Department of Microbiology / PhD (Microbiology)

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19576号 / 医博第4083号 / 新制||医||1013(附属図書館) / 32612 / 京都大学大学院医学研究科医学専攻 / (主査)教授 中川 一路, 教授 岩田 想, 教授 西渕 光昭 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Thesis advisor: Tim van Opijnen / Streptococcus pneumoniae is a prominent gram-positive commensal and opportunistic pathogen which possesses a large pan-genome. Significant strain-to-strain variability in genomic content drives the use of varied pathways to perform similar processes between strains. Considering this variation, we employ a set of 36 strains, representative of 78% of total pan-genome diversity, with which to perform functional studies. We previously determined the set of genes required by 22 of the 36 strains to maintain successful infection in a host, or the virulome. In this work, we sought to parse from the virulome the genes required specifically for nasopharyngeal adhesion, a crucial step in S. pneumoniae colonization and transmission, and often a precursor to invasive disease, as well as gene requirements for subversion of the macrophage. We performed in vitro attachment Tn-seq in the 22 strains to D562 human nasopharyngeal epithelial cells, identifying thirteen factors that exhibit requirements for adhesion, and preliminarily validated a proposed universal requirement for survival of the macrophage by a killing assay using J774A.1 murine migratory macrophages. / Thesis (BS) — Boston College, 2020. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: A&S Honors. / Discipline: Biology.

