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At least 19 recordsLinked to original sources
PubMed2024

Accessing and exploring the unusual chemistry by radical SAM-RiPP enzymes.

Radical SAM enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptides catalyze unusual transformations that lead to unique peptide scaffolds and building blocks. Several natural products from these pathways show encouraging antimicrobial activities and represent next-generation therapeutics for infectious diseases. These systems are uniquely configured to benefit from genome-mining approaches because minimal substrate and cognate modifying enzyme expression can reveal unique, chemically complex transformations that outperform late-stage chemical reactions. This report highlights the main strategies used to reveal these enzymatic transformations, which have relied mainly on genome mining using enzyme-first approaches. We describe the general biosynthetic components for rSAM enzymes and highlight emerging approaches that may broaden the discovery and study of rSAM-RiPP enzymes. The large number of uncharacterized rSAM proteins, coupled with their unpredictable transformations, will continue to be an essential and exciting resource for enzyme discovery.

S-Adenosylmethionine↗
PubMed2025

RRNPP quorum-sensing repertoires in the salivarius group genomes: overrepresentation and synchronous activation of SHP/Rgg systems in Streptococcus thermophilus.

UNLABELLED: In Bacillota, quorum sensing can be mediated by RRNPP regulators that are activated by autoinducing peptides (AIPs). In this study, we derived a hidden Markov model profile from a 3D-informed alignment to establish RRNPP repertoires for 527 genomes of streptococci in the salivarius group and identified probable AIPs. The salivarius group encompasses Streptococcus salivarius and Streptococcus vestibularis, which are part of the normal human oral microflora, and Streptococcus thermophilus, one of the most widely used bacteria in the dairy industry. We observed a large amount of plasticity in these repertoires, as well as profound differences among species. Notably, S. salivarius displayed an accumulation of ComR regulators, while S. thermophilus displayed an accumulation of Rgg regulators. The latter family included SHP-associated Rgg regulators, systems in which SHPs serve as AIPs; most of these regulators control the production of post-translationally modified peptides (RaS-RiPPs). Their level of richness contrasts with the genome reduction that accompanied S. thermophilus' adaptation to milk. We then used liquid chromatography-high resolution tandem mass spectrometry to analyze the activity of the eight most common SHP/Rgg systems by characterizing the SHPs and RaS-RiPPs found in the supernatants. We detected four SHPs and one RaS-RiPP that have never been seen before in S. thermophilus, and we showed that seven of the eight SHP/Rgg systems were functional. Finally, by simultaneously monitoring the amounts of both the SHPs and RaS-RiPPs, we demonstrated that the fates of these two peptide types differed during growth. SHP presence in the supernatant was transient, a pattern likely related to the peptides' signaling role. IMPORTANCE: Streptococcus thermophilus possesses an unusually high number of Rgg regulators, which are activated by SHP pheromones that control the production of RaS-RiPPs, peptides with cyclization motifs and growth inhibition properties. We conducted an in silico analysis of regulator repertoires across a wide range of strains; a subsequent experimental study revealed that the majority of the SHP/Rgg systems were functional. Employing an optimized liquid chromatography-high resolution tandem mass spectrometry protocol, we were able to better detect and follow SHP and RaS-RiPP accumulation. While RaS-RiPPs accumulated during growth, SHPs were only transiently present in the extracellular environment. This observation suggests that we could manipulate quorum sensing by adding SHPs to the growth medium and highlights the need to study the functions of the RaS-RiPPs.

Streptococcus thermophilus↗
PubMed2026

Substrate-Dependent Crosslinking by the Cytochrome P450 From Aminopyruvatide Biosynthesis.

Cytochrome P450s catalyze an array of reactions including crosslinking of aromatic side chains in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs). ApyO is a cytochrome P450 that forms a C─C bond between two tyrosines in a YLY motif in the substrate ApyA, the precursor peptide of the RiPP aminopyruvatide. We utilized cell-free translation to generate ApyA variants and probe the substrate tolerance of ApyO. Through AlphaFold-based modelling and in vitro assays, we show that ApyO accepts the 10 C-terminal residues of ApyA and requires a conserved Arg/Lys in the substrate. Inspired by substrate sequences in orthologous biosynthetic gene clusters, we substituted one of the tyrosine residues with a tryptophan and observed that ApyO catalyzed formation of an N─C bond between the indole of Trp and Cε2 of Tyr. ApyO unexpectedly catalyzed formation of a C─O bond between the two tyrosine residues when we substituted the leucine residue in the YLY motif with tyrosine or tryptophan. A peptide containing a biaryl linkage and C-terminal aminopyruvate displayed sub-nanomolar inhibition of select proteases, with the aminopyruvate group critical for activity. Overall, this study demonstrates plasticity in the manner of macrocyclization catalyzed by the P450 ApyO.

biosynthesis↗
PubMed2026

Genomic and biosynthetic landscape of high-temperature Daqu microbiome.

