An analysis of selected secretion systems of Pseudomonas species

Direct secretion systems which deliver molecules from one cell to another have huge significance in shaping bacterial communities or in determining the outcome of bacterial associations with eukaryotic organisms. This work examines the roles of the Type III Secretion System (T3SS) and the Type VI Secretion System (T6SS) systems of Pseudomonas, a widespread genus including clinical pathogens and biocontrol strains. Bioinformatic analysis of T6SS phylogeny and associated gene content within Pseudomonas identified several T6SS phylogenetic groups, and linked T6SS components VgrG and Hcp encoded outside of T6SS gene loci with their cognate T6SS phylogenetic groups. Remarkably, such “orphan” vgrG and hcp genes were found to occur in diverse, horizontally transferred, operons often containing putative T6SS accessory components and effectors. The prevalence of a widespread superfamily of T6SS lipase effectors (Tle) was assessed in metagenomes from various environments. The abundance of the Tle superfamily and individual families varied between niches, suggesting there is niche specific selection and specialisation of Tle. Experimental work also discovered that P. fluorescens F113 uses the SPI-1 T3SS to avoid amoeboid grazing in mixed populations. This finding may represent a significant aspect of F113 rhizocompetence, and the rhizocompetence of other Rhizobacteria

The Human Lung Viral Microbiome In Health And Disease

Vast and diverse microbial communities (the microbiome) are distinct at different human body sites and strongly influence health and disease. Specifically, the respiratory tract microbiome is thought to influence outcomes after lung transplantation, the only therapeutic option for end-stage lung diseases. Studies dissecting the role of the microbiome on pulmonary health should also include the viral microbiome (virome), which is less-studied due to unique challenges in identifying these small, diverse, self-replicating genetic elements. Organ transplantation is accompanied by immunosuppression, which can result in reactivation of latent viruses, transfer of viruses from organ donor to recipient, and increased susceptibility to viral infections. We therefore used high-throughput metagenomic approaches to study the virome of lung transplant recipients (LTRs). We first characterized the virome in LTRs and its relationship to clinically defined adverse events. We discovered that a family of eukaryotic viruses (Anelloviridae) is abundant in the lung and blood of LTRs and that their levels in the lungs were associated with primary graft dysfunction, a form of acute lung injury. Next, we investigated the temporal and spatial dynamics of the virome during lung transplantation and identified herpesviruses, parvoviruses, polyomaviruses, bacteriophage and complex anellovirus populations. We focused on the abundant anelloviruses by assembling genomes from shotgun metagenomic sequences and tracking their representation in the lung and blood of LTRs post-transplantation using a metric that accounts for inter-and intra-subject viral diversity. This analysis revealed that anellovirus populations move between lung allografts and the peripheral blood of LTRs. However, many uncharacterized sequences still existed in the metagenomic data generated in these studies. To address this, we developed a molecular and bioinformatics pipeline to mine public datasets and discovered a novel family of small, circular DNA viruses (Redondoviridae). Quantification of redondoviruses in human oro-respiratory samples showed an association with periodontal disease and acute illness. Overall, this work helps define the virome during lung transplantation and introduces a new family of human viruses, broadly demonstrating the importance of exploring the human virome

The mechanisms of evolutionary flexibility in earthworm genomes

Many individual organisms have latent phenotypic potentials which are never realised within their lifespans. This potential can include a huge diversity of dormant adaptations across the tree of life, such as the ability to tolerate radical changes in temperature, survive restricted nutrient availability, and resist toxins and parasites. Prior to unrealised phenotypic potentials are necessarily information potentials residing in a dormant state also. This thesis investigates the systematic interactions of facultative morphologies and atavistic adaptivity with the evolutionary systems which propagate them. Earthworms as models are for these purposes an almost archetypal form of a high-latent-potential organism. Examples abound of their thriving as peregrine species with near-global ranges

Bioinformatic insights into the diversity and evolution of bacterial toxins

Bacterial toxins are a broad category of molecules ranging from small organic compounds and peptides to large multi-domain or multi-meric enzymes. Several important diseases are caused primarily by bacterial toxins including botulism and diphtheria. Paradoxically, the same toxins have proven useful for the treatment of muscular disorders and cancer, respectively. Given their importance in medicine and their utility as drugs, it is desirable to attain a greater functional and mechanistic understanding of toxin families. However, a full description of any sequence's functionality must incorporate an understanding of the evolutionary processes that produced them, and currently little is known about these forces. Using a bioinformatic approach, this thesis presents analyses of three bacterial toxin families: clostridial neurotoxins, which cause botulism and tetanus; diphtheria toxins, which cause diphtheria; and large clostridial toxins, which contribute to the infections produced by various clostridia, including \textit{Clostridioides difficile}. The detection of toxin-related sequences from bacterial genomes allows the discovery of toxin variants that may have gone undetected by other methods of toxin identification. Based on the available genomic data, toxin families that cause disease in humans appear to be broader than previously imagined. Toxin-related sequences are capable of performing unique functions compared to the toxin variants more traditionally associated with human disease. By examining human toxins in evolutionary terms, it is possible to identify the functional innovations that have occurred to result in human specificity, as well as delve more deeply into the relationships between toxin sequences and their functions. Thus, the studies presented here provide examples of how the field of toxin biology, like many other disciplines, has much to gain from the genomic revolution

RNA, the Epicenter of Genetic Information

The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information. Key Features Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other. Integrates the influences of biochemistry and genetics on the landscape of molecular biology. Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress. Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA. Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology. Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers