bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Lateral Transfer of Genes Encoding Ferredoxins, Nitroreductases, NADH Oxidase, and Alcohol Dehydrogenase 3 from Anaerobic Prokaryotes to
Giardia
lamblia
and
Entamoeba
histolytica
Authors: Nixon Julie E. J. , Wang Amy , Field Jessica , Morrison Hilary G. , McArthur Andrew G. , Sogin Mitchell L. , Loftus Brendan J. , Samuelson John 
Published: December 2002

ABSTRACT

Giardia
lamblia
and
Entamoeba
histolytica
are amitochondriate, microaerophilic protists which use fermentation enzymes like those of bacteria to survive anaerobic conditions within the intestinal lumen. Genes encoding fermentation enzymes and related electron transport peptides (e.g., ferredoxins) in giardia organisms and amebae are hypothesized to be derived from either an ancient anaerobic eukaryote (amitochondriate fossil hypothesis), a mitochondrial endosymbiont (hydrogen hypothesis), or anaerobic bacteria (lateral transfer hypothesis). The goals here were to complete the molecular characterization of giardial and amebic fermentation enzymes and to determine the origins of the genes encoding them, when possible. A putative giardia [2Fe-2S]ferredoxin which had a hypothetical organelle-targeting sequence at its N terminus showed similarity to mitochondrial ferredoxins and the hydrogenosomal ferredoxin of
Trichomonas
vaginalis
(another luminal protist). However, phylogenetic trees were star shaped, with weak bootstrap support, so we were unable to confirm or rule out the endosymbiotic origin of the giardia [2Fe-2S]ferredoxin gene. Putative giardial and amebic 6-kDa ferredoxins, ferredoxin-nitroreductase fusion proteins, and oxygen-insensitive nitroreductases each tentatively supported the lateral transfer hypothesis. Although there were not enough sequences to perform meaningful phylogenetic analyses, the unique common occurrence of these peptides and enzymes in giardia organisms, amebae, and the few anaerobic prokaryotes suggests the possibility of lateral transfer. In contrast, there was more robust phylogenetic evidence for the lateral transfer of
G
.
lamblia
genes encoding an NADH oxidase from a gram-positive coccus and a microbial group 3 alcohol dehydrogenase from thermoanaerobic prokaryotes. In further support of lateral transfer, the
G
.
lamblia
NADH oxidase and
adh3
genes appeared to have an evolutionary history distinct from those of
E
.
histolytica
.
The Two Nuclei ofGiardiaEach Have Complete Copies of the Genome and Are Partitioned Equationally at Cytokinesis
Authors: Yu Li Zhi , Birky C. William , Adam Rodney D. 
Published: December 2002

ABSTRACTGiardia lambliais medically important as a cause of diarrhea and malabsorption throughout the world and is thought to be one of the earliest-branching eukaryotes on a phylogenetic tree. Nevertheless, the mechanisms of inheritance are largely unknown. The trophozoites ofGiardiaand other diplomonads are interesting in their possession of two nuclei that are identical or similar in several respects. They replicate at nearly the same time, have similar quantities of DNA, and are both transcriptionally active. We used fluorescence in situ hybridization to demonstrate that genes from each of the five chromosomes are found in both nuclei, confirming that each nucleus has at least one complete copy of the genome. This raises a second question. The alleles of a gene in different nuclei are expected to accumulate different mutations, but surprisingly, the degree of heterozygosity in a clone is very low. One possible mechanism for eliminating sequence differences between nuclei is that each daughter cell receives two copies of the same nucleus at cell division. We used trophozoites with a plasmid transfected into a single nucleus to demonstrate that the two nuclei are partitioned equationally at cytokinesis. The mechanism(s) by which homozygosity is maintained will require further investigation.
Involvement of
RAD9
-Dependent Damage Checkpoint Control in Arrest of Cell Cycle, Induction of Cell Death, and Chromosome Instability Caused by Defects in Origin Recognition Complex in
Saccharomyces cerevisiae
Authors: Watanabe Keiichi , Morishita Jun , Umezu Keiko , Shirahige Katsuhiko , Maki Hisaji 
Published: December 2002