As the core starter for Chinese Baijiu, high-temperature Daqu is produced through open solid-state fermentation with recurrent inoculation by mature Daqu, forming a rich yet largely untapped reservoir of genomes and bioactive compounds. This study constructs the High-temperature Daqu Fermentation Microbiome catalog using 463 metagenomes spanning the full fermentation cycle. The catalog comprises 4,264 metagenome-assembled genomes that are dereplicated into 252 representative genome-based species, 82 % of which are absent from current global food microbiome databases. It further contains 14.3 million non-redundant genes, of which 17.3 % are novel, and 17,031 biosynthetic gene clusters, of which 62.63 % are novel, thereby substantially expanding the known genomic and biosynthetic space of food microbiomes. Genome-resolved analyses revealed a U-shaped ecological trajectory, shifting from early Bacillus velezensis-enriched assemblages to transient dominance of lactic acid bacteria during peak thermogenesis, before returning in late fermentation to thermotolerant, spore-forming Bacillota and Actinomycetota. In parallel, biosynthetic potential was further organized into four recurrent, stage-enriched profiles, from RiPP-rich thermogenic states to mature-state assemblages enriched in PKS-, NRPS-, and terpene-related capacities, with Bacillus, Kroppenstedtia, and Saccharopolyspora constituting the principal biosynthetic reservoir. Together, this work uncovers a largely unexplored genomic and biosynthetic reservoir in high-temperature Daqu fermentation, providing a target resource for mining thermotolerant industrial enzymes, flavor-related genes, and bioactive metabolites with biotechnological potential.

Microbiota↗
PubMed1979

Multiple floppy valves: an echocardiographic syndrome.

Echocardiograms of 400 patients with mitral valve prolapse examined at the Peter Bent Brigham Hospital between 1974 and 1977 were reviewed. Eleven patients (3 per cent) were found to have prolapse (10 patients) or large excursion of the tricuspid valve (one patient) and large excursion of the aotric valve (four patients) or dilatation of the aotric root (seven patients) in addition to mitral valve prolapse. Two of these 11 patients underwent mitral valve replacement, and myxomatous degeneration of the valves was noted on pathologic examination. Almost half of the patients with multiple floppy valves (five of 11) had symptoms of congestive heart failure. In contrast to reported series of isolated mitral valve prolapse, in which female preponderance has been documented, 10 of the 11 patients were male. The syndrome of multiple floppy valves may represent either a unique entity or a more advanced form of the same process which underlies mitral valve prolapse.

Adult↗
PubMed2026

HP1α binding creates a local barrier against transcription activation and persists during chromatin decondensation.

Mouse pericentric heterochromatin forms compacted, transcriptionally silent domains, termed chromocenters, that are enriched in heterochromatin protein 1 (HP1). Whether HP1α represses chromocenters by binding locally or by maintaining a phase-separated compartment is unresolved. We investigated this question by recruiting transcriptional activators to mouse fibroblast chromocenters and quantifying repression at a transcription reporter. HP1α established a promoter-proximal barrier that suppressed weaker activators (VP16) but was overcome by stronger ones (VP64-p65-Rta [VPR] and p65). Activator-induced decondensation and transcription occurred without displacing HP1α or H3K9 trimethylation, and HP1α retained its granular distribution and stoichiometric binding dynamics. Multi-color super-resolution imaging revealed spatial segregation of transcribed and HP1α-bound regions at the nanodomain scale. A nanodomain model captured how repeat clusters independently transition between silenced and activated states. These data establish that HP1α and H3K9me3 act through independently switchable nanodomains, accounting for chromocenter regulation without invoking phase separation.

Animals↗
PubMed2026

An Acetyltransferase Conferring Self-Resistance of the Producer to Lasso Peptide Antibiotic Lariocidin.

