1,720,961 research outputs found
Insights into the Microbial Degradation of Rubber and Gutta-Percha by Analysis of the Complete Genome of Nocardia nova SH22a
No full textThe complete genome sequence of Nocardia nova SH22a was determined in light of the remarkable ability of rubber and guttapercha (GP) degradation of this strain. The genome consists of a circular chromosome of 8,348,532 bp with a G+C content of 67.77% and 7,583 predicted protein-encoding genes. Functions were assigned to 72.45% of the coding sequences. Among them, a large number of genes probably involved in the metabolism of xenobiotics and hardly degradable compounds, as well as genes that participate in the synthesis of polyketide-and/or nonribosomal peptide-type secondary metabolites, were detected. Based on in silico analyses and experimental studies, such as transposon mutagenesis and directed gene deletion studies, the pathways of rubber and GP degradation were proposed and the relationship between both pathways was unraveled. The genes involved include, inter alia, genes participating in cell envelope synthesis (long-chain-fatty-acid-AMP ligase and arabinofuranosyltransferase), beta-oxidation (alpha-methylacyl-coenzyme A [alpha-methylacyl-CoA] racemase), propionate catabolism (acyl-CoA carboxylase), gluconeogenesis (phosphoenolpyruvate carboxykinase), and transmembrane substrate uptake (Mce [mammalian cell entry] transporter). This study not only improves our insights into the mechanism of microbial degradation of rubber and GP but also expands our knowledge of the genus Nocardia regarding metabolic diversity.Deutsche Forschungsgemeinschaft [STE-386/10-1
Microbial Gutta-Percha Degradation Shares Common Steps with Rubber Degradation by Nocardia nova SH22a
No full textNocardia nova SH22a, a bacterium capable of degrading gutta-percha (GP) and natural rubber (NR), was used to investigate the GP degradation mechanism and the relations between the GP and NR degradation pathways. For this strain, a protocol of electroporation was systematically optimized, and an efficiency of up to 4.3 x 10(7) CFU per mu g of plasmid DNA was achieved. By applying this optimized protocol to N. nova SH22a, a Tn5096-based transposon mutagenesis library of this bacterium was constructed. Among about 12,000 apramycin-resistant transformants, we identified 76 stable mutants defective in GP or NR utilization. Whereas 10 mutants were specifically defective in GP utilization, the growth of the other 66 mutants was affected on both GP and NR. This indicated that the two degradation pathways are quite similar and share many common steps. The larger number of GP-degrading defective mutants could be explained in one of two ways: either (i) the GP pathway is more complex and harbors more specific steps or (ii) the steps for both pathways are almost identical, but in the case of GP degradation there are fewer enzymes involved in each step. The analysis of transposition loci and genetic studies on interesting genes confirmed the crucial role of an alpha-methylacyl-coenzyme A racemase in the degradation of both GP and NR. We also demonstrated the probable involvement of enzymes participating in oxidoreduction reactions, beta-oxidation, and the synthesis of complex cell envelope lipids in the degradation of GP.Deutsche Forschungsgemeinschaft [STE-386/10-1
The genome of Variovorax paradoxus strain TBEA6 provides new understandings for the catabolism of 3,3 '-thiodipropionic acid and hence the production of polythioesters
No full textThe betaproteobacterium Variovorax paradoxus strain TBEA6 is capable of using 3,3'-thiodipropionic acid (TDP) as sole carbon and energy source for growth. This thioether is employed for several industrial applications. It can be applied as precursor for the biotechnical production of polythioesters (PTE), which represent persistent bioplastics. Consequently, the genome of V. paradoxus strain TBEA6 was sequenced. The draft genome sequence comprises approximately 7.2 Mbp and 6852 predicted open reading frames. Furthermore, transposon mutagenesis to unravel the catabolism of TDP in strain TBEA6 was performed. Screening of 20,000 mutants mapped the insertions of Tn5::mob in 32 mutants, which all showed no growth with TDP as sole carbon source. Based on the annotated genome sequence together with transposon-induced mutagenesis, defined gene deletions, in silico analyses and comparative genomics, a comprehensive pathway for the catabolism of TDP is proposed: TDP is imported via the tripartite tricarboxcylate transport system and/or the TRAP-type dicarboxylate transport system. The initial cleavage of TDP into 3-hydroxypropionic acid (3HP) and 3-mercaptopropionic acid (3MP), which serves as precursor substrate for PTE synthesis, is most probably performed by the FAD-dependent oxidoreductase Fox. 3HP is presumably catabolized via malonate semialdehyde, whereas 3MP is oxygenated by the 3MP-dioxygenase Mdo yielding 3-sulfinopropionic acid (3SP). Afterwards, 3SP is linked to coenzyme A. The next step is the abstraction of sulfite by a desulfinase, and the resulting propionyl-CoA enters the central metabolism. Sulfite is oxidized to sulfate by the sulfite-oxidizing enzyme SoeABC and is subsequently excreted by the cells by the sulfate exporter Pse. (C) 2015 Published by Elsevier B.V
Unravelling the complete genome sequence of Advenella mimigardefordensis strain DPN7(T) and novel insights in the catabolism of the xenobiotic polythioester precursor 3,3 '-dithiodipropionate
