Quantitative bacterial transcriptomics with RNA-seq.
Abstract RNA sequencing has emerged as the premier approach to study bacterial transcriptomes. While the earliest published studies analyzed the data qualitatively, the data are readily digitized and lend themselves to quantitative analysis. High-resolution RNA sequence (RNA-seq) data allows transcriptional features (promoters, terminators, operons, among others) to be pinpointed on any bacterial transcriptome. Once the transcriptome is mapped, the activity of transcriptional features can be quantified. Here we highlight how quantitative transcriptome analysis can reveal biological insights and briefly discuss som...
Source: Current Opinion in Microbiology - December 4, 2014 Category: Microbiology Authors: Creecy JP, Conway T Tags: Curr Opin Microbiol Source Type: research

Ten years of pan-genome analyses.
Abstract Next generation sequencing technologies have engendered a genome sequence data deluge in public databases. Genome analyses have transitioned from single or few genomes to hundreds to thousands of genomes. Pan-genome analyses provide a framework for estimating the genomic diversity of the dataset at hand and predicting the number of additional whole genomes sequences that would be necessary to fully characterize that diversity. We review recent implementations of the pan-genome approach, its impact and limits, and we propose possible extensions, including analyses at the whole genome multiple sequence alig...
Source: Current Opinion in Microbiology - December 4, 2014 Category: Microbiology Authors: Vernikos G, Medini D, Riley DR, Tettelin H Tags: Curr Opin Microbiol Source Type: research

Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites.
Abstract Our knowledge of the extent and functional impact of lateral gene transfer (LGT) from prokaryotes to eukaryotes, outside of endosymbiosis, is still rather limited. Here we review the recent literature, focusing mainly on microbial parasites, indicating that LGT from diverse prokaryotes has played a significant role in the evolution of a number of lineages, and by extension throughout eukaryotic evolution. As might be expected, taxonomic biases for donor prokaryotes indicate that shared habitat is a major factor driving transfers. The LGTs identified predominantly affect enzymes from metabolic pathways, bu...
Source: Current Opinion in Microbiology - December 4, 2014 Category: Microbiology Authors: Hirt RP, Alsmark C, Embley TM Tags: Curr Opin Microbiol Source Type: research

The rest of the story: the microbiome and gastrointestinal infections.
Abstract Bacterial infectious diseases are studied primarily as a host-pathogen dyad. However it is increasingly apparent that the gut microbial community is an important participant in these interactions. The gut microbiota influences bacterial infections in a number of ways, including via bacterial metabolism, stimulation of host immunity and direct bacterial antagonism. This review focuses on recent findings highlighting the interplay between the gastrointestinal microbiota, its host and bacterial pathogens; and emphasizes how these interactions ultimately impact our understanding of infectious diseases. P...
Source: Current Opinion in Microbiology - December 2, 2014 Category: Microbiology Authors: Leslie JL, Young VB Tags: Curr Opin Microbiol Source Type: research

Taking the pseudo out of pseudogenes.
Abstract Pseudogenes are defined as fragments of once-functional genes that have been silenced by one or more nonsense, frameshift or missense mutations. Despite continuing increases in the speed of sequencing and annotating bacterial genomes, the identification and categorisation of pseudogenes remains problematic. Even when identified, pseudogenes are considered to be rare and tend to be ignored. On the contrary, pseudogenes are surprisingly prevalent and can persist for long evolutionary time periods, representing a record of once-functional genetic characteristics. Most importantly, pseudogenes provide an insi...
Source: Current Opinion in Microbiology - December 1, 2014 Category: Microbiology Authors: Goodhead I, Darby AC Tags: Curr Opin Microbiol Source Type: research

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.
We present an overview of these new technologies and the methods used to assemble long reads into complete genomes. PMID: 25461581 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - December 1, 2014 Category: Microbiology Authors: Koren S, Phillippy AM Tags: Curr Opin Microbiol Source Type: research

Legionella pneumophila: homeward bound away from the phagosome.
Abstract The intracellular pathogen Legionella pneumophila (Lp) survives and replicates inside a specialized vacuolar compartment that evades canonical phagosomal maturation. Through the action of a large number of effectors translocated into the host cytosol via the Dot/Icm type IV secretion system, Lp subverts host cell pathways to convert its nascent phagosome into an ER-derived compartment, the Legionella containing vacuole (LCV), which serves as bacterial replication niche. PMID: 25461578 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - November 27, 2014 Category: Microbiology Authors: Prashar A, Terebiznik MR Tags: Curr Opin Microbiol Source Type: research

