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Regulation and secretion of Xanthomonas virulence factorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Plant pathogenic bacteria of the genus Xanthomonas cause a variety of diseases in economically important monocotyledonous and dicotyledonous crop plants worldwide. Successful infection and bacterial multiplication in the host tissue often depend on the virulence factors secreted including adhesins, polysaccharides, LPS and degradative enzymes. One of the key pathogenicity factors is the type III secretion system, which injects effector proteins into the host cell cytosol to manipulate plant cellular processes such as basal defense to the benefit of the pathogen. The coordinated expression of bacterial virulence factors is ...
Source: FEMS Microbiology Reviews - November 18, 2009 Category: Microbiology Authors: Daniela Büttner, Ulla Bonas Source Type: journals

Conjugative DNA metabolism in Gram-negative bacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bacterial conjugation in Gram-negative bacteria is triggered by a signal that connects the relaxosome to the coupling protein (T4CP) and transferosome, a type IV secretion system. The relaxosome, a nucleoprotein complex formed at the origin of transfer (oriT), consists of a relaxase, directed to the nic site by auxiliary DNA-binding proteins. The nic site undergoes cleavage and religation during vegetative growth, but this is converted to a cleavage and unwinding reaction when a competent mating pair has formed. Here, we review the biochemistry of relaxosomes and ponder some of the remaining questions about the nature of t...
Source: FEMS Microbiology Reviews - November 17, 2009 Category: Microbiology Authors: Fernando de la Cruz, Laura S. Frost, Richard J. Meyer, Ellen L. Zechner Source Type: journals

Common trends in mutualism revealed by model associations between invertebrates and bacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mutually beneficial interactions between microorganisms and animals are a conserved and ubiquitous feature of biotic systems. In many instances animals, including humans, are dependent on their microbial associates for nutrition, defense, or development. To maintain these vital relationships, animals have evolved processes that ensure faithful transmission of specific microbial symbionts between generations. Elucidating mechanisms of transmission and symbiont specificity has been aided by the study of experimentally tractable invertebrate animals with diverse and highly evolved associations with microorganisms. Here, we re...
Source: FEMS Microbiology Reviews - November 10, 2009 Category: Microbiology Authors: John Chaston, Heidi Goodrich-Blair Source Type: journals

Extracellular biology of Myxococcus xanthusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Myxococcus xanthus has a lifecycle characterized by several social interactions. In the presence of prey, M. xanthus is a predator forming cooperatively feeding colonies, and in the absence of nutrients, M. xanthus cells interact to form multicellular, spore-filled fruiting bodies. Formation of both cellular patterns depends on extracellular functions including the extracellular matrix and intercellular signals. Interestingly, the formation of these patterns also depends on several activities that involve direct cell[ndash]cell contacts between M. xanthus cells or direct contacts between M. xanthus cells and the substratum...
Source: FEMS Microbiology Reviews - November 7, 2009 Category: Microbiology Authors: Anna Konovalova, Tobias Petters, Lotte Søgaard-Andersen Source Type: journals

A kinetic perspective on extracellular electron transfer by anode-respiring bacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In microbial fuel cells and electrolysis cells (MXCs), anode-respiring bacteria (ARB) oxidize organic substrates to produce electrical current. In order to develop an electrical current, ARB must transfer electrons to a solid anode through extracellular electron transfer (EET). ARB use various EET mechanisms to transfer electrons to the anode, including direct contact through outer-membrane proteins, diffusion of soluble electron shuttles, and electron transport through solid components of the extracellular biofilm matrix. In this review, we perform a novel kinetic analysis of each EET mechanism by analyzing the results av...
Source: FEMS Microbiology Reviews - October 10, 2009 Category: Microbiology Authors: César I. Torres, Andrew Kato Marcus, Hyung-Sool Lee, Prathap Parameswaran, Rosa Krajmalnik-Brown, Bruce E. Rittmann Source Type: journals

Free-living amoebae and their intracellular pathogenic microorganisms: risks for water qualityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An increasing number of microorganisms, including bacteria but also viruses and eukaryotes, have been described as benefiting from interaction with free-living amoebae (FLA). Beneficial interaction can be due to resistance to predation conferring ecological advantage, intracellular survival and/or intracellular proliferation. This review highlights the potential risk associated with amoebae by listing all known pathogenic microbial species for which growth and/or survival promotion by FLA (mainly Acanthamoeba spp.) has been demonstrated. It focuses on the susceptibility of amoebal and intra-amoebal bacteria to various cate...
Source: FEMS Microbiology Reviews - September 10, 2009 Category: Microbiology Authors: Vincent Thomas, Gerald McDonnell, Stephen P. Denyer, Jean-Yves Maillard Source Type: journals