No full textAdvenella mimigardefordensis strain DPN7(T) is a remarkable betaproteobacterium because of its extraordinary ability to use the synthetic disulfide 3,3'-dithiodipropionic acid (DTDP) as the sole carbon source and electron donor for aerobic growth. One application of DTDP is as a precursor substrate for biotechnically synthesized polythioesters (PTEs), which are interesting non-degradable biopolymers applicable for plastics materials. Metabolic engineering for optimization of PTE production requires an understanding of DTDP conversion. The genome of A. mimigardefordensis strain DPN7(T) was sequenced and annotated. The circular chromosome was found to be composed of 4740516 bp and 4112 predicted ORFs, whereas the circular plasmid consisted of 23610 bp and 24 predicted ORFs. The genes participating in DTDP catabolism had been characterized in detail previously, but knowing the complete genome sequence and with support of Tn5 : : mob-induced mutants, putatively involved transporter proteins and a transcriptional regulator were also identified. Most probably, DTDP is transported into the cell by a specific tripartite tricarboxylate transport system and is then cleaved by the disulfide reductase LpdA, sulfoxygenated by the 3-mercaptopropionate dioxygenase Mdo, activated by the CoA ligase SucCD and desulfinated by the acyl-CoA dehydrogenase-like desulfinase AcdA. Regulation of this pathway is presumably performed by a transcriptional regulator of the xenobiotic response element family. The excessive sulfate that is inevitably produced is secreted by the cells by a unique sulfate exporter of the CPA (cation : proton antiporter) superfamily
Role of Wax Ester Synthase/Acyl Coenzyme A:Diacylglycerol Acyltransferase in Oleaginous Streptomyces sp. Strain G25
No full textRecently, we isolated a novel Streptomyces strain which can accumulate extraordinarily large amounts of triacylglycerol (TAG) and consists of 64% fatty acids (dry weight) when cultivated with glucose and 50% fatty acids (dry weight) when cultivated with cellobiose. To identify putative gene products responsible for lipid storage and cellobiose utilization, we analyzed its draft genome sequence. A single gene encoding a wax ester synthase/acyl coenzyme A (CoA): diacylglycerol acyltransferase (WS/DGAT) was identified and heterologously expressed in Escherichia coli. The purified enzyme Atf(G25) showed acyltransferase activity with C-12-orC(16)-acyl-CoA, C-12 to C-18 alcohols, or dipalmitoyl glycerol. This acyltransferase exhibits 24% amino acid identity to the model enzyme AtfA from Acinetobacter baylyi but has high sequence similarities to WS/DGATs from other Streptomyces species. To investigate the impact of Atf(G25) on lipid accumulation, the respective gene, atf(G25), was inactivated in Streptomyces sp. strain G25. However, cells of the insertion mutant still exhibited DGAT activity and were able to store TAG, albeit in lower quantities and at lower rates than the wild-type strain. These findings clearly indicate that Atf(G25) has an important, but not exclusive, role in TAG biosynthesis in the novel Streptomyces isolate and suggest the presence of alternative metabolic pathways for lipid accumulation which are discussed in the present study
Involvement of Two Latex-Clearing Proteins during Rubber Degradation and Insights into the Subsequent Degradation Pathway Revealed by the Genome Sequence of Gordonia polyisoprenivorans Strain VH2
No full textThe increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber leads to huge challenges in waste management. Only a few bacteria are known to degrade rubber, and little is known about the mechanism of microbial rubber degradation. The genome of Gordonia polyisoprenivorans strain VH2, which is one of the most effective rubber-degrading bacteria, was sequenced and annotated to elucidate the degradation pathway and other features of this actinomycete. The genome consists of a circular chromosome of 5,669,805 bp and a circular plasmid of 174,494 bp with average GC contents of 67.0% and 65.7%, respectively. It contains 5,110 putative protein-coding sequences, including many candidate genes responsible for rubber degradation and other biotechnically relevant pathways. Furthermore, we detected two homologues of a latex-clearing protein, which is supposed to be a key enzyme in rubber degradation. The deletion of these two genes for the first time revealed clear evidence that latex-clearing protein is essential for the microbial utilization of rubber. Based on the genome sequence, we predict a pathway for the microbial degradation of rubber which is supported by previous and current data on transposon mutagenesis, deletion mutants, applied comparative genomics, and literature search
4
No full textVariovorax paradoxusB4 is able to utilize 2-mercaptosuccinate (MS) as sole carbon, sulfur and energy source. The whole genome of V.paradoxusB4 was sequenced, annotated and evaluated with special focus on genomic elements related to MS metabolism. The genome encodes two chromosomes harbouring 5795261 and 1353255bp. A total of 6753 putative protein-coding sequences were identified. Based on the genome and in combination with results from previous studies, a putative pathway for the degradation of MS could be postulated. The putative molybdopterin oxidoreductase identified during transposon mutagenesis probably catalyses the conversion of MS first into sulfinosuccinate and then into sulfosuccinate by successive transfer of oxygen atoms. Subsequently, the cleavage of sulfosuccinate yields oxaloacetate and sulfite, while the latter is oxidized to sulfate. The expression of the putative molybdopterin oxidoreductase was induced by MS, but not by gluconate, as confirmed by reverse transcriptase polymerase chain reaction. Further, in silico studies combined with experiments and comparative genomics revealed high metabolic diversity of strain B4. It bears a high potential as plant growth-promoting bacterium and as candidate for degradation and detoxification of xenobiotics and other hardly degradable substances. Additionally, the strain is of special interest for production of polythioesters with sulfur-containing precursors as MS
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
- …
