Aerial morphogenesis: enter the chaplins

The Best of Both Worlds-Streptomyces coelicolor and Streptomyces venezuelae as Model Species for Studying Antibiotic Production and Bacterial Multicellular Development

Streptomyces bacteria have been studied for more than 80 years thanks to their ability to produce an incredible array of antibiotics and other specialized metabolites and their unusual fungal-like development. Their antibiotic production capabilities have ensured continual interest from both academic and industrial sectors, while their developmental life cycle has provided investigators with unique opportunities to address fundamental questions relating to bacterial multicellular growth. Much of our understanding of the biology and metabolism of these fascinating bacteria, and many of the tools we use to manipulate these organisms, have stemmed from investigations using the model species Streptomyces coelicolor and Streptomyces venezuelae. Here, we explore the pioneering work in S. coelicolor that established foundational genetic principles relating to specialized metabolism and development, alongside the genomic and cell biology developments that led to the emergence of S. venezuelae as a new model system. We highlight key discoveries that have stemmed from studies of these two systems and discuss opportunities for future investigations that leverage the power and understanding provided by S. coelicolor and S. venezuelae.

Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin functional amyloids

Synergistic-aggregation and cross-seeding by two different proteins/peptides in the amyloid aggregation are well evident in various neurological disorders including Alzheimer’s disease. Here, we show co-storage of human Prolactin (PRL), which is associated with lactation in mammals, and neuropeptide galanin (GAL) as functional amyloids in secretory granules (SGs) of the female rat. Using a wide variety of biophysical studies, we show that irrespective of the difference in sequence and structure, both hormones facilitate their synergic aggregation to amyloid fibrils. Although each hormone possesses homotypic seeding ability, a unidirectional cross-seeding of GAL aggregation by PRL seeds and the inability of cross seeding by mixed fibrils suggest tight regulation of functional amyloid formation by these hormones for their efficient storage in SGs. Further, the faster release of functional hormones from mixed fibrils compared to the corresponding individual amyloid, suggests a novel mechanism of heterologous amyloid formation in functional amyloids of SGs in the pituitary.

The formation of plaques of proteins called ‘amyloids’ in the brain is one of the hallmark characteristics of both Alzheimer’s and Parkinson’s disease, but amyloids can form in many tissues and organs, often disrupting normal activity. A lot of the research into amyloids has focused on their role in disease, but it turns out that amyloids can also appear in healthy tissues. For example, some protein hormones form amyloids that act as storage depots, helping cells to release the hormone when it is needed.

Normally, amyloids are made mostly of a single type of protein or protein fragment associated with a particular disease like Alzheimer's. Often, this type of amyloid promotes plaque formation in other proteins, which aggravates other diseases (for example, the amyloids that form in Alzheimer’s can lead to Parkinson’s disease or type II diabetes getting worse).The plaques start growing from small amyloid fragments called seeds. In mixed amyloids – amyloids made of two types of proteins – seeds made of one protein can trigger the formation of amyloids of the other protein. This raises the question, is this true for hormones? The body often releases more than one hormone at a time from the same tissue; for example, the pituitary gland releases prolactin and galanin simultaneously. However, these hormones have completely different structures, so whether they can form a mixed amyloid is unclear.

To answer this question, Chatterjee et al. first determined that, within the pituitary gland of female rats, prolactin and galanin could be found together in the same cells, forming mixed amyloids. To understand out how this happens, Chatterjee et al. tried seeding new amyloids using either prolactin or galanin. This revealed that only prolactin seeds were able to trigger the formation of galanin amyloids. Chatterjee et al. also found that the mixed amyloids could release the hormones faster than amyloids made from either protein alone. Together, these results suggest that the collaboration between these two proteins may help maintain hormone balance in the body.

Problems with hormone storage and release lead to various human diseases, including prolactinoma. Understanding amyloid storage depots could reveal new ways to control hormone levels. Further research could also help to explain more about well-studied diseases linked to amyloids, like Alzheimer's.

