bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catabolite Repression Control ofnapF(Periplasmic Nitrate Reductase) Operon Expression inEscherichia coliK-12
Authors: Stewart Valley , Bledsoe Peggy J. , Chen Li-Ling , Cai Amie 
Published: December 2008

ABSTRACTEscherichia coli, a facultative aerobe, expresses two distinct respiratory nitrate reductases. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments, whereas the membrane-bound NarGHI enzyme functions during growth in nitrate-rich environments. Maximal expression of thenapFDAGHBCoperon encoding periplasmic nitrate reductase results from synergistic transcription activation by the Fnr and phospho-NarP proteins, acting in response to anaerobiosis and nitrate or nitrite, respectively. Here, we report that, during anaerobic growth with no added nitrate, less-preferred carbon sources stimulatednapFoperon expression by as much as fourfold relative to glucose. Deletion analysis identified a cyclic AMP receptor protein (Crp) binding site upstream of the NarP and Fnr sites as being required for this stimulation. ThenapDandnrfAoperon control regions fromShewanellaspp. also have apparent Crp and Fnr sites, and expression from theShewanella oneidensis nrfAcontrol region cloned inE. coliwas subject to catabolite repression. In contrast, the carbon source had relatively little effect on expression of thenarGHJIoperon encoding membrane-bound nitrate reductase under any growth condition tested. Carbon source oxidation state had no influence on synthesis of either nitrate reductase. The results suggest that the Fnr and Crp proteins may act synergistically to enhance NapABC synthesis during growth with poor carbon sources to help obtain energy from low levels of nitrate.
HicA of
Escherichia coli
Defines a Novel Family of Translation-Independent mRNA Interferases in Bacteria and Archaea
Authors: Jørgensen Mikkel G. , Pandey Deo P. , Jaskolska Milena , Gerdes Kenn 
Published: December 2008

ABSTRACT

Toxin-antitoxin (TA) loci are common in free-living bacteria and archaea. TA loci encode a stable toxin that is neutralized by a metabolically unstable antitoxin. The antitoxin can be either a protein or an antisense RNA. So far, six different TA gene families, in which the antitoxins are proteins, have been identified. Recently, Makarova et al. (K. S. Makarova, N. V. Grishin, and E. V. Koonin, Bioinformatics 22:2581-2584, 2006) suggested that the
hicAB
loci constitute a novel TA gene family. Using the
hicAB
locus of
Escherichia coli
K-12 as a model system, we present evidence that supports this inference: expression of the small HicA protein (58 amino acids [aa]) induced cleavage in three model mRNAs and tmRNA. Concomitantly, the global rate of translation was severely reduced. Using tmRNA as a substrate, we show that HicA-induced cleavage does not require the target RNA to be translated. Expression of HicB (145 aa) prevented HicA-mediated inhibition of cell growth. These results suggest that HicB neutralizes HicA and therefore functions as an antitoxin. As with other antitoxins (RelB and MazF), HicB could resuscitate cells inhibited by HicA, indicating that ectopic production of HicA induces a bacteriostatic rather than a bactericidal condition. Nutrient starvation induced strong
hicAB
transcription that depended on Lon protease. Mining of 218 prokaryotic genomes revealed that
hicAB
loci are abundant in bacteria and archaea.
Conjugative Interaction Induces Transposition of IS
Pst9
in
Pseudomonas stutzeri
AN10
Authors: Christie-Oleza J. A. , Lanfranconi M. P. , Nogales B. , Lalucat J. , Bosch R. 
Published: December 2008

