bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Long Terminal Repeat Retrotransposon of Fission Yeast Has Strong Preferences for Specific Sites of Insertion
Authors: Singleton Teresa L. , Levin Henry L. 
Published: December 2002

ABSTRACT

The successful dispersal of transposons depends on the critical balance between the fitness of the host and the ability of the transposon to insert into the host genome. One method transposons may use to avoid the disruption of coding sequences is to target integration into safe havens. We explored the interaction between the long terminal repeat retrotransposon Tf1 and the genome of the yeast
Schizosaccharomyces
pombe
. Using techniques that were specifically designed to detect integration of Tf1 throughout the genome and to avoid bias in this detection, we generated 51 insertion events. Although 60.2% of the genome of
S
.
pombe
is coding sequence, all but one of the insertions occurred in intergenic regions. We also found that Tf1 was significantly more likely to insert into intergenic regions that included polymerase II promoters than into regions between convergent gene pairs. Interestingly, 8 of the 51 insertion sites were isolated multiple times from genetically independent cultures. This result suggests that specific sites in intergenic regions are targeted by Tf1. Perhaps the most surprising observation was that per kilobase of nonrepetitive sequence, Tf1 was significantly more likely to insert into chromosome 3 than into one of the other two chromosomes. This preference was found not to be due to differences in the distribution or composition of intergenic sequences within the three chromosomes.
Saccharomyces
cerevisiae
C-Type Cyclin Ume3p/Srb11p Is Required for Efficient Induction and Execution of Meiotic Development
Authors: Cooper Katrina F. , Strich Randy 
Published: December 2002

ABSTRACT

The yeast C-type cyclin Ume3p/Srb11p and its cyclin-dependent kinase partner Ume5p/Srb10p repress the transcription of several genes required for meiotic recombination or meiosis I nuclear division. To relieve this repression, Srb11p is destroyed early in meiosis, prior to the first meiotic division. This report identifies two roles for Srb11p in regulating meiotic development. First,
SRB11
is required for the normal exit from the mitotic cell cycle prior to meiotic induction. Specifically, mutants lacking
SRB11
(
srb11
Δ) uncouple bud growth from chromosome segregation, producing small buds with nuclei. The bud growth defect is most likely due to the failure of
srb11
Δ mutants to reestablish polarized actin fibers at the bud tip following exposure to sporulation medium. Second, Srb11p is required for the efficient execution of meiosis I.
srb11
Δ mutants either exhibited a delay in performing meiosis I and meiosis II or skipped meiosis I entirely. This meiotic defect is not due to the activation of the recombination or spindle assembly checkpoint pathways. However, the expression of several meiotic genes is delayed and reduced in the mutant strains. These results suggest a positive role for Srb10-Srb11p in regulating the transcription program. This model is supported by the finding that overexpression of the meiotic inducer
IME2
partially restored the ability of
srb11
mutants to perform meiosis I. In conclusion, these findings indicate that Srb11p is required for both entry into and execution of the meiotic program, thus describing multiple roles for a C-type cyclin in the regulation of a developmental pathway.
Pumilio Homologue from
Saprolegnia parasitica
Specifically Expressed in Undifferentiated Spore Cysts
Authors: Andersson M. Gunnar , Cerenius Lage 
Published: December 2002

ABSTRACT

The expression of spore-specific marker transcripts at different stages of the asexual life cycle of
Saprolegnia parasitica
was analyzed. One of the markers, designated
puf1
, was found to be expressed transiently upon each of several cycles of zoospore encystment and reemergence. The transcript is induced immediately upon zoospore encystment and is rapidly lost when a cyst is triggered to germinate. In nongerminating cysts,
puf1
is maintained until a time point when the cysts can no longer be triggered to germinate and thus have become determined for zoospore reemergence. The results show that the cyst stage has two phases, of about equal duration, which are physiologically and transcriptionally distinct and that the transcriptional machinery of oomycetes is also active in nongerminating spores.
puf1
encodes a putative mRNA binding protein belonging to a conserved class of proteins including the
Drosophila melanogaster
Pumilio protein,
Caenorhabditis elegans
FBF, and
Saccharomyces cerevisiae
Puf5, all of which are involved in regulation of gene expression by posttranscriptional mechanisms.
Role of Uridylate-Specific Exoribonuclease Activity in
Trypanosoma brucei
RNA Editing
Authors: Igo Robert P. , Weston David S. , Ernst Nancy Lewis , Panigrahi Aswini K. , Salavati Reza , Stuart Kenneth 
Published: December 2002

