Download or read book Bacterial Integrative Mobile Genetic Elements written by Adam P. Roberts and published by CRC Press. This book was released on 2022-03-07 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: As our understanding of mobile genetic elements continues to grow we are gaining a deeper appreciation of their importance in shaping the bacterial genome and in the properties they confer to their bacterial hosts. These include, but are by no means limited to, resistance to antibiotics, and heavy metals, toxin production and increased virulence, production of antibiotics and the ability to utilize a diverse range of metabolic substrates. We are also gaining an understanding of diversity of these elements and their interactions with each other; a property which continually complicates any attempt to classify them. We are learning more about the molecular mechanisms by which they translocate to new genomic sites both within genomes and between different bacteria. This book provides a timely, state of the art update on the properties of an important selection of different bacterial integrative mobile genetic elements and the myriad of different ways in which they move and influence the biology of the host bacterium. The chapters are all written by authors who have undertaken pioneering work in their respective fields, making this book vital reading for all who are interested in the biology of bacteria and the mobile elements they carry.

Download or read book Mobile Genetic Elements written by Matthew George Durrant and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mobile genetic elements (MGEs) are genetic material that can mobilize and move either within a single organism's genome, or between the genomes of different organisms. An integrative mobile genetic element is one that can merge its genetic material with other genetic molecules to form a single genetic molecule, either DNA or RNA. Thanks to the work of pioneering scientists such as Nobel Laureate Barbara McClintock, our knowledge of how MGEs work and how they influence evolution has exploded and continues to grow to this day. MGEs and the enzymes that enable their mobilization (transposases, recombinases, integrases, resolvases, invertases, etc.) have been adapted as useful experimental and therapeutic tools. But there is still much to be learned about MGEs, and in the age of next-generation sequencing we have more tools than ever before to interrogate their function. In chapter 2, this dissertation introduces software that analyzes next-generation sequencing data to identify integrative mobile genetic elements and to genotype the precise genomic location of their insertion with respect to a reference genome. This bioinformatics tool, called MGEfinder, is applied in an analysis of thousands of publicly-available bacterial genomes, and this analysis sheds light on how MGEs allow bacteria to adapt, develop antibiotic resistance, and become more virulent and dangerous to their human hosts. In chapter 3, this tool and others are then adapted and used as a part of a genomic data mining pipeline to identify novel genetic elements and enzymes that have promise as genome engineering tools. Thousands of these site-specific integrases (also described as recombinases) were identified and stored in a database, and they were curated and prioritized to identify those that hold promise as human genome editing tools, specifically. Early validation experiments are promising. In addition to studies that focus on this main theme of mobile genetic elements, this dissertation introduces additional works related to the identification of small open reading frames (smORFs) in microbial genomes (chapter 4), and the transcriptomic and epigenomic response of a colorectal cancer cell line to the microbial metabolite butyrate (chapter 5). Together, these chapters demonstrate the importance of developing and applying tools to the study of mobile genetic elements more broadly, indicating the great scientific and therapeutic potential of these ubiquitous genetic elements.

Download or read book Effects of the Mobile Genetic Element ICEBs1 on Bacterial Host Fitness written by Joshua Mark Jones and published by . This book was released on 2020 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mobile genetic elements drive bacterial evolution by mediating horizontal gene transfer and by carrying cargo genes that confer important traits to host cells. Traits provided by mobile genetic elements include antibiotic resistance, novel metabolic capabilities, virulence factors, and the ability to form symbioses. Mobile genetic elements, especially Integrative Conjugative Elements (ICEs), are abundant in bacteria. Many do not contain cargo genes with known functions, but some likely carry novel types of cargo genes that provide traits beyond the scope of those currently attributed to mobile elements. In this thesis I describe the characterization of a fitness benefit provided by the mobile genetic element ICEBs1 to its bacterial host, Bacillus subtilis. Activation of ICEBs1 conferred a frequency-dependent selective advantage to host cells during biofilm formation and sporulation. The advantage was due to inhibition of biofilm-associated gene expression and delayed sporulation, which enabled ICEBs1 host cells to exploit their neighbors and grow more prior to sporulation. I identified a single gene within ICEBs1, ydcO, as both necessary and sufficient for the repression of development. Manipulation of host development programs allows ICEBs1 to increase host fitness. These findings highlight that cargo genes can alter existing aspects of physiology rather than providing entirely new traits, broadening our understanding of how mobile genetic elements influence their hosts.