ABSTRACT

IS
Pst9
is an IS
L3
-like insertion sequence (IS) that was recently described in the naphthalene-degrading organism
Pseudomonas stutzeri
strain AN10. In this paper we describe a novel strong IS regulation stimulus; transposition of IS
Pst9
is induced in all
P. stutzeri
AN10 cells after conjugative interaction with
Escherichia coli
. Thus, we observed that in all
P. stutzeri
AN10 cells that received genetic material by conjugation the IS
Pst9
genomic dose and/or distribution was changed. Furthermore, IS
Pst9
transposition was also observed when
P. stutzeri
AN10 cells were put in contact with the plasmidless conjugative strain
E. coli
S17-1λ

pir

, but not when they were put in contact with
E. coli
DH5α (a nonconjugative strain). The mechanism of IS
Pst9
transposition was analyzed, and transposition was shown to proceed by excision from the donor DNA using a conservative mechanism, which generated 3- to 10-bp deletions of the flanking DNA. Our results indicate that IS
Pst9
transposes, forming double-stranded DNA circular intermediates consisting of the IS and a 5-bp intervening DNA sequence probably derived from the IS
Pst9
flanking regions. The kinetics of IS circle formation are also described.
The Global Virulence Regulator PhcA Negatively Controls the
Ralstonia solanacearum hrp
Regulatory Cascade by Repressing Expression of the PrhIR Signaling Proteins
Authors: Yoshimochi Takeshi , Hikichi Yasufumi , Kiba Akinori , Ohnishi Kouhei 
Published: December 2008

ABSTRACT

PhcA positively and negatively regulates many genes responsible for pathogenicity of
Ralstonia solanacearum
. The type III secretion system-encoding
hrp
regulon is one of the negatively controlled operons. PhcA bound to the promoter region of
prhIR
and repressed its expression, demonstrating that PhcA shuts down the most upstream component of a signal transfer system for
hrpB
activation.
Trigger Factor from the Psychrophilic Bacterium
Psychrobacter frigidicola
Is a Monomeric Chaperone
Authors: Robin Sylvain , Togashi Denisio M. , Ryder Alan G. , Wall J. Gerard 
Published: December 2008

ABSTRACT

In eubacteria, trigger factor (TF) is the first chaperone to interact with newly synthesized polypeptides and assist their folding as they emerge from the ribosome. We report the first characterization of a TF from a psychrophilic organism. TF from
Psychrobacter frigidicola
(TF

Pf

) was cloned, produced in
Escherichia coli
, and purified. Strikingly, cross-linking and fluorescence anisotropy analyses revealed it to exist in solution as a monomer, unlike the well-characterized, dimeric
E. coli
TF (TF

Ec

). Moreover, TF

Pf

did not exhibit the downturn in reactivation of unfolded GAPDH (glyceraldehyde-3-phosphate dehydrogenase) that is observed with its
E. coli
counterpart, even at high TF/GAPDH molar ratios and revealed dramatically reduced retardation of membrane translocation by a model recombinant protein compared to the
E. coli
chaperone. TF

Pf

was also significantly more effective than TF

Ec

at increasing the yield of soluble and functional recombinant protein in a cell-free protein synthesis system, indicating that it is not dependent on downstream systems for its chaperoning activity. We propose that TF

Pf

differs from TF

Ec

in its quaternary structure and chaperone activity, and we discuss the potential significance of these differences in its native environment.
The Pentapeptide Repeat Proteins MfpA
Mt
and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex
Authors: Mérens Audrey , Matrat Stéphanie , Aubry Alexandra , Lascols Christine , Jarlier Vincent , Soussy Claude-James , Cavallo Jean-Didier , Cambau Emmanuelle 
Published: December 2008

