bluuebunny/crossref_metadata_2025_split huggingface dataset:
6S RNA Regulation of
pspF
Transcription Leads to Altered Cell Survival at High pH
Authors: Trotochaud Amy E. , Wassarman Karen M. 
Published: May 2006

ABSTRACT

6S RNA is a highly abundant small RNA that regulates transcription through direct interaction with RNA polymerase. Here we show that 6S RNA directly inhibits transcription of
pspF
, which subsequently leads to inhibition of
pspABCDE
and
pspG
expression. Cells without 6S RNA are able to survive at elevated pH better than wild-type cells due to loss of 6S RNA-regulation of
pspF
. This 6S RNA-dependent phenotype is eliminated in
pspF
-null cells, indicating that 6S RNA effects are conferred through PspF. Similar growth phenotypes are seen when PspF levels are increased in a 6S RNA-independent manner, signifying that changes to
pspF
expression are sufficient. Changes in survival at elevated pH most likely result from altered expression of
pspABCDE
and/or
pspG
, both of which require PspF for transcription and are indirectly regulated by 6S RNA. 6S RNA provides another layer of regulation in response to high pH during stationary phase. We propose that the normal role of 6S RNA at elevated pH is to limit the extent of the
psp
response under conditions of nutrient deprivation, perhaps facilitating appropriate allocation of diminishing resources.
Functional Genomics of Stress Response in
Pseudomonas putida
KT2440
Authors: Reva Oleg N. , Weinel Christian , Weinel Miryam , Böhm Kerstin , Stjepandic Diana , Hoheisel Jörg D. , Tümmler Burkhard 
Published: May 2006

ABSTRACT

The metabolically versatile soil bacterium
Pseudomonas putida
has to cope with numerous abiotic stresses in its habitats. The stress responses of
P. putida
KT2440 to 4°C, pH 4.5, 0.8 M urea, and 45 mM sodium benzoate were analyzed by determining the global mRNA expression profiles and screening for stress-intolerant nonauxotrophic Tn
5
transposon mutants. In 392 regulated genes or operons, 36 gene regions were differentially expressed by more than 2.5-fold, and 32 genes in 23 operons were found to be indispensable for growth during exposure to one of the abiotic stresses. The transcriptomes of the responses to urea, benzoate, and 4°C correlated positively with each other but negatively with the transcriptome of the mineral acid response. The CbrAB sensor kinase, the cysteine synthase CysM, PcnB and VacB, which control mRNA stability, and BipA, which exerts transcript-specific translational control, were essential to cope with cold stress. The
cyo
operon was required to cope with acid stress. A functional PhoP, PtsP, RelA/SpoT modulon, and adhesion protein LapA were necessary for growth in the presence of urea, and the outer membrane proteins OmlA and FepA and the phosphate transporter PstBACS were indispensable for growth in the presence of benzoate. A lipid A acyltransferase (PP0063) was a mandatory component of the stress responses to cold, mineral acid, and benzoate. Adaptation of the membrane barrier, uptake of phosphate, maintenance of the intracellular pH and redox status, and translational control of metabolism are key mechanisms of the response of
P. putida
to abiotic stresses.
Differential Activation of
Escherichia coli
Chemoreceptors by Blue-Light Stimuli
Authors: Wright Stuart , Walia Bharat , Parkinson John S. , Khan Shahid 
Published: May 2006

ABSTRACT

Enteric bacteria tumble, swim slowly, and are then paralyzed upon exposure to 390- to 530-nm light. Here, we analyze this complex response in
Escherichia coli
using standard fluorescence microscope optics for excitation at 440 ± 5 nm. The slow swimming and paralysis occurred only in dye-containing growth media or buffers. Excitation elicited complete paralysis within a second in 1 μM proflavine dye, implying specific motor damage, but prolonged tumbling in buffer alone. The tumbling half-response times were subsecond for onset but more than a minute for recovery. The response required the chemotaxis signal protein CheY and receptor-dependent activation of its kinase CheA. The study of deletion mutants revealed a specific requirement for either the aerotaxis receptor Aer or the chemoreceptor Tar but not the Tar homolog Tsr. The action spectrum of the wild-type response was consistent with a flavin, but the chromophores remain to be identified. The motile response processed via Aer was sustained, with recovery to either step-up or -down taking more than a minute. The response processed via Tar was transient, recovering on second time scales comparable to chemotactic responses. The response duration and amplitude were dependent on relative expression of Aer, Tar, and Tsr. The main response features were reproduced when each receptor was expressed singly from a plasmid in a receptorless host strain. However, time-resolved motion analysis revealed subtle kinetic differences that reflect the role of receptor cluster interactions in kinase activation-deactivation dynamics.
Utilization of the Methoxymalonyl-Acyl Carrier Protein Biosynthesis Locus for Cloning of the Tautomycin Biosynthetic Gene Cluster from
Streptomyces spiroverticillatus
Authors: Li Wenli , Ju Jianhua , Osada Hiroyuki , Shen Ben 
Published: May 2006

