scholarly journals The Gene Cluster for Agmatine Catabolism of Enterococcus faecalis: Study of Recombinant Putrescine Transcarbamylase and Agmatine Deiminase and a Snapshot of Agmatine Deiminase Catalyzing Its Reaction

2006 ◽  
Vol 189 (4) ◽  
pp. 1254-1265 ◽  
Author(s):  
José L. Llácer ◽  
Luis Mariano Polo ◽  
Sandra Tavárez ◽  
Benito Alarcón ◽  
Rebeca Hilario ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Enterococcus Faecalis ◽  
Duplication Event ◽  
Arginine Deiminase ◽  
Substrate Affinity ◽  
En Bloc ◽  
Carbamate Kinase ◽  
Atp Generation ◽  
Agmatine Deiminase ◽  
Covalent Catalysis

ABSTRACT Enterococcus faecalis makes ATP from agmatine in three steps catalyzed by agmatine deiminase (AgDI), putrescine transcarbamylase (PTC), and carbamate kinase (CK). An antiporter exchanges putrescine for agmatine. We have cloned the E. faecalis ef0732 and ef0734 genes of the reported gene cluster for agmatine catabolism, overexpressed them in Escherichia coli, purified the products, characterized them functionally as PTC and AgDI, and crystallized and X-ray diffracted them. The 1.65-Å-resolution structure of AgDI forming a covalent adduct with an agmatine-derived amidine reactional intermediate is described. We provide definitive identification of the gene cluster for agmatine catabolism and confirm that ornithine is a genuine but poor PTC substrate, suggesting that PTC (found here to be trimeric) evolved from ornithine transcarbamylase. N-(Phosphonoacetyl)-putrescine was prepared and shown to strongly (Ki = 10 nM) and selectively inhibit PTC and to improve PTC crystallization. We find that E. faecalis AgDI, which is committed to ATP generation, closely resembles the AgDIs involved in making polyamines, suggesting the recruitment of a polyamine-synthesizing AgDI into the AgDI pathway. The arginine deiminase (ADI) pathway of arginine catabolism probably supplied the genes for PTC and CK but not those for the agmatine/putrescine antiporter, and thus the AgDI and ADI pathways are not related by a single “en bloc” duplication event. The AgDI crystal structure reveals a tetramer with a five-blade propeller subunit fold, proves that AgDI closely resembles ADI despite a lack of sequence identity, and explains substrate affinity, selectivity, and Cys357-mediated-covalent catalysis. A three-tongued agmatine-triggered gating opens or blocks access to the active center.

scholarly journals Lmo0036, an ornithine and putrescine carbamoyltransferase in Listeria monocytogenes, participates in arginine deiminase and agmatine deiminase pathways and mediates acid tolerance

Microbiology ◽  
2011 ◽  
Vol 157 (11) ◽  
pp. 3150-3161 ◽  
Author(s):  
Jianshun Chen ◽  
Changyong Cheng ◽  
Ye Xia ◽  
Hanxin Zhao ◽  
Chun Fang ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Foodborne Pathogens ◽  
Foodborne Pathogen ◽  
Acid Tolerance ◽  
Arginine Deiminase ◽  
Transcriptional Level ◽  
Acidic Conditions ◽  
Acidic Environments ◽  
Agmatine Deiminase

Listeria monocytogenes is a foodborne pathogen causing listeriosis. Acid is one of the stresses that foodborne pathogens encounter most frequently. The ability to survive and proliferate in acidic environments is a prerequisite for infection. However, there is limited knowledge about the molecular basis of adaptation of L. monocytogenes to acid. Arginine deiminase (ADI) and agmatine deiminase (AgDI) systems are implicated in bacterial tolerance to acidic environments. Homologues of ADI and AgDI systems have been found in L. monocytogenes lineages I and II strains. Sequence analysis indicated that lmo0036 encodes a putative carbamoyltransferase containing conserved motifs and residues important for substrate binding. Lmo0036 acted as an ornithine carbamoyltransferase and putrescine carbamoyltransferase, representing the first example, to our knowledge, that catalyses reversible ornithine and putrescine carbamoyltransfer reactions. Catabolic ornithine and putrescine carbamoyltransfer reactions constitute the second step of ADI and AgDI pathways. However, the equilibrium of in vitro carbamoyltransfer reactions was overwhelmingly towards the anabolic direction, suggesting that catabolic carbamoyltransferase was probably the limiting step of the pathways. lmo0036 was induced at the transcriptional level when L. monocytogenes was subjected to low-pH stress. Its expression product in Escherichia coli exhibited higher catabolic carbamoyltransfer activities under acidic conditions. Consistently, absence of this enzyme impaired the growth of Listeria under mild acidic conditions (pH 4.8) and reduced its survival in synthetic human gastric fluid (pH 2.5), and corresponded to a loss in ammonia production, indicating that Lmo0036 was responsible for acid tolerance at both sublethal and lethal pH levels. Furthermore, Lmo0036 played a possible role in Listeria virulence.