ABSTRACT

MfpA
Mt
and QnrB4 are two newly characterized pentapeptide repeat proteins (PRPs) that interact with DNA gyrase. The
mfpA
Mt
gene is chromosome borne in
Mycobacterium tuberculosis
, while
qnrB4
is plasmid borne in enterobacteria. We expressed and purified the two PRPs and compared their effects on DNA gyrase, taking into account host specificity, i.e., the effect of MfpA
Mt
on
M. tuberculosis
gyrase and the effect of QnrB4 on
Escherichia coli
gyrase. Whereas QnrB4 inhibited
E. coli
gyrase activity only at concentrations higher than 30 μM, MfpA
Mt
inhibited all catalytic reactions of the
M. tuberculosis
gyrase described for this enzyme (supercoiling, cleavage, relaxation, and decatenation) with a 50% inhibitory concentration of 2 μM. We showed that the D87 residue in GyrA has a major role in the MfpA
Mt
-gyrase interaction, as D87H and D87G substitutions abolished MfpA
Mt
inhibition of
M. tuberculosis
gyrase catalytic reactions, while A83S modification did not. Since MfpA
Mt
and QnrB4 have been involved in resistance to fluoroquinolones, we measured the inhibition of the quinolone effect in the presence of each PRP. QnrB4 reversed quinolone inhibition of
E. coli
gyrase at 0.1 μM as described for other Qnr proteins, but MfpA
Mt
did not modify
M. tuberculosis
gyrase inhibition by fluoroquinolones. Crossover experiments showed that MfpA
Mt
also inhibited
E. coli
gyrase function, while QnrB4 did not reverse quinolone inhibition of
M. tuberculosis
gyrase. In conclusion, our in vitro experiments showed that MfpA
Mt
and QnrB4 exhibit opposite effects on DNA gyrase and that these effects are protein and species specific.
Chenodeoxycholate Is an Inhibitor of
Clostridium difficile
Spore Germination
Authors: Sorg Joseph A. , Sonenshein Abraham L. 
Published: December 2008

ABSTRACT

Some cholate derivatives that are normal components of bile can act with glycine to induce the germination of
Clostridium difficile
spores, but at least one bile component, chenodeoxycholate, does not induce germination. Here we show that chenodeoxycholate inhibits the germination of
C. difficile
spores in response to cholate and taurocholate.
Expression of
yeeK
during
Bacillus subtilis
Sporulation and Localization of YeeK to the Inner Spore Coat using Fluorescence Microscopy
Authors: Takamatsu Hiromu , Imamura Daisuke , Kuwana Ritsuko , Watabe Kazuhito 
Published: December 2008

ABSTRACT

The
yeeK
gene of
Bacillus subtilis
is predicted to encode a protein of 145 amino acids composed of 28% glycine, 23% histidine, and 12% tyrosine residues. Previous studies were unable to detect YeeK in wild-type spores; however, the 18-kDa YeeK polypeptide has been identified in
yabG
mutant spores. In this study, we analyze the expression and localization of YeeK to explore the relationship between YeeK and YabG. Northern hybridization analysis of wild-type RNA indicated that transcription of the
yeeK
gene, which was initiated 5 h after the onset of sporulation, was dependent on a SigK-containing RNA polymerase and the GerE protein. Genetic disruption of
yeeK
did not impair vegetative growth, development of resistant spores, or germination. Fluorescent microscopy of in-frame fusions of YeeK with green fluorescent protein (YeeK-GFP) and red fluorescent protein (YeeK-RFP) confirmed that YeeK assembles into the spore integument. CotE, SafA, and SpoVID were required for the proper localization of YeeK-GFP. Comparative analysis of YeeK-RFP and an in-frame GFP fusion of YabG indicated that YeeK colocalized with YabG in the spore coat. This is the first use of fluorescent proteins to show localization to different layers of the spore coat. Immunoblotting with anti-GFP antiserum indicated that YeeK-GFP was primarily synthesized as a 44-kDa molecule, which was then digested into a 29-kDa fragment that corresponded to the molecular size of GFP in wild-type spores. In contrast, a minimal amount of 44-kDa YeeK-GFP was digested in
yabG
mutant spores. Our findings demonstrate that YeeK is guided into the spore coat by CotE, SafA, and SpoVID. We conclude that YabG is directly or indirectly involved in the digestion of YeeK.
Purine Utilization byKlebsiella oxytocaM5al: Genes for Ring-Oxidizing and -Opening Enzymes
Authors: Pope Scott D. , Chen Li-Ling , Stewart Valley 
Published: December 2008