ABSTRACT

Tautomycin (TTM), a potent protein phosphatase inhibitor, consists of a polyketide chain containing a spiroketal moiety and an acyl chain bearing a dialkylmaleic anhydride structure. PCR using degenerate primers was used to clone genes from
Streptomyces spiroverticillatus
for formation of the methoxymalonyl-acyl carrier protein. This locus was found to contain five genes (
ttmC
,
ttmA
,
ttmD
,
ttmB
, and
ttmE
), one of which was used as a probe to clone the 110-kb TTM biosynthetic gene cluster. The involvement of the
ttmA
gene in TTM biosynthesis was confirmed by gene inactivation and mutation complementation experiments.
Bundle-Forming Pili and EspA Are Involved in Biofilm Formation by EnteropathogenicEscherichia coli
Authors: Moreira Cristiano G. , Palmer Kelli , Whiteley Marvin , Sircili Marcelo P. , Trabulsi Luiz R. , Castro Antonio F. P. , Sperandio Vanessa 
Published: May 2006

ABSTRACTMicrocolony formation is one of the initial steps in biofilm development, and in enteropathogenicEscherichia coli(EPEC) it is mediated by several adhesins, including the bundle-forming pilus (BFP) and the EspA filament. Here we report that EPEC forms biofilms on plastic under static conditions and a flowthrough continuous culture system. The abilities of several EPEC isogenic mutants to form biofilms were assessed. Adhesins such as BFP and EspA, important in microcolony formation on epithelial cells, are also involved in bacterial aggregation during biofilm formation on abiotic surfaces. Mutants that do not express BFP or EspA form more-diffuse biofilms than does the wild type. We also determined, usinggfptranscriptional fusions, that, consistent with the role of these adhesins in biofilms, the genes encoding BFP and EspA are expressed during biofilm formation. Finally, expression ofespAis controlled by a quorum-sensing (QS) regulatory mechanism, and the EPECqseAQS mutant also forms altered biofilms, suggesting that this signaling mechanism plays an important role in EPEC biofilm development. Taken together, these studies allowed us to propose a model of EPEC biofilm formation.
Identification of Methylation Sites in
Thermotoga maritima
Chemotaxis Receptors
Authors: Perez Eduardo , Zheng Haiyan , Stock Ann M. 
Published: May 2006

ABSTRACT

Adaptation in bacterial chemotaxis involves reversible methylation of specific glutamate residues within the cytoplasmic domains of methyl-accepting chemotaxis proteins. The specific sites of methylation in
Salmonella enterica
and
Escherichia coli
chemoreceptors, identified 2 decades ago, established a consensus sequence for methylation by methyltransferase CheR. Here we report the in vitro methylation of chemoreceptors from
Thermotoga maritima
, a hyperthermophile that has served as a useful source of chemotaxis proteins for structural analysis. Sites of methylation have been identified by liquid chromatography-mass spectrometry/mass spectrometry. Fifteen sites of methylation were identified within the cytoplasmic domains of four different
T. maritima
chemoreceptors. The results establish a consensus sequence for chemoreceptor methylation sites in
T. maritima
that is distinct from the previously identified consensus sequence for
E. coli
and
S. enterica
. These findings suggest that consensus sequences for posttranslational modifications in one organism may not be directly extrapolated to analogous modifications in other bacteria.
Genomic and Functional Analysis of the IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Its Transposon Tn
4655
Suggests Catabolic Gene Spread by a Tyrosine Recombinase
Authors: Sota Masahiro , Yano Hirokazu , Ono Akira , Miyazaki Ryo , Ishii Hidenori , Genka Hiroyuki , Top Eva M. , Tsuda Masataka 
Published: May 2006