ABSTRACT

Perturbation of origin firing in chromosome replication is a possible cause of spontaneous chromosome instability in multireplicon organisms. Here, we show that chromosomal abnormalities, including aneuploidy and chromosome rearrangement, were significantly increased in yeast diploid cells with defects in the origin recognition complex. The cell cycle of
orc1
-
4
/
orc1
-
4
temperature-sensitive mutant was arrested at the G
2
/M boundary, after several rounds of cell division at the restrictive temperature. However, prolonged incubation of the mutant cells at 37°C led to abrogation of G
2
arrest, and simultaneously the cells started to lose viability. A sharp increase in chromosome instability followed the abrogation of G
2
arrest. In
orc1
-
4
/
orc1
-
4 rad9
Δ/
rad9
Δ diploid cells grown at 37°C, G
2
arrest and induction of cell death were suppressed, while chromosome instability was synergistically augmented. These findings indicated that DNA lesions caused by a defect in Orc1p function trigger the
RAD9
-dependent checkpoint control, which ensures genomic integrity either by stopping the cell cycle progress until lesion repair, or by inducing cell death when the lesion is not properly repaired. At semirestrictive temperatures,
orc2
-
1
/
orc2
-
1
diploid cells demonstrated G
2
arrest and loss of cell viability, both of which require
RAD9
-dependent checkpoint control. However, chromosome instability was not induced in
orc2
-
1
/
orc2
-
1
cells, even in the absence of the checkpoint control. These data suggest that once cells lose the damage checkpoint control, perturbation of origin firing can be tolerated by the cells. Furthermore, although a reduction in origin-firing capacity does not necessarily initiate chromosome instability, the Orc1p possesses a unique function, the loss of which induces instability in the chromosome.
Myosin I Is Required for Hypha Formation in
Candida
albicans
Authors: Oberholzer U. , Marcil A. , Leberer E. , Thomas D. Y. , Whiteway M. 
Published: December 2002

ABSTRACT

The pathogenic yeast
Candida
albicans
can undergo a dramatic change in morphology from round yeast cells to long filamentous cells called hyphae. We have cloned the
CaMYO5
gene encoding the only myosin I in
C
.
albicans
. A strain with a deletion of both copies of
CaMYO5
is viable but cannot form hyphae under all hypha-inducing conditions tested. This mutant exhibits a higher frequency of random budding and a depolarized distribution of cortical actin patches relative to the wild-type strain. We found that polar budding, polarized localization of cortical actin patches, and hypha formation are dependent on a specific phosphorylation site on myosin I, called the “TEDS-rule” site. Mutation of this serine 366 to alanine gives rise to the null mutant phenotype, while a S366D mutation, the product of which mimics a phosphorylated serine, allows hypha formation. However, the S366D mutation still causes a depolarized distribution of cortical actin patches in budding cells, similar to that in the null mutant. The localization of CaMyo5-GFP together with cortical actin patches at the bud and hyphal tips is also dependent on serine 366. Intriguingly, the cortical actin patches in the majority of the hyphae of the mutant expressing

Camyo5
S366D

were depolarized, suggesting that although their distribution is dependent on myosin I localization, polarized cortical actin patches may not be required for hypha formation.
Nnf1p, Dsn1p, Mtw1p, and Nsl1p: a New Group of Proteins Important for Chromosome Segregation in
Saccharomyces cerevisiae
Authors: Euskirchen Ghia M. 
Published: December 2002

ABSTRACT

Previously, antibodies were raised against a nuclear envelope-enriched fraction of yeast, and the essential gene
NNF1
was cloned by reverse genetics. Here it is shown that the conditional
nnf1
-
17
mutant has decreased stability of a minichromosome in addition to mitotic spindle defects. I have identified the novel essential genes
DSN1, DSN3
, and
NSL1
through genetic interactions with
nnf1
-
17
. Dsn3p was found to be equivalent to the kinetochore protein Mtw1p. By indirect immunofluorescence, all four proteins, Nnf1p, Mtw1p, Dsn1p, and Nsl1p, colocalize and are found in the region of the spindle poles. Based on the colocalization of these four proteins, the minichromosome instability and the spindle defects seen in
nnf1
mutants, I propose that Nnf1p is part of a new group of proteins necessary for chromosome segregation.
Aspergillus
nidulans
swoF
Encodes an
N
-Myristoyl Transferase
Authors: Shaw Brian D. , Momany Cory , Momany Michelle 
Published: December 2002

