Identification of catalytically essential residues in Escherichia coli esterase by site-directed mutagenesis.

Escherichia coli esterase (EcE) is a member of the hormone-sensitive lipase family. We have analyzed the roles of the conserved residues in this enzyme (His103, Glu128, Gly163, Asp164, Ser165, Gly167, Asp262, Asp266 and His292) by site-directed mutagenesis. Among them, Gly163, Asp164, Ser165, and Gly167 are the components of a G-D/E-S-A-G motif. We showed that Ser165, Asp262, and His292 are the active-site residues of the enzyme. We also showed that none of the other residues, except for Asp164, is critical for the enzymatic activity. The mutation of Asp164 to Ala dramatically reduced the catalytic efficiency of the enzyme by the factor of 10(4) without seriously affecting the substrate binding. This residue is probably structurally important to make the conformation of the active-site functional.     

Identification of the gene encoding esterase, a homolog of hormone-sensitive lipase, from an oil-degrading bacterium, strain HD-1.

The gene encoding an esterase (HDE) was cloned from an oil-degrading bacterium, strain HD-1. HDE is a member of the hormone-sensitive lipase family and composed of 317 amino acid residues with a molecular weight of 33,633. The HDE-encoding gene was expressed in Escherichia coli, and the recombinant protein was purified and characterized. Amino acid sequence analysis indicated that the methionine residue was removed from its NH(2)-terminus. The good agreement of the molecular weights estimated by SDS-PAGE (35,000) and gel filtration (38,000) suggests that it acts in a monomeric form. HDE showed hydrolytic activity towards p-nitrophenyl esters of fatty acids with an acyl chain length of 2 to 14 and tributyrin, whereas it showed little hydrolytic activity towards p-nitrophenyl oleate (C(18)), tricaprylin and triolein. Determination of the kinetic parameters for the hydrolyses of the p-nitrophenyl substrates from C(2) to C(14) indicated that HDE shows a relatively broad substrate specificity. However, comparison of the k(cat)/K(m) values indicated that the C(10)-C(14) substrates are the most preferred ones. Such a preference for substrates with long acyl chains may be a characteristic of HDE.     

Protein structure databases with new web services for structural biology and biomedical research

The Protein Data Bank Japan (PDBj) curates, edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes approximately 25-30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, eF-site, as well as a search service for similar molecular surfaces, eF-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the utility of these tools in recognizing remote homologies between pairs of protein structures and in assigning putative biochemical functions to newly determined targets from structural genomics projects.     

Identification of five phospho-beta-glycosidases from Lactobacillus gasseri ATCC33323T cultured in lactose medium

Lactobacillus gasseri ATCC33323(T) has seven putative phospho-beta-glycosidase genes. Using column chromatography, we found that this strain cultured in lactose medium expresses five phospho-beta-glycosidases (LacG1, LacG2, Pbg1, Pbg2, and Pbg3), where these gene expressions can be suppressed by glucose. To our knowledge, this is the first report indicating that five glycosidases are induced from a single bacterial strain using a single carbon source, lactose.     

The assembly of the FtsZ ring at the mid-chloroplast division site depends on a balance between the activities of AtMinE1 and ARC11/AtMinD1

Chloroplast division comprises a sequence of events that facilitatesymmetric binary fission and that involve prokaryotic-like stromaldivision factors such as tubulin-like GTPase FtsZ and the divisionsite regulator MinD. In Arabidopsis, a nuclear-encoded prokaryoticMinE homolog, AtMinE1, has been characterized in terms of itseffects on a dividing or terminal chloroplast state in a limitedseries of leaf tissues. However, the relationship between AtMinE1expression and chloroplast phenotype remains to be fully elucidated.Here, we demonstrate that a T-DNA insertion mutation in AtMinE1results in a severe inhibition of chloroplast division, producingmotile dots and short filaments of FtsZ. In AtMinE1 sense (overexpressor)plants, dividing chloroplasts possess either single or multipleFtsZ rings located at random intervals and showing constrictiondepth, mainly along the chloroplast polarity axis. The AtMinE1sense plants displayed equivalent chloroplast phenotypes toarc11, a loss-of-function mutant of AtMinD1 which forms replicatingmini-chloroplasts. Furthermore, a certain population of FtsZrings formed within developing chloroplasts failed to initiateor progress the membrane constriction of chloroplasts and consequentiallyto complete chloroplast fission in both AtMinE1 sense and arc11/atminD1plants. Our present data thus demonstrate that the chloroplastdivision site placement involves a balance between the opposingactivities of AtMinE1 and AtMinD1, which acts to prevent FtsZring formation anywhere outside of the mid-chloroplast. In addition,the imbalance caused by an AtMinE1 dominance causes multiple,non-synchronous division events at the single chloroplast level,as well as division arrest, which becomes apparent as the chloroplastsmature, in spite of the presence of FtsZ rings.     

