Cell Cycle Regulation and Development in Alphaproteobacteria


Book Description

This book provides a comprehensive overview of the cell cycle regulation and development in Alphaproteobacteria. Cell cycle and cellular differentiation are fascinating biological phenomena that are highly regulated in all organisms. In the last decades, many laboratories around the world have been investigating these processes in Alphaproteobacteria. This bacterial class comprises important bacterial species, studied by fundamental and applied research. The complexity of cell cycle regulation and many examples of cellular differentiations in this bacterial group represent the main motives of this book. The book starts with discussing the regulation of cell cycle in alphaproteobacterial species from a system biology perspective. The following chapters specifically focus on the model species Caulobacter crescentus multiple layers of regulation, from transcriptional cascades to proteolysis and dynamic subcellular regulation of cell cycle regulators. In addition, the cell division process, chromosome segregation and growth of the cell envelope is described in detail. The last part of the book covers examples of non-Caulobacter alphaproteobacterial models, such as Agrobacterium tumefaciens, Brucella species and Sinorhizobium meliloti and also discusses possible applications. This book will be of interest to researchers in microbiology and cell biology labs working on cell cycle regulation and development.




Bacterial Transcription Factors and the Cell Cycle, 2nd edition


Book Description

Analogous to the eukaryotic G1, S and M phase of the cell cycle, the bacterial cell cycle can be classified into independent stages. Slowly growing bacterial cells undergo three different stages, B-, C- and D-phase, respectively, while the cell cycle of fast-growing bacteria involves at least two independent cycles: the chromosome replication and the cell division. The oscillation in gene expression regulated by transcription factors, and proteolysis mediated by ClpXP, are closely correlated with progression of the cell cycle. Indeed, it has been shown that DnaA couples DNA replication initiation with the expression of the two oscillating regulators GcrA and CtrA, and the DnaA/GcrA/CtrA regulatory cascade drives the forward progression of the Caulobacter cell cycle. Furthermore, it has been found that: the DnaA oscillation in Eschericha coli and Caulobacter crescentus plays an important role in the cell cycle coordination; RpoS in Coxiella regulates the gene expression involved in the developmental cycle; the SigB and SinR transcription factors control whether cells remain in or leave a biofilm responding to metabolic conditions in Bacillus subtilis; similarly, BolA in most Gram-negative bacteria turns off motility and turns on biofilm development as a transcription factor; CtrA regulates cell division and outer membrane composition of the pathogen Brucella abortus; an essential transcription factor SciP enhances robustness of Caulobacter cell cycle regulation. Interestingly, transcription factors mediated metabolism fluctuations are also related to progression of the cell cycle. It has been shown that: CggR and Cra factors are involved in the flux-signaling metabolite fructose-1,6-bisphosphate; IclR mediates para-hydroxybenzoate catabolism in Streptomyces coelicolor; CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria; and these metabolism changes affect cell growth. In line with the argument, AspC-mediated aspartate metabolism coordinates the E. coli cell cycle. However, the molecular mechanisms of maintaining the proper cell cycle progression through coordination of transcription factors mediated gene transcription oscillation, cellular metabolism with the cell cycle are not yet well-established. This Research Topic is intended to cover the spectrum of cell cycle regulatory mechanisms, in particular the coordination of transcription factor mediated gene transcription oscillations, and the cellular metabolisms associated with the cell cycle. We welcome all types of articles including Original Research, Review, and Mini Review. The subject areas of interest include but are not limited to: 1. Cell cycle coordination through gene expression and expression oscillation mediated by transcription factors. 2. Regulation of the cell cycle by proteolysis oscillation. 3. Coordination of the cell cycle with metabolism fluctuation. 4. DNA methylation fluctuation and the cell cycle. 5. Novel transcription factors and gene expression patterns associated with the cell cycle.




Regulation of Motility, the Cell Cycle, and Magnetosome Formation in Magnetospirillum Magneticum AMB-1