ABSTRACT

Polar growth is a fundamental process in filamentous fungi and is necessary for disease initiation in many pathogenic systems. Previously,
swoF
was identified in
Aspergillus
nidulans
as a single-locus, temperature-sensitive (
ts
) mutant aberrant in both polarity establishment and polarity maintenance. The
swoF
gene was cloned by complementation of the
ts
phenotype and sequenced. The derived protein sequence had high identity with
N
-myristoyl transferases (NMTs) found in fungi, plants, and animals. In addition, wild-type growth at restrictive temperature was partially restored by the addition of myristic acid to the growth medium. Sequencing revealed that the mutation in
swoF
changes the conserved aspartic acid 369 to a tyrosine. The predicted
A
.
nidulans
SwoF protein, SwoFp, was homology modeled based on crystal structures of NMTs from
Saccharomyces
cerevisiae
and
Candida
albicans
. The D369Y
swoF
mutation is on the opposite face of the protein, distal to the myristoyl coenzyme A and peptide substrate binding sites. In wild-type NMTs, D369 appears to stabilize a structural β-strand bend through two hydrogen bonds and an ionic interaction. These stabilizing bonds are abolished in the D369Y mutant. We hypothesize that a substrate of SwoFp must be myristoylated for proper polarity establishment and maintenance. The mutation prevents the proper function of SwoFp at restrictive temperature and thus blocks polar growth.
The Mold-Specific
MS8
Gene Is Required for Normal Hypha Formation in the Dimorphic Pathogenic Fungus
Histoplasma capsulatum
Authors: Tian Xianbin , Shearer Glenmore 
Published: December 2002

ABSTRACT

The dimorphic fungus
Histoplasma capsulatum
is the etiologic agent of one of the most common systemic mycoses of humans, histoplasmosis. In the environment,
H. capsulatum
grows in a differentiated mold form and shifts to an undifferentiated yeast form after mold fragments or spores are inhaled. This mold-to-yeast shift is required for disease. Little is known about the molecular biology of dimorphism in
Histoplasma
, and most studies have been directed toward yeast-specific genes. While it is important to examine the role of genes upregulated in the yeast morphotype, genes which are silenced in the yeast (i.e., mold-specific genes) may also play a critical role in dimorphism. To begin to examine this hypothesis, we report here the first misexpression and knockout analysis of a mold-specific gene in
Histoplasma
. The strongly expressed
MS8
gene encodes a predicted 21-kDa protein extremely rich in glycine and glutamine. Forced expression of
MS8
driven by the
TEF1
promoter in yeast did not alter the yeast morphology at 37°C or mold formation at 25°C. Yeast expressing
MS8
did exhibit clumping in liquid medium and formed “sticky” colonies on agar plates. Allelic replacement of
MS8
was accomplished by a positive-negative selection procedure.
ms8
knockout mutants formed apparently normal yeast at 37°C but gave rise to aberrant mycelia at 25°C. The mold colonies of the knockouts were less than half as large as normal, had a granular surface, produced a dark-red pigment, and formed short hyphae which were 40% wider with a distinctive twisted “zig-zag” shape.
Mating-Type-Specific and Nonspecific PAK Kinases Play Shared and Divergent Roles in
Cryptococcus neoformans
Authors: Wang Ping , Nichols Connie B. , Lengeler Klaus B. , Cardenas Maria E. , Cox Gary M. , Perfect John R. , Heitman Joseph 
Published: December 2002

ABSTRACT

Cryptococcus neoformans
is an opportunistic fungal pathogen with a defined sexual cycle involving fusion of haploid
MAT
α and
MAT
a cells. Virulence has been linked to the mating type, and
MAT
α cells are more virulent than congenic
MAT
a cells. To study the link between the mating type and virulence, we functionally analyzed three genes encoding homologs of the p21-activated protein kinase family:
STE20
α,
STE20
a, and
PAK1
. In contrast to the
STE20
genes that were previously shown to be in the mating-type locus, the
PAK1
gene is unlinked to the mating type. The
STE20
α,
STE20
a, and
PAK1
genes were disrupted in serotype A and D strains of
C. neoformans
, revealing central but distinct roles in mating, differentiation, cytokinesis, and virulence.
ste20
α
pak1
and
ste20
a
pak1
double mutants were synthetically lethal, indicating that these related kinases share an essential function. In summary, our studies identify an association between the
STE20
α gene, the
MAT
α locus, and virulence in a serotype A clinical isolate and provide evidence that PAK kinases function in a MAP kinase signaling cascade controlling the mating, differentiation, and virulence of this fungal pathogen.
Distinct Signaling Pathways from the Circadian Clock Participate in Regulation of Rhythmic Conidiospore Development in
Neurospora crassa
Authors: Correa Alejandro , Bell-Pedersen Deborah 
Published: December 2002

