from turkeys is characteristic of a unique clonal group of erythromycin-susceptible strains and that IVS can be acquired by these strains via natural transformation to erythromycin resistance.
Influences of Infaunal Burrows on the Community Structure and Activity of Ammonia-Oxidizing Bacteria in Intertidal Sediments
Authors: Satoh Hisashi , Nakamura Yoshiyuki , Okabe Satoshi 
Published: December 2006

ABSTRACT

Influences of infaunal burrows constructed by the polychaete (
Tylorrhynchus heterochaetus
) on O
2
concentrations and community structures and abundances of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in intertidal sediments were analyzed by the combined use of a 16S rRNA gene-based molecular approach and microelectrodes. The microelectrode measurements performed in an experimental system developed in an aquarium showed direct evidence of O
2
transport down to a depth of 350 mm of the sediment through a burrow. The 16S rRNA gene-cloning analysis revealed that the betaproteobacterial AOB communities in the sediment surface and the burrow walls were dominated by
Nitrosomonas
sp. strain Nm143-like sequences, and most of the clones in
Nitrospira
-like NOB clone libraries of the sediment surface and the burrow walls were related to the
Nitrospira marina
lineage. Furthermore, we investigated vertical distributions of AOB and NOB in the infaunal burrow walls and the bulk sediments by real-time quantitative PCR (Q-PCR) assay. The AOB and
Nitrospira
-like NOB-specific 16S rRNA gene copy numbers in the burrow walls were comparable with those in the sediment surfaces. These numbers in the burrow wall at a depth of 50 to 55 mm from the surface were, however, higher than those in the bulk sediment at the same depth. The microelectrode measurements showed higher NH
4
+
consumption activity at the burrow wall than those at the surrounding sediment. This result was consistent with the results of microcosm experiments showing that the consumption rates of NH
4
+
and total inorganic nitrogen increased with increasing infaunal density in the sediment. These results clearly demonstrated that the infaunal burrows stimulated O
2
transport into the sediment in which otherwise reducing conditions prevailed, resulting in development of high NH
4
+
consumption capacity. Consequently, the infaunal burrow became an important site for NH
4
+
consumption in the intertidal sediment.
Reduced Dietary Intake of Carbohydrates by Obese Subjects Results in Decreased Concentrations of Butyrate and Butyrate-Producing Bacteria in Feces
Authors: Duncan Sylvia H. , Belenguer Alvaro , Holtrop Grietje , Johnstone Alexandra M. , Flint Harry J. , Lobley Gerald E. 
Published: December 2006

ABSTRACT

Weight loss diets for humans that are based on a high intake of protein but low intake of fermentable carbohydrate may alter microbial activity and bacterial populations in the large intestine and thus impact on gut health. In this study, 19 healthy, obese (body mass index range, 30 to 42) volunteers were given in succession three different diets: maintenance (M) for 3 days (399 g carbohydrate/day) and then high protein/medium (164 g/day) carbohydrate (HPMC) and high protein/low (24 g/day) carbohydrate (HPLC) each for 4 weeks. Stool samples were collected at the end of each dietary regimen. Total fecal short-chain fatty acids were 114 mM, 74 mM, and 56 mM (
P
< 0.001) for M, HPMC, and HPLC diets, respectively, and there was a disproportionate reduction in fecal butyrate (18 mM, 9 mM, and 4 mM, respectively;
P
< 0.001) with decreasing carbohydrate. Major groups of fecal bacteria were monitored using nine 16S rRNA-targeted fluorescence in situ hybridization probes, relative to counts obtained with the broad probe Eub338. No significant change was seen in the relative counts of the bacteroides (Bac303) (mean, 29.6%) or the clostridial cluster XIVa (Erec482, 23.3%), cluster IX (Prop853, 9.3%), or cluster IV (Fprau645, 11.6%; Rbro730 plus Rfla729, 9.3%) groups. In contrast, the
Roseburia
spp. and
Eubacterium rectale
subgroup of cluster XIVa (11%, 8%, and 3% for M, HPMC, and HPLC, respectively;
P
< 0.001) and bifidobacteria (4%, 2.1%, and 1.9%, respectively;
P
= 0.026) decreased as carbohydrate intake decreased. The abundance of butyrate-producing bacteria related to
Roseburia
spp. and
E. rectale
correlated well with the decline in fecal butyrate.
Rugosity in
Grimontia hollisae
Authors: Curtis S. K. , Kothary M. H. , Blodgett R. J. , Raybourne R. B. , Ziobro G. C. , Tall B. D. 
Published: December 2006