ABSTRACT

The naphthalene-catabolic (
nah
) genes on the incompatibility group P-9 (IncP-9) self-transmissible plasmid NAH7 from
Pseudomonas putida
G7 are some of the most extensively characterized genetic determinants for bacterial aerobic catabolism of aromatic hydrocarbons. In contrast to the detailed studies of its catabolic cascade and enzymatic functions, the biological characteristics of plasmid NAH7 have remained unclear. Our sequence determination in this study together with the previously deposited sequences revealed the entire structure of NAH7 (82,232 bp). Comparison of NAH7 with two other completely sequenced IncP-9 catabolic plasmids, pDTG1 and pWW0, revealed that the three plasmids share very high nucleotide similarities in a 39-kb region encoding the basic plasmid functions (the IncP-9 backbone). The backbone of NAH7 is phylogenetically more related to that of pDTG1 than that of pWW0. These three plasmids carry their catabolic gene clusters at different positions on the IncP-9 backbone. All of the NAH7-specified
nah
genes are located on a class II transposon, Tn
4655
. Our analysis of the Tn
4655
-encoded site-specific recombination system revealed that (i) a novel tyrosine recombinase, TnpI, catalyzed both the intra- and intermolecular recombination between two copies of the
attI
site, (ii) the functional
attI
site was located within a 119-bp segment, and (iii) the site-specific strand exchange occurred within a 30-bp segment in the 41-bp CORE site. Our results and the sequence data of other naphthalene-catabolic plasmids, pDTG1 and pND6-1, suggest a potential role of the TnpI-
attI
recombination system in the establishment of these catabolic plasmids.
Role of Dipicolinic Acid in Resistance and Stability of Spores of
Bacillus subtilis
with or without DNA-Protective α/β-Type Small Acid-Soluble Proteins
Authors: Setlow Barbara , Atluri Swaroopa , Kitchel Ryan , Koziol-Dube Kasia , Setlow Peter 
Published: May 2006

ABSTRACT

Dipicolinic acid (DPA) comprises ∼10% of the dry weight of spores of
Bacillus
species. Although DPA has long been implicated in spore resistance to wet heat and spore stability, definitive evidence on the role of this abundant molecule in spore properties has generally been lacking.
Bacillus subtilis
strain FB122 (
sleB spoVF
) produced very stable spores that lacked DPA, and sporulation of this strain with DPA yielded spores with nearly normal DPA levels. DPA-replete and DPA-less FB122 spores had similar levels of the DNA protective α/β-type small acid-soluble spore proteins (SASP), but the DPA-less spores lacked SASP-γ. The DPA-less FB122 spores exhibited similar UV resistance to the DPA-replete spores but had lower resistance to wet heat, dry heat, hydrogen peroxide, and desiccation. Neither wet heat nor hydrogen peroxide killed the DPA-less spores by DNA damage, but desiccation did. The inability to synthesize both DPA and most α/β-type SASP in strain PS3664 (
sspA sspB sleB spoVF
) resulted in spores that lost viability during sporulation, at least in part due to DNA damage. DPA-less PS3664 spores were more sensitive to wet heat than either DPA-less FB122 spores or DPA-replete PS3664 spores, and the latter also retained viability during sporulation. These and previous results indicate that, in addition to α/β-type SASP, DPA also is extremely important in spore resistance and stability and, further, that DPA has some specific role(s) in protecting spore DNA from damage. Specific roles for DPA in protecting spore DNA against damage may well have been a major driving force for the spore's accumulation of the high levels of this small molecule.
Maltose and Maltodextrin Utilization by
Bacillus subtilis
Authors: Schönert Stefan , Seitz Sabine , Krafft Holger , Feuerbaum Eva-Anne , Andernach Iris , Witz Gabriele , Dahl Michael K. 
Published: May 2006

ABSTRACT

Bacillus subtilis
can utilize maltose and maltodextrins that are derived from polysaccharides, like starch or glycogen. In this work, we show that maltose is taken up by a member of the phosphoenolpyruvate-dependent phosphotransferase system and maltodextrins are taken up by a maltodextrin-specific ABC transporter. Uptake of maltose by the phosphoenolpyruvate-dependent phosphotransferase system is mediated by maltose-specific enzyme IICB (MalP; synonym, GlvC), with an apparent

K
m

of 5 μM and a
V
max
of 91 nmol · min
−1
· (10
10
CFU)
−1
. The maltodextrin-specific ABC transporter is composed of the maltodextrin binding protein MdxE (formerly YvdG), with affinities in the low micromolar range for maltodextrins, and the membrane-spanning components MdxF and MdxG (formerly YvdH and YvdI, respectively), as well as the energizing ATPase MsmX. Maltotriose transport occurs with an apparent

