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Functional viral metagenomics and the next generation of molecular tools.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The enzymes of bacteriophages and other viruses have been essential research tools since the first days of molecular biology. However, the current repertoire of viral enzymes only hints at their overall potential. The most commonly used enzymes are derived from a surprisingly small number of cultivated viruses, which is remarkable considering the extreme abundance and diversity of viruses revealed over the past decade by metagenomic analysis. To access the treasure trove of enzymes hidden in the global virosphere and develop them for research, therapeutic and diagnostic uses, improvements are needed in our ability to r...
Source: Trends in Microbiology - November 5, 2009 Category: Microbiology Authors: Schoenfeld T, Liles M, Wommack KE, Polson SW, Godiska R, Mead D Tags: Trends Microbiol Source Type: journals

Bacterial tyrosine kinases: novel targets for antibacterial therapy?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The resistance of pathogenic bacteria to current antibiotics has become a crucial public health problem. To combat this resistance, there is a constant need for antibacterial drugs with new modes of action on therapeutic targets. Recent data have shown that a variety of cellular processes essential for bacterial survival and virulence are regulated by the phosphorylation of certain endogenous proteins catalyzed by specific tyrosine kinases. In this article, I highlight a selection of recent findings that confirm the central role of protein tyrosine phosphorylation in the control of bacterial physiology. Based on this k...
Source: Trends in Microbiology - October 21, 2009 Category: Microbiology Authors: Cozzone AJ Tags: Trends Microbiol Source Type: journals

Actinobacteria as mutualists: general healthcare for insects?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mutualistic microorganisms are well known to play a key role in providing nutrients for successful growth and reproduction in many insects. Several recent studies indicate that they can be equally important for the protection of the host and its nutritional resources against pathogen attack. In particular, different actinobacteria have been found to defend ants, beetles and wasps against detrimental microorganisms by producing antibiotics. The extraordinary abilities of actinobacteria to exploit a wide variety of carbon and nitrogen sources and their extensive repertoire of secondary metabolites probably predispose thi...
Source: Trends in Microbiology - October 21, 2009 Category: Microbiology Authors: Kaltenpoth M Tags: Trends Microbiol Source Type: journals

Can filamentous fungi form biofilms?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The discovery of biofilm formation in bacteria and yeasts has led to a better understanding of microbial ecology and to new insights into the mechanisms of virulence and persistence of pathogenic microorganisms. However, it is generally assumed that filamentous fungi, some of which have a significant impact on our health or our economy, do not form biofilms. In contrast to this assumption, here we discuss recent findings supporting the hypothesis that surface-associated filamentous fungi can form biofilms. Based on these findings and on previous models for bacterial and yeast systems, we propose preliminary criteria an...
Source: Trends in Microbiology - October 12, 2009 Category: Microbiology Authors: Harding MW, Marques LL, Howard RJ, Olson ME Tags: Trends Microbiol Source Type: journals

Role of virus-encoded microRNAs in herpesvirus biology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs (miRNAs) are short RNAs of about 22 nucleotides in length that post-transcriptionally regulate gene expression by binding to 3' untranslated regions of mRNAs, thereby inducing translational silencing. Recently, more than 140 miRNAs have been identified in the genomes of herpesviruses. Deciphering their role in viral biology requires the identification of target genes, a challenging task because miRNAs require only limited complementarity. The subject of this review will be the herpesvirus miRNAs and their respective target genes that have been determined experimentally to date. These miRNAs regulate fundament...
Source: Trends in Microbiology - October 11, 2009 Category: Microbiology Authors: Boss IW, Plaisance KB, Renne R Tags: Trends Microbiol Source Type: journals

Ecological strategies of protists and their symbiotic relationships with prokaryotic microbes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Protistan species are found in almost every environment on our planet, and have adapted in many ways to survive and thrive under dramatically different conditions. Some of the most diverse adaptations involve symbiotic relationships with prokaryotes. Described symbioses primarily involve heterotrophic protists, including ciliates, Rhizaria (amoebae, foraminifera, radiolaria) and flagellate taxa. Recently there has been an increase in reports of environmental isolates that represent novel associations, which suggest that the symbioses are probably more widespread than conventionally thought. Future work will need to exp...
Source: Trends in Microbiology - October 11, 2009 Category: Microbiology Authors: Gast RJ, Sanders RW, Caron DA Tags: Trends Microbiol Source Type: journals