Microbial pathogenesis and host defense in the nematode C. elegans.
Abstract Epithelial cells line the surfaces of the body, and are on the front lines of defense against microbial infection. Like many other metazoans, the nematode Caenorhabditis elegans lacks known professional immune cells and relies heavily on defense mediated by epithelial cells. New results indicate that epithelial defense in C. elegans can be triggered through detection of pathogen-induced perturbation of core physiology within host cells and through autophagic defense against intracellular and extracellular pathogens. Recent studies have also illuminated a diverse array of pathogenic attack strategies used ...
Source: Current Opinion in Microbiology - November 27, 2014 Category: Microbiology Authors: Cohen LB, Troemel ER Tags: Curr Opin Microbiol Source Type: research

Post-modern pathogens: surprising activities of translocated effectors from E. coli and Legionella.
Abstract Many bacterial pathogens have the ability to manipulate cellular processes and interfere with host cell function through the translocation of bacterial 'effector' proteins. Dedicated protein secretion machines from Gram-negative pathogens, including type III, type IV and type VI secretion systems, inject virulence proteins into infected cells, altering normal cell physiology, including cell structure, metabolism, trafficking and signalling. While effectors were once thought to exert an effect simply by their localization and binding to host cell proteins, increasingly effectors are being recognised as enz...
Source: Current Opinion in Microbiology - November 25, 2014 Category: Microbiology Authors: Pearson JS, Zhang Y, Newton HJ, Hartland EL Tags: Curr Opin Microbiol Source Type: research

New insights into the role of Bartonella effector proteins in pathogenesis.
Abstract The facultative intracellular bacteria Bartonella spp. share a common infection strategy to invade and colonize mammals in a host-specific manner. Following transmission by blood-sucking arthropods, Bartonella are inoculated in the derma and then spread, via two sequential enigmatic niches, to the blood stream where they cause a long-lasting intra-erythrocytic bacteraemia. The VirB/VirD4 type IV secretion system (VirB/D4 T4SS) is essential for the pathogenicity of most Bartonella species by injecting an arsenal of effector proteins into host cells. These bacterial effector proteins share a modular archite...
Source: Current Opinion in Microbiology - November 25, 2014 Category: Microbiology Authors: Siamer S, Dehio C Tags: Curr Opin Microbiol Source Type: research

Novel receptors for bacterial protein toxins.
Abstract While bacterial effectors are often directly introduced into eukaryotic target cells by various types of injection machines, toxins enter the cytosol of host cells from endosomal compartments or after retrograde transport via Golgi from the ER. A first crucial step of toxin-host interaction is receptor binding. Using optimized protocols and new methods novel toxin receptors have been identified, including metalloprotease ADAM 10 for Staphylococcus aureus α-toxin, laminin receptor Lu/BCAM for Escherichia coli cytotoxic necrotizing factor CNF1, lipolysis stimulated lipoprotein receptor (LSR) for Clost...
Source: Current Opinion in Microbiology - November 22, 2014 Category: Microbiology Authors: Schmidt G, Papatheodorou P, Aktories K Tags: Curr Opin Microbiol Source Type: research

The application of genomics to tracing bacterial pathogen transmission.
Abstract New sequencing technologies have made it possible to generate bacterial genomes at clinically relevant timescales and price levels. The use of whole-genome sequencing (WGS) has proved useful for investigating transmission at different scales. WGS data are highly effective at determining whether individuals are part of the same transmission chain, making it possible to detect probable direct transmission events, delimit the extent of local nosocomial or community-based outbreaks, and identify worldwide patterns of spread and long-term dynamics of bacterial pathogens. Making the most of WGS data will probab...
Source: Current Opinion in Microbiology - November 22, 2014 Category: Microbiology Authors: Croucher NJ, Didelot X Tags: Curr Opin Microbiol Source Type: research

Neisseria meningitidis: pathogenesis and immunity.
Abstract The recent advances in cellular microbiology, genomics, and immunology has opened new horizons in the understanding of meningococcal pathogenesis and in the definition of new prophylactic intervention. It is now clear that Neissera meningitidis has evolved a number of surface structures to mediate interaction with host cells and a number of mechanisms to subvert the immune system and escape complement-mediated killing. In this review we report the more recent findings on meningococcal adhesion and on the bacteria-complement interaction highlighting the redundancy of these mechanisms. An effective vaccine ...
Source: Current Opinion in Microbiology - November 22, 2014 Category: Microbiology Authors: Pizza M, Rappuoli R Tags: Curr Opin Microbiol Source Type: research

