Diversity, classification and evolution of CRISPR-Cas systems.
Abstract The bacterial and archaeal CRISPR-Cas systems of adaptive immunity show remarkable diversity of protein composition, effector complex structure, genome locus architecture and mechanisms of adaptation, pre-CRISPR (cr)RNA processing and interference. The CRISPR-Cas systems belong to two classes, with multi-subunit effector complexes in Class 1 and single-protein effector modules in Class 2. Concerted genomic and experimental efforts on comprehensive characterization of Class 2 CRISPR-Cas systems led to the identification of two new types and several subtypes. The newly characterized type VI systems are the ...
Source: Current Opinion in Microbiology - June 9, 2017 Category: Microbiology Authors: Koonin EV, Makarova KS, Zhang F Tags: Curr Opin Microbiol Source Type: research

Beyond the canonical strategies of horizontal gene transfer in prokaryotes.
, Muniesa M Abstract Efforts to identify and characterize strategies for horizontal gene transfer (HGT) in prokaryotes could have overlooked some mechanisms that do not entirely fit in with the canonical ones most often described (conjugation of plasmids, phage transduction and transformation). The difficulty in distinguishing the different HGT strategies could have contributed to underestimate their real extent. Here we review non classical HGT strategies: some that require mobile genetic elements (MGEs) and others independent of MGE. Among those strategies that require MGEs, there is a range of newly reported, h...
Source: Current Opinion in Microbiology - June 7, 2017 Category: Microbiology Authors: García-Aljaro C, Ballesté E, Muniesa M Tags: Curr Opin Microbiol Source Type: research

Guaranteeing a captive audience: coordinated regulation of gene transfer agent (GTA) production and recipient capability by cellular regulators.
Abstract Gene transfer agents (GTAs) are bacteriophage-like particles produced by many prokaryotes. Several members of the Alphaproteobacteria produce a class of genetically-related GTAs that is best studied in Rhodobacter capsulatus. DNA transfer by the R. capsulatus GTA (RcGTA) combines aspects of both transduction and natural transformation, as recipient cells require a natural transformation-like system to incorporate donated DNA. The genes involved in RcGTA production and recipient capability are located at multiple loci in the bacterial genome; however, a conserved phosphorelay containing the response regula...
Source: Current Opinion in Microbiology - June 6, 2017 Category: Microbiology Authors: Westbye AB, Beatty JT, Lang AS Tags: Curr Opin Microbiol Source Type: research

Making serine integrases work for us.
This article summarizes our current knowledge of serine integrase structure and mechanism, then outlines key factors that affect the performance of these phage recombination systems. Recently published studies, that have expanded the repertoire of available systems and reveal system-specific characteristics, will help us to choose the best integrases for envisaged applications. PMID: 28599144 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - June 6, 2017 Category: Microbiology Authors: Stark WM Tags: Curr Opin Microbiol Source Type: research

Evolution of commensal bacteria in the intestinal tract of mice.
rdo I Abstract Hundreds of different bacterial species inhabit our intestines and contribute to our health status, with significant loss of species diversity typically observed in disease conditions. Within each microbial species a great deal of diversity is hidden and such intra-specific variation is also key to the proper homeostasis between the host and its microbial inhabitants. Indeed, it is at this level that new mechanisms of antibiotic resistance emerge and pathogenic characteristics evolve. Yet, our knowledge on intra-species variation in the gut is still limited and an understanding of the evolutionary m...
Source: Current Opinion in Microbiology - June 4, 2017 Category: Microbiology Authors: Sousa A, Frazão N, Ramiro RS, Gordo I Tags: Curr Opin Microbiol Source Type: research

Towards a taxonomy of conjugative plasmids.
Abstract Conjugative plasmids are the keystone of horizontal gene transfer. Metagenomic research and clinical understanding of plasmid transmission beg for a taxonomical approach to conjugative plasmid classification. Up to now, a meaningful classification was difficult to achieve for lack of appropriate analytical tools. The advent of the genomic era revolutionized the landscape, offering a plethora of plasmid sequences as well as bioinformatic analytical tools. Given the need and the opportunity, in view of the available evidence, a taxonomy of conjugative plasmids is proposed in the hope that it will leverage p...
Source: Current Opinion in Microbiology - June 3, 2017 Category: Microbiology Authors: Fernandez-Lopez R, Redondo S, Garcillan-Barcia MP, de la Cruz F Tags: Curr Opin Microbiol Source Type: research

