101,672 research outputs found
Cytochromes P450 involved in bacterial RiPP biosyntheses
No full textRibosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of secondary metabolites that have garnered scientific attention due to their complex scaffolds with potential roles in medicine, agriculture, and chemical ecology. RiPPs derive from the cleavage of ribosomally synthesized proteins and additional modifications, catalyzed by various enzymes to alter the peptide backbone or side chains. Of these enzymes, cytochromes P450 (P450s) are a superfamily of heme-thiolate proteins involved in many metabolic pathways, including RiPP biosyntheses. In this review, we focus our discussion on P450 involved in RiPP pathways and the unique chemical transformations they mediate. Previous studies have revealed a wealth of P450s distributed across all domains of life. While the number of characterized P450s involved in RiPP biosyntheses is relatively small, they catalyze various enzymatic reactions such as C-C or C-N bond formation. Formation of some RiPPs is catalyzed by more than one P450, enabling structural diversity. With the continuous improvement of the bioinformatic tools for RiPP prediction and advancement in synthetic biology techniques, it is expected that further cytochrome P450-mediated RiPP biosynthetic pathways will be discovered.
SUMMARY: The presence of genes encoding P450s in gene clusters for ribosomally synthesized and post-translationally modified peptides expand structural and functional diversity of these secondary metabolites, and here, we review the current state of this knowledge
Nachweis eines RiPP-Precursors auf Peptid-Ebene
No full textRibosomally synthesized and post-translationally modified peptides (RiPPs) are a group of secondary metabolites with unique biosynthetic pathways resulting in a wide variety of structures and bioactivities. RiPP biosynthesis is a two-stage process. First, linear precursor peptides consisting of an N-terminal leader sequence, a core sequence and an optional C-terminal recognition sequence are translated by classical ribosomal translation. After this, the linear precursor is heavily modified by an assembly of tailoring enzymes yielding the mature, often cyclized product. A set of potential RiPP precursors has been identified in the genome of the fungus Trichoderma reesei in a recent genome mining approach and gene cluster activity was demonstrated on the transcriptome level. The aim of this thesis was to determine whether the precursor/leader sequence mRNA is translated into the corresponding precursor/leader peptides. To this end, extracts of wild type and RiPP knockout strains of T. reesei were subjected to quantitative LCIMS-MS/MS analysis. Different protease digestion strategies were tested to maximize sequence coverage of the RiPP precursor. By employing a simple extraction procedure followed by nanoLC-IMS-MS/MS analysis and a common proteomics database search, the translation of the precursor mRNA into the corresponding peptide could be verified. Moreover, several extraction and analysis approaches were tested on model RiPPs produced in the fungus Aspergillus flavus to develop an efficient method for the analysis of mature RiPPs which will set a basis for the discovery and identification of RiPPs with yet unknown structure in T. reesei. The second part of this thesis compares the efficiency of different sample preparation methods for proteomics with a special focus on sub-microgram sample input. A recently published paramagnetic bead-based approach (single-pot, solid-phase enhanced sample preparation, SP3) for sample preparation was compared to an established in-solution digestion method and a commercially available kit for sample preparation (PreOmics). The SP3 approach was further optimized by adopting different peptide cleanup strategies in order to increase the number of identified proteins. It was shown that for protein amounts above 10 μg, an increase in protein identifications can be achieved by employing an additional desalting step
Research fronts in library and information science in Spain
No full textPublications and author cocitations in library and information science in Spain during the period from 1985 to 1994 were analyzed as a measure of the structure, specificity and composition of research fronts in this country. A cocitation matrix developed from an ad hoc database was subjected to cluster analysis, multidimensional scaling and principal components analysis, The resulting cocitation maps identified specific areas of r~search and their knowledge bases. We inferred the degree of consolidation of the discipline of library and information science, and of the subdisciplines informetrics, librarianship and university affiliation, from the research activities revealed. In this respect, the conclusions from the study show the existence of several research fronts in Spanish literature the contents of which are in most cases difficult to compare with those in other countries. A lesser degree of maturity of research in this field is shown
Letter, [Author unclear] to Paulina T. Merritt
No full textHandwritten letter to Paulina Merritt from an unknown author, October 1, 1876.