ABSTRACT

Several different environmental signals can induce asexual spore development (conidiation) and expression of developmentally regulated genes in
Neurospora crassa
. However, under constant conditions, where no environmental cues for conidiation are present, the endogenous circadian clock in
N. crassa
promotes daily rhythms in expression of known developmental genes and of conidiation. We anticipated that the same pathway of gene regulation would be followed during clock-controlled conidiation and environmental induction of conidiation and that the circadian clock would need only to control the initial developmental switch. Previous experiments showed that high-level developmental induction of the clock-controlled genes
eas
(
ccg-2
) and
ccg-1
requires the developmental regulatory proteins FL and ACON-2, respectively, and normal developmental induction of
fl
mRNA expression requires ACON-2. We demonstrate that the circadian clock regulates rhythmic
fl
gene expression and that
fl
rhythmicity requires ACON-2. However, we find that clock regulation of
eas
(
ccg-2
) is normal in an
fl
mutant strain and
ccg-1
expression is rhythmic in an
acon-2
mutant strain. Together, these data point to the endogenous clock and the environment following separate pathways to regulate conidiation-specific gene expression.
Outside-In Signaling of Cellulose Synthesis by a Spore Coat Protein in
Dictyostelium
Authors: West Christopher M. , Zhang Ping , McGlynn Aiko C. , Kaplan Lee 
Published: December 2002

ABSTRACT

The spore coat of
Dictyostelium
is formed de novo from proteins secreted from vesicles and cellulose synthesized across the plasma membrane as differentiating spores rise up the stalk. The mechanism by which these events are coordinated is not understood. In the course of experiments designed to test the function of the inner layer coat protein SP85 (PsB), expression of a specific partial length fragment was found to interrupt coat assembly after protein secretion and prior to cellulose synthesis in 85% of the cells. This fragment consisted of SP85's N-terminal domain, containing prespore vesicle targeting information, and its Cys-rich C1 domain. The effect of the NC1 fusion was not cell autonomous in interstrain chimeras, suggesting that it acted at the cell surface. SP85-null spores presented an opposite phenotype in which spores differentiated prematurely before reaching the top of the stalk, and cellulose was slightly overproduced in a disorganized fashion. A similar though less severe phenotype occurred when a fusion of the N and C2 domains was expressed. In a double mutant, absence of SP85 was epistatic to NC1 expression, suggesting that NC1 inhibited SP85 function. Together, these results suggest the existence of an outside-in signaling pathway that constitutes a checkpoint to ensure that cellulose synthesis does not occur until coat proteins are properly organized at the cell surface and stalk formation is complete. Checkpoint execution is proposed to be regulated by SP85, which is in turn under the influence of other coat proteins that interact with SP85 via its C1 and C2 domains.
Role of Histone Deacetylation in Developmentally Programmed DNA Rearrangements in
Tetrahymena thermophila
Authors: Duharcourt Sandra , Yao Meng-Chao 
Published: December 2002

ABSTRACT

In
Tetrahymena
, as in other ciliates, development of the somatic macronucleus during conjugation involves extensive and reproducible rearrangements of the germ line genome, including chromosome fragmentation and excision of internal eliminated sequences (IESs). The molecular mechanisms controlling these events are poorly understood. To investigate the role that histone acetylation may play in the regulation of these processes, we treated
Tetrahymena
cells during conjugation with the histone deacetylase inhibitor trichostatin A (TSA). We show that TSA treatment induces developmental arrests in the early stages of conjugation but does not significantly affect the progression of conjugation once the mitotic divisions of the zygotic nucleus have occurred. Progeny produced from TSA-treated cells were examined for effects on IES excision and chromosome breakage. We found that TSA treatment caused partial inhibition of excision of five out of the six IESs analyzed but did not affect chromosome breakage at four different sites. TSA treatment greatly delayed in some cells and inhibited in most the excision events in the developing macronucleus. It also led to loss of the specialized subnuclear localization of the chromodomain protein Pdd1p that is normally associated with DNA elimination. We propose a model in which underacetylated nucleosomes mark germ line-limited sequences for excision.
Evolutionary Analyses of the Small Subunit of Glutamate Synthase: Gene Order Conservation, Gene Fusions, and Prokaryote-to- Eukaryote Lateral Gene Transfers
Authors: Andersson Jan O. , Roger Andrew J. 
Published: December 2002