ABSTRACT

Grimontia hollisae
, formerly
Vibrio hollisae
, produces both smooth and rugose colonial variants. The rugose colony phenotype is characterized by wrinkled colonies producing copious amounts of exopolysaccharide. Cells from a rugose colony grown at 30°C form rugose colonies, while the same cells grown at 37°C form smooth colonies, which are characterized by a nonwrinkled, uncrannied appearance. Stress response studies revealed that after exposure to bleach for 30 min, rugose survivors outnumbered smooth survivors. Light scatter information obtained by flow cytometry indicated that rugose cells clumped into clusters of three or more cells (average, five cells) and formed two major clusters, while smooth cells formed only one cluster of single cells or doublets. Fluorescent lectin-binding flow cytometry studies revealed that the percentages of rugose cells that bound either wheat germ agglutinin (WGA) or
Galanthus nivalis
lectin (GNL) were greater than the percentages of smooth cells that bound the same lectins (WGA, 35% versus 3.5%; GNL, 67% versus 0.21%). These results indicate that the rugose exopolysaccharide consists partially of
N
-acetylglucosamine and mannose. Rugose colonies produced significantly more biofilm material than did smooth colonies, and rugose colonies grown at 30°C produced more biofilm material than rugose colonies grown at 37°C. Ultrastructurally, rugose colonies show regional cellular differentiation, with apical and lateral colonial regions containing cells embedded in a matrix stained by Alcian Blue. The cells touching the agar surface are packed tightly together in a palisade-like manner. The central region of the colony contains irregularly arranged, fluid-filled spaces and loosely packed chains or arrays of coccoid and vibrioid cells. Smooth colonies, in contrast, are flattened, composed of vibrioid cells, and lack distinct regional cellular differences. Results from suckling mouse studies showed that both orally fed rugose and smooth variants elicited significant, but similar, amounts of fluid accumulated in the stomach and intestines. These observations comprise the first report of expression and characterization of rugosity by
G. hollisae
and raise the possibility that expression of rugose exopolysaccharide in this organism is regulated at least in part by growth temperature.
Role of Cdc42-Cla4 Interaction in the Pheromone Response of
Saccharomyces cerevisiae
Authors: Heinrich Melanie , Köhler Tim , Mösch Hans-Ulrich 
Published: December 2006

ABSTRACT

In
Saccharomyces cerevisiae
, the highly conserved Rho-type GTPase Cdc42 is essential for cell division and controls cellular development during mating and invasive growth. The role of Cdc42 in mating has been controversial, but a number of previous studies suggest that the GTPase controls the mitogen-activated protein (MAP) kinase cascade by activating the p21-activated protein kinase (PAK) Ste20. To further explore the role of Cdc42 in pheromone-stimulated signaling, we isolated novel alleles of
CDC42
that confer resistance to pheromone. We find that in
CDC42
(
V36A
) and
CDC42
(
V36A
,
I182T
) mutant strains, the inability to undergo pheromone-induced cell cycle arrest correlates with reduced phosphorylation of the mating MAP kinases Fus3 and Kss1 and with a decrease in mating efficiency. Furthermore, Cdc42(V36A) and Cdc42(V36A, I182T) proteins show reduced interaction with the PAK Cla4 but not with Ste20. We also show that deletion of
CLA4
in a
CDC42
(
V36A
,
I182T
) mutant strain suppresses pheromone resistance and that overexpression of
CLA4
interferes with pheromone-induced cell cycle arrest and MAP kinase phosphorylation in
CDC42
wild-type strains. Our data indicate that Cla4 has the potential to act as a negative regulator of the mating pathway and that this function of the PAK might be under control of Cdc42. In conclusion, our study suggests that control of pheromone signaling by Cdc42 not only depends on Ste20 but also involves interaction of the GTPase with Cla4.
Genome-Wide Analysis of C/D and H/ACA-Like Small Nucleolar RNAs in
Leishmania major
Indicates Conservation among Trypanosomatids in the Repertoire and in Their rRNA Targets
Authors: Liang Xue-hai , Hury Avraham , Hoze Ehud , Uliel Shai , Myslyuk Inna , Apatoff Avihay , Unger Ron , Michaeli Shulamit 
Published: December 2006