Induction of serotonin accumulation by feeding of rice striped stem borer in rice leaves

Tryptophan (Trp)-related secondary metabolism has been implicated in the defense against pathogen infection and insect feeding in various gramineous species. Recently, we also reported that rice plant accumulated serotonin and tryptamine as well as their amide compounds coupled with phenolic acids in response to the infection by fungal pathogen. These compounds were likely to play an important role in the formation of physical barrier to the invading pathogens. To extend our study to elucidate the defensive role of Trp-derived secondary metabolism in gramineous plants, we examined in this study whether it is activated in response to herbivore attack as well. Third leaves of rice plant were fed on by third instar larvae of rice striped stem borer for 24 h or 48 h. The analysis of four Trp-derived metabolites including tryptamine, serotonin feruloyltryptamine (FerTry) and p-coumaroylserotonin (CouSer) by liquid chromatography coupled with tandem mass spectrometry revealed that their contents clearly increased in response to the larvae feeding. The respective amounts of tryptamine, serotonin, FerTry and CouSer in the larvae-fed leaves were 12-, 3.5-, 33- and 140-fold larger than those in control leaves 48 h after the start of feeding.Key words: rice, Oryza sativa, Gramineae, serotonin, secondary metabolism, rice striped stem borer, Chilo suppressalisPlants defend themselves from environmental stresses by utilizing secondary metabolism. One of major biological stresses that plants have to cope with is attack by herbivorous insects. In the interactions with herbivorous insects, various secondary metabolites that are derived from tryptophan (Trp) pathway have been shown to play defensive roles in plants including gramineous species. For example, benzoxazinone glucosides in wheat (Triticum aestivum), rye (Secale sereale) and maize (Zea mays) express toxic and antifeeding effects on herbivorous insects.^1,2 Benzoxazinones are biosynthesized from indole-3-glycerol phosphate, an intermediate of Trp synthesis.^3,4 Another example of those compounds is gramine in barley (Hordeum vulgare). Gramine is a Trp-rerived indole amine,⁵ and has been received attention in the resistance mainly against aphids on the basis of its toxicity and deterrence.⁶We recently found that Trp-derived secondary metabolism is also involved in defense responses of rice (Oryza sativa) leaves to infection by brown spot fungus (Bipolaris oryzae).⁷ The infection of the fungus activates Trp biosynthesis and accumulation of serotonin and of smaller amounts of tryptamine, feruloyltryptamine (FerTry) and p-coumaroylserotonin (CouSer). In addition, the enhancement of serotonin peroxidase activity and incorporation of serotonin in the cell walls were detected. Thus, it is very likely that that serotonin-derived materials deposit in cell walls after oxidative polymerization to constitute a part of physical defense system of rice, which may be reminiscent of the wound sloughing in animals. These findings prompted us to investigate whether Trp-related secondary metabolism is also involved in the defense of rice plant against the attack by insects, as in the cases of other gramineous plants mentioned above. While the response of plants to pathogenic infection is generally different from that to insect herbivory, Trp-derived secondary metabolites have occasionally been implicated in both responses.^8–10 Here, we report the results of our study to examine the effects of herbivory by rice striped stem borer (Chilo suppressalis) on the Trp derived secondary metabolism in rice leaves.Rice (cv. Nipponbare) leaves were incubated with larvae of C. suppressalis in a feeding tube assembled according to Oikawa et al.,⁸ Aerial parts of two 12-day-old rice seedlings were excised, and their cutting ends were immersed in distilled water in a vial. Three third instar larvae of C. suppressalis were put on the leaves, and the leaves with larvae were covered by a plastic tube. For comparison, the control leaves were wounded by razor blade at the start of the incubation. After incubation for 24 h or 48 h with 16/8 h LD cycle at 28°C, the leaves were extracted with 10 volumes of 80% methanol, and analyzed by liquid chromatography coupled with tandem mass spectrometry in multiple reaction monitoring mode.As shown in Figure 1, the contents of tryptamine and serotonin increased along with time in the larvae-fed leaves. The respective contents of tryptamine and serotonin in the leaves were 12- and 3.5-fold larger than those in control leaves 48 h after the start of feeding. The accumulation of FerTry and CouSer was also observed after larvae feeding with the contents being 33- and 140-fold larger than those in control leaves, respectively. Their contents, however, were approximately 10-fold smaller than the corresponding amines.Open in a separate windowFigure 1Accumulation of Trp derived metabolites in the leaves attacked by rice striped stem borer. Chemical structures of analyzed compounds (A). The contents of tryptamine (B), serotonin (B), FerTry (C) and CouSer (D) were determined by LC-MS/MS analysis. The third leaves of 12-d-old rice seedlings were fed on by rice striped stem borer (brack bars) or wounded by razor blade as control (white bars). After incubation, the leaves were extracted by 80% methanol. The contents of metabolites at time 0 are represented as gray bars.In the interaction of rice plant with B. oryzae, serotonin was shown to be incorporated into cell walls as a part of physical defense system.⁷ In an analogous way, modification of cell walls by serotonin might function in sealing the sites injured by insect feeding to protect the leaves from desiccation, and opportunistic and insect-mediated infection by microorganisms. Indeed, at the cutting edge of the leaves, the formation of brown materials was observed. In addition, since serotonin is a neurotransmitter of insects and tryptamine has been indicated to be a neuroactive substance, their accumulation might directly affect behavior and physiology of some insects. High concentrations of tryptamine have been shown to express anti-oviposition activity toward Bemisia tabaci¹¹ and anti-feeding activities toward Malacosoma disstria and Manduca sexta.¹²The low levels of serotonin, tryptamine and their amides in the control leaves suggest that these compounds are induced in response to some components produced during the interaction between the plant and the herbivore. In this relation, it has been shown that elicitors are present in the saliva of some herbivous insects, which induce volatile emission from the plant to attracts their natural enemies.^13,14 Induction of Trp-derived secondary metabolites by the herbivore attack may likely be a result of recognition of some insect-derived molecules by rice leaves, similarly to the induction of volatile emission.The induced accumulation of indole amines and their hydroxycinnamic acid amides in the rice leaves attacked by C. suppressalis suggests that a common signaling pathway might be involved in the responses to pathogen infection and insect feeding. However, the composition of induced compounds was different between the responses to the two biological stresses. The content of tryptamine in the larvae-fed leaves was comparable to that reported in the B. oryzae-infected leaves, whereas the amount of serotonin (approximately 35 nmol/gFW) was much smaller than that in the infected leaves (approximately 250 nmol/gFW). This characteristic was similar to the response of rice leaves to methyl jasmonate (MeJA), which also induced accumulation of these Trp-derived secondary metabolites.⁷ The strong activation of the conversion of tryptamine to serotonin may require infection-specific signals.The serotonin accumulation in rice appears to be similar to the accumulation of gramine in barley in several aspects. Gramine accumulation has been demonstrated to be induced by either infection by pathogens⁹ or infestation by the aphid Schizaphis graminum.¹⁰ In addition, the gene encoding N-methyltransferase that catalyzes the final reaction in the gramine biosynthetic pathway is upregulated by MeJA, suggesting gramine synthesis is at least partly under the control of jasmonate signaling pathway.^15,16 The inducible serotonin production may be an archetypal form of the biosynthesis of more complicated indole amine in barley.     