Download or read book Interactions Between Mobile Genetic Elements and Their Bacterial Hosts written by Emily Lauryn Clark and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integrative and conjugative elements (ICEs) are widespread mobile genetic elements that facilitate the spread of many important genes, including those involved in antibiotic resistance, metabolism, pathogenesis, or symbiosis. These elements are also powerful tools for genetic analyses and engineering. ICEs are typically found integrated in a host chromosome. Either stochastically, or upon some signal, they can excise, undergo DNA processing events, be transferred through encoded conjugation machinery into a neighboring cell, and stably integrate into the new chromosome. Interactions between an ICE and its hosts throughout the life cycle can influence the efficiency of acquisition by new hosts. In this work, I investigated and compared the interactions that two ICEs, Tn916 and ICEBs1, have with their host cells. First, I explored how the different functional modules of these elements impact how efficiently they are transferred into different host species. I generated hybrid conjugative elements that merge functions of both elements to increase transfer efficiencies, presenting exciting potential to be used for genetic engineering. Next, I investigated a previously unknown ability of Tn916 to cause a growth arrest and kill its host cell. I took genetic approaches to determine that two Tn916-encoded genes interact with a defective phage-like element in the B. subtilis chromosome to elicit some of these effects. Finally, I evaluated the integration site selection of Tn916 in the B. subtilis chromosome, identifying several hundred unique AT-rich insertion sites, one of which is a "hot spot" for integration. I found that a host nucleoid-associated protein does not influence integration site selection. I conclude this body of work with a discussion of how the efficient spread of an element is shaped by its interactions with host cells and other horizontally acquired elements

Download or read book Interplay Between an Integrative and Conjugative Element and Its Bacterial Host written by Saria Armena McKeithen-Mead and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integrative and conjugative elements (ICEs) are considered the most abundant conjugative elements. ICEs are MGEs that reside integrated into their host chromosome, excise, and transfer their DNA via conjugation (involving a type IV secretion system) into a recipient. During acquisition, the element must switch from a replicating element to a quiescent element capable of integrating for stable acquisition.

Download or read book Mobile DNA III written by Michael Chandler and published by John Wiley & Sons. This book was released on 2020-07-24 with total page 1321 pages. Available in PDF, EPUB and Kindle. Book excerpt: An exploration of the raw power of genetic material to refashion itself to any purpose... Virtually all organisms contain multiple mobile DNAs that can move from place to place, and in some organisms, mobile DNA elements make up a significant portion of the genome. Mobile DNA III provides a comprehensive review of recent research, including findings suggesting the important role that mobile elements play in genome evolution and stability. Editor-in-Chief Nancy L. Craig assembled a team of multidisciplinary experts to develop this cutting-edge resource that covers the specific molecular mechanisms involved in recombination, including a detailed structural analysis of the enzymes responsible presents a detailed account of the many different recombination systems that can rearrange genomes examines the tremendous impact of mobile DNA in virtually all organisms Mobile DNA III is valuable as an in-depth supplemental reading for upper level life sciences students and as a reference for investigators exploring new biological systems. Biomedical researchers will find documentation of recent advances in understanding immune-antigen conflict between host and pathogen. It introduces biotechnicians to amazing tools for in vivo control of designer DNAs. It allows specialists to pick and choose advanced reviews of specific elements and to be drawn in by unexpected parallels and contrasts among the elements in diverse organisms. Mobile DNA III provides the most lucid reviews of these complex topics available anywhere.

