Template Domain Research Articles

Theoretical Studies on the Catalytic Mechanism and Cyclization Pattern of Fungal Polyketide Synthase Product Template Domain

AbstractAromatic polyketides are pharmaceutically significant natural products. Product template (PT) domains from fungal non‐reducing polyketide synthases (NR‐PKSs) control the regioselective aldol cyclization of highly reactive polyketide intermediates, whose instabilities have hindered experimental studies. The molecular basis of PT‐catalyzed cyclization and aromatization remain ambiguous. Herein, we conducted MD simulations and QM/MM calculations to explore the catalytic mechanHism and the cyclization pattern of PksA PT specific for C4−C9. The cyclization mediated by PksA PT is initiated by the C4 deprotonation followed by the aldol condensation in C4−C9 register. PTs which evolve from ancient PKS dehydratases (DHs) perform dehydration reactions to aromatize the cyclized intermediates. In PksA PT, the catalytic His1345 and Asp1543 are responsible for aldol cyclization and aromatization steps, respectively. A keto‐enol tautomerism at C3 assists in the elimination reaction catalyzed by Asp1543 with a water molecule network, different from most DHs of PKSs. The C2−C7 aldol cyclization in PksA PT can occur, but the subsequent dehydration step is kinetically unfeasible and thermodynamically unfavorable, suggesting that the aromatization steps determine the C4−C9 cyclization mode of PksA PT. Overall, these computational investigations provide detailed mechanistic insights into the regiospecific intramolecular cyclization and aromatization controlled by fungal PksA PT.

Functional Interactions of Kluyveromyces lactis Telomerase Reverse Transcriptase with the Three-Way Junction and the Template Domains of Telomerase RNA.

The ribonucleoprotein telomerase contains two essential components: telomerase RNA (TER) and telomerase reverse transcriptase (TERT, Est2 in yeast). A small portion of TER, termed the template, is copied by TERT onto the chromosome ends, thus compensating for sequence loss due to incomplete DNA replication and nuclease action. Although telomerase RNA is highly divergent in sequence and length across fungi and mammals, structural motifs essential for telomerase function are conserved. Here, we show that Est2 from the budding yeast Kluyveromyces lactis (klEst2) binds specifically to an essential three-way junction (TWJ) structure in K. lactis TER, which shares a conserved structure and sequence features with the essential CR4-CR5 domain of vertebrate telomerase RNA. klEst2 also binds specifically to the template domain, independently and mutually exclusive of its interaction with TWJ. Furthermore, we present the high-resolution structure of the klEst2 telomerase RNA-binding domain (klTRBD). Mutations introduced in vivo in klTRBD based on the solved structure or in TWJ based on its predicted RNA structure caused severe telomere shortening. These results demonstrate the conservation and importance of these domains and the multiple protein–RNA interactions between Est2 and TER for telomerase function.

Highly Ordered Porous Inorganic Structures via Block Copolymer Lithography: An Application of the Versatile and Selective Infiltration of the "Inverse" P2VP-b-PS System.

A facile and versatile strategy was developed to produce highly ordered porous metal oxide structures via block copolymer (BCP) lithography. Phase separation of poly(2-vinylpyridine)-b-polystyrene (P2VP-b-PS) was induced by solvent vapor annealing in a nonselective solvent environment to fabricate cylindrical arrays. In this work, we thoroughly analyzed the effects of the film thickness, solvent annealing time, and temperature on the ordering of a P2VP-majority system for the first time, resulting in "inverse" structures. Reflectometry, atomic force microscopy, scanning electron microscopy, energy-dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy (XPS), and transmission electron microscopy were used to characterize the formation of the highly ordered BCP morphology and the subsequently produced metal oxide film. At 40 min solvent annealing time, hexagonally close packed structures were produced with cylinder diameters ∼40 nm. Subsequently, the BCP films were infiltrated with different metal cations. Metal ions (Cr, Fe, Ni, and Ga) selectively infiltrated the P2VP domain, while the PS did not retain any detectable amount of metal precursor. This gave rise to a metal oxide porous structure after a UV/ozone (UVO) treatment. The results showed that the metal oxide structures demonstrated high fidelity compared to the BCP template and cylindrical domains presented a similar size to the previous PS structure. Moreover, XPS analyses revealed the complete elimination of the BCP template and confirmed the presence of the metal oxides. These metal oxides were used as hard masks for pattern transfer via dry etching as a further application. Silicon nanopores were fabricated mimicking the BCP template and demonstrated a pore depth of ∼50 nm. Ultimately, this strategy can be applied to create different inorganic nanostructures for a diverse range of applications, for example, solar cells, diodes, and integrated circuits. Furthermore, by optimizing the etching parameters, deeper structures can be obtained via ICP/RIE processes, leading to many potential applications.

