Microbial diversity of hypersaline environments: a metagenomic approach.
ke RT Abstract Recent studies based on metagenomics and other molecular techniques have permitted a detailed knowledge of the microbial diversity and metabolic activities of microorganisms in hypersaline environments. The current accepted model of community structure in hypersaline environments is that the square archaeon Haloquadratum waslbyi, the bacteroidete Salinibacter ruber and nanohaloarchaea are predominant members at higher salt concentrations, while more diverse archaeal and bacterial taxa are observed in habitats with intermediate salinities. Additionally, metagenomic studies may provide insight into th...
Source: Current Opinion in Microbiology - June 5, 2015 Category: Microbiology Authors: Ventosa A, de la Haba RR, Sánchez-Porro C, Papke RT Tags: Curr Opin Microbiol Source Type: research

From the blood to the brain: avenues of eukaryotic pathogen dissemination to the central nervous system.
Abstract Infection of the central nervous system (CNS) is a significant cause of morbidity and mortality, and treatments available to combat the highly debilitating symptoms of CNS infection are limited. The mechanisms by which pathogens in the circulation overcome host immunity and breach the blood-brain barrier are active areas of investigation. In this review, we discuss recent work that has significantly advanced our understanding of the avenues of pathogen dissemination to the CNS for four eukaryotic pathogens of global health importance: Toxoplasma gondii, Plasmodium falciparum, Trypanosoma brucei, and Crypt...
Source: Current Opinion in Microbiology - June 2, 2015 Category: Microbiology Authors: Ueno N, Lodoen MB Tags: Curr Opin Microbiol Source Type: research

Posttranslational regulation of microbial metabolism.
We present recent advances in elucidating the role of these regulatory layers, focusing on posttranslational modifications and allosteric interactions. As the systematic mapping of posttranslational regulatory events has now become possible, the next challenge is to identify those regulatory events that are functionally relevant under a given condition. PMID: 26048423 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - June 2, 2015 Category: Microbiology Authors: Kochanowski K, Sauer U, Noor E Tags: Curr Opin Microbiol Source Type: research

Metagenomics of extreme environments.
Abstract Whether they are exposed to extremes of heat or cold, or buried deep beneath the Earth's surface, microorganisms have an uncanny ability to survive under these conditions. This ability to survive has fascinated scientists for nearly a century, but the recent development of metagenomics and 'omics' tools has allowed us to make huge leaps in understanding the remarkable complexity and versatility of extremophile communities. Here, in the context of the recently developed metagenomic tools, we discuss recent research on the community composition, adaptive strategies and biological functions of extremophiles....
Source: Current Opinion in Microbiology - June 1, 2015 Category: Microbiology Authors: Cowan DA, Ramond JB, Makhalanyane TP, De Maayer P Tags: Curr Opin Microbiol Source Type: research

Antimicrobial interactions: mechanisms and implications for drug discovery and resistance evolution.
Abstract Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs' joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further id...
Source: Current Opinion in Microbiology - May 29, 2015 Category: Microbiology Authors: Bollenbach T Tags: Curr Opin Microbiol Source Type: research

Microbial bet-hedging: the power of being different.
Abstract Bet-hedging is an evolutionary theory that describes how risk spreading can increase fitness of a genotype in an unpredictably changing environment. To achieve risk spreading, maladapted phenotypes develop within isogenic populations that may be fit for a future environment. In recent years, various observations of microbial phenotypic heterogeneity have been denoted as bet-hedging strategies, sometimes without sufficient evidence to support this claim. Here, we discuss selected examples of microbial phenotypic heterogeneity that so far do seem consistent with the evolutionary theory concept of bet-hedgin...
Source: Current Opinion in Microbiology - May 26, 2015 Category: Microbiology Authors: Grimbergen AJ, Siebring J, Solopova A, Kuipers OP Tags: Curr Opin Microbiol Source Type: research

Adaptive strategies in the double-extremophilic prokaryotes inhabiting soda lakes.
Abstract Haloalkaliphiles are double extremophilic organisms thriving both at high salinity and alkaline pH. Although numerous haloalkaliphilic representatives have been identified among Archaea and Bacteria over the past 15 years, the adaptations underlying their prosperity at haloalkaline conditions are scarcely known. A multi-level adaptive strategy was proposed to occur in haloalkaliphilic organisms isolated from saline alkaline and soda environments including adjustments in the cell wall structure, plasma membrane lipid composition, membrane transport systems, bioenergetics, and osmoregulation. Isolation of c...
Source: Current Opinion in Microbiology - May 26, 2015 Category: Microbiology Authors: Banciu HL, Muntyan MS Tags: Curr Opin Microbiol Source Type: research