ABSTRACTThe enterobacteriumKlebsiella oxytocauses a variety of inorganic and organic nitrogen sources, including purines, nitrogen-rich compounds that are widespread in the biosphere. We have identified a 23-gene cluster that encodes the enzymes for utilizing purines as the sole nitrogen source. Growth and complementation tests with insertion mutants, combined with sequence comparisons, reveal functions for the products of these genes. Here, we report our characterization of 12 genes, one encoding guanine deaminase and the others encoding enzymes for converting (hypo)xanthine to allantoate. Conventionally, xanthine dehydrogenase, a broadly distributed molybdoflavoenzyme, catalyzes sequential hydroxylation reactions to convert hypoxanthine via xanthine to urate. Our results show that these reactions inK. oxytocaare catalyzed by a two-component oxygenase (HpxE-HpxD enzyme) homologous to Rieske nonheme iron aromatic-ring-hydroxylating systems, such as phthalate dioxygenase. Our results also reveal previously undescribed enzymes involved in urate oxidation to allantoin, catalyzed by a flavoprotein monooxygenase (HpxO enzyme), and in allantoin conversion to allantoate, which involves allantoin racemase (HpxA enzyme). The pathway also includes the recently described PuuE allantoinase (HpxB enzyme). The HpxE-HpxD and HpxO enzymes were discovered independently by de la Riva et al. (L. de la Riva, J. Badia, J. Aguilar, R. A. Bender, and L. Baldoma, J. Bacteriol. 190:7892-7903, 2008). Thus, several enzymes in thisK. oxytocapurine utilization pathway differ from those in other microorganisms. Isofunctional homologs of these enzymes apparently are encoded by other species, includingAcinetobacter,Burkholderia,Pseudomonas,Saccharomyces, andXanthomonas.
Comparison of Responses to Double-Strand Breaks betweenEscherichia coliandBacillus subtilisReveals Different Requirements for SOS Induction
Authors: Simmons Lyle A. , Goranov Alexi I. , Kobayashi Hajime , Davies Bryan W. , Yuan Daniel S. , Grossman Alan D. , Walker Graham C. 
Published: December 2008

ABSTRACTDNA double-strand breaks are particularly deleterious lesions that can lead to genomic instability and cell death. We investigated the SOS response to double-strand breaks in bothEscherichia coliandBacillus subtilis. InE. coli, double-strand breaks induced by ionizing radiation resulted in SOS induction in virtually every cell.E. colistrains incapable of SOS induction were sensitive to ionizing radiation. In striking contrast, we found that inB. subtilisboth ionizing radiation and a site-specific double-strand break causes induction of prophage PBSX and SOS gene expression in only a small subpopulation of cells. These results show that double-strand breaks provoke global SOS induction inE. colibut not inB. subtilis. Remarkably, RecA-GFP focus formation was nearly identical following ionizing radiation challenge in bothE. coliandB. subtilis, demonstrating that formation of RecA-GFP foci occurs in response to double-strand breaks but does not require or result in SOS induction inB. subtilis. Furthermore, we found thatB. subtiliscells incapable of inducing SOS had near wild-type levels of survival in response to ionizing radiation. Moreover,B. subtilisRecN contributes to maintaining low levels of SOS induction during double-strand break repair. Thus, we found that the contribution of SOS induction to double-strand break repair differs substantially betweenE. coliandB. subtilis.
Functional Roles of
arcA
,
etrA
, Cyclic AMP (cAMP)-cAMP Receptor Protein, and
cya
in the Arsenate Respiration Pathway in
Shewanella
sp. Strain ANA-3
Authors: Murphy Julie N. , Durbin K. James , Saltikov Chad W. 
Published: December 2008

