Engineering of complex polyketide biosynthesis — insights from sequencing of the monensin biosynthetic gene cluster

The biosynthesis of complex reduced polyketides is catalysed in actinomycetes by large multifunctional enzymes, the modular Type I polyketide synthases (PKSs). Most of our current knowledge of such systems stems from the study of a restricted number of macrolide-synthesising enzymes. The sequencing of the genes for the biosynthesis of monensin A, a typical polyether ionophore polyketide, provided the first genetic evidence for the mechanism of oxidative cyclisation through which polyethers such as monensin are formed from the uncyclised products of the PKS. Two intriguing genes associated with the monensin PKS cluster code for proteins, which show strong homology with enzymes that trigger double bond migrations in steroid biosynthesis by generation of an extended enolate of an unsaturated ketone residue. A similar mechanism operating at the stage of an enoyl ester intermediate during chain extension on a PKS could allow isomerisation of an E double bond to the Z isomer. This process, together with epoxidations and cyclisations, form the basis of a revised proposal for monensin formation. The monensin PKS has also provided fresh insight into general features of catalysis by modular PKSs, in particular into the mechanism of chain initiation. Journal of Industrial Microbiology & Biotechnology (2001) 27, 360–367. Received 18 March 2001/ Accepted in revised form 09 July 2001     

Salinomycin biosynthesis reversely regulates the β-oxidation pathway in Streptomyces albus by carrying a 3-hydroxyacyl-CoA dehydrogenase gene in its biosynthetic gene cluster

Streptomyces is well known for synthesis of many biologically active secondary metabolites, such as polyketides and non-ribosomal peptides. Understanding the coupling mechanisms of primary and secondary metabolism can help develop strategies to improve secondary metabolite production in Streptomyces. In this work, Streptomyces albus ZD11, an oil-preferring industrial Streptomyces strain, was proved to have a remarkable capability to generate abundant acyl-CoA precursors for salinomycin biosynthesis with the aid of its enhanced β-oxidation pathway. It was found that the salinomycin biosynthetic gene cluster contains a predicted 3-hydroxyacyl-CoA dehydrogenase (FadB3), which is the third enzyme of β-oxidation cycle. Deletion of fadB3 significantly reduced the production of salinomycin. A variety of experimental evidences showed that FadB3 was mainly involved in the β-oxidation pathway rather than ethylmalonyl-CoA biosynthesis and played a very important role in regulating the rate of β-oxidation in S. albus ZD11. Our findings elucidate an interesting coupling mechanism by which a PKS biosynthetic gene cluster could regulate the β-oxidation pathway by carrying β-oxidation genes, enabling Streptomyces to efficiently synthesize target polyketides and economically utilize environmental nutrients.     

Analysis of seven genes from the eryAI –eryK region of the erythromycin biosynthetic gene cluster in Saccharopolyspora erythraea

The gene cluster (ery) governing the biosynthesis of the macrolide antibiotic erythromycin A by Saccharopolyspora erythraea contains, in addition to the eryA genes encoding the polyketide synthase, two regions containing genes for later steps in the pathway. The region 5′ of eryA, and lying between eryA and the gene eryK, which is known to encode the C-12 hydroxylase, has been sequenced and shown to contain seven additional open reading frames (ORFs 13–19). On the basis of sequence similarities, roles are proposed for several of these ORFs in the biosynthesis of the deoxysugar mycarose and the deoxyaminosugar desosamine. A chromosomal mutant carrying a deletion in ORF15 has been constructed and shown to accumulate 3-O-mycarosyl-erythronolide B, as expected for an eryC mutant. Similarly, a chromosomal mutant carrying a deletion in ORF16 has been constructed and shown to accumulate erythronolide B, as expected for an eryB mutant.     

