Cyanochelins, an overlooked class of widely distributed cyanobacterial siderophores, discovered by silent gene cluster awakening.

Cyanobacteria require iron for growth and often inhabit iron-limited habitats, yet only a few siderophores are known to be produced by them. We report that cyanobacterial genomes frequently encode PKS/NRPS biosynthetic pathways for synthesis of lipopeptides featuring β -hydroxyaspartate ( β -OH-Asp), a residue known to be involved in iron chelation. Iron starvation triggered the synthesis of β -OH-Asp lipopeptides in the cyanobacteria Rivularia sp. PCC 7116, Leptolyngbya sp. NIES-3755 and Rubidibacter lacunae KORDI 51-2. The induced compounds were confirmed to bind iron by mass spectrometry and were capable of Fe 3+ to Fe 2+ photoreduction accompanied by their cleavage, when exposed to sunlight. The siderophore from Rivularia , named cyanochelin A, was structurally characterized by MS and NMR and contains a hydrophobic tail bound to phenolate and oxazole moieties followed by five amino acids including two modified aspartate residues for iron chelation. Phylogenomic analysis revealed twenty-six additional cyanochelin-like gene clusters across a broad range of cyanobacterial lineages. Our data suggests that cyanochelins and related compounds are widespread, β -OH-Asp-featuring cyanobacterial siderophores produced by phylogenetically distant species upon iron starvation. Production of photolabile siderophores by phototrophic cyanobacteria raises questions to what extent the compounds facilitate iron monopolization by the producer or provide Fe 2+ for the whole microbial community via photoreduction. Significance: All living organisms depend on iron as an essential cofactor for indispensable enzymes. However, the sources of bioavailable iron are often limited. To face this problem, microorganisms synthesize low molecular weight metabolites capable of iron scavenging - the siderophores. Although cyanobacteria inhabit the majority of the Earth's ecosystems, their repertoire of known siderophores is remarkably poor. Their genomes are known to harbour a rich variety of gene clusters with unknown function. Here we report the awakening of a widely distributed class of silent gene clusters by iron starvation, yielding cyanochelins, β -hydroxy aspartate lipopeptides involved in iron acquisition. Our results expand the limited arsenal of known cyanobacterial siderophores and propose products with ecological function to a number of previously silent gene clusters.

Recent Advances in Silent Gene Cluster Activation in Streptomyces

Natural products (NPs) are critical sources of drug molecules for decades. About two-thirds of natural antibiotics are produced by Streptomyces. Streptomyces have a large number of secondary metabolite biosynthetic gene clusters (SM-BGCs) that may encode NPs. However, most of these BGCs are silent under standard laboratory conditions. Hence, activation of these silent BGCs is essential to current natural products discovery research. In this review, we described the commonly used strategies for silent BGC activation in Streptomyces from two aspects. One focused on the strategies applied in heterologous host, including methods to clone and reconstruct BGCs along with advances in chassis engineering; the other focused on methods applied in native host which includes engineering of promoters, regulatory factors, and ribosomes. With the metabolic network being elucidated more comprehensively and methods optimized more high-thoroughly, the discovery of NPs will be greatly accelerated.

Epigenetics and expression of key genes associated with cardiac fibrosis: NLRP3, MMP2, MMP9, CCN2/CTGF and AGT

Aims: Excessive inflammatory signaling and pathological remodeling of the extracellular matrix drive cardiac fibrosis and require changes in gene expression. Materials and methods: Using bioinformatics, both tissue-specific expression profiles and epigenomic profiles of some genes critical for cardiac fibrosis were examined, namely, NLRP3, MMP2, MMP9, CCN2/CTGF, AGT (encodes angiotensin II precursors) and hsa-mir-223 (post-transcriptionally regulates NLRP3). Results: In monocytes, neutrophils, fibroblasts, venous cells, liver and brain, enhancers or super-enhancers were found that correlate with high expression of these genes. One enhancer extended into a silent gene neighbor. These enhancers harbored tissue-specific foci of DNA hypomethylation, open chromatin and transcription factor binding. Conclusions: This study identified previously undescribed enhancers containing hypomethylated transcription factor binding subregions that are predicted to regulate expression of these cardiac fibrosis-inducing genes.