ABSTRACT

Lateral gene transfer has been identified as an important mode of genome evolution within prokaryotes. Except for the special case of gene transfer from organelle genomes to the eukaryotic nucleus, only a few cases of lateral gene transfer involving eukaryotes have been described. Here we present phylogenetic and gene order analyses on the small subunit of glutamate synthase (encoded by
gltD
) and its homologues, including the large subunit of sulfide dehydrogenase (encoded by
sudA
). The scattered distribution of the
sudA
and
sudB
gene pair and the phylogenetic analysis strongly suggest that lateral gene transfer was involved in the propagation of the genes in the three domains of life. One of these transfers most likely occurred between a prokaryote and an ancestor of diplomonad protists. Furthermore, phylogenetic analyses indicate that the gene for the small subunit of glutamate synthase was transferred from a low-GC gram-positive bacterium to a common ancestor of animals, fungi, and plants. Interestingly, in both examples, the eukaryotes encode a single gene that corresponds to a conserved operon structure in prokaryotes. Our analyses, together with several recent publications, show that lateral gene transfers from prokaryotes to unicellular eukaryotes occur with appreciable frequency. In the case of the genes for sulfide dehydrogenase, the transfer affected only a limited group of eukaryotes—the diplomonads—while the transfer of the glutamate synthase gene probably happened earlier in evolution and affected a wider range of eukaryotes.
Molecular Characterization of a Cystathionine Beta-Synthase Gene,
CBS1
, in
Magnaporthe
grisea
Authors: Lo Sze Chung Clive , Hamer Lisbeth , Hamer John E. 
Published: December 2002

ABSTRACT

CBS1
from
Magnaporthe
grisea
is a structural and functional homolog of the cystathionine β-synthase (CBS) gene from
Saccharomyces
cerevisiae
. Our studies indicated that
M
.
grisea
can utilize homocysteine and methionine through a CBS-independent pathway. The results also revealed responses of
M
.
grisea
to homocysteine that are reminiscent of human homocystinuria.
Toxoplasma gondii
Cyclic GMP-Dependent Kinase: Chemotherapeutic Targeting of an Essential Parasite Protein Kinase
Authors: Donald Robert G. K. , Allocco John , Singh Suresh B. , Nare Bakela , Salowe Scott P. , Wiltsie Judyann , Liberator Paul A. 
Published: December 2002

ABSTRACT

The trisubstituted pyrrole 4-[2-(4-fluorophenyl)-5-(1-methylpiperidine-4-yl)-1H-pyrrol-3-yl]pyridine (compound 1) has in vivo activity against the apicomplexan parasites
Toxoplasma gondii
and
Eimeria tenella
in animal models. The presumptive molecular target of this compound in
E. tenella
is cyclic GMP-dependent protein kinase (PKG). Native PKG purified from
T. gondii
has kinetic and pharmacologic properties similar to those of the
E. tenella
homologue, and both have been functionally expressed as recombinant proteins in
T. gondii
. Computer modeling of parasite PKG was used to predict catalytic site amino acid residues that interact with compound 1. The recombinant laboratory-generated mutants
T. gondii
PKG T761Q or T761M and the analogous
E. tenella
T770 alleles have reduced binding affinity for, and are not inhibited by, compound 1. By all other criteria, PKG with this class of catalytic site substitution is indistinguishable from wild-type enzyme. A genetic disruption of
T. gondii
PKG can only be achieved if a complementing copy of PKG is provided in
trans
, arguing that PKG is an essential protein. Strains of
T. gondii
, disrupted at the genomic PKG locus and dependent upon the
T. gondii
T761-substituted PKGs, are as virulent as wild type in mice. However, unlike mice infected with wild-type
T. gondii
that are cured by compound 1, mice infected with the laboratory-generated strains of
T. gondii
do not respond to treatment. We conclude that PKG represents the primary molecular target responsible for the antiparasitic efficacy of compound 1.