bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salt Stress-Induced Changes in the Transcriptome, Compatible Solutes, and Membrane Lipids in the Facultatively Phototrophic Bacterium Rhodobacter sphaeroides
Authors: Tsuzuki Minoru , Moskvin Oleg V. , Kuribayashi Masayuki , Sato Kiichi , Retamal Susana , Abo Mitsuru , Zeilstra-Ryalls Jill , Gomelsky Mark 
Published: September 2011

ABSTRACT

Responses to NaCl stress were investigated in phototrophically grown
Alphaproteobacterium Rhodobacter sphaeroides
by transcriptome profiling, mutational analysis, and measurements of compatible solutes and membrane phospholipids. After exposure to salt stress, genes encoding two putative glycine betaine uptake systems,
proVWX
and
betS
, were highly upregulated. Mutational analysis revealed that BetS, not ProVWX, was the primary transporter of this compatible solute. Upon the addition of salt, exogenous glycine betaine was taken up rapidly, and maximal intracellular levels were reached within minutes. In contrast, synthesis of another important compatible solute in
R. sphaeroides
, trehalose, increased slowly following salt stress, reaching maximal levels only after several hours. This accumulation pattern was consistent with the more gradual increase in salt-induced transcription of the trehalose biosynthesis operon
otsBA
. Several genes encoding putative transcription factors were highly induced by salt stress. Multiple copies of one of these factors,
crpO
(RSP1275), whose product is a member of the cyclic AMP receptor protein/fumarate and nitrate reduction regulator (CRP/FNR) family, improved NaCl tolerance. When
crpO
was provided in multicopy, expression of genes for synthesis or transport of compatible solutes was unaltered, but the membrane phospholipid composition became biased toward that found in salt-stressed cells. Collectively, this study characterized transcriptional responses to salt stress, correlated changes in transcription with compatible solute accumulation rates, identified the main glycine betaine transporter and trehalose synthase, characterized salt-induced changes in phospholipid composition, and uncovered a transcription factor associated with changes in phospholipids. These findings set the stage for deciphering the salt stress-responsive regulatory network in
R. sphaeroides
.
Formation of Polyhydroxyalkanoate in Aerobic Anoxygenic Phototrophic Bacteria and Its Relationship to Carbon Source and Light Availability
Authors: Xiao Na , Jiao Nianzhi 
Published: September 2011

ABSTRACT

Aerobic anoxygenic phototrophic bacteria (AAPB) are unique players in carbon cycling in the ocean. Cellular carbon storage is an important mechanism regulating the nutrition status of AAPB but is not yet well understood. In this paper, six AAPB species (
Dinoroseobacter
sp. JL1447,
Roseobacter denitrificans
OCh 114,
Roseobacter litoralis
OCh 149,
Dinoroseobacter shibae
DFL 12
T
,
Labrenzia alexandrii
DFL 11
T
, and
Erythrobacter longus
DSMZ 6997) were examined, and all of them demonstrated the ability to form the carbon polymer polyhydroxyalkanoate (PHA) in the cell. The PHA in
Dinoroseobacter
sp. JL1447 was identified as poly-beta-hydroxybutyrate (PHB) according to evidence from Fourier transform infrared spectroscopy, differential scanning calorimetry, and
1
H nuclear magnetic resonance spectroscopy examinations. Carbon sources turned out to be critical for PHA production in AAPB. Among the eight media tested with
Dinoroseobacter
sp. JL1447, sodium acetate, giving a PHA production rate of 72%, was the most productive carbon source, followed by glucose, with a 68% PHA production rate. Such PHA production rates are among the highest recorded for all bacteria. The C/N ratio of substrates was verified by the experiments as another key factor in PHA production. In the case of
R. denitrificans
OCh 114, PHA was not detected when the organism was cultured at C/N ratios of <2 but became apparent at C/N ratios of >3. Light is also important for the formation of PHA in AAPB. In the case of
Dinoroseobacter
sp. JL1447, up to a one-quarter increase in PHB production was observed when the culture underwent growth in a light-dark cycle compared to growth completely in the dark.
Partial Genome Assembly for a Candidate Division OP11 Single Cell from an Anoxic Spring (Zodletone Spring, Oklahoma)
Authors: Youssef Noha H. , Blainey Paul C. , Quake Stephen R. , Elshahed Mostafa S. 
Published: September 2011

