from Karlijn C. Bastiaansen, Wilbert Bitter and María A. Llamas writing in Bacterial Regulatory Networks:
Gene expression in bacteria is mainly controlled at the level of transcription initiation. To achieve this process a number of different mechanisms have evolved, one of which is the utilization of alternative sigma factors. Sigma factors are small proteins that associate with the RNA polymerase core enzyme (RNAPc) and direct it to specific promoter sequences, where they initiate gene transcription. Bacteria are able to regulate transcription initiation by synthesizing and activating different sigma factors that recognize different promoter consensus sequences. The largest group of alternative sigma factors consists of the so-called extracytoplasmic function (ECF) sigma factors that regulate gene expression in response to cell envelope stresses or environmental stimuli. The activity of ECF sigma factors is controlled by anti-sigma factors and a complex cascade of regulated (proteolytic) modifications. In gram-negative bacteria, ECF sigma factors are also controlled by cell-surface signalling (CSS), a regulatory system that includes an outer membrane receptor in the signal transduction pathway. In this chapter we will discuss the general composition and function of ECF sigma factors and their role in cell envelope stress responses and CSS.
Further reading: Bacterial Regulatory Networks Related publications
from Moshe Szyf writing in Epigenetics: A Reference Manual:
The DNA molecule contains within its chemical structure two layers of information. The DNA sequence that bears the ancestral genetic information and the pattern of distribution of covalently bound methyl groups to cytosines in DNA. While the genetic information is similar in all tissues in the individual, the pattern of distribution of methylation across the genome is cell-type specific. DNA methylation is an important regulator of gene function. Recent data that will be discussed here that supports the hypothesis that DNA methylation is a reversible biological signal. This expands the potential role of DNA methylation beyond embryogenesis to other time-points in life and to post mitotic tissues such as the brain. DNA methylation is proposed to act as a genomic response to both physical and social signals from the environment at different time points in life and to serve as a genomic memory of these exposures at different time scales, stably altering gene expression programming and thus modulating the physical and behavioral phenotypes to respond to these environments. It is hypothesized that DNA methylation provides within the structure of the DNA a dynamic interface between the changing world around us and the relatively fixed and stable genome.
Further reading: Epigenetics: A Reference Manual
from Eivind Almaas, Per Bruheim, Rahmi Lale and Svein Valla writing in Systems Microbiology: Current Topics and Applications:
The functional repertoire of an organism's metabolic network is closely linked to its phenotype and potential for utility in metabolic engineering applications. In this chapter, we discuss a systems biology view of Escherichia coli metabolism by integrating current genome-scale computational modelling approaches with available molecular genetics tools, as well as the experimental framework for metabolite and metabolic flux determination.
Further reading: Systems Microbiology Related publications
from J. Maxwell Dow, Yvonne McCarthy, Karen O'Donovan, Delphine Caly and Robert P. Ryan writing in Bacterial Regulatory Networks:
Cyclic di-GMP is now recognised as an almost universal second messenger in eubacteria that acts to regulate a wide range of functions including developmental transitions, adhesion, biofilm formation, motility and the synthesis of virulence factors. Cyclic di-GMP is synthesised from two GTP molecules by diguanylate cyclases that have a GGDEF domain and degraded by phosphodiesterases with either an EAL or HD-GYP domain. These proteins often have associated signal input domains, suggesting that their enzymatic activity may be modulated by different environmental or cellular cues. Cyclic di-GMP exerts a regulatory action through binding to diverse receptors that include a small protein domain called PilZ, transcription factors, enzymatically-inactive GGDEF, EAL or HD-GYP domains and riboswitches. The multiplicity of GGDEF, EAL and HD-GYP proteins together with a range of receptors within the same bacterial cell indicates the considerable complexity of cyclic di-GMP signalling. This has led to the concept of discrete pools of the nucleotide that are generated locally and act to influence intimately associated targets. A number of signalling proteins may be organised in a regulatory network to control a common function(s). Understanding cyclic di-GMP signalling may afford strategies for inhibition of biofilm formation and virulence factor synthesis in bacterial pathogens.
Further reading: Bacterial Regulatory Networks Related publications
from John M. Pfeffer, Patrick J. Moynihan, Chelsea A. Clarke, Chris Vandenende and Anthony J. Clarke writing in Bacterial Glycomics: Current Research, Technology and Applications:
Lytic transglycosylases are an important class of bacterial enzymes that act on peptidoglycan with the same substrate specificity as lysozyme. Unlike the latter enzymes however, the lytic transglycosylases are not hydrolases, but instead cleave the glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anydromuramyl product. They are ubiquitous in bacteria which produce a complement of different forms that are responsible for creating space within the peptidoglycan sacculus for its biosynthesis and recycling, cell division, and the insertion of cell-envelope spanning structures, such as flagella and secretion systems. Given their catastrophic autolytic potential, the activity of lytic transglycosylases must be tightly controlled within the producing cells. Three modes of control at the enzymatic level have been identified: the modification of substrate, membrane association and complex formation, and the production of proteinaceous inhibitors. These modes of control and their potential as new targets for antibacterials are discussed.
Further reading: Bacterial Glycomics: Current Research, Technology and Applications
from Anne N. Reid and Leslie Cuthbertson writing in Bacterial Glycomics: Current Research, Technology and Applications:
Capsular polysaccharides (CPSs) and exopolysaccharides (EPSs) enhance bacterial survival in the environment, contribute to symbiotic interactions between plants and bacteria, and mediate interactions between plant and animal pathogens and their hosts. Bacteria express a wide array of CPS and EPS structures that are assembled by one of three distinct mechanisms. The Wzy-dependent polymerization system is characterized by the synthesis of lipid-linked repeat units in the cytoplasm, and their block-wise polymerization at the periplasmic face of the inner membrane. The resulting polymer is transported across the outer membrane (in Gram-negative organisms) via a channel formed by an outer membrane polysaccharide export (OPX) protein. The ATP-binding cassette (ABC) transporter-dependent system is defined by the synthesis of full-length CPS chains in the cytoplasm, their ABC transporter-dependent export across the inner membrane, and their subsequent transport across the outer membrane, presumably via a channel formed by an OPX protein. In the synthase-dependent system, a single enzyme achieves polymer initiation, synthesis and export across the membrane. This chapter describes these modes of CPS and EPS assembly, highlighting recent findings and identifying areas where further research is warranted.
Further reading: Bacterial Glycomics: Current Research, Technology and Applications