Complex formation between macromolecules constitutes the foundation of most cellular processes. Most known complexes are made up of two or more proteins interacting in order to build a functional entity and therefore enabling activities which the single proteins could otherwise not fulfill. With the increasing knowledge about noncoding RNAs (ncRNAs) it has become evident that, similar to proteins, many of them also need to form a complex to be functional. This functionalization is usually executed by specific or global RNA-binding proteins (RBPs) that are specialized binders of a certain class of ncRNAs. For instance, the enterobacterial global RBPs Hfq and ProQ together bind >80 % of the known small regulatory RNAs (sRNAs), a class of ncRNAs involved in post-transcriptional regulation of gene expression. However, identification of RNA-protein interactions so far was performed individually by employing low-throughput biochemical methods and thereby hindered the discovery of such interactions, especially in less studied organisms such as Gram-positive bacteria. Using gradient profiling by sequencing (Grad-seq), the present thesis aimed to establish high-throughput, global RNA/protein complexome resources for Escherichia coli and Streptococcus pneumoniae in order to provide a new way to investigate RNA-protein as well as protein-protein interactions in these two important model organisms. In E. coli, Grad-seq revealed the sedimentation profiles of 4,095 (∼85 % of total) transcripts and 2,145 (∼49 % of total) proteins and with that reproduced its major ribonucleoprotein particles. Detailed analysis of the in-gradient distribution of the RNA and protein content uncovered two functionally unknown molecules—the ncRNA RyeG and the small protein YggL—to be ribosomeassociated. Characterization of RyeG revealed it to encode for a 48 aa long, toxic protein that drastically increases lag times when overexpressed. YggL was shown to be bound by the 50S subunit of the 70S ribosome, possibly indicating involvement of YggL in ribosome biogenesis or translation of specific mRNAs. S. pneumoniae Grad-seq detected 2,240 (∼88 % of total) transcripts and 1,301 (∼62 % of total) proteins, whose gradient migration patterns were successfully reconstructed, and thereby represents the first RNA/protein complexome resource of a Gram-positive organism. The dataset readily verified many conserved major complexes for the first time in S. pneumoniae and led to the discovery of a specific interaction between the 3’!5’ exonuclease Cbf1 and the competence-regulating ciadependent sRNAs (csRNAs). Unexpectedly, trimming of the csRNAs by Cbf1 stabilized the former, thereby promoting their inhibitory function. cbf1 was further shown to be part of the late competence genes and as such to act as a negative regulator of competence. / Makromoleküle, die Komplexe bilden, sind die Grundlage der meisten zellulären Prozesse. Die meisten bekannten Komplexe bestehen aus zwei oder mehr Proteinen, die interagieren, um eine funktionelle Einheit zu bilden. Diese Interaktionen ermöglichen Funktionen, die die einzelnen Proteine nicht erfüllen könnten. Wachsende wissenschaftliche Erkenntnisse über nichtkodierende RNAs (ncRNAs) haben gezeigt, dass, analog zu Proteinen, auch viele ncRNAs Komplexe bilden müssen, um ihre Funktionen ausüben zu können. Diese Funktionalisierung wird normalerweise von spezifischen oder globalen RNA-bindenden Proteinen (RBPs), die auf eine bestimmte Klasse an ncRNAs spezialisiert sind, durchgeführt. So binden beispielsweise die in Enterobakterien verbreiteten globalen RBPs Hfq und ProQ zusammen >80 % der bekannten kleinen regulatorischen RNAs (sRNAs)—eine Klasse der ncRNAs, die in die posttranskriptionelle Genexpressionsregulation involviert ist. RNA-Protein-Interaktionen wurden bisher anhand einzelner Moleküle und mithilfe von biochemischen Methoden mit niedrigem Durchsatz identifiziert, was die Entdeckung solcher Interaktionen erschwert hat. Dies gilt insbesondere für Organismen, die seltener Gegenstand der Forschung sind, wie beispielsweise grampositive Bakterien. Das Ziel dieser Doktorarbeit war es, mittels gradient profiling by sequencing (Grad-seq) globale Hochdurchsatzkomplexomdatensätze der RNA-ProteinInteraktionen in Escherichia coli und Streptococcus pneumoniae zu generieren. Diese Datensätze ermöglichen es auf eine neue Art und Weise RNA-Protein- und ProteinProtein-Interaktionen in diesen wichtigen Modellorganismen zu untersuchen. Die E. coli Grad-seq-Daten beinhalten die Sedimentationsprofile von 4095 Transkripten (∼85 % des Transkriptoms) und 2145 Proteinen (∼49 % des Proteoms), mit denen die wichtigsten Ribonukleoproteine reproduziert werden konnten. Die detaillierte Analyse der Verteilung von RNAs und Proteinen im Gradienten zeigte, dass zwei Moleküle, deren Funktionen bisher unbekannt waren—die ncRNA RyeG und das kleine Protein YggL—ribosomenassoziiert sind. Durch weitere Charakterisierung konnte gezeigt werden, dass RyeG für ein toxisches Protein mit einer Länge von 48 Aminosäuren kodiert, das bei Überexpression die Latenzphase drastisch verlängert. Für YggL konnte eine Interaktion mit der 50S Untereinheit von 70S Ribosomen nachgewiesen werden, was auf eine potenzielle Funktion in der Biogenese von Ribosomen oder bei der Translation bestimmter mRNAs hindeutet. Die S. pneumoniae Grad-seq Daten beinhalten 2240 Transkripte (∼88 % des Transkriptoms) und 1301 Proteine (∼62 % des Proteoms), deren Migrationsprofile im Gradienten erfolgreich rekonstruiert werden konnten. Dieser RNA/ProteinKomplexomdatensatz eines grampositiven Organismus ermöglichte erstmalig die Verifizierung der wichtigsten konservierten Komplexe von S. pneumoniae. Weiterhin konnte eine spezifische Interaktion der 3’!5’-Exonuklease Cbf1 mit den ciadependent sRNAs (csRNAs), die an der Regulation von Kompetenz beteiligt sind, nachgewiesen werden. Überraschenderweise stabilisiert das von Cbf1 durchgeführte Kürzen der csRNAs die selbigen, was deren inhibitorische Funktion unterstützt. Darüber hinaus konnte gezeigt werden, dass cbf1 eines der späten Kompetenzgene ist und als solches als negativer Regulator der Kompetenz agiert.

This study evaluates the ecology of Streptococcus pneumoniae (SP) nasopharynx (NP) colonization in response to the pneumococcal conjugate vaccines, specifically 7-Valent Pneumococcal Conjugate Vaccine (2000-2009), 13-Valent Pneumococcal Conjugate Vaccine (2010-2023) and 20-Valent Pneumococcal Conjugate Vaccine (2023-future date). It is anticipated that the replacement of PCV13 with PCV20, a pneumococcal conjugate vaccine with 7 additional polysaccharide conjugates to CRM197 will enhance the protection against non-vaccine serotypes which are in circulation in communities. The project will evaluate the dynamic changes in pneumococcal colonization over the 5-year time line from 2021-2026. Pneumococcal nasopharynx colonization is detected through nasopharyngeal culture and molecular techniques. The primary source of pneumococcal transmission occurs among the pediatric population and between children and adults. The impact of PCV7 and 13 on pneumococcal colonization over the prior 20 years created a herd effect that resulted in a reduction in pneumococcal disease in unimmunized children and adults. Studies of NP colonization has led to a deeper understanding of pneumococcal conjugate vaccine (PCV) effectiveness and the role of herd immunity in protecting the population, the emergence of replacement serotypes, the variation in invasive capability of each serotype and evolution of antimicrobial resistance resulting from the evolving ecology. In this 5-year-study, researchers at the Pelton Lab in Boston Medical Center set out to understand the prevalence of NP carriage of 13vPnC serotypes, the 7 unique 20vPnC serotypes and NVST (non-vaccine serotypes) within the pediatric population prior to and subsequent to the introduction of PCV 20 (Fall 2023).

