ScienceDirect Publication: Trends in Microbiology
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Caught in a TRAP: substrate-binding proteins in secondary transport
24 Jul 2010 at 1:54pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 23 July 2010
Marcus, Fischer , Qian Yi, Zhang , Roderick E., Hubbard , Gavin H., Thomas
Substrate-binding protein (SBP)-dependent secondary transporters are ubiquitous in prokaryotes yet poorly characterised. Recently, the structures of over 10 prokaryotic SBPs have been solved, which we compare here to consider their impact on our understanding of transporter function and evolution. Seven structures are from tripartite ATP-independent periplasmic (TRAP) transporters of the DctP-type, which have similar overall structures distinct from SBPs used by ATP-binding cassette (ABC) transporters, despite recognising a range of substrates. A defining feature of substrate recognition in the DctP?TRAP SBPs is the formation of a salt bridge between a highly conserved arginine and a carboxylate group in the substrate,...
Deep-sea piezosphere and piezophiles: geomicrobiology and biogeochemistry
20 Jul 2010 at 1:53pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 19 July 2010
Jiasong, Fang , Li, Zhang , Dennis A., Bazylinski
The deep-sea piezosphere accounts for approximately 75% of the total ocean volume and hosts active and diverse biological communities. Evidence obtained thus far suggests that the microbial biomass present in the piezosphere is significant. Continued international interest in exploring the deep ocean provides impetus to increase our understanding of the deep-sea piezosphere and of the influence of piezophilic microbial communities on the global ocean environment and on biogeochemical cycling occurring in the deep sea. Here, we review the diversity, metabolic characteristics, geomicrobiology and biogeochemistry of the deep-sea piezophiles.
Unlocking pathogen genotyping information for public health by mathematical m...
19 Jul 2010 at 2:00pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 17 July 2010
Mirjam, Kretzschmar , M., Gabriela M. Gomes , Roel A., Coutinho , James S., Koopman
Molecular typing and mathematical modeling have gone through rapid development in the past decade. Both offer new insights into the epidemiology of infectious diseases, thereby contributing to a better understanding of transmission dynamics. Infectious disease surveillance and control benefit from the optimum use of these techniques. In this paper, we review recent developments and propose methods to integrate pathogen ecology and molecular evolution based on their common dependence on the underlying host contact patterns.
A phylum level perspective on bacterial cell envelope architecture
15 Jul 2010 at 1:59pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 14 July 2010
Iain C., Sutcliffe
Improved understanding of the bacterial phylogenetic tree has allowed the distinction of at least 25 phyla with cultured representatives. This review surveys the diversity of cell envelope types present in these phyla and emphasises that it is important to define bacterial cell envelopes according to whether they have one (monoderm) or two (diderm) cellular membranes and, in the latter case, lipopolysaccharide as well. A comparative genomics approach, facilitated by the recent vast expansion in genome sequence information, is used here to survey the distribution of key lipopolysaccharide biosynthesis enzymes across the bacterial world and to consider alternative diderm cell envelope...
Microbial nanoscopy: a closer look at microbial cell surfaces
13 Jul 2010 at 2:06pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 12 July 2010
Vincent, Dupres , David, Alsteens , Guillaume, Andre , Yves F., Dufrêne
How cell envelope constituents are spatially organised and how they interact with the environment are key questions in microbiology. Unlike other bioimaging tools, atomic force microscopy (AFM) provides information about the nanoscale surface architecture of living cells and about the localization and interactions of their individual constituents. These past years have witnessed remarkable advances in our use of the AFM molecular toolbox to observe and force probe microbial cells. Recent milestones include the real-time imaging of the nanoscale organization of cell walls, the quantification of subcellular chemical heterogeneities, the mapping and functional analysis of individual cell wall constituents and the...
Distinct gene set in two different lineages of ammonia-oxidizing archaea supp...
3 Jul 2010 at 3:00pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 2 July 2010
Anja, Spang , Roland, Hatzenpichler , Céline, Brochier-Armanet , Thomas, Rattei , Patrick, Tischler , ...
Globally distributed archaea comprising ammonia oxidizers of moderate terrestrial and marine environments are considered the most abundant archaeal organisms on Earth. Based on 16S rRNA phylogeny, initial assignment of these archaea was to the Crenarchaeota. By contrast, features of the first genome sequence from a member of this group suggested that they belong to a novel phylum, the Thaumarchaeota. Here, we re-investigate the Thaumarchaeota hypothesis by including two newly available genomes, that of the marine ammonia oxidizer Nitrosopumilus maritimus and that of Nitrososphaera gargensis, a representative of another evolutionary lineage within this group predominantly detected in terrestrial environments. Phylogenetic studies...
Editorial Board
2 Jul 2010 at 1:56pm
Publication year: 2010
Source: Trends in Microbiology, Volume 18, Issue 7, July 2010, Page i
[No author name available]
Strong FtsZ is with the force: mechanisms to constrict bacteria
1 Jul 2010 at 1:54pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 1 July 2010
Jesús, Mingorance , Germán, Rivas , Marisela, Vélez , Paulino, Gómez-Puertas , Miguel, Vicente
FtsZ, the best-known prokaryotic division protein, assembles at midcell with other proteins forming a ring during septation. Widely conserved in bacteria, FtsZ represents the ancestor of tubulin. In the presence of GTP it forms polymers able to associate into multi-stranded flexible structures. FtsZ research is aimed at determining the role of the Z-ring in division, describing the polymerization and potential force-generating mechanisms and evaluating the roles of nucleotide exchange and hydrolysis. Systems to reconstruct the FtsZ ring in vitro have been described and some of its mechanical properties have been reproduced using in silico modeling. We discuss current research in...