ABSTRACT
Members of candidate division OP11 are widely distributed in terrestrial and marine ecosystems, yet little information regarding their metabolic capabilities and ecological role within such habitats is currently available. Here, we report on the microfluidic isolation, multiple-displacement-amplification, pyrosequencing, and genomic analysis of a single cell (ZG1) belonging to candidate division OP11. Genome analysis of the ∼270-kb partial genome assembly obtained showed that it had no particular similarity to a specific phylum. Four hundred twenty-three open reading frames were identified, 46% of which had no function prediction. In-depth analysis revealed a heterotrophic lifestyle, with genes encoding endoglucanase, amylopullulanase, and laccase enzymes, suggesting a capacity for utilization of cellulose, starch, and, potentially, lignin, respectively. Genes encoding several glycolysis enzymes as well as formate utilization were identified, but no evidence for an electron transport chain was found. The presence of genes encoding various components of lipopolysaccharide biosynthesis indicates a Gram-negative bacterial cell wall. The partial genome also provides evidence for antibiotic resistance (β-lactamase, aminoglycoside phosphotransferase), as well as antibiotic production (bacteriocin) and extracellular bactericidal peptidases. Multiple mechanisms for stress response were identified, as were elements of type I and type IV secretion systems. Finally, housekeeping genes identified within the partial genome were used to demonstrate the OP11 affiliation of multiple hitherto unclassified genomic fragments from multiple database-deposited metagenomic data sets. These results provide the first glimpse into the lifestyle of a member of a ubiquitous, yet poorly understood bacterial candidate division.
Vacuolar Protein Sorting Genes Regulate Mat Formation in Saccharomyces cerevisiae by Flo11p-Dependent and -Independent Mechanisms
Authors: Sarode Neha , Miracle Bethany , Peng Xin , Ryan Owen , Reynolds Todd B. 
Published: September 2011

ABSTRACT

Saccharomyces cerevisiae
generates complex biofilms called mats on low-density (0.3%) agar plates. The mats can be morphologically divided into two regions: (i) hub, the interior region characterized by the presence of wrinkles and channels, and (ii) rim, the smooth periphery. Formation of mats depends on the adhesin Flo11p, which is also required for invasive growth, a phenotype in which the
S. cerevisiae
yeasts grow as chains of cells that dig into standard-density (2%) agar plates. Although both invasive growth and mat formation depend on Flo11p, mutations that perturb the multivesicular body (MVB) protein sorting pathway inhibit mat formation in a
FLO11
-independent manner. These mutants, represented by
vps27
Δ, disrupt mat formation but do not affect invasive growth,
FLO11
gene or protein expression, or Flo11p localization. In contrast, an overlapping subset of MVB mutants (represented by ESCRT [endosomal sorting complex required for transport] complex genes such as
VPS25
) interrupt the Rim101p signal transduction cascade, which is required for
FLO11
expression, and thus block both invasive growth and mat formation. In addition, this report shows that mature Flo11p is covalently associated with the cell wall and shed into the extracellular matrix of the growing mat.
A GCN2-Like Eukaryotic Initiation Factor 2 Kinase Increases the Viability of Extracellular Toxoplasma gondii Parasites
Authors: Konrad Christian , Wek Ronald C. , Sullivan William J. 
Published: September 2011