Functional microbiology of soda lakes.
Abstract Soda lakes represent unique permanently haloalkaline system. Despite the harsh conditions, they are inhabited by abundant, mostly prokaryotic, microbial communities. This review summarizes results of studies of main functional groups of the soda lake prokaryotes responsible for carbon, nitrogen and sulfur cycling, including oxygenic and anoxygenic phototrophs, aerobic chemolithotrophs, fermenting and respiring anaerobes. The main conclusion from this work is that the soda lakes are very different from other high-salt systems in respect to microbial richness and activity. The reason for this difference is ...
Source: Current Opinion in Microbiology - May 26, 2015 Category: Microbiology Authors: Sorokin DY, Banciu HL, Muyzer G Tags: Curr Opin Microbiol Source Type: research

The Apicomplexan CDC/MACPF-like pore-forming proteins.
Abstract Pore-forming proteins (PFPs) encompass a broad family of proteins that are used for virulence or immune defense. Members of the cholesterol-dependent cytolysins (CDCs) and membrane attack complex/perforin (MACPF) family of PFPs form large β-barrel pores in the membrane. The CDC/MACPF proteins contain a characteristic four-stranded β-sheet that is flanked by two α-helical bundles, which unfold to form two transmembrane β-hairpins. Apicomplexan eukaryotic parasites express CDC/MACPFs termed perforin-like proteins (PLPs). Here we review recent studies that provide key insights into the a...
Source: Current Opinion in Microbiology - May 26, 2015 Category: Microbiology Authors: Wade KR, Tweten RK Tags: Curr Opin Microbiol Source Type: research

Metagenomics meets time series analysis: unraveling microbial community dynamics.
Abstract The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic patterns, help to build predictive models or, on the contrary, quantify irregularities that make community behavior unpredictable. Microbial communities can change abruptly in response to small perturbations, linked to changing conditions or the presence of multiple stable states. With sufficient samples or ti...
Source: Current Opinion in Microbiology - May 22, 2015 Category: Microbiology Authors: Faust K, Lahti L, Gonze D, de Vos WM, Raes J Tags: Curr Opin Microbiol Source Type: research

Leishmania survival in the macrophage: where the ends justify the means.
Abstract Macrophages are cells of the immune system that mediate processes ranging from phagocytosis to tissue homeostasis. Leishmania has evolved ingenious ways to adapt to life in the macrophage. The GP63 metalloprotease, which disables key microbicidal pathways, has recently been found to disrupt processes ranging from antigen cross-presentation to nuclear pore dynamics. New studies have also revealed that Leishmania sabotages key metabolic and signaling pathways to fuel parasite growth. Leishmania has also been found to induce DNA methylation to turn off genes controlling microbicidal pathways. These novel fin...
Source: Current Opinion in Microbiology - May 15, 2015 Category: Microbiology Authors: Arango Duque G, Descoteaux A Tags: Curr Opin Microbiol Source Type: research

Oxygen sensing by protozoans: how they catch their breath.
Abstract Cells must know the local levels of available oxygen and either adapt accordingly or relocate to more favorable environments. Prolyl 4-hydroxylases (P4Hs) are emerging as universal cellular oxygen sensors. In animals, these oxygen sensors respond to decreased oxygen availability by up-regulating hypoxia-inducible transcription factors. In protozoa, the P4Hs appear to activate E3-SCF ubiquitin ligase complexes via a glycosylation-dependent mechanism, potentially to turn over their proteomes. Intracellular parasites are impacted by both types of oxygen-sensing pathways. Since parasites are exposed to divers...
Source: Current Opinion in Microbiology - May 15, 2015 Category: Microbiology Authors: West CM, Blader IJ Tags: Curr Opin Microbiol Source Type: research

Non-random distribution of macromolecules as driving forces for phenotypic variation.
;ller S Abstract Clonal populations employ many strategies of diversification to deal with constraints. All these strategies result in the generation of different phenotypes with diverse functions. Events like cell division are major sources of phenotypic variability due to the unequal partitioning of cellular components. In this review we concentrate on passive and active mechanisms cells employ to distribute macromolecules between their offspring. Different types of segregation are described, addressing both metabolically pertinent molecules such as PHA/PHB or polyphosphates, and components that adversely affect...
Source: Current Opinion in Microbiology - May 11, 2015 Category: Microbiology Authors: Jahn M, Günther S, Müller S Tags: Curr Opin Microbiol Source Type: research