The carp–goldfish nucleocytoplasmic hybrid has mitochondria from the carp as the nuclear donor species

It is widely accepted that mitochondria and its DNA (mtDNA) exhibit strict maternal inheritance, with sperm contributing no or non-detectable mitochondria to the next generation. In fish, nuclear transfer (NT) through the combination of a donor nucleus and an enucleated oocyte can produce fertile nucleocytoplasmic hybrids (NCHs) even between different genera and subfamilies. One of the best studied fish NCHs is CyCa produced by transplanting the nuclei plus cytoplasm from the common carp (Cyprinus carpio var. wuyuanensis) into the oocytes of the wild goldfish (Carassius auratus), which has been propagated by self-mating for three generations. These NCH fish thus provide a unique model to study the origin of mitochondria. Here we report the complete mtDNA sequence of the CyCa hybrid and its parental species carp and goldfish as nuclear donor and cytoplasm host, respectively. Interestingly, the mtDNA of NCH fish CyCa is 99.69% identical to the nuclear donor species carp, and 89.25% identical to the oocyte host species goldfish. Furthermore, an amino acid sequence comparison of 13 mitochondrial proteins reveals that CyCa is 99.68% identical to the carp and 87.68% identical to the goldfish. On an mtDNA-based phylogenetic tree, CyCa is clustered with the carp but separated from the goldfish. A real-time PCR analysis revealed the presence of carp mtDNA but the absence of goldfish mtDNA. These results demonstrate – for the first time to our knowledge – that the mtDNA of a NCH such as CyCa fish may originate from its nuclear donor rather than its oocyte host.     

Arabidopsis thaliana as a model for the study of plant–virus co-evolution

Understanding plant–virus coevolution requires wild systems in which there is no human manipulation of either host or virus. To develop such a system, we analysed virus infection in six wild populations of Arabidopsis thaliana in Central Spain. The incidence of five virus species with different life-styles was monitored during four years, and this was analysed in relation to the demography of the host populations. Total virus incidence reached 70 per cent, which suggests a role of virus infection in the population structure and dynamics of the host, under the assumption of a host fitness cost caused by the infection. Maximum incidence occurred at early growth stages, and co-infection with different viruses was frequent, two factors often resulting in increased virulence. Experimental infections under controlled conditions with two isolates of the most prevalent viruses, cauliflower mosaic virus and cucumber mosaic virus, showed that there is genetic variation for virus accumulation, although this depended on the interaction between host and virus genotypes. Comparison of Q_ST-based genetic differentiations between both host populations with F_ST genetic differentiation based on putatively neutral markers suggests different selection dynamics for resistance against different virus species or genotypes. Together, these results are compatible with a hypothesis of plant–virus coevolution.     

Preimplantation diagnosis of the β1 integrin knockout mutation as a model for aneuploid gene testing

The autosomal beta1 integrin knockout mouse mutation was selected as a model to experimentally determine preimplantation diagnosis test reliability for autosomal gene deletions and duplications. In experiment 1, which analyzed 198 individually disaggregated single blastomeres, the observed test frequencies matched the mathematically predicted frequencies calculated from the independently derived values of 90% normal allele amplification, 92% mutant allele amplification, 4% alternate allele contamination, and 4% failure to transfer amplifiable target DNA into the PCR reaction mix. This experiment correctly predicted a normal embryonic phenotype in 143 (99.3%) of the 144 phenotypically normal autosomal recessive results. Experiment 2 compared single biopsied blastomere test results to test results on the remaining embryonic cells cultured 1 week until trophoblast outgrowth. Single biopsied blastomere analysis correctly predicted a normal autosomal recessive phenotype in 87 (98%) of the 89 embryos that would have been selected for implantation. Experiment 3 compared the PCR results of two biopsied blastomeres tested independently to the PCR result from the remaining cultured blastomeres to improve test reliability. Given that embryos would have been implanted only when two normal results were obtained, 17 of 17 phenotypically normal embryos would have been implanted from among the 44 embryos tested. These experiment 3 results are consistent with the mathematical prediction that about 99.9% of embryos implanted with two unaffected biopsied blastomere results would have had a phenotypically normal genotype.     