Prolamellar bodies formed by cyanobacterial protochlorophyllide oxidoreductase in Arabidopsis

In angiosperms, chlorophyll biosynthesis is light dependent. A key factor in this process is protochlorophyllide oxidoreductase (POR), which requires light to catalyze the reduction of protochlorophyllide to chlorophyllide. It is believed that this protein originated from an ancient cyanobacterial enzyme that was introduced into proto‐plant cells during the primary symbiosis. Here we report that PORs from the cyanobacteria Gloeobacter violaceus PCC7421 and Synechocystis sp. PCC6803 function in plastids. First, we found that the G. violaceus POR shows a higher affinity to its substrate protochlorophyllide than the Synechocystis POR but a similar affinity to plant PORs. Secondly, the reduced size of prolamellar bodies caused by a knockdown mutation of one of the POR genes, PORA, in Arabidopsis could be complemented by heterologous expression of the cyanobacterial PORs. Photoactive protochlorophyllide in the etioplasts of the complementing lines, however, was retained at a low level as in the parent PORA knockdown mutant, indicating that the observed formation of prolamellar bodies was irrelevant to the assembly of photoactive protochlorophyllide. This work reveals a new view on the formation of prolamellar bodies and provides new clues about the function of POR in the etioplast–chloroplast transition.     

