bluuebunny/crossref_metadata_2025_split huggingface dataset:
Special Sm Core Complex Functions in Assembly of the U2 Small Nuclear Ribonucleoprotein of
Trypanosoma brucei
Authors: Preußer Christian , Palfi Zsofia , Bindereif Albrecht 
Published: June 2009

ABSTRACT

The processing of polycistronic pre-mRNAs in trypanosomes requires the spliceosomal small ribonucleoprotein complexes (snRNPs) U1, U2, U4/U6, U5, and SL, each of which contains a core of seven Sm proteins. Recently we reported the first evidence for a core variation in spliceosomal snRNPs; specifically, in the trypanosome U2 snRNP, two of the canonical Sm proteins, SmB and SmD3, are replaced by two U2-specific Sm proteins, Sm15K and Sm16.5K. Here we identify the U2-specific, nuclear-localized U2B″ protein from
Trypanosoma brucei
. U2B″ interacts with a second U2 snRNP protein, U2-40K (U2A′), which in turn contacts the U2-specific Sm16.5K/15K subcomplex. Together they form a high-affinity, U2-specific binding complex. This trypanosome-specific assembly differs from the mammalian system and provides a functional role for the Sm core variation found in the trypanosomal U2 snRNP.
Adaptations in the Glucose Metabolism of Procyclic
Trypanosoma brucei
Isolates from Tsetse Flies and during Differentiation of Bloodstream Forms
Authors: van Grinsven Koen W. A. , Van Den Abbeele Jan , Van den Bossche Peter , van Hellemond Jaap J. , Tielens Aloysius G. M. 
Published: June 2009

ABSTRACT

Procyclic forms of
Trypanosoma brucei
isolated from the midguts of infected tsetse flies, or freshly transformed from a strain that is close to field isolates, do not use a complete Krebs cycle. Furthermore, short stumpy bloodstream forms produce acetate and are apparently metabolically preadapted to adequate functioning in the tsetse fly.
β-Glucanase Eng2 Is Required for Ascus Wall Endolysis after Sporulation in the Fission Yeast
Schizosaccharomyces pombe
Authors: Encinar del Dedo Javier , Dueñas Encarnación , Arnáiz Yolanda , del Rey Francisco , Vázquez de Aldana Carlos R. 
Published: June 2009

ABSTRACT

Meiosis is the developmental program by which sexually reproducing diploid organisms generate haploid gametes. In yeast, meiosis is followed by spore morphogenesis. When
Schizosaccharomyces pombe
diploid cells undergo meiosis, they differentiate into asci containing four haploid ascospores that are highly resistant to environmental stress. The formation of the ascospore wall requires the activity of several enzymes involved in the biosynthesis and modification of its components, such as α- and β-glucan synthases. Once the spores are completely mature, the wall of the ascus undergoes an endolytic process that results in the release of ascospores from the ascus, allowing their dispersal into the environment. This process requires the activity of the endo-α-1,3-glucanase Agn2. Here, we focus on the characterization of the endo-β-1,3-glucanase Eng2, which is also required for ascospore release from the ascus. Although Eng2 is present during the mitotic cycle, the protein accumulates after meiosis II. The expression of
eng2
+
is required for the efficient release of ascospores, as shown by placing
eng2
+
under the control of a repressible promoter. Furthermore, a point mutation that destroys the catalytic activity of the protein results in a phenotype similar to that of the mutant strain. Finally, we demonstrate that exogenous addition of purified Eng2 releases the ascospores from asci generated by an
eng2
Δ mutant. We propose that Eng2 would act together with Agn2 to completely hydrolyze the ascus wall, thereby assisting in the release of ascospores in
S. pombe
.
Isolation and Characterization ofXenorhabdus nematophilaTransposon Insertion Mutants Defective in Lipase Activity against Tween
Authors: Richards Gregory R. , Vivas Eugenio I. , Andersen Aaron W. , Rivera-Santos Delmarie , Gilmore Sara , Suen Garret , Goodrich-Blair Heidi 
Published: June 2009