The impact of genomics on population genetics of parasitic diseases.
Abstract Parasites, defined as eukaryotic microbes and parasitic worms that cause global diseases of human and veterinary importance, span many lineages in the eukaryotic Tree of Life. Historically challenging to study due to their complicated life-cycles and association with impoverished settings, their inherent complexities are now being elucidated by genome sequencing. Over the course of the last decade, projects in large sequencing centers, and increasingly frequently in individual research labs, have sequenced dozens of parasite reference genomes and field isolates from patient populations. This 'tsunami' of ...
Source: Current Opinion in Microbiology - November 20, 2014 Category: Microbiology Authors: Hupalo DN, Bradic M, Carlton JM Tags: Curr Opin Microbiol Source Type: research

Editorial overview: Growth and development: eukaryotes.
r M PMID: 25467419 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - November 19, 2014 Category: Microbiology Authors: Bölker M Tags: Curr Opin Microbiol Source Type: research

Neutrophil serine proteases in antibacterial defense.
Abstract Neutrophil serine proteases (NSPs) are critical for the effective functioning of neutrophils and greatly contribute to immune protection against bacterial infections. Thanks to their broad substrate specificity, these chymotrypsin-like proteases trigger multiple reactions that are detrimental to bacterial survival such as direct bacterial killing, generation of antimicrobial peptides, inactivation of bacterial virulence factors and formation of neutrophil extracellular traps. Recently, the importance of NSPs in antibacterial defenses has been further underscored by discoveries of unique bacterial evasion ...
Source: Current Opinion in Microbiology - November 18, 2014 Category: Microbiology Authors: Stapels DA, Geisbrecht BV, Rooijakkers SH Tags: Curr Opin Microbiol Source Type: research

Targeting of plant pattern recognition receptor-triggered immunity by bacterial type-III secretion system effectors.
Abstract During infection, microbes are detected by surface-localized pattern recognition receptors (PRRs), leading to an innate immune response that prevents microbial ingress. Therefore, successful pathogens must evade or inhibit PRR-triggered immunity to cause disease. In the past decade, a number of type-III secretion system effector (T3Es) proteins from plant pathogenic bacteria have been shown to suppress this layer of innate immunity. More recently, the detailed mechanisms of action have been defined for several of these effectors. Interestingly, effectors display a wide array of virulence targets, being ab...
Source: Current Opinion in Microbiology - November 13, 2014 Category: Microbiology Authors: Macho AP, Zipfel C Tags: Curr Opin Microbiol Source Type: research

Antimicrobial inflammasomes: unified signalling against diverse bacterial pathogens.
Abstract Inflammasomes - molecular platforms for caspase-1 activation - have emerged as common hubs for a number of pathways that detect and respond to bacterial pathogens. Caspase-1 activation results in the secretion of bioactive IL-1β and IL-18 and pyroptosis, and thus launches a systemic immune and inflammatory response. In this review we discuss signal transduction leading to 'canonical' and 'non-canonical' activation of caspase-1 through the involvement of upstream caspases. Recent studies have identified a growing number of regulatory networks involving guanylate binding proteins, protein kinases, ubiq...
Source: Current Opinion in Microbiology - November 13, 2014 Category: Microbiology Authors: Eldridge MJ, Shenoy AR Tags: Curr Opin Microbiol Source Type: research

Salmonella enterica: living a double life in epithelial cells.
Abstract Intracellular bacterial pathogens can occupy a membrane-bound vacuole or live freely within the cytosol of mammalian cells. Many studies have shown that the enteric bacterium, Salmonella enterica serovar Typhimurium (S. Typhimurium), is a vacuolar pathogen. Recent data, however, have revealed that within epithelial cells there are subpopulations of vacuolar and cytosolic Salmonella. Release from the Salmonella-containing vacuole leads to transcriptional reprogramming of bacteria and their robust replication in the cytosol. Eventually, epithelial cell death via pyroptosis results in cell lysis, proinflamma...
Source: Current Opinion in Microbiology - November 11, 2014 Category: Microbiology Authors: Knodler LA Tags: Curr Opin Microbiol Source Type: research

