Highlights • RNA-seq has become the method of choice for bacterial transcriptomics. • Differential RNA-seq (dRNA-seq) distinguishes primary and processed transcripts. • dRNA-seq provides global TSS maps and other transcriptome information. • dRNA-seq is generic and has been applied to many different species.
Highlights • Antibiotics are used extensively in the swine industry. • Pigs can be a source of antibiotic resistant organisms that impact on human health. • Extended spectrum β-lactamase (ESBL) producing bacteria are an increasing problem. • Resistance genes on plasmids enhance transmissibility of ESBLs. • Antibiotic resistant strains of zoonotic organisms such as methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus suis are of concern.
Highlights • Cryptococcus has an unusual morphological transition in vivo to generate enlarged titan cells. • Titan cells are greater than 15 μm in diameter, have a thick cell wall, and highly cross-linked capsule. • Titan cells are produced in both mammalian and invertebrate infections. • Titan cells are important for cryptococcal pathogenesis.
Extracytoplasmic function sigma factors (ECFs) represent a fundamental and widely distributed principle of bacterial signal transduction that connects the perception of a stimulus (input) with the induction of an appropriate set of genes (output). In recent years, comparative genomics analyses have not only allowed a systematic and functional classification of ECFs but also indicated the presence of numerous novel and widely conserved mechanisms of ECF-dependent signaling. Some of these novel systems have been experimentally characterized and uncovered unique features not previously observed. These studies demonstrate that ECF-dependent signaling is much more versatile and diverse than has been appreciated before. They also indicate that the majority of mechanisms that regulate ECF activity still remain to be discovered and characterized.
Following the pioneering screens for small regulatory RNAs (sRNAs) in Escherichia coli in 2001, sRNAs are now being identified in almost every branch of the eubacterial kingdom. Experimental strategies have become increasingly important for sRNA discovery, thanks to increased availability of tiling arrays and fast progress in the development of high-throughput cDNA sequencing (RNA-Seq). The new technologies also facilitate genome-wide discovery of potential target mRNAs by sRNA pulse-expression coupled to transcriptomics, and immunoprecipitation with RNA-binding proteins such as Hfq. Moreover, the staggering rate of new sRNAs demands mechanistic analysis of target regulation. We will also review the available toolbox for wet lab-based research, including in vivo and in vitro reporter systems, genetic methods and biochemical co-purification of sRNA interaction partners.
Highlights ► Characterization of mucosal biofilms. ► Current models to study mucosal biofilms: vaginal, oral mucosal and denture biofilm model. ► Bacterial– C. albicans interactions. ► Host immune responses in biofilms.
Highlights • The yeast C. albicans is a commensal and pathogen of humans and other mammals. • Iron and zinc are sequestered in mammalian blood and tissues but not in the gut. • C. albicans virulence requires specialized mechanisms for acquiring host iron and zinc. • Limitation of iron uptake promotes C. albicans commensalism in the gut.
Highlights • Hsp90 governs fungal drug resistance, morphogenesis and virulence. • Hsp90 inhibitors in clinical development enhance antifungal efficacy in vivo. • Chaperone network components provide new targets to minimize host toxicity. • Co-chaperones, lysine deacetylases, kinases, and phosphatases are key effectors. • Hsp90 provides a fungal Achilles’ heel, with broad therapeutic potential.
The signal transduction pathway governing the sigma(E)-dependent cell envelope stress response in Escherichia coli communicates information from the periplasm to sigma(E) in the cytoplasm via a regulated proteolytic cascade that results in the destruction of the membrane-bound antisigma factor, RseA, and the release of sigma(E) to direct transcription. Regulated proteolysis is used for signal transduction in all domains of life, and these pathways bear remarkable similarities in their architecture and the proteases involved. Work with the pathway governing the sigma(E) response has elucidated key design principles that ensure a rapid yet graded response that is buffered from inappropriate activation. Structural and biochemical studies of the proteases that mediate signal transduction reveal the molecular underpinnings enabling this design.
Highlights • Mass spectrometry techniques are powerful tools in studying specialized metabolites production from microbial colonies. • Direct analysis of microbial colonies can be used for clinical strain identification. • Microbial imaging mass spectrometry is able to visualize surface and secreted metabolites from microbial colonies. • Real-time mass spectrometry techniques enable the direct mass spectrometric interrogation of living microbial colonies. • Tandem mass spectrometry based molecular networking and emerging algorithms enable global molecular analysis of microbial metabolites.
Recently published work indicates that reversible Nε -lysine ( Nε -Lys) acetylation of proteins in bacteria may be as diverse, and as important for cellular function, as it has been reported in eukaryotes for the last five decades. In addition to biochemical and genetic approaches, proteomic studies have identified Nε -Lys acetylation of proteins and enzymes involved in diverse cellular activities such as transcription, translation, stress response, detoxification, and especially carbohydrate and energy metabolism. These findings provide a platform for elucidating the molecular mechanisms behind modulation of enzyme activity by Nε -Lys acetylation, as well as for understanding how the prokaryotic cell maintains homeostasis in a changing environment.
The signal transduction pathway governing the σE -dependent cell envelope stress response in Escherichia coli communicates information from the periplasm to σE in the cytoplasm via a regulated proteolytic cascade that results in the destruction of the membrane-bound antisigma factor, RseA, and the release of σE to direct transcription. Regulated proteolysis is used for signal transduction in all domains of life, and these pathways bear remarkable similarities in their architecture and the proteases involved. Work with the pathway governing the σE response has elucidated key design principles that ensure a rapid yet graded response that is buffered from inappropriate activation. Structural and biochemical studies of the proteases that mediate signal transduction reveal the molecular underpinnings enabling this design.
The Streptomyces life cycle encompasses three well established developmental stages: vegetative hyphae, aerial hyphae and spores. Many regulators governing the transitions between these life cycle stages have been identified, and recent work is shedding light on their specific functions. A new discovery has shown Streptomyces can deviate from this classic life cycle through a process termed 'exploration', where cells rapidly traverse solid surfaces. Exploration does not require any of the traditional developmental regulators, and therefore provides an exciting new context in which to uncover novel developmental pathways. Here, we summarize our understanding of how Streptomyces exploration is controlled, and we speculate on how insight into classical regulation and stress response systems can inform future research into the regulation of exploratory growth.