K
m

of 1.4 μM and a
V
max
of 4.7 nmol · min
−1
· (10
10
CFU)
−1
.
Metabolism of Isovanillate, Vanillate, and Veratrate by
Comamonas testosteroni
Strain BR6020
Authors: Providenti Miguel A. , O'Brien Jason M. , Ruff Jürgen , Cook Alasdair M. , Lambert Iain B. 
Published: May 2006

ABSTRACT

In
Comamonas testosteroni
strain BR6020, metabolism of isovanillate (iVan; 3-hydroxy-4-methoxybenzoate), vanillate (Van; 4-hydroxy-3-methoxybenzoate), and veratrate (Ver; 3,4-dimethoxybenzoate) proceeds via protocatechuate (Pca; 3,4-dihydroxybenzoate). A 13.4-kb locus coding for the catabolic enzymes that channel the three substrates to Pca was cloned. O demethylation is mediated by the phthalate family oxygenases IvaA (converts iVan to Pca and Ver to Van) and VanA (converts Van to Pca and Ver to iVan). Reducing equivalents from NAD(P)H are transferred to the oxygenases by the class IA oxidoreductase IvaB. Studies using whole cells, cell extracts, and reverse transcriptase PCR showed that degradative activity and expression of
vanA
,
ivaA
, and
ivaB
are inducible. In succinate- and Pca-grown cells, there is negligible degradative activity towards Van, Ver, and iVan and little to no expression of
vanA
,
ivaA
, and
ivaB
. Growth on Van or Ver results in production of oxygenases with activity towards Van, Ver, and iVan and expression of
vanA
,
ivaA
, and
ivaB
. With iVan-grown cultures,
ivaA
and
ivaB
are expressed, and in assays with whole cells, production of the iVan oxygenase is observed, but there is little activity towards Van or Ver. In cell extracts, though, Ver metabolism is observed, which suggests that the system mediating iVan uptake in whole cells does not mediate Ver uptake.
The Genome of the Obligately Intracellular Bacterium
Ehrlichia canis
Reveals Themes of Complex Membrane Structure and Immune Evasion Strategies
Authors: Mavromatis K. , Doyle C. Kuyler , Lykidis A. , Ivanova N. , Francino M. P. , Chain P. , Shin M. , Malfatti S. , Larimer F. , Copeland A. , Detter J. C. , Land M. , Richardson P. M. , Yu X. J. , Walker D. H. , McBride J. W. , Kyrpides N. C. 
Published: May 2006

ABSTRACT

Ehrlichia canis
, a small obligately intracellular, tick-transmitted, gram-negative, α-proteobacterium, is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the
E. canis
genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, 17 putative pseudogenes, and a substantial proportion of noncoding sequence (27%). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences and a unique serine-threonine bias associated with the potential for O glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein families associated with immune evasion were identified, one of which contains poly(G-C) tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Genes associated with pathogen-host interactions were identified, including a small group encoding proteins (
n
= 12) with tandem repeats and another group encoding proteins with eukaryote-like ankyrin domains (
n
= 7).
Functional Analysis of Glucan Binding Protein B from
Streptococcus mutans
Authors: Mattos-Graner Renata O. , Porter Kristen A. , Smith Daniel J. , Hosogi Yumiko , Duncan Margaret J. 
Published: May 2006

ABSTRACT

Mutans streptococci are major etiological agents of dental caries, and several of their secreted products contribute to bacterial accumulation on teeth. Of these,
Streptococcus mutans
glucan binding protein B (GbpB) is a novel, immunologically dominant protein. Its biological function is unclear, although GbpB shares homology with a putative peptidoglycan hydrolase from
S. agalactiae
and
S. pneumoniae
, indicative of a role in murein biosynthesis. To determine the cellular function of GbpB, we used several approaches to inactivate the gene, analyze its expression, and identify interacting proteins. None of the transformants analyzed were true
gbpB
mutants, since they all contained both disrupted and wild-type gene copies, and expression of functional GbpB was always conserved. Thus, the inability to obtain viable
gbpB
null mutants supports the notion that
gbpB
is an essential gene. Northern blot and real-time PCR analyses suggested that induction of
gbpB
expression in response to stress was a strain-dependent phenomenon. Proteins that interacted with GbpB were identified in pull-down and coimmunoprecipitation assays, and these data suggest that GbpB interacts with ribosomal protein L7/L12, possibly as part of a protein complex involved in peptidoglycan synthesis and cell division.
The X-Ray Structure of the Haloalcohol Dehalogenase HheA from
Arthrobacter
sp. Strain AD2: Insight into Enantioselectivity and Halide Binding in the Haloalcohol Dehalogenase Family
Authors: de Jong René M. , Kalk Kor H. , Tang Lixia , Janssen Dick B. , Dijkstra Bauke W. 
Published: May 2006