ABSTRACT

Microbial arsenate respiration can enhance arsenic release from arsenic-bearing minerals—a process that can cause arsenic contamination of water. In
Shewanella
sp. strain ANA-3, the arsenate respiration genes (
arrAB
) are induced under anaerobic conditions with arsenate and arsenite. Here we report how genes that encode anaerobic regulator (
arcA
and
etrA
[
fnr
homolog]) and carbon catabolite repression (
crp
and
cya
) proteins affect arsenate respiration in ANA-3. Transcription of
arcA
,
etrA
, and
crp
in ANA-3 was similar in cells grown on arsenate and cells grown under aerobic conditions. ANA-3 strains lacking
arcA
and
etrA
showed minor to moderate growth defects, respectively, with arsenate. However,
crp
was essential for growth on arsenate. In contrast to the wild-type strain,
arrA
was not induced in the
crp
mutant in cultures shifted from aerobic to anaerobic conditions containing arsenate. This indicated that cyclic AMP (cAMP)-cyclic AMP receptor (CRP) activates
arr
operon transcription. Computation analysis for genome-wide CRP binding motifs identified a putative binding motif within the
arr
promoter region. This was verified by electrophoretic mobility shift assays with cAMP-CRP and several DNA probes. Lastly, four putative adenylate cyclase (
cya
) genes were identified in the genome. One particular
cya
-like gene was differentially expressed under aerobic versus arsenate respiration conditions. Moreover, a double mutant lacking two of the
cya
-like genes could not grow with arsenate as a terminal electron acceptor; exogenous cAMP could complement growth of the double
cya
mutant. It is concluded that the components of the carbon catabolite repression system are essential to regulating arsenate respiratory reduction in
Shewanella
sp. strain ANA-3.
Streptomyces
Telomeres Contain a Promoter
Authors: Lin Yuh-ru , Hahn Mi-Young , Roe Jung-Hye , Huang Tzu-Wen , Tsai Hsiu-Hui , Lin Yung-Feng , Su Tsung-Sheng , Chan Yu-Jiun , Chen Carton W. 
Published: December 2008

ABSTRACT

Bidirectional replication of the linear chromosomes and plasmids of
Streptomyces
spp. results in single-strand overhangs at their 3′ ends, which contain extensive complex palindromic sequences. The overhangs are believed to be patched by DNA synthesis primed by a terminal protein that remains covalently bound to the 5′ ends of the telomeres. We discovered that in vitro a conserved 167-bp telomere DNA binds strongly to RNA polymerase holoenzyme and exhibits promoter activities stronger than those of an rRNA operon. In vivo, the telomere DNA exhibited promoter activity in both orientations on a circular plasmid in
Streptomyces
. The telomere promoter is also active on a linear plasmid during exponential growth. Such promoter activity in a telomere has not hitherto been observed in eukaryotic or prokaryotic replicons.
Streptomyces
telomere promoters may be involved in priming the terminal Okazaki fragment (during replication) replicative transfer (during conjugation), or expression of downstream genes (including a conserved
ttrA
helicase-like gene involved in conjugal transfer). Interestingly, the
Streptomyces
telomeres also function as a promoter in
Escherichia coli
and as a transcription enhancer in yeast.
Control of Gluconate Utilization in
Sinorhizobium meliloti
Authors: Steele Tyler T. , Fowler Christopher W. , Griffitts Joel S. 
Published: December 2008

ABSTRACT

The
Sinorhizobium meliloti
megaplasmid pSymA has previously been implicated in gluconate utilization. We report a locus on pSymA encoding a putative tripartite ATP-independent periplasmic (TRAP) transporter that is required for gluconate utilization. The expression of this locus is negatively regulated by a GntR family regulator encoded adjacent to the transporter operon.
Mycobacterium aviumGenes MAV_5138 and MAV_3679 Are Transcriptional Regulators That Play a Role in Invasion of Epithelial Cells, in Part by Their Regulation of CipA, a Putative Surface Protein Interacting with Host Cell Signaling Pathways
Authors: Harriff Melanie J. , Danelishvili Lia , Wu Martin , Wilder Cara , McNamara Michael , Kent Michael L. , Bermudez Luiz E. 
Published: December 2008