The Streptomyces viridochromogenes product template domain represents an evolutionary intermediate between dehydratase and aldol cyclase of type I polyketide synthases

The product template (PT) domains act as an aldol cyclase to control the regiospecific aldol cyclization of the extremely reactive poly-β-ketone intermediate assembled by an iterative type I polyketide synthases (PKSs). Up to now, only the structure of fungal PksA PT that mediates the first-ring cyclization via C4–C9 aldol cyclization is available. We describe here the structural and computational characterization of a bacteria PT domain that controls C2–C7 cyclization in orsellinic acid (OSA) synthesis. Mutating the catalytic H949 of the PT abolishes production of OSA and results in a tetraacetic acid lactone (TTL) generated by spontaneous O-C cyclization of the acyl carrier protein (ACP)-bound tetraketide intermediate. Crystal structure of the bacterial PT domain closely resembles dehydrase (DH) domains of modular type I PKSs in the overall fold, dimerization interface and His-Asp catalytic dyad organization, but is significantly different from PTs of fungal iterative type I PKSs. QM/MM calculation suggests that the catalytic H949 abstracts a proton from C2 and transfers it to C7 carbonyl to mediate the cyclization reaction. According to structural similarity to DHs and functional similarity to fungal PTs, we propose that the bacterial PT represents an evolutionary intermediate between the two tailoring domains of type I PKSs.

Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products.

Many biologically active natural products are synthesized by nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and their hybrids. These megasynthetases contain modules possessing distinct catalytic domains that allow for substrate initiation, chain extension, processing and termination. At the end of a module, a terminal domain, usually a thioesterase (TE), is responsible for catalyzing the release of the NRPS or PKS as a linear or cyclized product. In this review, we address the general cyclization mechanism of the TE domain, including oligomerization and the fungal C-C bond forming Claisen-like cyclases (CLCs). Additionally, we include examples of cyclization catalysts acting within or at the end of a module. Furthermore, condensation-like (CT) domains, terminal reductase (R) domains, reductase-like domains that catalyze Dieckmann condensation (RD), thioesterase-like Dieckmann cyclases, trans-acting TEs from the penicillin binding protein (PBP) enzyme family, product template (PT) domains and others will also be reviewed. The studies summarized here highlight the remarkable diversity of NRPS and PKS cyclization catalysts for the production of biologically relevant, complex cyclic natural products and related compounds.

Physical Activity Interventions for Individuals With a Mild Traumatic Brain Injury:: A Scoping Review.

To document the characteristics, measured outcomes, and effectiveness of physical activity (PA) interventions designed to improve health-related outcomes in individuals with a mild traumatic brain injury (mTBI) to assist in rehabilitation quality improvement efforts of a TBI rehabilitation program. A scoping review following a 6-step iterative framework search across 5 databases (MEDLINE, CINAHL, PsycINFO, SPORTDiscuss, and EMBASE) and the gray literature (Google) was performed. Selected PA interventions were designed for individuals of all ages and any mechanism of injury (eg, sports-related and falls). Data were charted, collated, and summarized according to the Consensus on Exercise Reporting Template checklist and domains of the International Classification of Functioning, Disability and Health. Involvement of clinical experts ensured tailoring of the knowledge synthesis to meet clinical needs. Thirty-five articles and 14 gray literature records were retained. Five types of PA interventions were identified with the majority being multimodal. Reporting of PA intervention characteristics was highly variable across studies; many details necessary for intervention replication are missing. Study outcomes focused primarily on improving body functions and symptoms of mTBI, and less frequently on activities, participation, and health-related quality of life. The methodological quality of studies varies. Identified PA intervention types offer various management options for healthcare providers. PA interventions may improve a wide range of health-related outcomes supporting the inclusion of PA in the management of individuals of all ages with mTBI. Higher-quality research and better reporting about intervention characteristics is however needed.

In silico Targeting, inhibition and analysis of polyketide synthase enzyme in Aspergillus ssp.