Warum Mikroorganismen Naturstoffe produzieren

A key role in the communication between fungi and bacteria is played by natural products. Many of their encoding gene clusters are silent under standard laboratory conditions. Interspecies “talk” between microorganisms represents an ecological trigger to activate such silent gene clusters and leads to the formation of novel natural products by the involved species. The understanding of both the activation of silent gene clusters and the ecological function of the produced compounds is of importance to reveal functional microbial interactions required to shape microbiomes.

Targeted induction of a silent fungal gene cluster encoding the bacteria-specific germination inhibitor fumigermin

Microorganisms produce numerous secondary metabolites (SMs) with various biological activities. Many of their encoding gene clusters are silent under standard laboratory conditions because for their activation they need the ecological context, such as the presence of other microorganisms. The true ecological function of most SMs remains obscure, but understanding of both the activation of silent gene clusters and the ecological function of the produced compounds is of importance to reveal functional interactions in microbiomes. Here, we report the identification of an as-yet uncharacterized silent gene cluster of the fungus Aspergillus fumigatus, which is activated by the bacterium Streptomyces rapamycinicus during the bacterial-fungal interaction. The resulting natural product is the novel fungal metabolite fumigermin, the biosynthesis of which requires the polyketide synthase FgnA. Fumigermin inhibits germination of spores of the inducing S. rapamycinicus, and thus helps the fungus to defend resources in the shared habitat against a bacterial competitor.

Discovery of Two New Sorbicillinoids by Overexpression of the Global Regulator LaeA in a Marine-Derived Fungus Penicillium dipodomyis YJ-11

Overexpression of the global regulator LaeA in a marine-derived fungal strain of Penicillium dipodomyis YJ-11 induced obvious morphological changes and metabolic variations. Further chemical investigation of the mutant strain afforded a series of sorbicillinoids including two new ones named 10,11-dihydrobislongiquinolide (1) and 10,11,16,17-tetrahydrobislongiquinolide (2), as well as four known analogues, bislongiquinolide (3), 16,17-dihydrobislongiquinolide (4), sohirnone A (5), and 2′,3′-dihydrosorbicillin (6). The results support that the global regulator LaeA is a useful tool in activating silent gene clusters in Penicillium strains to obtain previously undiscovered compounds.

Triggering the expression of a silent gene cluster from genetically intractable bacteria results in scleric acid discovery

The characterisation of scleric acid, a new natural product from a silent and cryptic gene cluster from genetically intractable bacteria, and its biosynthesis are reported.

Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells

Many adult tissues contain postmitotic cells as old as the host organism. The only organelle that does not turn over in these cells is the nucleus, and its maintenance represents a formidable challenge, as it harbors regulatory proteins that persist throughout adulthood. Here we developed strategies to visualize two classes of such long-lived proteins, histones and nucleoporins, to understand the function of protein longevity in nuclear maintenance. Genome-wide mapping of histones revealed specific enrichment of long-lived variants at silent gene loci. Interestingly, nuclear pores are maintained by piecemeal replacement of subunits, resulting in mosaic complexes composed of polypeptides with vastly different ages. In contrast, nondividing quiescent cells remove old nuclear pores in an ESCRT-dependent manner. Our findings reveal distinct molecular strategies of nuclear maintenance, linking lifelong protein persistence to gene regulation and nuclear integrity.

The Silent Cooperator: An Epigenetic Model for Emergence of Altruistic Traits in Biological Systems

Spatial evolutionary game theory explains how cooperative traits can survive the intense competition in biological systems. If the spatial distribution allows cooperators to interact with each other frequently, the benefits of cooperation will outweigh the losses due to exploitation by selfish organisms. However, for a cooperative behavior to get established in a system, it needs to be found initially in a sufficiently large cluster to allow a high frequency of intracooperator interactions. Since mutations are rare events, this poses the question of how cooperation can arise in a biological system in the first place. We present a simple model which captures two concepts from genetics that can explain how evolution overcomes the emergence problem. The first concept is, often in nature, a gene may not express its phenotype except under specific environmental conditions, rendering it to be a “silent” gene. The second key idea is that a neutral gene, one that does not harm or improve an organism’s survival chances, can still spread through a population if it is physically near to another gene that is positively selected. Through these two ideas, our model offers a possible solution to the fundamental problem of emergence of cooperation in biological systems.