scholarly journals Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Haijian Du ◽  
Wenyan Zhang ◽  
Wensi Zhang ◽  
Weijia Zhang ◽  
Hongmiao Pan ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Cluster ◽  
Geomagnetic Field ◽  
Evolutionary Biology ◽  
Genomic Analysis ◽  
Magnetotactic Bacteria ◽  
Duplication Event ◽  
Comparative Genomic ◽  
Content Type ◽  
Evolutionary Trajectories

ABSTRACT The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth’s geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria. Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria. The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria. IMPORTANCE A diversity of organisms can sense the geomagnetic field for the purpose of navigation. Magnetotactic bacteria are the most primitive magnetism-sensing organisms known thus far and represent an excellent model system for the study of the origin, evolution, and mechanism of microbial magnetoreception (or magnetotaxis). The present study is the first report focused on magnetosome gene cluster duplication in the Alphaproteobacteria, which suggests the important role of gene duplication in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria. A novel scenario for the evolution of magnetotaxis in the Alphaproteobacteria is proposed and may provide new insights into evolution of magnetoreception of higher species.

scholarly journals Structure, Regulation, and Putative Function of the Arginine Deiminase System of Streptococcus suis

2006 ◽  
Vol 188 (2) ◽  
pp. 361-369 ◽  
Author(s):  
Petra Gruening ◽  
Marcus Fulde ◽  
Peter Valentin-Weigand ◽  
Ralph Goethe
Keyword(s):  
Binding Site ◽  
Streptococcus Suis ◽  
Arginine Deiminase ◽  
Knockout Mutant ◽  
Transcription Regulator ◽  
Protective Antigens ◽  
Ornithine Carbamoyl Transferase ◽  
Young Pigs ◽  
Arginine Repressor ◽  
Carbamate Kinase

ABSTRACT Streptococcus suis is an important cause of infectious diseases in young pigs. Little is known about the virulence factors or protective antigens of S. suis. Recently, we have identified two proteins of the arginine deiminase system (ADS) of S. suis, which were temperature induced and expressed on the streptococcal surface (N. Winterhoff, R. Goethe, P. Gruening, M. Rohde, H. Kalisz, H. E. Smith, and P. Valentin-Weigand, J. Bacteriol. 184:6768-6776, 2002). In the present study, we analyzed the complete ADS of S. suis. Due to their homologies to the recently published S. gordonii ADS genes, the genes for arginine deiminase, ornithine carbamoyl-transferase, and carbamate kinase, which were previously designated adiS, octS, and ckS, respectively, were renamed arcA, arcB, and arcC, respectively. Our data revealed that arcA, arcB, and arcC of the S. suis ADS are transcribed from an operon (arcABC operon). Additionally, putative ADS-associated genes were cloned and sequenced which, however, did not belong to the arcABC operon. These were the flpS gene upstream of the arcABC operon with homology to the flp transcription regulator of S. gordonii and the arcD, arcT, arcH, and argR genes downstream of the arcABC operon with high homologies to a putative arginine-ornithine antiporter, a putative dipeptidase of S. gordonii, a putative β-N-acetylhexosaminidase of S. pneumoniae, and a putative arginine repressor of S. gordonii, respectively. The transcriptional start point of the arcABC operon was determined, and promoter analysis provided evidence that multiple factors contribute to the regulation of the ADS. Thus, a putative binding site for a transcription regulator of the Crp/Fnr family, an ArgR-binding site, and two cis-acting catabolite response elements were identified in the promoter-operator region of the operon. Consistent with this, we could demonstrate that the ADS of S. suis is inducible by arginine and reduced O2 tension and subject to carbon catabolite repression. Furthermore, comparing an arcA knockout mutant in which expression of the three operon-encoded proteins was abolished with the parental wild-type strain showed that the arcABC operon of S. suis contributes to survival under acidic conditions.

