bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic BacteriumXanthomonas campestrispv. vesicatoria Revealed by the Complete Genome Sequence
Authors: Thieme Frank , Koebnik Ralf , Bekel Thomas , Berger Carolin , Boch Jens , Büttner Daniela , Caldana Camila , Gaigalat Lars , Goesmann Alexander , Kay Sabine , Kirchner Oliver , Lanz Christa , Linke Burkhard , McHardy Alice C. , Meyer Folker , Mittenhuber Gerhard , Nies Dietrich H. , Niesbach-Klösgen Ulla , Patschkowski Thomas , Rückert Christian , Rupp Oliver , Schneiker Susanne , Schuster Stephan C. , Vorhölter Frank-Jörg , Weber Ernst , Pühler Alfred , Bonas Ulla , Bartels Daniela , Kaiser Olaf 
Published: October 2005

ABSTRACTThe gram-negative plant-pathogenic bacteriumXanthomonas campestrispv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying bacterial infection strategies. Here, we present the whole-genome sequence of the pepper-pathogenicXanthomonas campestrispv. vesicatoria strain 85-10, which comprises a 5.17-Mb circular chromosome and four plasmids. The genome has a high G+C content (64.75%) and signatures of extensive genome plasticity. Whole-genome comparisons revealed a gene order similar to bothXanthomonas axonopodispv. citri andXanthomonas campestrispv. campestris and a structure completely different fromXanthomonas oryzaepv. oryzae. A total of 548 coding sequences (12.2%) are unique toX. campestrispv. vesicatoria. In addition to a type III secretion system, which is essential for pathogenicity, the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gram-negative bacteria. Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogensLegionella pneumophilaandCoxiella burnetii. Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.
An Expression-Driven Approach to the Prediction of Carbohydrate Transport and Utilization Regulons in theHyperthermophilic BacteriumThermotoga maritima
Authors: Conners Shannon B. , Montero Clemente I. , Comfort Donald A. , Shockley Keith R. , Johnson Matthew R. , Chhabra Swapnil R. , Kelly Robert M. 
Published: October 2005

ABSTRACTComprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bacteriumThermotoga maritimaon 14 monosaccharide and polysaccharide substrates was undertaken with the goal of proposing carbohydrate specificities for transport systems and putative transcriptional regulators. Saccharide-induced regulons were predicted through the complementary use of comparative genomics, mixed-model analysis of genome-wide microarray expression data, and examination of upstream sequence patterns. The results indicate thatT. maritimarelies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. Roles in uptake of specific carbohydrates were suggested for members of the expanded Opp/Dpp family of ABC transporters. In this family, phylogenetic relationships among transport systems revealed patterns of possible duplication and divergence as a strategy for the evolution of new uptake capabilities. The presence of GC-rich hairpin sequences between substrate-binding proteins and other components of Opp/Dpp family transporters offers a possible explanation for differential regulation of transporter subunit genes. Numerous improvements toT. maritimagenome annotations were proposed, including the identification of ABC transport systems originally annotated as oligopeptide transporters as candidate transporters for rhamnose, xylose, β-xylan, andβ -glucans and identification of genes likely to encode proteins missing from current annotations of the pentose phosphate pathway. Beyond the information obtained forT. maritima, the present study illustrates how expression-based strategies can be used for improving genome annotation in other microorganisms, especially those for which genetic systems are unavailable.
A Mycothiol Synthase Mutant of
Mycobacterium smegmatis
Produces Novel Thiols and Has an Altered Thiol Redox Status
Authors: Newton Gerald L. , Ta Philong , Fahey Robert C. 
Published: October 2005

