Vitamin B6 metabolism and underground metabolic routes in the Gram-positive bacterium Bacillus subtilis

Genome-reduced bacteria give the opportunity to study essential gene functions but also give the starting point for biotechnological production pathways. The MiniBacillus project aims to produce a genome reduced Bacillus subtilis strain with only a defined set of necessary genes. To identify new deletable genes, we studied the vitamin B6 metabolic pathway since the active form of vitamin B6 pyridoxal-5’-phosphate (PLP) is involved in about 4% of all known enzymatic reactions. In the Gram-positive soil bacterium B. subtilis at least 65 vitamin B6-dependent proteins were identified. In this study, mainly three aspects of vitamin B6 metabolism were studied: The PdxST vitamin B6 synthesis complex, transport and detoxication of vitamin B6 and, the role of the low molecular weight (LMW) thiol bacillithiol (BSH) together with the ytoQ gene in a heterologous vitamin B6 synthesis pathway. In B. subtilis vitamin B6 is produced by a complex of PdxS and PdxT. The glutaminase domain PdxT cleaves off ammonia from glutamine and transfers it to the synthase domain PdxS. Vitamin B6 even can be produced by PdxS in absence of PdxT, when high concentrations of ammonium are present. A suppressor screen was performed with the pdxT mutant on medium containing low amounts of ammonium and an amplification of a 15 kb region including the pdxS gene was identified as the main suppression mechanism. Moreover, in some suppressors the ammonium channel nrgA was upregulated, leading to a growth advantage especially when pdxS was not overexpressed. Besides that, the pdxS gene and its promotor region did not acquire beneficial mutations even if the amplification relevant recombinase gene recA was deleted. Furthermore, the nucleobase:cation symporter family proteins and the ECF transporter were excluded as vitamin B6 transporters and an upregulation of the Ars operon was identified as a detoxification mechanism for toxic PL levels. A PL-auxotroph B. subtilis mutant harboring only the last two genes of the DXP-dependent vitamin B6 synthesis pathway from E. coli, formed suppressor mutants, which deleted the bacillithiol synthesis gene bshC and upregulated the ytoQ gene. It was shown that cultivation on medium containing cysteine repealed the beneficial effect. Cysteine can also act as a LMW thiol indicating a role of YtoQ and BSH in oxidative stress response. Furthermore, a proposed underground metabolism pathway for the synthesis of PLP could be excluded, involving the genes cpgA, serA, serS and thrB. To increase general fitness and get insights about deleterious effects of the genome reduction in the MiniBacillus strains, the two genome-reduced strains PG10 (36% reduction) and PG39 (40% reduction) were evolved in complex medium. For PG39 a deregulation of genes mainly involved in oxidative stress response was identified as suppression mechanism. In PG10 over 25 genes harbored mutations. Interestingly, a downregulation of the mhqNOP operon was found, which was identified as highly upregulated in the strain.2021-07-2

Die FRBR customization im Datenformat der Music Encoding Initiative (MEI)

Vor dem Hintergrund des digitalen Wandels und der Entwicklung virtueller Forschungsumgebungen wird eine stärkere Kooperation von Bibliotheken und Forschungsinstitutionen künftig unabdingbar sein. Die zunehmende Internationalisierung in Bereichen der Datenaufbereitung stellt wachsende Anforderungen an Bibliotheken wie auch Forschungsinstitutionen. Die vorliegende Arbeit thematisiert die Implementierung des Modells der Functional Requirements for Bibliographic Records (FRBR)im Datenformat der Music Encoding Initiative (MEI), welches sich in den letzten Jahren als Standard zur Codierung von Musiknotation etabliert hat und sehr detaillierte Möglichkeiten auch zur Erfassung von Metadaten bietet. Ziel dieser Kombination ist es ausdrücklich, größtmögliche Kompatibilität zwischen den in musikwissenschaftlichen Projekten erarbeiteten, MEI-basierten Forschungsdaten und bibliothekarischen Erschließungstechniken herzustellen. Die Vorteile einer solchen Erweiterung erscheinen gerade vor dem Hintergrund der bevorstehenden Umstellung auf RDA als überaus lohnenswert.Following the digital turn and the increasing availability and usefulness of virtual research environments, a stronger collaboration between libraries and research institutions will become an essential prerequisite for future projects. The increasing internationalization in the field of data curation and management leads to higher requirements for libraries and research institutions. This study deals with the implementation of the model of the Functional Requirements for Bibliographic Records(FRBR)in the data framework of the Music Encoding Initiative (MEI), which received much recognition as a standard for encoding music notation in recent years. MEI offers manifold possibilities to store detailed metadata and aims at providing maximum compatibility between the data generated by musicological research projects and best-practice cataloging principles in libraries. Given the upcoming transition to RDA, this combination seems timely and highly promising