scholarly journals Catabolism of Branched-Chain α-Keto Acids in Enterococcus faecalis: the bkd Gene Cluster, Enzymes, and Metabolic Route

1999 ◽  
Vol 181 (17) ◽  
pp. 5433-5442 ◽  
Author(s):  
Donald E. Ward ◽  
R. Paul Ross ◽  
Coen C. van der Weijden ◽  
Jacky L. Snoep ◽  
Al Claiborne
Keyword(s):  
Gene Cluster ◽  
Enterococcus Faecalis ◽  
Specific Activity ◽  
Pyruvate Dehydrogenase Complex ◽  
Type Conversion ◽  
Metabolic Route ◽  
Keto Acids ◽  
Genes Encoding ◽  
Lipoamide Dehydrogenase ◽  
Branched Chain

ABSTRACT Genes encoding a branched-chain α-keto acid dehydrogenase fromEnterococcus faecalis 10C1, E1α (bkdA), E1β (bkdB), E2 (bkdC), and E3 (bkdD), were found to reside in the gene cluster ptb-buk-bkdDABC. The predicted products of ptb and buk exhibited significant homology to the phosphotransbutyrylase and butyrate kinase, respectively, from Clostridium acetobutylicum. Activity and redox properties of the purified recombinant enzyme encoded bybkdD indicate that E. faecalis has a lipoamide dehydrogenase that is distinct from the lipoamide dehydrogenase associated with the pyruvate dehydrogenase complex. Specific activity of the ptb gene product expressed in Escherichia coli was highest with the substrates valeryl-coenzyme A (CoA), isovaleryl-CoA, and isobutyryl-CoA. In cultures, a stoichiometric conversion of α-ketoisocaproate to isovalerate was observed, with a concomitant increase in biomass. We propose that α-ketoisocaproate is converted via the BKDH complex to isovaleryl-CoA and subsequently converted into isovalerate via the combined actions of theptb and buk gene products with the concomitant phosphorylation of ADP. In contrast, an E. faecalis bkdmutant constructed by disruption of the bkdA gene did not benefit from having α-ketoisocaproate in the growth medium, and conversion to isovalerate was less than 2% of the wild-type conversion. It is concluded that the bkd gene cluster encodes the enzymes that constitute a catabolic pathway for branched-chain α-keto acids that was previously unidentified inE. faecalis.

scholarly journals AsnB is responsible for peptidoglycan precursor amidation in Clostridium difficile in the presence of vancomycin

Microbiology ◽  
2020 ◽  
Vol 166 (6) ◽  
pp. 567-578 ◽  
Author(s):  
Fariza Ammam ◽  
Delphine Patin ◽  
Héloise Coullon ◽  
Didier Blanot ◽  
Thierry Lambert ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Gene Cluster ◽  
Enterococcus Faecalis ◽  
Type Species ◽  
Asparagine Synthetase ◽  
Structure Modification ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Peptidoglycan Structure

Clostridium difficile 630 possesses a cryptic but functional gene cluster vanG Cd homologous to the vanG operon of Enterococcus faecalis . Expression of vanG Cd in the presence of subinhibitory concentrations of vancomycin is accompanied by peptidoglycan amidation on the meso-DAP residue. In this paper, we report the presence of two potential asparagine synthetase genes named asnB and asnB2 in the C. difficile genome whose products were potentially involved in this peptidoglycan structure modification. We found that asnB expression was only induced when C. difficile was grown in the presence of vancomycin, yet independently from the vanG Cd resistance and regulation operons. In addition, peptidoglycan precursors were not amidated when asnB was inactivated. No change in vancomycin MIC was observed in the asnB mutant strain. In contrast, overexpression of asnB resulted in the amidation of most of the C. difficile peptidoglycan precursors and in a weak increase of vancomycin susceptibility. AsnB activity was confirmed in E. coli . In contrast, the expression of the second asparagine synthetase, AsnB2, was not induced in the presence of vancomycin. In summary, our results demonstrate that AsnB is responsible for peptidoglycan amidation of C. difficile in the presence of vancomycin.