Haloviruses of archaea, bacteria, and eukaryotes.
Abstract Hypersaline environments up to near saturation are rich reservoirs of extremophilic viruses. One milliliter of salt water may contain up to 10(9) viruses which can also be trapped inside salt crystals. To date, most of the ∼100 known halovirus isolates infect extremely halophilic archaea, although a few bacterial and eukaryotic viruses have also been described. These isolates comprise tailed and tailless icosahedral, pleomorphic, and lemon-shaped viruses which have been classified according to features such as host range, genome type, and replication. Recent studies have revealed that viruses can be g...
Source: Current Opinion in Microbiology - April 28, 2015 Category: Microbiology Authors: Atanasova NS, Oksanen HM, Bamford DH Tags: Curr Opin Microbiol Source Type: research

Toxoplasma's ways of manipulating the host transcriptome via secreted effectors.
Abstract The obligate intracellular parasite Toxoplasma gondii strikes a subtle balance with the host immune system that not only prevents host death but also promotes parasite persistence. Although being enclosed within a parasitophorous vacuole, the parasite actively interfaces with host cell signaling pathways, thereby directing host cell responses. To this end, T. gondii delivers effector proteins into the host cell that co-opt host transcription factors and eventually modulate gene expression. Aside from the secretory Rhoptry organelles initially described as the main source of such effectors, Dense Granules ...
Source: Current Opinion in Microbiology - April 23, 2015 Category: Microbiology Authors: Hakimi MA, Bougdour A Tags: Curr Opin Microbiol Source Type: research

Ensuring transmission through dynamic host environments: host-pathogen interactions in Plasmodium sexual development.
Abstract A renewed global commitment to malaria elimination lends urgency to understanding the biology of Plasmodium transmission stages. Recent progress toward uncovering the mechanisms underlying Plasmodium falciparum sexual differentiation and maturation reveals potential targets for transmission-blocking drugs and vaccines. The identification of parasite factors that alter sexual differentiation, including extracellular vesicles and a master transcriptional regulator, suggest that parasites make epigenetically controlled developmental decisions based on environmental cues. New insights into sexual development,...
Source: Current Opinion in Microbiology - April 7, 2015 Category: Microbiology Authors: Dantzler KW, Ravel DB, Brancucci NM, Marti M Tags: Curr Opin Microbiol Source Type: research

Prokaryotic functional gene diversity in the sunlit ocean: Stumbling in the dark.
Abstract Prokaryotes are extremely abundant in the ocean where they drive biogeochemical cycles. The recent development and application of -omics techniques has provided an astonishing amount of information revealing the existence of a vast diversity of functional genes and a large heterogeneity within each gene. The big challenge for microbial ecologists is now to understand the ecological relevance of this variability for ecosystem functioning, a question that remains largely understudied. This brief review highlights some of the latest advances in the study of the diversity of biogeochemically relevant function...
Source: Current Opinion in Microbiology - April 6, 2015 Category: Microbiology Authors: Ferrera I, Sebastian M, Acinas SG, Gasol JM Tags: Curr Opin Microbiol Source Type: research

Microsporidia-host interactions.
Abstract Microsporidia comprise one of the largest groups of obligate intracellular pathogens and can infect virtually all animals, but host response to these fungal-related microbes has been poorly understood. Several new studies of the host transcriptional response to microsporidia infection have found infection-induced regulation of genes involved in innate immunity, ubiquitylation, metabolism, and hormonal signaling. In addition, microsporidia have recently been shown to exploit host recycling endocytosis for exit from intestinal cells, and to interact with host degradation pathways. Microsporidia infection ha...
Source: Current Opinion in Microbiology - April 3, 2015 Category: Microbiology Authors: Szumowski SC, Troemel ER Tags: Curr Opin Microbiol Source Type: research

Guiding bioprocess design by microbial ecology.
r B Abstract Industrial bioprocess development is driven by profitability and eco-efficiency. It profits from an early stage definition of process and biocatalyst design objectives. Microbial bioprocess environments can be considered as synthetic technical microbial ecosystems. Natural systems follow Darwinian evolution principles aiming at survival and reproduction. Technical systems objectives are eco-efficiency, productivity, and profitable production. Deciphering technical microbial ecology reveals differences and similarities of natural and technical systems objectives, which are discussed in this review in v...
Source: Current Opinion in Microbiology - March 30, 2015 Category: Microbiology Authors: Volmer J, Schmid A, Bühler B Tags: Curr Opin Microbiol Source Type: research