Iron–sulfur cluster biosynthesis: characterization of IscU–IscS complex formation and a structural model for sulfide delivery to the [2Fe–2S] assembly site

Recent work on the bacterial iron–sulfur cluster (isc) family of gene products, and eukaryotic homologs, has advanced the molecular understanding of cellular mechanisms of iron–sulfur cluster biosynthesis. Members of the IscS family are pyridoxyl-5′-phosophate dependent proteins that deliver inorganic sulfide during assembly of the [2Fe–2S] cluster on the IscU scaffold protein. Herein it is demonstrated through calorimetry, fluorescence, and protein stability measurements that Thermotoga maritima IscS forms a 1:1 complex with IscU in a concentration-dependent manner (K _D varying from 6 to 34 μM, over an IscS concentration range of approximately 2–50 μM). Docking simulations of representative IscU and IscS proteins reveal critical contact surfaces at the N-terminal helix of IscU and a C-terminal loop comprising a chaperone binding domain. Consistent with the isothermal titration calorimetry results described here, an overall dominant contribution of charged surfaces with a change in the molar heat capacity of binding, ΔC _p ~ 199.8 kcal K⁻¹ mol⁻¹, is observed that accounts for approximately 10% of the total accessible surface area at the binding interface. Both apo and holo IscUs and homologs were found to bind to IscS in an enthalpically driven reaction with comparable K _D values. Both helix and loop regions are highly conserved among phylogenetically diverse organisms from a pool of archael, bacterial, fungal, and mammalian representatives.     

The detection of a de novo allele of the Glu-1Dx gene in wheat–rye hybrid offspring

Key message

This study provides a link between a de novo gene and novel phenotype in wheat–rye hybrids that can be used as a model for induced de novo genetic variation.

Abstract

Wide hybridization can produce de novo DNA variation that may cause novel phenotypes. However, there is still a lack of specific links between changed genes and novel phenotypes in wide hybrids. The well-studied high-molecular-weight glutenin subunit (HMW-GS) genes in tribe Triticeae provide a useful model for addressing this issue. In this study, we investigated the feasibility of a wheat–rye hybridization method for inducing de novo phenotypes using the Glu-1Dx2.2 subunit as an example. We developed three hexaploid wheat lines with normal fertility and a Glu-1Dx2.2 variant, named Glu-1Dx2.2 ^v , derived from three F₁ hybrids. The wild-type Glu-1Dx2.2 has two direct repeats of 295 bp length separated by an intervening 101 bp in its central repetitive region. In the mutant Glu-1Dx2.2 ^v , one copy of the repeats and the intervening sequence were deleted, probably through homology-dependent illegitimate recombination (IR). This study provides a direct link between a de novo allele and novel phenotype. Our results indicate that the wheat–rye method may be a useful tool to induce de novo genetic variations that broaden the genetic diversity for wheat improvement.     

Exclusion of the C/D box snoRNA gene cluster HBII-52 from a major role in Prader–Willi syndrome

Prader–Willi syndrome (PWS) and Angelman syndrome (AS) are distinct neurogenetic disorders caused by the loss of function of imprinted genes in 15q11–q13. The maternally expressed UBE3A gene is affected in AS. Four protein-encoding genes (MKRN3, MAGEL2, NDN and SNURF-SNRPN) and several small nucleolar (sno) RNA genes (HBII-13, HBII-436, HBII-85, HBII-438A, HBII-438B and HBII-52) are expressed from the paternal chromosome only but their contribution to PWS is unclear. To examine the role of the HBII-52 snoRNA genes, we have reinvestigated an AS family with a submicroscopic deletion spanning UBE3A and flanking sequences. By fine mapping of the centromeric deletion breakpoint in this family, we have found that the deletion affects all of the 47 HBII-52 genes. Since the complete loss of the HBII-52 genes in family members who carry the deletion on their paternal chromosome is not associated with an obvious clinical phenotype, we conclude that HBII-52 snoRNA genes do not play a major role in PWS. However, we cannot exclude the possibility that the loss of HBII-52 has a phenotypic effect when accompanied by the loss of function of other genes in 15q11–q13.Electronic Database Information: accession numbers and URLs for data presented herein are as follows: for PAR-4 (accession number AF019617), deletion junction fragment (L15422): GenBank, ; for Angelman syndrome [MIM105830]: Online Mendelian Inheritance in Man (OMIM),     

The stationary distribution of a sample from the Wright–Fisher diffusion model with general small mutation rates

Journal of Mathematical Biology - The stationary distribution of a sample taken from a Wright–Fisher diffusion with general small mutation rates is found using a coalescent approach. The...     