ABSTRACT

Mycobacteria and other actinomycetes do not produce glutathione but make mycothiol (MSH; AcCys-GlcN-Ins) that has functions similar to those of glutathione and is essential for growth of
Mycobacterium tuberculosis
. Mycothiol synthase (MshD) catalyzes N acetylation of Cys-GlcN-Ins to produce MSH in
Mycobacterium smegmatis
mc
2
155, and Cys-GlcN-Ins is maintained at a low level. The mycothiol synthase mutant, the
mshD
::Tn
5
mutant, produces high levels of Cys-GlcN-Ins along with two novel thiols,
N
-formyl-Cys-GlcN-Ins and
N
-succinyl-Cys-GlcN-Ins, and a small amount of MSH. The nonenzymatic reaction of acyl-coenzyme A (CoA) with Cys-GlcN-Ins to produce acyl-Cys-GlcN-Ins is a facile reaction under physiologic conditions, with succinyl-CoA being an order of magnitude more reactive than acetyl-CoA. The uncatalyzed reaction rates are adequate to account for the observed production of
N
-succinyl-Cys-GlcN-Ins and MSH under physiologic conditions. It was shown that the
N
-acyl-Cys-GlcN-Ins compounds are maintained in a substantially reduced state in the mutant but that Cys-GlcN-Ins exists in disulfide forms at 5 to 40% at different stages of growth. MSH was able to facilitate reduction of
N
-succinyl-Cys-GlcN-Ins disulfide through thiol-disulfide exchange, but
N
-formyl-Cys-GlcN-Ins was ineffective. The oxidized state of Cys-GlcN-Ins in cells appears to result from a high susceptibility to autoxidation and a low capacity of the cell to reduce its disulfide forms. The mutant exhibited no enhanced sensitivity to hydrogen peroxide,
tert
-butyl hydroperoxide, or cumene hydroperoxide relative to the parent strain, suggesting that the most abundant thiol,
N
-formyl-Cys-GlcN-Ins, functions as a substitute for MSH.
Genetic and Functional Characterization of theEscherichia coliBarA-UvrY Two-Component System: Point Mutations in the HAMP Linker of the BarA Sensor Give a Dominant-Negative Phenotype
Authors: Tomenius Henrik , Pernestig Anna-Karin , Méndez-Catalá Claudia F. , Georgellis Dimitris , Normark Staffan , Melefors Öjar 
Published: October 2005

ABSTRACTThe BarA-UvrY two-component system family is strongly associated with virulence but is poorly understood at the molecular level. During our attempts to complement abarAdeletion mutant, we consistently generated various mutated BarA proteins. We reasoned that characterization of the mutants would help us to better understand the signal transduction mechanism in tripartite sensors. This was aided by the demonstrated ability to activate the UvrY regulator with acetyl phosphate independently of the BarA sensor. Many of the mutated BarA proteins had poor complementation activity but could counteract the activity of the wild-type sensor in a dominant-negative fashion. These proteins carried point mutations in or near the recently identified HAMP linker, previously implicated in signal transduction between the periplasm and cytoplasm. This created sensor proteins with an impaired kinase activity and a net dephosphorylating activity. Using further site-directed mutagenesis of a HAMP linker-mutated protein, we could demonstrate that the phosphoaccepting aspartate 718 and histidine 861 are crucial for the dephosphorylating activity. Additional analysis of the HAMP linker-mutated BarA sensors demonstrated that a dephosphorylating activity can operate via phosphotransfer within a tripartite sensor dimer in vivo. This also means that a tripartite sensor can be arranged as a dimer even in the dephosphorylating mode.
Gene Cloning and Molecular Characterization of an Extracellular Poly(l-Lactic Acid) Depolymerase fromAmycolatopsissp. Strain K104-1
Authors: Matsuda Emiko , Abe Naoki , Tamakawa Hideyuki , Kaneko Jun , Kamio Yoshiyuki 
Published: October 2005

ABSTRACTWe have isolated a polylactide or poly(l-lactic acid) (PLA)-degrading bacterium,Amycolatopsissp. strain K104-1, and purified PLA depolymerase (PLD) from the culture fluid of the bacterium. Here, we cloned and expressed thepldgene encoding PLD inStreptomyces lividans1326 and characterized a recombinant PLD (rPLD) preparation. We also describe the processing mechanism from nascent PLD to mature PLD. Thepldgene encodes PLD as a 24,225-Da polypeptide consisting of 238 amino acids. Biochemical and Western immunoblot analyses of PLD and its precursors revealed that PLD is synthesized as a precursor (prepro-type), requiring proteolytic cleavage of the N-terminal 35-amino-acid extension including the 26-amino-acid signal sequence and 9-residue prosequence to generate the mature enzyme of 20,904 Da. The cleavage of the prosequence was found to be autocatalytic. PLD showed about 45% similarity to many eukaryotic serine proteases. In addition, three amino acid residues, H57, D102, and S195(chymotrypsin numbering), which are implicated in forming the catalytic triad necessary for cleavage of amide bond of substrates in eukaryotic serine proteases, were conserved in PLD as residues H74, D111, and S197. The G193residue (chymotrypsin numbering), which is implicated in forming an oxyanion hole with residue S195and forms an important hydrogen bond for interaction with the carbonyl group of the scissile peptide bond, was also conserved in PLD. The functional analysis of the PLD mutants H74A, D111A, and S197A revealed that residues H74, D111, and S197are important for the depolymerase and caseinolytic activities of PLD and for cleavage of the prosequence from pro-type PLD to form the mature one. The PLD preparation had elastase activity which was not inhibited by 1 mM elastatinal, which is 10 times higher than needed for complete inhibition of porcine pancreatic elastase. The rPLD preparation degraded PLA with an average molecular mass of 220 kDa into lactic acid dimers through lactic acid oligomers and finally into lactic acid. The PLD preparation bound to high polymers of 3-hydoxybutyrate, ε-caprolacton, and butylene succinate as well as PLA, but it degraded only PLA.
Rhamnolipids Modulate Swarming Motility Patterns ofPseudomonas aeruginosa
Authors: Caiazza Nicky C. , Shanks Robert M. Q. , O'Toole G. A. 
Published: October 2005