The advent of genome-wide association studies for bacteria.
Abstract Significant advances in sequencing technologies and genome-wide association studies (GWAS) have revealed substantial insight into the genetic architecture of human phenotypes. In recent years, the application of this approach in bacteria has begun to reveal the genetic basis of bacterial host preference, antibiotic resistance, and virulence. Here, we consider relevant differences between bacterial and human genome dynamics, apply GWAS to a global sample of Mycobacterium tuberculosis genomes to highlight the impacts of linkage disequilibrium, population stratification, and natural selection, and finally co...
Source: Current Opinion in Microbiology - March 25, 2015 Category: Microbiology Authors: Chen PE, Shapiro BJ Tags: Curr Opin Microbiol Source Type: research

DNA methylation in bacteria: from the methyl group to the methylome.
ús J Abstract Formation of C(5)-methyl-cytosine, N(4)-methyl-cytosine, and N(6)-methyl-adenine in bacterial genomes is postreplicative, and occurs at specific targets. Base methylation can modulate the interaction of DNA-binding proteins with their cognate sites, and controls chromosome replication, correction of DNA mismatches, cell cycle-coupled transcription, and formation of epigenetic lineages by phase variation. During four decades, the roles of DNA methylation in bacterial physiology have been investigated by analyzing the contribution of individual methyl groups or small methyl group clusters to the...
Source: Current Opinion in Microbiology - March 25, 2015 Category: Microbiology Authors: Sánchez-Romero MA, Cota I, Casadesús J Tags: Curr Opin Microbiol Source Type: research

Microbes in flow.
Abstract Microbes often live in moving fluids. Despite the multitude of implications that flow has on microbial ecology and environmental microbiology, only recently have experimental tools and conceptual frameworks from fluid physics been applied systematically to further our knowledge of the behavior of microbes in flow. This nascent research field, which truly straddles biology and physics, has already produced important contributions to our understanding of the physical interaction between microbes and flow, both in bulk fluid and close to surfaces, at the same time revealing the richness and complexity of the...
Source: Current Opinion in Microbiology - March 23, 2015 Category: Microbiology Authors: Rusconi R, Stocker R Tags: Curr Opin Microbiol Source Type: research

Intracellular detection of viral nucleic acids.
Abstract Successful clearance of a microbial infection depends on the concerted action of both the innate and adaptive arms of the immune system. Accurate recognition of an invading pathogen is the first and most crucial step in eliciting effective antimicrobial defense mechanisms. In recent years, remarkable progress has been made towards understanding the molecular details of how the innate immune system recognizes microbial signatures, commonly called pathogen-associated molecular patterns (PAMPs). For viral pathogens, nucleic acids-both viral genomes and viral replication products-represent a major class of PA...
Source: Current Opinion in Microbiology - March 17, 2015 Category: Microbiology Authors: Sparrer KM, Gack MU Tags: Curr Opin Microbiol Source Type: research

Editorial overview: Cell regulation: When you think you know it all, there is another layer to be discovered.
g A PMID: 25708065 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - February 20, 2015 Category: Microbiology Authors: Gross CA, Gründling A Tags: Curr Opin Microbiol Source Type: research

How to train your microbe: methods for dynamically characterizing gene networks.
Abstract Gene networks regulate biological processes dynamically. However, researchers have largely relied upon static perturbations, such as growth media variations and gene knockouts, to elucidate gene network structure and function. Thus, much of the regulation on the path from DNA to phenotype remains poorly understood. Recent studies have utilized improved genetic tools, hardware, and computational control strategies to generate precise temporal perturbations outside and inside of live cells. These experiments have, in turn, provided new insights into the organizing principles of biology. Here, we introduce t...
Source: Current Opinion in Microbiology - February 9, 2015 Category: Microbiology Authors: Castillo-Hair SM, Igoshin OA, Tabor JJ Tags: Curr Opin Microbiol Source Type: research