The molecular and cellular basis of pathogenesis in melioidosis: how does Burkholderia pseudomallei cause disease?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Melioidosis, a febrile illness with disease states ranging from acute pneumonia or septicaemia to chronic abscesses, was first documented by Whitmore & Krishnaswami (1912). The causative agent, Burkholderia pseudomallei, was subsequently identified as a motile, gram-negative bacillus, which is principally an environmental saprophyte. Melioidosis has become an increasingly important disease in endemic areas such as northern Thailand and Australia (Currie et al., 2000). This health burden, plus the classification of B. pseudomallei as a category B biological agent (Rotz et al., 2002), has resulted in an escalation of researc...
Source: FEMS Microbiology Reviews - September 2, 2009 Category: Microbiology Authors: Natalie R. Lazar Adler, Brenda Govan, Meabh Cullinane, Marina Harper, Ben Adler, John D. Boyce Source Type: journals

DNA base repair – recognition and initiation of catalysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Endogenous DNA damage induced by hydrolysis, reactive oxygen species and alkylation modifies DNA bases and the structure of the DNA duplex. Numerous mechanisms have evolved to protect cells from these deleterious effects. Base excision repair is the major pathway for removing base lesions. However, several mechanisms of direct base damage reversal, involving enzymes such as transferases, photolyases and oxidative demethylases, are specialized to remove certain types of photoproducts and alkylated bases. Mismatch excision repair corrects for misincorporation of bases by replicative DNA polymerases. The determination of the ...
Source: FEMS Microbiology Reviews - July 30, 2009 Category: Microbiology Authors: Bjørn Dalhus, Jon K. Laerdahl, Paul H. Backe, Magnar Bjørås Source Type: journals

Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaeaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the ...
Source: FEMS Microbiology Reviews - July 23, 2009 Category: Microbiology Authors: Wriddhiman Ghosh, Bomba Dam Source Type: journals

Identity and ecophysiology of filamentous bacteria in activated sludgeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Excessive growth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) can cause serious operational problems. With some filaments there may be the problem of bulking, where inadequate flocculation and settling of the biomass in the secondary clarifier results in a carryover of solids with the final treated liquid effluent. Their proliferation often encourages the development of stable foams on the surface of the reactors, and these foams may impact negatively on plant performance and operation. The availability of culture-independent molecular methods now allows us to identify many of the more co...
Source: FEMS Microbiology Reviews - July 20, 2009 Category: Microbiology Authors: Per Halkjær Nielsen, Caroline Kragelund, Robert J. Seviour, Jeppe Lund Nielsen Source Type: journals

Deciphering the hunting strategy of a bacterial wolfpackEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Myxococcus xanthus is a common soil bacterium with an intricate multicellular lifestyle that continues to challenge the way in which we conceptualize the capabilities of prokaryotic organisms. Myxococcus xanthus is the preferred laboratory representative from the Myxobacteria, a family of organisms distinguished by their ability to form highly structured biofilms that include tentacle-like packs of surface-gliding cell groups, synchronized rippling waves of oscillating cells and massive spore-filled aggregates that protrude upwards from the substratum to form fruiting bodies. But most of the Myxobacteria are also predators...
Source: FEMS Microbiology Reviews - June 24, 2009 Category: Microbiology Authors: James E. Berleman, John R. Kirby Source Type: journals

Generational coexistence and ancestor's inhibition in bacterial populationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Generational coexistence in structured environments raises the possibility of a competition between ancestors and descendents. This type of kin competition, and in particular, the possibility that descendents might actively repress the ancestor's dominance, has been rarely considered in microbial evolutionary ecology. The recent discovery of the phenomenon of stationary-phase contact-dependent inhibition of bacterial ancestor cells by late descendents provides a new theoretical perspective to analyze intrapopulational evolutionary changes. The ancestor's inhibition effect might accelerate such changes, particularly when th...
Source: FEMS Microbiology Reviews - June 5, 2009 Category: Microbiology Authors: Fernando Baquero, Marc Lemonnier Source Type: journals