Microbial disease and the coral holobiont.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Tropical coral reefs harbour a reservoir of enormous biodiversity that is increasingly threatened by direct human activities and indirect global climate shifts. Emerging coral diseases are one serious threat implicated in extensive reef deterioration through disruption of the integrity of the coral holobiont - a complex symbiosis between the coral animal, endobiotic alga and an array of microorganisms. In this article, we review our current understanding of the role of microorganisms in coral health and disease, and highlight the pressing interdisciplinary research priorities required to elucidate the mechanisms of dis...
Source: Trends in Microbiology - October 9, 2009 Category: Microbiology Authors: Bourne DG, Garren M, Work TM, Rosenberg E, Smith GW, Harvell CD Tags: Trends Microbiol Source Type: journals

Life in the inflamed intestine, Salmonella style.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The lower gastrointestinal tract is densely populated with resident microbial communities (microbiota), which do not elicit overt host responses but rather provide benefit to the host, including niche protection from pathogens. However, introduction of bacteria into the underlying tissue evokes acute inflammation. Non-typhoidal Salmonella serotypes (NTS) elicit this stereotypic host response by actively penetrating the intestinal epithelium and surviving in tissue macrophages. Initial responses generated by bacterial host cell interaction are amplified in tissue through the interleukin (IL)-18/interferon-gamma and IL-2...
Source: Trends in Microbiology - October 8, 2009 Category: Microbiology Authors: Santos RL, Raffatellu M, Bevins CL, Adams LG, Tükel C, Tsolis RM, Bäumler AJ Tags: Trends Microbiol Source Type: journals

Endofungal bacteria as producers of mycotoxins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mycotoxins are compounds of fungal origin that can adversely affect human, animal and plant health through food spoilage or infection, even to the point of epidemics such as turkey X disease and ergotism. The biosynthetic pathways of various mycotoxins (such as aflatoxin and fumonisins) are generally well understood. However, two examples have recently been described where a mycotoxin is not synthesized by the fungus itself but by bacteria residing within the fungal cytosol. These discoveries have implications in various fields, such as ecology, medicine and food processing. PMID: 19800796 [PubMed - as supplied by ...
Source: Trends in Microbiology - September 30, 2009 Category: Microbiology Authors: Lackner G, Partida-Martinez LP, Hertweck C Tags: Trends Microbiol Source Type: journals

Dealing with low pH: entry and exit of alphaviruses and flaviviruses.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The alphaviruses and flaviviruses include many important human pathogens, such as the dengue, West Nile, and Chikungunya viruses. These enveloped viruses infect cells by a membrane fusion reaction triggered by the low pH in endosomes. Fusion is mediated by viral membrane proteins through their acid-dependent conversion from a dimer on the virus surface to a homotrimer inserted into the host cell membrane. Here we review recent studies on the regulatory mechanisms that silence these fusion proteins during virus exit and that sense low pH and mediate protein refolding during virus entry. We discuss results using truncate...
Source: Trends in Microbiology - September 28, 2009 Category: Microbiology Authors: Martín CS, Liu CY, Kielian M Tags: Trends Microbiol Source Type: journals

The search for the fungal tree of life.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Fungi comprise a diverse kingdom of eukaryotes that are characterized by a typically filamentous but sometimes unicellular vegetative form, and heterotrophic, absorptive nutrition. Their simple morphologies and variable ecological strategies have confounded efforts to elucidate their limits, phylogenetic relationships, and diversity. Here we review progress in developing a phylogenetic classification of Fungi since Darwin's On the Origin of Species. Knowledge of phylogenetic relationships has been driven by the available characters that have ranged from morphological and ultrastructural to biochemical and genomic. ...
Source: Trends in Microbiology - September 23, 2009 Category: Microbiology Authors: McLaughlin DJ, Hibbett DS, Lutzoni F, Spatafora JW, Vilgalys R Tags: Trends Microbiol Source Type: journals

Medical countermeasures to protect humans from anthrax bioterrorism.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article summarizes the most important medical countermeasures that have mostly been developed since the 2001 events, and highlights current problems and possible avenues for future research. PMID: 19781945 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - September 22, 2009 Category: Microbiology Authors: Bouzianas DG Tags: Trends Microbiol Source Type: journals