Book Description

Despite their diminutive size and seemingly simple construction, bacteria lead remarkably complex lives. In order to fulfill their biological roles of growth and reproduction, they must integrate a wealth of information about their environment and, depending upon the suitability of the available conditions for survival, they can act to relocate themselves to more preferred locales. Doing so requires that bacteria be able to sense environmental stimuli and relay signals induced by those stimuli to various locomotive apparatuses. Once a cell has fulfilled its nutrient quota to support replication, cell division can occur. Cell division is also intricately timed and regulated in bacterial cells, which are now known to possess intracellular organization, cytoskeletal features, and, in some species, compartmentalization. Therefore, division of a bacterial cell must coordinate disassembly, reassortment, and segregation of these cell biological features. In this work, I investigate the connection between the cell cycle and bacterial organelle formation in the magnetotactic bacterium Magnetospirillum magneticum AMB-1. Magnetotactic bacteria, including AMB-1, are defined by their ability to synthesize chains of intracellular membrane-bounded magnetic minerals, which facilitate bacterial alignments with and responses to geomagnetic fields. To determine the role of the cell cycle in governing the production of these bacterial organelles, called magnetosomes, I disrupted homologs of regulatory factors known to control the progression of the cell cycle as well as polar organelle development in related Alphaproteobacteria. Surprisingly, mutants in the CtrA regulatory pathway were viable, indicating alternative mechanisms of cell cycle progression in AMB-1; in addition, magnetosome formation was also unaffected. Notably, motility was the only feature of AMB-1 disrupted by the CtrA pathway mutations. While subsequent studies to probe upstream regulators of motility in AMB-1 failed to yield additional insight, my results suggest a terminal role for CtrA in the transcription of flagellar biosynthesis genes. This role appears to be ancestral in the Alphaproteobacteria. Further, I have developed protocols which should enable future investigations of the cell cycle in AMB-1 and the temporal changes in gene expression which allow its progression. Preliminary studies indicate that genes involved in signal transduction and possibly magnetosome membrane formation vary their expression throughout the AMB-1 cell cycle. Continued investigation of the connections between the CtrA pathway, magnetosome gene expression, and the cell cycle may elucidate regulation of motility in magnetotactic bacteria and illustrate novel mechanisms of cell cycle progression in these unique organisms.




Coordination of Cell Envelope Biogenesis and Cell Division by an Essential Two-component Signaling System in Alphaproteobacteria


Book Description

Prokaryotes depend on a number of two-component systems (TCSs) to rapidly sense and respond to environmental stimuli. These TCSs, comprised of a signaling histidine kinase and cognate response regulator, are critical for bacterial signal integration and cellular response to external or internal cues. Commonly, these systems function to regulate the expression of target genes, or initiate larger regulatory cascades, to coordinate this response. Bacteria rely on several well-studied envelope stress response TCSs to monitor extracytoplasmic and cell envelope homeostasis as well as respond to antibiotics, toxins, host immune factors, osmotic and desiccation stress to promote survival. Other TCSs are important regulators of essential processes including cell cycle dynamics and cell wall biosynthesis. However, these systems tend to be poorly conserved and/or studied in Gram-negative bacteria. As a result, little is known about this regulation in Îł-proteobacteria. Therefore, one goal of my thesis project was to provide insight into these processes using the Gram-negative Îł-proteobacterium Rhodobacter sphaeroides as a model. This purple non-sulfur bacterium remodels the cell envelope under low oxygen conditions by increasing lipid content and creating intracytoplasmic membrane invaginations (ICM) that protrude from the cytoplasmic membrane and house the cell's photosynthetic machinery. Thus, we hypothesized that Rb. sphaeroides would be amenable to perturbation to identify the genetic basis and regulation of cell envelope remodeling and biosynthesis. First, I characterized a previously unidentified histidine kinase (CenK) with no known cognate response regulator that when disrupted, produced cells with altered cell morphology and hypersensitivity to compounds inhibiting peptidoglycan synthesis. This work defined the TCS that this kinase belongs in and identified an essential response regulator (CenR) as its cognate pair. Utilizing gain of function and loss of function alleles, I assayed the predicted function of CenR in transcriptional regulation and determined that this TCS regulates the expression of cell division, outer membrane biogenesis, and peptidoglycan cell wall biosynthesis and assembly. Consistent with its activity in Rb. sphaeroides, I found that many Îł-proteobacteria contain a homologous TCS and provide evidence for its conserved function in these microbes. Expanding on this work, I utilized the cell morphological changes produced by increasing the activity of the CenKR TCS to probe poorly understood spatial and temporal cell division processes in Rb. sphaeroides. I showed that the localization of the outer membrane lipoprotein Pal is key to proper localization of peptidoglycan biosynthesis and the coordination of bacterial cytoskeletal proteins MreB and FtsZ. By monitoring the localization of these essential proteins, I developed a model for how these systems function in wild type cells as well as how their disruption leads to TCS mutant phenotypes. Therefore, I propose CenKR is an unusual and essential regulator of outer membrane homeostasis and division. I further propose that genetic manipulation of this TCS has and can continue to provide new insights into poorly understood process of cell elongation, cell division, and cell envelope biogenesis in Rb. sphaeroides and other Îł-proteobacteria.