ABSTRACT

Editing of mitochondrial mRNAs in kinetoplastid protozoa occurs by a series of enzymatic steps that insert and delete uridylates (U's) as specified by guide RNAs (gRNAs). The characteristics of the 3" exonuclease activity that removes the U's following cleavage during deletion editing were determined by using an in vitro precleaved deletion assay that is based on ATPase subunit 6 pre-mRNA and gA6[14] gRNA. The exonuclease in partially purified editing complexes is specific for U's. The specificity occurs in the absence of gRNA, but its activity is enhanced by the presence of gRNA. The 3" pre-mRNA fragment enhances the specificity, but not the efficiency, of U removal. The activity is sensitive to the 5" phosphate of the 3" fragment, which is not required for U removal. The ability of the 3" U's to base pair with purines in the gRNA protects them from removal, suggesting that the U-specific 3" exonuclease (exoUase) is specific for U's which are not base paired. ExoUase is stereospecific and cannot remove (

R
p

)α-thio-U. The specificity of the exoUase activity thus contributes to the precision of RNA editing.
CulB, a Putative Ubiquitin Ligase Subunit, Regulates Prestalk Cell Differentiation and Morphogenesis in
Dictyostelium
spp
Authors: Wang Bin , Kuspa Adam 
Published: December 2002

ABSTRACT

Dictyostelium
amoebae accomplish a starvation-induced developmental process by aggregating into a mound and forming a single fruiting body with terminally differentiated spores and stalk cells.
culB
was identified as the gene disrupted in a developmental mutant with an aberrant prestalk cell differentiation phenotype. The
culB
gene product appears to be a homolog of the cullin family of proteins that are known to be involved in ubiquitin-mediated protein degradation. The
culB
mutants form supernumerary prestalk tips atop each developing mound that result in the formation of multiple small fruiting bodies. The prestalk-specific gene
ecmA
is expressed precociously in
culB
mutants, suggesting that prestalk cell differentiation occurs earlier than normal. In addition, when
culB
mutant cells are mixed with wild-type cells, they display a cell-autonomous propensity to form stalk cells. Thus, CulB appears to ensure that the proper number of prestalk cells differentiate at the appropriate time in development. Activation of cyclic AMP-dependent protein kinase (PKA) by disruption of the regulatory subunit gene (
pkaR
) or by overexpression of the catalytic subunit gene (
pkaC
) enhances the prestalk/stalk cell differentiation phenotype of the
culB
mutant. For example,
culB
−
pkaR
−
cells form stalk cells without obvious multicellular morphogenesis and are more sensitive to the prestalk O (pstO) cell inducer DIF-1. The sensitized condition of PKA activation reveals that CulB may govern prestalk cell differentiation in
Dictyostelium
, in part by controlling the sensitivity of cells to DIF-1, possibly by regulating the levels of one or more proteins that are rate limiting for prestalk differentiation.
A New, Expressed Multigene Family Containing a Hot Spot for Insertion of Retroelements Is Associated with Polymorphic Subtelomeric Regions of
Trypanosoma brucei
Authors: Bringaud Frédéric , Biteau Nicolas , Melville Sara E. , Hez Stéphanie , El-Sayed Najib M. , Leech Vanessa , Berriman Matthew , Hall Neil , Donelson John E. , Baltz Théo 
Published: December 2002

ABSTRACT

We describe a novel gene family that forms clusters in subtelomeric regions of
Trypanosoma brucei
chromosomes and partially accounts for the observed clustering of retrotransposons. The
ingi
and ribosomal inserted mobile element (RIME) non-LTR retrotransposons share 250 bp at both extremities and are the most abundant putatively mobile elements, with about 500 copies per haploid genome. From cDNA clones and subsequently in the
T. brucei
genomic DNA databases, we identified 52 homologous gene and pseudogene sequences, 16 of which contain a RIME and/or
ingi
retrotransposon inserted at exactly the same relative position. Here these genes are called the
RHS
family, for retrotransposon hot spot. Comparison of the protein sequences encoded by
RHS
genes (21 copies) and pseudogenes (24 copies) revealed a conserved central region containing an ATP/GTP-binding motif and the RIME/
ingi
insertion site. The RHS proteins share between 13 and 96% identity, and six subfamilies,
RHS1
to
RHS6
, can be defined on the basis of their divergent C-terminal domains. Immunofluorescence and Western blot analyses using RHS subfamily-specific immune sera show that RHS proteins are constitutively expressed and occur mainly in the nucleus. Analysis of Genome Survey Sequence databases indicated that the
Trypanosoma brucei
diploid genome contains about 280
RHS
(pseudo)-genes. Among the 52 identified
RHS
(pseudo)genes, 48 copies are in three
RHS
clusters located in subtelomeric regions of chromosomes Ia and II and adjacent to the active bloodstream form expression site in
T. brucei
strain TREU927/4 GUTat10.1.
RHS
genes comprise the remaining sequence of the size-polymorphic “repetitive region” described for
T. brucei
chromosome I, and a homologous gene family is present in the
Trypanosoma cruzi
genome.
Neurospora
Clock-Controlled Gene 9 (
ccg-9
) Encodes Trehalose Synthase: Circadian Regulation of Stress Responses and Development
Authors: Shinohara Mari L. , Correa Alejandro , Bell-Pedersen Deborah , Dunlap Jay C. , Loros Jennifer J. 
Published: December 2002

