bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of Heterozygosity at an Unlinked Genomic Locus Is Responsible for the Phenotype of a Candida albicans
sap4
Δ
sap5
Δ
sap6
Δ Mutant
Authors: Dunkel Nico , Morschhäuser Joachim 
Published: November 2010

ABSTRACT

The diploid genome of the pathogenic yeast
Candida albicans
exhibits a high degree of heterozygosity. Genomic alterations that result in a loss of heterozygosity at specific loci may affect phenotypes and confer a selective advantage under certain conditions. Such genomic rearrangements can also occur during the construction of
C. albicans
mutants and remain undetected. The
SAP2
gene on chromosome R encodes a secreted aspartic protease that is induced and required for growth of
C. albicans
when proteins are the only available nitrogen source. In strain SC5314, the two
SAP2
alleles are functionally divergent because of differences in their regulation. Basal expression of the
SAP2
-
2
allele, but not the
SAP2
-
1
allele, provides the proteolytic degradation products that serve as inducers for full
SAP2
induction. A triple mutant lacking the
SAP4
,
SAP5
, and
SAP6
genes, which are located on chromosome 6, has previously been reported to have a growth defect on proteins, suggesting that one of the encoded proteases is required for
SAP2
expression. Here we show that this
sap4
Δ
sap5
Δ
sap6
Δ mutant has become homozygous for chromosome R and lost the
SAP2
-
2
allele. Replacement of one of the
SAP2
-
1
copies in this strain by
SAP2
-
2
and its regulatory region restored the ability of the
sap4
Δ
sap5
Δ
sap6
Δ mutant to utilize proteins as the sole nitrogen source. This is an illustrative example of how loss of heterozygosity at a different genomic locus can cause the mutant phenotype attributed to targeted deletion of a specific gene in
C. albicans
.
The Peptidoglycan of
Mycobacterium abscessus
Is Predominantly Cross-Linked by
l
,
d
-Transpeptidases
Authors: Lavollay Marie , Fourgeaud Martine , Herrmann Jean-Louis , Dubost Lionel , Marie Arul , Gutmann Laurent , Arthur Michel , Mainardi Jean-Luc 
Published: November 2010

ABSTRACT

Few therapeutic alternatives remain for the treatment of infections due to multiresistant
Mycobacterium abscessus
. Here we show that the peptidoglycans of the “rough” and “smooth” morphotypes contain predominantly 3→3 cross-links generated by
l
,
d
-transpeptidases, indicating that these enzymes are attractive targets for the development of efficient drugs.
Isolation and Characterization of P1 Adhesin, a Leg Protein of the Gliding Bacterium
Mycoplasma pneumoniae
Authors: Nakane Daisuke , Adan-Kubo Jun , Kenri Tsuyoshi , Miyata Makoto 
Published: November 2010

ABSTRACT

Mycoplasma pneumoniae
, a pathogen causing human pneumonia, binds to solid surfaces at its membrane protrusion and glides by a unique mechanism. In this study, P1 adhesin, which functions as a “leg” in gliding, was isolated from mycoplasma culture and characterized. Using gel filtration, blue-native polyacrylamide gel electrophoresis (BN-PAGE), and chemical cross-linking, the isolated P1 adhesin was shown to form a complex with an accessory protein named P90. The complex included two molecules each of P1 adhesin and P90 (protein B), had a molecular mass of about 480 kDa, and was observed by electron microscopy to form 20-nm-diameter spheres. Partial digestion of isolated P1 adhesin by trypsin showed that the P1 adhesin molecule can be divided into three domains, consistent with the results from trypsin treatment of the cell surface. Sequence analysis of P1 adhesin and its orthologs showed that domain I is well conserved and that a transmembrane segment exists near the link between domains II and III.
Identification of Nocobactin NA Biosynthetic Gene Clusters inNocardia farcinica
Authors: Hoshino Yasutaka , Chiba Kazuhiro , Ishino Keiko , Fukai Toshio , Igarashi Yasuhiro , Yazawa Katsukiyo , Mikami Yuzuru , Ishikawa Jun 
Published: November 2010