Sexual reproduction in Aspergillus species of medical or economical importance: why so fastidious?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Heterothallism is dependent upon the obligatory cross-mating between self-sterile homokaryotic individuals and represents a common pattern of sexuality in yeasts and molds. Heterothallic reproductive cycles have recently been discovered in three Aspergillus species of medical and economic importance, namely Aspergillus fumigatus,A. parasiticus and A. flavus. Together with Aspergillus udagawae (Neosartorya udagawae), heterothallism has now been discovered in a total of four aspergilli that affect human health or economy. These fungi appear to express relatively low levels of fertility compared to other heterothallic or ...
Source: Trends in Microbiology - September 21, 2009 Category: Microbiology Authors: Kwon-Chung KJ, Sugui JA Tags: Trends Microbiol Source Type: journals

Ancient ESCRTs and the evolution of binary fission.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Eukaryotic and prokaryotic orthologs of tubulin play key roles in DNA segregation and cell division processes. Remarkably, recent studies have revealed that cell division can occur in the absence of this highly conserved protein. Members of the hyperthermophilic crenarchaea, that lack tubulin-like proteins, undergo division by binary fission. Here we review how this process is dependent on archaeal homologs of the eukaryotic 'endosomal sorting complex required for transport' (ESCRT) system - an apparatus that plays a pivotal role in a wide range of membrane manipulation processes. Thus, two distinct machineries to driv...
Source: Trends in Microbiology - September 21, 2009 Category: Microbiology Authors: Samson RY, Bell SD Tags: Trends Microbiol Source Type: journals

Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Rhizobia are phylogenetically disparate alpha- and beta-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen (N(2)) in symbiosis with legumes. All rhizobia elicit the formation of root - or occasionally stem - nodules, plant organs dedicated to the fixation and assimilation of nitrogen. Bacterial colonization of these nodules culminates in a remarkable case of sustained intracellular infection in plants. Rhizobial phylogenetic diversity raised the question of whether these soil bacteria shared a common core of symbiotic genes. In this article, we review the cumulative ...
Source: Trends in Microbiology - September 16, 2009 Category: Microbiology Authors: Masson-Boivin C, Giraud E, Perret X, Batut J Tags: Trends Microbiol Source Type: journals

Bacteriophages as model organisms for virus emergence research.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Viruses fully emerge by gaining the ability to sustainably infect new host populations. When the hosts are humans, emerging viruses can present major public health issues, as exemplified by the AIDS pandemic. Therefore, heuristic approaches to identify nascent diseases before they become pandemic would be valuable. Unfortunately, the current patient-based and epidemiological approaches are ill-suited in this regard because they are largely responsive and not predictive. Alternative approaches based on virus evolutionary ecology might have greater potential to predict virus emergence. However, given the difficulties enc...
Source: Trends in Microbiology - September 15, 2009 Category: Microbiology Authors: Dennehy JJ Tags: Trends Microbiol Source Type: journals

Killing me softly: chlamydial use of proteolysis for evading host defenses.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Chlamydial infections in humans cause severe health problems, including blinding trachoma and sexually transmitted diseases. Although the involved pathogenic mechanisms remain unclear, the ability to replicate and maintain long-term residence in the infected cells seems to significantly contribute to chlamydial pathogenicity. These obligate intracellular parasites maintain a delicate balance between exploiting and protecting their host: they occupy intracellular space and acquire nutrients from the infected cells, but at the same time they have to maintain the integrity of the host cells for the completion of their int...
Source: Trends in Microbiology - September 15, 2009 Category: Microbiology Authors: Zhong G Tags: Trends Microbiol Source Type: journals

Are essential genes really essential?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gene essentiality has emerged as an often-asked question in the wake of bacterial genome sequencing and a renaissance in studies of prokaryotic physiology. Genome-scale efforts at describing essential gene sets have necessarily been carried out under standard and tractable growth conditions in a laboratory setting. In addition to reinforcing our understanding of core bacterial physiology, these studies have also uncovered large numbers of essential genes encoding proteins whose functions remain poorly described. Studies of these and other elements of core physiology have naturally followed and several paradoxes, relati...
Source: Trends in Microbiology - September 15, 2009 Category: Microbiology Authors: D'Elia MA, Pereira MP, Brown ED Tags: Trends Microbiol Source Type: journals

