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Jon Clardy

Publications and source records attributed to Jon Clardy.

At least 37 records · Page 2Linked to original sources
PubMed2005

Coil-to-helix transition and ligand release of Bombyx mori pheromone-binding protein.

The transport of hydrophobic insect pheromones through the aqueous medium surrounding their receptors is assisted by pheromone-binding proteins (PBPs). The protein from the silkworm moth Bombyx mori, BmorPBP, exhibits a pH-dependent conformational change postulated to trigger the release of the pheromone bombykol to its receptor. At low pH, an alpha-helix occupies the same binding pocket that houses the pheromone in the BmorPBP-bombykol complex at high pH. We have determined the crystal structure of apo BmorPBP at a resolution of 2.3 angstroms and pH 7.5, which has surprisingly a structure similar to the A-form. These data suggest that BmorPBP undergoes a ligand-dependent conformational change in addition to the previously described pH-dependent conformational change. Analysis of the alpha-helix occupying the binding pocket reveals an amphipathic helix with three acidic residues along one face that are conserved among lepidopteran PBPs and may be involved in a conformational transition of BmorPBP at the receptor membrane.

Amino Acid Sequence↗
PubMed2005

Using genomics to deliver natural products from symbiotic bacteria.

The availability of some natural products with promising anticancer activity has been limited because they are synthesized by symbiotic bacteria associated with specific animals. Recent research has identified the clusters of bacterial genes responsible for their synthesis, so that the molecules can be synthesized in alternative, easily cultured bacteria.

Bacteria↗
PubMed2005

N-acyl derivatives of arginine and tryptophan isolated from environmental DNA expressed in Escherichia coli.

Heterologous expression of microbial DNA extracted directly from environmental samples (environmental DNA, eDNA) in easily cultured hosts can provide access to natural products produced by previously uncultured bacteria. This report describes the characterization of antibacterially active long-chain N-acyl derivatives of tryptophan and arginine that are produced by eDNA clones hosted in Escherichia coli. The sequencing and subcloning of the proposed N-acyl amino acid synthases (NASs) for each family of natural products are also described. [reaction: see text]

Arginine↗
PubMed2005

Bacterial printing press that regenerates its ink: contact-printing bacteria using hydrogel stamps.

This paper describes the use of micropatterned agarose stamps prepared by molding against PDMS masters to print patterns of bacteria on agar plates. Topographically patterned agarose stamps were inked with suspensions of bacteria; these stamps generated patterns of bacteria with features as small as 200 microm over areas as large as 50 cm2. Stamps with many small features (>200 microm) were used to study patterns of bacteria growing on media containing gradients of small molecules; stamps with larger features (>750 microm) were used to print different strains of bacteria simultaneously. The stamp transfers only a small percentage of cells that are on its surface to the agar at a time; it is thus possible to replica-pattern hundreds of times with a single inking. The use of soft stamps provides other useful functions. Stamps are easily customized to provide a range of patterns. When culture media is included in the agarose stamp, cells divide and thrive on the surface. The resulting "living stamp" regenerates its "ink" and can be used to pattern surfaces repetitively for a month. This method is rapid, reproducible, convenient, and can be used to control the pattern, spacing, and orientation between colonies of different bacteria.

Aliivibrio fischeri↗
PubMed2005

The psammaplysenes, specific inhibitors of FOXO1a nuclear export.

A small collection of marine natural product extracts was screened for compounds that would compensate lost tumor suppressor functionality in PTEN-deficient cells. From the most active extract, the previously unreported bromotyrosine derivative, psammaplysene A (1), was identified. Psammaplysene A compensates for PTEN loss by relocalizing the transcription factor FOXO1a to the nucleus.

Active Transport, Cell Nucleus↗
PubMed2004

Lessons from natural molecules.

Natural products have inspired chemists and physicians for millennia. Their rich structural diversity and complexity has prompted synthetic chemists to produce them in the laboratory, often with therapeutic applications in mind, and many drugs used today are natural products or natural-product derivatives. Recent years have seen considerable advances in our understanding of natural-product biosynthesis. Coupled with improvements in approaches for natural-product isolation, characterization and synthesis, these could be opening the door to a new era in the investigation of natural products in academia and industry.