ABSTRACTWe identified the biosynthetic gene clusters of the siderophore nocobactin NA. Thenbtclusters, which were discovered as genes highly homologous to the mycobactin biosynthesis genes by the genomic sequencing ofNocardia farcinicaIFM 10152, consist of 10 genes separately located at two genomic regions. The gene organization of thenbtclusters and the predicted functions of thenbtgenes, particularly the cyclization and epimerization domains, were in good agreement with the chemical structure of nocobactin NA. Disruptions of thenbtAandnbtEgenes, respectively, reduced and abolished the productivity of nocobactin NA. The heterologous expression of thenbtSgene revealed that this gene encoded a salicylate synthase. These results indicate that thenbtclusters are responsible for the biosynthesis of nocobactin NA. We also found putative IdeR-binding sequences upstream of thenbtA, -G, -H, -S, and -Tgenes, whose expression was more than 10-fold higher in the low-iron condition than in the high-iron condition. These results suggest thatnbtgenes are regulated coordinately by IdeR protein in an iron-dependent manner. The ΔnbtEmutant was found to be impaired in cytotoxicity against J774A.1 cells, suggesting that nocobactin NA production is required for virulence ofN. farcinica.
Structural and Functional Insights into
Aeropyrum pernix
OppA, a Member of a Novel Archaeal OppA Subfamily
Authors: Balestrieri M. , Gogliettino M. , Fiume I. , Pocsfalvi G. , Catara G. , Rossi M. , Palmieri G. 
Published: November 2010

ABSTRACT

In this study we gain insight into the structural and functional characterization of the
Aeropyrum pernix
oligopeptide-binding protein (OppA
Ap
) previously identified from the extracellular medium of an
Aeropyrum pernix
cell culture at late stationary phase. OppA
Ap
showed an N-terminal Q32 in a pyroglutamate form and C-terminal processing at the level of a threonine-rich region probably involved in protein membrane anchoring. Moreover, the OppA
Ap
protein released into the medium was identified as a “nicked” form composed of two tightly associated fragments detachable only under strong denaturing conditions. The cleavage site E569-G570 seems be located on an exposed surface loop that is highly conserved in several three-dimensional (3D) structures of dipeptide/oligopeptide-binding proteins from different sources. Structural and biochemical properties of the nicked protein were virtually indistinguishable from those of the intact form. Indeed, studies of the entire bacterially expressed OppA
Ap
protein owning the same N and C termini of the nicked form supported these findings. Moreover, in the middle exponential growth phase, OppA
Ap
was found as an intact cell membrane-associated protein. Interestingly, the native exoprotein OppA
Ap
was copurified with a hexapeptide (EKFKIV) showing both lysines methylated and possibly originating from an
A. pernix
endogenous stress-induced lipoprotein. Therefore, the involvement of OppA
Ap
in the recycling of endogenous proteins was suggested to be a potential physiological function. Finally, a new OppA from
Sulfolobus solfataricus
, SSO1288, was purified and preliminarily characterized, allowing the identification of a common structural/genetic organization shared by all “true” archaeal OppA proteins of the dipeptide/oligopeptide class.
Genome Copy Numbers and Gene Conversion in Methanogenic Archaea
Authors: Hildenbrand Catherina , Stock Tilmann , Lange Christian , Rother Michael , Soppa Jörg 
Published: November 2010