Editorial overview: Growth and development: prokaryotes: An emerging integrated view of the bacterial chromosome, from the genome to the nucleoid.
PMID: 25467420 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - November 7, 2014 Category: Microbiology Authors: Boccard F Tags: Curr Opin Microbiol Source Type: research

The bacterial nucleoid: nature, dynamics and sister segregation.
Abstract Recent studies reveal that the bacterial nucleoid has a defined, self-adherent shape and an underlying longitudinal organization and comprises a viscoelastic matrix. Within this shape, mobility is enhanced by ATP-dependent processes and individual loci can undergo ballistic off-equilibrium movements. In Escherichia coli, two global dynamic nucleoid behaviors emerge pointing to nucleoid-wide accumulation and relief of internal stress. Sister segregation begins with local splitting of individual loci, which is delayed at origin, terminus and specialized interstitial snap regions. Globally, as studied in sev...
Source: Current Opinion in Microbiology - November 5, 2014 Category: Microbiology Authors: Kleckner N, Fisher JK, Stouf M, White MA, Bates D, Witz G Tags: Curr Opin Microbiol Source Type: research

Integrated circuits: how transcriptional silencing and counter-silencing facilitate bacterial evolution.
Abstract Horizontal gene transfer is a major contributor to bacterial evolution and diversity. For a bacterial cell to utilize newly-acquired traits such as virulence and antibiotic resistance, new genes must be integrated into the existing regulatory circuitry to allow appropriate expression. Xenogeneic silencing of horizontally-acquired genes by H-NS or other nucleoid-associated proteins avoids adventitious expression and can be relieved by other DNA-binding counter-silencing proteins in an environmentally-responsive and physiologically-responsive manner. Biochemical and genetic analyses have recently demonstrat...
Source: Current Opinion in Microbiology - November 5, 2014 Category: Microbiology Authors: Will WR, Navarre WW, Fang FC Tags: Curr Opin Microbiol Source Type: research

Liaison alcaline: Pals entice non-endosomal ESCRTs to the plasma membrane for pH signaling.
st HN Abstract The alkaline pH-responsive Pal/Rim signal transduction pathway mediating regulation of gene expression by ambient pH has been extensively studied in Aspergillus nidulans and Saccharomyces cerevisiae. In A. nidulans, PalH, PalI, PalF, PalC, PalA and PalB are required for the proteolytic activation of the executing transcription factor PacC. Although necessary, Pal proteins are insufficient to transmit the signal, which additionally requires ESCRT-I, II and Vps20 with Snf7 in ESCRT-III. Although this initially suggested cooperation between a plasma membrane sensor and an ESCRT-containing Pal complex o...
Source: Current Opinion in Microbiology - November 1, 2014 Category: Microbiology Authors: Peñalva MA, Lucena-Agell D, Arst HN Tags: Curr Opin Microbiol Source Type: research

Multilayer chromosome organization through DNA bending, bridging and extrusion.
Abstract All living cells have to master the extraordinarily extended and tangly nature of genomic DNA molecules - in particular during cell division when sister chromosomes are resolved from one another and confined to opposite halves of a cell. Bacteria have evolved diverse sets of proteins, which collectively ensure the formation of compact and yet highly dynamic nucleoids. Some of these players act locally by changing the path of DNA through the bending of its double helical backbone. Other proteins have wider or even global impact on chromosome organization, for example by interconnecting two distant segments...
Source: Current Opinion in Microbiology - November 1, 2014 Category: Microbiology Authors: Gruber S Tags: Curr Opin Microbiol Source Type: research

RNA polymerase: chromosome domain boundary maker and regulator of supercoil density.
Abstract Most bacterial chromosomes and plasmids are covalently closed circular molecules that are maintained in a dynamic supercoiled state. Average supercoil density differs significantly between Escherichia coli and Salmonella. Two related questions are: What protein(s) create supercoil domain boundaries in a bacterial chromosome? and How is supercoil density regulated in different bacterial species? RNA polymerase plays pivotal roles in both of these topological phenomena. PMID: 25460807 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - November 1, 2014 Category: Microbiology Authors: Higgins NP Tags: Curr Opin Microbiol Source Type: research

