Exploring Protein Interactions on a Minimal Type II Polyketide Synthase Using a Yeast Two-Hybrid System

Interactions between proteins that form the ’minimal’ type II polyketide synthase in the doxorubicin producing biosynthetic pathway from Streptomyces peucetius were investigated using a yeast two-hybrid system (Y2H). Proteins that function as the so called ’chain length factor’ (DpsB) and putative transacylase (DpsD) were found to interact with the ketosynthase subunit (DpsA), which can also interact with itself. On the basis of these results we propose a head-to-tail homodimeric structure, which is consistent with previously published in vivo mutagenesis studies. No interactions were found between the acyl-carrier protein (DpsG) and any of the other constituents of the complex, however, transient interactions, not detectable using the Y2H system, cannot be discounted and warrant further investigation

Exploring Protein Interactions on a Minimal Type II Polyketide Synthase Using a Yeast Two-Hybrid System

Interactions between proteins that form the ’minimal’ type II polyketide synthase in the doxorubicin producing biosynthetic pathway from Streptomyces peucetius were investigated using a yeast two-hybrid system (Y2H). Proteins that function as the so called ’chain length factor’ (DpsB) and putative transacylase (DpsD) were found to interact with the ketosynthase subunit (DpsA), which can also interact with itself. On the basis of these results we propose a head-to-tail homodimeric structure, which is consistent with previously published in vivo mutagenesis studies. No interactions were found between the acyl-carrier protein (DpsG) and any of the other constituents of the complex, however, transient interactions, not detectable using the Y2H system, cannot be discounted and warrant further investigation

Why are plant–soil feedbacks so unpredictable, and what to do about it?

1.The study of feedbacks between plants and soils (plant‐soil feedbacks; PSFs) is receiving increased attention. However, PSFs have been mostly studied in isolation of abiotic and biotic drivers that could affect their strength and direction. This is problematic because it has led to limited predictive power of PSFs in ‘the real world’, leaving large knowledge gaps in our ability to predict how PSFs contribute to ecosystem processes and functions. 2.Here, we present a synthetic framework to elucidate how abiotic and biotic drivers affect PSFs. We focus on two key abiotic drivers (temperature and soil moisture) and two key biotic drivers (aboveground plant consumers and belowground top‐down control of pathogens and mutualists). We focus on these factors because they are known drivers of plants and soil organisms and the ecosystem processes they control, and hence would be expected to strongly influence PSFs. 3.Our framework describes the proposed mechanisms behind these drivers and explores their effects on PSFs. We demonstrate the impacts of these drivers using the fast‐ to slow‐growing plant economics spectrum. We use this well‐established paradigm because plants on opposite ends of this spectrum differ in their relationships with soil biota and have developed contrasting strategies to cope with abiotic and biotic environmental conditions. 4.Finally, we present suggestions for improved experimental designs and scientific inference that will capture and elucidate the influence of above‐ and belowground drivers on PSFs. By establishing the role of abiotic and biotic drivers of PSFs, we will be able to make more robust predictions of how PSFs impact on ecosystem function

Horizontal transfer of a natterin-like toxin encoding gene within the holobiont of the reef building coral Acropora digitifera (Cnidaria:Anthozoa: Scleractinia) and across multiple animal linages

Phylogenetic evidence is provided for horizontal transfer of a natterin-like toxin encoding gene from fungi into the genome of the coral Acropora digitifera. Sequencing analysis of the coral tissues supported that a fungal taxon predicted to be the most likely gene donor was represented in the coral microbiome. Further bioinformatics data suggested widespread recruitment of the natterin-like gene into venomous terrestrial invertebrates, and repositioning of this gene to non-toxic functions in non-venomous teleost fish

A Deep XMM-Newton Survey of M33: Point Source Catalog, Source Detection and Characterization of Overlapping Fields