Exploring the inner membrane proteome of Escherichia coli: which proteins are eluding detection and why?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Proteins embedded in membranes are important for helping the cell adapt to changes in the extracellular milieu and often play key roles in the life cycles of pathogenic microbes. Bioinformatic predictions can provide an estimate of membrane proteins, but experimental approaches of detection are required for a deeper understanding of their functions. To determine the effectiveness of experimental detection approaches, here we collate and discuss data from available proteomic analyses on the inner (or cytoplasmic) membrane of Escherichia coli. We compile a list of proteins that have been experimentally detected and by co...
Source: Trends in Microbiology - September 15, 2009 Category: Microbiology Authors: Bernsel A, Daley DO Tags: Trends Microbiol Source Type: journals

The use of mushroom-forming fungi for the production of N-glycosylated therapeutic proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The market for N-glycosylated therapeutic proteins represents multi-billion dollars in sales and is growing more than 10% each year. This requires cost-effective production platforms that display correct and homogeneous N-glycosylation. Based on recent results, we propose to use mushroom-forming basidiomycetes for the production of N-glycosylated therapeutic proteins. PMID: 19758804 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - September 13, 2009 Category: Microbiology Authors: Berends E, Scholtmeijer K, Wösten HA, Bosch D, Lugones LG Tags: Trends Microbiol Source Type: journals

An "omics" approach to uropathogenic Escherichia coli vaccinology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19758805 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - September 13, 2009 Category: Microbiology Authors: Sivick KE, Mobley HL Tags: Trends Microbiol Source Type: journals

On the facultative requirement of the bacterial RNA chaperone, Hfq.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The pleiotropic post-transcriptional regulator Hfq is an RNA chaperone that facilitates pairing interactions between small regulatory RNAs (sRNAs) and their mRNA targets in several bacteria. However, this classical pattern, derived from the Escherichia coli model, is not applicable to the whole bacterial kingdom. In this article we discuss the facultative requirement for Hfq for sRNA-mRNA duplex formation among bacteria and the specific features of the Hfq protein and RNA duplexes that might account for the dispensability or requirement of the chaperone. Apparent links between the need for Hfq, the GC content of bacter...
Source: Trends in Microbiology - September 1, 2009 Category: Microbiology Authors: Jousselin A, Metzinger L, Felden B Tags: Trends Microbiol Source Type: journals

Migrating microbes and planetary protection.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Since the dawn of the space age, humans have wrestled with concerns about planetary cross-contamination. Spacecraft launched from Earth can transport hitchhiker microbes to new worlds on both robotic and crewed vehicles. As plans proceed for future life detection and human exploration missions, planetary protection considerations are again uppermost on the agendas of mission planners, and microbiologists have an important role to play. PMID: 19726193 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - August 30, 2009 Category: Microbiology Authors: Nicholson WL, Schuerger AC, Race MS Tags: Trends Microbiol Source Type: journals

Infrequent marine-freshwater transitions in the microbial world.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Until recently, the evolutionary relationships between marine and freshwater microbes were unclear, but the use of molecular phylogenies is beginning to shed light on this subject. An increasing amount of studies are showing that marine and freshwater microbes (including viruses) are usually not closely related, often grouping into distinct marine and freshwater phylogenetic clusters, similar to what has been reported before for macroorganisms. These studies indicate that marine-freshwater transitions have been infrequent events during the diversification of microbes and that most of these transitions occurred a long t...
Source: Trends in Microbiology - August 30, 2009 Category: Microbiology Authors: Logares R, Bråte J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K Tags: Trends Microbiol Source Type: journals

LPxTG surface proteins of enterococci.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Enterococci have become an important cause of nosocomial infections since the late 1980s. Several surface proteins have been implicated in contributing to infections caused by Enterococcus faecalis and Enterococcus faecium. Understanding the in vivo function of enterococcal surface proteins, particularly their role in directing interactions with the host during infection, is essential to explain the success of enterococci as nosocomial pathogens. Here we review current knowledge of enterococcal LPxTG surface proteins, including aggregation substance, enterococcal surface protein, three collagen-binding microbial surfac...
Source: Trends in Microbiology - August 30, 2009 Category: Microbiology Authors: Hendrickx AP, Willems RJ, Bonten MJ, van Schaik W Tags: Trends Microbiol Source Type: journals