A novel XRE family regulator that controls antibiotic production and development in Streptomyces coelicolor

Although the genome of the Streptomyces model strain S. coelicolor was sequenced nearly two decades ago, the function of many annotated genes has not been verified, including that of gene sco1979, which was predicted to encode a transcriptional regulator of the xenobiotic response element (XRE) family. In this study, we showed that SCO1979 represses its own transcription and that deletion of sco1979 from S. coelicolor markedly enhanced production of three antibiotics, which are actinorhodin (ACT), undecylprodigiosin (RED), and calcium-dependent antibiotic (CDA), suggesting that SCO1979 represses their biosynthesis. We demonstrated that transcription of genes in the ACT, RED, and CDA pathways was generally increased in the mutant strain Δ1979 compared with levels in the wild-type strain M145. Additionally, purified recombinant SCO1979 interacted with DNA sequences upstream of sco1979 and actII-orf4, redZ, and cdaR, the pathway-specific regulators for the three pathways, implying that SCO1979 potentially regulates the ACT, RED, and CDA pathways via their specific regulators. In addition, disruption of sco1979 led to the notably delayed formation of aerial mycelium and spores, and consistent with this, transcription of genes associated with aerial hyphae and spore formation, such as chp and rdl, and ram, was reduced in Δ1979, implying the involvement of SCO1979 in cellular development control as well. In summary, our findings demonstrated that SCO1979 is a pleiotropic regulator with roles in both secondary metabolism and morphological development in S. coelicolor. KEY POINTS: • SCO1979 is a novel Streptomyces regulator of the XRE family. • SCO1979 regulates its own transcription. • SCO1979 regulates antibiotic production and cellular development.

Protein Nanofibrils as Storage Forms of Peptide Drugs and Hormones

Amyloids are highly organized cross β-sheet protein nanofibrils that are associated with both diseases and functions. Thermodynamically amyloids are stable structures as they represent the lowest free energy state that proteins can attain. However, recent studies suggest that amyloid fibrils can be dissociated by a change in environmental parameters such as pH and ionic strength. This reversibility of amyloids can not only be associated with disease, but function as well. In disease-associated amyloids, fibrils can act as reservoirs of cytotoxic oligomers. Recently, in higher organisms such as mammals, hormones were found to be stored in amyloid-like state, where these were reported to act as a reservoir of functional monomers. These hormone amyloids can dissociate to monomers upon release from the secretory granules, and subsequently bind to their respective receptors and perform their functions. In this book chapter, we describe in detail how these protein nanofibrils represent the densest possible peptide packing and are suitable for long-term storage. Thus, mimicking the feature of amyloids to release functional monomers, it is possible to formulate amyloid-based peptide/protein drugs, which can be used for sustained release.

Deletion of MtrA Inhibits Cellular Development of Streptomyces coelicolor and Alters Expression of Developmental Regulatory Genes

The developmental life cycle of Streptomyces species includes aerial hyphae formation and spore maturation, two distinct developmental processes that are controlled, respectively, by two families of developmental regulatory genes, bld and whi. In this study, we show that the response regulator MtrA (SCO3013) is critical for normal development of aerial hyphae in S. coelicolor and related species. ΔmtrA, a deletion mutant of the response regulator gene mtrA, exhibited the bald phenotype typical of bld mutants defective in aerial mycelium formation, with formation either much delayed or absent depending on the culture medium. Transcriptional analysis indicated that MtrA activates multiple genes involved in formation of aerial mycelium, including chp, rdl, and ram genes, as well as developmental regulatory genes of the bld and whi families. However, the major regulatory gene bldD showed enhanced expression in ΔmtrA, suggesting it is repressed by MtrA. electrophoretic mobility shift assays indicated that MtrA binds upstream of several genes with altered expression in ΔmtrA, including bldD and whiI, and sequences similar to the consensus binding sequence for MtrA of another actinomycete, Mycobacterium tuberculosis, were found in the bound sites. A loosely conserved recognition sequence containing two short, direct repeats was identified for MtrA of S. coelicolor and was validated using mutational analysis. MtrA homologs are widely distributed among Streptomyces species, and as with S. coelicolor, deletion of the mtrA homologs sve_2757 from S. venezuelae and sli_3357 from S. lividans resulted in conditional bald morphology. Our study suggests a critical and conserved role for MtrA in Streptomyces development.

