Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development

The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of the Rhodococcus oleaginous metabolism, we sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction assigned 2017 enzymatic reactions to the 8632 R. opacus PD630 genes we identified. Of these, 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. Rhodococcus synthesizes uncommon straight-chain odd-carbon fatty acids in high abundance and stores them as TAGs. We have identified these to be pentadecanoic, heptadecanoic, and cis-heptadecenoic acids. To identify bioconversion pathways, we screened R. opacus PD630, R. jostii RHA1, Ralstonia eutropha H16, and C. glutamicum 13032 for growth on 190 compounds. The results of the catabolic screen, phylogenetic analysis of the TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy.Cambridge-MIT InstituteMassachusetts Institute of Technology. (Seed Grant program)Shell Oil CompanyNational Institute of Allergy and Infectious Diseases (U.S.)United States. National Institutes of HealthNational Institutes of Health. Department of Health and Human Services (Contract No. HHSN272200900006C

Approccio molecolare alla risoluzione di sistematizzazioni controverse: il caso di Acanthodasys caribbeanensis Hochberg & Atherton (Gastrotricha: Thaumastodermatidae)

Lo status tassonomico di alcuni gastrotrichi caraibici recentemente descritti come Acanthodasys caribbeanensis \ue8 incerto poich\ue9 alcune importati caratteristiche morfologiche li avvicinerebbero piuttosto al genere Diplodasys. La scoperta in Sardegna di gastrotrichi simili ha offerto l'opportunit\ue0 di intraprendere uno studio filogenetico su base molecolare al fine di chiarirne la collocazione sistematica. I gastrotrichi sardi sono stati rinvenuti nell'isola di Budelli nel settembre 2010 a 30 metri di profondit\ue0. Le ricostruzioni filogenetiche derivano da analisi MP, ML e inferenza Bayesiana condotte su sequenze del gene 18S rDNA provenienti dagli esemplari sardi e 40 altre specie inclusa A. caribbeanensis raccolta nelle US-Virgin Islands. Gli alberi filogenetici ottenuti mostrano topologie ampiamente sovrapponibili e in generale ben supportate statisticamente. Ipotesi, classiche e recenti, circa i rapporti filogenetici all'interno della famiglia Thaumastodermatidae risultano confermate. Nell'ambito dei Diplodasyinae, Acanthodasys caribbeanensis e gli individui sardi appaiono riuniti in un sottoclade mai strettamente alleato con Acanthodasys. Nell'indicare una maggiore affinit\ue0 degli animali investigati con specie del genere Diplodasys i risultati rendono manifesta l'opportunit\ue0 di provvedere ad una loro ri-collocazione sistematica. Prima di intraprendere i passi formali riteniamo tuttavia necessario aggiungere robustezza alle analisi migliorando il campionamento tassonomico con il coinvolgimento di altre specie di Diplodasyinae

Probing gastrotrich taxonomy with DNA barcoding

Gastrotrichs represent a phylum of basal metazoans, living both in marine and freshwater environments, dimensionally comprised between 80 µm and 3 mm. Though taxonomic and biogeographic knowledge has been improved in the last years, little is known about the molecular aspects of this group. The aim of this study was to analyze these organisms by means of DNA barcoding which is a well-known technique consisting in the use of a gene sequence to affiliate an organism to a known species or to a new taxon. In this research, mitochondrial gene cytochrome oxidase I (COI) was used to identify gastrotrichs. It’s important to notice that no Gastrotrich COI sequence has been deposited in GenBank so far. Sampling of different populations of Turbanella cornuta and Paraturbanella teissieri, species considered to have a wide distribution, was carried out in Adriatic, Ligurian and Tyrrhenian Sea (Italy), Baltic Sea (Sweden), Atlantic Ocean (Canary Islands) and Arabian Gulf (Kuwait). DNA was extracted from some specimens, COI sequence amplified through PCR, and in the end the product was purified and sequenced. The obtained sequences were analyzed with NJ, MP and Bayesian Inference. It was possible to group in monophyletic clades, morphologically similar specimens belonging both to the same population and to diversely geographically distant populations. In particular, analyses revealed that specimens of T. cornuta from Adriatic, Ligurian, and Baltic Sea and Arabian Gulf can be considered distinct species, although similar. These results show that barcoding allows a more precise specific identification of Gastrotrichs; therefore this technique appears to be clearly useful when dealing with cryptic species, not easily distinguishable just by means of morphological characters. The wide application of this method will be of true interest also in reconsidering on new bases the paradoxical cosmopolitan distribution of several species

An integrate approach to the description and systematization of a new genus and species of marine Gastrotricha