N–Cα Bond Cleavage Catalyzed by a Multinuclear Iron Oxygenase from a Divergent Methanobactin-like RiPP Gene Cluster
No full textDUF692 multinuclear iron oxygenases (MNIOs) are an emerging family of tailoring enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs). Three members, MbnB, TglH, and ChrH, have been characterized to date and shown to catalyze unusual and complex transformations. Using a co-occurrence-based bioinformatic search strategy, we recently generated a sequence similarity network of MNIO-RiPP operons that encode one or more MNIOs adjacent to a transporter. The network revealed >1,000 unique gene clusters, evidence of an unexplored biosynthetic landscape. In this work, we assess an MNIO-RiPP cluster from the network that is encoded in proteobacteria and actinobacteria. The cluster, which we have termed mov (for methanobactin-like operon in Vibrio), encodes a 23-residue precursor peptide, two MNIOs, a RiPP recognition element, and a transporter. Using both in vivo and in vitro methods, we show that one MNIO, homologous to MbnB, installs an oxazolone-thioamide at a Thr-Cys dyad in the precursor. Subsequently, the second MNIO catalyzes N–Cα bond cleavage of the penultimate Asn to generate a C-terminally amidated peptide. This transformation expands the reaction scope of the enzyme family, marks the first ex-ample of an MNIO-catalyzed modification that does not involve Cys, and sets the stage for future exploration of other MNIO-RiPP
Handwritten biographical information on Paulina T. McClung Merritt
No full textA handwritten biography of Paulina T. McClung Merritt by an unknown author, 1892.
Heterogeneous and tissue-specific regulation of effector T cell responses by IFN-gamma during Plasmodium berghei ANKA infection.
No full textIFN-γ and T cells are both required for the development of experimental cerebral malaria during Plasmodium berghei ANKA infection. Surprisingly, however, the role of IFN-γ in shaping the effector CD4(+) and CD8(+) T cell response during this infection has not been examined in detail. To address this, we have compared the effector T cell responses in wild-type and IFN-γ(-/-) mice during P. berghei ANKA infection. The expansion of splenic CD4(+) and CD8(+) T cells during P. berghei ANKA infection was unaffected by the absence of IFN-γ, but the contraction phase of the T cell response was significantly attenuated. Splenic T cell activation and effector function were essentially normal in IFN-γ(-/-) mice; however, the migration to, and accumulation of, effector CD4(+) and CD8(+) T cells in the lung, liver, and brain was altered in IFN-γ(-/-) mice. Interestingly, activation and accumulation of T cells in various nonlymphoid organs was differently affected by lack of IFN-γ, suggesting that IFN-γ influences T cell effector function to varying levels in different anatomical locations. Importantly, control of splenic T cell numbers during P. berghei ANKA infection depended on active IFN-γ-dependent environmental signals--leading to T cell apoptosis--rather than upon intrinsic alterations in T cell programming. To our knowledge, this is the first study to fully investigate the role of IFN-γ in modulating T cell function during P. berghei ANKA infection and reveals that IFN-γ is required for efficient contraction of the pool of activated T cells
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Pelevin’s Trinity in the novel “t”: author – protagonist – reader
No full textThe article attempts to interpret Pelevin's artistic strategy in the novel "T" by exploring its subject organization and addressing the key problems of the author, the protagonist, and the reader as they are seen by the researcher. The article analyzes the peculiarities of constructing the narrative reality in the novel "T", and goes on to discuss Pelevin's philosophic models of the development of the humankind, and the emergence of his new anthropology
N–Cα Bond Cleavage Catalyzed by a Multinuclear Iron Oxygenase from a Divergent Methanobactin-like RiPP Gene Cluster
No full textDUF692
multinuclear iron oxygenases (MNIOs) are an emerging family
of tailoring enzymes involved in the biosynthesis of ribosomally synthesized
and post-translationally modified peptides (RiPPs). Three members,
MbnB, TglH, and ChrH, have been characterized to date and shown to
catalyze unusual and complex transformations. Using a co-occurrence-based
bioinformatic search strategy, we recently generated a sequence similarity
network of MNIO-RiPP operons that encode one or more MNIOs adjacent
to a transporter. The network revealed >1000 unique gene clusters,
evidence of an unexplored biosynthetic landscape. Herein, we assess
an MNIO-RiPP cluster from this network that is encoded in Proteobacteria
and Actinobacteria. The cluster, which we have termed mov (for methanobactin-like operon in Vibrio), encodes
a 23-residue precursor peptide, two MNIOs, a RiPP recognition element,
and a transporter. Using both in vivo and in vitro methods, we show
that one MNIO, homologous to MbnB, installs an oxazolone-thioamide
at a Thr-Cys dyad in the precursor. Subsequently, the second MNIO
catalyzes N–Cα bond cleavage of the penultimate Asn to
generate a C-terminally amidated peptide. This transformation
expands the reaction scope of the enzyme family, marks the first example
of an MNIO-catalyzed modification that does not involve Cys, and sets
the stage for future exploration of other MNIO-RiPPs
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