ABSTRACT

Toxoplasmosis is a significant opportunistic infection caused by the protozoan parasite
Toxoplasma gondii
, an obligate intracellular pathogen that relies on host cell nutrients for parasite proliferation.
Toxoplasma
parasites divide until they rupture the host cell, at which point the extracellular parasites must survive until they find a new host cell. Recent studies have indicated that phosphorylation of
Toxoplasma
eukaryotic translation initiation factor 2-alpha (TgIF2α) plays a key role in promoting parasite viability during times of extracellular stress. Here we report the cloning and characterization of a TgIF2α kinase designated TgIF2K-D that is related to GCN2, a eukaryotic initiation factor 2α (eIF2α) kinase known to respond to nutrient starvation in other organisms. TgIF2K-D is present in the cytosol of both intra- and extracellular
Toxoplasma
parasites and facilitates translational control through TgIF2α phosphorylation in extracellular parasites. We generated a
TgIF2K-D
knockout parasite and demonstrated that loss of this eIF2α kinase leads to a significant fitness defect that stems from an inability of the parasite to adequately adapt to the environment outside host cells. This phenotype is consistent with that reported for our nonphosphorylatable TgIF2α mutant (S71A substitution), establishing that TgIF2K-D is the primary eIF2α kinase responsible for promoting extracellular viability of
Toxoplasma
. These studies suggest that eIF2α phosphorylation and translational control are an important mechanism by which vulnerable extracellular parasites protect themselves while searching for a new host cell. Additionally, TgIF2α is phosphorylated when intracellular parasites are deprived of nutrients, but this can occur independently of TgIF2K-D, indicating that this activity can be mediated by a different TgIF2K.
Sex Determination in the First-Described Sexual Fungus
Authors: Idnurm Alexander 
Published: September 2011

ABSTRACT

The original report of sex in fungi dates 2 centuries ago to the species
Syzygites megalocarpus
(Mucoromycotina). The organism was subsequently used in 1904 to represent self-fertile homothallic species when the concepts of heterothallism and homothallism were developed for the fungal kingdom. In this study, two putative
sex
/
MAT
loci were identified in individual strains of
S. megalocarpus
, accounting for its homothallic behavior. The strains encode both of the high-mobility-group domain-containing proteins, SexM and SexP, flanked by RNA helicase and glutathione oxidoreductase genes that are found adjacent to the mating-type loci in other Mucoromycotina species. The presence of pseudogenes and the arrangement of genes suggest that the origin of homothallism in this species is from a heterothallic relative, obtained via a chromosomal rearrangement to switch two alleles into two separated loci within a single genetic background. Similar events have given rise to homothallic species from heterothallic species in ascomycete fungi, demonstrating that conserved forces shape the evolution of sex determination and speciation in highly diverged fungi.
Diversity in Requirement of Genetic and Epigenetic Factors for Centromere Function in Fungi
Authors: Roy Babhrubahan , Sanyal Kaustuv 
Published: September 2011

ABSTRACT

A centromere is a chromosomal region on which several proteins assemble to form the kinetochore. The centromere-kinetochore complex helps in the attachment of chromosomes to spindle microtubules to mediate segregation of chromosomes to daughter cells during mitosis and meiosis. In several budding yeast species, the centromere forms in a DNA sequence-dependent manner, whereas in most other fungi, factors other than the DNA sequence also determine the centromere location, as centromeres were able to form on nonnative sequences (neocentromeres) when native centromeres were deleted in engineered strains. Thus, in the absence of a common DNA sequence, the cues that have facilitated centromere formation on a specific DNA sequence for millions of years remain a mystery. Kinetochore formation is facilitated by binding of a centromere-specific histone protein member of the centromeric protein A (CENP-A) family that replaces a canonical histone H3 to form a specialized centromeric chromatin structure. However, the process of kinetochore formation on the rapidly evolving and seemingly diverse centromere DNAs in different fungal species is largely unknown. More interestingly, studies in various yeasts suggest that the factors required for
de novo
centromere formation (establishment) may be different from those required for maintenance (propagation) of an already established centromere. Apart from the DNA sequence and CENP-A, many other factors, such as posttranslational modification (PTM) of histones at centric and pericentric chromatin, RNA interference, and DNA methylation, are also involved in centromere formation, albeit in a species-specific manner. In this review, we discuss how several genetic and epigenetic factors influence the evolution of structure and function of centromeres in fungal species.
Sampangine Inhibits Heme Biosynthesis in both Yeast and Human
Authors: Huang Zhiwei , Chen Kaifu , Xu Tao , Zhang Jianhuai , Li Yongxiang , Li Wei , Agarwal Ameeta K. , Clark Alice M. , Phillips John D. , Pan Xuewen 
Published: September 2011