Regulatory small RNAs from the 3' regions of bacterial mRNAs.
Abstract Most studies of small regulatory RNAs in bacteria have focussed on conserved transcripts in intergenic regions. However, several recent developments including single-nucleotide resolution transcriptome profiling by RNA-seq and increased knowledge of the cellular targets of the RNA chaperone Hfq suggest that the bacterial world of functional small RNAs is more diverse. One emerging class are small RNAs that are identical to the 3' regions of known mRNAs, but are produced either by transcription from internal promoters or by mRNA processing. Using several recently discovered examples of such sRNAs, we discu...
Source: Current Opinion in Microbiology - February 9, 2015 Category: Microbiology Authors: Miyakoshi M, Chao Y, Vogel J Tags: Curr Opin Microbiol Source Type: research

Diagnosing oxidative stress in bacteria: not as easy as you might think.
Abstract Microorganisms are vulnerable to elevated levels of intracellular reactive oxygen species (ROS). This situation has led to proposals that many natural stresses might be toxic specifically because they accelerate endogenous ROS formation. Such a mechanism has been convincingly demonstrated for redox-cycling compounds. However, the evidence is much weaker for most other stressors. The hypothesis that clinical antibiotics generate lethal ROS stress has attracted much attention, and the author discusses some aspects of evidence that support or oppose this idea. Importantly, even if all cellular electron flow ...
Source: Current Opinion in Microbiology - February 6, 2015 Category: Microbiology Authors: Imlay JA Tags: Curr Opin Microbiol Source Type: research

Growth rate and cell size: a re-examination of the growth law.
Abstract Research into the mechanisms regulating bacterial cell size has its origins in a single paper published over 50 years ago. In it Schaechter and colleagues made the observation that the chemical composition and size of a bacterial cell is a function of growth rate, independent of the medium used to achieve that growth rate, a finding that is colloquially referred to as 'the growth law'. Recent findings hint at unforeseen complexity in the growth law, and suggest that nutrients rather than growth rate are the primary arbiter of size. The emerging picture suggests that size is a complex, multifactorial pheno...
Source: Current Opinion in Microbiology - February 4, 2015 Category: Microbiology Authors: Vadia S, Levin PA Tags: Curr Opin Microbiol Source Type: research

Microbial individuality: how single-cell heterogeneity enables population level strategies.
Abstract Much of our knowledge of microbial life is only a description of average population behaviours, but modern technologies provide a more inclusive view and reveal that microbes also have individuality. It is now acknowledged that isogenic cell-to-cell heterogeneity is common across organisms and across different biological processes. This heterogeneity can be regulated and functional, rather than just reflecting tolerance to noisy biochemistry. Here, we review recent advances in our understanding of microbial heterogeneity, with an emphasis on the pervasiveness of heterogeneity, the mechanisms that sustain ...
Source: Current Opinion in Microbiology - February 4, 2015 Category: Microbiology Authors: Martins BM, Locke JC Tags: Curr Opin Microbiol Source Type: research

Diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes.
Abstract Sporulation allows bacteria to survive adverse conditions and is essential to the lifecycle of some obligate anaerobes. In Bacillus subtilis, the sporulation-specific sigma factors, σ(F), σ(E), σ(G), and σ(K), activate compartment-specific transcriptional programs that drive sporulation through its morphological stages. The regulation of these sigma factors was predicted to be conserved across the Firmicutes, since the regulatory proteins controlling their activation are largely conserved. However, recent studies in (Pepto)Clostridium difficile, Clostridium acetobutylicum, Clostrid...
Source: Current Opinion in Microbiology - January 31, 2015 Category: Microbiology Authors: Fimlaid KA, Shen A Tags: Curr Opin Microbiol Source Type: research

H-NS and RNA polymerase: a love-hate relationship?
Abstract Histone-like nucleoid structuring (H-NS) protein is a component of bacterial chromatin and influences gene expression both locally and on a global scale. Although H-NS is broadly considered a silencer of transcription, the mechanisms by which H-NS inhibits gene expression remain poorly understood. Here we discuss recent advances in the context of a 'love-hate' relationship between H-NS and RNA polymerase, in which these factors recognise similar DNA sequences but interfere with each other's activity. Understanding the complex relationship between H-NS and RNA polymerase may unite the multiple models that ...
Source: Current Opinion in Microbiology - January 29, 2015 Category: Microbiology Authors: Landick R, Wade JT, Grainger DC Tags: Curr Opin Microbiol Source Type: research