Fungal diversity is negatively affected by habitat fragmentation: a meta-analysis.
Abstract Fungi are ubiquitous organisms around the world with important roles in ecosystem functioning and services, but knowledge about how habitat fragmentation affect fungal diversity is spread in different trophic groups, studied regions and experimental approaches. We performed a meta-analysis to synthesize the available information to glimpse general patterns of habitat fragmentation effects on fungal diversity. The habitat fragmentation process consistently affect fungal diversity through isolation, area size and increasing edge proportion, albeit this trend may differ between both the type of response vari...
Source: Current Opinion in Microbiology - June 1, 2017 Category: Microbiology Authors: Grilli G, Longo S, Huais PY, Pereyra M, Verga E, Urcelay C, Galetto L Tags: Curr Opin Microbiol Source Type: research

Themes and variations in gene regulation by extracytoplasmic function (ECF) sigma factors.
Abstract The ECF sigma family was identified 23 years ago as a distinct group of σ(70)-like factors. ECF sigma factors have since emerged as a major form of bacterial signal transduction that can be grouped into over 50 phylogenetically distinct subfamilies. Advances in our understanding of these sigma factors and the signaling pathways governing their activity have elucidated conserved features as well as aspects that have evolved over time. All ECF sigma factors are predicted to share a common streamlined domain structure and mode of promoter interaction. The activity of most ECF sigma factors is controlle...
Source: Current Opinion in Microbiology - May 30, 2017 Category: Microbiology Authors: Sineva E, Savkina M, Ades SE Tags: Curr Opin Microbiol Source Type: research

Transposable phages, DNA reorganization and transfer.
Abstract Transposable bacteriophages have long been known to necessarily and randomly integrate their DNA in their host genome, where they amplify by successive rounds of replicative transposition, profoundly reorganizing that genome. As a result of such transposition, a conjugative element (plasmid or genomic island), can either become integrated in the chromosome or receive chromosome segments, which can then be transferred to new hosts by conjugation. In recent years, more and more transposable phages have been isolated or detected by sequence similarity searches in a wide range of bacteria, supporting the idea...
Source: Current Opinion in Microbiology - May 25, 2017 Category: Microbiology Authors: Toussaint A, Rice PA Tags: Curr Opin Microbiol Source Type: research

Temperate bacteriophages as regulators of host behavior.
Abstract Bacteriophages are ubiquitous and affect most facets of life, from evolution of bacteria, through ecology and global biochemical cycling to human health. The interactions between phages and bacteria often lead to biological novelty and an important milestone in this process is the ability of phages to regulate their host's behavior. In this review article, we will focus on newly reported cases that demonstrate how temperate phages regulate bacterial gene expression and behavior in a variety of bacterial species, pathogenic and environmental. This regulation is mediated by diverse mechanisms such as transc...
Source: Current Opinion in Microbiology - May 22, 2017 Category: Microbiology Authors: Argov T, Azulay G, Pasechnek A, Stadnyuk O, Ran-Sapir S, Borovok I, Sigal N, Herskovits AA Tags: Curr Opin Microbiol Source Type: research

An evolutionary perspective on plasmid lifestyle modes.
n T Abstract Plasmids are extra-chromosomal genetic elements whose ecology and evolution depend on their genetic repertoire and interaction with the host. We review the events that lead to transitions between plasmid lifestyle modes - invasion, host range, plasmid persistence and adaptation - from a plasmid perspective. Plasmid lifestyle is determined by various traits, including mobility, stability and indispensability that vary in their magnitude. Transitions between the plasmid lifestyles, invasion, host range, plasmid persistence and adpatation, are caused by the interplay between plasmid traits and host biolo...
Source: Current Opinion in Microbiology - May 21, 2017 Category: Microbiology Authors: Hülter N, Ilhan J, Wein T, Kadibalban AS, Hammerschmidt K, Dagan T Tags: Curr Opin Microbiol Source Type: research

Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer.
Abstract Bacteriophages and archaeal viruses contribute, through lysogenic conversion or transduction, to the horizontal transfer of genetic material between microbial genomes. Recent genomics, metagenomics, and single cell studies have shown that lysogenic conversion is widespread and provides hosts with adaptive traits often associated with biotic interactions. The quantification of the evolutionary impact of transduction has lagged behind and requires further theoretical and experimental work. Nevertheless, recent studies suggested that generalized transduction plays a role in the transfer of antibiotic resista...
Source: Current Opinion in Microbiology - May 17, 2017 Category: Microbiology Authors: Touchon M, Moura de Sousa JA, Rocha EP Tags: Curr Opin Microbiol Source Type: research

