Jun Maki

Identification and characterization of a putative endolysin encoded by episomal phage phiSM101 of Clostridium perfringens

Clostridium perfringens produces potent toxins and histolytic enzymes, causing various diseases including life-threatening fulminant diseases in humans and other animals. Aiming at utilizing a phage endolysin as a therapeutic alternative to antibiotics, we surveyed the genome and bacteriophage sequences of C. perfringens. A phiSM101 muramidase gene (psm) revealed by this study can be assumed to encode an N-acetylmuramidase, since the N-terminal catalytic domain deduced from the gene shows high homology of those of N-acetylmuramidases. The psm gene is characteristic in that it is present in phiSM101, an episomal phage of enterotoxigenic C. perfringens type A strain, SM101, and also in that homologous genes are present in the genomes of all five C. perfringens toxin types. The psm gene was cloned and expressed in Escherichia coli as a protein histidine-tagged at the N-terminus (Psm-his). Psm-his was purified to homogeneity by nickel-charged immobilized metal affinity chromatography and anion-exchange chromatography. The purified enzyme lysed cells of all C. perfringens toxin types but not other clostridial species tested, as was shown by a turbidity reduction assay. These results indicate the Psm-his is useful as a cell-wall lytic enzyme and also suggest that it is potentially useful for biocontrol of this organism.

X‐ray structure of a novel endolysin encoded by episomal phage phiSM101 of Clostridium perfringens

Gram‐positive bacteria possess a thick cell wall composed of a mesh polymer of peptidoglycans, which provides physical protection. Endolysins encoded by phages infecting bacteria can hydrolyse peptidoglycans in the bacterial cell wall, killing the host bacteria immediately. The endolysin (Psm) encoded by episomal phage phiSM101 of enterotoxigenic Clostridium perfringens type A strain SM101 exhibits potent lytic activity towards most strains of Clostridium perfringens. Psm has an N‐terminal catalytic domain highly homologous to N‐acetylmuramidases belonging to the glycoside hydrolase 25 family, and C‐terminal tandem repeated bacterial Src homology 3 (SH3_3) domains as the cell wall‐binding domain. The X‐ray structure of full‐length Psm and a catalytic domain of Psm in complex with N‐acetylglucosamine were determined to elucidate the catalytic reaction and cell wall recognition mechanisms of Psm. The results showed that Psm may have adopted a neighbouring‐group mechanism for the catalytic hydrolysing reaction in which the N‐acetyl carbonyl group of the substrate was involved in the formation of an oxazolinium ion intermediate. Based on structural comparisons with other endolysins and a modelling study, we proposed that tandem repeated SH3_3 domains of Psm recognized the peptide side‐chains of peptidoglycans to assist the catalytic domain hydrolysing the glycan backbone.

The Vibrio parahaemolyticus Small RNA RyhB Promotes Production of the Siderophore Vibrioferrin by Stabilizing the Polycistronic mRNA

High-affinity iron acquisition in Vibrio parahaemolyticus is mediated by the cognate siderophore vibrioferrin. We have previously reported that the vibrioferrin biosynthesis operon (pvsOp) is regulated at the transcriptional level by the iron-responsive repressor Fur (T. Tanabe, T. Funahashi, H. Nakao, S. Miyoshi, S. Shinoda, and S. Yamamoto, J. Bacteriol. 185:6938-6949, 2003). In this study, we identified the Fur-regulated small RNA RyhB and the RNA chaperone Hfq protein as additional regulatory proteins of vibrioferrin biosynthesis. We found that vibrioferrin production was greatly impaired in both the ryhB and hfq deletion mutants, and a TargetRNA search (http://snowwhite.wellesley.edu/targetRNA/index2.html) revealed that the 5-untranslated region of pvsOp mRNA (pvsOp 5-UTR) contains a potential base-pairing region required for the formation of the RyhB-pvsOp 5-UTR duplex. An electrophoresis mobility shift assay indicated that RyhB can directly bind to the pvsOp 5-UTR with the aid of Hfq. Rifampin chase experiments indicated that the half-life of pvsOp mRNA in the ryhB and hfq mutants was approximately 3-fold shorter than that in the parental strain, suggesting that both RyhB and Hfq are engaged in the stabilization of pvsOp mRNA. Chrome azurol S assays followed by electrophoresis mobility shift assays and rifampin chase experiments carried out for mutant strains indicated that base pairing between RyhB and the pvsOp 5-UTR results in an increase in the stability of pvsOp mRNA, thereby leading to the promotion of vibrioferrin production. It is unprecedented that RyhB confers increased stability on a polycistronic mRNA involved in siderophore biosynthesis as a direct target.