Aflatoxins are toxic and carcinogenic components produced by some Aspergillus species such as Aspergillus flavus. Polyketide synthases enzyme (PKS) plays a central role in aflatoxin s biosynthesis of in Aspergillus flavus, especially the product template (PT) domain, which controls the aldol cyclization of the polyketide forerunner during the biosynthesis of the aflatoxin pathway process. Here, we apply the in silico approaches to validate 623 natural components obtained from the South African Natural Compound Database (SANCDB), to distinguish the PT domain s prospected inhibitors. From the 623 compounds, docking results showed that there are 330 different compounds with energy binding lower than the natural substrate (palmitic acid or PLM) of the Product Templet domain (PT). Three factors were selected to determine the best 10 inhibiting components; 1) energy binding, 2) the strengthen chemical interactions, 3) the drug-likeness. The top ten inhibiting components are kraussianone 6, kraussianone 1, neodiospyrin, clionamine D, bromotopsentin, isodiospyrin, spongotine A, kraussianone 3, 14β-Hydroxybufa-3,5,20,22-tetraenolide and kraussianone 7. The chemical interactions between 3HRQ domain and the natural substrate in the active site amino acids are highly similar to the 3HRQ with the top ten components, but the main differences are in the binding energy which is the best in the top ten ligands. Those ten components give successful inhibition with PT domain which will lead to the formula to be used for inhibition and control aflatoxin contamination of agriculture crop yields and lessen the degree of harming and sicknesses that are coming about because of acquiring measures of aflatoxin.

Evolutionary and biochemical analyses reveal conservation of the Brassicaceae telomerase ribonucleoprotein complex.

The telomerase ribonucleoprotein complex (RNP) is essential for genome stability and performs this role through the addition of repetitive DNA to the ends of chromosomes. The telomerase enzyme is composed of a reverse transcriptase (TERT), which utilizes a template domain in an RNA subunit (TER) to reiteratively add telomeric DNA at the ends of chromosomes. Multiple TERs have been identified in the model plant Arabidopsis thaliana. Here we combine a phylogenetic and biochemical approach to understand how the telomerase RNP has evolved in Brassicaceae, the family that includes A. thaliana. Because of the complex phylogenetic pattern of template domain loss and alteration at the previously characterized A. thaliana TER loci, TER1 and TER2, across the plant family Brassicaceae, we bred double mutants from plants with a template deletion at AtTER1 and T-DNA insertion at AtTER2. These double mutants exhibited no telomere length deficiency, a definitive indication that neither of these loci encode a functional telomerase RNA. Moreover, we determined that the telomerase components TERT, Dyskerin, and the KU heterodimer are under strong purifying selection, consistent with the idea that the TER with which they interact is also conserved. To test this hypothesis further, we analyzed the substrate specificity of telomerase from species across Brassicaceae and determined that telomerase from close relatives bind and extend substrates in a similar manner, supporting the idea that TERs in different species are highly similar to one another and are likely encoded from an orthologous locus. Lastly, TERT proteins from across Brassicaceae were able to complement loss of function tert mutants in vivo, indicating TERTs from other species have the ability to recognize the native TER of A. thaliana. Finally, we immunoprecipitated the telomerase complex and identified associated RNAs via RNA-seq. Using our evolutionary data we constrained our analyses to conserved RNAs within Brassicaceae that contained a template domain. These analyses revealed a highly expressed locus whose disruption by a T-DNA resulted in a telomeric phenotype similar to the loss of other telomerase core proteins, indicating that the RNA has an important function in telomere maintenance.

Productivity, performance, and portability for computational fluid dynamics applications

Hardware trends over the last decade show increasing complexity and heterogeneity in high performance computing architectures, which presents developers of CFD applications with three key challenges; the need for achieving good performance, being able to utilise current and future hardware by being portable, and doing so in a productive manner. These three appear to contradict each other when using traditional programming approaches, but in recent years, several strategies such as template libraries and Domain Specific Languages have emerged as a potential solution; by giving up generality and focusing on a narrower domain of problems, all three can be achieved.This paper gives an overview of the state-of-the-art for delivering performance, portability, and productivity to CFD applications, ranging from high-level libraries that allow the symbolic description of PDEs to low-level techniques that target individual algorithmic patterns. We discuss advantages and challenges in using each approach, and review the performance benchmarking literature that compares implementations for hardware architectures and their programming methods, giving an overview of key applications and their comparative performance.

