bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Arabidopsis Small G Protein ROP2 Is Activated by Light in Guard Cells and Inhibits Light-Induced Stomatal Opening
Authors: Jeon Byeong Wook , Hwang Jae-Ung , Hwang Youngkyu , Song Won-Yong , Fu Ying , Gu Ying , Bao Fang , Cho Daeshik , Kwak June M. , Yang Zhenbiao , Lee Youngsook 
Published: January 2008

Abstract
ROP small G proteins function as molecular switches in diverse signaling processes. Here, we investigated signals that activate ROP2 in guard cells. In guard cells of Vicia faba expressing Arabidopsis thaliana constitutively active (CA) ROP2 fused to red fluorescent protein (RFP-CA-ROP2), fluorescence localized exclusively at the plasma membrane, whereas a dominant negative version of RFP-ROP2 (DN-ROP2) localized in the cytoplasm. In guard cells expressing green fluorescent protein–ROP2, the relative fluorescence intensity at the plasma membrane increased upon illumination, suggesting that light activates ROP2. Unlike previously reported light-activated factors, light-activated ROP2 inhibits rather than accelerates light-induced stomatal opening; stomata bordered by guard cells transformed with CA-rop2 opened less than controls upon light irradiation. When introduced into guard cells together with CA-ROP2, At RhoGDI1, which encodes a guanine nucleotide dissociation inhibitor, inhibited plasma membrane localization of CA-ROP2 and abolished the inhibitory effect of CA-ROP2 on light-induced stomatal opening, supporting the negative effect of active ROP2 on stomatal opening. Mutant rop2 Arabidopsis guard cells showed phenotypes similar to those of transformed V. faba guard cells; CA-rop2 stomata opened more slowly and to a lesser extent, and DN-rop2 stomata opened faster than wild-type stomata in response to light. Moreover, in rop2 knockout plants, stomata opened faster and to a greater extent than wild-type stomata in response to light. Thus, ROP2 is a light-activated negative factor that attenuates the extent of light-induced changes in stomatal aperture. The inhibition of light-induced stomatal opening by light-activated ROP2 suggests the existence of feedback regulatory mechanisms through which stomatal apertures may be finely controlled.
Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution
Authors: Salse Jérôme , Bolot Stéphanie , Throude Michaël , Jouffe Vincent , Piegu Benoît , Quraishi Umar Masood , Calcagno Thomas , Cooke Richard , Delseny Michel , Feuillet Catherine 
Published: January 2008

AbstractThe grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.
A Genomic Map of Viroid RNA Motifs Critical for Replication and Systemic Trafficking
Authors: Zhong Xuehua , Archual Anthony J. , Amin Amy A. , Ding Biao 
Published: January 2008

AbstractRNA replication and systemic trafficking play significant roles in developmental regulation and host–pathogen interactions. Viroids are the simplest noncoding eukaryotic RNA pathogens and genetic units that are capable of autonomous replication and systemic trafficking and offer excellent models to investigate the role of RNA structures in these processes. Like other RNAs, the predicted secondary structure of a viroid RNA contains many loops and bulges flanked by double-stranded helices, the biological functions of which are mostly unknown. Using Potato spindle tuber viroid infection of Nicotiana benthamiana as the experimental system, we tested the hypothesis that these loops/bulges are functional motifs that regulate replication in single cells or trafficking in a plant. Through a genome-wide mutational analysis, we identified multiple loops/bulges essential or important for each of these biological processes. Our results led to a genomic map of viroid RNA motifs that mediate single-cell replication and systemic trafficking, respectively. This map provides a framework to enable high-throughput studies on the tertiary structures and functional mechanisms of RNA motifs that regulate viroid replication and trafficking. Our model and approach should also be valuable for comprehensive investigations of the replication and trafficking motifs in other RNAs.
Requirement for the Budding Yeast Polo Kinase Cdc5 in Proper Microtubule Growth and Dynamics
Authors: Park Chong J. , Park Jung-Eun , Karpova Tatiana S. , Soung Nak-Kyun , Yu Li-Rong , Song Sukgil , Lee Kyung H. , Xia Xue , Kang Eugene , Dabanoglu Ilknur , Oh Doo-Yi , Zhang James Y. , Kang Young Hwi , Wincovitch Stephen , Huffaker Tim C. , Veenstra Timothy D. , McNally James G. , Lee Kyung S. 
Published: January 2008