ABSTRACT

The circadian clock of
Neurospora crassa
regulates the rhythmic expression of a number of genes encoding diverse functions which, as an ensemble, are adaptive to life in a rhythmic environment of alternating levels of light and dark, warmth and coolness, and dryness and humidity. Previous differential screens have identified a number of such genes based solely on their cycling expression, including clock-controlled gene 9 (
ccg-9
). Sequence analysis now shows the predicted CCG-9 polypeptide to be homologous to a novel form of trehalose synthase; as such it would catalyze the synthesis of the disaccharide trehalose, which plays an important role in protecting many cells from environmental stresses. Consistent with this, heat, glucose starvation, and osmotic stress induce
ccg-9
transcript accumulation. Surprisingly, however, a parallel role in development is suggested by the finding that inactivation of
ccg-9
results in altered conidiophore morphology and abolishes the normal circadian rhythm of asexual macroconidial development. Examination of a clock component, FRQ, in the
ccg-9
-null strain revealed normal cycling, phosphorylation, and light induction, indicating that loss of the conidiation rhythm is not due to changes in either the circadian oscillator or light input into the clock but pointing instead to a defect in circadian output. These data imply an interplay between a role of trehalose in stress protection and an apparent requirement for trehalose in clock regulation of conidiation under constant environmental conditions. This requirement can be bypassed by a daily light signal which drives a light-entrained rhythm in conidiation in the
ccg-9
-null strain; this bypass suggests that the trehalose requirement is related to clock control of development and not to the developmental process itself. Circadian control of trehalose synthase suggests a link between clock control of stress responses and that of development.
Yeast Rpi1 Is a Putative Transcriptional Regulator That Contributes to Preparation for Stationary Phase
Authors: Sobering Andrew K. , Jung Un Sung , Lee Kyung S. , Levin David E. 
Published: December 2002

ABSTRACT

The
RPI1
gene of
Saccharomyces cerevisiae
was identified initially as a dosage suppressor of the heat shock sensitivity associated with overexpression of
RAS2
(J. Kim and S. Powers, Mol. Cell. Biol. 11:3894–3904, 1991). Based on its failure to suppress mutationally activated
RAS2
,
RPI1
was proposed to be a negative regulator of the Ras/cyclic AMP (cAMP) pathway that functions at a point upstream of Ras. We isolated
RPI1
as a high-copy-number suppressor of the cell lysis defect associated with a null mutation in the
MPK1
gene, which encodes the mitogen-activated protein kinase of the cell wall integrity-signaling pathway. Although the sequence of Rpi1 is not informative about its function, we present evidence that this protein resides in the nucleus, possesses a transcriptional activation domain, and affects the mRNA levels of several cell wall metabolism genes. In contrast to the previous report, we found that
RPI1
overexpression suppresses defects associated with mutational hyperactivation of the Ras/cAMP pathway at all points including constitutive mutations in the cAMP-dependent protein kinase. We present additional genetic and biochemical evidence that Rpi1 functions independently of and in opposition to the Ras/cAMP pathway to promote preparations for the stationary phase. Among these preparations is a fortification of the cell wall that is antagonized by Ras pathway activity. This observation reveals a novel link between the Ras/cAMP pathway and cell wall integrity. Finally, we propose that inappropriate expression of
RPI1
during log phase growth drives fortification of the cell wall and that this behavior is responsible for suppression of the
mpk1
cell lysis defect.
Adenylyl Cyclase Functions Downstream of the Gα Protein Gpa1 and Controls Mating and Pathogenicity of
Cryptococcus neoformans
Authors: Alspaugh J. Andrew , Pukkila-Worley Read , Harashima Toshiaki , Cavallo Lora M. , Funnell Deanna , Cox Gary M. , Perfect John R. , Kronstad James W. , Heitman Joseph 
Published: December 2002