Management of multipartite genomes: the Vibrio cholerae model.
zel D Abstract A minority of bacterial species has been found to carry a genome divided among several chromosomes. Among these, all Vibrio species harbor a genome split into two chromosomes of uneven size, with distinctive replication origins whose replication firing involves common and specific factors. Most of our current knowledge on replication and segregation in multi-chromosome bacteria has come from the study of Vibrio cholerae, which is now the model organism for this field. It has been firmly established that replication of the two V. cholerae chromosomes is temporally regulated and coupled to the cell cy...
Source: Current Opinion in Microbiology - October 30, 2014 Category: Microbiology Authors: Val ME, Soler-Bistué A, Bland MJ, Mazel D Tags: Curr Opin Microbiol Source Type: research

Making connections: snapshots of chlamydial type III secretion systems in contact with host membranes.
Abstract Chlamydiae are obligate intracellular bacterial pathogens with an unusual biphasic lifecycle, which is underpinned by two bacterial forms of distinct structure and function. Bacterial entry and replication require a type III secretion system (T3SS), a widely conserved nanomachine responsible for the translocation of virulence effectors into host cells. Recent cell biology experiments supported by electron and cryo-electron tomography have provided fresh insights into Chlamydia-host interactions. In this review, we highlight some of the recent advances, particularly the in situ analysis of T3SSs in contact...
Source: Current Opinion in Microbiology - October 24, 2014 Category: Microbiology Authors: Dumoux M, Nans A, Saibil HR, Hayward RD Tags: Curr Opin Microbiol Source Type: research

The role of mitochondria in cytosolic-nuclear iron-sulfur protein biogenesis and in cellular iron regulation.
f U Abstract Mitochondria are indispensable in eukaryotes because of their function in the maturation of cytosolic and nuclear iron-sulfur proteins that are essential for DNA synthesis and repair, tRNA modification, and protein translation. The mitochondrial Fe/S cluster assembly machinery not only generates the organelle's iron-sulfur proteins, but also extra-mitochondrial ones. Biogenesis of the latter proteins requires the mitochondrial ABC transporter Atm1 that exports a sulfur-containing compound in a glutathione-dependent fashion. The process is further assisted by the cytosolic iron-sulfur protein assembly ...
Source: Current Opinion in Microbiology - October 22, 2014 Category: Microbiology Authors: Lill R, Srinivasan V, Mühlenhoff U Tags: Curr Opin Microbiol Source Type: research

Spatial organization of bacterial chromosomes.
Abstract Bacterial chromosomes are organized in stereotypical patterns that are faithfully and robustly regenerated in daughter cells. Two distinct spatial patterns were described almost a decade ago in our most tractable model organisms. In recent years, analysis of chromosome organization in a larger and more diverse set of bacteria and a deeper characterization of chromosome dynamics in the original model systems have provided a broader and more complete picture of both chromosome organization and the activities that generate the observed spatial patterns. Here, we summarize these different patterns highlightin...
Source: Current Opinion in Microbiology - October 17, 2014 Category: Microbiology Authors: Wang X, Rudner DZ Tags: Curr Opin Microbiol Source Type: research

Challenges posed by extracellular vesicles from eukaryotic microbes.
Abstract Extracellular vesicles (EV) produced by eukaryotic microbes play an important role during infection. EV release is thought to benefit microbial invasion by delivering a high concentration of virulence factors to distal host cells or to the cytoplasm of a host cell. EV can significantly impact the outcome of host-pathogen interaction in a cargo-dependent manner. Release of EV from eukaryotic microbes poses unique challenges when compared to their bacterial or archaeal counterparts. Firstly, the membrane-bound organelles within eukaryotes facilitate multiple mechanisms of vesicle generation. Secondly, the f...
Source: Current Opinion in Microbiology - October 17, 2014 Category: Microbiology Authors: Wolf JM, Casadevall A Tags: Curr Opin Microbiol Source Type: research

Cell cycle regulation by the bacterial nucleoid.
Abstract Division site selection presents a fundamental challenge to all organisms. Bacterial cells are small and the chromosome (nucleoid) often fills most of the cell volume. Thus, in order to maximise fitness and avoid damaging the genetic material, cell division must be tightly co-ordinated with chromosome replication and segregation. To achieve this, bacteria employ a number of different mechanisms to regulate division site selection. One such mechanism, termed nucleoid occlusion, allows the nucleoid to protect itself by acting as a template for nucleoid occlusion factors, which prevent Z-ring assembly over t...
Source: Current Opinion in Microbiology - October 17, 2014 Category: Microbiology Authors: Adams DW, Wu LJ, Errington J Tags: Curr Opin Microbiol Source Type: research