ABSTRACT

The azaoxoaporphine alkaloid sampangine exhibits strong antiproliferation activity in various organisms. Previous studies suggested that it somehow affects heme metabolism and stimulates production of reactive oxygen species (ROS). In this study, we show that inhibition of heme biosynthesis is the primary mechanism of action by sampangine and that increases in the levels of reactive oxygen species are secondary to heme deficiency. We directly demonstrate that sampangine inhibits heme synthesis in the yeast
Saccharomyces cerevisiae
. It also causes accumulation of uroporphyrinogen and its decarboxylated derivatives, intermediate products of the heme biosynthesis pathway. Our results also suggest that sampangine likely works through an unusual mechanism—by hyperactivating uroporhyrinogen III synthase—to inhibit heme biosynthesis. We also show that the inhibitory effect of sampangine on heme synthesis is conserved in human cells. This study also reveals a surprising essential role for the interaction between the mitochondrial ATP synthase and the electron transport chain.
An Erythrocyte Cytoskeleton-Binding Motif in Exported Plasmodium falciparum Proteins
Authors: Kilili Geoffrey K. , LaCount Douglas J. 
Published: September 2011

ABSTRACT

Binding of exported malaria parasite proteins to the host cell membrane and cytoskeleton contributes to the morphological, functional, and antigenic changes seen in
Plasmodium falciparum
-infected erythrocytes. One such exported protein that targets the erythrocyte cytoskeleton is the mature parasite-infected erythrocyte surface antigen (MESA), which interacts with the N-terminal 30-kDa domain of protein 4.1R via a 19-residue sequence. We report here that the MESA erythrocyte cytoskeleton-binding (MEC) domain is present in at least 13 other
P. falciparum
proteins predicted to be exported to the host cell. An alignment of the putative cytoskeleton-binding sequences revealed a conserved aspartic acid at the C terminus that was omitted from the originally reported binding domain. Mutagenesis experiments demonstrated that this aspartic acid was required for the optimal binding of MESA to inside-out vesicles (IOVs) prepared from erythrocytes. Using pulldown assays, we characterized the binding of fragments encoding the MEC domains from PFE0040c/MESA and six other proteins (PF10_0378, PFA0675w, PFB0925w, PFD0095c, PFF1510w, and PFI1790w) to IOVs. All seven proteins bound to IOVs, with MESA showing the strongest affinity in saturation binding experiments. We further examined the interaction of the MEC domain proteins with components of the erythrocyte cytoskeleton and showed that MESA, PF10_0378, and PFA0675w coprecipitated full-length 4.1R from lysates prepared from IOVs. These data demonstrated that the MEC motif is present and functional in at least six other
P. falciparum
proteins that are exported to the host cell cytoplasm.
Regulation of
perR
Expression by Iron and PerR in Campylobacter jejuni
Authors: Kim Minkyeong , Hwang Sunyoung , Ryu Sangryeol , Jeon Byeonghwa 
Published: September 2011

ABSTRACT

Campylobacter jejuni
is a leading food-borne pathogen causing gastroenteritis in humans. Although OxyR is a widespread oxidative stress regulator in many Gram-negative bacteria,
C. jejuni
lacks OxyR and instead possesses the metalloregulator PerR. Despite the important role played by PerR in oxidative stress defense, little is known about the factors influencing
perR
expression in
C. jejuni
. In this study, a
perR
promoter-
lacZ
fusion assay demonstrated that iron significantly reduced the level of
perR
transcription, whereas other metal ions, such as copper, cobalt, manganese, and zinc, did not affect
perR
transcription. Notably, a
perR
mutation substantially increased the level of
perR
transcription and in
trans
complementation restored the transcriptional changes, suggesting
perR
is transcriptionally autoregulated in
C. jejuni
. In the
perR
mutant, iron did not repress
perR
transcription, indicating the iron dependence of
perR
expression results from
perR
autoregulation. Electrophoretic mobility shift assays showed that PerR binds to the
perR
promoter, and DNase I footprinting assays identified a PerR binding site overlapping the −35 region of the two
perR
promoters, further supporting
perR
autoregulation at the transcriptional level. Alignment of the PerR binding sequence in the
perR
promoter with the regulatory region of other PerR regulon genes of
C. jejuni
revealed a 16-bp consensus PerR binding sequence, which shares high similarities to the
Bacillus subtilis
PerR box. The results of this study demonstrated that PerR directly interacts with the
perR
promoter and regulates
perR
transcription and that
perR
autoregulation is responsible for the repression of
perR
transcription by iron in
C. jejuni
.
Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems
Authors: Makarova Kira S. , Wolf Yuri I. , Snir Sagi , Koonin Eugene V. 
Published: September 2011