ABSTRACTTheMycobacterium aviumcomplex (MAC) is an important group of opportunistic pathogens for birds, cattle, swine, and immunosuppressed humans. Although invasion of epithelial cells lining the intestine is the chief point of entry for these organisms, little is known about the mechanisms by which members of the MAC are taken up by these cells. Studies withM. aviumhave shown that cytoskeletal rearrangement via activation of the small G-protein Cdc42 is involved and that this activation is regulated in part by theM. avium fadD2gene. ThefadD2gene indirectly regulates a number of genes upon exposure to HEp-2 cells, including transcriptional regulators, membrane proteins, and secreted proteins. Overexpression of two fadD2-associated regulators (MAV_5138 and MAV_3679) led to increased invasion of HEp-2 cells, as well as altered expression of other genes. The protein product of one of the regulated genes, named CipA, has domains that resemble the PXXP motif of human Piccolo proteins, which bind SH3 domains in proteins involved in the scaffold complex formed during cytoskeletal rearrangement. Although CipA was not detected in the cytoplasm of HEp-2 cells exposed toM. avium, the recombinant protein was shown to be potentially expressed on the surface ofMycobacterium smegmatisincubated with HEp-2 cells and, possibly, to interact with human Cdc42. The interaction was then confirmed by showing that CipA activates Cdc42. These results suggest that members of theM. aviumcomplex have a novel mechanism for activating cytoskeletal rearrangement, prompting uptake by host epithelial cells, and that this mechanism is regulated in part byfadD2, MAV_5138, and MAV_3679.
Swimming Motility Mutants of Marine
Synechococcus
Affected in Production and Localization of the S-Layer Protein SwmA
Authors: McCarren J. , Brahamsha B. 
Published: December 2008

ABSTRACT

The S-layer protein SwmA is required for nonflagellar swimming in marine
Synechococcus
. An analysis of mutations in seven genes at two loci in the
Synechococcus
sp. strain WH8102 genome indicates that a multicomponent transporter and glycosyltransferases are required for the production and proper localization of SwmA.
Y4lO of
Rhizobium
sp. Strain NGR234 Is a Symbiotic Determinant Required for Symbiosome Differentiation
Authors: Yang Feng-Juan , Cheng Li-Li , Zhang Ling , Dai Wei-Jun , Liu Zhe , Yao Nan , Xie Zhi-Ping , Staehelin Christian 
Published: December 2008

ABSTRACT

Type 3 (T3) effector proteins, secreted by nitrogen-fixing rhizobia with a bacterial T3 secretion system, affect the nodulation of certain host legumes. The open reading frame y4lO of
Rhizobium
sp. strain NGR234 encodes a protein with sequence similarities to T3 effectors from pathogenic bacteria (the YopJ effector family). Transcription studies showed that the promoter activity of y4lO depended on the transcriptional activator TtsI. Recombinant Y4lO protein expressed in
Escherichia coli
did not acetylate two representative mitogen-activated protein kinase kinases (human MKK6 and MKK1 from
Medicago truncatula
), indicating that YopJ-like proteins differ with respect to their substrate specificities. The y4lO gene was mutated in NGR234 (strain NGRΩ
y4lO
) and in NGRΩ
nopL
, a mutant that does not produce the T3 effector NopL (strain NGRΩ
nopL
Ω
y4lO
). When used as inoculants, the symbiotic properties of the mutants differed.
Tephrosia vogelii, Phaseolus vulgaris
cv. Yudou No. 1, and
Vigna unguiculata
cv. Sui Qing Dou Jiao formed pink effective nodules with NGR234 and NGRΩ
nopL
Ω
y4lO
. Nodules induced by NGRΩ
y4lO
were first pink but rapidly turned greenish (ineffective nodules), indicating premature senescence. An ultrastructural analysis of the nodules induced by NGRΩ
y4lO
revealed abnormal formation of enlarged infection droplets in ineffective nodules, whereas symbiosomes harboring a single bacteroid were frequently observed in effective nodules induced by NGR234 or NGRΩ
nopL
Ω
y4lO
. It is concluded that Y4lO is a symbiotic determinant involved in the differentiation of symbiosomes. Y4lO mitigated senescence-inducing effects caused by the T3 effector NopL, suggesting synergistic effects for Y4lO and NopL in nitrogen-fixing nodules.