The periplastidal compartment: a naturally minimized eukaryotic cytoplasm.
Abstract Many important algae groups like diatoms, dinoflagellates and 'kelp' but also apicomplexan parasites evolved in secondary endosymbiosis. Here, a eukaryote-eukaryote endosymbiosis created chimeric cells, in which a eukaryotic symbiont was reduced to a complex plastid. Although having lost nearly all of the eukaryotic compartments of the symbiont, a tiny lumen representing the remnant of the cytoplasm of the symbiont is still present in most of these organisms. This compartment, the periplastidal compartment, shows different degrees of reductions as in two algal groups the former nucleus is still present in...
Source: Current Opinion in Microbiology - October 15, 2014 Category: Microbiology Authors: Grosche C, Hempel F, Bolte K, Zauner S, Maier UG Tags: Curr Opin Microbiol Source Type: research

Evolution, dynamics and specialized functions of glycosomes in metabolism and development of trypanosomatids.
e;pez M, Michels PA Abstract Kinetoplastea such as trypanosomatid parasites contain specialized peroxisomes that uniquely contain enzymes of the glycolytic pathway and other parts of intermediary metabolism and hence are called glycosomes. Their specific enzyme content can vary strongly, quantitatively and qualitatively, between different species and during the parasites' life cycle. The correct sequestering of enzymes has great importance for the regulation of the trypanosomatids' metabolism and can, dependent on environmental conditions, even be essential. Glycosomes also play a pivotal role in life-cycle regula...
Source: Current Opinion in Microbiology - October 14, 2014 Category: Microbiology Authors: Szöör B, Haanstra JR, Gualdrón-López M, Michels PA Tags: Curr Opin Microbiol Source Type: research

Mechanisms for chromosome segregation.
We describe the latest advances in segregation of bacterial chromosomes with emphasis on the different pair and release mechanisms. PMID: 25460797 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - October 13, 2014 Category: Microbiology Authors: Bouet JY, Stouf M, Lebailly E, Cornet F Tags: Curr Opin Microbiol Source Type: research

Endosymbiotic theory for organelle origins.
Abstract Endosymbiotic theory goes back over 100 years. It explains the similarity of chloroplasts and mitochondria to free-living prokaryotes by suggesting that the organelles arose from prokaryotes through (endo)symbiosis. Gene trees provide important evidence in favour of symbiotic theory at a coarse-grained level, but the finer we get into the details of branches in trees containing dozens or hundreds of taxa, the more equivocal evidence for endosymbiotic events sometimes becomes. It seems that either the interpretation of some endosymbiotic events are wrong, or something is wrong with the interpretations of s...
Source: Current Opinion in Microbiology - October 9, 2014 Category: Microbiology Authors: Zimorski V, Ku C, Martin WF, Gould SB Tags: Curr Opin Microbiol Source Type: research

Fungal peroxisomes as biosynthetic organelles.
Abstract Peroxisomes are nearly ubiquitous single-membrane organelles harboring multiple metabolic pathways beside their prominent role in the β-oxidation of fatty acids. Here we review the diverse metabolic functions of peroxisomes in fungi. A variety of fungal metabolites are at least partially synthesized inside peroxisomes. These include the essential co-factor biotin but also different types of secondary metabolites. Peroxisomal metabolites are often derived from acyl-CoA esters in for example β-oxidation intermediates. In several ascomycetes a subtype of peroxisomes has been identified that is meta...
Source: Current Opinion in Microbiology - October 8, 2014 Category: Microbiology Authors: Stehlik T, Sandrock B, Ast J, Freitag J Tags: Curr Opin Microbiol Source Type: research

The chromosomal accommodation and domestication of mobile genetic elements.
Abstract Prokaryotes are constantly being infected by large mobile genetic elements (MGEs) such as conjugative elements and temperate phages. The fitness of these elements is tightly linked with the evolutionary success of the host. This leads to selection against disruptive effects their integration might have on the organization and structure of the chromosome. Seamless genetic accommodation of the mobile elements also involves silencing infectious mechanisms and expressing functions adaptive to the host. Ironically, these characteristics favor the host ability to domesticate the mobile element. Recent data sugg...
Source: Current Opinion in Microbiology - October 8, 2014 Category: Microbiology Authors: Touchon M, Bobay LM, Rocha EP Tags: Curr Opin Microbiol Source Type: research