1-nm-Wide Hydrated Dipole Arrays Regulate AuNW Assembly on Striped Monolayers in Nonpolar Solvent

Summary We show that striped phases of horizontally oriented phospholipids presenting 1-nm-wide orientable dipole arrays can order and straighten flexible 2-nm-diameter gold nanowires (AuNWs) with lengths (up to 1 μm) that greatly exceed the template pitch (∼7.5 nm). AuNW ordering can extend over areas > 100 μm2. Whereas wires bundle in solution, with contact between ligand shells, wires adsorbing to the template separate to much larger center-to-center distances (e.g., 12–30 nm) near multiples of the template pitch, consistent with repulsive interactions between wires emerging during interactions with dipole arrays in the template. AuNW assembly was carried out in cyclohexane, a nonpolar solvent. Interestingly, we found that wire ordering was contingent on the extent of phospholipid headgroup hydration and the presence of excess oleylamine, which assembled into hemicylindrical micelles around the hydrated headgroups. Together, these components generated a protected polar environment that enabled the phospholipid headgroups to function collectively to regulate AuNW assembly.

Docking analysis of hexanoic acid and quercetin with seven domains of polyketide synthase A provided insight into quercetin-mediated aflatoxin biosynthesis inhibition in Aspergillus flavus

Studies on phytochemicals as anti-aflatoxigenic agents have gained importance including quercetin. Thus, to understand the molecular mechanism behind inhibition of aflatoxin biosynthesis by quercetin, interaction study with polyketide synthase A (PksA) of Aspergillus flavus was undertaken. The 3D structure of seven domains of PksA was modeled using SWISS-MODEL server and docking studies were performed by Autodock tools-1.5.6. Docking energies of both the ligands (quercetin and hexanoic acid) were compared with each of the domains of PksA enzyme. Binding energy for quercetin was lesser that ranged from - 7.1 to - 5.25kcal/mol in comparison to hexanoic acid (- 4.74 to - 3.54kcal/mol). LigPlot analysis showed the formation of 12H bonds in case of quercetin and 8H bonds in hexanoic acid. During an interaction with acyltransferase domain, both ligands showed H bond formation at Arg63 position. Also, in product template domain, quercetin creates four H bonds in comparison to one in hexanoic acid. Our quantitative RT-PCR analysis of genes from aflatoxin biosynthesis showed downregulation of pksA, aflD, aflR, aflP and aflS at 24h time point in comparison to 7h in quercetin-treated A. flavus. Overall results revealed that quercetin exhibited the highest level of binding potential (more number of H bonds) with PksA domain in comparison to hexanoic acid; thus, quercetin possibly inhibits via competitively binding to the domains of polyketide synthase, a key enzyme of aflatoxin biosynthetic pathway. Further, we propose that key enzymes from aflatoxin biosynthetic pathway in aflatoxin-producing Aspergilli could be explored further using other phytochemicals as inhibitors.

Spherically Directed Synthesis and Enhanced Cellular Internalization of Metal-Crosslinked DNA Micelles

Using spherically directed reduction of metal ions, a facile and universal method for in situ crosslinking of DNA micelles is described. By incorporating a series of specific template domains into lipid-DNA monomers, copper-, silver-, and gold-crosslinked DNA micelles are formed. By combining characterization results and simulation algorithms, accurate structural profiling of DNA micelles is achieved for the first time. The prepared metal-crosslinked DNA micelles show obvious merits, including one-step formation of core structure and ligand corona, facile size tunability, monodispersity, stability against salt-induced aggregation, high utilization of DNA ligand, mild synthesis conditions, and less time consumption and better internalization. Based on our spherically directed synthesis, metal-crosslinked DNA micelle flares were further prepared for effective intracellular imaging by integrating an aptamer-toehold strategy. In addition, we extended the strategy to cholesterol-based double-stranded DNA micelles, giving strong evidence that our method is not only universal but also flexible.

An integrated and restructive probe mediated strand displacement amplification strategy for sensitive and specific DNA methyltransferase activity detection

Herein, an integrated and restructive probe mediated strand displacement amplification (SDA) strategy is developed for sensitive and specific DNA MTase activity detection. The probe is specially designed with a hairpin structure, which encloses the MTase recognition site in the stem and seals the SDA primer and template in the loop. Under the action of DNA MTase, the probe is methylated and cleaved by DpnI endonuclease, causing its stem truncated. The truncated structure then reconstructs with a shrunken loop and a partially-hybridized duplex of stem, drawing the SDA primer and template domains close to trigger cascade amplification. Numerous G-quadruplexes are produced and intercalated by N-methyl-mesoporphyrin IX (NMM) to generate enhanced fluorescent signal. This strategy detects MTase activity down to 0.063 U/mL, and well distinguishes Dam MTase from its analogues. It is further applied for the MTase detection in biological samples and MTase inhibition analysis. The strategy will provide a promising tool for detection MTase activity in biomedical study and early cancer diagnosis.