Complexity of cyanobacterial exopolysaccharides: composition, structures, inducing factors and putative genes involved in their biosynthesis and assemblyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cyanobacterial extracellular polymeric substances (EPS) are mainly composed of high-molecular-mass heteropolysaccharides, with variable composition and roles according to the microorganism and the environmental conditions. The number of constituents [ndash] both saccharidic and nonsaccharidic [ndash] and the complexity of structures give rise to speculations on how intricate their biosynthetic pathways could be, and how many genes may be involved in their production. However, little is known regarding the cyanobacterial EPS biosynthetic pathways and regulating factors. This review organizes available information on cyanoba...
Source: FEMS Microbiology Reviews - May 16, 2009 Category: Microbiology Authors: Sara Pereira, Andrea Zille, Ernesto Micheletti, Pedro Moradas-Ferreira, Roberto De Philippis, Paula Tamagnini Source Type: journals

Bacterial strain typing in the genomic eraEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We described and compared the applications of genotyping methods to the study of bacterial strain diversity. We also discussed the selection of appropriate genotyping methods and the challenges of bacterial strain typing, described the current trends of genotyping methods, and investigated the progresses allowed by the availability of genomic sequences. (Source: FEMS Microbiology Reviews)
Source: FEMS Microbiology Reviews - May 7, 2009 Category: Microbiology Authors: Wenjun Li, Didier Raoult, Pierre-Edouard Fournier Source Type: journals

Molecular and infection biology of the horse pathogen Rhodococcus equiEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The soil actinomycete Rhodococcus equi is a pulmonary pathogen of young horses and AIDS patients. As a facultative intracellular bacterium, R. equi survives and multiplies in macrophages and establishes its specific niche inside the host cell. Recent research into chromosomal virulence factors and into the role of virulence plasmids in infection and host tropism has presented novel aspects of R. equi infection biology and pathogenicity. This review will focus on new findings in R. equi biology, the trafficking of R. equi-containing vacuoles inside host cells, factors involved in virulence and host resistance and on host[nd...
Source: FEMS Microbiology Reviews - April 24, 2009 Category: Microbiology Authors: Kristine von Bargen, Albert Haas Source Type: journals

Environmental factors shaping the ecological niches of ammonia-oxidizing archaeaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
For more than 100 years it was believed that bacteria were the only group responsible for the oxidation of ammonia. However, recently, a new strain of archaea bearing a putative ammonia monooxygenase subunit A (amoA) gene and able to oxidize ammonia was isolated from a marine aquarium tank. Ammonia-oxidizing archaea (AOA) were subsequently discovered in many ecosystems of varied characteristics and even found as the predominant causal organisms in some environments. Here, we summarize the current knowledge on the environmental conditions related to the presence of AOA and discuss the possible site-related properties. Consi...
Source: FEMS Microbiology Reviews - April 22, 2009 Category: Microbiology Authors: Tuba H. Erguder, Nico Boon, Lieven Wittebolle, Massimo Marzorati, Willy Verstraete Source Type: journals

Fungal apoptosis: function, genes and gene functionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cells of all living organisms are programmed to self-destruct under certain conditions. The most well known form of programmed cell death is apoptosis, which is essential for proper development in higher eukaryotes. In fungi, apoptotic-like cell death occurs naturally during aging and reproduction, and can be induced by environmental stresses and exposure to toxic metabolites. The core apoptotic machinery in fungi is similar to that in mammals, but the apoptotic network is less complex and of more ancient origin. Only some of the mammalian apoptosis-regulating proteins have fungal homologs, and the number of protein famili...
Source: FEMS Microbiology Reviews - April 21, 2009 Category: Microbiology Authors: Amir Sharon, Alin Finkelstein, Neta Shlezinger, Ido Hatam Source Type: journals

Bacteriophage and their lysins for elimination of infectious bacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
When phages were originally identified, the possibility of using them as antibacterial agents against pathogens was immediately recognized and put into practise based on the knowledge available at the time. However, with the advent of antibiotics a decline in the use of phage as therapeutics followed. Phages did, however, become more useful in the study of fundamental aspects of molecular biology and in the diagnostic laboratory for the identification of pathogenic bacteria. More recently, the original application of phage as therapeutics to treat human and animal infections has been rekindled, particularly in an era where...
Source: FEMS Microbiology Reviews - April 18, 2009 Category: Microbiology Authors: Sarah O'Flaherty, R. Paul Ross, Aidan Coffey Source Type: journals