Peroxisomal quality control mechanisms.
Abstract Peroxisomes are ubiquitous organelles that harbor diverse metabolic pathways, which are essential for normal cell performance. Conserved functions of these organelles are hydrogen peroxide metabolism and β-oxidation. Cells employ multiple quality control mechanisms to ensure proper peroxisome function and to protect peroxisomes from damage. These involve the function of molecular chaperones, a peroxisomal Lon protease and autophagic removal of dysfunctional organelles. In addition, multiple mechanisms exist to combat peroxisomal oxidative stress. Here, we outline recent advances in our understanding ...
Source: Current Opinion in Microbiology - October 8, 2014 Category: Microbiology Authors: Kumar S, Kawałek A, van der Klei IJ Tags: Curr Opin Microbiol Source Type: research

New approaches to understanding the spatial organization of bacterial genomes.
We describe the power of these techniques, highlighting the major advances they have produced while also discussing their limitations. PMID: 25305533 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - October 7, 2014 Category: Microbiology Authors: Le TB, Laub MT Tags: Curr Opin Microbiol Source Type: research

The role of mitochondria in fungal aging.
Abstract Time-dependent impairments of mitochondrial function play a key role in biological aging. Work on fungal aging models has been instrumental in unraveling basic mechanisms leading to mitochondrial dysfunction and the identification of different pathways active in keeping mitochondria 'healthy' over time. Pathways including those involved in reactive oxygen scavenging, repair of damage, proteostasis, mitochondrial dynamics, and biogenesis, are interconnected and part of a complex quality control system. The individual components of this network are limited in capacity. However, if the capacity of one pathwa...
Source: Current Opinion in Microbiology - October 6, 2014 Category: Microbiology Authors: Bernhardt D, Hamann A, Osiewacz HD Tags: Curr Opin Microbiol Source Type: research

The antibiotic resistome: what's new?
Abstract The antibiotic resistome is dynamic and ever expanding, yet its foundations were laid long before the introduction of antibiotics into clinical practice. Here, we revisit our theoretical framework for the resistome concept and consider the many factors that influence the evolution of novel resistance genes, the spread of mobile resistance elements, and the ramifications of these processes for clinical practice. Observing the trends and prevalence of genes within the antibiotic resistome is key to maintaining the efficacy of antibiotics in the clinic. PMID: 25280222 [PubMed - as supplied by publisher]...
Source: Current Opinion in Microbiology - September 30, 2014 Category: Microbiology Authors: Perry JA, Westman EL, Wright GD Tags: Curr Opin Microbiol Source Type: research

Collective antibiotic resistance: mechanisms and implications.
Abstract In collective resistance, microbial communities are able to survive antibiotic exposures that would be lethal to individual cells. In this review, we explore recent advances in understanding collective resistance in bacteria. The population dynamics of 'cheating' in a system with cooperative antibiotic inactivation have been described, providing insight into the demographic factors that determine resistance allele frequency in bacteria. Extensive work has elucidated mechanisms underlying collective resistance in biofilms and addressed questions about the role of cooperation in these structures. Additional...
Source: Current Opinion in Microbiology - September 27, 2014 Category: Microbiology Authors: Vega NM, Gore J Tags: Curr Opin Microbiol Source Type: research

Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory.
Abstract In this review, we demonstrate how game theory can be a useful first step in modeling and understanding interactions among bacteria that produce and resist antibiotics. We introduce the basic features of evolutionary game theory and explore model microbial systems that correspond to some classical games. Each game discussed defines a different category of social interaction with different resulting population dynamics (exclusion, coexistence, bistability, cycling). We then explore how the framework can be extended to incorporate some of the complexity of natural microbial communities. Overall, the game th...
Source: Current Opinion in Microbiology - September 27, 2014 Category: Microbiology Authors: Conlin PL, Chandler JR, Kerr B Tags: Curr Opin Microbiol Source Type: research

Quorum sensing peptides mediating interspecies bacterial cell death as a novel class of antimicrobial agents.
Abstract mazEF is a toxin-antitoxin stress-induced module which is abundant on the chromosome of most bacteria including pathogens and most extensively studied in Escherichia coli. E. coli mazEF mediated cell death is a population phenomenon requiring the quorum-sensing (QS) 'Extracellular Death Factor' (EDF), the E. coli peptide NNWNN. E. coli mazEF-mediated cell death can also be triggered by different QS peptides secreted by the Gram positive bacterium Bacillus subtilis and the Gram negative bacterium Pseudomonas aeruginosa. Thus, the different EDFs belong to a family of QS peptides that mediates interspecies c...
Source: Current Opinion in Microbiology - September 19, 2014 Category: Microbiology Authors: Kumar S, Engelberg-Kulka H Tags: Curr Opin Microbiol Source Type: research