Plant-insect-pathogen interactions: a naturally complex m énage à trois.
Plant-insect-pathogen interactions: a naturally complex ménage à trois. Curr Opin Microbiol. 2017 May 06;37:54-60 Authors: Franco FP, Moura DS, Vivanco JM, Silva-Filho MC Abstract Under environmental conditions, plants are constantly exposed to a wide range of biotic interactions, which include insects, and pathogens. Usually scientists are tempted to study each association individually, which reduces the complexity of the interaction. This restricted view of the problem does not consider that plants are the ballroom in which a multitude of organisms are constantly interacting with each ...
Source: Current Opinion in Microbiology - May 6, 2017 Category: Microbiology Authors: Franco FP, Moura DS, Vivanco JM, Silva-Filho MC Tags: Curr Opin Microbiol Source Type: research

The impact of nutrition on intestinal bacterial communities.
Abstract What we eat influences the species composition of our gut microbiota. This is not only because diet composition determines the supply of substrates for microbial growth (in the form of dietary residue, mainly fibre, that reaches the large intestine) but also because of impacts on gut transit and the gut environment. In turn the metabolic activities of the gut microbiota, which have important health consequences, are influenced by diet and diet-driven changes in microbiota composition. Better understanding of the metabolic capabilities and host-interactions of dominant members of the gut microbiota will ai...
Source: Current Opinion in Microbiology - May 6, 2017 Category: Microbiology Authors: Flint HJ, Duncan SH, Louis P Tags: Curr Opin Microbiol Source Type: research

Mechanisms of stabilization of integrative and conjugative elements.
Abstract Integrative and conjugative elements (ICEs) are nearly ubiquitous in microbial genomes and influence their evolution by providing adaptive functions to their host and by enhancing genome plasticity and diversification. For a long-time, it has been assumed that by integrating into the chromosome of their host, these self-transmissible elements were passively inherited in subsequent generations. Recent findings point to a much more complex story that includes multiple strategies used by ICEs to leverage maintenance in cell populations such as transient replication, active partition of the excised circular i...
Source: Current Opinion in Microbiology - May 5, 2017 Category: Microbiology Authors: Burrus V Tags: Curr Opin Microbiol Source Type: research

Mobile self-splicing introns and inteins as environmental sensors.
Abstract Self-splicing introns and inteins are often mobile at the level of the genome. Although these RNA and protein elements, respectively, are generally considered to be selfish parasites, group I and group II introns and inteins can be triggered by environmental cues to splice and/or to mobilize. These cues include stressors such as oxidizing agents, reactive oxygen and nitrogen species, starvation, temperature, osmolarity and DNA damage. Their sensitivity to these stimuli leads to a carefully choreographed dance between the mobile element and its host that is in tune with the cellular environment. This respo...
Source: Current Opinion in Microbiology - May 5, 2017 Category: Microbiology Authors: Belfort M Tags: Curr Opin Microbiol Source Type: research

Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery.
in EV Abstract A casposon, a member of a distinct superfamily of archaeal and bacterial self-synthesizing transposons that employ a recombinase (casposase) homologous to the Cas1 endonuclease, appears to have given rise to the adaptation module of CRISPR-Cas systems as well as the CRISPR repeats themselves. Comparison of the mechanistic features of the reactions catalyzed by the casposase and the Cas1-Cas2 heterohexamer, the CRISPR integrase, reveals close similarity but also important differences that explain the requirement of Cas2 for integration of short DNA fragments, the CRISPR spacers. PMID: 28472712 [...
Source: Current Opinion in Microbiology - May 1, 2017 Category: Microbiology Authors: Krupovic M, Béguin P, Koonin EV Tags: Curr Opin Microbiol Source Type: research

In and out-contribution of natural transformation to the shuffling of large genomic regions.
Abstract Naturally competent bacteria can pull free DNA from their surroundings. This incoming DNA can serve various purposes, ranging from acting as a source of nutrients or DNA stretches for repair to the acquisition of novel genetic information. The latter process defines the natural competence for transformation as a mode of horizontal gene transfer (HGT) and led to its discovery almost a century ago. However, although it is widely accepted that natural competence can contribute to the spread of genetic material among prokaryotes, the question remains whether this mode of HGT can foster the transfer of larger ...
Source: Current Opinion in Microbiology - April 27, 2017 Category: Microbiology Authors: Blokesch M Tags: Curr Opin Microbiol Source Type: research

The shrinking human gut microbiome.
Abstract Mammals harbor complex assemblages of gut bacteria that are deeply integrated with their hosts' digestive, immune, and neuroendocrine systems. Recent work has revealed that there has been a substantial loss of gut bacterial diversity from humans since the divergence of humans and chimpanzees. This bacterial depauperation began in humanity's ancient evolutionary past and has accelerated in recent years with the advent of modern lifestyles. Today, humans living in industrialized societies harbor the lowest levels of gut bacterial diversity of any primate for which metagenomic data are available, a condition...
Source: Current Opinion in Microbiology - April 27, 2017 Category: Microbiology Authors: Moeller AH Tags: Curr Opin Microbiol Source Type: research