ABSTRACTWe identifiedXenorhabdus nematophilatransposon mutants with defects in lipase activity. One of the mutations, inyigL, a conserved gene of unknown function, resulted in attenuated virulence againstManduca sextainsects. We discuss possible connections between lipase production, YigL, and specific metabolic pathways.
Phylogenetic Ubiquity and Shuffling of the Bacterial RecBCD and AddAB Recombination Complexes
Authors: Cromie Gareth A. 
Published: June 2009

ABSTRACT

RecBCD and AddAB are bacterial enzymes that share similar helicase and nuclease activities and initiate repair of DNA double-strand breaks by homologous recombination. Examination of the phylogenetic distribution of AddAB and RecBCD revealed that one or the other complex is present in most sequenced bacteria. In addition, horizontal gene transfer (HGT) events involving
addAB
and
recBCD
appear to be common, with the genes encoding one complex frequently replacing those encoding the other. HGT may also explain the unexpected identification of archaeal
addAB
genes. More than 85% of
addAB
and
recBCD
genes are clustered on the genome, suggesting operon structures. A few organisms, including the
Mycobacteria
, encode multiple copies of these complexes of either the same or mixed classes. The possibility that the enzymatic activities of the AddAB and RecBCD enzymes promote their horizontal transfer is discussed, and the distribution of AddAB/RecBCD is compared to that of the RecU/RuvC resolvases. Finally, it appears that two sequence motifs, the Walker A box involved in ATP binding and an iron-sulfur-cysteine cluster, are present only in subsets of AddB proteins, suggesting the existence of mechanistically distinct classes of AddB.
Optical Mapping Reveals a Large Genetic Inversion between Two Methicillin-Resistant
Staphylococcus aureus
Strains
Authors: Shukla Sanjay K. , Kislow Jennifer , Briska Adam , Henkhaus John , Dykes Colin 
Published: June 2009

ABSTRACT

Staphylococcus aureus
is a highly versatile and evolving bacterium of great clinical importance.
S. aureus
can evolve by acquiring single nucleotide polymorphisms and mobile genetic elements and by recombination events. Identification and location of novel genomic elements in a bacterial genome are not straightforward, unless the whole genome is sequenced. Optical mapping is a new tool that creates a high-resolution, in situ ordered restriction map of a bacterial genome. These maps can be used to determine genomic organization and perform comparative genomics to identify genomic rearrangements, such as insertions, deletions, duplications, and inversions, compared to an in silico (virtual) restriction map of a known genome sequence. Using this technology, we report here the identification, approximate location, and characterization of a genetic inversion of ∼500 kb of a DNA element between the NRS387 (USA800) and FPR3757 (USA300) strains. The presence of the inversion and location of its junction sites were confirmed by site-specific PCR and sequencing. At both the left and right junction sites in NRS387, an IS
1181
element and a 73-bp sequence were identified as inverted repeats, which could explain the possible mechanism of the inversion event.
CtrA, a Global Response Regulator, Uses a Distinct Second Category of Weak DNA Binding Sites for Cell Cycle Transcription Control in
Caulobacter crescentus
Authors: Spencer William , Siam Rania , Ouimet Marie-Claude , Bastedo D. Patrick , Marczynski Gregory T. 
Published: June 2009

ABSTRACT

CtrA controls cell cycle programs of chromosome replication and genetic transcription. Phosphorylated CtrA∼P exhibits high affinity (dissociation constant [

K
d

], <10 nM) for consensus TTAA-N7-TTAA binding sites with “typical” (N = 7) spacing. We show here that
ctrA
promoters P1 and P2 use low-affinity (

K
d

, >500 nM) CtrA binding sites with “atypical” (N ≠ 7) spacing. Footprints demonstrated that phosphorylated CtrA∼P does not exhibit increased affinity for “atypical” sites, as it does for sites in the replication origin. Instead, high levels of CtrA (>10 μM) accumulate, which can drive CtrA binding to “atypical” sites. In vivo cross-linking showed that when the stable CtrAΔ3 protein persists during the cell cycle, the “atypical” sites at
ctrA
and
motB
are persistently bound. Interestingly, the cell cycle timing of
ctrA
P1 and P2 transcription is not altered by persistent CtrAΔ3 binding. Therefore, operator DNA occupancy is not sufficient for regulation, and it is the cell cycle variation of CtrA∼P phosphorylation that provides the dominant “activation” signal. Protein dimerization is one potential means of “activation.” The glutathione
S
-transferase (GST) protein dimerizes, and fusion with CtrA (GST-CtrA) creates a stable dimer with enhanced affinity for TTAA motifs. Electrophoretic mobility shift assays with GST-CtrA revealed cooperative modes of binding that further distinguish the “atypical” sites. GST-CtrA also binds a single TTAA motif in
ctrA
P1 aided by DNA in the extended TTAACCAT motif. We discuss how “atypical” sites are a common yet distinct category of CtrA regulatory sites and new implications for the working and evolution of cell cycle control networks.
CsrRS Regulates Group BStreptococcusVirulence Gene Expression in Response to Environmental pH: a New Perspective on Vaccine Development
Authors: Santi Isabella , Grifantini Renata , Jiang Sheng-Mei , Brettoni Cecilia , Grandi Guido , Wessels Michael R. , Soriani Marco 
Published: June 2009