ABSTRACT

Previous studies revealed that one species of methanogenic archaea,
Methanocaldococcus jannaschii
, is polyploid, while a second species,
Methanothermobacter thermoautotrophicus
, is diploid. To further investigate the distribution of ploidy in methanogenic archaea, species of two additional genera—
Methanosarcina acetivorans
and
Methanococcus maripaludis
—were investigated
. M. acetivorans
was found to be polyploid during fast growth (
t
D
= 6 h; 17 genome copies) and oligoploid during slow growth (doubling time = 49 h; 3 genome copies).
M. maripaludis
has the highest ploidy level found for any archaeal species, with up to 55 genome copies in exponential phase and ca. 30 in stationary phase. A compilation of archaeal species with quantified ploidy levels reveals a clear dichotomy between Euryarchaeota and Crenarchaeota: none of seven euryarchaeal species of six genera is monoploid (haploid), while, in contrast, all six crenarchaeal species of four genera are monoploid, indicating significant genetic differences between these two kingdoms. Polyploidy in asexual species should lead to accumulation of inactivating mutations until the number of intact chromosomes per cell drops to zero (called “Muller's ratchet”). A mechanism to equalize the genome copies, such as gene conversion, would counteract this phenomenon. Making use of a previously constructed heterozygous mutant strain of the polyploid
M. maripaludis
we could show that in the absence of selection very fast equalization of genomes in
M. maripaludis
took place probably via a gene conversion mechanism. In addition, it was shown that the velocity of this phenomenon is inversely correlated to the strength of selection.
Role of the F1 Region in theEscherichia coliAerotaxis Receptor Aer
Authors: Campbell Asharie J. , Watts Kylie J. , Johnson Mark S. , Taylor Barry L. 
Published: November 2010

ABSTRACTInEscherichiacoli, the aerotaxis receptor Aer is an atypical receptor because it senses intracellular redox potential. The Aer sensor is a cytoplasmic, N-terminal PAS domain that is tethered to the membrane by a 47-residue F1 linker. Here we investigated the function, topology, and orientation of F1 by employing random mutagenesis, cysteine scanning, and disulfide cross-linking. No native residue was obligatory for function, most deleterious substitutions had radically different side chain properties, and all F1 mutants but one were functionally rescued by the chemoreceptor Tar. Cross-linking studies were consistent with the predicted α-helical structure in the N-terminal F1 region and demonstrated trigonal interactions among the F1 linkers from three Aer monomers, presumably within trimer-of-dimer units, as well as binary interactions between subunits. Using heterodimer analyses, we also demonstrated the importance of arginine residues near the membrane interface, which may properly anchor the Aer protein in the membrane. By incorporating these data into a homology model of Aer, we developed a model for the orientation of the Aer F1 and PAS regions in an Aer lattice that is compatible with the known dimensions of the chemoreceptor lattice. We propose that the F1 region facilitates the orientation of PAS and HAMP domains during folding and thereby promotes the stability of the PAS and HAMP domains in Aer.
Acyl-Homoserine Lactone Binding to and Stability of the Orphan
Pseudomonas aeruginosa
Quorum-Sensing Signal Receptor QscR
Authors: Oinuma Ken-Ichi , Greenberg E. Peter 
Published: November 2010

ABSTRACT

The
Pseudomonas aeruginosa
transcription factor QscR responds to a variety of fatty acyl-homoserine lactones (HSLs), including
N
-3-oxododecanoyl-HSL (3OC12-HSL), which is produced and detected by the
P. aeruginosa
quorum-sensing circuit LasI and LasR. As is true for LasR and many other acyl-HSL-dependent transcription factors, production of soluble QscR in sufficient amounts for purification requires growth of recombinant bacteria in the presence of an appropriate acyl-HSL. QscR is thought to bind 3OC12-HSL relatively weakly compared to LasR, and unlike LasR, binding of purified QscR to target DNA was shown to strongly depend on exogenously added 3OC12-HSL. We show that purified QscR is dimeric at sufficiently high concentrations and monomeric at lower concentrations. Furthermore, QscR bound 3OC12-HSL more tightly than previously believed. Purified QscR retained 3OC12-HSL, and at sufficiently high concentrations, it bound target DNA in the absence of added 3OC12-HSL. We also obtained soluble QscR from recombinant
Escherichia coli
grown in the presence of
N
-3-oxohexanoyl-HSL (3OC6-HSL) instead of 3OC12-HSL, and because 3OC6-HSL bound much more loosely to QscR than other acyl-HSLs tested, we were able to exchange 3OC6-HSL with other acyl-HSLs
in vitro
and then estimate binding affinities of QscR for different acyl-HSLs and for target DNA. Our data support a model whereby QscR polypeptides fold properly in the absence of an acyl-HSL, but soluble, acyl-HSL-free QscR does not accumulate because it is subject to rapid aggregation or proteolysis.
Fur and the Novel Regulator YqjI Control Transcription of the Ferric Reductase Gene
yqjH
in
Escherichia coli
Authors: Wang Suning , Wu Yun , Outten F. Wayne 
Published: November 2010