In sandy samples from South-West Thailand we found numerous macrodasyidan gastrotrichs belonging to an undescribed species. The abundance and originality of the specimens prompted us to undertake a deep survey of both morphological and molecular traits aiming at the unbiased systematization of the new taxon. Using several microscopical techniques (DIC, SEM and CLSM) we investigated the external and internal anatomy plus the muscular and nervous systems. The Thai gastrotrichs are vermiform, up to 800 μm in total length; the head is well defined and, provided at its posterior edges with a pair of leaf-like sensorial organs; the posterior half of the body appears slightly wider than the anterior region and terminates in a single lobe. The adhesive apparatus includes tubes of the anterior, ventrolateral, posterior and dorsal series. Pharynx is about ¼ of the total body length and shows pores at its posterior 3/4. Adults exhibit maturing eggs and a bulky, muscular caudal organ but, surprisingly, not the frontal organ nor the (usual) spermatozoa. Falloidin reaction indicated that the muscular system organization follows the usual macrodasyidan plan. The nervous system, revealed with antibodies against RF-amide and serotonin (5HT), is present in the central, peripheral and stomatogastrich compartments. The brain consists of paired RF-positive perikarya connected by three dorsal- and a single ventral commissures, plus paired 5HT-positive cells joined by a dorsal commissure. Paired RF- and 5HT-positive neurites run ventrally along all the body length and coalesced at the posterior end. While the anatomical details of the new species appear unique among known genera, ongoing molecular analysis will help (us) clarify its phylogenetic position within the order

Synthetic Strategy toward γ-Keto Nitriles and Their Biocatalytic Conversion to Asymmetric γ-Lactones

Asymmetric γ-hydroxy nitriles are valuable intermediates because hydrolysis of the nitriles can result in an intramolecular cyclization to chiral γ-lactones, which have a variety of biological uses. Starting with an assortment of different aldehydes (alkyl and aryl) a 4-step synthesis of γ-keto nitriles was developed. These prochiral substrates were then screened against a library of ketoreductases for their ability to stereoselectively reduce the carbonyl. Enzymes from the short chain dehydrogenase family showed activity and these enzymatic reactions were scaled up to produce a diverse set of chiral γ-lactones

Single versus Double Cu(I) Catalyzed [3 + 2] Azide/Platinum Diacetylide Cycloaddition Reactions

This report focuses on Cu­(I) catalyzed cycloaddition reactions between organic azides and the platinum diacetylide complexes <i>trans</i>-(PR₃)₂Pt­(CCR′)₂ (where PR₃ = P­(OEt)₃, PEt₃, P^<i>n</i>Bu₃, PPhMe₂, PPh₃, and PBn₃; and R′ = H, Ph, and <i>p</i>-PhNO₂). Pt­(II)-Diacetylides supported by P­(OEt)₃, PEt₃, P^<i>n</i>Bu₃, and PPhMe₂ react with benzyl azide to provide <i>syn</i>/<i>anti</i> isomers of double cycloaddition products. In contrast, Pt­(II)-diacetylide complexes supported by PPh₃ and PBn₃ afford single cycloaddition products, exclusively. Steric congestion enforced by the larger phosphines PPh₃ and PBn₃ prevent the second cycloaddition. Ground state DFT computations provide some insight into the divergent reactivity and indicate that the π-acidity of the phosphine ligands is a variable in the single vs double cycloaddition outcome

Single versus Double Cu(I) Catalyzed [3 + 2] Azide/Platinum Diacetylide Cycloaddition Reactions

This report focuses on Cu­(I) catalyzed cycloaddition reactions between organic azides and the platinum diacetylide complexes <i>trans</i>-(PR₃)₂Pt­(CCR′)₂ (where PR₃ = P­(OEt)₃, PEt₃, P^<i>n</i>Bu₃, PPhMe₂, PPh₃, and PBn₃; and R′ = H, Ph, and <i>p</i>-PhNO₂). Pt­(II)-Diacetylides supported by P­(OEt)₃, PEt₃, P^<i>n</i>Bu₃, and PPhMe₂ react with benzyl azide to provide <i>syn</i>/<i>anti</i> isomers of double cycloaddition products. In contrast, Pt­(II)-diacetylide complexes supported by PPh₃ and PBn₃ afford single cycloaddition products, exclusively. Steric congestion enforced by the larger phosphines PPh₃ and PBn₃ prevent the second cycloaddition. Ground state DFT computations provide some insight into the divergent reactivity and indicate that the π-acidity of the phosphine ligands is a variable in the single vs double cycloaddition outcome

Single versus Double Cu(I) Catalyzed [3 + 2] Azide/Platinum Diacetylide Cycloaddition Reactions

This report focuses on Cu­(I) catalyzed cycloaddition reactions between organic azides and the platinum diacetylide complexes <i>trans</i>-(PR₃)₂Pt­(CCR′)₂ (where PR₃ = P­(OEt)₃, PEt₃, P^<i>n</i>Bu₃, PPhMe₂, PPh₃, and PBn₃; and R′ = H, Ph, and <i>p</i>-PhNO₂). Pt­(II)-Diacetylides supported by P­(OEt)₃, PEt₃, P^<i>n</i>Bu₃, and PPhMe₂ react with benzyl azide to provide <i>syn</i>/<i>anti</i> isomers of double cycloaddition products. In contrast, Pt­(II)-diacetylide complexes supported by PPh₃ and PBn₃ afford single cycloaddition products, exclusively. Steric congestion enforced by the larger phosphines PPh₃ and PBn₃ prevent the second cycloaddition. Ground state DFT computations provide some insight into the divergent reactivity and indicate that the π-acidity of the phosphine ligands is a variable in the single vs double cycloaddition outcome