Pathogenesis, parasitism and mutualism in the trophic space of microbe?plant ...
1 Jul 2010 at 1:54pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 1 July 2010
Adrian C., Newton , Bruce D.L., Fitt , Simon D., Atkins , Dale R., Walters , Tim J., Daniell
Microbe?host interactions can be categorised as pathogenic, parasitic or mutualistic, but in practice few examples exactly fit these descriptions. New molecular methods are providing insights into the dynamics of microbe?host interactions, with most microbes changing their relationship with their host at different life-cycle stages or in response to changing environmental conditions. Microbes can transition between the trophic states of pathogenesis and symbiosis and/or between mutualism and parasitism. In plant-based systems, an understanding of the true ecological niche of organisms and the dynamic state of their trophic interactions with their hosts has important implications for agriculture, including crop rotation, disease control...
What's in a name? The semantics of quorum sensing
22 Jun 2010 at 2:38pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 21 June 2010
Thomas G., Platt , Clay, Fuqua
The expression of many bacterial phenotypes is regulated according to the concentration of chemical cues that they or other bacteria produce, a process often termed quorum sensing (QS). Many aspects of the environment can affect cue concentration. Thus these molecules might be indirect proxies for any one or combination of environmental factors. Recent research suggests that the adaptive significance of QS varies depending on its evolutionary and ecological context. Consequently, some researchers have proposed new terms, each emphasizing different adaptive functions, for the QS process. However, these new terms generate potential for a semantic quagmire and perpetuate the questionable notion...
Molecular adaptations to psychrophily: the impact of ?omic? technologies
19 Jun 2010 at 1:30pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 18 June 2010
Ana, Casanueva , Marla, Tuffin , Craig, Cary , Don A., Cowan
The ability of cold-adapted microorganisms (generally referred to as psychrophiles) to survive is the result of molecular evolution and adaptations which, together, counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. These physiological adaptations are seen at many levels. Against a background of detailed comparative protein structural analyses, the recent surge of psychrophile proteome, genome, metagenome and transcriptome sequence data has triggered a series of sophisticated analyses of changes in global protein composition. These studies have revealed consistent and statistically robust changes in amino acid composition, interpreted as evolutionary mechanisms designed to destabilise protein...
Diversification and focusing: strategies of microbial culture collections
9 Jun 2010 at 1:15pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 9 June 2010
Erko, Stackebrandt
Implementation of quality measures, compliance with the Convention on Biological Diversity (CBD), and adoption of latest bioinformatics tools are among the main steps to be taken by microbial culture collections in order to provide resources for the emerging area of the knowledge-based bioeconomy. These measures have to be introduced side by side with the deposition of increasingly phylogenetically and physiologically diverse microbiological organisms. However, the necessary expansion of human resources and infrastructure is moving slowly, if at all. Furthermore, considering that the vast majority of microbial isolates do not find their way into public collections, a strategy should be devised...
Revealing the dynamics of polymicrobial infections: implications for antibiot...
2 Jun 2010 at 1:19pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 1 June 2010
Geraint B., Rogers , Lucas R., Hoffman , Marvin, Whiteley , Thomas V.W., Daniels , Mary P., Carroll , ...
As a new generation of culture-independent analytical strategies emerge, the amount of data on polymicrobial infections will increase dramatically. For these data to inform clinical thinking, and in turn to maximise benefits for patients, an appropriate framework for their interpretation is required. Here, we use cystic fibrosis (CF) lower airway infections as a model system to examine how conceptual and technological advances can address two clinical questions that are central to improved management of CF respiratory disease. Firstly, can markers of the microbial community be identified that predict a change in infection dynamics and clinical outcomes? Secondly, can these new...
Change is in the air
2 Jun 2010 at 1:19pm
Publication year: 2010
Source: Trends in Microbiology, Volume 18, Issue 6, June 2010, Page 233
Gail, Teitzel
Clanistics: a multi-level perspective for harvesting unrooted gene trees
1 Jun 2010 at 1:14pm
Publication year: 2010
Source: Trends in Microbiology, In Press, Corrected Proof, Available online 31 May 2010
François-Joseph, Lapointe , Philippe, Lopez , Yan, Boucher , Jeremy, Koenig , Eric, Bapteste
Prokaryotic evolution takes place within and between genomes, when significant amounts of genes are transferred and recombined between interacting genetic partners. These non-tree-like evolutionary processes, intertwined with events of vertical descent, lead to a massive production of unrooted trees in which branches, nodes and groupings have different biological meanings than for the rooted trees usually studied by phylogenetics. Such unrooted gene trees can not only inform us about organismal phylogeny, but also about the variety of evolutionary, genetic, functional and ecological relationships affecting a plurality of evolutionary units, at multiple levels ? from genes, groups of genes, organisms and consortia,...

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