Lost in transcription: transient errors in information transfer.
Abstract Errors in information transfer from DNA to RNA to protein are inevitable. Here, we focus on errors that occur in nascent transcripts during transcription, epimutations. Recent approaches using novel cDNA library preparation and next-generation sequencing begin to directly determine the rate of epimutation and allow analysis of the epimutational spectrum of transcription errors, the type and sequence context of the errors produced in a transcript by an RNA polymerase. The phenotypic consequences of transcription errors have been assessed using both forward and reverse epimutation systems. These studies rev...
Source: Current Opinion in Microbiology - January 28, 2015 Category: Microbiology Authors: Gordon AJ, Satory D, Halliday JA, Herman C Tags: Curr Opin Microbiol Source Type: research

Editorial overview: Genomics: The era of genomically-enabled microbiology.
PMID: 25636516 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - January 27, 2015 Category: Microbiology Authors: Hall N, Hinton J Tags: Curr Opin Microbiol Source Type: research

Guiding divisome assembly and controlling its activity.
Abstract Cell division in bacteria requires the construction of two new polar caps for the daughter cells. To constrict the cell membrane and build these new surface layers, bacteria employ a multiprotein machine called the divisome. Over the years, most of the essential division proteins have been identified and localized to the ring-like divisome apparatus. The challenge now is to determine the molecular function of these factors, how they cooperate to bring about the dramatic transformation of the mother cell envelope, and what coordinates their activity with other major cell cycle events. In this review, we di...
Source: Current Opinion in Microbiology - January 27, 2015 Category: Microbiology Authors: Tsang MJ, Bernhardt TG Tags: Curr Opin Microbiol Source Type: research

How do bacteria tune translation efficiency?
Abstract Bacterial proteins are translated with precisely determined rates to meet cellular demand. In contrast, efforts to express recombinant proteins in bacteria are often met with large unpredictability in their levels of translation. The disconnect between translation of natural and synthetic mRNA stems from the lack of understanding of the strategy used by bacteria to tune translation efficiency (TE). The development of array-based oligonucleotide synthesis and ribosome profiling provides new approaches to address this issue. Although the major determinant for TE is still unknown, these high-throughput studi...
Source: Current Opinion in Microbiology - January 27, 2015 Category: Microbiology Authors: Li GW Tags: Curr Opin Microbiol Source Type: research

Diversity in (p)ppGpp metabolism and effectors.
Abstract Bacteria produce guanosine tetraphosphate and pentaphosphate, collectively named (p)ppGpp, in response to a variety of environmental stimuli. These two remarkable molecules regulate many cellular processes, including the central dogma processes and metabolism, to ensure survival and adaptation. Work in Escherichia coli laid the foundation for understanding the molecular details of (p)ppGpp and its cellular functions. As recent studies expand to other species, it is apparent that there exists considerable variation, with respect to not only (p)ppGpp metabolism, but also to its mechanism of action. From an ...
Source: Current Opinion in Microbiology - January 27, 2015 Category: Microbiology Authors: Liu K, Bittner AN, Wang JD Tags: Curr Opin Microbiol Source Type: research

Functional genomic and metagenomic approaches to understanding gut microbiota-animal mutualism.
Abstract Accumulating data sets of gut microbiome by next-generation sequencing allow us to gain a comprehensive view of the functional diversity of the gut-associated metagenome. However, many microbiome functions are unknown and/or have only been predicted, and may not necessarily reflect the in vivo function within a gut niche. Functional genomic and metagenomic approaches have been successfully applied to broaden the understanding of invertebrate and vertebrate gut microbiome involved in diverse functions, including colonization ability, nutritional processing, antibiotic resistance, microbial physiology and m...
Source: Current Opinion in Microbiology - January 24, 2015 Category: Microbiology Authors: Yoon SS, Kim EK, Lee WJ Tags: Curr Opin Microbiol Source Type: research

Ser/Thr phosphorylation as a regulatory mechanism in bacteria.
Abstract This review will discuss some recent work describing the role of Ser/Thr phosphorylation as a post-translational mechanism of regulation in bacteria. I will discuss the interaction between bacterial eukaryotic-like Ser/Thr kinases (eSTKs) and two-component systems as well as hints as to physiological function of eSTKs and their cognate eukaryotic-like phosphatases (eSTPs). In particular, I will highlight the role of eSTKs and eSTPs in the regulation of peptidoglycan metabolism and protein synthesis. In addition, I will discuss how data from phosphoproteomic surveys suggest that Ser/Thr phosphorylation pla...
Source: Current Opinion in Microbiology - January 24, 2015 Category: Microbiology Authors: Dworkin J Tags: Curr Opin Microbiol Source Type: research