ABSTRACTTo identify factors involved in the response of group B streptococci (GBS) to environmental pH, we performed a comparative global gene expression analysis of GBS at acidic and neutral pHs. We found that the transcription of 317 genes was increased at pH 5.5 relative to that at pH 7.0, while 61 genes were downregulated. The global response to acid stress included the differential expression of genes involved in transport, metabolism, stress response, and virulence. Known vaccine candidates, such as BibA and pilus components, were also regulated by pH. We observed that many of the genes involved in the GBS response to pH are known to be controlled by the CsrRS two-component system. Comparison of the regulon of wild-type strain 2603 V/R with that of acsrRSdeletion mutant strain revealed that the pH-dependent regulation of 90% of the downregulated genes and 59.3% of the up-regulated genes in strain 2603 V/R was CsrRS dependent and that many virulence factors were overexpressed at high pH. Beta-hemolysin regulation was abrogated by selective inactivation ofcsrS, suggesting the implication of the CsrS protein in pH sensing. These results imply that the translocation of GBS from the acidic milieu of the vagina to the neutral pH of the neonatal lung signals the up-regulation of GBS virulence factors and conversion from a colonizing to an invasive phenotype. In addition, the fact that increased exposure of BibA on the bacterial surface at pH 7.0 induced opsonophagocytic killing of GBS in immune serum highlights the importance of pH regulation in the protective efficacy of specific antibodies to surface-exposed GBS proteins.
Polyamines Are Not Required for Aerobic Growth of
Escherichia coli
: Preparation of a Strain with Deletions in All of the Genes for Polyamine Biosynthesis
Authors: Chattopadhyay Manas K. , Tabor Celia White , Tabor Herbert 
Published: June 2009

ABSTRACT

A strain of
Escherichia coli
was constructed in which all of the genes involved in polyamine biosynthesis—
speA
(arginine decarboxylase),
speB
(agmatine ureohydrolase),
speC
(ornithine decarboxylase),
spe D
(adenosylmethionine decarboxylase),
speE
(spermidine synthase),
speF
(inducible ornithine decarboxylase),
cadA
(lysine decarboxylase), and
ldcC
(lysine decarboxylase)—had been deleted. Despite the complete absence of all of the polyamines, the strain grew indefinitely in air in amine-free medium, albeit at a slightly (ca. 40 to 50%) reduced growth rate. Even though this strain grew well in the absence of the amines in air, it was still sensitive to oxygen stress in the absence of added spermidine. In contrast to the ability to grow in air in the absence of polyamines, this strain, surprisingly, showed a requirement for polyamines for growth under strictly anaerobic conditions.
Enhancement of the Synthesis of RpoE and StpA by Polyamines at the Level of Translation in
Escherichia coli
under Heat Shock Conditions
Authors: Terui Yusuke , Higashi Kyohei , Tabei Yuzuru , Tomitori Hideyuki , Yamamoto Kaneyoshi , Ishihama Akira , Igarashi Kazuei , Kashiwagi Keiko 
Published: June 2009