Selective adaptor dependent protein degradation in bacteria.
Abstract Energy dependent proteolysis is essential for all life, but uncontrolled degradation leads to devastating consequences. In bacteria, oligomeric AAA+ proteases are responsible for controlling protein destruction and are regulated in part by adaptor proteins. Adaptors are regulatory factors that shape protease substrate choice by either restricting or enhancing substrate recognition in several ways. In some cases, protease activity or assembly itself requires adaptor binding. Adaptors can also alter specificity by acting as scaffolds to tether particular substrates to already active proteases. Finally, hier...
Source: Current Opinion in Microbiology - April 27, 2017 Category: Microbiology Authors: Kuhlmann NJ, Chien P Tags: Curr Opin Microbiol Source Type: research

Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world.
Abstract The Th17 cell composition in the murine gut is strikingly dependent on the presence of the commensal segmented filamentous bacteria (SFB). SFB potently stimulates innate and adaptive immune responses and protects the host from pathogens both in and outside of the gut, partly due to its unique ability to promote a Th17-fostering environment. Recent work has highlighted the role of the tight adherence of SFB to the intestinal surface in mediating the potent immunostimulatory potential of SFB. Progress has also been made in our understanding of how SFB fosters this protective immune environment on the cellul...
Source: Current Opinion in Microbiology - April 25, 2017 Category: Microbiology Authors: Schnupf P, Gaboriau-Routhiau V, Sansonetti PJ, Cerf-Bensussan N Tags: Curr Opin Microbiol Source Type: research

Managing the plant microbiome for biocontrol fungi: examples from Hypocreales.
Abstract Feeding an increasing global population requires continued improvements in agricultural efficiency and productivity. Meeting estimated future production levels requires the adoption of practices that increase output without environmental degradation associated with external inputs to supplement nutrition or control pests. Enriching the community of microbes associated with plants in agricultural systems for those providing ecosystem services such as pest control is one possible component towards achieving sustainable productivity increases. In this review we explore the current state of knowledge for Hypo...
Source: Current Opinion in Microbiology - April 22, 2017 Category: Microbiology Authors: Kepler RM, Maul JE, Rehner SA Tags: Curr Opin Microbiol Source Type: research

Membrane vesicles and horizontal gene transfer in prokaryotes.
Abstract Membrane vesicles (MVs) are released from all living cells. MVs are lumen-containing spheres of lipid-bilayers derived from the cell surface. MVs are biologically active and contain various components, including genetic material. Both chromosomal and plasmid DNA, as well as different types of RNA have been detected in MVs. Vesicle-mediated transfer of genes coding for antibiotic resistance, virulence and metabolic traits has been reported in Gram-negative and Gram-positive bacteria and in Archaea. MVs can persist over time in natural environments. Here we review the characteristics of and the role of MVs ...
Source: Current Opinion in Microbiology - April 22, 2017 Category: Microbiology Authors: Domingues S, Nielsen KM Tags: Curr Opin Microbiol Source Type: research

Ecological patterns of seed microbiome diversity, transmission, and assembly.
Abstract Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently act as the initial inoculum for the plant microbiota. The purpose of this mini-review is to provide an overview of current knowledge on the diversity, structure and role of the seed microbiota. The relative importance of the mode of transmission (vertical vs horizontal) of the microbial entities composing the seed microbiota as well as the potential connections existing between seed and other plant habitats such as the anthosphere and the spermosphere is discussed. Finally the governing processes...
Source: Current Opinion in Microbiology - April 21, 2017 Category: Microbiology Authors: Shade A, Jacques MA, Barret M Tags: Curr Opin Microbiol Source Type: research

Life in earth - the root microbiome to the rescue?
Abstract Manipulation of the soil microbiome holds great promise for contributing to more environmentally benign agriculture, with soil microbes such as Pseudomonas promoting plant growth and effectively suppressing pathogenic microorganisms. Next-generation sequencing has enabled a new generation of research into soil microbiomes, presenting the opportunity to better understand and exploit these valuable resources. Soil bacterial communities are both highly complex and variable, and contain vast interspecies and intraspecies diversity, both of which respond to environmental variation. Therefore, we propose that a...
Source: Current Opinion in Microbiology - April 21, 2017 Category: Microbiology Authors: Mauchline TH, Malone JG Tags: Curr Opin Microbiol Source Type: research