The soil microbiome, a reservoir of antibiotic-producing bacteria, also harbors resistance determinants encoded within antibiotic biosynthetic gene clusters (BGCs). Studying self-resistance mechanisms, which have evolved in producers to protect against their own toxic metabolites, provides critical insights into the evolution of resistance and the potential vulnerabilities of new antibiotics and can facilitate the production of natural products in heterologous hosts. Here, we describe the self-resistance mechanism to lariocidin (LAR), a recently discovered lasso peptide antibiotic that inhibits the ribosomal machinery and exhibits antibacterial activity against key pathogens. We identified and characterized an N-acetyltransferase enzyme (LrcE) encoded within the LAR BGC that mediates self-resistance in LAR-producing Paenibacillus sp. M2. LrcE is a member of the GCN5-related N-acetyltransferase (GNAT) superfamily and performs site-specific acetylation of LAR at a critical lysine residue. This modification disrupts ribosomal binding, thereby reducing LAR's antibacterial activity. Using in silico modeling, we predicted a conserved acetyl-CoA-binding motif and an LAR-binding region on LrcE. Bioinformatic analysis revealed LrcE homologues in environmental but not clinically relevant pathogens, suggesting a limited risk of horizontal gene transfer and, therefore, supporting the further development of LAR as a next-generation antibiotic.

Anti-Bacterial Agents↗
PubMed1978

Generation of b-wave currents in the skate retina.

Potassium kinetics within the skate retina were monitored extracellularly with K+-selective electrodes. Two sources of K+ efflux were detected in response to photic stimulation: one in the distal retina in the region of the outer plexiform layer, and the other at a more proximal location near the border between the inner nuclear and inner plexiform layers. The magnitude of the K+ efflux at these retinal depths was affected differently by spot and full-field illumination, suggesting that the two sources originate from different classes of neuron. There is evidence that both sources are associated with current sinks provided by the Müller cells, thereby establishing radial current paths along the lengths of these elements. We have proposed a model in which asymmetries in the magnitudes of these currents give rise to the b-wave of the electroretinogram. Extracellular field potentials recorded differentially at various retinal depths, and in response to changes in stimulus configuration, were consistent with predictions of the model.

Animals↗
PubMed1976

Peroxidase uptake by photoreceptor terminals of the skate retina.

The photoreceptors of dark-adapted skate retinas bathed in a Ringer solution containing horseradish peroxidase (HRP) incorporate the tracer into membrane-bound compartments within the synaptic terminal of the cell; after 1 or 2 h of incubation, approx. 10-38% of the synaptic vesicles were labeled. The receptors appeared to be functioning normally throughout the incubation period, since electrical potentials of normal amplitude could be elicited in response to dimphotic stimuli. However, it was possible to block the uptake of peroxidase by a regimen of light adaptation that effectively suppressed light-induced activity in the electroretinogram. If, during incubation with peroxidase, retinas were exposed at 10-min intervals to an intense 1-ms flash from a xenon discharge tube, the receptor terminals were almost completely devoid of peroxidase; fewer than 2% of the vesicles were labeled. The suppression of HRP uptake could also be achieved in dark-adapted retinas by adding magnesium to the bathing solution, suggesting that calcium is necessary for transmitter release from vesicles in the receptor terminals. These findings are consistent with the view that vertebrate photoreceptors discharge a neurotransmitter in darkness, and that light decreases the release of this substance. It seems likely that the incorporation of peroxidase into vesicles of physiologically active receptor terminals reflects a mechanism for the retrieval of vesicle membrane after exocytosis.

Animals↗
PubMed1977

The proximal negative response and visual adaptation in the skate retina.

The proximal negative response (PNR), a complex extracellular potential derived mainly from amacrine cell activity, was studied in the all-rod retina of the skate. Tetrodotoxin (10(-6) mg/ml) did not affect either the waveform or the latency of the response, indicating that the PNR reflects the graded, nonregenerative components of the amacrine cell potential. As regards its adaptive properties, the PNR exhibited both the extreme sensitivity to weak background light and the slow time course of light and dark adaptation that are characteristic of other responses from the proximal retina. Thus, the PNR, like the b-wave and ganglion cell discharge, appears to reflect adaptive processes located within the neural network of the inner retina.

Adaptation, Ocular↗
PubMed1977

Rhodopsin photoproducts and rod sensitivity in the skate retina.