ABSTRACT

In many organisms, polo kinases appear to play multiple roles during M-phase progression. To provide new insights into the function of the budding yeast polo kinase Cdc5, we generated novel temperature-sensitive
cdc5
mutants by mutagenizing the C-terminal noncatalytic polo box domain, a region that is critical for proper subcellular localization. One of these mutants,
cdc5-11
, exhibited a temperature-sensitive growth defect with an abnormal spindle morphology. Strikingly, provision of a moderate level of benomyl, a microtubule-depolymerizing drug, permitted
cdc5-11
cells to grow significantly better than the isogenic
CDC5
wild type in a FEAR (cdc Fourteen Early Anaphase Release)-independent manner. In addition,
cdc5-11
required
MAD2
for both cell growth and the benomyl-remedial phenotype. These results suggest that
cdc5-11
is defective in proper spindle function. Consistent with this view,
cdc5-11
exhibited abnormal spindle morphology, shorter spindle length, and delayed microtubule regrowth at the nonpermissive temperature. Overexpression of
CDC5
moderately rescued the
spc98-2
growth defect. Interestingly, both Cdc28 and Cdc5 were required for the proper modification of the spindle pole body components Nud1, Slk19, and Stu2 in vivo. They also phosphorylated these three proteins in vitro. Taken together, these observations suggest that concerted action of Cdc28 and Cdc5 on Nud1, Slk19, and Stu2 is important for proper spindle functions.
Evolutionary Dynamics of Light-Independent Protochlorophyllide Oxidoreductase Genes in the Secondary Plastids of Cryptophyte Algae
Authors: Fong Anna , Archibald John M. 
Published: January 2008

ABSTRACT
Plastid genes encoding light-independent protochlorophyllide oxidoreductase (LIPOR) subunits were isolated from cryptophyte algae, the first example of such genes in plastids of secondary endosymbiotic origin. The presence of functional and nonfunctional copies of LIPOR genes in cryptophytes suggests that light-independent chlorophyll biosynthesis is a nonessential pathway in these organisms.
Gene Overexpression/Suppression Analysis of Candidate Virulence Factors of
Candida albicans
Authors: Fu Yue , Luo Guanpingsheng , Spellberg Brad J. , Edwards John E. , Ibrahim Ashraf S. 
Published: January 2008

ABSTRACT

We developed a conditional overexpression/suppression genetic strategy in
Candida albicans
to enable simultaneous testing of gain or loss of function in order to identify new virulence factors. The strategy involved insertion of a strong, tetracycline-regulated promoter in front of the gene of interest. To validate the strategy, a library of genes encoding glycosylphosphatidylinositol (GPI)-anchored surface proteins was screened for virulence phenotypes in vitro. During the screening, overexpression of
IFF4
was found to increase the adherence of
C. albicans
to plastic and to human epithelial cells, but not endothelial cells. Consistent with the in vitro results,
IFF4
overexpression modestly increased the tissue fungal burden during murine vaginal candidiasis. In addition to the in vitro screening tests,
IFF4
overexpression was found to increase
C. albicans
susceptibility to neutrophil-mediated killing. Furthermore,
IFF4
overexpression decreased the severity of hematogenously disseminated candidiasis in normal mice, but not in neutropenic mice, again consistent with the in vitro phenotype. Overexpression of 12 other GPI proteins did not affect normal GPI protein cell surface accumulation, demonstrating that the overexpression strategy did not affect the cell capacity for making such proteins. These data indicate that the same gene can increase or decrease candidal virulence in distinct models of infection, emphasizing the importance of studying virulence genes in different anatomical contexts. Finally, these data validate the use of a conditional overexpression/suppression genetic strategy to identify candidal virulence factors.
Toxoplasma gondii
and
Cryptosporidium parvum
Lack Detectable DNA Cytosine Methylation
Authors: Gissot Mathieu , Choi Sang-Woon , Thompson Reid F. , Greally John M. , Kim Kami 
Published: January 2008

ABSTRACT

Epigenetic factors play a role in the expression of virulence traits in Apicomplexa. Apicomplexan genomes encode putative DNA cytosine methylation enzymes. To assess the presence of cytosine methylation of
Toxoplasma gondii
and
Cryptosporidium parvum
DNA, we used mass spectrometry analysis and confirmed that these organisms lack detectable methylcytosine in their DNA.
The Min System as a General Cell Geometry Detection Mechanism: Branch Lengths in Y-ShapedEscherichia coliCells Affect Min Oscillation Patterns and Division Dynamics
Authors: Varma Archana , Huang Kerwyn Casey , Young Kevin D. 
Published: January 2008