ABSTRACT

Iron acquisition in aerobic habitats is complicated by the low solubility of ferric hydroxides. Siderophores that bind ferric iron with high affinity are used to mobilize iron. The reduction of ferric iron to the ferrous form can be coupled to the release of iron from siderophores. Iron is also stored intracellularly as a ferric mineral in proteins, such as ferritin, and must be reduced during release. In
Escherichia coli
, the
yqjH
gene encodes a putative ferric siderophore reductase that is also part of the Fur regulon. Here we show that YqjH has ferric reductase activity and is required for iron homeostasis in
E. coli
. Divergently transcribed from
yqjH
is the
yqjI
gene, which encodes a novel member of the winged-helix family of transcriptional regulators and also contains an N-terminal extension similar to the Ni
2+
-binding C-terminal tail of SlyD. Deletion of
yqjI
leads to constitutive high-level activity of the
yqjH
and
yqjI
promoters. Purified YqjI binds inverted repeat target sequences within the
yqjH
and
yqjI
promoters. We also observed that YqjI-dependent transcriptional repression is reduced when cells are exposed to elevated nickel levels, resulting in increased expression of
yqjH
and
yqjI
. YqjI binding to nickel or iron reduces YqjI DNA-binding activity
in vitro
. Furthermore, we found that elevated nickel stress levels disrupt iron homeostasis in
E. coli
and that deletion of
yqjH
increases nickel toxicity. Our results suggest that the YqjI protein controls expression of
yqjH
to help maintain iron homeostasis under conditions (such as elevated cellular nickel levels) that disrupt iron metabolism.
Differences in MinC/MinD Sensitivity between Polar and Internal Z Rings in
Escherichia coli
Authors: Shen Bang , Lutkenhaus Joe 
Published: November 2010

ABSTRACT

In
Escherichia coli
the Z ring has the potential to assemble anywhere along the cell length but is restricted to midcell by the action of negative regulatory systems, including Min. In the current model for the Min system, the MinC/MinD division inhibitory complex is evenly distributed on the membrane and can disrupt Z rings anywhere in the cell; however, MinE spatially regulates MinC/MinD by restricting it to the cell poles, thus allowing Z ring formation at midcell. This model assumes that Z rings formed at different cellular locations have equal sensitivity to MinC/MinD in the absence of MinE. However, here we report evidence that differences in MinC/MinD sensitivity between polar and nonpolar Z rings exists even when there is no MinE. MinC/MinD at proper levels is able to block minicell production in
Δmin
strains without increasing the cell length, indicating that polar Z rings are preferentially blocked. In the FtsZ-I374V strain (which is resistant to MinC
C
/MinD), wild-type morphology can be easily achieved with MinC/MinD in the absence of MinE. We also show that MinC/MinD at proper levels can rescue the lethal phenotype of a
min slmA
double deletion mutant, which we think is due to the elimination of polar Z rings (or FtsZ structures), which frees up FtsZ molecules for assembly of Z rings at internal sites to rescue division and growth. Taken together, these data indicate that polar Z rings are more susceptible to MinC/MinD than internal Z rings, even when MinE is absent.
Membrane Topology and DNA-Binding Ability of the Streptococcal CpsA Protein
Authors: Hanson Brett R. , Lowe Beth A. , Neely Melody N. 
Published: November 2010