The late photoproducts that result from the isomerization of rhodopsin have been identified in the isolated all-rod retina of the skate by means of rapid spectrophotometry. The sequence in which these intermediates form and decay could be described by a scheme that incorporates two pathways for the degradation of metarhodopsin II (MII) to retinol: one via metarhodopsin III (MIII) and the other (which bypasses MIII) through retinal. Computer simulation of the model yielded rate constants and spectral absorbance coefficients for the late photoproducts which fit experimental data obtained at temperatures ranging from 7 degrees C to 27 degrees C. Comparing the kinetics of the thermal reactions with the changes in rod threshold that occur during dark adaptation indicated that the decay of MII and the fall in receptor thresholds exhibit similarities with regard to their temperature dependence. However, the addition of 2 mM hydroxylamine to a perfusate bathing the retina greatly accelerated the photochemical reactions, but had no significant effect on the rate of recovery of rod sensitivity. It appears, therefore, that the late bleaching intermediates do not control the sensitivities of skate rods during dark adaptation.

Animals↗
PubMed1978

Formation, conversion, and utilization of isorhodopsin, rhodopsin, and porphyropsin by rod photoreceptors in the Xenopus retina.

The visual pigment content of rod photoreceptors in Xenopus larvae was reduced greater than 90% through a combination of vitamin A-deficient diet and constant light. Thereafter, a dose of either all-trans-retinol or 9-cis-retinal was injected intramuscularly, leading to the formation of a rhodopsin (lambdamax 504 nm) or isorhodopsin (lambdamax 487-493 nm) pigment, respectively. Electrophysiological measurements were made of the threshold and spectral sensitivity of the aspartate-isolated PIII (photoreceptoral) component of the electroretinogram. These measures established that either rhodopsin or isorhodopsin subserved visual transduction with the same efficiency as the 519 nm porphyropsin pigment encountered normally. When animals with rhodopsin or isorhodopsin were kept in darkness or placed on a cyclical lighting regimen for 8 days, retinal densitometry showed that either pigment was being converted to porphyropsin; significantly more porphyropsin was formed as a result of cyclical lighting than after complete darkness.

Animals↗
PubMed1978

Purification of the extracellular opacity factor of a strain of group A Streptococcus M type 2.

The extracellular Opacity Factor elaborated by a strain of group A streptococcus M type 2 was purified by ammonium sulphate precipitation, DEAE-cellulose and hydroxylapatite column chromatography and Sephadex G-200 gel filtration. Gel filtration experiments indicated that the Opacity Factor is consituted of high molecular weight proteins or protein aggregates which appear to dissociate into subunits of 66000 minimum molecular weight as determined by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. The purified preparations had no group A carbohydrate of T protein antigens. Passive haemagglutination and indirect immunofluorescence tests indicated that Opacity Factor is distinct from the M type 2 protein antigen.

Antibody Formation↗
PubMed1977

Synthesis of stereospecifically deuterated phenylalamines and determination of their configuration.

1. Starting from trans-cinnamic acid a chiral (-)3-phenyl-[2,3-2H]propionic acid has been synthesized using Clostridium kiuyveri cells as catalyst. 2. The chiral dideuterated acid has been converted by chemical methods to a mixture of (2R) and (2S)-phenyl[2,3-2H]-alanine. 3. By means of 1H nuclear magnetic resonance spectroscopy and the action of D and L-amino acid oxidase the configuration of the phenylalamine has been shown to be (2R, 3S) and (2S, 3S), respectively. The labelled phenylalanine is thus sterically and isotopically homogenous at position 3 but heterogenous at position 2.

Amino Acid Oxidoreductases↗
PubMed1977

Stereospecificity of phenylpyruvate tautomerase. A convenient method for the preparation of chirally labelled phenylpyruvates.

1. By 1H nuclear magnetic resonance spectroscopy it has been shown that phenylpyruvate tautomerase from beef kidney catalyses the stereospecific exchange of one of the enantiotopic 3H-atoms in the side-chain of the substrate with solvent protons, the rate of spontaneous exchange being slow under physiological conditions. 2. Using monodeuterated phenylpyruvate of known absolute configuration it has been shown that the tautomerase removes specifically the 3-pro-R hydrogen atom of the substrate. 3. The circular dichroism spectra of the two enantiomeric 3-phenyl-[3-2H]pyruvates have been determined. 4. Some implications of these findings for the investigation of the metabolism of aromatic amino acids are discussed.

Circular Dichroism↗