Bacillus: Cellular and Molecular Biology | Book
Caister Academic Press
University of Freiburg, Germany
xvi + 454
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Bacillus subtilis is one of the best understood prokaryotes in terms of molecular biology and cell biology. Its superb genetic amenability and relatively large size have provided powerful tools to investigate a bacterium in all possible aspects. Recent improvements in technology have provided novel and amazing insights into the dynamic structure of this single cell organism. The organism is a model for differentiation, gene/protein regulation and cell cycle events in bacteria.
This book presents an overview of the most recent exciting new research fields and provides a picture of the major cytological aspects of a model bacterium. The authors present the most recent knowledge on topics such as the replication and segregation of the chromosome, cell division, replication and growth, the cell cycle, transcription, translation, regulation, the actin cyctoskeleton, the cell membrane and cell wall, biofilm formation and sporulation. Also covered are DNA repair, the regulation of transcription through RNA molecules, and the regulation of protein activity through proteolysis. The authors seamlessly merge the fields of bacterial cell biology and molecular biology to provide an integral view of the bacterial cell, providing an understanding of the way a bacterial cell functions as a whole entity and in 3D, i.e. how it is spatially organized, and even how bacterial cells communicate with each other, or give their life for the sake of the whole community.
An essential book for anyone interested in Bacillus, cell biology or bacterial genetics and molecular biology.
"This will be valuable to researchers in the area of bacterial genetics, protein synthesis, cell division and sporulation. It may be appropriate for advanced graduate students as well. It provides a valuable resource of recent data in one place." from Doodys (2007)
"a most comprehensive and authoritative account on the latest research ... perfect as a reference for advanced undergraduate and graduate-level courses ... A must read for anybody interested in just about any aspect of bacterial research." from Internat. Microbiol. (2007) 10: 227
"This book is highly recommended ... Suited for both students and highly-learned professionals!!" from J. Microbiol. Methods (2007) 71: 90-91
"... a compulsory purchase for specialist research laboratories." from SGM Microbiology Today (2007)
Table of contents
1. Replication of the Bacillus subtilis Chromosome
Philippe Noirot, Patrice Polard and Marie-Françoise Noirot-Gros
Eubacteria have evolved multicomponent protein machines, termed replisomes, that 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 possible 'roadblocks' encountered on the DNA template, and c) promote 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 the 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
Humberto Sanchez, Begoña Carrasco, Silvia Ayora and Juan C. Alonso
All organisms have developed a variety of repair mechanisms, with recombination being the ultimate step for DNA repair and for promoting re-establishment of replication forks that are stalled or collapsed. This review summarises our current knowledge on the cellular response to DNA damage in Bacillus subtilis cells. Cytological approaches now confirm previous observations from genetic and biochemical analyses, which suggested that recombinational repair, and especially double-strand break repair, is choreographed by multi-protein complexes that are organised into focal assemblies tightly regulated and coordinated with other essential processes, such as DNA replication, and chromosomal segregation.
3. Chromosome Segregation
Peter L. Graumann
The Bacillus subtilis chromosome with its 2 mm contour length is compacted into a 1 µm large nucleoid, and sister chromosomes are separated into opposite cell poles during ongoing replication through an active intracellular machinery. The machinery consists of several elements that have a defined subcelluar localization, and appear to work hand in hand. Replication occurs in the centrally located replication apparatus that optimally positions duplicated chromosome regions to be moved towards opposite cell poles, through an as yet unknown motor that may involve bacterial actin-like filaments. Separated regions appear to be compacted within each cell half by the SMC condensation complex, which forms subcellular assemblies within each cell half. Dedicated recombination enzymes, topoisomerases and a DNA pump ensure complete separation of occurring chromosome dimers, chromosome termini that are intertwined or chromosomes that may be trapped within the division septum, respectively.
4. Cell Division
Cell division in rod-shaped bacteria like Bacillus subtilis is carried out by a contractile protein ring, known as the divisome or septalsome, which is made up of about a dozen different polypeptides. This sophisticated macromolecular machine, which is centered around the tubulin-like protein FtsZ, is capable of promoting the coordinated invagination of the cell membrane and cell wall to create the so-called division septum. The goal of this chapter is to provide an overview of the mechanism of septum formation in B. subtilis. Emphasis will be placed on describing the properties of the individual division proteins and how they assemble into the divisome complex, and on a discussion of the regulatory mechanisms that ensure that septum formation will happen with great spatial and temporal precision at every cell cycle. In addition, the peculiar asymmetric division that happens during B. subtilis sporulation will be described.
5. The Organisation of Transcription and Translation
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 of transcription and translation 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
In this chapter I will focus on regulatory mechanisms in Bacillus subtilis that are mediated through noncoding RNAs. Traditionally, bacterial genetic regulation is assumed to occur at the level of transcription initiation through the use of transcription factors. Regulatory mechanisms that take place post-transcription initiation are treated as anomalies - as exceptions to the rule. Although it is likely that regulation of transcription initiation by global factors will constitute the majority of overall bacterial regulation, the actual degree to which posttranscriptional regulation occurs is still unknown. As testament to this fact, the past several years have led to a rapid expansion in the understanding of posttranscriptional regulation in B. 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, regulation at the posttranscriptional level is a vital layer of bacterial genetic circuitry that still remains to be fully revealed.
7. General and Regulatory Proteolysis in Bacillus subtilis
Kü ad Turgay
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 B. 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 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 and MamK proteins) are involved in cell shape determination, DNA segregation, cell polarity, 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 helical structures that 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 cytoskeleton and the extracellular proteins that carry out cell wall biosynthesis and degradation, probably linked through the MreCD and/or other membrane proteins. 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, Girbe Buist, Mark J.J.B. Sibbald, Jessica C. Zweers, Jean-Yves F. Dubois and Harold Tjalsma
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 role 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 current knowledge gaps are discussed in order to give a comprehensive overview of the in's and out's 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, the bacterium is metabolically active and uses 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 a highly resistant spore. In the spore state, the bacterium is metabolically dormant, and its genetic material, protected in the core of the spore, can endure a variety of challenges, including radiation, heat and 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-transcriptional 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 more than 70 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.
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(EAN: 9781904455127 9781913652296 Subjects: [bacteriology] [microbiology] [molecular microbiology] [genomics] [environmental microbiology] )