Color me bad: microbial pigments as virulence factors.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A hallmark feature of several pathogenic microbes is the distinctive color of their colonies when propagated in the clinical laboratory. Such pigmentation comes in a variety of hues, and has often proven useful in presumptive clinical diagnosis. Recent advances in microbial pigment biochemistry and the genetic basis of pigment production have sometimes revealed a more sinister aspect to these curious materials that change the color of reflected light by selective light absorbance. In many cases, the microbial pigment contributes to disease pathogenesis by interfering with host immune clearance mechanisms or by exhibiti...
Source: Trends in Microbiology - August 30, 2009 Category: Microbiology Authors: Liu GY, Nizet V Tags: Trends Microbiol Source Type: journals

Microbial TIR domains: not necessarily agents of subversion?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Toll/interleukin-1 receptor (TIR) domain plays a crucial role in the mammalian innate immune response. Recently, proteins containing TIR domains have been described in bacteria and it has been suggested that these bacterial proteins are involved in subversion of the vertebrate immune system. Here we describe the distribution of TIR-domain proteins among bacteria, fungi, archaea and viruses and evaluate the subversion hypothesis in the light of our findings. We suggest that most TIR domains in bacteria have nothing to do with subverting eukaryotic cells; instead, TIR domains function simply as general purpose protei...
Source: Trends in Microbiology - August 26, 2009 Category: Microbiology Authors: Spear AM, Loman NJ, Atkins HS, Pallen MJ Tags: Trends Microbiol Source Type: journals

What did Darwin say about microbes, and how did microbiology respond?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Although it is commonly assumed that Darwin had nothing to say about microbes, he did in fact say quite a lot. He included microbes in his Beagle studies of the geographical distribution of organisms and used microscopic organisms as explicit exemplars of how adaptation did not imply increasing complexity. Darwin often discussed microrganismal classification, origins and experimentation in his correspondence. But despite his interests in microbial phenomena, Darwin's impact on microbiological thinking of the late nineteenth century was negligible. This limited response may be connected to today's assumptions about Darw...
Source: Trends in Microbiology - August 10, 2009 Category: Microbiology Authors: O'Malley MA Tags: Trends Microbiol Source Type: journals

Outer membrane translocation: numerical protein secretion nomenclature in question in mycobacteria.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19674902 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - August 9, 2009 Category: Microbiology Authors: Desvaux M, Hébraud M, Talon R, Henderson IR Tags: Trends Microbiol Source Type: journals

Type VII secretion in mycobacteria: classification in line with cell envelope structure.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bacteria with an outer membrane are faced with a double hydrophobic barrier for protein secretion. To achieve this, several different secretion machineries have evolved. In a recent Opinion article in this journal, Mickaël Desvaux and colleagues [Desvaux, M., et al. (2009) Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends in microbiology] discuss the nomenclature of these secretion systems. Although we agree that consensus in nomenclature is important, here we discuss an important point that was overlooked. PMID: 19660950 [PubMed - as supplied by publisher] (Sour...
Source: Trends in Microbiology - August 3, 2009 Category: Microbiology Authors: Bitter W, Houben EN, Luirink J, Appelmelk BJ Tags: Trends Microbiol Source Type: journals

Brucella regulators: self-control in a hostile environment.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Brucella is an important zoonotic pathogen for which no human vaccine exists. In an infected host, Brucella resides in macrophages but must coordinate expression of multiple virulence factors for successful cell entry and trafficking to acquire this replicative niche. Brucella responds to environmental signals to regulate virulence strategies that circumvent or blunt the host immune response. The Brucella quorum sensing system is a nexus of control for several Brucella virulence factors including flagellar genes and the type IV secretion system. Other sensory transduction systems, such as BvrRS and the newly described ...
Source: Trends in Microbiology - August 3, 2009 Category: Microbiology Authors: Rambow-Larsen AA, Petersen EM, Gourley CR, Splitter GA Tags: Trends Microbiol Source Type: journals

Mineral weathering by bacteria: ecology, actors and mechanisms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Soil microbes play an essential role in the environment by contributing to the release of key nutrients from primary minerals that are required not only for their own nutrition but also for that of plants. Although the role of fungi in mineral weathering is beginning to be elucidated, the relative impact of bacteria in this process and the molecular mechanisms involved remain poorly understood. Here, we discuss the ecological relevance of bacterial weathering, mainly in the soil and especially in acidic forest ecosystems, which strongly depend on mineral weathering for their sustainability. We also present highlights f...
Source: Trends in Microbiology - August 3, 2009 Category: Microbiology Authors: Uroz S, Calvaruso C, Turpault MP, Frey-Klett P Tags: Trends Microbiol Source Type: journals