Animals↗
PubMed2004

Transglutaminase 5 is regulated by guanine-adenine nucleotides.

Transglutaminases (TGases) are Ca2+-dependent enzymes capable of catalysing transamidation of glutamine residues to form intermolecular isopeptide bonds. Nine distinct TGases have been described in mammals, and two of them (types 2 and 3) are regulated by GTP/ATP. TGase2 hydrolyses GTP and is therefore a bifunctional enzyme. In the present study, we report that TGase5 is also regulated by nucleotides. We have identified the putative TGase5 GTP-binding pocket by comparative amino acid sequence alignment and homology-derived three-dimensional modelling. GTP and ATP inhibit TGase5 cross-linking activity in vitro, and Ca2+ is capable of completely reversing this inhibition. In addition, TGase5 mRNA is not restricted to epidermal tissue, but is also present in different adult and foetal tissues, suggesting a role for TGase5 outside the epidermis. These results reveal the reciprocal actions of Ca2+ and nucleotides with respect to TGase5 activity. Taken together, these results indicate that TGases are a complex family of enzymes regulated by calcium, with at least three of them, namely TGase2, TGase3 and TGase5, also being regulated by ATP and GTP.

Adenosine Triphosphate↗
PubMed2004

Tyrosol is a quorum-sensing molecule in Candida albicans.

The human fungal pathogen Candida albicans shows a significant lag in growth when diluted into fresh minimal medium. This lag is abolished by the addition of conditioned medium from a high-density culture. The active component of conditioned medium is tyrosol, which is released into the medium continuously during growth. Under conditions permissive for germ-tube formation, tyrosol stimulates the formation of these filamentous protrusions. Because germ-tube formation is inhibited by farnesol, another quorum-sensing molecule, this process must be under complex positive and negative control by environmental conditions. The identification of tyrosol as an autoregulatory molecule has important implications on the dynamics of growth and morphogenesis in Candida.

Base Sequence↗
PubMed2004

Berkeleydione and berkeleytrione, new bioactive metabolites from an acid mine organism.

[structure: see text] Two novel hybrid polyketide-terpenoid metabolites were isolated from a Penicillium sp. growing in the Berkeley Pit Lake of Butte, Montana. Their structures were deduced by spectroscopic analysis and confirmed by single-crystal X-ray analysis on berkeleydione (1). Both compounds inhibited matrix metalloproteinase-3 and caspase-1, and berkeleydione showed activity toward non-small-cell lung cancer in NCI's human cell line antitumor screen.

Acids↗
PubMed2004

A further study of the cytotoxic constituents of a milnamide-producing sponge.

A reinvestigation of Auletta sp. yielded the novel compound milnamide C (3) plus the known compounds milnamide A (1), milnamide B (hemiasterlin) (2), jasplakinolide (5), and geodiamolides A (6), D (7), E (8), and G (9). The isolation work was guided by cytoskeletal bioactivity data. Compounds 2 and 3 were shown to cause microtubule depolymerization, and 6-9 were shown to cause microfilament disruption. This biological activity and the structural elucidation of 3, including X-ray analysis, are reported here. [structure: see text]

Animals↗
PubMed2004

Palmitoylputrescine, an antibiotic isolated from the heterologous expression of DNA extracted from bromeliad tank water.

Heterologous expression of large fragments of microbial DNA extracted directly from environmental samples (environmental DNA, or eDNA) in easily cultured hosts should provide access to some of the natural products produced by previously uncultured bacteria. The natural product antibiotic palmitoylputrescine (1) was isolated from Escherichia coli transformed with a cosmid (pCSLF16) containing DNA extracted directly from Costa Rican bromeliad tank water. In this report we describe the characterization of this antibiotic and its biosynthetic gene.

Anti-Bacterial Agents↗
PubMed2004

Long-chain N-acyltyrosine synthases from environmental DNA.