ABSTRACT

The signaling molecule cyclic AMP (cAMP) is a ubiquitous second messenger that enables cells to detect and respond to extracellular signals. cAMP is generated by the enzyme adenylyl cyclase, which is activated or inhibited by the Gα subunits of heterotrimeric G proteins in response to ligand-activated G-protein-coupled receptors. Here we identified the unique gene (
CAC1
) encoding adenylyl cyclase in the opportunistic fungal pathogen
Cryptococcus neoformans
. The
CAC1
gene was disrupted by transformation and homologous recombination. In stark contrast to the situation for
Saccharomyces cerevisiae
, in which adenylyl cyclase is essential,
C. neoformans cac1
mutant strains were viable and had no vegetative growth defect. Furthermore,
cac1
mutants maintained the yeast-like morphology of wild-type cells, in contrast to the constitutively filamentous phenotype found upon the loss of adenylyl cyclase in another basidiomycete pathogen,
Ustilago maydis
. Like
C. neoformans
mutants lacking the Gα protein Gpa1,
cac1
mutants were mating defective and failed to produce two inducible virulence factors: capsule and melanin. As a consequence,
cac1
mutant strains were avirulent in animal models of cryptococcal meningitis. Reintroduction of the wild-type
CAC1
gene or the addition of exogenous cAMP suppressed
cac1
mutant phenotypes. Moreover, the overexpression of adenylyl cyclase restored mating and virulence factor production in
gpa1
mutant strains. Physiological studies revealed that the Gα protein Gpa1 and adenylyl cyclase controlled cAMP production in response to glucose, and no cAMP was detectable in extracts from
cac1
or
gpa1
mutant strains. These findings provide direct evidence that Gpa1 and adenylyl cyclase function in a conserved signal transduction pathway controlling cAMP production, hyphal differentiation, and virulence of this human fungal pathogen.
Isolation and Characterization of Two Ammonium Permease Genes,
meaA
and
mepA
, from
Aspergillus nidulans
Authors: Monahan Brendon J. , Fraser James A. , Hynes Michael J. , Davis Meryl A. 
Published: December 2002

ABSTRACT

Ammonium and the analogue methylammonium are taken into the cell by active transport systems which constitute a family of transmembrane proteins that have been identified in fungi, bacteria, plants, and animals. Two genes from
Aspergillus
nidulans
,
mepA
and
meaA
, which encode ammonium transporters with different affinities have been characterized. The MepA transporter exhibits the highest affinity for methylammonium (
K

m
0

, 44.3 μM); in comparison, the
K

m

for MeaA is 3.04 mM. By use of targeted gene replacement strategies,
meaA
and
mepA
deletion mutants were created. Deletion of both
meaA
and
mepA
resulted in the inability of the strain to grow on ammonium concentrations of less than 10 mM. The single
meaA
deletion mutant exhibited reduced growth at the same concentrations, whereas the
mepA
deletion mutant displayed wild-type growth. Interestingly, multiple copies of
mepA
were found to complement the methylammonium resistance phenotype conferred by the deletion of
meaA
. The expression profiles for
mepA
and
meaA
differed; the
mepA
transcript was detected only in nitrogen-starved cultures, whereas
meaA
was expressed under both ammonium-sufficient and nitrogen starvation conditions. Together, these results indicate that MeaA constitutes the major ammonium transport activity and is required for the optimal growth of
A
.
nidulans
on ammonium as the sole nitrogen source and that MepA probably functions in scavenging low concentrations of ammonium under nitrogen starvation conditions.
CDC42 Is Required for Polarized Growth in Human Pathogen
Candida albicans
Authors: Ushinsky Sophia C. , Harcus Doreen , Ash Josee , Dignard Daniel , Marcil Anne , Morchhauser Joachim , Thomas David Y. , Whiteway Malcolm , Leberer Ekkehard 
Published: December 2002