Deposition of a recombinant peptide in ER-derived protein bodies by retention with cysteine-rich prolamins in transgenic rice seed

A 7Crp peptide composed of seven major human T cell epitopes derived from the Japanese cedar pollen allergens Cry j 1 and Cry j 2 is an ideal tolerogen for peptide immunotherapy against Japanese cedar pollinosis. To maximize the accumulation level of the 7Crp peptide in transgenic rice seed, we tested endosperm specific promoters and intracellular localizations suitable for stable accumulation. A 7Crp peptide carrying the KDEL ER retention signal directed by the 2.3-kb promoter of the glutelin GluB-1, which contains a signal peptide, accumulated at the highest level of about 60 μg/grain. Notably, the 7Crp peptide predominantly accumulated in ER-derived protein bodies irrespective of the presence of various sorting signals or expression as a fusion protein with glutelin. We attribute this abnormal pattern of accumulation to the formation of disulfide bonds between the 7Crp peptide and cysteine-rich (Cys-rich) prolamin storage proteins. Furthermore, the formation of these aggregates induced the chaperone proteins BiP and PDI as an ER stress response.     

DNA Sequencing and Homologous Expression of a Small Peptide Conferring Immunity to Gassericin A,a Circular Bacteriocin Produced by Lactobacillus gasseri LA39

Gassericin A, produced by Lactobacillus gasseri LA39, is a hydrophobic circular bacteriocin. The DNA region surrounding the gassericin A structural gene, gaaA, was sequenced, and seven open reading frames (ORFs) of 3.5 kbp (gaaBCADITE) were found with possible functions in gassericin A production, secretion, and immunity. The deduced products of the five consecutive ORFs gaaADITE have homology to those of genes involved in butyrivibriocin AR10 production, although the genetic arrangements are different in the two circular bacteriocin genes. GaaI is a small, positively charged hydrophobic peptide of 53 amino acids containing a putative transmembrane segment. Heterologous expression and homologous expression of GaaI in Lactococcus lactis subsp. cremoris MG1363 and L. gasseri JCM1131^T, respectively, were studied. GaaI-expressing strains exhibited at least sevenfold-higher resistance to gassericin A than corresponding control strains, indicating that gaaI encodes an immunity peptide for gassericin A. Comparison of GaaI to peptides with similar characteristics found in the circular bacteriocin gene loci is discussed.Bacteriocins are antimicrobial peptides that act primarily against related bacterial species. The classification of bacteriocins remains controversial. Here, we use the classification of Maqueda et al. (30): class I (lantibiotics); class II (nonlantibiotics) with subclasses IIa (antilisteral pediocin-like bacteriocins), IIb (two-peptide bacteriocins), and IIc (leaderless bacteriocins); class III (large heat-labile bacteriocins); and class IV (circular bacteriocins linked at the N- and C-terminal amino acids).Nine class IV circular bacteriocins have been reported to date. They can be further divided into two major groups by using their primary structures, biochemical characteristics, and genetic arrangements. One group is the family of enterocin AS-48 (32), the first circular bacteriocin described (in 1994), which includes circularin A (25) and uberolysin (40). The other group is the family of gassericin A (19, 21), the second bacteriocin found (in 1998), which includes acidocin B (28), reutericin 6 (with a primary structure 100% identical to that of gassericin A) (22, 23), butyrivibriocin AR10 (17), and carnocyclin A, from Carnobacterium maltaromaticum UAL307 (33). The lantibiotic-like subtilosin A produced by Bacillus subtilis subsp. subtilis strain 168 (24) is an orphan member of the class IV bacteriocins. The gassericin A family of bacteriocins have been isolated from various bacterial species in several countries, suggesting the bacteriocin genes may be associated with transferable genetic elements.The bacteriocins of lactic acid bacteria (LAB) and bacteriocin-producing LAB strains isolated from foods are promising food preservative candidates, and strains of human origin are expected to be probiotics that could help to prevent the growth of harmful bacteria in food and the human intestine. Lactobacillus gasseri belongs to the Lactobacillus acidophilus group of LAB, which are natural inhabitants of the human intestinal tract (35), and many L. gasseri strains have been shown to produce bacteriocins (16, 20). Gassericin A was produced by L. gasseri LA39 isolated from the feces of a human infant; it has bactericidal activity against the food-borne pathogens Listeria monocytogenes, Bacillus cereus, and Staphylococcus aureus (16). Recently, using proteose peptone, some strains of L. gasseri containing LA39 were successfully cultured in reconstituted skim milk and cheese whey, where L. gasseri LA39 produced gassericin A; these low-cost, safe media could be used to improve the safety of biopreservation (1). Gassericin A has been purified and characterized, and its structural gene (gaaA) has been cloned and sequenced (21, 22). Determination of the complete chemical structure of gassericin A showed that the bacteriocin belongs to class IV and consists of 58 amino acid residues linked at the N and C termini (19). Little is known about the mechanisms of secretion and circularization of gassericin A and immunity to the circular bacteriocin.Here, we sequenced six genes surrounding gaaA thought to be related to production of and immunity to gassericin A and examined the homologous and heterologous expression of a small hydrophobic peptide, GaaI; we found that gaaI is an immunity gene providing protection against gassericin A.