A prototype two-partner secretion pathway: the Haemophilus influenzae HMW1 and HMW2 adhesin systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nontypable Haemophilus influenzae is a common cause of human disease and initiates infection by colonizing the upper respiratory tract. Adherence to respiratory epithelium is an important step in the process of colonization and is influenced by adhesive proteins called adhesins. In approximately 80% of nontypable H. influenzae isolates, the major adhesins are related proteins called HMW1 and HMW2. Here, we summarize recent advances in our understanding of HMW1 and HMW2 as prototype members of the bacterial two-partner secretion pathway and examples of the expanding number of bacterial glycoproteins, highlighting experi...
Source: Trends in Microbiology - August 3, 2009 Category: Microbiology Authors: St Geme JW, Yeo HJ Tags: Trends Microbiol Source Type: journals

Controlling injection: regulation of type III secretion in enterohaemorrhagic Escherichia coli.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Type III secretion (T3S) systems enable the injection of bacterial proteins through membrane barriers into host cells, either from outside the host cell or from within a vacuole. This system is required for colonization of their ruminant reservoir hosts by enterohaemorrhagic Escherichia coli (EHEC) and might also be important for the etiology of disease in the incidental human host. T3S systems of E. coli inject a cocktail of proteins into epithelial cells that enables bacterial attachment and promotes longer-term colonization in the animal. Here, we review recent progress in our understanding of the regulation of T3S ...
Source: Trends in Microbiology - August 3, 2009 Category: Microbiology Authors: Tree JJ, Wolfson EB, Wang D, Roe AJ, Gally DL Tags: Trends Microbiol Source Type: journals

Symbiont-mediated protection in insect hosts.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microbes influence the ecology and evolution of their hosts in a variety of ways, including the formation of life-long beneficial or detrimental parasitic infections. Understanding the molecular and biochemical events that underpin symbiosis - beneficial or parasitic - has been a long-term goal of molecular symbiosis research. In addition to beneficial symbionts provisioning scarce resources to their hosts, a growing body of evidence shows that bacterial symbionts can protect their hosts from parasitic symbionts and predators. Here, we review recent theoretical predictions and experimental observations of symbiont-medi...
Source: Trends in Microbiology - August 3, 2009 Category: Microbiology Authors: Brownlie JC, Johnson KN Tags: Trends Microbiol Source Type: journals

Infection strategies of filamentous microbes described with the Gene Ontology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Filamentous microbes that form highly developed symbiotic associations (ranging from pathogenesis to mutualism) with their hosts include fungi, oomycetes and actinomycete bacteria. These organisms share many common features in growth, development and infection and have evolved similar strategies for neutralizing host defense responses to establish symbioses. Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced genomes of filamentous organisms. Analysis of the available genomes has provided useful information about genes that might be important for host infection and co...
Source: Trends in Microbiology - July 2, 2009 Category: Microbiology Authors: Torto-Alalibo T, Meng S, Dean RA Tags: Trends Microbiol Source Type: journals

Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Gene Ontology (GO) is a structured controlled vocabulary developed to describe the roles and locations of gene products in a consistent manner and in a way that can be shared across organisms. The unicellular fungus Candida albicans is similar in many ways to the model organism Saccharomyces cerevisiae but, as both a commensal and a pathogen of humans, differs greatly in its lifestyle. With an expanding at-risk population of immunosuppressed patients, increased use of invasive medical procedures, the increasing prevalence of drug resistance and the emergence of additional Candida species as serious pathogens, it ha...
Source: Trends in Microbiology - July 2, 2009 Category: Microbiology Authors: Arnaud MB, Costanzo MC, Shah P, Skrzypek MS, Sherlock G Tags: Trends Microbiol Source Type: journals

Viewing the microbial world through the lens of the Gene Ontology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19577929 [PubMed - as supplied by publisher] (Source: Trends in Microbiology)
Source: Trends in Microbiology - July 2, 2009 Category: Microbiology Authors: Tyler BM Tags: Trends Microbiol Source Type: journals