Gene cassettes and cassette arrays in mobile resistance integronsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gene cassettes are small mobile elements, consisting of little more than a single gene and recombination site, which are captured by larger elements called integrons. Several cassettes may be inserted into the same integron forming a tandem array. The discovery of integrons in the chromosome of many species has led to the identification of thousands of gene cassettes, mostly of unknown function, while integrons associated with transposons and plasmids carry mainly antibiotic resistance genes and constitute an important means of spreading resistance. An updated compilation of gene cassettes found in sequences of such 'mobil...
Source: FEMS Microbiology Reviews - April 15, 2009 Category: Microbiology Authors: Sally R. Partridge, Guy Tsafnat, Enrico Coiera, Jonathan R. Iredell Source Type: journals

Multiple chaperonins in bacteria – why so many?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A significant proportion of bacteria express two or more chaperonin genes. Chaperonins are a group of molecular chaperones, defined by sequence similarity, required for the folding of some cellular proteins. Chaperonin monomers have a mass of c. 60 kDa, and are typically found as large protein complexes containing 14 subunits arranged in two rings. The mechanism of action of the Escherichia coli GroEL protein has been studied in great detail. It acts by binding to unfolded proteins and enabling them to fold in a protected environment where they do not interact with any other proteins. GroEL can assist the folding of many p...
Source: FEMS Microbiology Reviews - April 7, 2009 Category: Microbiology Authors: Peter A. Lund Source Type: journals

Tellurite: history, oxidative stress, and molecular mechanisms of resistanceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The perceived importance of tellurium (Te) in biological systems has lagged behind selenium (Se), its lighter sister in the Group 16 chalcogens, because of tellurium's lower crustal abundance, lower oxyanion solubility and biospheric mobility and the fact that, unlike Se, Te has yet to be found to be an essential trace element. Te applications in electronics, optics, batteries and mining industries have expanded during the last few years, leading to an increase in environmental Te contamination, thus renewing biological interest in Te toxicity. This chalcogen is rarely found in the nontoxic, elemental state (Te0), but its ...
Source: FEMS Microbiology Reviews - April 2, 2009 Category: Microbiology Authors: Thomas Girard Chasteen, Derie Esteban Fuentes, Juan Carlos Tantaleán, Claudio Christian Vásquez Source Type: journals

The diversity of conjugative relaxases and its application in plasmid classificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bacterial conjugation is an efficient and sophisticated mechanism of DNA transfer among bacteria. While mobilizable plasmids only encode a minimal MOB machinery that allows them to be transported by other plasmids, conjugative plasmids encode a complete set of transfer genes (MOB+T4SS). The only essential ingredient of the MOB machinery is the relaxase, the protein that initiates and terminates conjugative DNA processing. In this review we compared the sequences and properties of the relaxase proteins contained in gene sequence databases. Proteins were arranged in families and phylogenetic trees constructed from the family...
Source: FEMS Microbiology Reviews - March 29, 2009 Category: Microbiology Authors: María Pilar Garcillán-Barcia, María Victoria Francia, Fernando de la Cruz Source Type: journals

Pilin gene variation in Neisseria gonorrhoeae: reassessing the old paradigmsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Neisseria gonorrhoeae displays considerable potential for antigenic variation as shown in human experimental studies. Various surface antigens can change either by antigenic variation using RecA-dependent recombination schemes (e.g. PilE antigenic variation) or, alternatively, through phase variation (on/off switching) in a RecA-independent fashion (e.g. Opa and lipooligosaccharide phase variation). PilE antigenic variation has been well documented over the years. However, with the availability of the N. gonorrhoeae FA1090 genome sequence, considerable genetic advances have recently been made regarding the mechanistic cons...
Source: FEMS Microbiology Reviews - March 23, 2009 Category: Microbiology Authors: Stuart A. Hill, John K. Davies Source Type: journals

Genesis, effects and fates of repeats in prokaryotic genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe how repeats are created and how they can be found in genomes. We then focus on the functional and genomic consequences of repeats that dictate their fate. (Source: FEMS Microbiology Reviews)
Source: FEMS Microbiology Reviews - March 13, 2009 Category: Microbiology Authors: Todd J. Treangen, Anne-Laure Abraham, Marie Touchon, Eduardo P.C. Rocha Source Type: journals