Using comparative genomics to drive new discoveries in microbiology.
Abstract Bioinformatics looks to many microbiologists like a service industry. In this view, annotation starts with what is known from experiments in the lab, makes reasonable inferences of which genes match other genes in function, builds databases to make all that we know accessible, but creates nothing truly new. Experiments lead, then biocuration and computational biology follow. But the astounding success of genome sequencing is changing the annotation paradigm. Every genome sequenced is an intercepted coded message from the microbial world, and as all cryptographers know, it is easier to decode a thousand me...
Source: Current Opinion in Microbiology - January 21, 2015 Category: Microbiology Authors: Haft DH Tags: Curr Opin Microbiol Source Type: research

On the evolution of bacterial multicellularity.
Abstract Multicellularity is one of the most prevalent evolutionary innovations and nowhere is this more apparent than in the bacterial world, which contains many examples of multicellular organisms in a surprising array of forms. Due to their experimental accessibility and the large and diverse genomic data available, bacteria enable us to probe fundamental aspects of the origins of multicellularity. Here we discuss examples of multicellular behaviors in bacteria, the selective pressures that may have led to their evolution, possible origins and intermediate stages, and whether the ubiquity of apparently converge...
Source: Current Opinion in Microbiology - January 15, 2015 Category: Microbiology Authors: Lyons NA, Kolter R Tags: Curr Opin Microbiol Source Type: research

Post-translational modifications as key regulators of bacterial metabolic fluxes.
Abstract In order to survive and compete in natural settings, bacteria must excel at quickly adapting their metabolism to fluctuations in nutrient availability and other environmental variables. This necessitates fast-acting post-translational regulatory mechanisms, that is, allostery or covalent modification, to control metabolic flux. While allosteric regulation has long been a well-established strategy for regulating metabolic enzyme activity in bacteria, covalent post-translational modes of regulation, such as phosphorylation or acetylation, have previously been regarded as regulatory mechanisms employed prima...
Source: Current Opinion in Microbiology - January 15, 2015 Category: Microbiology Authors: Pisithkul T, Patel NM, Amador-Noguez D Tags: Curr Opin Microbiol Source Type: research

Rethinking transcription coupled DNA repair.
Abstract Nucleotide excision repair (NER) is an evolutionarily conserved, multistep process that can detect a wide variety of DNA lesions. Transcription coupled repair (TCR) is a subpathway of NER that repairs the transcribed DNA strand faster than the rest of the genome. RNA polymerase (RNAP) stalled at DNA lesions mediates the recruitment of NER enzymes to the damage site. In this review we focus on a newly identified bacterial TCR pathway in which the NER enzyme UvrD, in conjunction with NusA, plays a major role in initiating the repair process. We discuss the tradeoff between the new and conventional models of...
Source: Current Opinion in Microbiology - January 14, 2015 Category: Microbiology Authors: Kamarthapu V, Nudler E Tags: Curr Opin Microbiol Source Type: research

Oxidative stress protection by polyphosphate-new roles for an old player.
Abstract Inorganic polyphosphate is a universally conserved biopolymer whose association with oxidative stress resistance has been documented in many species, but whose mode of action has been poorly understood. Here we review the recent discovery that polyphosphate functions as a protein-protective chaperone, examine the mechanisms by which polyphosphate-metal ion interactions reduce oxidative stress, and summarize polyphosphate's roles in regulating general stress response pathways. Given the simple chemical structure and ancient pedigree of polyphosphate, these diverse mechanisms are likely to be broadly releva...
Source: Current Opinion in Microbiology - January 9, 2015 Category: Microbiology Authors: Gray MJ, Jakob U Tags: Curr Opin Microbiol Source Type: research

Temporal and evolutionary dynamics of two-component signaling pathways.
Abstract Bacteria sense and respond to numerous environmental signals through two-component signaling pathways. Typically, a given stimulus will activate a sensor histidine kinase to autophosphorylate and then phosphotransfer to a cognate response regulator, which can mount an appropriate response. Although these signaling pathways often appear to be simple switches, they can also orchestrate surprisingly sophisticated and complex responses. These temporal dynamics arise from several key regulatory features, including the bifunctionality of histidine kinases as well as positive and negative feedback loops. Two-com...
Source: Current Opinion in Microbiology - January 9, 2015 Category: Microbiology Authors: Salazar ME, Laub MT Tags: Curr Opin Microbiol Source Type: research