Entwicklung von Schulungsmaterialien für Einsatzmöglichkeiten von MEI im bibliothekarischen Bereich

Das Datenformat der Music Encoding Initiative (MEI) ist ein XML-basiertes Framework zur Codierung von Musiknotation bzw. Musikalien, das in Anlehnung an die Erkenntnisse der Text Encoding Initiative (TEI) auf den Bereich der Musik entwickelt wurde. Eine der Besonderheiten dieses Formats besteht darin, dass neben den musikalischen Daten auch sehr umfangreiche und detaillierte Metadaten zur bibliographischen Erfassung musikalischer Quellen abgelegt werden können. Durch die Vielseitigkeit des Formats sowie durch seine robuste Beschaffenheit eignet sich MEI besonders gut für die Langzeitarchivierung von Daten und ist damit für einen Einsatz in musikwissenschaftlichen wie bibliothekarischen Bereichen prädestiniert. Im Sommer 2012 entstanden in dem von der Deutschen Forschungsgemeinschaft (DFG) sowie dem National Endowment for the Humanities (NEH) gemeinsam geförderten Projekt „Digital Music Notation Data Model and Prototype Delivery System“ Schulungsmaterialien zur Erschließung von Notentexten und zur Erfassung relevanter Metadaten mit MEI. Diese sollen die Leistungsfähigkeit von MEI veranschaulichen und Geisteswissenschaftler, Bibliothekare, Editoren und Informatiker an das Format heranführen.The Music Encoding Initiative (MEI) is an XML-based framework for the encoding of music notation and accordingly sheet music. Along the findings of the Text Encoding Initiative (TEI) it was developed for the field of music. One of the distinguishing features of the format is that it not only supports detailed encodings of music notation, but also accommodates comprehensive and detailed metadata for bibliographical recordings of musical sources. Due to its versatility and its robust characteristics MEI is particularly suitable for long-term archiving of data and is thus predestined for use in both fields of musicology and library services. Within the project “Digital Music Notation Data Model and Prototype Delivery System” jointly funded by the German Research Foundation (DFG) and the National Endowment of the Humanities (NEH), in summer 2012 training materials have been developed for indexing musical texts and for capturing relevant metadata with MEI. They aim at demonstrating the efficiency of MEI and intend to introduce it to humanities scholars, librarians, editors and computer scientists

Eine rätselhafte Verbindung: Literarisch-musikalische Studien zu Robert Schumanns Drei-Werke-Einheit op. 79, op. 98a und op. 98b

Die vorliegende Arbeit unternimmt ein Gedankenspiel. Sie eröffnet den LeserInnen eine neuartige Perspektive auf drei Werke Robert Schumanns, die in enger zeitlicher Abfolge im Jahre 1849 entstanden sind und sich allesamt mit der Kunstfigur Mignon aus Johann Wolfgang von Goethes Bildungsroman »Wilhelm Meisters Lehrjahre« befassen: dem Liederalbum für die Jugend op. 79, den Liedern und Gesängen aus Goethes »Wilhelm Meister« op. 98a und dem Requiem für Mignon op. 98b. Wäre es denkbar, dass Schumann gezielt Verbindungen zwischen den drei Werken gesetzt hat, um sie als eine Einheit zu kennzeichnen? Erwächst aus dieser Drei-Werke-Einheit dann vielleicht etwas viel Größeres: eine Erzählumgebung, mit deren Hilfe Schumann – wie er selbst dem Musikkritiker Franz Brendel einmal schrieb – der Musik etwas über die Zeit erzählt? Die neue Werkform des »Musikalischen Bildungszyklus«, die hier geschaffen wird, ist Ausdruck einer lebendigen Kunst und eines Künstlers, der ein Bewusstsein für sein eigenes Künstler-Sein schafft