Microbial amyloids--functions and interactions within the host

The aggregation of proteins into amyloid fibers is a common characteristic of many neurodegenerative disorders including Alzheimer's, Parkinson's, and prion diseases. Amyloid formation was originally characterized in these systems and is traditionally viewed as a consequence of protein misfolding and aggregation. An emerging field of study brings functional amyloids, like those produced by bacteria, into the scientific mainstream, and demonstrates a ubiquitous role for amyloids in living systems. This review aims to summarize what is known about the bacterial amyloids and their interactions within various host environments.

Molecular interpretation of ACTH-β-endorphin coaggregation: relevance to secretory granule biogenesis

Peptide/protein hormones could be stored as non-toxic amyloid-like structures in pituitary secretory granules. ACTH and β-endorphin are two of the important peptide hormones that get co-stored in the pituitary secretory granules. Here, we study molecular interactions between ACTH and β-endorphin and their colocalization in the form of amyloid aggregates. Although ACTH is known to be a part of ACTH-β-endorphin aggregate, ACTH alone cannot aggregate into amyloid under various plausible conditions. Using all atom molecular dynamics simulation we investigate the early molecular interaction events in the ACTH-β-endorphin system, β-endorphin-only system and ACTH-only system. We find that β-endorphin and ACTH formed an interacting unit, whereas negligible interactions were observed between ACTH molecules in ACTH-only system. Our data suggest that ACTH is not only involved in interaction with β-endorphin but also enhances the stability of mixed oligomers of the entire system.

Recruitment of class I hydrophobins to the air:water interface initiates a multi-step process of functional amyloid formation

Class I fungal hydrophobins form amphipathic monolayers composed of amyloid rodlets. This is a remarkable case of functional amyloid formation in that a hydrophobic:hydrophilic interface is required to trigger the self-assembly of the proteins. The mechanism of rodlet formation and the role of the interface in this process have not been well understood. Here, we have studied the effect of a range of additives, including ionic liquids, alcohols, and detergents, on rodlet formation by two class I hydrophobins, EAS and DewA. Although the conformation of the hydrophobins in these different solutions is not altered, we observe that the rate of rodlet formation is slowed as the surface tension of the solution is decreased, regardless of the nature of the additive. These results suggest that interface properties are of critical importance for the recruitment, alignment, and structural rearrangement of the amphipathic hydrophobin monomers. This work gives insight into the forces that drive macromolecular assembly of this unique family of proteins and allows us to propose a three-stage model for the interface-driven formation of rodlets.

Functional amyloids signal their arrival

Amyloids have traditionally been associated with misfolded protein aggregates and debilitating neurodegenerative diseases. However, a growing number of functional amyloids have now been described that demonstrate that amyloid formation can be an integral part of normal cellular physiology. Functional amyloid production is highly regulated, and the resulting fibers serve a variety of roles for the cells that produce them. A new role for amyloid as storage reservoirs for peptide hormones within mammalian secretory granules has been discovered. More than 30 different peptide hormones have been found to form amyloids in vitro, and both rats and mice have been shown to store hormone amyloid deposits in secretory granules. Thus, the emerging evidence adds to the diverse roles of amyloid and raises intriguing questions for both the peptide hormone and the functional amyloid fields.

Amyloids: not only pathological agents but also ordered nanomaterials

Amyloid fibers constitute one of the most abundant and important naturally occurring self-associated assemblies. A variety of protein and peptide molecules with various amino acid sequences form these highly stable and well-organized assemblies under diverse conditions. These assemblies display phase states ranging from liquid crystals to rigid nanotubes. The potential applications of these supramolecular assemblies exceed those of synthetic polymers since the building blocks may introduce biological function in addition to mechanical properties. Here we review the structural characteristics of amyloidal supramolecular assemblies, their potential use as either natural or de novo designed sequences, and the range of applications that have been demonstrated so far.