The Complex Transcriptional Landscape of Caulobacter Crescentus


Book Description

One of the central aspects of the biological program that guide the development of an organism is embedded in the regulated and sequential expression of genes as development progresses. A large part of this regulation is achieved through the temporal activation and repression of transcriptional initiation by the selective binding of regulatory proteins, such as transcription factors, to promoters during specific stages of development. Thus, being able to globally and precisely identify these processes are important steps in gaining a systems-level insight and understanding of the developmental program. The cell cycle of Caulobacter crescentus, an alpha-proteobacteria that undergoes cell differentiation and asymmetric cell division, has been used extensively as a model organism to study bacterial development. A cyclical and integrated genetic circuit involving five master regulatory proteins, including DnaA, GcrA, CtrA, and SciP, and the DNA methyl-transferase CcrM, whose presence and activities oscillate in space and time, orchestrate the many facets of the Caulobacter cell cycle including DNA replication, DNA methylation, organelle biogenesis, and cytokinesis. This genetic circuit is at the core of the Caulobacter developmental program. While microarrays have shown 19% of mRNAs undergo changes in RNA level during the cell cycle and development, it is unclear exactly which regulatory factors of the core circuit drive the changes in transcription at each specific locus, and how these regulatory factors act combinatorially to effect transcriptional outcomes has not been systematically dissected. In order to achieve these goals and to further define the transcriptional regulatory landscape that guides the cell cycle, a thorough and global analysis of Caulobacter transcription as a function of the cell cycle and developmental progression is needed. In this thesis, I devised a novel protocol combining 5' rapid amplification of cDNA ends (5' RACE) and high-throughput sequencing to globally map the precise locations of transcriptional start sites (TSSs) in the Caulobacter genome, measured their transcription levels at multiple times in the cell cycle, and identified their transcription factor binding sites. Using the TSSs identified and a RNA sequencing dataset, I made a functional annotation of operons and other transcriptional units in the genome. A large number of antisense transcripts were identified, and many of them are within essential cell cycle-regulated genes, including two master regulators, a previous unknown feature of the core cell cycle control circuit. Many critical genes and operons have multiple promoters, and these promoters are often independently regulated. Furthermore, approximately 25% of the cell cycle-regulated promoters are co-regulated by two or more master regulatory proteins of the core genetic circuit. These results revealed surprising transcriptional complexity and uncovered multiple new layers of transcriptional control mediating the bacterial cell cycle and development and represent the first in-depth analysis of TSS control in as a function bacterial cell cycle and developmental progression.




Prokaryotic Metabolism and Physiology


Book Description

Extensive and up-to-date review of key metabolic processes in bacteria and archaea and how metabolism is regulated under various conditions.




Comparative Virology


Book Description

Comparative Virology provides an integrated comparison of viruses, based on their chemical and morphological characteristics. These descriptions will not only give the reader a background but also a detailed analysis of the various groups. In some instances the groups are still host related, as in the case of bacteriophages and polyhedral insect viruses. In others, for instance in pox viruses, the group comprises viruses of vertebrates and invertebrates. The hosts of the bacilliform Rhabdovirales range from man and other warm-blooded vertebrates through invertebrate animals to plants. A special chapter is devoted to viruses devoid of protein—a group that is of great interest and that has only recently been recognized. Since there is historical and practical interest in écologie groupings, such as arboviruses and oncogenic viruses, chapters on such groups have also been included. The book opens with a discussion on the classification of viruses. Chapters dealing with DNA viruses and RNA viruses follow, and the ecologically and disease-oriented groups complete the volume. It is hoped that ""Comparative Virology"" will help bring unity to the science of virology through the comparative approach that is not dependent on virus-host interactions. The combined efforts of eminent contributors to discuss and evaluate new information will hopefully benefit all who are interested in virology




Asymmetric Cell Division in Development, Differentiation and Cancer


Book Description

This book provides readers with an overview of the frequent occurrence of asymmetric cell division. Employing a broad range of examples, it highlights how this mode of cell division constitutes the basis of multicellular organism development and how its misregulation can lead to cancer. To underline such developmental correlations, readers will for example gain insights into stem cell fate and tumor growth. In turn, subsequent chapters include descriptions of asymmetric cell division from unicellular organisms to humans in both physiological and pathological conditions. The book also illustrates the importance of this process for evolution and our need to understand the background mechanisms, offering a valuable guide not only for students in the field of developmental biology but also for experienced researchers from neighboring fields.







Cellular Ecophysiology of Microbe


Book Description

This book assembles concisely written chapters by world-leaders in the field summarizing recent advances in understanding microbial responses to hydrocarbons. Subjects treated include mechanisms of sensing, hydrocarbon tolerance and degradation as well as an overview on hydrophobic modification of biomolecules. Other chapters are dedicated to issues related to the reduced bioavailability of hydrocarbons, which differentiates this class of compounds form many others, but which of central importance to understand the ecophysiological consequences. This book should be standard literature in any laboratory working in this area.