Microbial communities associated with plants: learning from nature to apply it in agriculture.
Abstract It is a new consensus that any living organism depends on its partners to strive under environmental conditions along their living period. Plants are also highly dependent on their associated microbes, which can support its development and proper protection under stressors. Along their evolution, plants learned to interact to soil microbiota, extracting their utmost capacity to provide resources for plant development and successful colonization of terrestrial systems, where the great soil biodiversity is keen on properly exert this role. Functional systems, such as the rhizosphere, provide evidences of th...
Source: Current Opinion in Microbiology - April 21, 2017 Category: Microbiology Authors: Andreote FD, Pereira E Silva MC Tags: Curr Opin Microbiol Source Type: research

Upscaling of fungal-bacterial interactions: from the lab to the field.
Abstract Fungal-bacterial interactions (FBI) are an integral component of microbial community networks in terrestrial ecosystems. During the last decade, the attention for FBI has increased tremendously. For a wide variety of FBI, information has become available on the mechanisms and functional responses. Yet, most studies have focused on pairwise interactions under controlled conditions. The question to what extent such studies are relevant to assess the importance of FBI for functioning of natural microbial communities in real ecosystems remains largely unanswered. Here, the information obtained by studying a t...
Source: Current Opinion in Microbiology - April 21, 2017 Category: Microbiology Authors: de Boer W Tags: Curr Opin Microbiol Source Type: research

Jasmonic acid signalling and the plant holobiont.
Abstract The plant holobiont - which is the plant and its associated microbiome - is increasingly viewed as an evolving entity. Some interacting microbes that compose the microbiome assist plants in combating pathogens and herbivorous insects. However, knowledge of the factors that influence the microbiome in the context of defence signalling pathways is still in its infancy. Recent research reported that changes in jasmonic acid (JA) and salicylic acid signalling affects the root microbiome of Arabidopsis thaliana. This review aims to present the hypothesis that the JA pathway represents a novel mechanism for mic...
Source: Current Opinion in Microbiology - April 21, 2017 Category: Microbiology Authors: Carvalhais LC, Schenk PM, Dennis PG Tags: Curr Opin Microbiol Source Type: research

The unseen rhizosphere root-soil-microbe interactions for crop production.
Abstract The underground root-soil-microbe interactions are extremely complex, but vitally important for aboveground plant growth, health and fitness. The pressure to reduce our reliance on agrochemicals, and sustainable efforts to develop agriculture makes rhizosphere interactions' research a hotspot. Recent advances provide new insights about the signals, pathways, functions and mechanisms of these interactions. In this review, we provide an overview about recent progress in rhizosphere interaction networks in crops. We also discuss a holistic view of the root-soil-rhizomicrobiome interactions achieved through t...
Source: Current Opinion in Microbiology - April 20, 2017 Category: Microbiology Authors: Zhang R, Vivanco JM, Shen Q Tags: Curr Opin Microbiol Source Type: research

Class 1 integrons as invasive species.
Abstract Clinical class 1 integrons are a major contributor to the evolution and dissemination of antibiotic resistance. The conserved motifs of these integrons suggest that a single, recent ancestor gave rise to all current variants. They have had a spectacular increase in distribution and abundance over the last 100 years, exhibiting many similarities to invasive species that prosper under human impacts. They have spread into over 70 bacterial species of medical importance, are commonly resident in the gut of humans and domesticated animals, and have invaded every continent, including Antarctica. They have done ...
Source: Current Opinion in Microbiology - April 14, 2017 Category: Microbiology Authors: Gillings MR Tags: Curr Opin Microbiol Source Type: research

Regulation of antibiotic-resistance by non-coding RNAs in bacteria.
Abstract Antibiotic resistance genes are commonly regulated by sophisticated mechanisms that activate gene expression in response to antibiotic exposure. Growing evidence suggest that cis-acting non-coding RNAs play a major role in regulating the expression of many resistance genes, specifically those which counteract the effects of translation-inhibiting antibiotics. These ncRNAs reside in the 5'UTR of the regulated gene, and sense the presence of the antibiotics by recruiting translating ribosomes onto short upstream open reading frames (uORFs) embedded in the ncRNA. In the presence of translation-inhibiting ant...
Source: Current Opinion in Microbiology - April 14, 2017 Category: Microbiology Authors: Dar D, Sorek R Tags: Curr Opin Microbiol Source Type: research

Diverse mobilization strategies facilitate transfer of non-conjugative mobile genetic elements.
Abstract Conjugation is a dominant mechanism of horizontal gene transfer and substantially contributes to the plasticity and evolvability of prokaryotic genomes. The impact of conjugation on genetic flux extends well beyond self-transmissible conjugative elements, because non-conjugative 'mobilizable elements' utilize other elements' conjugative apparatus for transfer. Bacterial genome comparisons highlight plasmids as vehicles for dissemination of pathogenesis and antimicrobial-resistance determinants, but for most non-conjugative plasmids, a mobilization mechanism is not apparent. Recently we discovered many Sta...
Source: Current Opinion in Microbiology - April 6, 2017 Category: Microbiology Authors: Ramsay JP, Firth N Tags: Curr Opin Microbiol Source Type: research