Amyloid Fibrils: From Disease to Design. New Biomaterial Applications for Self-Assembling Cross-β Fibrils

Amyloid fibrils are self-assembling protein aggregates. They are essentially insoluble and resilient nanofibres that offer great potential as materials for nanotechnology and bionanotechnology. Fibrils are associated with several debilitating diseases, for example Alzheimer’s disease, but recent advances suggest they also have positive functions in nature and can be formed in vitro from generic proteins. This article explores how the unique nanotopography and advantageous properties of fibrils may be used to develop tools for probing cell behaviour, protein-based biomimetic materials for supporting cells, or platforms for biosensors and enzyme immobilization.

Insight into the structure of amyloid fibrils from the analysis of globular proteins

The conversion from soluble states into cross-β fibrillar aggregates is a property shared by many different proteins and peptides and was hence conjectured to be a generic feature of polypeptide chains. Increasing evidence is now accumulating that such fibrillar assemblies are generally characterized by a parallel in-register alignment of β-strands contributed by distinct protein molecules. Here we assume a universal mechanism is responsible for β-structure formation and deduce sequence-specific interaction energies between pairs of protein fragments from a statistical analysis of the native folds of globular proteins. The derived fragment–fragment interaction was implemented within a novel algorithm, prediction of amyloid structure aggregation (PASTA), to investigate the role of sequence heterogeneity in driving specific aggregation into ordered self-propagating cross-β structures. The algorithm predicts that the parallel in-register arrangement of sequence portions that participate in the fibril cross-β core is favoured in most cases. However, the antiparallel arrangement is correctly discriminated when present in fibrils formed by short peptides. The predictions of the most aggregation-prone portions of initially unfolded polypeptide chains are also in excellent agreement with available experimental observations. These results corroborate the recent hypothesis that the amyloid structure is stabilised by the same physicochemical determinants as those operating in folded proteins. They also suggest that side chain–side chain interaction across neighbouring β-strands is a key determinant of amyloid fibril formation and of their self-propagating ability.

In many fatal neurodegenerative diseases, including Alzheimer, Parkinson, and spongiform encephalopathies, proteins aggregate into specific fibrous structures to form insoluble plaques known as amyloid. The amyloid structure may also play a nonaberrant role in different organisms. Many globular proteins, folding to their biologically functional native structures in vivo, can be induced to aggregate into amyloid-like fibrils under suitable conditions in vitro. One hallmark of amyloid structure is a specific supramolecular architecture called cross-beta structure, held together by hydrogen bonds extending repeatedly along the fibril axis, but intermolecular interactions are yet unknown at the amino-acid level except for very few cases. In this study, the authors present an algorithm, called prediction of amyloid structure aggregation (PASTA), to computationally predict which portions of a given protein or peptide sequence forming amyloid fibrils are stabilizing the corresponding cross-beta structure and the specific intermolecular pattern of hydrogen-bonded amino acids. PASTA is based on the assumption that the same amino acid–specific interactions stabilizing hydrogen bond patterns in native structures of globular proteins are also employed by nature in amyloid structure. The successful comparison of the authors' prediction with available experimental data supports the existence of a unique framework to describe protein folding and aggregation.

Production of fungal antibiotics using polymeric solid supports in solid-state and liquid fermentation