The heterologous expression of DNA extracted directly from environmental samples (environmental DNA [eDNA]) in easily cultured hosts provides access to natural products produced by previously inaccessible microorganisms. When eDNA cosmid libraries were screened in Escherichia coli for antibacterially active clones, long-chain N-acyltyrosine-producing clones were found in every eDNA library. These apparently common natural products have not been previously described from screening extracts of cultured bacteria for biologically active natural products. Of the 11 long-chain N-acyl amino acid synthases (NASs) that were characterized, 10 are unique sequences. A predicted protein of previously unknown function from Nitrosomonas europaea, a gram-negative nitrifying beta-proteobacterium, is 14 to 37% identical to eDNA NASs. When cloned into E. coli, this open reading frame confers the production of long-chain N-acyltyrosines to the host and is therefore the first NAS from a cultured bacterium to be functionally characterized. Understanding the role that long-chain N-acyl amino acids play in soil microbial communities should now be feasible with the identification of a cultured organism that has the genetic capacity to produce these compounds.

Acylation↗
PubMed2003

Unusual C25 steroids produced by a sponge-derived Penicillium citrinum.

[structure: see text] Structurally unique steroids, isocyclocitrinol A (1) and 22-acetylisocyclocitrinol A (2), were isolated from the extract of a saltwater culture of sponge-derived Penicilliun citrinum. The structures were established by analysis of 1D and 2D NMR data. The absolute structures were determined on the basis of X-ray structure analysis and application of modified Mosher's method. Furthermore, the structure of cyclocitrinol (3a) previously isolated from a terrestrial P. citrinum was revised as 3b. Compounds 1 and 2 showed weak antibacterial activity against Staphylococcus epidermidis and Enterococcus durans.

Animals↗
PubMed2003

The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2.

Mutations in palmitoyl protein thioesterase-1 (PPT1) have been found to cause the infantile form of neuronal ceroid lipofuscinosis, which is a lysosomal storage disorder characterized by impaired degradation of fatty acid-modified proteins with accumulation of amorphous granular deposits in cortical neurons, leading to mental retardation and death. Palmitoyl protein thioesterase-2 (PPT2) is a second lysosomal hydrolase that shares a 26% identity with PPT1. A previous study had suggested that palmitoyl-CoA was the preferred substrate of PPT2. Furthermore, PPT2 did not hydrolyze palmitate from the several S-palmitoylated protein substrates. Interestingly, PPT2 deficiency in a recent transgenic mouse model is associated with a form of neuronal ceroid lipofuscinosis, suggesting that PPT1 and -2 perform non-redundant roles in lysosomal thioester catabolism. In the current paper, we present the crystal structure of PPT2 at a resolution of 2.7 A. Comparisons of the structures of PPT1 and -2 show very similar architectural features; however, conformational differences in helix alpha4 lead to a solvent-exposed lipid-binding groove in PPT1. The limited space between two parallel loops (beta3-alphaA and beta8-alphaF) located immediately above the lipid-binding groove in PPT2 restricts the binding of fatty acids with bulky head groups, and this binding groove is significantly larger in PPT1. This structural difference accounts for the ability of PPT2 to hydrolyze an unbranched structure such as palmitoyl-CoA but not palmitoylcysteine or palmitoylated proteins. Furthermore, differences in fatty acid chain length specificity of PPT1 and -2, also reported here, are explained by the structure and may provide a biochemical basis for their non-redundant roles.

Amino Acid Sequence↗
PubMed2003

Synthesis of long-chain fatty acid enol esters isolated from an environmental DNA clone.

[structure: see text] Long-chain fatty acid enol ester 1 is the major metabolite of a new family of small molecules isolated from the heterologous expression of environmentally derived DNA. A versatile synthesis of 1, in which an aromatic acetaldehyde is O-acylated with a long-chain acyl chloride allowed for the rapid construction of both the isolated product (1) and a number of structural analogues (including 8, 17, and 18).

Acyl Carrier Protein↗