Regulation of CRISPR-Cas adaptive immune systems.
Abstract CRISPR-Cas systems are prokaryotic immune systems that allow defense against invasion by foreign genetic elements. Through the acquisition of genetic memory representing prior exposure, the CRISPR-Cas machinery identifies complementary nucleic acids and mediates their destruction. Since their discovery, CRISPR-Cas research has exploded, with major progress into their mechanism and biotechnological application. In contrast, we are only beginning to understand how CRISPR-Cas activity is regulated. Recent studies have uncovered both conserved regulatory pathways, in addition to more specific mechanisms. Iden...
Source: Current Opinion in Microbiology - March 27, 2017 Category: Microbiology Authors: Patterson AG, Yevstigneyeva MS, Fineran PC Tags: Curr Opin Microbiol Source Type: research

Modulation of host cell apoptotic pathways by intracellular pathogens.
n A Abstract Nearly all steps of the host cell apoptotic cascade can be subverted by intracellular microorganisms. Some pathogens modulate early steps and interfere with sensing of extracellular signals, cellular stress or signal transduction; others target Bcl-2 proteins, caspases, or inhibitor of apoptosis proteins (IAPs). In many cases the exact molecular mechanisms leading to interference with the host cell apoptotic cascade are still unknown. However, there are some examples where bacterial factors that modulate host cell death have been identified. In this review we will summarize recent findings on how intr...
Source: Current Opinion in Microbiology - March 17, 2017 Category: Microbiology Authors: Friedrich A, Pechstein J, Berens C, Lührmann A Tags: Curr Opin Microbiol Source Type: research

Toxin-antitoxin systems: reversible toxicity.
Abstract Toxin-antitoxin (TA) systems encoded on the plasmids and chromosomes of bacteria are emerging as key players in stress adaptation. In particular, they have been implicated in the induction of persisters non-growing cells that can evade antibiotic exposure. TA toxins operate by a diverse range of mechanisms, either destructive or conservative, leading to the reversible growth arrest of bacterial cells. Whilst the molecular mechanisms of intoxication are now well understood, we still have very little information on how corrupted cells reawaken. Alongside the phenomenon of conditional cooperativity, new evid...
Source: Current Opinion in Microbiology - March 6, 2017 Category: Microbiology Authors: Hall AM, Gollan B, Helaine S Tags: Curr Opin Microbiol Source Type: research

Distance-dependent danger responses in bacteria.
Abstract The last decade has seen a resurgence in our understanding of the diverse mechanisms that bacteria use to kill one another. We are also beginning to uncover the responses and countermeasures that bacteria use when faced with specific threats or general cues of potential danger from bacterial competitors. In this Perspective, we propose that diverse offensive and defensive responses in bacteria have evolved to offset dangers detected at different distances. Thus, while volatile organic compounds provide bacterial cells with a warning at the greatest distance, diffusible compounds like antibiotics or contac...
Source: Current Opinion in Microbiology - March 1, 2017 Category: Microbiology Authors: Westhoff S, van Wezel GP, Rozen DE Tags: Curr Opin Microbiol Source Type: research

The divisome at 25: the road ahead.
Abstract The identification of the FtsZ ring by Bi and Lutkenhaus in 1991 was a defining moment for the field of bacterial cell division. Not only did the presence of the FtsZ ring provide fodder for the next 25 years of research, the application of a then cutting-edge approach-immunogold labeling of bacterial cells-inspired other investigators to apply similarly state-of-the-art technologies in their own work. These efforts have led to important advances in our understanding of the factors underlying assembly and maintenance of the division machinery. At the same time, significant questions about the mechanisms c...
Source: Current Opinion in Microbiology - February 27, 2017 Category: Microbiology Authors: den Blaauwen T, Hamoen LW, Levin PA Tags: Curr Opin Microbiol Source Type: research

Exploring functional membrane microdomains in bacteria: an overview.
Abstract Recent studies show that internal organization of bacterial cells is more complex than previously appreciated. A clear example of this is the assembly of the nanoscale membrane platforms termed functional membrane microdomains. The lipid composition of these regions differs from that of the surrounding membrane; these domains confine a set of proteins involved in specific cellular processes such as protease secretion and signal transduction. It is currently thought that functional membrane microdomains act as oligomerization platforms and promote efficient oligomerization of interacting protein partners i...
Source: Current Opinion in Microbiology - February 23, 2017 Category: Microbiology Authors: Lopez D, Koch G Tags: Curr Opin Microbiol Source Type: research