We have obtained a deep 8-field XMM-Newton mosaic of M33 covering the galaxy out to the D$_{25}$ isophote and beyond to a limiting 0.2--4.5 keV unabsorbed flux of 5$\times$10$^{-16}$ erg cm$^{-2}$ s$^{-1}$ (L${>}$4$\times$10$^{34}$ erg s$^{-1}$ at the distance of M33). These data allow complete coverage of the galaxy with high sensitivity to soft sources such as diffuse hot gas and supernova remnants. Here we describe the methods we used to identify and characterize 1296 point sources in the 8 fields. We compare our resulting source catalog to the literature, note variable sources, construct hardness ratios, classify soft sources, analyze the source density profile, and measure the X-ray luminosity function. As a result of the large effective area of XMM-Newton below 1 keV, the survey contains many new soft X-ray sources. The radial source density profile and X-ray luminosity function for the sources suggests that only $\sim$15% of the 391 bright sources with L${>}$3.6$\times$10$^{35}$ erg s$^{-1}$ are likely to be associated with M33, and more than a third of these are known supernova remnants. The log(N)--log(S) distribution, when corrected for background contamination, is a relatively flat power-law with a differential index of 1.5, which suggests many of the other M33 sources may be high-mass X-ray binaries. Finally, we note the discovery of an interesting new transient X-ray source, which we are unable to classify.Comment: 26 pages, 6 tables, 13 figures, accepted for publication in ApJ

Observation of modified hadronization in relativistic Au+Au collisions: a promising signature for deconfined quark-gluon matter

Measurements of identified particles from Au+Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV are reviewed. Emphasis is placed on nuclear modification, baryon-to-meson ratios, and elliptic flow at intermediate transverse momentum ($1.5 < p_T < 5$ GeV/c). Possible connections between (1) these measurements, (2) the running coupling for static quark anti-quark pairs at finite temperature, and (3) the creation of a deconfined quark-gluon phase are presented. Modifications to hadronization in Au+Au collisions are proposed as a likely signature for the creation of deconfined colored matter.Comment: 8 pages, 5 figures, invited talk at the Strange Quark Matter 2004 conference, Cape Town, South Afric

Od sekvencije DNA do kemijske strukture – pretraživanje mikrobnih genomskih i metagenomskih skupova podataka radi pronalaženja novih prirodnih spojeva

Rapid mining of large genomic and metagenomic data sets for modular polyketide synthases, non-ribosomal peptide synthetases and hybrid polyketide synthase/non-ribosomal peptide synthetase biosynthetic gene clusters has been achieved using the generic computer program packages ClustScan and CompGen. These program packages perform the annotation with the hierarchical structuring into polypeptides, modules and domains, as well as storage and graphical presentations of the data. This aims to achieve the most accurate predictions of the activities and specificities of catalytically active domains that can be made with present knowledge, leading to a prediction of the most likely chemical structures produced by these enzymes. The program packages also allow generation of novel clusters by homologous recombination of the annotated genes in silico. ClustScan and CompGen were used to construct a custom database of known compounds (CSDB) and of predicted entirely novel recombinant products (r-CSDB) that can be used for in silico screening with computer aided drug design technology. The use of these programs has been exemplified by analysing genomic sequences from terrestrial prokaryotes and eukaryotic microorganisms, a marine metagenomic data set and a newly discovered example of a \u27shared metabolic pathway\u27 in marine-microbial endosymbiosis.Brzo pretraživanje genomskih i metagenomskih skupova podataka, modularnih biosintetskih genskih nakupina poliketid sintaza i sintetaza neribosomalno sintetiziranih peptida, postignuto je primjenom generičkih računalnih programskih paketa ClustScan i CompGen. Ti programski paketi provode anotaciju hijerarhijskim strukturiranjem podataka na polipeptide, module i domene, te pohranu i grafičku prezentaciju tih podataka. Na temelju dosadašnjih spoznaja, nastoji se postići najtočnije moguće predviđanje aktivnosti i specifičnosti katalitički aktivnih domena, što vodi prema predviđanju najvjerojatnijih kemijskih struktura koje ti enzimi mogu sintetizirati. Programski paketi ClustScan i CompGen omogućuju generiranje novih genskih nakupina homolognom rekombinacijom anotiranih gena u uvjetima in silico, a upotrijebljeni su i za konstrukciju vlastitih baza podataka poznatih poliketidnih i peptidnih supstancija (CSDB) te potpuno novih poliketidnih i peptidnih supstancija produkata rekombinacije (r-CSDB). Ti će se produkti rekombinacije moći upotrijebiti za izbor supstancija s potencijalnom biološkom aktivnošću pomoću računalom vođenog dizajna lijekova u uvjetima in silico. Primjenjivost programskih paketa ClustScan i CompGen dokazana je u analizi genomskih sekvencija prokariotskih i eukariotskih mikroorganizama što žive u tlu, analizi metagenomske skupine podataka u uzorku iz morske vode, a i na nedavno opisanom primjeru \u27zajedničkog metaboličkoga puta\u27 u mikrobnog endosimbionta morske životinje