ABSTRACTInEscherichia coli, division site placement is regulated by the dynamic behavior of the MinCDE proteins, which oscillate from pole to pole and confine septation to the centers of normal rod-shaped cells. Some current mathematical models explain these oscillations by considering interactions among the Min proteins without recourse to additional localization signals. So far, such models have been applied only to regularly shaped bacteria, but here we test these models further by employing aberrantly shapedE. colicells as miniature reactors. The locations of MinCDE proteins fused to derivatives of green fluorescent protein were monitored in branched cells with at least three conspicuous poles. MinCDE most often moved from one branch to another in an invariant order, following a nonreversing clockwise or counterclockwise direction over the time periods observed. In cells with two short branches or nubs, the proteins oscillated symmetrically from one end to the other. The locations of FtsZ rings were consistent with a broad MinC-free zone near the branch junctions, and Min rings exhibited the surprising behavior of moving quickly from one possible position to another. Using a reaction-diffusion model that reproduces the observed MinCD oscillations in rod-shaped and roundE. coli, we predict that the oscillation patterns in branched cells are a natural response of Min behavior in cellular geometries having different relative branch lengths. The results provide further evidence that Min protein oscillations act as a general cell geometry detection mechanism that can locate poles even in branched cells.
Protein Subassemblies of theHelicobacter pyloriCag Type IV Secretion System Revealed by Localization and Interaction Studies
Authors: Kutter Stefan , Buhrdorf Renate , Haas Jürgen , Schneider-Brachert Wulf , Haas Rainer , Fischer Wolfgang 
Published: January 2008

ABSTRACTType IV secretion systems are possibly the most versatile protein transport systems in gram-negative bacteria, with substrates ranging from small proteins to large nucleoprotein complexes. In many cases, such as thecagpathogenicity island ofHelicobacter pylori, genes encoding components of a type IV secretion system have been identified due to their sequence similarities to prototypical systems such as the VirB system ofAgrobacterium tumefaciens. The Cag type IV secretion system contains at least 14 essential apparatus components and several substrate translocation and auxiliary factors, but the functions of most components cannot be inferred from their sequences due to the lack of similarities. In this study, we have performed a comprehensive sequence analysis of all essential or auxiliary Cag components, and we have used antisera raised against a subset of components to determine their subcellular localization. The results suggest that the Cag system contains functional analogues to all VirB components except VirB5. Moreover, we have characterized mutual stabilization effects and performed a comprehensive yeast two-hybrid screening for potential protein-protein interactions. Immunoprecipitation studies resulted in identification of a secretion apparatus subassembly at the outer membrane. Combining these data, we provide a first low-resolution model of the Cag type IV secretion apparatus.
Functional Overlap but Lack of Complete Cross-Complementation of
Streptococcus mutans
and
Escherichia coli
YidC Orthologs
Authors: Dong Yuxia , Palmer Sara R. , Hasona Adnan , Nagamori Shushi , Kaback H. Ronald , Dalbey Ross E. , Brady L. Jeannine 
Published: January 2008

