Bacillus: Cellular and Molecular Biology (Second edition)
"high quality diagrams and figures" (Doodys)
"a thorough reference" (Book News)
"carefully edited book" (Biospektrum)
Caister Academic Press
University of Freiburg, Germany
xii + 398
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Bacillus subtilis has become widely adopted as a model organism for laboratory studies and is one of the best understood prokaryotes in terms of molecular and cellular biology. Its superb genetic amenability and relatively large size have provided powerful tools to investigate a bacterium in all possible aspects.
Extensively revised and updated, the new edition of this valuable reference work provides a comprehensive and up-to-date analysis of the current knowledge and new research in Bacillus molecular and cellular biology. Under the expert guidance of the editor Peter Graumann, renowned authors from around the world have contributed critical reviews on the most recent and topical research. Subjects covered include chromosome replication, DNA repair, chromosome segregation, cell division, transcription and translation, RNA-mediated regulation, general and regulatory proteolysis, the actin-like MreB cytoskeleton, the membrane proteome, the cell wall, endospore formation, biofilms, multicellularity and social behaviour, competence and transformation.
An essential book for anyone interested in Bacillus and an important reference volume for those working in fields as diverse as medicine, biotechnology, agriculture, food and industry. A recommended book for all microbiology laboratories.
"comprehensive and up-to-date" from IFIS
"The book contains some very high quality diagrams and figures ... It also comes with useful Internet tools ... This comprehensive book presents current scientific studies on the cellular processes of Bacillus species ... The book is well organized" from Doodys
"... a thorough reference to Bacillus subtilis." from Ref. Res. Book News
"As in the first edition Graumann has brought together top authors who critically review the high-level topics and classify the current literature in an excellent manner ... This carefully edited book of Graumann\'s should be in the collection of every group that works with B. subtilis." from Biospektrum (2012) 18: 681.
Table of contents
1. Replication of the Bacillus subtilis Chromosome
Marie-Françoise Noirot-Gros, Patrice Polard and Philippe Noirot
Eubacteria have evolved multicomponent protein machines, termed replisomes, which duplicate their chromosomes rapidly and accurately. Extensive studies in the model bacteria Escherichia coli and Bacillus subtilis have revealed that in addition to the replication core machinery, other proteins are necessary to form a functional replication fork. Specific subsets of proteins mediate: a) the assembly of the replisome at the chromosomal origin of replication [initiation]; b) the progression of the replication forks along the chromosome [elongation] and their maintenance by providing solutions for replication restart, which are adapted to overcome possible 'roadblocks' encountered on the DNA template; and c) the physiological arrest of replication when chromosome duplication is completed [termination]. Within the cell, DNA replication takes place within a factory positioned at the cell centre. This review summarises recent knowledge about chromosomal replication in Bacillus subtilis and related Gram-positive bacteria. It is focused on the events governing the assembly and the fate of the replication fork, describes protein networks connected with the replisome, and emphasises several novel aspects of DNA replication in this group of bacteria.
2. Dynamics of DNA Double-strand Break Repair in Bacillus subtilis
Begoña Carrasco, Paula P. Cardenas, Cristina Cañas, Tribuhwuan Yadav, Carolina E. César, Silvia Ayora and Juan C. Alonso
All organisms have developed a variety of DNA repair mechanisms to cope with DNA lesions. Homologous recombination (HR), which uses a homologous template to restore lost information at the break site, is the ultimate step for repair of one- or two-ended double strands breaks (DSBs) and for promoting the re-establishment of replication forks. Genetic and cytological approaches were used to analyze the requirements of exponentially growing Bacillus subtilis cells to survive chemical or physical agents that generate one- or two-ended DSBs and the choreography of DSB repair. The damage-induced multi-protein complex (recombinosome), organised into focal assemblies, has been confirmed by biochemical approaches. HR is coordinated with other essential processes, such as DNA replication, transcription and chromosomal segregation. When DSB recognition or end resection is severely impaired or an intact homologous template is not available the DNA ends of two-ended DSBs are repaired via non-homologous end joining.
3. Chromosome Segregation
Peter L. Graumann
After a bit more than a decade of the use of GFP - or immuno-fluorescence microscopy to study bacterial chromosome segregation, it has become clear that this process is highly organized, temporally as well as spatially, and that a mitotic-like machinery exists that actively moves apart sister chromosomes. Several key factors in this process have been identified, and at least a rough overall picture can be drawn on how chromosomes are separated so highly rapidly and efficiently. Bacillus subtilis has a circular chromosome. Replication initiates at the origin of replication that is defined as 0 degrees, and two replication forks proceed bidirectionally to converge at the terminus region, which is defined as 180 degrees. All other regions on the chromosome are defined as the corresponding site on a circle. DNA replication occurs in the cell centre, and duplicated regions are moved away from the cell centre towards opposite cell poles. This process is driven by an active motor that involves bacterial actin-like proteins, whose mode of action is still unknown. A dedicated protein complex called SMC forms two subcellular centres that organize newly duplicated chromosome regions within each cell half, setting up the spatial organization that characterizes bacterial chromosome segregation. Several proteins, including topoisomerases, DNA translocases and recombinases, ensure that entangled sister chromosomes or chromosome dimers can be completely separated into the future daughter cells shortly before cell division occurs at the middle of the cells.