scholarly journals Structural and Functional Analysis of the Gene Cluster Encoding the Enzymes of the Arginine Deiminase Pathway ofLactobacillus sake

1998 ◽  
Vol 180 (16) ◽  
pp. 4154-4159 ◽  
Author(s):  
Manuel Zúñiga ◽  
Marie Champomier-Verges ◽  
Monique Zagorec ◽  
Gaspar Pérez-Martínez
Keyword(s):  
Genomic Library ◽  
Arginine Deiminase ◽  
Degenerate Primers ◽  
Pcr Screening ◽  
Lactobacillus Sake ◽  
Arginine Catabolism ◽  
Carbamate Kinase ◽  
Encoding Gene ◽  
Ornithine Transcarbamoylase ◽  
Encoding Genes

ABSTRACT Lactobacillus sake can use arginine via the arginine deiminase (ADI) pathway. We designed degenerate primers based on an alignment of known sequences of ornithine transcarbamoylase (OTC)-encoding genes in order to amplify the L. sakecounterpart sequences by PCR. Screening a genomic library of L. sake in λEMBL3 allowed us to isolate a clone containing a 10-kbL. sake genomic DNA insert. Sequence analysis revealed that the genes involved in arginine catabolism were clustered and encoded ADI (arcA), OTC (arcB), carbamate kinase (arcC), and a putative carrier with high similarity to the arginine/ornithine antiporter of Pseudomonas aeruginosa(arcD). Additionally, a putative transaminase-encoding gene (arcT) was located in this region. The genes followed the order arcA arcB arcC arcT arcD, which differs from that found in other microorganisms. arcA, arcB,arcC, and arcD mutants were constructed, and the ADI pathway was impaired in all of them. Transcriptional studies indicated that arcA gene is subject to catabolite repression, and under the conditions used, several transcripts could be detected, suggesting the existence of different initiation sites or processing of a larger mRNA.

scholarly journals Expression of the Agmatine Deiminase Pathway in Enterococcus faecalis Is Activated by the AguR Regulator and Repressed by CcpA and PTSMan Systems

PLoS ONE ◽  
2013 ◽  
Vol 8 (10) ◽  
pp. e76170 ◽  
Author(s):  
Cristian Suárez ◽  
Martín Espariz ◽  
Víctor S. Blancato ◽  
Christian Magni
Keyword(s):  
Enterococcus Faecalis ◽  
Agmatine Deiminase

Enzymes of agmatine degradation and the control of their synthesis in Streptococcus faecalis

1982 ◽  
Vol 152 (2) ◽  
pp. 676-681
Author(s):  
J P Simon ◽  
V Stalon
Keyword(s):  
Energy Source ◽  
Catabolite Repression ◽  
Type Strain ◽  
Wild Type Strain ◽  
Arginine Deiminase ◽  
The Other ◽  
Wild Type ◽  
Streptococcus Faecalis ◽  
Agmatine Deiminase ◽  
Sole Energy

Streptococcus faecalis ATCC 11700 uses agmatine as its sole energy source for growth. Agmatine deiminase and putrescine carbamoyltransferase are coinduced by growth on agmatine. Glucose and arginine were found to exert catabolite repression on the agmatine deiminase pathway. Four mutants unable to utilize agmatine as an energy source, isolated from the wild-type strain, exhibited three distinct phenotypes. Two of these strains showed essentially no agmatine deiminase, one mutant showed negligible activity of putrescine carbamoyltransferase, and one mutant was defective in both activities. Two carbamate kinases are present in S. faecalis, one belonging to the arginine deiminase pathway, the other being induced by growth on agmatine. These two enzymes have the same molecular weight, 82,000, and seem quite different in size from the kinases isolated from other streptococci.

The High Biofilm-Encoding Bee Locus: A Second Pilus Gene Cluster in Enterococcus faecalis?

2009 ◽  
Vol 59 (2) ◽  
pp. 206-211 ◽  
Author(s):  
Susanne Schlüter ◽  
Charles M. A. P. Franz ◽  
Frank Gesellchen ◽  
Oliver Bertinetti ◽  
Friedrich W. Herberg ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Enterococcus Faecalis
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