New RNA-seq approaches for the study of bacterial pathogens.
Abstract Understanding how bacteria cause disease requires knowledge of which genes are expressed and how they are regulated during infection. While RNA-seq is now a routine method for gene expression analysis in bacterial pathogens, the past years have also witnessed a surge of novel RNA-seq based approaches going beyond standard mRNA profiling. These include variations of the technique to capture post-transcriptional networks controlled by small RNAs and to discover associated RNA-binding proteins in the pathogen itself. Dual RNA-seq analyzing pathogen and host simultaneously has revealed roles of noncoding RNAs...
Source: Current Opinion in Microbiology - February 16, 2017 Category: Microbiology Authors: Saliba AE, C Santos S, Vogel J Tags: Curr Opin Microbiol Source Type: research

RNA-based control mechanisms of Clostridium difficile.
Abstract Clostridium difficile (CD)-associated diarrhoea is currently the most prevalent nosocomial diarrhoea worldwide. Many characteristics of CD pathogenicity remain poorly understood. Recent data strongly indicate the importance of an RNA network for the control of gene expression in CD. More than 200 regulatory RNAs have been identified by deep sequencing and targeted approaches, including Hfq-dependent trans riboregulators, cis-antisense RNAs, CRISPR RNAs, and c-di-GMP-responsive riboswitches. These regulatory RNAs are involved in the control of major processes in the CD infection cycle, for example motility...
Source: Current Opinion in Microbiology - February 16, 2017 Category: Microbiology Authors: Soutourina O Tags: Curr Opin Microbiol Source Type: research

Breaking the population barrier by single cell analysis: one host against one pathogen.
Abstract Most of our understanding of the host-bacterium interaction has come from studies of bulk populations. In reality, highly adaptable and dynamic host cells and bacteria engage in complex, diverse interactions. This complexity necessarily limits the depth of understanding that can be gained with bulk population measurements. Here, we will review the merit of single cell analysis to characterize this diversity that can trigger heterogeneous outcomes. We will discuss heterogeneity of bacterial and host populations, differences in host microenvironments, technological advances that facilitate the analysis of r...
Source: Current Opinion in Microbiology - February 16, 2017 Category: Microbiology Authors: Mills E, Avraham R Tags: Curr Opin Microbiol Source Type: research

Robust peptidoglycan growth by dynamic and variable multi-protein complexes.
Abstract In Gram-negative bacteria such as Escherichia coli the peptidoglycan sacculus resides in the periplasm, a compartment that experiences changes in pH value, osmolality, ion strength and other parameters depending on the cell's environment. Hence, the cell needs robust peptidoglycan growth mechanisms to grow and divide under different conditions. Here we propose a model according to which the cell achieves robust peptidoglycan growth by employing dynamic multi-protein complexes, which assemble with variable composition from freely diffusing sets of peptidoglycan synthases, hydrolases and their regulators, w...
Source: Current Opinion in Microbiology - February 15, 2017 Category: Microbiology Authors: Pazos M, Peters K, Vollmer W Tags: Curr Opin Microbiol Source Type: research

Emerging insights into the biology of typhoid toxin.
;n JE Abstract Typhoid toxin is a unique A2B5 exotoxin and an important virulence factor for Salmonella Typhi, the cause of typhoid fever. In the decade since its initial discovery, great strides have been made in deciphering the unusual biological program of this toxin, which is fundamentally different from related toxins in many ways. Purified typhoid toxin administered to laboratory animals causes many of the symptoms of typhoid fever, suggesting that typhoid toxin is a central factor in this disease. Further advances in understanding the biology of this toxin will help guide the development of badly needed dia...
Source: Current Opinion in Microbiology - February 14, 2017 Category: Microbiology Authors: Fowler CC, Chang SJ, Gao X, Geiger T, Stack G, Galán JE Tags: Curr Opin Microbiol Source Type: research

Structure and function of HWE/HisKA2-family sensor histidine kinases.
Abstract Sensor histidine kinases regulate adaptive cellular responses to changes in the chemical or physical state of the environment. HWE/HisKA2-family kinases comprise a subset of histidine kinases that is defined by unique sequence motifs in both the catalytic and non-catalytic regions. Recent crystal structures have defined conserved intramolecular interactions that inform models of kinase regulation that are unique to the HWE/HisKA2 superfamily. Emerging genetic, biochemical and genomic data indicate that, unlike typical histidine kinases, HWE/HisKA2 kinases do not generally signal via classical DNA-binding ...
Source: Current Opinion in Microbiology - February 10, 2017 Category: Microbiology Authors: Herrou J, Crosson S, Fiebig A Tags: Curr Opin Microbiol Source Type: research