Regulation of natural genetic transformation and acquisition of transforming DNA in Streptococcus pneumoniaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The ability of pneumococci to take up naked DNA from the environment and permanently incorporate the DNA into their genome by recombination has been exploited as a valuable research tool for 80 years. From being viewed as a marginal phenomenon, it has become increasingly clear that horizontal gene transfer by natural transformation is a powerful mechanism for generating genetic diversity, and that it has the potential to cause severe problems for future treatment of pneumococcal disease. This process constitutes a highly efficient mechanism for spreading [beta]-lactam resistance determinants between streptococcal strains a...
Source: FEMS Microbiology Reviews - March 10, 2009 Category: Microbiology Authors: Ola Johnsborg, Leiv Sigve Håvarstein Source Type: journals

Side effects of antibiotics on genetic variabilityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In recent years, there has been accumulating evidence that antibiotics, besides their antimicrobial action, potentially have a number of undesired side effects that can, at least in some cases, promote genetic variability of bacteria. In addition to resistant variants, antibiotics have also been shown to select mutator clones, thus stimulating evolution towards further resistance. Furthermore, mutations, recombination and horizontal gene transfer have been reported to be somehow affected when bacteria are exposed to subinhibitory concentrations of certain antibiotics. These findings may have implications for the use of ant...
Source: FEMS Microbiology Reviews - February 28, 2009 Category: Microbiology Authors: Alejandro Couce, Jesús Blázquez Source Type: journals

Bacterial translocation motors investigated by single molecule techniquesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Translocation of DNA and protein fibers through narrow constrictions is a ubiquitous and crucial activity of bacterial cells. Bacteria use specialized machines to support macromolecular movement. A very important step toward a mechanistic understanding of these translocation machines is the characterization of their physical properties at the single molecule level. Recently, four bacterial transport processes have been characterized by nanomanipulation at the single molecule level, DNA translocation by FtsK and SpoIIIE, DNA import during transformation, and the related process of a type IV pilus retraction. With all four p...
Source: FEMS Microbiology Reviews - February 26, 2009 Category: Microbiology Authors: Jean-Francois Allemand, Berenike Maier Source Type: journals

The genetic transformation machinery: composition, localization, and mechanismEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Natural genetic transformation is widely distributed in bacteria. It is a genetically programmed process that is inherent to the species. Transformation requires a specialized membrane-associated machinery for uptake of exogenous double-stranded DNA. It also requires dedicated cytosolic proteins, some of which have been characterized only recently, for the processing of internalized single-stranded DNA fragments into recombination products. A series of observations made in Bacillus subtilis and Streptococcus pneumoniae led to the recent emergence of a picture of a unique, highly integrated machine localized at the cell pol...
Source: FEMS Microbiology Reviews - February 18, 2009 Category: Microbiology Authors: Jean-Pierre Claverys, Bernard Martin, Patrice Polard Source Type: journals

Orphan LuxR regulators of quorum sensingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bacteria can modulate their behavior by releasing and responding to the accumulation of signal molecules. This population co-ordination, referred to as quorum sensing, is prevalent in Gram-negative and Gram-positive bacteria. The essential constituents of quorum-sensing systems include a signal producer, or synthase, and a cognate transcriptional regulator that responds to the accumulated signal molecules. With the availability of bacterial genome sequences and an increased elucidation of quorum-sensing circuits, genes that code for additional transcriptional regulators, usually in excess of the synthase, have been identif...
Source: FEMS Microbiology Reviews - February 15, 2009 Category: Microbiology Authors: Arati V. Patankar, Juan E. González Source Type: journals

Determinants of phase variation rate and the fitness implications of differing rates for bacterial pathogens and commensalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Phase variation (PV) of surface molecules and other phenotypes is a major adaptive strategy of pathogenic and commensal bacteria. Phase variants are produced at high frequencies and in a reversible manner by hypermutation or hypervariable methylation in specific regions of the genome. The major mechanisms of PV involve site-specific recombination, homologous recombination, simple sequence DNA repeat tracts or epigenetic modification by the dam methylase. PV rates of some of these mechanisms are subject to the influence of genome maintenance pathways such as DNA replication, recombination and repair while others are indepen...
Source: FEMS Microbiology Reviews - February 13, 2009 Category: Microbiology Authors: Christopher D. Bayliss Source Type: journals