The chromaffin granule — Plasma membrane interaction as a model for exocytosis: Quantitative release of the soluble granular content

Bovine adrenal medullary plasma membranes induce the release of soluble components from chromaffin granules in a Ca²⁺ dependent manner. This interaction can be modulated by changing the temperature. Correlation of the concentrations of four released soluble markers (catecholamines, soluble protein, ATP and dopamine-β-hydroxylase) in samples incubated at different temperatures revealed that those markers were liberated simultaneously. Their ratio did not differ significantly from the ratio measured in chromaffin granule lysates. These results suggest the release of the total granular content upon incubation with plasma membranes. Further analysis of the free catecholamines showed a preferential release of adrenalin.     

Protection of scaffold protein Isu from degradation by the Lon protease Pim1 as a component of Fe–S cluster biogenesis regulation

Iron–sulfur (Fe–S) clusters, essential protein cofactors, are assembled on the mitochondrial scaffold protein Isu and then transferred to recipient proteins via a multistep process in which Isu interacts sequentially with multiple protein factors. This pathway is in part regulated posttranslationally by modulation of the degradation of Isu, whose abundance increases >10-fold upon perturbation of the biogenesis process. We tested a model in which direct interaction with protein partners protects Isu from degradation by the mitochondrial Lon-type protease. Using purified components, we demonstrated that Isu is indeed a substrate of the Lon-type protease and that it is protected from degradation by Nfs1, the sulfur donor for Fe–S cluster assembly, as well as by Jac1, the J-protein Hsp70 cochaperone that functions in cluster transfer from Isu. Nfs1 and Jac1 variants known to be defective in interaction with Isu were also defective in protecting Isu from degradation. Furthermore, overproduction of Jac1 protected Isu from degradation in vivo, as did Nfs1. Taken together, our results lead to a model of dynamic interplay between a protease and protein factors throughout the Fe–S cluster assembly and transfer process, leading to up-regulation of Isu levels under conditions when Fe–S cluster biogenesis does not meet cellular demands.     

The gene for the α-subunit of ATPase: a site of homologous recombination in plant mitochondrial DNA also functions in somatic hybrid cells

Summary Segments of mitochondrial DNA (mtDNA) carrying the gene for the -subunit of F₁-ATPase (atpA) were detected by Southern hybridization with atpA from pea as probe. In the case of Nicotiana langsdorffii, we identified four fragments that are derived from combinations of two different 5 and two different 3 flanking regions of atpA. All four types share the coding region, suggesting that they result from homologous recombination in the coding region of atpA. By contrast, N. glauca generated only one analogous fragment, which indicated the existence of only a single type of atpA in N. glauca. In the case of somatic hybrids obtained by fusion between protoplasts from N. langsdorffii and N. glauca, analysis with EcoRI or HindIII detected three new fragments in addition to the parental fragments. These new fragments can be explained by homologous recombination within the coding region of atpA. Our results show that the coding region of atpA is involved not only in intragenomic homologous recombination but can also be involved in homologous recombination between two parental mitochondrial genomes of somatic hybrids.     

Evaluation of different protocols for the analysis of lipophilic plant metabolites by gas chromatography–mass spectrometry using potato as a model

In the analysis of lipophilic plant metabolites by gas chromatography?Cmass spectrometry a step is required to release fatty acids and other analytes from complex molecules. Seven alternative methods were compared to the standard method of 1% H₂SO₄/50°C/16?h using Desirée and Phureja potato tubers as models. With two sodium methoxide alkali-catalysed methods (0.5?M NaOCH₃/50°C/1 and 16?h) recoveries of ferulic acids increased, long chain fatty acids and sterols decreased, 2-hydroxy acids were negligible, solanidine was absent and ??5-avenasterol isomerisation was minimal. Using a harsh alkali hydrolysis (1.0?M KOH/120°C/24?h) followed by a mild methylation (1% H₂SO₄/50°C/1.5?h), recoveries of polyunsaturated fatty acids were poor, sterols decreased but ??5-avenasterol isomerisation was minimal. With a mild alkali hydrolysis (0.5?M NaOH/100°C/5?min) followed by methylation with boron trifluoride (14%BF₃/100°C/30?min) recoveries of sterols and 2-hydroxy fatty acids were similar to the standard method and ??5-avenasterol isomerisation was high. Lower ferulic acid recoveries, absence of solanidine and overestimation of fatty alcohols were evident in both methods involving alkali hydrolysis. Three different methods using hydrochloric acid (1.00?M HCl/70°C/5?h, 0.63?M HCl/110°C/2?h and 2.00?M HCl/50°C/24?h) all gave increased recoveries of 2-hydroxy acids, ferulic acids, solanidine and sterols, although ??5-avenasterol isomerisation increased. Hydrochloric acid methods are recommended for studies requiring quantitative determinations (i.e. concentration of metabolite in sample). Either the hydrochloric acid methods or the standard sulphuric acid method are suggested for determining relative concentrations between samples, although there is a requirement for further studies.     