ABSTRACT

Haloalcohol dehalogenases are bacterial enzymes that cleave the carbon-halogen bond in short aliphatic vicinal haloalcohols, like 1-chloro-2,3-propanediol, some of which are recalcitrant environmental pollutants. They use a conserved Ser-Tyr-Arg catalytic triad to deprotonate the haloalcohol oxygen, which attacks the halogen-bearing carbon atom, producing an epoxide and a halide ion. Here, we present the X-ray structure of the haloalcohol dehalogenase HheA
AD2
from
Arthrobacter
sp. strain AD2 at 2.0-Å resolution. Comparison with the previously reported structure of the 34% identical enantioselective haloalcohol dehalogenase HheC from
Agrobacterium radiobacter
AD1 shows that HheA
AD2
has a similar quaternary and tertiary structure but a much more open substrate-binding pocket. Docking experiments reveal that HheA
AD2
can bind both enantiomers of the haloalcohol substrate 1-
p
-nitrophenyl-2-chloroethanol in a productive way, which explains the low enantiopreference of HheA
AD2
. Other differences are found in the halide-binding site, where the side chain amino group of Asn182 is in a position to stabilize the halogen atom or halide ion in HheA
AD2
, in contrast to HheC, where a water molecule has taken over this role. These results broaden the insight into the structural determinants that govern reactivity and selectivity in the haloalcohol dehalogenase family.
Active Transcription of rRNA Operons Is a Driving Force for the Distribution of RNA Polymerase in Bacteria: Effect of Extrachromosomal Copies of
rrnB
on the In Vivo Localization of RNA Polymerase
Authors: Cabrera Julio E. , Jin Ding J. 
Published: May 2006

ABSTRACT

In contrast to eukaryotes, bacteria such as
Escherichia coli
contain only one form of RNA polymerase (RNAP), which is responsible for all cellular transcription. Using an RNAP-green fluorescent protein fusion protein, we showed previously that
E. coli
RNAP is partitioned exclusively in the nucleoid and that stable RNA synthesis, particularly rRNA transcription, is critical for concentrating a significant fraction of RNAP in transcription foci during exponential growth. The extent of focus formation varies under different physiological conditions, supporting the proposition that RNAP redistribution is an important element for global gene regulation. Here we show that extra, plasmid-borne copies of an rRNA operon recruit RNAP from the nucleoid into the cytoplasmic space and that this is accompanied by a reduction in the growth rate. Transcription of an intact rRNA operon is not necessary, although a minimal transcript length is required for this phenotype. Replacement of the ribosomal promoters with another strong promoter, P
tac
, abolished the effect. These results demonstrate that active synthesis from rRNA promoters is a major driving force for the distribution of RNAP in bacteria. The implications of our results for the regulation of rRNA synthesis and cell growth are discussed.
Salt Stress inDesulfovibrio vulgarisHildenborough: an Integrated Genomics Approach
Authors: Mukhopadhyay Aindrila , He Zhili , Alm Eric J. , Arkin Adam P. , Baidoo Edward E. , Borglin Sharon C. , Chen Wenqiong , Hazen Terry C. , He Qiang , Holman Hoi-Ying , Huang Katherine , Huang Rick , Joyner Dominique C. , Katz Natalie , Keller Martin , Oeller Paul , Redding Alyssa , Sun Jun , Wall Judy , Wei Jing , Yang Zamin , Yen Huei-Che , Zhou Jizhong , Keasling Jay D. 
Published: May 2006

ABSTRACTThe ability ofDesulfovibrio vulgarisHildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced byD. vulgarisin its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation ofD. vulgariscells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profiling, and electron microscopy, we used a systems approach to explore the effects of excess NaCl onD. vulgaris. In this study we demonstrated that import of osmoprotectants, such as glycine betaine and ectoine, is the primary mechanism used byD. vulgaristo counter hyperionic stress. Several efflux systems were also highly up-regulated, as was the ATP synthesis pathway. Increases in the levels of both RNA and DNA helicases suggested that salt stress affected the stability of nucleic acid base pairing. An overall increase in the level of branched fatty acids indicated that there were changes in cell wall fluidity. The immediate response to salt stress included up-regulation of chemotaxis genes, although flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The results of an extensive NaCl stress analysis were compared with microarray data from a KCl stress analysis, and unlike many other bacteria,D. vulgarisresponded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response inD. vulgaristhat can be compared to those in other microorganisms.