ABSTRACT
Many streptococcal pathogens require a polysaccharide capsule for survival in the host during systemic infection. The highly conserved CpsA protein is proposed to be a transcriptional regulator of capsule production in streptococci, although the regulatory mechanism is unknown. Hydropathy plots of CpsA predict an integral membrane protein with 3 transmembrane domains and only 27 cytoplasmic residues, whereas other members of the LytR_cpsA_psr protein family are predicted to have a single transmembrane domain. This unique topology, with the short cytoplasmic domain, membrane localization, and large extracellular domain, suggests a novel mechanism of transcriptional regulation. Therefore, to determine the actual membrane topology of CpsA, specific protein domains were fused to beta-galactosidase or alkaline phosphatase. Enzymatic assays confirmed that the predicted membrane topology for CpsA is correct. To investigate how this integral membrane protein may be functioning in regulation of capsule transcription, purified full-length and truncated forms of CpsA were used in electrophoretic mobility shift assays to characterize the ability to bind the capsule operon promoter. Assays revealed that full-length, purified CpsA protein binds specifically to DNA containing the capsule promoter region. Furthermore, the large extracellular domain is not required for DNA binding, but all cytoplasmic regions of CpsA are necessary and sufficient for specific binding to the capsule operon promoter. This is the first demonstration of a member of this protein family interacting with its target DNA. Taken together, CpsA, as well as other members of the LytR_cpsA_psr protein family, appears to utilize a unique mechanism of transcriptional regulation.
Genome Annotation and Intraviral Interactome for the
Streptococcus pneumoniae
Virulent Phage Dp-1
Authors: Sabri Mourad , Häuser Roman , Ouellette Marc , Liu Jing , Dehbi Mohammed , Moeck Greg , García Ernesto , Titz Björn , Uetz Peter , Moineau Sylvain 
Published: November 2010

ABSTRACT

Streptococcus pneumoniae
causes several diseases, including pneumonia, septicemia, and meningitis. Phage Dp-1 is one of the very few isolated virulent
S. pneumoniae
bacteriophages, but only a partial characterization is currently available. Here, we confirmed that Dp-1 belongs to the family
Siphoviridae
. Then, we determined its complete genomic sequence of 56,506 bp. It encodes 72 open reading frames, of which 44 have been assigned a function. We have identified putative promoters, Rho-independent terminators, and several genomic clusters. We provide evidence that Dp-1 may be using a novel DNA replication system as well as redirecting host protein synthesis through queuosine-containing tRNAs. Liquid chromatography-mass spectrometry analysis of purified phage Dp-1 particles identified at least eight structural proteins. Finally, using comprehensive yeast two-hybrid screens, we identified 156 phage protein interactions, and this intraviral interactome was used to propose a structural model of Dp-1.
Contributions of Multiple Binding Sites and Effector-Independent Binding to CodY-Mediated Regulation inBacillus subtilis
Authors: Belitsky Boris R. , Sonenshein Abraham L. 
Published: November 2010