Post-transcriptional regulation of type III secretion in plant and animal pathogens.
Abstract Type III secretion systems (T3SS) serve as a primary anti-host defense mechanism for many Gram-negative plant and animal pathogens. T3SS production is tightly controlled and activated by host-associated signals. Although transcriptional responses represent a significant component of the activation cascade, recent studies have uncovered diverse post-transcriptional mechanisms that also contribute to T3SS production. Targets for post-transcriptional control are often AraC/XylS transcription factors that promote T3SS gene expression. Commons mechanisms of post-transcriptional regulation include direct contro...
Source: Current Opinion in Microbiology - February 9, 2017 Category: Microbiology Authors: Schulmeyer KH, Yahr TL Tags: Curr Opin Microbiol Source Type: research

If it transcribes, we can sequence it: mining the complexities of host-pathogen-environment interactions using RNA-seq.
r C Abstract Host-pathogen interactions are exceedingly complex because they involve multiple host tissues, often occur in the context of normal microflora, and can span diverse microenvironments. Although decades of gene expression studies have provided detailed insights into infection processes, technical challenges have restricted experiments to single pathogenic species or host tissues. RNA-sequencing (RNA-seq) has revolutionized the study of gene expression because in addition to quantifying transcriptional output, it allows detection and characterization of all transcripts in a genome. Here, we review how re...
Source: Current Opinion in Microbiology - February 9, 2017 Category: Microbiology Authors: Colgan AM, Cameron AD, Kröger C Tags: Curr Opin Microbiol Source Type: research

Inflammatory disease caused by intestinal pathobionts.
Abstract Environmental and intrinsic factors that alter microbiota structure can trigger aberrant immune responses. The resulting states of dysbiosis take many forms characterized by overrepresentation of pro-inflammatory organisms and pathobionts and loss of beneficial commensals further aggravating the inflammatory state. The pathogenic potential of the dysbiotic community can be linked to specific organisms in some cases but accumulating evidence suggests that intestinal inflammatory diseases are driven by collective functions of highly variable polymicrobial communities. Key challenges are to gain sufficient k...
Source: Current Opinion in Microbiology - February 9, 2017 Category: Microbiology Authors: Zechner EL Tags: Curr Opin Microbiol Source Type: research

The ins and outs of cyclic di-GMP signaling in Vibrio cholerae.
iz FH Abstract The second messenger nucleotide cyclic dimeric guanosine monophosphate (c-di-GMP) governs many cellular processes in the facultative human pathogen Vibrio cholerae. This organism copes with changing environmental conditions in aquatic environments and during transitions to and from human hosts. Modulation of c-di-GMP allows V. cholerae to shift between motile and sessile stages of life, thus allowing adaptation to stressors and environmental conditions during its transmission cycle. The V. cholerae genome encodes a large set of proteins predicted to degrade and produce c-di-GMP. A subset of these en...
Source: Current Opinion in Microbiology - February 4, 2017 Category: Microbiology Authors: Conner JG, Zamorano-Sánchez D, Park JH, Sondermann H, Yildiz FH Tags: Curr Opin Microbiol Source Type: research

Systematic probing of the bacterial RNA structurome to reveal new functions.
Abstract RNA folds into intricate structures. Recent discoveries using next-generation sequencing (NGS) approaches have revealed unprecedented structural complexity with a pivotal role in regulating RNA function and stability. Here, we present new discoveries from the transcriptome-wide determination of RNA structuromes in bacteria and discuss emerging concepts in the role of mRNA structures in regulating transcription, translation and degradation. We also provide critical viewpoints on the use of NGS approaches for elucidating of RNA structuromes at the systems level. PMID: 28160611 [PubMed - as supplied by ...
Source: Current Opinion in Microbiology - February 1, 2017 Category: Microbiology Authors: Ignatova Z, Narberhaus F Tags: Curr Opin Microbiol Source Type: research

Geometric protein localization cues in bacterial cells.
Abstract Bacterial cells are highly organized at a molecular level. Understanding how specific proteins localize to their proper subcellular address has been a major challenge in bacterial cell biology. One mechanism, which appears to be increasingly more common, is the use of 'geometric cues' for protein localization. In this model, certain shape-sensing proteins recognize, and preferentially embed into, either negatively or positively curved (concave or convex, respectively) membranes. Here, we review examples of bacterial proteins that reportedly localize by sensing geometric cues and highlight emerging mechani...
Source: Current Opinion in Microbiology - January 19, 2017 Category: Microbiology Authors: Updegrove TB, Ramamurthi KS Tags: Curr Opin Microbiol Source Type: research