Od sekvencije DNA do kemijske strukture – pretraživanje mikrobnih genomskih i metagenomskih skupova podataka radi pronalaženja novih prirodnih spojeva

Rapid mining of large genomic and metagenomic data sets for modular polyketide synthases, non-ribosomal peptide synthetases and hybrid polyketide synthase/non-ribosomal peptide synthetase biosynthetic gene clusters has been achieved using the generic computer program packages ClustScan and CompGen. These program packages perform the annotation with the hierarchical structuring into polypeptides, modules and domains, as well as storage and graphical presentations of the data. This aims to achieve the most accurate predictions of the activities and specificities of catalytically active domains that can be made with present knowledge, leading to a prediction of the most likely chemical structures produced by these enzymes. The program packages also allow generation of novel clusters by homologous recombination of the annotated genes in silico. ClustScan and CompGen were used to construct a custom database of known compounds (CSDB) and of predicted entirely novel recombinant products (r-CSDB) that can be used for in silico screening with computer aided drug design technology. The use of these programs has been exemplified by analysing genomic sequences from terrestrial prokaryotes and eukaryotic microorganisms, a marine metagenomic data set and a newly discovered example of a \u27shared metabolic pathway\u27 in marine-microbial endosymbiosis.Brzo pretraživanje genomskih i metagenomskih skupova podataka, modularnih biosintetskih genskih nakupina poliketid sintaza i sintetaza neribosomalno sintetiziranih peptida, postignuto je primjenom generičkih računalnih programskih paketa ClustScan i CompGen. Ti programski paketi provode anotaciju hijerarhijskim strukturiranjem podataka na polipeptide, module i domene, te pohranu i grafičku prezentaciju tih podataka. Na temelju dosadašnjih spoznaja, nastoji se postići najtočnije moguće predviđanje aktivnosti i specifičnosti katalitički aktivnih domena, što vodi prema predviđanju najvjerojatnijih kemijskih struktura koje ti enzimi mogu sintetizirati. Programski paketi ClustScan i CompGen omogućuju generiranje novih genskih nakupina homolognom rekombinacijom anotiranih gena u uvjetima in silico, a upotrijebljeni su i za konstrukciju vlastitih baza podataka poznatih poliketidnih i peptidnih supstancija (CSDB) te potpuno novih poliketidnih i peptidnih supstancija produkata rekombinacije (r-CSDB). Ti će se produkti rekombinacije moći upotrijebiti za izbor supstancija s potencijalnom biološkom aktivnošću pomoću računalom vođenog dizajna lijekova u uvjetima in silico. Primjenjivost programskih paketa ClustScan i CompGen dokazana je u analizi genomskih sekvencija prokariotskih i eukariotskih mikroorganizama što žive u tlu, analizi metagenomske skupine podataka u uzorku iz morske vode, a i na nedavno opisanom primjeru \u27zajedničkog metaboličkoga puta\u27 u mikrobnog endosimbionta morske životinje