ABSTRACTCodY is a branched-chain amino acid-responsive transcriptional regulator that controls, directly or indirectly, the expression of more than 100 genes and operons inBacillus subtilis. Using DNase I footprinting and gel-shift experiments, we identified two CodY-binding regions upstream of aB. subtilisgene (bcaP, previously known asyhdG) that encodes a transporter of branched-chain amino acids. Mutational analysis revealed that both CodY-binding regions contribute to repressionin vivoand do so independently of each other. Thus, a single CodY-binding site is apparently sufficient for substantial CodY-dependent regulation. By analyzing affinities of wild-type and mutant CodY-binding sites for CodY and their regulation by wild-type CodY and forms of CodY with various levels of activation by branched-chain amino acids, we concluded that unliganded CodY cannot repress transcriptionin vivoand that the level of endogenously produced effectors is sufficient for CodY-mediated regulation of promoters with stronger sites. Because the sites with higher affinity apparently respond to lower concentrations of CodY effectors and saturate faster as the concentrations of effectors increase, having two sites of binding with different affinities for CodY permits a promoter to respond to a wider range of intracellular concentrations of effectors.
Rok Regulates
yuaB
Expression during Architecturally Complex Colony Development of
Bacillus subtilis
168
Authors: Kovács Ákos T. , Kuipers Oscar P. 
Published: November 2010

ABSTRACT

Transcriptome analysis of a
Bacillus subtilis rok
strain that showed reduced complex colony structure formation revealed significant downregulation of the
yuaB
gene. Overexpression of
yuaB
restored structure formation in the
rok
strain. We show that transcription of
yuaB
is indirectly regulated by Rok, independently from its previously described AbrB-dependent regulation.
Chemotaxis to the Quorum-Sensing Signal AI-2 Requires the Tsr Chemoreceptor and the Periplasmic LsrB AI-2-Binding Protein
Authors: Hegde Manjunath , Englert Derek L. , Schrock Shanna , Cohn William B. , Vogt Christian , Wood Thomas K. , Manson Michael D. , Jayaraman Arul 
Published: November 2010

ABSTRACTAI-2 is an autoinducer made by many bacteria. LsrB binds AI-2 in the periplasm, and Tsr is thel-serine chemoreceptor. We show that AI-2 strongly attractsEscherichia coli. Both LsrB and Tsr are necessary for sensing AI-2, but AI-2 uptake is not, suggesting that LsrB and Tsr interact directly in the periplasm.
Complete Genome Sequence of
Bifidobacterium
longum
subsp.
longum
BBMN68, a New Strain from a Healthy Chinese Centenarian
Authors: Hao Yanling , Huang Dawei , Guo Huiyuan , Xiao Man , An Haoran , Zhao Liang , Zuo Fanglei , Zhang Bing , Hu Songnian , Song Shuhui , Chen Shangwu , Ren Fazheng 
Published: November 2010

ABSTRACT

Bifidobacterium
longum
subsp.
longum
BBMN68 was isolated from the feces of a healthy centenarian living in an area of BaMa, Guangxi, China, known for longevity. Here we report the main genome features of
B
.
longum
strain BBMN68 and the identification of several predicted proteins associated with the ecological niche of longevity.
Primosomal Proteins DnaD and DnaB Are Recruited to Chromosomal Regions Bound by DnaA inBacillus subtilis
Authors: Smits Wiep Klaas , Merrikh Houra , Bonilla Carla Yaneth , Grossman Alan D. 
Published: November 2010

ABSTRACTThe initiation of DNA replication requires the binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication,oriC. DnaA also binds to many sites around the chromosome, outsideoriC, and acts as a transcription factor at several of these. In low-G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase atoriC, and this depends on DnaA. DnaD and DnaB also are required to load the replicative helicase outsideoriCduring replication restart, independently of DnaA. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA inBacillus subtilis. This association was dependent on DnaA, and the order of recruitment was the same as that atoriC, but it was independent of a functionaloriCand suggests that DnaD and DnaB do not require open complex formation for the stable association with DNA. These secondary binding regions for DnaA could be serving as a reservoir for excess DnaA, DnaD, and DnaB to help properly regulate replication initiation and perhaps are analogous to the proposed function of thedatAlocus inEscherichia coli. Alternatively, DnaD and DnaB might modulate the activity of DnaA at the secondary binding regions. All three of these proteins are widely conserved and likely have similar functions in a range of organisms.