Mechanisms of egg contamination by Salmonella EnteritidisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Salmonella Enteritidis (SE) has been the major cause of the food-borne salmonellosis pandemic in humans over the last 20 years, during which contaminated hen's eggs were the most important vehicle of the infection. Eggs can be contaminated on the outer shell surface and internally. Internal contamination can be the result of penetration through the eggshell or by direct contamination of egg contents before oviposition, originating from infection of the reproductive organs. Once inside the egg, the bacteria need to cope with antimicrobial factors in the albumen and vitelline membrane before migration to the yolk can occur. ...
Source: FEMS Microbiology Reviews - January 21, 2009 Category: Microbiology Authors: Inne Gantois, Richard Ducatelle, Frank Pasmans, Freddy Haesebrouck, Richard Gast, Tom J. Humphrey, Filip Van Immerseel Source Type: journals

Roles of DNA adenine methylation in host–pathogen interactions: mismatch repair, transcriptional regulation, and moreEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The DNA adenine methyltransferase (Dam methylase) of Gammaproteobacteria and the cell cycle-regulated methyltransferase (CcrM) methylase of Alphaproteobacteria catalyze an identical reaction (methylation of adenosine moieties using S-adenosyl-methionine as a methyl donor) at similar DNA targets (GATC and GANTC, respectively). Dam and CcrM are of independent evolutionary origin. Each may have evolved from an ancestral restriction-modification system that lost its restriction component, leaving an 'orphan' methylase devoted solely to epigenetic genome modification. The formation of 6-methyladenine reduces the thermodynamic s...
Source: FEMS Microbiology Reviews - January 19, 2009 Category: Microbiology Authors: Martin G. Marinus, Josep Casadesus Source Type: journals

Shuffling genes around in hot environments: the unique DNA transporter of Thermus thermophilusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Natural transformation permits the transport of DNA through bacterial membranes and represents a dominant mode for the transfer of genetic information between bacteria and between microorganisms of distant evolutionary lineages and even between members of different domains. This phenomenon, known as horizontal, or lateral, gene transfer, has been a major force for genome plasticity over evolutionary history, and is largely responsible for the spread of fitness-enhancing traits, including antibiotic resistance and virulence factors. In particular, for adaptation of prokaryotes to extreme environments, lateral gene transfer ...
Source: FEMS Microbiology Reviews - January 17, 2009 Category: Microbiology Authors: Beate Averhoff Source Type: journals

Functional role of bacterial multidrug efflux pumps in microbial natural ecosystemsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Multidrug efflux pumps have emerged as relevant elements in the intrinsic and acquired antibiotic resistance of bacterial pathogens. In contrast with other antibiotic resistance genes that have been obtained by virulent bacteria through horizontal gene transfer, genes coding for multidrug efflux pumps are present in the chromosomes of all living organisms. In addition, these genes are highly conserved (all members of the same species contain the same efflux pumps) and their expression is tightly regulated. Together, these characteristics suggest that the main function of these systems is not resisting the antibiotics used ...
Source: FEMS Microbiology Reviews - January 16, 2009 Category: Microbiology Authors: Jose Luis Martinez, María Blanca Sánchez, Laura Martínez-Solano, Alvaro Hernandez, Leonor Garmendia, Alicia Fajardo, Carolina Alvarez-Ortega Source Type: journals

From the Chief EditorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: FEMS Microbiology Reviews)
Source: FEMS Microbiology Reviews - January 7, 2009 Category: Microbiology Authors: Dieter Haas Source Type: journals

The importance of being persistent: heterogeneity of bacterial populations under antibiotic stressEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
While the DNA sequence is largely responsible for transmitting phenotypic traits over evolutionary time, organisms are also considerably affected by phenotypic variations that persist for more than one generation, with no direct change in the organisms' DNA sequence. In contrast to genetic variation, which is passed on over many generations, the phenotypic variation generated by nongenetic mechanisms is difficult to study due to the inherently limited life time of states that are not encoded in the DNA sequence, but makes it possible for the 'memory' of past environments to influence future organisms. One striking example ...
Source: FEMS Microbiology Reviews - January 7, 2009 Category: Microbiology Authors: Orit Gefen, Nathalie Q. Balaban Source Type: journals