Polyketide mimetics yield structural and mechanistic insights into product template domain function in nonreducing polyketide synthases

Product template (PT) domains from fungal nonreducing polyketide synthases (NR-PKSs) are responsible for controlling the aldol cyclizations of poly-β-ketone intermediates assembled during the catalytic cycle. Our ability to understand the high regioselective control that PT domains exert is hindered by the inaccessibility of intrinsically unstable poly-β-ketones for in vitro studies. We describe here the crystallographic application of "atom replacement" mimetics in which isoxazole rings linked by thioethers mimic the alternating sites of carbonyls in the poly-β-ketone intermediates. We report the 1.8-Å cocrystal structure of the PksA PT domain from aflatoxin biosynthesis with a heptaketide mimetic tethered to a stably modified 4'-phosphopantetheine, which provides important empirical evidence for a previously proposed mechanism of PT-catalyzed cyclization. Key observations support the proposed deprotonation at C4 of the nascent polyketide by the catalytic His1345 and the role of a protein-coordinated water network to selectively activate the C9 carbonyl for nucleophilic addition. The importance of the 4'-phosphate at the distal end of the pantetheine arm is demonstrated to both facilitate delivery of the heptaketide mimetic deep into the PT active site and anchor one end of this linear array to precisely meter C4 into close proximity to the catalytic His1345. Additional structural features, docking simulations, and mutational experiments characterize protein-substrate mimic interactions, which likely play roles in orienting and stabilizing interactions during the native multistep catalytic cycle. These findings afford a view of a polyketide "atom-replaced" mimetic in a NR-PKS active site that could prove general for other PKS domains.

Isogeometric computation reuse method for complex objects with topology-consistent volumetric parameterization

Volumetric spline parameterization and computational efficiency are two main challenges in isogeometric analysis (IGA). To tackle this problem, we propose a framework of computation reuse in IGA on a set of three-dimensional models with similar semantic features. Given a template domain, B-spline based consistent volumetric parameterization is first constructed for a set of models with similar semantic features. An efficient quadrature-free method is investigated in our framework to compute the entries of stiffness matrix by Bézier extraction and polynomial approximation. In our approach, evaluation on the stiffness matrix and imposition of the boundary conditions can be pre-computed and reused during IGA on a set of CAD models. Examples with complex geometry are presented to show the effectiveness of our methods, and efficiency similar to the computation in linear finite element analysis can be achieved for IGA taken on a set of models.

Structural and Biochemical Analysis of Protein–Protein Interactions Between the Acyl‐Carrier Protein and Product Template Domain

AbstractIn fungal non‐reducing polyketide synthases (NR‐PKS) the acyl‐carrier protein (ACP) carries the growing polyketide intermediate through iterative rounds of elongation, cyclization and product release. This process occurs through a controlled, yet enigmatic coordination of the ACP with its partner enzymes. The transient nature of ACP interactions with these catalytic domains imposes a major obstacle for investigation of the influence of protein–protein interactions on polyketide product outcome. To further our understanding about how the ACP interacts with the product template (PT) domain that catalyzes polyketide cyclization, we developed the first mechanism‐based crosslinkers for NR‐PKSs. Through in vitro assays, in silico docking and bioinformatics, ACP residues involved in ACP–PT recognition were identified. We used this information to improve ACP compatibility with non‐cognate PT domains, which resulted in the first gain‐of‐function ACP with improved interactions with its partner enzymes. This advance will aid in future combinatorial biosynthesis of new polyketides.

Structural and Biochemical Analysis of Protein-Protein Interactions Between the Acyl-Carrier Protein and Product Template Domain.

In fungal non-reducing polyketide synthases (NR-PKS) the acyl-carrier protein (ACP) carries the growing polyketide intermediate through iterative rounds of elongation, cyclization and product release. This process occurs through a controlled, yet enigmatic coordination of the ACP with its partner enzymes. The transient nature of ACP interactions with these catalytic domains imposes a major obstacle for investigation of the influence of protein-protein interactions on polyketide product outcome. To further our understanding about how the ACP interacts with the product template (PT) domain that catalyzes polyketide cyclization, we developed the first mechanism-based crosslinkers for NR-PKSs. Through in vitro assays, in silico docking and bioinformatics, ACP residues involved in ACP-PT recognition were identified. We used this information to improve ACP compatibility with non-cognate PT domains, which resulted in the first gain-of-function ACP with improved interactions with its partner enzymes. This advance will aid in future combinatorial biosynthesis of new polyketides.