Fusobacterium nucleatum: a commensal-turned pathogen.
This article reviews its implication in adverse pregnancy outcomes (chorioamnionitis, preterm birth, stillbirth, neonatal sepsis, preeclampsia), GI disorders (colorectal cancer, inflammatory bowel disease, appendicitis), cardiovascular disease, rheumatoid arthritis, respiratory tract infections, Lemierre's syndrome and Alzheimer's disease. The virulence mechanisms involved in the diseases are discussed, with emphasis on its colonization, systemic dissemination, and induction of host inflammatory and tumorigenic responses. The FadA adhesin/invasin conserved in F. nucleatum is a key virulence factor and a potential diagnosti...
Source: Current Opinion in Microbiology - January 7, 2015 Category: Microbiology Authors: Han YW Tags: Curr Opin Microbiol Source Type: research

Editorial overview: Host-microbe interactions: Bacteria.
PMID: 25560922 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - January 2, 2015 Category: Microbiology Authors: Holden DW, Philpott DJ Tags: Curr Opin Microbiol Source Type: research

Bacterial-induced cell reprogramming to stem cell-like cells: new premise in host-pathogen interactions.
Abstract Bacterial pathogens employ a myriad of strategies to alter host tissue cell functions for bacterial advantage during infection. Recent advances revealed a fusion of infection biology with stem cell biology by demonstrating developmental reprogramming of lineage committed host glial cells to progenitor/stem cell-like cells by an intracellular bacterial pathogen Mycobacterium leprae. Acquisition of migratory and immunomodulatory properties of such reprogrammed cells provides an added advantage for promoting bacterial spread. This presents a previously unseen sophistication of cell manipulation by hijacking ...
Source: Current Opinion in Microbiology - December 22, 2014 Category: Microbiology Authors: Hess S, Rambukkana A Tags: Curr Opin Microbiol Source Type: research

Bacteriophage-mediated spread of bacterial virulence genes.
ck RP Abstract Bacteriophages are types of viruses that infect bacteria. They are the most abundant and diverse entities in the biosphere, and influence the evolution of most bacterial species by promoting gene transfer, sometimes in unexpected ways. Although pac-type phages can randomly package and transfer bacterial DNA by a process called generalized transduction, some mobile genetic elements have developed elegant and sophisticated strategies to hijack the phage DNA-packaging machinery for their own transfer. Moreover, phage-like particles (gene transfer agents) have also evolved, that can package random piece...
Source: Current Opinion in Microbiology - December 18, 2014 Category: Microbiology Authors: Penadés JR, Chen J, Quiles-Puchalt N, Carpena N, Novick RP Tags: Curr Opin Microbiol Source Type: research

Emerging themes in bacterial autophagy.
Abstract The role of autophagy in the control of intracellular bacterial pathogens, also known as xenophagy, is well documented. Here, we highlight recent advances in the field of xenophagy. We review the importance of bacterial targeting by ubiquitination, diacylglycerol (DAG) or proteins such as Nod1, Nod2, NDP52, p62, NBR1, optineurin, LRSAM1 and parkin in the process of xenophagy. The importance of metabolic sensors, such as mTOR and AMPK, in xenophagy induction is also discussed. We also review the in vitro and in vivo evidence that demonstrate a global role for xenophagy in the control of bacterial growth. F...
Source: Current Opinion in Microbiology - December 9, 2014 Category: Microbiology Authors: Sorbara MT, Girardin SE Tags: Curr Opin Microbiol Source Type: research

Freund's adjuvant, NOD2 and mycobacteria.
Abstract Purpose: Mycobacterium tuberculosis contributed to the discovery of delayed-type hypersensitivity and cell-mediated immunity. However, the biochemical basis for the immunogenicity of the mycobacterial cell wall has until recently remained unknown. Recent findings: Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) responds to bacterial peptidolycan-derived muramyl dipeptide (MDP). Whereas most bacteria produce N-acetyl MDP, mycobacteria produce an unusual modified form of MDP, called N-glycolyl MDP. Disruption of N-glycolyl MDP synthesis in mycobacteria greatly diminishes the contributi...
Source: Current Opinion in Microbiology - December 4, 2014 Category: Microbiology Authors: Behr MA, Divangahi M Tags: Curr Opin Microbiol Source Type: research