DNA bridging and antibridging: a role for bacterial nucleoid-associated proteins in regulating the expression of laterally acquired genesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Horizontal DNA transfer plays a major role in the evolution of bacteria. It allows them to acquire new traits rapidly and these may confer fitness advantages as the bacteria compete with others in the environment. Historically, the mechanisms of horizontal DNA transfer, chiefly conjugation, transformation and transduction, have received a great deal of attention. Less attention has been focused on the regulatory problems that may accompany the acquisition of new genes by lateral routes. How are these genes integrated into the existing regulatory circuits of the cell? Does a process of 'plug-and-play' operate, or are the ne...
Source: FEMS Microbiology Reviews - December 23, 2008 Category: Microbiology Authors: Charles J. Dorman, Kelly A. Kane Source Type: journals

Escherichia coli O157:H7 colonization in small domestic ruminantsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Enterohaemorrhagic Escherichia coli O157:H7 was first implicated in human disease in the early 1980s, with ruminants cited as the primary reservoirs. Preliminary studies indicated cattle to be the sole source of E. coli O157:H7 outbreaks in humans; however, further epidemiological studies soon demonstrated that E. coli O157:H7 was widespread in other food sources and that a number of transmission routes existed. More recently, small domestic ruminants (sheep and goats) have emerged as important sources of E. coli O157:H7 human infection, particularly with the widespread popularity of petting farms and the increased use of ...
Source: FEMS Microbiology Reviews - December 17, 2008 Category: Microbiology Authors: Roberto M. La Ragione, Angus Best, Martin J. Woodward, Andrew D. Wales Source Type: journals

Colonization outwith the colon: plants as an alternative environmental reservoir for human pathogenic enterobacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Members of the Enterobacteriaceae have the capacity to adapt to a wide variety of environments and can be isolated from a range of host species across biological kingdoms. Bacteria that are pathogenic to animals, in particular humans, are increasingly found to be transmitted through the food chain by fruits and vegetables. Rather than simply contaminating plant surfaces, there is a growing body of evidence to show that these bacteria actively interact with plants and can colonize them as alternative hosts. This review draws together evidence from studies that investigate proven and potential mechanisms involved in coloniza...
Source: FEMS Microbiology Reviews - December 10, 2008 Category: Microbiology Authors: Nicola Holden, Leighton Pritchard, Ian Toth Source Type: journals

A phylogenomic analysis of bacterial helix–turn–helix transcription factorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present here a reassessment of bacterial helix[ndash]turn[ndash]helix regulator diversity in different organisms from a multidisciplinary perspective, on the interface that links metabolism, ecology and phylogeny, further sustained by a statistically based approach. The present revision brought to light evidence of patterns among families of regulators, suggesting that multiple selective forces modulate the number and kind of regulators present in a given genome. Besides being an important step towards understanding the adaptive traits that influence the microbial responses to the varying environment on the very first a...
Source: FEMS Microbiology Reviews - December 9, 2008 Category: Microbiology Authors: Catarina L. Santos, Fernando Tavares, Jean Thioulouse, Philippe Normand Source Type: journals

Genome-scale models of bacterial metabolism: reconstruction and applicationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into ba...
Source: FEMS Microbiology Reviews - December 4, 2008 Category: Microbiology Authors: Maxime Durot, Pierre-Yves Bourguignon, Vincent Schachter Source Type: journals

Toward minimal bacterial cells: evolution vs. designEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recent technical and conceptual advances in the biological sciences opened the possibility of the construction of newly designed cells. In this paper we review the state of the art of cell engineering in the context of genome research, paying particular attention to what we can learn on naturally reduced genomes from either symbiotic or free living bacteria. Different minimal hypothetically viable cells can be defined on the basis of several computational and experimental approaches. Projects aiming at simplifying living cells converge with efforts to make synthetic genomes for minimal cells. The panorama of this particula...
Source: FEMS Microbiology Reviews - December 4, 2008 Category: Microbiology Authors: Andrés Moya, Rosario Gil, Amparo Latorre, Juli Peretó, Maria Pilar Garcillán-Barcia, Fernando de la Cruz Source Type: journals

The sociobiology of biofilmsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Biofilms are densely packed communities of microbial cells that grow on surfaces and surround themselves with secreted polymers. Many bacterial species form biofilms, and their study has revealed them to be complex and diverse. The structural and physiological complexity of biofilms has led to the idea that they are coordinated and cooperative groups, analogous to multicellular organisms. We evaluate this idea by addressing the findings of microbiologists from the perspective of sociobiology, including theories of collective behavior (self-organization) and social evolution. This yields two main conclusions. First, the app...
Source: FEMS Microbiology Reviews - December 4, 2008 Category: Microbiology Authors: Carey D. Nadell, Joao B. Xavier, Kevin R. Foster Source Type: journals