4. Cell Division
Cell division is the process of generating two viable descendants from a progenitor cell. This involves two coordinated events: the replication and segregation of the bacterial chromosome and the splitting of the progenitor cell by cytokinesis, which in bacteria is also known as septum formation. Bacterial cells have developed a remarkably sophisticated protein machine capable of precisely splitting a progenitor cell at the right place and time in every cell cycle. This machine, which is known as the divisome or septalsome, is based on a contractile protein ring, as in the case of eukaryotes. In contrast to eukaryotic cells, however, which use actin and myosin in their contractile protein ring, the bacterial contractile machine is based on the tubulin-like protein FtsZ. Here we review the mechanism of cytokinesis in Bacillus subtilis.
5. The Organisation of Transcription and Translation
Peter Lewis and Xiao Yang
The traditional view of transcription and translation within the cell was that of a very closely coupled process where translating ribosomes assembled on the nascent transcript as it was produced by transcribing RNA polymerase. Whilst this close physical coupling is undoubtedly important, it seems clear now that a number of other events are significant with respect to the physical organization of these two processes within the cell. Transcription is crudely segregated into two regions within the nucleoid where either stable (r- and t-) RNA, or mRNA transcription predominate. Translation by polysomes is probably enriched at cell poles, whereas the assembly of initiation complexes, and maybe some transcriptionally linked ribosomes may occur throughout the nucleoid.
6. RNA-mediated Regulation in Bacillus subtilis
Wade C. Winkler
Bacterial genetic regulation is generally assumed to occur at the level of transcription initiation through the use of transcription factors. Regulatory mechanisms that take place post-transcription initiation are sometimes treated as anomalies - as exceptions to the rule. However, the actual degree of usage for post-initiation regulatory strategies in bacteria still remains to be fully determined. As evidence to this fact, recent research has significantly expanded the general understanding of post-initiation regulation in Bacillus subtilis and other bacteria. Regulatory RNAs are now predicted to control expression of numerous fundamental biochemical pathways that together constitute greater than 4% of the B. subtilis genome. Therefore, post-initiation regulation is a vital layer of bacterial genetic circuitry that still remains to be fully revealed.
7. General and Regulatory Proteolysis in Bacillus subtilis
Proteolysis is an important part of many fundamental cellular processes. The intricate involvement of proteases and peptidases in protein quality control, general stress response, control of regulatory networks and development in Bacillus subtilis are introduced in this review. Especially the more recent developments on the role of AAA+ proteins and their adaptor proteins in regulated and general proteolysis and the role of regulated intra-membrane proteolysis and membrane proteases in signal transduction are discussed.
8. The Actin-like MreB Cytoskeleton
Prokaryotic cells possess filamentous proteins, analogous to eukaryotic cytoskeletal proteins, that play a key role in the spatial organization of essential cellular processes. The bacterial homologues of actin (MreB, ParM, MamK and AlfA and Alps proteins) are involved in cell shape determination, DNA segregation, cell polarity, cell motility and other functions that require the targeting and accurate positioning of proteins and molecular complexes in the cell. In Bacillus subtilis, MreB homologues (MreB, Mbl and MreBH) assemble into dynamic helical-like structures along the sidewalls, which control morphogenesis by actively directing the growth of the cylindrical cell wall (elongation). The ultimate morphology of the cell is believed to depend on a dynamic interplay between the intracellular MreB proteins and the extracellular proteins that carry up cell wall biosynthesis and degradation, probably linked through MreCD and/or other membrane proteins such as RodZ. Recent findings rule out an essential function of the MreB isoforms of B. subtilis in chromosome segregation, but it is still possible that MreB is involved in this process. The general properties of the MreB proteins, relative to eukaryotic actin and to other prokaryotic homologues of actin, and the known functions of the MreB cytoskeleton in B. subtilis and other bacteria, will be discussed in this chapter.
9. Ins and Outs of the Bacillus subtilis Membrane Proteome
Jan Maarten van Dijl, Annette Dreisbach, Marcin J. Skwark, Mark J.J.B. Sibbald, Harold Tjalsma, Jessica C. Zweers and Girbe Buist
Bacterial homeostasis is largely determined by a phospholipid bilayer that encloses the cytoplasm. The proteins residing in this cytoplasmic membrane are responsible for communication between the cytoplasm and extracytoplasmic cell compartments or the extracellular milieu of the cell. This chapter deals with the cytoplasmic membrane proteome of Bacillus subtilis. Specifically, we address current views on the roles of membrane proteins in homeostasis, their membrane targeting and retention signals, machinery for membrane insertion, localization of membrane proteins, membrane protein degradation and, finally, the identified and predicted composition of the B. subtilis membrane proteome. Known mechanisms and knowledge gaps are discussed to give a comprehensive overview of the ins and outs of the B. subtilis membrane proteome.