Download or read book Consequences of a Mobile Genetic Element Integrated at Secondary Locations written by Kayla Lynne Menard and published by . This book was released on 2013 with total page 96 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integrative and conjugative elements (ICEs) are widespread mobile genetic elements that are integrated in bacterial chromosomes, but can excise and transfer to a recipient through conjugation. ICEs are important agents of evolution, contributing to the acquisition of new traits, including antibiotic resistance. Many ICEs are site-specific in that they integrate preferentially into a primary attachment site in the bacterial chromosome. Site-specific ICEs can integrate into secondary locations, but little is known about the consequences of integration. Using ICEBs1, a site-specific ICE from Bacillus subtilis, I found that integration into secondary attachment sites is detrimental to both ICEBs1 and the host cell. Integration at secondary locations is detrimental to ICEBsJ. Once integrated in the chromosome, excision of ICEBs1 from all secondary attachment sites analyzed was either reduced (4 sites) or undetectable (3 sites) compared to ICEBs1 excision from the primary site. Additionally, from two of the four secondary sites that exhibited reduced but detectable excision, the excised, circular form of ICEBs1 was present at lower levels than expected, indicating that circular ICEBs1 may be unstable. Defects in excision and stability of ICEBs] severely limit its ability to spread to other cells. Integration at secondary locations is detrimental to the host cell. Induction of ICEBs1 gene expression in secondary integration sites resulted in a defect in cell proliferation and/or viability, as well as induction of the SOS response. These effects are likely due to DNA damage resulting from plasmid-like, rolling-circle replication of the excision-defective ICEBs1 in the chromosome. Consistent with this model, deletion of ICEBs] replication genes (nicK and helP) alleviated the proliferation and viability defects. Implications for the evolution of ICEs. These previously unrecognized detrimental effects may provide selective pressure against propagation of ICEBs1 in secondary attachment sites. Such detrimental effects could explain the maintenance and prevalence of site-specific integration among ICEs.

Download or read book Interactions Between an Integrative and Conjugative Element and Its Bacterial Host written by Mark Michael Harden (Jr.) and published by . This book was released on 2021 with total page 137 pages. Available in PDF, EPUB and Kindle. Book excerpt: Conjugative elements are mobile genetic elements that can transfer from a donor bacterium to a recipient via an element-encoded type IV secretion system. Integrative and conjugative elements (ICEs) are an abundant class of conjugative element. ICEs are typically integrated into the bacterial host chromosome, but under certain conditions, or stochastically, they can excise from the chromosome and transfer to a recipient. ICEs likely interact with their bacterial host at every stage of their life cycle, but few of these interactions have been characterized. In this work I sought to 1) identify bacterial host factors necessary for efficient transfer of the integrative and conjugative element ICEBs1 to a recipient, and 2) determine whether the ICEBs1-encoded cell wall-modifying enzyme CwlT acts on the cell wall of the donor bacterium, the recipient bacterium, or both. I used CRISPR interference to induce a knockdown of individual essential Bacillus subtilis genes, and then screened for gene knockdowns that caused an acute defect in transfer of ICEBs1. I found that wall teichoic acids were necessary in both ICEBs1 donors and recipients for efficient conjugative transfer. I found that depletion of wall teichoic acids caused cells involved in ICEBs1 conjugation to sustain lethal envelope damage caused by active conjugation machinery. Conjugative elements must bypass the cell wall of both the donor and recipient cells in a mating pair. Conjugative elements encode cell wall hydrolases that are required for efficient transfer, which are presumed to partly degrade the cell wall of the donor bacterium during conjugation. In order to investigate the role of the ICEBs1-encoded cell wall hydrolase CwlT in conjugation, I generated cell wall-less (L-form) strains of B. subtilis which could donate or receive ICEBs1. In the absence of either the donor or recipient cell wall, CwlT was dispensable for efficient transfer. This finding indicates that CwlT acts on both the donor and recipient cell wall in a mating pair.