Streptococcus pneumoniae (the pneumococcus) is one of the leading causes of death due to infectious disease in the world, with over one million deaths being attributed to this bacterium each year. While the majority of these deaths occur in children in developing nations, significant morbidity and mortality in the developed world, especially in the elderly, can be attributed to pneumococcal diseases such as bacterial pneumonia and meningitis. This is despite the near-universal use of anti-pneumococcal vaccines in these parts of the world. The work presented in this thesis describes the ways in which resident nasal macrophages respond to nasopharyngeal pneumococcal colonization, allowing for the protection of immunocompetent individuals from these diseases. This thesis describes the role of the macrophage scavenger receptor MARCO in recognizing the bacterium upon colonization, and the chain of events that are subsequently established. I have found that MARCO is vital in orchestrating the clearance of pneumococci from the nasopharynx in an expedient manner, as well as preventing the swift spread of bacteria to other tissues of the body early on in colonization. I also outline a role for regulatory micro-RNAs present in macrophages in the mounting of this anti-pneumococcal response via the induction of specific T cell populations. The collection of data found herein is an important resource for those attempting to understand the complex narrative that takes place between the pneumococcus and the innate immune system during a colonizing event and will lead to further discovery on how healthy individuals escape fatal pneumococcal disease. / Thesis / Doctor of Philosophy (PhD) / The bacterium Streptococcus pneumoniae is one of the most dangerous pathogens in the world, accounting for more one million deaths every year worldwide. This bacterium is also very common, with approximately one third of all people having some S. pneumoniae in their noses at any given time. The goal of this thesis is to provide a better understanding of how our immune cells interact with S. pneumoniae when it first enters our noses and how these initial interactions prevent healthy people from becoming sick. I have found that white blood cells called macrophages are crucial to these interactions. Macrophages are able to ‘eat’ the bacteria using a specialized protein called MARCO to grab onto them. This information will be vital in trying to develop new vaccines and treatments for S. pneumoniae-related diseases like bacterial pneumonia (lung infection) and meningitis (brain infection).

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Thesis advisor: Tim van Opijnen / Thesis advisor: Michelle Meyer / Although bacteria are often studied as planktonic or free-living organisms, they frequently grow in complex surface-attached communities known as biofilms. Biofilms are communities of microorganisms attached to surfaces and embedded in a self-produced extracellular matrix. Biofilms are dynamic structures analogous to human settlements shaped by space and environment. These microbial communities fulfill critical roles in multiple infections in the human body. Streptococcuspneumoniae is a human pathogen that can cause biofilm-associated infections in various tissues and organs. This thesis offers a unique outlook for the study of S. pneumoniae biofilms by combining in vitro, genome-wide, and in vivo experiments to elucidate the complex population dynamics of S. pneumoniae biofilms. Existing methods to cultivate S. pneumoniae biofilms fail to fully capture the complexity of these communities, and most studies are limited to short periods of time. We developed a robust in vitro assay to grow S. pneumoniae biofilms. This assay can be maintained forever rather than days. We then use this robust assay to study their behavior in vivo and monitor disease outcomes. After establishing clear differences in biofilm and dispersal samples, we monitor population dynamics using genome-wide techniques (Tn-seq, RNA-seq and WGS) to provide some insights into this complex mode of growth. This work includes the first global identification of genetic requirements during biofilm establishment in two different S. pneumoniae strains using Tn-Seq. Coupled with our transcriptomic analysis, we found that genes involved in multiple pathways, such as capsule biosynthesis, nucleotide metabolism, and stress response, contributed to biofilm growth. Lastly, we studied the development of antibiotic resistance to three different types of antibiotics under S. pneumoniae biofilm conditions. We revealed common adaptive pathways to achieve biofilm growth and antibiotic resistance (antibiotic target genes), as well as novel routes of adaptation to develop resistance. Our findings add to the growing body of knowledge in the field of bacterial genetics and antimicrobial resistance, paving the way for future research and therapeutic advancement. / Thesis (PhD) — Boston College, 2023. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.