ABSTRACTPseudomonas aeruginosais capable of twitching, swimming, and swarming motility. The latter form of translocation occurs on semisolid surfaces, requires functional flagella and biosurfactant production, and results in complex motility patterns. From the point of inoculation, bacteria migrate as defined groups, referred to as tendrils, moving in a coordinated manner capable of sensing and responding to other groups of cells. We were able to show thatP. aeruginosaproduces extracellular factors capable of modulating tendril movement, and genetic analysis revealed that modulation of these movements was dependent on rhamnolipid biosynthesis. AnrhlBmutant (deficient in mono- and dirhamnolipid production) and anrhlCmutant (deficient in dirhamnolipid production) exhibited altered swarming patterns characterized by irregularly shaped tendrils. In addition, agar supplemented with rhamnolipid-containing spent supernatant inhibited wild-type (WT) swarming, whereas agar supplemented with spent supernatant from mutants that do not make rhamnolipids had no effect on WTP. aeruginosaswarming. Addition of purified rhamnolipids to swarming medium also inhibited swarming motility of the WT strain. We also show that asadBmutant does not sense and/or respond to other groups of swarming cells and this mutant was capable of swarming on media supplemented with rhamnolipid-containing spent supernatant or purified rhamnolipids. The abilities to produce and respond to rhamnolipids in the context of group behavior are discussed.
Role of the Nfo (YqfS) and ExoA Apurinic/Apyrimidinic Endonucleases in Protecting
Bacillus subtilis
Spores from DNA Damage
Authors: Salas-Pacheco José M. , Setlow Barbara , Setlow Peter , Pedraza-Reyes Mario 
Published: October 2005

ABSTRACT

The
Bacillus subtilis
enzymes ExoA and Nfo (originally termed YqfS) are endonucleases that can repair apurinic/apyrimidinic (AP) sites and strand breaks in DNA. We have analyzed how the lack of ExoA and Nfo affects the resistance of growing cells and dormant spores of
B. subtilis
to a variety of treatments, some of which generate AP sites and DNA strand breaks. The lack of ExoA and Nfo sensitized spores (termed α
−
β
−
) lacking the majority of their DNA-protective α/β-type small, acid-soluble spore proteins (SASP) to wet heat. However, the lack of these enzymes had no effect on the wet-heat resistance of spores that retained α/β-type SASP. The lack of either ExoA or Nfo sensitized wild-type spores to dry heat, but loss of both proteins was necessary to sensitize α
−
β
−
spores to dry heat. The lack of ExoA and Nfo also sensitized α
−
β
−
, but not wild-type, spores to desiccation. In contrast, loss of ExoA and Nfo did not sensitize growing cells or wild-type or α
−
β
−
spores to hydrogen peroxide or
t
-butylhydroperoxide. Loss of ExoA and Nfo also did not increase the spontaneous mutation frequency of growing cells.
exoA
expression took place not only in growing cells, but also in the forespore compartment of the sporulating cell. These results, together with those from previous work, suggest that ExoA and Nfo are additional factors that protect
B. subtilis
spores from DNA damage accumulated during spore dormancy.
Expression Dynamics of Arsenic Respiration and Detoxification in
Shewanella
sp. Strain ANA-3
Authors: Saltikov Chad W. , Wildman Richard A. , Newman Dianne K. 
Published: October 2005