ABSTRACT

Small nucleolar RNAs (snoRNAs) are a large group of noncoding RNAs that exist in eukaryotes and archaea and guide modifications such as 2′-
O
-ribose methylations and pseudouridylation on rRNAs and snRNAs. Recently, we described a genome-wide screening approach with
Trypanosoma brucei
that revealed over 90 guide RNAs. In this study, we extended this approach to analyze the repertoire of the closely related human pathogen
Leishmania major
. We describe 23 clusters that encode 62 C/Ds that can potentially guide 79 methylations and 37 H/ACA-like RNAs that can potentially guide 30 pseudouridylation reactions. Like
T. brucei
,
Leishmania
also contains many modifications and guide RNAs relative to its genome size. This study describes 10 H/ACAs and 14 C/Ds that were not found in
T. brucei
. Mapping of 2′-O-methylations in rRNA regions rich in modifications suggests the existence of trypanosomatid-specific modifications conserved in
T. brucei
and
Leishmania
. Structural features of C/D snoRNAs, such as copy number, conservation of boxes, K turns, and intragenic and extragenic base pairing, were examined to elucidate the great variation in snoRNA abundance. This study highlights the power of comparative genomics for determining conserved features of noncoding RNAs.
GAS2
and
GAS4
, a Pair of Developmentally Regulated Genes Required for Spore Wall Assembly in
Saccharomyces cerevisiae
Authors: Ragni Enrico , Coluccio Alison , Rolli Eleonora , Rodriguez-Peña José Manuel , Colasante Gaia , Arroyo Javier , Neiman Aaron M. , Popolo Laura 
Published: December 2006

ABSTRACT

The
GAS
multigene family of
Saccharomyces cerevisiae
is
composed of five paralogs (
GAS1
to
GAS5
).
GAS1
is the only one of these genes that has been
characterized to date. It encodes a
glycosylphosphatidylinositol-anchored protein functioning as aβ
(1,3)-glucan elongase and required for proper cell wall
assembly during vegetative growth. In this study, we characterize the
roles of the
GAS2
and
GAS4
genes. These genes are
expressed exclusively during sporulation. Their mRNA levels showed a
peak at 7 h from induction of sporulation and then decreased.
Gas2 and Gas4 proteins were detected and reached maximum levels between
8 and 10 h from induction of sporulation, a time roughly
coincident with spore wall assembly. The double null
gas2
gas4
diploid mutant showed a severe reduction in the
efficiency of sporulation, an increased permeability of the spores to
exogenous substances, and production of inviable spores, whereas the
single
gas2
and
gas4
null diploids were similar to
the parental strain. An analysis of spore ultrastructure indicated that
the loss of Gas2 and Gas4 proteins affected the proper attachment of
the glucan to the chitosan layer, probably as a consequence of the lack
of coherence of the glucan layer. The ectopic expression of
GAS2
and
GAS4
genes in a
gas1
null mutant
revealed that these proteins are redundant versions of Gas1p
specialized to function in a compartment at a pH value close to
neutral.
Endoplasmic Reticulum Retention Signal-Dependent Glycylation of the Hsp70/Grp170-Related Pgp1p in
Tetrahymena
Authors: Xie Rong , Clark Kathleen M. , Gorovsky Martin A. 
Published: December 2006

ABSTRACT

Glycylation is an uncommon posttranslational modification. It has been found that tubulin glycylation is essential for cell survival in
Tetrahymena
. Here we describe
PGP1
, a
Tetrahymena
gene encoding an Hsp70 homologue that is a novel glycylated protein. Pgp1p is a conserved glycoprotein that localizes within the lumen of the endoplasmic reticulum (ER). We demonstrate that
PGP1
is essential for viability and present evidence that both glycosylation and ER retention are necessary but not sufficient for glycylation.