ABSTRACT
The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic “sinks” that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxins-antitoxins and an important role of horizontal mobility in the evolution of these islands.
Recognition of β-Strand Motifs by RseB Is Required for σ
E
Activity in Escherichia coli
Authors: Kulp Adam , Kuehn Meta J. 
Published: September 2011

ABSTRACT

Gram-negative bacteria react to misfolded proteins in the envelope through a myriad of different stress response pathways. This cohort of pathways allows the bacteria to specifically respond to different types of damage, and many of these have been discovered to have key roles in the virulence of bacterial pathogens. Misfolded outer membrane proteins (OMPs) are typically recognized by the σ
E
pathway, a highly conserved envelope stress response pathway. We examined the features of misfolded OMPs with respect to their ability to generate envelope stress responses. We determined that the secondary structure, particularly the potential to form β strands, is critical to inducing the σ
E
response in an RseB-dependent manner. The sequence of the potential β-strand motif modulates the strength of the σ
E
response generated by the constructs. By understanding the details of how such stress response pathways are activated, we can gain a greater understanding of how bacteria survive in harsh environments.
Determination of Borrelia Surface Lipoprotein Anchor Topology by Surface Proteolysis
Authors: Chen Shiyong , Kumru Ozan S. , Zückert Wolfram R. 
Published: September 2011

ABSTRACT

We used a surface trypsinolysis assay to probe accessibility of the membrane-proximal N-terminal tether peptides of
Borrelia
surface lipoproteins OspA and Vsp1. Our findings with both wild-type and mutant proteins are only compatible with the anchoring of these surface lipoproteins in the outer leaflet of the outer spirochetal membrane.
An Atypical Phr Peptide Regulates the Developmental Switch Protein RapH
Authors: Mirouze Nicolas , Parashar Vijay , Baker Melinda D. , Dubnau David A. , Neiditch Matthew B. 
Published: September 2011

ABSTRACT

Under conditions of nutrient limitation and high population density, the bacterium
Bacillus subtilis
can initiate a variety of developmental pathways. The signaling systems regulating
B. subtilis
differentiation are tightly controlled by switch proteins called Raps, named after the founding members of the family, which were shown to be
r
esponse regulator
a
spartate
p
hosphatases. A
phr
gene encoding a secreted pentapeptide that regulates the activity of its associated Rap protein was previously identified downstream of 8 of the chromosomally encoded
rap
genes. We identify and validate here the sequence of an atypical Phr peptide, PhrH, by
in vivo
and
in vitro
analyses. Using a luciferase reporter bioassay combined with
in vitro
experiments, we found that PhrH is a hexapeptide (TDRNTT), in contrast to the other characterized Phr pentapeptides. We also determined that
phrH
expression is driven by a promoter lying within
rapH
. Unlike the previously identified dedicated σ
H
-driven
phr
promoters, it appears that
phrH
expression most likely requires σ
A
. Furthermore, we show that PhrH can antagonize both of the known activities of RapH: the dephosphorylation of Spo0F and the sequestration of ComA, thus promoting the development of spores and the competent state. Finally, we propose that PhrH is the prototype of a newly identified class of Phr signaling molecules consisting of six amino acids. This class likely includes PhrI, which regulates RapI and the expression, excision, and transfer of the mobile genetic element ICE
Bs
1.