ABSTRACT

Oxa/YidC/Alb family proteins are chaperones involved in membrane protein insertion and assembly.
Streptococcus mutans
has two YidC paralogs. Elimination of
yidC2
, but not
yidC1
, results in stress sensitivity with decreased membrane-associated F
1
F
o
ATPase activity and an inability to initiate growth at low pH or high salt concentrations (A. Hasona, P. J. Crowley, C. M. Levesque, R. W. Mair, D. G. Cvitkovitch, A. S. Bleiweis, and L. J. Brady, Proc. Natl. Acad. Sci. USA 102:17466-17471, 2005). We now show that
Escherichia coli
YidC complements for acid tolerance, and partially for salt tolerance, in
S. mutans
lacking
yidC2
and that
S. mutans
YidC1 or YidC2 complements growth in liquid medium, restores the proton motive force, and functions to assemble the F
1
F
o
ATPase in a previously engineered
E. coli
YidC depletion strain (J. C. Samuelson, M. Chen, F. Jiang, I. Moller, M. Wiedmann, A. Kuhn, G. J. Phillips, and R. E. Dalbey, Nature 406:637-641, 2000). Both YidC1 and YidC2 also promote membrane insertion of known YidC substrates in
E. coli
; however, complete membrane integrity is not fully replicated, as evidenced by induction of phage shock protein A. While both function to rescue
E. coli
growth in broth, a different result is observed on agar plates: growth of the YidC depletion strain is largely restored by 247YidC2, a hybrid
S. mutans
YidC2 fused to the YidC targeting region, but not by a similar chimera, 247YidC1, nor by YidC1 or YidC2. Simultaneous expression of YidC1 and YidC2 improves complementation on plates. This study demonstrates functional redundancy between YidC orthologs in gram-negative and gram-positive organisms but also highlights differences in their activity depending on growth conditions and species background, suggesting that the complete functional spectrum of each is optimized for the specific bacteria and environment in which they reside.
Mutagenesis of the C1 Oxidation Pathway in
Methanosarcina barkeri
: New Insights into the Mtr/Mer Bypass Pathway
Authors: Welander Paula V. , Metcalf William W. 
Published: January 2008

ABSTRACT

A series of
Methanosarcina barkeri
mutants lacking the genes encoding the enzymes involved in the C1 oxidation/reduction pathway were constructed. Mutants lacking the methyl-tetrahydromethanopterin (H
4
MPT):coenzyme M (CoM) methyltransferase-encoding operon (Δ
mtr
), the methylene-H
4
MPT reductase-encoding gene (Δ
mer
), the methylene-H
4
MPT dehydrogenase-encoding gene (Δ
mtd
), and the formyl-methanofuran:H
4
MPT formyl-transferase-encoding gene (Δ
ftr
) all failed to grow using either methanol or H
2
/CO
2
as a growth substrate, indicating that there is an absolute requirement for the C1 oxidation/reduction pathway for hydrogenotrophic and methylotrophic methanogenesis. The mutants also failed to grow on acetate, and we suggest that this was due to an inability to generate the reducing equivalents needed for biosynthetic reactions. Despite their lack of growth on methanol, the Δ
mtr
and Δ
mer
mutants were capable of producing methane from this substrate, whereas the Δ
mtd
and Δ
ftr
mutants were not. Thus, there is an Mtr/Mer bypass pathway that allows oxidation of methanol to the level of methylene-H
4
MPT in
M. barkeri
. The data further suggested that formaldehyde may be an intermediate in this bypass; however, no methanol dehydrogenase activity was found in Δ
mtr
cell extracts, nor was there an obligate role for the formaldehyde-activating enzyme (Fae), which has been shown to catalyze the condensation of formaldehyde and H
4
MPT in vitro. Both the Δ
mer
and Δ
mtr
mutants were able to grow on a combination of methanol plus acetate, but they did so by metabolic pathways that are clearly distinct from each other and from previously characterized methanogenic pathways.
Functional Characterization of MigA and WapR: Putative Rhamnosyltransferases Involved in Outer Core Oligosaccharide Biosynthesis ofPseudomonas aeruginosa
Authors: Poon Karen K. H. , Westman Erin L. , Vinogradov Evgeny , Jin Shouguang , Lam Joseph S. 
Published: January 2008

ABSTRACTPseudomonas aeruginosalipopolysaccharide (LPS) contains two glycoforms of core oligosaccharide (OS); one form is capped with O antigen through an α-1,3-linkedl-rhamnose (l-Rha), while the other is uncapped and contains an α-1,6-linkedl-Rha. Two genes in strain PAO1,wapR(PA5000) andmigA(PA0705), encode putative glycosyltransferases associated with core biosynthesis. We propose that WapR and MigA are the rhamnosyltransferases responsible for the two linkages ofl-Rha to the core. Knockout mutants with mutations in both genes were generated. ThewapRmutant produced LPS lacking O antigen, and addition ofwapRintranscomplemented this defect. ThemigAmutant produced LPS with a truncated outer core and showed no reactivity to outer core-specific monoclonal antibody (MAb) 5C101. Complementation of this mutant withmigArestored reactivity of the LPS to MAb 5C101. Interestingly, LPS from the complementedmigAstrain was not reactive to MAb 18-19 (specific for the core-plus-one O repeat). This was due to overexpression of MigA in the complemented strain that caused an increase in the proportion of the uncapped core OS, thereby decreasing the amount of the core-plus-one O repeat, indicating that MigA has a regulatory role. The structures of LPS from both mutants were elucidated using nuclear magnetic resonance spectroscopy and mass spectrometry. The capped core of thewapRmutant was found to be truncated and lacked α-1,3-l-Rha. In contrast, uncapped core OS from themigAmutant lacked α-1,6-l-Rha. These results provide evidence that WapR is the α-1,3-rhamnosyltransferase, while MigA is the α-1,6-rhamnosyltransferase.
Conjugal Transfer of the
Salmonella enterica
Virulence Plasmid in the Mouse Intestine
Authors: García-Quintanilla Meritxell , Ramos-Morales Francisco , Casadesús Josep 
Published: January 2008