Metagenomics approaches in systems microbiologyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The world of microorganisms comprises a vast diversity of live organisms, each with its individual set of genes, cellular components and metabolic reactions that interact within the cell and communicate with the environment in many different ways. There is a strong imperative to gain a broader view of the wired and interconnected cellular and environmental processes as a whole via the systems microbiology approach in order to understand and predict ecosystem functioning. On the other hand, currently we experience a rise of metagenomics as an emerging tool to study communities of uncultured microorganisms. In this review, w...
Source: FEMS Microbiology Reviews - December 2, 2008 Category: Microbiology Authors: José M. Vieites, María-Eugenia Guazzaroni, Ana Beloqui, Peter N. Golyshin, Manuel Ferrer Source Type: journals

Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The bacterial cell-envelope consists of a complex arrangement of lipids, proteins and carbohydrates that serves as the interface between a microorganism and its environment or, with pathogens, a human host. Escherichia coli has long been investigated as a leading model system to elucidate the fundamental mechanisms underlying microbial cell-envelope biology. This includes extensive descriptions of the molecular identities, biochemical activities and evolutionary trajectories of integral transmembrane proteins, many of which play critical roles in infectious disease and antibiotic resistance. Strikingly, however, only half ...
Source: FEMS Microbiology Reviews - December 1, 2008 Category: Microbiology Authors: Juan Javier Díaz-Mejía, Mohan Babu, Andrew Emili Source Type: journals

Global phenotypic characterization of bacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The measure of the quality of a systems biology model is how well it can reproduce and predict the behaviors of a biological system such as a microbial cell. In recent years, these models have been built up in layers, and each layer has been growing in sophistication and accuracy in parallel with a global data set to challenge and validate the models in predicting the content or activities of genes (genomics), proteins (proteomics), metabolites (metabolomics), and ultimately cell phenotypes (phenomics). This review focuses on the latter, the phenotypes of microbial cells. The development of Phenotype MicroArrays, which att...
Source: FEMS Microbiology Reviews - December 1, 2008 Category: Microbiology Authors: Barry R. Bochner Source Type: journals

The dynamic genetic repertoire of microbial communitiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-ba...
Source: FEMS Microbiology Reviews - December 1, 2008 Category: Microbiology Authors: Paul Wilmes, Sheri L. Simmons, Vincent J. Denef, Jillian F. Banfield Source Type: journals

Microbial systems biology: bottom up and top downEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: FEMS Microbiology Reviews)
Source: FEMS Microbiology Reviews - November 29, 2008 Category: Microbiology Authors: Víctor de Lorenzo, Michael Galperin Source Type: journals

Generation of multiple cell types in Bacillus subtilisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bacillus subtilis is a Gram-positive bacterium that is well known for its ability to differentiate into metabolically inactive spores that are highly resistant to environmental stresses. In fact, populations of genetically identical B. subtilis comprise numerous distinct cell types. In addition to spores, cells can become genetically competent, motile, produce extracellular matrix or degradative enzymes, or secrete toxins that allow them to cannibalize their neighbors. Many of the cell fates listed above appear to be mutually exclusive. In this review, we discuss how individual cells within a population control their gene ...
Source: FEMS Microbiology Reviews - November 23, 2008 Category: Microbiology Authors: Daniel Lopez, Hera Vlamakis, Roberto Kolter Source Type: journals

A global view of antibiotic resistanceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Antibiotic resistance is one of the few examples of evolution that can be addressed experimentally. The present review analyses this resistance, focusing on the networks that regulate its acquisition and its effect on bacterial physiology. It is widely accepted that antibiotics and antibiotic resistance genes play fundamental ecological roles [ndash] as weapons and shields, respectively [ndash] in shaping the structures of microbial communities. Although this Darwinian view of the role of antibiotics is still valid, recent work indicates that antibiotics and resistance mechanisms may play other ecological roles and strongl...
Source: FEMS Microbiology Reviews - November 21, 2008 Category: Microbiology Authors: Jose Luis Martinez, Alicia Fajardo, Leonor Garmendia, Alvaro Hernandez, Juan Francisco Linares, Laura Martínez-Solano, María Blanca Sánchez Source Type: journals