Controlled vocabularies for microbial virulence factors.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Knowledge about pathogenesis is increasing dramatically, and most of this information is stored in the scientific literature or in sequence databases. This information can be made more accessible by the use of ontologies or controlled vocabularies. Recently, several ontologies, controlled vocabularies and databases have been developed or adapted for virulence factors and their roles in pathogenesis. Here, we discuss these systems, how they are being used in research and the challenges that remain for developing and applying ontologies for virulence factors. PMID: 19577471 [PubMed - as supplied by publisher] (Source...
Source: Trends in Microbiology - July 1, 2009 Category: Microbiology Authors: Korves T, Colosimo ME Tags: Trends Microbiol Source Type: journals

Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The quest to characterize each of the genes of the yeast Saccharomyces cerevisiae has propelled the development and application of novel high-throughput (HTP) experimental techniques. To handle the enormous amount of information generated by these techniques, new bioinformatics tools and resources are needed. Gene Ontology (GO) annotations curated by the Saccharomyces Genome Database (SGD) have facilitated the development of algorithms that analyze HTP data and help predict functions for poorly characterized genes in S. cerevisiae and other organisms. Here, we describe how published results are incorporated into GO ann...
Source: Trends in Microbiology - July 1, 2009 Category: Microbiology Authors: Christie KR, Hong EL, Cherry JM Tags: Trends Microbiol Source Type: journals

Applying the Gene Ontology in microbial annotation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The ever-increasing number of microbial sequencing projects necessitates a standardized system for the capture of genomic data to ensure that the flood of information produced can be effectively utilized. The Gene Ontology (GO) provides the standard for gene product annotations in the areas of molecular function, biological process and cellular component. A recent effort by the Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has produced more than 800 new GO terms specific for annotating interactions between microbes and their hosts and other symbiotic interactions. In addition, there have been changes and ad...
Source: Trends in Microbiology - July 1, 2009 Category: Microbiology Authors: Giglio MG, Collmer CW, Lomax J, Ireland A Tags: Trends Microbiol Source Type: journals

Understanding animal viruses using the Gene Ontology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Understanding the effects of viral infection has typically focused on specific virus-host interactions such as tissue tropism, immune responses and histopathology. However, modeling viral pathogenesis requires information about the functions of gene products from both virus and host, and how these products interact. Recent developments in the functional annotation of genomes using Gene Ontology (GO) and in modeling functional interactions among gene products, together with an increased interest in systems biology, provide an excellent opportunity to generate global interaction models for viral infection. Here, we revie...
Source: Trends in Microbiology - July 1, 2009 Category: Microbiology Authors: McCarthy FM, Mahony TJ, Parcells MS, Burgess SC Tags: Trends Microbiol Source Type: journals

Gene Ontology for type III effectors: capturing processes at the host-pathogen interface.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Disease development is determined by the interplay of host defense processes and pathogen factors that subvert defenses and remodel the host for parasitic benefit. The goal of the Plant-Associated Microbe Gene Ontology (PAMGO) interest group is the development of Gene Ontology (GO) terms that capture the range of biological processes occurring between hosts and symbionts (from mutualists to pathogens). Here, the application of the new GO terms to type III effector proteins (T3Es) from the plant pathogen Pseudomonas syringae serves as an example to systematically document the available extensive data and to reveal share...
Source: Trends in Microbiology - June 30, 2009 Category: Microbiology Authors: Lindeberg M, Collmer A Tags: Trends Microbiol Source Type: journals

What we can learn about Escherichia coli through application of Gene Ontology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
How we classify the genes, products and complexes that are present or absent in genomes, transcriptomes, proteomes and other datasets helps us place biological objects into subsystems with common functions, see how molecular functions are used to implement biological processes and compare the biology of different species and strains. Gene Ontology (GO) is one of the most successful systems for classifying biological function. Although GO is widely used for eukaryotic genomics, it has not yet been widely used for bacterial systems. The potential applications of GO are currently limited by the need to improve the annotat...
Source: Trends in Microbiology - June 30, 2009 Category: Microbiology Authors: Hu JC, Karp PD, Keseler IM, Krummenacker M, Siegele DA Tags: Trends Microbiol Source Type: journals