ABSTRACT

Cdc42p is a member of the RAS superfamily of GTPases and plays an essential role in polarized growth in many eukaryotic cells. We cloned the
Candida albicans CaCDC42
by functional complementation in
Saccharomyces cerevisiae
and analyzed its function in
C. albicans
. A double deletion of
CaCDC42
was made in a
C. albicans
strain containing
CaCDC42
under the control of the
PCK1
promoter. When expression of the heterologous copy of
CaCDC42
was repressed in this strain, the cells ceased proliferation. These arrested cells were large, round, and unbudded and contained predominantly two nuclei. The
PCK1
-mediated overexpression of wild-type CaCdc42p had no effect on cells. However, in cells overexpressing CaCdc42p containing the dominant-negative D118A substitution, proliferation was blocked and the arrested cells were large, round, unbudded, and multinucleated, similar to the phenotype of the
cdc42
double-deletion strain. Cells overexpressing CaCdc42p containing the hyperactive G12V substitution also ceased proliferation in yeast growth medium; in this case the arrested cells were multinucleated and multibudded. An intact CAAX box is essential for the phenotypes associated with either CaCdc42p
G12V
or CaCdc42p
D118A
ectopic expression, suggesting that membrane attachment is involved in CaCdc42p function. In addition, the lethality caused by ectopic expression of CaCdc42p
G12V
was suppressed by deletion of
CST20
but not by deletion of
CaCLA4
. CaCdc42p function was also examined under hypha-inducing conditions. Cdc42p depletion prior to hyphal induction trapped cells in a round, unbudded state, while depletion triggered at the same time as hyphal induction permitted the initiation of germ tubes that failed to be extended. Ectopic expression of either the G12V or D118A substitution protein modified hyphal formation in a CAAX box-dependent manner. Thus, CaCdc42p function appears important for polarized growth of both the yeast and hyphal forms of
C. albicans
.
Heat Stress Activates the Yeast High-Osmolarity Glycerol Mitogen-Activated Protein Kinase Pathway, and Protein Tyrosine Phosphatases Are Essential under Heat Stress
Authors: Winkler Astrid , Arkind Christopher , Mattison Christopher P. , Burkholder Anne , Knoche Kathryn , Ota Irene 
Published: December 2002

ABSTRACT

The yeast high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathway has been characterized as being activated solely by osmotic stress. In this work, we show that the Hog1 MAPK is also activated by heat stress and that Sho1, previously identified as a membrane-bound osmosensor, is required for heat stress activation of Hog1. The two-component signaling protein, Sln1, the second osmosensor in the HOG pathway, was not involved in heat stress activation of Hog1, suggesting that the Sho1 and Sln1 sensors discriminate between stresses. The possible function of Hog1 activation during heat stress was examined, and it was found that the
hog1
Δ strain does not recover as rapidly from heat stress as well as the wild type. It was also found that protein tyrosine phosphatases (PTPs) Ptp2 and Ptp3, which inactivate Hog1, have two functions during heat stress. First, they are essential for survival at elevated temperatures, preventing lethality due to Hog1 hyperactivation. Second, they block inappropriate cross talk between the HOG and the cell wall integrity MAPK pathways, suggesting that PTPs are important for maintaining specificity in MAPK signaling pathways.
Altered Phosphotransfer in an Activated Mutant of the
Saccharomyces cerevisiae
Two-Component Osmosensor Sln1p
Authors: Ault A. D. , Fassler J. S. , Deschenes R. J. 
Published: December 2002

ABSTRACT

The
SLN1
two-component signaling pathway of
Saccharomyces cerevisiae
utilizes a multistep phosphorelay mechanism to control osmotic stress responses via the
HOG1
mitogen-activated protein kinase pathway and the transcription factor Skn7p. Sln1p consists of a sensor kinase module that undergoes histidine autophosphorylation and a receiver module that autocatalytically transfers the phosphoryl group from histidine to aspartate. The Sln1p aspartyl phosphate is then transferred to Ypd1p, which in turn transfers the phosphoryl group to a conserved aspartate on one of two response regulators, Ssk1p and Skn7p. Activated alleles of
SLN1
(
sln1*
) were previously identified that appear to increase the level of phosphorylation of downstream targets Ssk1p and Skn7p. In principle, the phenotype of
sln1
* alleles could arise from an increase in autophosphorylation or phosphotransfer activities or a decrease in an intrinsic or extrinsic dephosphorylation activity. Genetic analysis of the activated mutants has been unable to distinguish between these possibilities. In this report, we address this issue by analyzing phosphorelay and phosphohydrolysis reactions involving the Sln1p-associated receiver. The results are consistent with a model in which the activated phenotype of the
sln1
* allele,
sln1
-
22
, arises from a shift in the phosphotransfer equilibrium from Sln1p to Ypd1p, rather than from impaired dephosphorylation of the system in response to osmotic stress.