ABSTRACT

BALB/c mice were infected with two
Salmonella enterica
serovar Typhimurium strains, one of which lacked the virulence plasmid. Transconjugants were found at high frequencies in the mouse feces and at low frequencies in the liver and the spleen, suggesting that mating occurred in the gut. Laboratory conditions that mimic those of the small intestine (microaerophilic growth in the presence of 0.3 M NaCl) increased the frequency of virulence plasmid transfer. Sodium deoxycholate, which is found at high concentrations in the duodenum, and sodium propionate, which is abundant in the large intestine, reduced the conjugation frequency. Feces inhibited conjugation. Altogether, these observations suggested that transfer of the virulence plasmid occurred in the distal portion of the small intestine. Conjugation trials in ileal loops provided direct evidence that conjugal transfer of the
Salmonella
virulence plasmid occurs in the ileum in mice.
Identification of the Archaeal
alg7
Gene Homolog (Encoding
N
-Acetylglucosamine-1-Phosphate Transferase) of the N-Linked Glycosylation System by Cross-Domain Complementation in
Saccharomyces cerevisiae
Authors: Shams-Eldin Hosam , Chaban Bonnie , Niehus Sebastian , Schwarz Ralph T. , Jarrell Ken F. 
Published: January 2008

ABSTRACT

The Mv1751 gene product is thought to catalyze the first step in the N-glycosylation pathway in
Methanococcus voltae
. Here, we show that a conditional lethal mutation in the
alg7
gene (
N
-acetylglucosamine-1-phosphate transferase) in
Saccharomyces cerevisiae
was successfully complemented with Mv1751, highlighting a rare case of cross-domain complementation.
Phosphate Acquisition Components of the
Myxococcus xanthus
Pho Regulon Are Regulated by both Phosphate Availability and Development
Authors: Whitworth David E. , Holmes Antony B. , Irvine Alistair G. , Hodgson David A. , Scanlan David J. 
Published: January 2008

ABSTRACT

In many organisms, phosphatase expression and phosphate (P) uptake are coordinately regulated by the Pho regulon. In
Myxococcus xanthus
P limitation initiates multicellular development, a process associated with changes in phosphatase expression. We sought here to characterize the link between P acquisition and development in this bacterium, an organism capable of preying upon other microorganisms as a sole nutrient source.
M. xanthus
seems to possess no significant internal P stores, as reducing the P concentration to less than 10 μM retarded growth within one doubling time. Pyrophosphate, polyphosphate, and glyceraldehyde-3-phosphate could support growth as sole P sources, although many other P-containing biomolecules could not (including nucleic acids and phospholipids). Several Pho regulon promoters were found to be highly active during vegetative growth, and P limitation specifically induced
pstSCAB
, AcPA1, and
pho3
promoter activity and repressed
pit
expression. Enhanced
pstSCAB
and
pho3
promoter activities in a
phoP4
mutant (in the presence of high and low concentrations of P) suggested that PhoP4 acts as a repressor of these genes. However, in a
phoP4
background, the activities of
pstSCAB
remained P regulated, suggesting that there is additional regulation by a P-sensitive factor. Initiation of multicellular development caused immediate down-regulation of Pho regulon genes and caused
pstSCAB
and
pho3
promoter activities to become P insensitive. Hence, P acquisition components of the
M. xanthus
Pho regulon are regulated by both P availability and development, with developmental down-regulation overriding up-regulation by P limitation. These observations suggest that when development is initiated, subsequent changes in P availability become irrelevant to the population, which presumably has sufficient intrinsic P to ensure completion of the developmental program.