Characterization of a gene encoding the outer membrane receptor for ferric enterobactin in Aeromonas hydrophila ATCC 7966(T).

Aeromonas hydrophila ATCC 7966(T) produces a catecholate siderophore amonabactin in response to iron starvation. In this study, we determined that this strain utilizes exogenously supplied enterobactin (Ent) for growth under iron-limiting conditions. A homology search of the A. hydrophila ATCC 7966(T) genomic sequence revealed the existence of a candidate gene encoding a protein homologous to Vibrio parahaemolyticus IrgA that functions as the outer membrane receptor for ferric Ent. SDS-PAGE showed induction of IrgA under iron-limiting conditions. The growth of the double mutant of irgA and entA (one of the amonabactin biosynthetic genes) was restored when it was complemented with irgA in the presence of Ent. Moreover, a growth assay of three isogenic tonB mutants indicated that the tonB2 system exclusively provides energy for IrgA to transport ferric Ent. Finally, reverse transcriptase-quantitative PCR revealed that the transcription of irgA and the TonB2 system cluster genes is iron-regulated, consistently with the presence of a predicted Fur box in the promoter region.

Regulation of the Expression of the Vibrio parahaemolyticus peuA Gene Encoding an Alternative Ferric Enterobactin Receptor

A pvsB-vctA-irgA triple deletion mutant of Vibrio parahaemolyticus can utilize enterobactin under iron-limiting conditions by inducing a previously undescribed receptor, PeuA (VPA0150), in response to extracellular alkaline pH and enterobactin. In silico analyses revealed the existence of a two-component regulatory system operon, peuRS, immediately upstream of peuA, which constitutes an operon with the TonB2 system genes. Both the peuRS and peuA-tonB2 operons were found to be upregulated under iron-limiting conditions in a ferric uptake regulator (Fur)-dependent manner. The involvement of peuA and peuRS in enterobactin utilization was analyzed by complementation experiments using deletion mutants. Primer extension analysis indicated that, under iron-limiting conditions, the transcription of peuA was initiated from the +1 site at pH 7.0 and from both the +1 and +39 sites at pH 8.0 in the presence of enterobactin. The +39 transcript was absent from the peuRS deletion mutant. Secondary structure prediction of their 5′-untranslated regions suggested that translation initiation is blocked in the +1 transcript, but not in the +39 transcript. Consistent with this, in vitro translation analysis demonstrated that production of PeuA was determined only by the +39 transcript. These studies establish a novel gene regulation mechanism in which the two-component regulatory system PeuRS enhances expression of the alternative +39 transcript that possesses non-inhibitory structure, allowing the peuA expression to be regulated at the translation stage.

Identification and characterization of Aeromonas hydrophila genes encoding the outer membrane receptor of ferrioxamine B and an AraC-type transcriptional regulator

We found that, under iron-limiting conditions, Aeromonas hydrophila ATCC 7966T could utilize the xenosiderophore desferrioxamine B (DFOB) for growth by inducing the expression of its own outer membrane receptor. Two consecutive genes, desR and desA, were selected as candidates involved in DFOB utilization. The presence of the ferric-uptake regulator boxes in their promoters suggested that these genes are under iron-dependent regulation. Mutation of desA, a gene that encodes the outer membrane receptor of ferrioxamine B, disrupted the growth of the amonabactin-deficient mutant in the presence of DFOB. β-Galactosidase reporter assays and reverse transcriptase-quantitative PCR demonstrated that desR, a gene that encodes an AraC-like regulator homolog is required for the induction of desA transcription in the presence of DFOB and under iron-limiting conditions. The functions of desA and desR were analyzed using complementation experiments. Our data provided evidence that DesA is powered primarily by the TonB2 system. Graphical Abstract Proposed model for DesR (AraC-type transcriptional regulator)-mediated transcriptional regulation of desA (encoding the outer membrane receptor for ferrioxamine B) gene in Aeromonas hydrophila.