ABSTRACT

Proteins whose synthesis is enhanced by polyamines at the level of translation were identified with a polyamine-requiring mutant cultured in the presence of 0.1% glucose and 0.02% glutamate at 42°C. Polyamines had a greater effect on cell growth at 42°C than at 37°C. At 42°C, the synthesis of RpoE (σ
24
) and StpA, which are involved in the transcription of a number of heat shock response genes, was stimulated by polyamines at the level of translation. In the
rpoE
and
stpA
mRNAs, a Shine-Dalgarno (SD) sequence is located at 13 and 12 nucleotides, respectively, upstream of the initiation codon AUG. When the SD sequences were moved to the more common position 7 nucleotides upstream of the initiation codon AUG, the degree of polyamine stimulation was reduced, although the level of RpoE and StpA synthesis was markedly increased. The mechanism underlying polyamine stimulation of RpoE synthesis was then studied. Polyamine stimulation of RpoE synthesis was reduced by changing the bulged-out structure in the initiation site of
rpoE
mRNA, although the level of RpoE synthesis increased. A selective structural change of this bulged-out region induced by spermidine at 42°C was observed by circular dichroism. Polyamine stimulation of fMet-tRNA binding to ribosomes at 42°C also disappeared by changing the bulged-out structure in the initiation site of
rpoE
mRNA. The results suggest that polyamines enhance the synthesis of RpoE by changing the bulged-out structure in the initiation site of
rpoE
mRNA.
Role of the σD-Dependent Autolysins inBacillus subtilisPopulation Heterogeneity
Authors: Chen Rui , Guttenplan Sarah B. , Blair Kris M. , Kearns Daniel B. 
Published: June 2009

ABSTRACTExponentially growing populations ofBacillus subtiliscontain two morphologically and functionally distinct cell types: motile individuals and nonmotile multicellular chains. Motility differentiation arises because RNA polymerase and the alternative sigma factor σDactivate expression of flagellin in a subpopulation of cells. Here we demonstrate that the peptidoglycan-remodeling autolysins under σDcontrol, LytC, LytD, and LytF, are expressed in the same subpopulation of cells that complete flagellar synthesis. Morphological heterogeneity is explained by the expression of LytF that is necessary and sufficient for cell separation. Moreover, LytC is required for motility but not at the level of cell separation or flagellum biosynthesis. Rather, LytC appears to be important for flagellar function, and motility was restored to aLytCmutant by mutation of eitherlonA, encoding the LonA protease, or a gene encoding a previously unannotated swarming motility inhibitor, SmiA. We conclude that heterogeneous activation of σD-dependent gene expression is sufficient to explain both the morphological heterogeneity and functional heterogeneity present in vegetativeB. subtilispopulations.
Site-Directed Mutagenesis Identifies a Molecular Switch Involved in Copper Sensing by the Histidine Kinase CinS in
Pseudomonas putida
KT2440
Authors: Quaranta Davide , McEvoy Megan M. , Rensing Christopher 
Published: June 2009

ABSTRACT

In the presence of copper,
Pseudomonas putida
activates transcription of
cinAQ
via the two-component system CinS-CinR. The CinS-CinR TCS was responsive to 0.5 μM copper and was specifically activated only by copper and silver. Modeling studies of CinS identified a potential copper binding site containing H37 and H147. CinS mutants with H37R and H147R mutations had an almost 10-fold reduced copper-dependent induction of
cinAQ
compared to the wild type.
Effect of Perturbation of ATP Level on the Activity and Regulation of Nitrogenase in
Rhodospirillum rubrum
Authors: Zhang Yaoping , Pohlmann Edward L. , Roberts Gary P. 
Published: June 2009

ABSTRACT

Nitrogenase activity in
Rhodospirillum rubrum
and in some other photosynthetic bacteria is regulated in part by the availability of light. This regulation is through a posttranslational modification system that is itself regulated by P
II
homologs in the cell. P
II
is one of the most broadly distributed regulatory proteins in nature and directly or indirectly senses nitrogen and carbon signals in the cell. However, its possible role in responding to light availability remains unclear. Because P
II
binds ATP, we tested the hypothesis that removal of light would affect P
II
by changing intracellular ATP levels, and this in turn would affect the regulation of nitrogenase activity. This in vivo test involved a variety of different methods for the measurement of ATP, as well as the deliberate perturbation of intracellular ATP levels by chemical and genetic means. To our surprise, we found fairly normal levels of nitrogenase activity and posttranslational regulation of nitrogenase even under conditions of drastically reduced ATP levels. This indicates that low ATP levels have no more than a modest impact on the P
II
-mediated regulation of NifA activity and on the posttranslational regulation of nitrogenase activity. The relatively high nitrogenase activity also shows that the ATP-dependent electron flux from dinitrogenase reductase to dinitrogenase is also surprisingly insensitive to a depleted ATP level. These in vivo results disprove the simple model of ATP as the key energy signal to P
II
under these conditions. We currently suppose that the ratio of ADP/ATP might be the relevant signal, as suggested by a number of recent in vitro analyses.
CodY Activates Transcription of a Small RNA inBacillus subtilis
Authors: Preis Heike , Eckart Rita A. , Gudipati Rajani K. , Heidrich Nadja , Brantl Sabine 
Published: June 2009