Holling's “hungry mantid” model for the invertebrate functional response considered as a Markov process. Part I: The full model and some of its limits

In this paper we give an analytical reformulation of Holling's (1966) simulation model for invertebrate predatory behaviour. To this end we represent a population of predators as a frequency distribution over a space of (physiological) states. The functional response of a predator is calculated from the (stable) equilibrium distribution of its state as a function of prey density.Starting from the general model various other models are obtained by limit processes, some of them new and some of them old. The more interesting of which will be studied in further papers in this series.List of Notation a rate constant of digestion - b maximum of rate constant of prey encounter in the mantid - b maximum pursuit duration in the mantid (_p(0)) - c satiation threshold for search - c satiation threshold for pursuit in the mantid: c=c(b-D_s/v)/b - D _m maximum sighting distance - D _p pursuit distance - D _s strike distance - expectation operator - f, f ₀ rate of change of satiation during search - f ₁ rate of change of satiation during prey handling - F functional response: number of prey eaten per unit of time by one predator - g rate constant of effective prey encounter in the gobbler and sucker - g₀ rate constant of prey encounter - g₁ probability of no prey loss from pursuit - g₂ probability of no prey escaping during pursuit - H Holling secretary correction factor in the sucker: fraction of the time spent searching - k _R density of R - k_T probability density of maximum prey handling time - K probability that maximum prey handling time is _e, i.e. pursuit duration is zero - K _R distribution function of R - N number of prey caught - p (marginal) density of S - p₀ density of S in search - p₁ simultaneous density of S and T - P probability - p ₁ marginal density of S in handling prey - q probability of strike success - R ratio of realized to maximum sighting distance - s, S satiation - satiation axis - t time - handling time axis - u eating speed - U homogeneous(0,1) random variable - v pursuit speed - V exponential(1) random variable - w prey weight - W exponential(_m) random variable - x prey density - ratio of maximum successful pursuit duration to meal duration (_pm/_e) - _pm - relative duration of successful pursuit (_p/_pm) - ratio of shortest to largest sighting distance - x_e - time already spent handling a prey item - rate of prey loss during prey handling - prey escape rate during pursuit - prey biomass density (xw) - , T maximum time still to be spent handling a prey item - _e meal duration - _m maximum handling time ( _e+ _p) - _p duration of successful pursuit - _pm maximum duration of successful pursuit (_p(0)) - hazard rate - _m maximum of hazard rate - scaled functional response (wF) - minimal i-state space     

The library model for satellite DNA evolution: a case study with the rodents of the genus Ctenomys (Octodontidae) from the Iberá marsh, Argentina

On the basement of the library model of satellite DNA evolution is the differential amplification of subfamilies through lineages diversification. However, this idea has rarely been explored from an experimental point of view. In the present work, we analyzed copy number and sequence variability of RPCS (repetitive PvuII Ctenomys sequence), the major satellite DNA present in the genomes of the rodents of the genus Ctenomys, in a closely related group of species and forms inhabiting the Iberá marsh in Argentina. We studied the dependence of these two parameters at the intrapopulation level because in the case of interbreeding genomes, differences in RPCS copy number are due to recent amplification/contraction events. We found an inverse relationship among RPCS copy number and sequence variability: amplifications lead to a decrease in sequence variability, by means of biased homogenization of the overall satellite DNA, prevailing few variants. On the contrary, the contraction events that involve tandems of homogeneous monomers contribute-by default-minor variants to become "evident", which otherwise were undetectable. On the other hand, all the RPCS sequence variants are totally or partially shared by all the studied populations. As a whole, these results are comprehensible if these RPCS variants preexisted in the common ancestor of this Ctenomys group.