ABSTRACT

Because arsenate [As(V)] reduction by bacteria can significantly enhance arsenic mobility in the environment, it is important to be able to predict when this activity will occur. Currently, two bacterial systems are known that specifically reduce As(V), namely, a respiratory system (encoded by the
arr
genes) and a detoxification system (encoded by the
ars
genes). Here we analyze the conditions under which these two systems are expressed in
Shewanella
sp. strain ANA-3. The
ars
system is expressed under both aerobic and anaerobic conditions, whereas the
arr
system is only expressed anaerobically and is repressed by oxygen and nitrate. When cells are grown on As(V), the
arr
system is maximally induced during exponential growth, with peak expression of the
ars
system occurring at the beginning of stationary phase. Both the
arr
and
ars
systems are specifically induced by arsenite [As(III)], but the
arr
system is activated by a concentration of As(III) that is 1,000 times lower than that required for the
arsC
system (≤100 nM versus ≤100 μM, respectively). A double mutant was constructed that does not reduce As(V) under any growth conditions. In this strain background, As(V) is capable of inducing the
arr
system at low micromolar concentrations, but it does not induce the
ars
system. Collectively, these results demonstrate that the two As(V) reductase systems in ANA-3 respond to different amounts and types of inorganic arsenic.
Bile Salts Modulate Expression of the CmeABC Multidrug Efflux Pump inCampylobacter jejuni
Authors: Lin Jun , Cagliero Cédric , Guo Baoqing , Barton Yi-Wen , Maurel Marie-Christine , Payot Sophie , Zhang Qijing 
Published: October 2005

ABSTRACTCmeABC, a multidrug efflux pump, is involved in the resistance ofCampylobacter jejunito a broad spectrum of antimicrobial agents and is essential forCampylobactercolonization in animal intestine by mediating bile resistance. Previously, we have shown that expression of this efflux pump is under the control of a transcriptional repressor named CmeR. Inactivation of CmeR or mutation in thecmeABCpromoter (PcmeABC) region derepressescmeABC, leading to overexpression of this efflux pump. However, it is unknown if the expression ofcmeABCcan be conditionally induced by the substrates it extrudes. In this study, we examined the expression ofcmeABCin the presence of various antimicrobial compounds. Although the majority of the antimicrobials tested did not affect the expression ofcmeABC, bile salts drastically elevated the expression of this efflux operon. The induction was observed with both conjugated and unconjugated bile salts and was in a dose- and time-dependent manner. Experiments using surface plasmon resonance demonstrated that bile salts inhibited the binding of CmeR to PcmeABC, suggesting that bile compounds are inducing ligands of CmeR. The interaction between bile salts and CmeR likely triggers conformational changes in CmeR, resulting in reduced binding affinity of CmeR to PcmeABC. Bile did not affect the transcription ofcmeR, indicating that altered expression ofcmeRis not a factor in bile-induced overexpression ofcmeABC. In addition to the CmeR-dependent induction, some bile salts (e.g., taurocholate) also activated the expression ofcmeABCby a CmeR-independent pathway. Consistent with the elevated production of CmeABC, the presence of bile salts in culture media resulted in increased resistance ofCampylobacterto multiple antimicrobials. These findings reveal a new mechanism that modulates the expression ofcmeABCand further support the notion that bile resistance is a natural function of CmeABC.
CpsE from Type 2Streptococcus pneumoniaeCatalyzes the Reversible Addition of Glucose-1-Phosphate to a Polyprenyl Phosphate Acceptor, Initiating Type 2 Capsule Repeat Unit Formation
Authors: Cartee Robert T. , Forsee W. Thomas , Bender Matthew H. , Ambrose Karita D. , Yother Janet 
Published: October 2005