ABSTRACTRegulatory small RNAs (sRNAs) in bacterial genomes have become a focus of research over the past 8 years. Whereas more than 100 such sRNAs have been found inEscherichia coli, relatively little is known about sRNAs in gram-positive bacteria. Using a computational approach, we identified two sRNAs in intergenic regions of theBacillus subtilisgenome, SR1 and SR2 (renamed BsrF). Recently, we demonstrated that SR1 inhibits the translation initiation of the transcriptional activator AhrC. Here, we describe detection of BsrF, its expression profile, and its regulation by CodY. Furthermore, we mapped the secondary structure of BsrF. BsrF is expressed in complex and minimal media in all growth phases inB. subtilisand, with a similar expression profile, also inBacillus amyloliquefaciens. Neither overexpression nor deletion ofbsrFaffected the growth ofB. subtilis. BsrF was found to be long-lived in complex and minimal media. Analysis of 13 putative transcription factor binding sites upstream ofbsrFrevealed only an effect for CodY. Here, we showed by using Northern blotting,lacZreporter gene fusions, in vitro transcription, and DNase I footprinting that the transcription ofbsrFis activated by CodY in the presence of branched-chain amino acids and GTP. Furthermore, BsrF transcription was increased 1.5- to 2-fold by glucose in the presence of branched-chain amino acids, and this increase was independent of the known glucose-dependent regulators. BsrF is the second target for which transcriptional activation by CodY has been discovered.
Characterization of the
Synechocystis
Strain PCC 6803 Penicillin-Binding Proteins and Cytokinetic Proteins FtsQ and FtsW and Their Network of Interactions with ZipN
Authors: Marbouty Martial , Mazouni Khalil , Saguez Cyril , Cassier-Chauvat Corinne , Chauvat Franck 
Published: June 2009

ABSTRACT

Because very little is known about cell division in noncylindrical bacteria and cyanobacteria, we investigated 10 putative cytokinetic proteins in the unicellular spherical cyanobacterium
Synechocystis
strain PCC 6803. Concerning the eight penicillin-binding proteins (PBPs), which define three classes, we found that
Synechocystis
can survive in the absence of one but not two PBPs of either class A or class C, whereas the unique class B PBP (also termed FtsI) is indispensable. Furthermore, we showed that all three classes of PBPs are required for normal cell size. Similarly, the putative FtsQ and FtsW proteins appeared to be required for viability and normal cell size. We also used a suitable bacterial two-hybrid system to characterize the interaction web among the eight PBPs, FtsQ, and FtsW, as well as ZipN, the crucial FtsZ partner that occurs only in cyanobacteria and plant chloroplasts. We showed that FtsI, FtsQ, and ZipN are self-interacting proteins and that both FtsI and FtsQ interact with class A PBPs, as well as with ZipN. Collectively, these findings indicate that ZipN, in interacting with FtsZ and both FtsI and FtQ, plays a similar role to the
Escherichia coli
FtsA protein, which is missing in cyanobacteria and chloroplasts.
Genome Sequence of the Emerging Pathogen
Helicobacter canadensis
Authors: Loman N. J. , Snyder L. A. S. , Linton J. D. , Langdon R. , Lawson A. J. , Weinstock G. M. , Wren B. W. , Pallen M. J. 
Published: June 2009

ABSTRACT

We determined the genome sequence of the type strain of
Helicobacter canadensis
, an emerging human pathogen with diverse animal reservoirs. Potential virulence determinants carried by the genome include systems for N-linked glycosylation and capsular export. A protein-based phylogenetic analysis places
H. canadensis
close to
Wolinella succinogenes
.