Phenalenone Polyketide Cyclization Catalyzed by Fungal Polyketide Synthase and Flavin-Dependent Monooxygenase.

Phenalenones are polyketide natural products that display diverse structures and biological activities. The core of phenalenones is a peri-fused tricyclic ring system cyclized from a linear polyketide precursor via an unresolved mechanism. Toward understanding the unusual cyclization steps, the phn biosynthetic gene cluster responsible for herqueinone biosynthesis was identified from the genome of Penicillium herquei. A nonreducing polyketide synthase (NR-PKS) PhnA was shown to synthesize the heptaketide backbone and cyclize it into the angular, hemiketal-containing naphtho-γ-pyrone prephenalenone. The product template (PT) domain of PhnA catalyzes only the C4-C9 aldol condensation, which is unprecedented among known PT domains. The transformation of prephenalenone to phenalenone requires an FAD-dependent monooxygenase (FMO) PhnB, which catalyzes the C2 aromatic hydroxylation of prephenalenone and ring opening of the γ-pyrone ring simultaneously. Density functional theory calculations provide insights into why the hydroxylated intermediate undergoes an aldol-like phenoxide-ketone cyclization to yield the phenalenone core. This study therefore unveiled new routes and biocatalysts for polyketide cyclization.

The Distant Siblings-A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis.

In recent years, the influx of newly sequenced fungal genomes has enabled sampling of secondary metabolite biosynthesis on an unprecedented scale. However, explanations of extant diversity which take into account both large-scale phylogeny reconstructions and knowledge gained from multiple genome projects are still lacking. We analyzed the evolutionary sources of genetic diversity in aromatic polyketide biosynthesis in over 100 model fungal genomes. By reconciling the history of over 400 nonreducing polyketide synthases (NR-PKSs) with corresponding species history, we demonstrate that extant fungal NR-PKSs are clades of distant siblings, originating from a burst of duplications in early Pezizomycotina and thinned by extensive losses. The capability of higher fungi to biosynthesize the simplest precursor molecule (orsellinic acid) is highlighted as an ancestral trait underlying biosynthesis of aromatic compounds. This base activity was modified during early evolution of filamentous fungi, toward divergent reaction schemes associated with biosynthesis of, for example, aflatoxins and fusarubins (C4–C9 cyclization) or various anthraquinone derivatives (C6–C11 cyclization). The functional plasticity is further shown to have been supplemented by modularization of domain architecture into discrete pieces (conserved splice junctions within product template domain), as well as tight linkage of key accessory enzyme families and divergence in employed transcriptional factors. Although the majority of discord between species and gene history is explained by ancient duplications, this landscape has been altered by more recent duplications, as well as multiple horizontal gene transfers. The 25 detected transfers include previously undescribed events leading to emergence of, for example, fusarubin biosynthesis in Fusarium genus. Both the underlying data and the results of present analysis (including alternative scenarios revealed by sampling multiple reconciliation optima) are maintained as a freely available web-based resource: http://cropnet.pl/metasites/sekmet/nrpks_2014.

Bioinformatical analysis of the sequences, structures and functions of fungal polyketide synthase product template domains.

The product template (PT) domains, specifically in fungal non-reducing polyketide synthases (NR-PKSs), mediate the regioselective cyclization of polyketides dominating the final structures. However, up to date, the systematic knowledge about PT domains has been insufficient. In present study, the relationships between sequences, structures and functions of the PT domains were analyzed with 661 NR-PKS sequences. Based on the phylogenetic analysis, the PT domains were classified into prominent eight groups (I–VIII) corresponding with the representative compounds and cyclization regioselectivity (C2-C7, C4-C9, and C6-C11). Most of the cavity lining residue (CLR) sites in all groups were common, while the regional CLR site mutations resulted in the appearance of finger-like regions with different orientation. The cavity volumes and shapes, even the catalytic dyad positions of PT domains in different groups were corresponding with characteristic cyclization regioselectivity and compound sizes. The conservative residues in PT sequences were responsible for the cyclization functions and the evolution of the key residues resulted in the differentiations of cyclization functions. The above findings may help to better understand the cyclization mechanisms of PT domains and even predict the structural types of the aromatic polyketide products.