ABSTRACTThe majority of the 90 capsule types made by the gram-positive pathogenStreptococcus pneumoniaeare assembled by a block-type mechanism similar to that utilized by the Wzy-dependent O antigens and capsules of gram-negative bacteria. In this mechanism, initiation of repeat unit formation occurs by the transfer of a sugar to a lipid acceptor. InS. pneumoniae, this step is catalyzed by CpsE, a protein conserved among the majority of capsule types. Membranes fromS. pneumoniaetype 2 strain D39 andEscherichia colicontaining recombinant Cps2E catalyzed incorporation of [14C]Glc from UDP-[14C]Glc into a lipid fraction in a Cps2E-dependent manner. The Cps2E-dependent glycolipid product from both membranes was sensitive to mild acid hydrolysis, suggesting that Cps2E was catalyzing the formation of a polyprenyl pyrophosphate Glc. Addition of exogenous polyprenyl phosphates ranging in size from 35 to 105 carbons to D39 andE. colimembranes stimulated Cps2E activity. The stimulation was due, in part, to utilization of the exogenous polyprenyl phosphates as an acceptor. The glycolipid product synthesized in the absence of exogenous polyprenyl phosphates comigrated with a 60-carbon polyprenyl pyrophosphate Glc. When 10 or 100 μM UMP was added to reaction mixtures containing D39 membranes, Cps2E activity was inhibited 40% and 80%, respectively. UMP, which acted as a competitive inhibitor of UDP-Glc, also stimulated Cps2E to catalyze the reverse reaction, with synthesis of UDP-Glc from the polyprenyl pyrophosphate Glc. These data indicated that Cps2E was catalyzing the addition of Glc-1-P to a polyprenyl phosphate acceptor, likely undecaprenyl phosphate.
Regulation of thepspAVirulence Factor and EssentialpcsBMurein Biosynthetic Genes by the Phosphorylated VicR (YycF) Response Regulator inStreptococcus pneumoniae
Authors: Ng Wai-Leung , Tsui Ho-Ching Tiffany , Winkler Malcolm E. 
Published: October 2005

ABSTRACTThe VicRK (YycFG) two-component regulatory system (TCS) is required for virulence of the human respiratory pathogenStreptococcus pneumoniae(pneumococcus). The VicR (YycF) response regulator (RR) is essential through its positive regulation ofpcsB, which encodes an extracellular protein that mediates murein biosynthesis. To determine other genes that are regulated by VicR, we performed microarray analyses on a unique ΔvicRdeletion mutant, which was constructed by uncoupling regulation ofpcsB. Results from these microarray experiments support the idea that the VicR RR exerts strong positive regulation on the transcription of a set of genes encoding important surface proteins, including the PspA virulence factor, two proteins (Spr0096 and Spr1875) containing LysM peptidoglycan-binding domains, and a putative membrane protein (Spr0709) of unknown function. To demonstrate direct regulation, we performed band shift and footprinting experiments using purified unphosphorylated VicR and phosphorylated VicR-P, which was prepared by reaction with acetyl phosphate. VicR and VicR-P bound to regions upstream ofpcsB,pspA,spr0096,spr1875, andspr0709.Phosphorylation of VicR to VicR-P increased the apparent strength and changed the nature of binding to these regions. DNase I footprinting of VicR and VicR-P bound to regions upstream ofpcsB,pspA,spr0096, andspr1875showed protection of extended regions containing a degenerate sequence related to a previously proposed consensus. These combined approaches did not support autoregulation of thevicRKXoperon or substantive direct regulation of fatty acid biosynthesis by VicR or VicR-P. However, the ΔvicRmutant required fatty acids in some conditions, which supports the notion that the VicRK TCS may mediate membrane integrity as well as murein biosynthesis and virulence factor expression inS. pneumoniae.
Nocturnal Production of Endospores in Natural Populations ofEpulopiscium-Like Surgeonfish Symbionts
Authors: Flint Joseph F. , Drzymalski Dan , Montgomery W. Linn , Southam Gordon , Angert Esther R. 
Published: October 2005

ABSTRACTPrior studies have described a morphologically diverse group of intestinal microorganisms associated with surgeonfish. Despite their diversity of form, 16S rRNA gene surveys and fluorescent in situ hybridizations indicate that these bacteria are low-G+C gram-positive bacteria related toEpulopisciumspp. Many of these bacteria exhibit an unusual mode of reproduction, developing multiple offspring intracellularly. Previous reports have suggested that someEpulopiscium-like symbionts produce dormant or phase-bright intracellular offspring. Close relatives ofEpulopiscium, such asMetabacterium polysporaandClostridium lentocellum, are endospore-forming bacteria, which raises the possibility that the phase-bright offspring are endospores. Structural evidence and the presence of dipicolinic acid demonstrate that phase-bright offspring ofEpulopiscium-like bacteria are true endospores. In addition, endospores are formed as part of the normal daily life cycle of these bacteria. In the populations studied, mature endospores were seen only at night and the majority of cells in a given population produced one or two endospores per mother cell. Phylogenetic analyses confirmed the close relationship between the endospore-forming surgeonfish symbionts characterized here and previously describedEpulopisciumspp. The broad distribution of endospore formation among theEpulopisciumphylogenetic group raises the possibility that sporulation is a characteristic of the group. We speculate that spore formation inEpulopiscium-like symbionts may be important for dispersal and may also enhance survival in the changing conditions of the fish intestinal tract.