10. The Cell Wall of Bacillus subtilis
The cell wall of Bacillus subtilis is a rigid structure on the outside of the cell that forms the first barrier between the bacterium and the environment, and at the same time maintains cell shape and withstands the pressure generated by the cell's turgor. In this chapter, the chemical composition of peptidoglycan, teichoic and teichuronic acids, the polymers that comprise the cell wall, and the biosynthetic pathways involved in their synthesis will be discussed, as well as the architecture of the cell wall. B. subtilis has been the first bacterium for which the role of an actin-like cytoskeleton in cell shape determination and peptidoglycan synthesis was identified and for which the entire set of peptidoglycan synthesizing enzymes has been localised. The role of the cytoskeleton in shape generation and maintenance will be discussed and results from other model organisms will be compared to what is known for B. subtilis. Finally, outstanding questions in the field of cell wall synthesis will be discussed.
11. Genomics and Cellular Biology of Endospore Formation
Bacteria of the genera Bacillus and Clostridium can be found in two distinct states. In the vegetative state, bacteria are metabolically active and use available nutrients to grow and divide by binary fission, a process that generates two identical daughter cells. By contrast, when nutrients are scarce, a developmental program of endospore formation (sporulation) is initiated, resulting in the production of highly resistant spores. In the spore state, bacteria are metabolically dormant, and their genetic material, protected in the core of the spore, can endure a variety of challenges, including exposure to radiation, elevated temperatures and noxious chemicals. Sporulation is a complex process, which requires the generation of two distinct cell types: a forespore and a larger mother cell. The progression of the developmental program is controlled by two exquisitely regulated cell type-specific lines of gene expression that run in parallel and are connected at the post-translational level. Various genetic screens and genome-wide transcriptional analyses have identified more than 600 genes that are expressed in the course of sporulation. The function of several of these genes has been characterized in detail and subcellular localization data are available for at least 90 sporulation proteins. Thus, sporulation constitutes one of the best characterized developmental programs at the molecular and cellular levels.
12. Multicellularity and Social Behaviour in Bacillus subtilis
José Eduardo González-Pastor
Most of the knowledge about Bacillus subtilis derives from studies of laboratory strains growing as planktonic cultures, in which all the individual cells are considered identical. Recently, the study of a natural and undomesticated isolate has revealed that B. subtilis cells display multicellular and social features that were lost in the laboratory strains, which were selected over generations for easy manipulation. In undomesticated strains, certain environmental conditions trigger cells of this bacterium to form multicellular communities where sporulation takes place, and to exhibit some particular social traits, like swarming motility and the fratricide of sibling cells or cannibalism during sporulation. Interestingly, some of these behaviours are based in the heterogeneity of the B. subtilis populations, which has been determined using cell biological techniques like fluorescence and light microscopy. This chapter outlines the genetic pathways governing the transition from a unicellular to a multicellular stage, swarming motility and cannibalism. The biological relevance of these alternative lifestyles is discussed.
13. Competence and Transformation
Competence for transformation enables bacteria to take up exogenous DNA. The imported DNA can integrate into the chromosome by homologous recombination or anneal to form a self replicating plasmid. Development of competence in Bacillus subtilis is tightly regulated as a function of cell density during entry into the stationary growth phase. Additionally, competence occurs only in a small subpopulation of B. subtilis cells. Development of competence is switch-like and controlled by the concentration of the master regulator ComK. Quantitative analysis at the single cell level in conjunction with mathematical modeling allowed understanding of development and decline of competence at the systems level. In the current model, a complex regulatory network maintains the concentration of ComK below a threshold concentration for switching into the competent state. In the stationary growth phase, noisy expression of ComK triggers competence development as individual cells reach the threshold concentration due to random fluctuations. Competent cells express specialized proteins (late competence proteins) for binding, importing, and recombining external DNA. Cytosolic and transmembrane proteins accumulate at a single or both cell poles. Application of external DNA triggers movement of various proteins involved in recombination away from the pole, most likely undergoing search for homologous regions on the chromosome. These findings provide good evidence for a concerted action of DNA import and recombination, promoting the idea that a spatially organized and modular multiprotein machine has evolved for efficient transformation. This machine powers efficient and irreversible DNA import and can work against considerable external forces.
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(EAN: 9781904455974 9781912530489 Subjects: [microbiology] [bacteriology] [medical microbiology] [molecular microbiology] [genomics] )