Download or read book The Pangenome written by Hervé Tettelin and published by Springer Nature. This book was released on 2020-04-30 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.

Download or read book Structure and Function of the Bacterial Genome written by Charles J. Dorman and published by John Wiley & Sons. This book was released on 2020-04-28 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents an integrated view of the expression of bacterial genetic information, genome architecture and function, and bacterial physiology and pathogenesis This book blends information from the very latest research on bacterial chromosome and nucleoid architecture, whole-genome analysis, cell signaling, and gene expression control with well-known gene regulation paradigms from model organisms (including pathogens) to give readers a picture of how information flows from the environment to the gene, modulating its expression and influencing the competitive fitness of the microbe. Structure and Function of the Bacterial Genome explores the governance of the expression of the genes that make a bacterium what it is, and updates the basics of gene expression control with information about transcription promoter structure and function, the role of DNA as a regulatory factor (in addition to its role as a carrier of genetic information), small RNAs, RNAs that sense chemical signals, ribosomes and translation, posttranslational modification of proteins, and protein secretion. It looks at the forces driving the conservation and the evolution of the dynamic genome and offers chapters that cover DNA replication, DNA repair, plasmid biology, recombination, transposition, the roles of repetitive DNA sequences, horizontal gene transfer, the defense of the genome by CRISPR-Cas, restriction enzymes, Argonaute proteins and BREX systems. The book finishes with a chapter that gives an integrated overview of genome structure and function. Blends knowledge of gene regulatory mechanisms with a consideration of nucleoid structure and dynamics Offers a 'DNA-centric' approach to considering transcription control Views horizontal gene transfer from a gene regulation perspective Assesses the opportunities and limitations of designing synthetic microbes or rewiring existing ones Structure and Function of the Bacterial Genome is an ideal book for graduate and undergraduate students studying microbial cell biology, bacterial pathogenesis, gene regulation, and molecular microbiology. It will also appeal to principal investigators conducting research on these and related topics and researchers in synthetic biology and other arms of biotechnology.

Download or read book Horizontal Gene Pool written by Christopher M. Thomas and published by CRC Press. This book was released on 2003-09-02 with total page 459 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria are the most ubiquitous of all organisms. Responsible for a number of diseases and for many of the chemical cycles on which life depends, they are genetically adaptable. Vital to this adaptability is the existence of autonomous genetic elements-plasmids-which promote genetic exchange and recombination. The genes carried by any particular plasmid may be found in only a few individuals of any species but can also be shared with other species and thus constitute a horizontal gene pool. This book explains the various contributions that plasmids make to this pool: the replication, stable inheritance and transfer modules, the phenotypic markers they carry, the way they evolve, the ways they contribute to their host population and the approaches that we use to study and classify them. It also looks at what we know about their activity in natural communities and the way that they interact with other mobile elements to promote bacterial evolution.

Download or read book Specificity and Benefits of an Exclusion Mechanism for a Mobile Genetic Element in Bacillus Subtilis written by Kathleen Patricia Davis and published by . This book was released on 2019 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: The horizontal transfer of mobile genetic elements, including Integrative and Conjugative Elements (ICEs), plays an essential role in bacterial evolution by helping to promote the spread of genes involved in antibiotic and heavy metal resistance, metabolism, symbiosis, and pathogenicity. Like conjugative plasmids, ICEs spread to new hosts by conjugative transfer through Type 4 Secretion Systems (T4SSs) encoded in the ICE DNA, however unlike plasmids, ICEs are usually found integrated into the host chromosome except for immediately prior to, during and after conjugative transfer. Almost all plasmids and some ICEs have an exclusion mechanism, which prevents acquisition of a second copy of the element via conjugative transfer. ICEBs1 has an exclusion mechanism in which the ICEBs1 exclusion protein YddJ targets the conjugation machinery protein ConG, the VirB6 homolog in the ICEBs1 T4SS, to prevent transfer from a would-be donor cell. My work described in this thesis involves a mutagenesis and enrichment screen which isolated exclusion-resistant, transfer-competent mutations in ConG, and swap experiments with ICEBs1 and ICEBat1 ConG and YddJ homologs demonstrating that YddJ targets its cognate ConG for exclusion, and that YddJ and ConG together determine the specificity of exclusion. I identified regions of ConG and YddJ that are essential for exclusion specificity, and found that YddJ-mediated exclusion protects donor cells from serving as recipients during or immediately after they serve as donors. These findings further our understanding of regulation of horizontal gene transfer, particularly in Gram-positive bacteria. They provide further evidence of a conserved target in exclusion, the VirB6 homologs, and indicate that different mobile genetic elements can employ exclusion systems for different reasons.