Persistence: a copacetic and parsimonious hypothesis for the existence of non-inherited resistance to antibiotics.
wu KI Abstract We postulate that phenotypic resistance to antibiotics, persistence, is not an evolved (selected-for) character but rather like mutation, an inadvertent product of different kinds of errors and glitches. The rate of generation of these errors is augmented by exposure to these drugs. The genes that have been identified as contributing to the production of persisters are analogous to the so-called mutator genes; they modulate the rate at which these errors occur and/or are corrected. In theory, these phenotypically resistant bacteria can retard the rate of microbiological cure by antibiotic treatment....
Source: Current Opinion in Microbiology - August 1, 2014 Category: Microbiology Authors: Levin BR, Concepción-Acevedo J, Udekwu KI Tags: Curr Opin Microbiol Source Type: research

Editorial overview: Host-microbe interactions: parasites: sensing and responding to the changing environment: le life of protozoan parasites.
ngh M PMID: 25081632 [PubMed - as supplied by publisher] (Source: Current Opinion in Microbiology)
Source: Current Opinion in Microbiology - July 28, 2014 Category: Microbiology Authors: Guillén N, Duraisingh M Tags: Curr Opin Microbiol Source Type: research

Reactive oxygen species and the bacterial response to lethal stress.
Abstract Bacteria are killed by a variety of lethal stressors, some of which promote a cascade of reactive oxygen species (ROS). Perturbations expected to alter ROS accumulation affect the lethal action of diverse antibacterials, leading to the hypothesis that killing by these agents can involve ROS-mediated self-destruction. Recent challenges to the hypothesis are considered, particularly with respect to complexities in assays that distinguish primary damage from the cellular response to that damage. Also considered are bifunctional factors that are protective at low stress levels but destructive at high levels. ...
Source: Current Opinion in Microbiology - July 28, 2014 Category: Microbiology Authors: Zhao X, Drlica K Tags: Curr Opin Microbiol Source Type: research

Reactive dirty fragments: implications for tuberculosis drug discovery.
Abstract Reactive multi-target fragments, old synthetic antimycobacterials that are activated inside Mycobacterium tuberculosis bacilli and are smaller than the usual drug-like, single-target molecules, represent critical components of current tuberculosis chemotherapies. Recent studies showed that para-aminosalicylic acid is recognized as a substrate by dihydropteroate synthase and poisons the downstream folate pathway. Pyrazinamide, a key relapse-reducing drug, is metabolized by an amidase and the reaction product interferes with trans-translation, membrane potential and other targets. However, the mechanism of ...
Source: Current Opinion in Microbiology - July 28, 2014 Category: Microbiology Authors: Gopal P, Dick T Tags: Curr Opin Microbiol Source Type: research

Bacterial gasotransmitters: an innate defense against antibiotics.
Abstract In recent decades, there has been growing interest in the field of gasotransmitters, endogenous gaseous signaling molecules (NO, H2S, and CO), as regulators of a multitude of biochemical pathways and physiological processes. Most of the concerted effort has been on eukaryotic gasotransmitters until the subsequent discovery of bacterial counterparts. While the fundamental aspects of bacterial gasotransmitters remain undefined and necessitate further research, we will discuss a known specific role they play in defense against antibiotics. Considering the current dilemma of multidrug-resistant bacteria we co...
Source: Current Opinion in Microbiology - July 28, 2014 Category: Microbiology Authors: Luhachack L, Nudler E Tags: Curr Opin Microbiol Source Type: research

Emerging mass spectrometry techniques for the direct analysis of microbial colonies.
Abstract One of the emerging areas in microbiology is detecting specialized metabolites produced by microbial colonies and communities with mass spectrometry. In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies. Mass spectrometry techniques such as imaging mass spectrometry and real-time mass spectrometry allow two and three-dimensional visualization of the distribution of metabolites, often with minimal sample pretreatment. The speed in which molecules are captured using these methods requi...
Source: Current Opinion in Microbiology - July 24, 2014 Category: Microbiology Authors: Fang J, Dorrestein PC Tags: Curr Opin Microbiol Source Type: research