Stand und Perspektiven der Nutzung von MEI in der Musikwissenschaft und in Bibliotheken

Ausgehend von einer Darstellung der (an TEI angelehnten) Entwicklung von MEI werden die Forschungsperspektiven des Einsatzes dieses für wissenschaftliche Zwecke geschaffenen Formats und speziell das Potential seines umfangreichen Header-Bereichs beschrieben. Am Beispiel der Rolle von Faksimiles in Editionen wird deutlich, wie dieses Format zu einer neuen Zusammenarbeit von Wissenschaft und Bibliotheken beitragen kann.Starting from the description of the development of MEI (which has to be seen in parallel with TEI) the paper deals with the perspectives of the usage of this format, which was designed for scholarly purposes and, in the library context, has high potentials especially in the header-section. The role of facsimiles in editions illustrates how this format might contribute to a new way of collaboration between the scholarly and the library world

Projektmanagement in digitalen Forschungsprojekten. Ein Leitfaden für interdisziplinäre und kooperative Drittmittelprojekte im Umfeld Digitaler Editionen

Komprecht AM, Röwenstrunk D. Projektmanagement in digitalen Forschungsprojekten. Ein Leitfaden für interdisziplinäre und kooperative Drittmittelprojekte im Umfeld Digitaler Editionen. In: Stadler P, Richts K, eds. "Ei, dem alten Herrn zoll' ich Achtung gern'". Festschrift für Joachim Veit zum 60. Geburtstag. München: Allitera; 2016: 509-522

A Survey of Pyridoxal 5′-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis

The B6 vitamer pyridoxal 5′-phosphate (PLP) is a co-factor for proteins and enzymes that are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all kingdoms of life. Here we provide an overview about the PLP-dependent proteins from the Gram-positive soil bacterium Bacillus subtilis. Since B. subtilis serves as a model system in basic research and as a production host in industry, knowledge about the PLP-dependent proteins could facilitate engineering the bacteria for biotechnological applications. The survey revealed that the majority of the PLP-dependent proteins are involved in metabolic pathways like amino acid biosynthesis and degradation, biosynthesis of antibacterial compounds, utilization of nucleotides as well as in iron and carbon metabolism. Many PLP-dependent proteins participate in de novo synthesis of the co-factors biotin, folate, heme, and NAD+ as well as in cell wall metabolism, tRNA modification, regulation of gene expression, sporulation, and biofilm formation. A surprisingly large group of PLP-dependent proteins (29%) belong to the group of poorly characterized proteins. This review underpins the need to characterize the PLP-dependent proteins of unknown function to fully understand the “PLP-ome” of B. subtilis

United, Linked, Connected – A Data Model for the Inventory of the Former Detmold Court Theatre (1825–1875), or: How Library Inventory History Can also Be Told

Library forms of cataloging may differ greatly from the cataloging requirements of musicological research projects: They are often not detailed enough and do not take a close enough look at aspects of content relevant to research, such as handwritten entries in materials, etc. Library catalog entries of individual documents stand on their own for historical reasons, but usually do not reflect relationships to other surviving materials. This observation was the starting point for the Detmold Court Theatre Project, a six-year research project (September 2014 – January 2021) that looked at the interconnectedness of different surviving materials of a 19th century theatre company that existed from 1825 to 1875. This project dealt with a very detailed form of inventory indexing in order to hand over and make accessible the formerly related materials in their entirety. This form of indexing was called ‘contextual deep indexing’. This special form of indexing took into account not only the pure performance materials but also the surviving theatre files, such as fee books, revenue and expense documents, stock lists, director’s books, role and costume books, etc. […]. It was the first attempt to carry out such a form of indexing on the basis of the MEI and TEI encoding standards for a large repertory. For this purpose, a data model was needed that focuses on the linking of MEI and TEI data and enables the linking of different surviving library holdings, with a focus on a FRBR-based indexing of performance materials and associated performers as well as the structure of the theatre. […] The paper summarizes the results of this pilot project. It addresses the particularities and requirements of an inventory development that does not focus on individual objects, but on the relationship between different objects (and subjects). It presents a document-oriented (not object-oriented) data model that uses library materials to revive an entire network of a long-gone organization