Download or read book Antimicrobial Resistance written by World Health Organization and published by . This book was released on 2014 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: Summary report published as technical document with reference number: WHO/HSE/PED/AIP/2014.2.

Download or read book Microbial Megaplasmids written by Edward Schwartz and published by Springer Science & Business Media. This book was released on 2009-01-29 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Megaplasmids are extrachromosomal genetic elements in the size range of 100 kb and larger. They are found in physiologically and phylogenetically diverse groups of bacteria and archaea. By definition, megaplasmids are not essential for the viability of their hosts under all growth conditions, but paradoxically many megaplasmids carry the genetic information for the defining and characteristic traits of the organism in which they reside. Microbial Megaplasmids reviews our knowledge of the extensively studied representatives, such as the catabolic plasmids of the pseudomonads, the rhizobial Sym plasmids, the Ti plasmids of the genus Agrobacterium and the giant enterobacterial virulence plasmids. It also presents snapshots of more recently discovered megaplasmids. The contribution of megaplasmids to the biology of their hosts is described, highlighting the interactions between megaplasmid and chromosomal genes.

Download or read book Comparative Genomics written by João Carlos Setubal and published by Springer Nature. This book was released on with total page 622 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Type IV Secretion in Gram Negative and Gram Positive Bacteria written by Steffen Backert and published by Springer. This book was released on 2018-03-13 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: Type IV secretion systems (T4SSs) are highly versatile membrane-associated transporter machines used by Gram-negative and Gram-positive bacteria to deliver substrate molecules to a large variety of target cells. This volume summarizes our current knowledge of the large variety and structural diversity of T4SSs in pathogenic Escherichia, Agrobacterium, Legionella, Coxiella, Bartonella, Helicobacter, Enterococcus and other species. Divided into 13 chapters contributed by leading experts, it presents findings that significantly enhance our understanding of how various pathogens manipulate host cell functions to trigger bacterial uptake, promote intracellular growth, suppress defense mechanisms and of how bacteria spread antibiotic resistances, thus facilitating bacterial colonization and disease development. The book is an invaluable source of information for researchers and clinicians.

Download or read book Characterization of an Exclusion Mechanism in an Integrative and Conjugative Element in Bacillus Subtilis written by Monika Maria Masumi Avello and published by . This book was released on 2018 with total page 84 pages. Available in PDF, EPUB and Kindle. Book excerpt: Horizontal gene transfer is the acquisition of new genetic material that can confer novel phenotypes to bacteria and contribute to their evolution. Conjugation is an important mechanism of horizontal gene transfer that involves the direct transfer of DNA between two cells and is mediated by mobile genetic elements encoding type IV secretion systems. Conjugative elements prevent redundant transfer by a mechanism known as exclusion that inhibits their cognate secretion systems. Exclusion is prevalent among conjugative elements, suggesting it is advantageous and potentially essential. Yet very few exclusion mechanisms are characterized, and the advantages they provide are not well understood. My work characterizes the exclusion mechanism of an integrative and conjugative element found in a Gram-positive bacterium. In combination with several other studies, my results point to a potentially conserved mechanism and novel benefits of this phenomenon, furthering our understanding of how mobile genetic elements regulate their transfer, impact their bacterial hosts, and mediate horizontal gene transfer.