Describing commonalities in microbial effector delivery using the Gene Ontology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Myriad symbiotic microbes, ranging from mutualistic through to pathogenic, deliver 'effector' molecules into the cytoplasm or cellular milieu of their hosts to facilitate colonization. Among ecologically and evolutionarily diverse taxa, analogous processes and structures exist to facilitate effector delivery. These include syringe-like injection (bacteria and nematodes), common host-targeting signals (oomycetes and protozoans) and specialized intercellular structures (fungi and oomycetes). Here, we briefly introduce readers to the Gene Ontology (GO), a controlled vocabulary to facilitate comparative genomics of diverse...
Source: Trends in Microbiology - June 30, 2009 Category: Microbiology Authors: Chibucos MC, Tseng TT, Setubal JC Tags: Trends Microbiol Source Type: journals

Why do bacteria engage in homologous recombination?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Microbiologists have long recognized that the uptake and incorporation of homologous DNA from outside the cell is a common feature of bacteria, with important implications for their evolution. However, the exact reasons why bacteria engage in homologous recombination remain elusive. This Opinion article aims to reinvigorate the debate by examining the costs and benefits that homologous recombination could engender in natural populations of bacteria. It specifically focuses on the hypothesis that homologous recombination is selectively maintained because the genetic variation it generates improves the response of bacter...
Source: Trends in Microbiology - June 1, 2009 Category: Microbiology Authors: Vos M Tags: Trends Microbiol Source Type: journals

A modular master on the move: the Tn916 family of mobile genetic elements.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Tn916 family is a group of mobile genetic elements that are widespread among many commensal and pathogenic bacteria. These elements are found primarily, but not exclusively, in the Firmicutes. They are integrated into the bacterial genome and are capable of conjugative transfer to a new host and, often, intracellular transposition to a different genomic site - hence their name: 'conjugative transposons', or 'integrative conjugative elements'. An increasing variety of Tn916 relatives are being reported from different bacteria, harbouring genes coding for resistance to various antibiotics and the potential to encode ...
Source: Trends in Microbiology - June 1, 2009 Category: Microbiology Authors: Roberts AP, Mullany P Tags: Trends Microbiol Source Type: journals

Lipoteichoic acid biosynthesis: two steps forwards, one step sideways?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Lipoteichoic acids (LTAs) are membrane-anchored molecules in the cell envelopes of Gram-positive bacteria. Until recently, they were considered to be restricted to the Firmicutes, which include important pathogens such as Staphylococcus aureus and Streptococcus pneumoniae. Polyanionic LTAs have fundamentally important roles in divalent cation retention within the Gram-positive cell envelope and thereby influence bacterial cell division. Thus, LTA biosynthesis provides an attractive target for the development of novel antimicrobial interventions. Recent studies, notably two investigations of S. aureus and another of Bac...
Source: Trends in Microbiology - June 1, 2009 Category: Microbiology Authors: Rahman O, Dover LG, Sutcliffe IC Tags: Trends Microbiol Source Type: journals

For absent friends: life without recombination in mutualistic gamma-proteobacteria.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Almost all cellular organisms employ RecA orthologues to guide the strand invasion reactions necessary for DNA recombination and repair. One of the few exceptions to this orthodoxy is a group of gamma-proteobacteria flourishing in obligate intracellular symbiosis with insects and deep-sea clams. The apparent inability of these bacteria to commence the recombinational exchange process seems to confer genetic stability by preventing any further rearrangements or lateral transfer events. Although debate has centred on the absence of selected recombination functions and their impact on a fixed genomic architecture, no expl...
Source: Trends in Microbiology - June 1, 2009 Category: Microbiology Authors: Sharples GJ Tags: Trends Microbiol Source Type: journals

Ancient micronauts: interplanetary transport of microbes by cosmic impacts.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent developments in microbiology, geophysics and planetary sciences raise the possibility that the planets in our solar system might not be biologically isolated. Hence, the possibility of lithopanspermia (the interplanetary transport of microbial passengers inside rocks) is presently being re-evaluated, with implications for the origin and evolution of life on Earth and within our solar system. Here, I summarize our current understanding of the physics of impacts, space transport of meteorites, and the potentiality of microorganisms to undergo and survive interplanetary transfer. PMID: 19464895 [PubMed - in pro...
Source: Trends in Microbiology - June 1, 2009 Category: Microbiology Authors: Nicholson WL Tags: Trends Microbiol Source Type: journals