The use of inert absorbent polymeric supports for cellular attachment in solid-state fungal fermentation influenced growth, morphology, and production of bioactive secondary metabolites. Two filamentous fungi exemplified the utility of this approach to facilitate the discovery of new antimicrobial compounds. Cylindrocarpon sp. LL-Cyan426 produced pyrrocidines A and B and Acremonium sp. LL-Cyan416 produced acremonidins A-E when grown on agar bearing moist polyester-cellulose paper and generated distinctly different metabolite profiles than the conventional shaken or stationary liquid fermentations. Differences were also apparent when tenfold concentrated methanol extracts from these fermentations were tested against antibiotic-susceptible and antibiotic-resistant Gram-positive bacteria, and zones of inhibition were compared. Shaken broth cultures of Acremonium sp. or Cylindrocarpon sp. showed complex HPLC patterns, lower levels of target compounds, and high levels of unwanted compounds and medium components, while agar/solid support cultures showed significantly increased yields of pyrrocidines A and B and acremonidins A-E, respectively. This method, mixed-phase fermentation (fermentation with an inert solid support bearing liquid medium), exploited the increase in surface area available for fungal growth on the supports and the tendency of some microorganisms to adhere to solid surfaces, possibly mimicking their natural growth habits. The production of dimeric anthraquinones by Penicillium sp. LL-WF159 was investigated in liquid fermentation using various inert polymeric immobilization supports composed of polypropylene, polypropylene cellulose, polyester-cellulose, or polyurethane. This culture produced rugulosin, skyrin, flavomannin, and a new bisanthracene, WF159-A, after fermentation in the presence and absence of polymeric supports for mycelial attachment. The physical nature of the different support systems influenced culture morphology and relative metabolite yields, as determined by HPLC analysis and measurement of antimicrobial activity. The application of such immobilized-cell fermentation methods under solid and liquid conditions facilitated the discovery of new antibiotic compounds, and offers new approaches to fungal fermentation for natural product discovery.

Evolution of plant pathogenicity in Streptomyces

Among the multitude of soil-inhabiting, saprophytic Streptomyces species are a growing number of plant pathogens that cause economically important diseases, including potato scab. Streptomyces scabies is the dominant pathogenic species worldwide, but is only one of many that cause very similar disease symptoms on plants. Molecular genetic analysis is beginning to identify the mechanisms used by plant pathogenic species to manipulate their hosts. The nitrated dipeptide phytotoxin, thaxtomin, inhibits cellulose biosynthesis in expanding plant tissues, stimulates Ca2+ spiking, and causes cell death. A secreted necrogenic protein, Nec1, contributes to virulence on diverse plant species. The thaxtomin biosynthetic genes and nec1 lie on a large mobilizable PAI, along with other putative virulence genes including a cytokinin biosynthetic pathway and a saponinase homolog. The PAI is mobilized during conjugation and site-specifically inserts in the linear chromosome of recipient species, accounting for the emergence of new pathogens in agricultural systems. The recently available genome sequence of S. scabies will accelerate research on host-pathogen interactions.

Curli biogenesis and function

Curli are the major proteinaceous component of a complex extracellular matrix produced by many Enterobacteriaceae. Curli were first discovered in the late 1980s on Escherichia coli strains that caused bovine mastitis, and have since been implicated in many physiological and pathogenic processes of E. coli and Salmonella spp. Curli fibers are involved in adhesion to surfaces, cell aggregation, and biofilm formation. Curli also mediate host cell adhesion and invasion, and they are potent inducers of the host inflammatory response. The structure and biogenesis of curli are unique among bacterial fibers that have been described to date. Structurally and biochemically, curli belong to a growing class of fibers known as amyloids. Amyloid fiber formation is responsible for several human diseases including Alzheimer's, Huntington's, and prion diseases, although the process of in vivo amyloid formation is not well understood. Curli provide a unique system to study macromolecular assembly in bacteria and in vivo amyloid fiber formation. Here, we review curli biogenesis, regulation, role in biofilm formation, and role in pathogenesis.

Amyloids--a functional coat for microorganisms

Amyloids are filamentous protein structures approximately 10 nm wide and 0.1-10 mum long that share a structural motif, the cross-beta structure. These fibrils are usually associated with degenerative diseases in mammals. However, recent research has shown that these proteins are also expressed on bacterial and fungal cell surfaces. Microbial amyloids are important in mediating mechanical invasion of abiotic and biotic substrates. In animal hosts, evidence indicates that these protein structures also contribute to colonization by activating host proteases that are involved in haemostasis, inflammation and remodelling of the extracellular matrix. Activation of proteases by amyloids is also implicated in modulating blood coagulation, resulting in potentially life-threatening complications.