Structural and biochemical characterization of the Clostridium perfringens autolysin catalytic domain

Bacterial autolysins can partially hydrolyze cell wall peptidoglycans into small sections to regulate cell separation/division and the growth phase. Clostridium perfringens autolysin (Acp) has an N‐terminal cell wall‐binding domain and a C‐terminal catalytic domain with glucosaminidase activity that belongs to the glycoside hydrolase 73 family. Here, we determined the X‐ray structure of the Acp catalytic domain (AcpCD) at 1.76 Å resolution. AcpCD has a unique crescent‐shaped structure, forming a deep groove for substrate‐binding at the center of the protein. The modeling study of the enzyme/substrate complex demonstrated that the length of the substrate‐binding groove is closely related to the glucosaminidase activity. Mutagenesis analysis showed that AcpCD likely adopts a neighboring‐group mechanism for the catalytic reaction.

Identification and characterization of a cluster of genes involved in biosynthesis and transport of acinetoferrin, a siderophore produced by Acinetobacter haemolyticus ATCC 17906T

Acinetobacter haemolyticus ATCC 17906(T) is known to produce the siderophore acinetoferrin under iron-limiting conditions. Here, we show that an operon consisting of eight consecutive genes, named acbABCD and actBCAD, participates in the biosynthesis and transport of acinetoferrin, respectively. Transcription of the operon was found to be iron-regulated by a putative Fur box located in the promoter region of the first gene, acbA. Homology searches suggest that acbABCD and actA encode enzyme proteins involved in acinetoferrin biosynthesis and an outer-membrane receptor for ferric acinetoferrin, respectively. Mutants defective in acbA and actA were unable to produce acinetoferrin or to express the ferric acinetoferrin receptor under iron-limiting conditions. These abilities were rescued by complementation of the mutants with native acbA and actA genes. Secondary structure analysis predicted that the products of actC and actD may be inner-membrane proteins with 12 membrane-spanning helices that belong to the major facilitator superfamily proteins. ActC showed homology to Sinorhizobium meliloti RhtX, which has been characterized as an inner-membrane importer for ferric rhizobactin 1021 structurally similar to acinetoferrin. Compared to the parental ATCC 17906(T) strain, the actD mutant displayed about a 35u200a% reduction in secretion of acinetoferrin, which was restored by complementation with actD, suggesting that ActD acts as an exporter of the siderophore. Finally, the actB product was significantly similar to hypothetical proteins in certain bacteria, in which genes encoding ActBCA homologues are arranged in the same order as in A. haemolyticus ATCC 17906(T). However, the function of ActB remains to be clarified.

Identification of Characteristic Phenolic Constituents in Mousouchiku Extract Used as Food Additives

Mousouchiku extract is prepared from the bamboo-sheath of Phyllostachys heterocycla MITF. (Poaceae), and is registered as a food manufacturing agent in the List of Existing Food Additives in Japan. This study describes the chromatographic evaluation of characteristic components of this extract to obtain the chemical data needed for standardized specifications. We isolated 12 known compounds from this extract: 5-hydroxymethyl-2-furfural, 4-hydroxybenzoic acid, trans-p-coumaric acid, trans-ferulic acid, N,N-diferuloylputrescine, 4-hydroxypropiophenone, β-arbutin, tachioside, isotachioside, 3,4-dihydroxypropiophenone 3-O-glucoside, koaburaside, and (+)-lyoniresinol 9-O-glucoside. Moreover, a new propiophenone glycoside, propiophenone 4-O-(6-β-D-xylosyl)-β-D-glucoside (propiophenone 4-O-primeveroside), was isolated. The structure of each isolated compound was elucidated based on NMR and MS data or direct HPLC comparisons with authentic samples. Among the isolates, (+)-lyoniresinol 9-O-glucoside was found to be the major ingredients of the extract as observed using HPLC analysis. However, 2,6-dimethoxy-1,4-benzoquinone, which is considered the main constituent of mousouchiku extract, was only detected as a trace constituent and not isolated in this study.

A Novel Methodology for Synthesis of 1,5,6-Trisubstituted 2(1H)-Pyrazinones of Biological Interest

In this report, we describe a new method for the synthesis of densely functionalized 2(1H)-pyrazinones. Treatment of mesoionic 1,3-oxazolium-5-olates with carbanions derived from activated methylene isocyanides (p-toluenesulfonylmethyl isocyanide (TosMIC) and ethyl isocyanoacetate) causes a novel ring transformation affording 2(1H)-pyrazinones in moderate to high yields. The cytotoxicity and antibacterial activity of some of the obtained products were studied and some of the products exhibited tumor-specific cytotoxicity.