Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi

Background: Haloquadratum walsbyi represents up to 80 % of cells in NaCl-saturated brines worldwide, but is notoriously difficult to maintain under laboratory conditions. In order to establish the extent of genetic diversity in a natural population of this microbe, we screened a H. walsbyi enriched metagenomic fosmid library and recovered seven novel version of its cell-wall associated genomic island. The fosmid inserts were sequenced and analysed. Results: The novel cell-wall associated islands delineated two major clades within H. walsbyi. The islands predominantly contained genes putatively involved in biosynthesis of surface layer, genes encoding cell surface glycoproteins and genes involved in envelope formation. We further found that these genes are maintained in the population and that the diversity of this region arises through homologous recombination but also through the action of mobile genetic elements, including viruses. Conclusions: The population of H. walsbyi in the studied saltern brine is composed of numerous clonal lineages that differ in surface structures including the cell wall. This type of variation probably reflects a number of mechanisms that minimize the infection rate of predating virusesAll authors were supported by project MICROGEN (Programa CONSOLIDER-INGENIO 2010 CSD2009-00006) from the Spanish Ministerio de Ciencia e Innovación.FR-V and AMBC received support from MEDIMAX BFPU2013- 48007-P from the Spanish Ministerio de Economía y CompetitividadMaCuMBA Project 311975 of the European Commission FP7ACOMP/2014/024, AORG 2014/032 and PROMETEO II/2014/012. LP received support from Ministry for School and Sports of the Republic of Slovenia under Slovenian Research Agency program P1-0198

Mobile DNA and evolution in the 21st century

Scientific history has had a profound effect on the theories of evolution. At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write (RW) memory system rather than an organism blueprint. Genome sequencing has documented the importance of mobile DNA activities and major genome restructuring events at key junctures in evolution: exon shuffling, changes in cis-regulatory sites, horizontal transfer, cell fusions and whole genome doublings (WGDs). The natural genetic engineering functions that mediate genome restructuring are activated by multiple stimuli, in particular by events similar to those found in the DNA record: microbial infection and interspecific hybridization leading to the formation of allotetraploids. These molecular genetic discoveries, plus a consideration of how mobile DNA rearrangements increase the efficiency of generating functional genomic novelties, make it possible to formulate a 21st century view of interactive evolutionary processes. This view integrates contemporary knowledge of the molecular basis of genetic change, major genome events in evolution, and stimuli that activate DNA restructuring with classical cytogenetic understanding about the role of hybridization in species diversification

Finding a Needle in the Virus Metagenome Haystack - Micro-Metagenome Analysis Captures a Snapshot of the Diversity of a Bacteriophage Armoire

Viruses are ubiquitous in the oceans and critical components of marine microbial communities, regulating nutrient transfer to higher trophic levels or to the dissolved organic pool through lysis of host cells. Hydrothermal vent systems are oases of biological activity in the deep oceans, for which knowledge of biodiversity and its impact on global ocean biogeochemical cycling is still in its infancy. In order to gain biological insight into viral communities present in hydrothermal vent systems, we developed a method based on deep-sequencing of pulsed field gel electrophoretic bands representing key viral fractions present in seawater within and surrounding a hydrothermal plume derived from Loki's Castle vent field at the Arctic Mid-Ocean Ridge. The reduction in virus community complexity afforded by this novel approach enabled the near-complete reconstruction of a lambda-like phage genome from the virus fraction of the plume. Phylogenetic examination of distinct gene regions in this lambdoid phage genome unveiled diversity at loci encoding superinfection exclusion- and integrase-like proteins. This suggests the importance of fine-tuning lyosgenic conversion as a viral survival strategy, and provides insights into the nature of host-virus and virus-virus interactions, within hydrothermal plumes. By reducing the complexity of the viral community through targeted sequencing of prominent dsDNA viral fractions, this method has selectively mimicked virus dominance approaching that hitherto achieved only through culturing, thus enabling bioinformatic analysis to locate a lambdoid viral “needle" within the greater viral community “haystack". Such targeted analyses have great potential for accelerating the extraction of biological knowledge from diverse and poorly understood environmental viral communities

Insights into bacterial genome composition through variable target GC content profiling

This study presents a new computational method for guanine (G) and cytosine (C), or GC, content profiling based on the idea of multiple resolution sampling (MRS). The benefit of our new approach over existing techniques follows from its ability to locate significant regions without prior knowledge of the sequence, nor the features being sought. The use of MRS has provided novel insights into bacterial genome composition. Key findings include those that are related to the core composition of bacterial genomes, to the identification of large genomic islands (in Enterobacterial genomes), and to the identification of surface protein determinants in human pathogenic organisms (e.g., Staphylococcus genomes). We observed that bacterial surface binding proteins maintain abnormal GC content, potentially pointing to a viral origin. This study has demonstrated that GC content holds a high informational worth and hints at many underlying evolutionary processes. For online Supplementary Material, see www.liebertonline.com

Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies

Background: Arctic Mesorhizobium strain N33 was isolated from nodules of the legume Oxytropis arctobia in Canada’s eastern Arctic. This symbiotic bacterium can grow at temperatures ranging from 0 to 30 °C, fix nitrogen at 10 °C, and is one of the best known cold-adapted rhizobia. Despite the economic potential of this bacterium for northern regions, the key molecular mechanisms of its cold adaptation remain poorly understood. Results: Using a microarray printed with 5760 Arctic Mesorhizobium genomic clones, we performed a partial transcriptome analysis of strain N33 grown under eight different temperature conditions, including both sustained and transient cold treatments, compared with cells grown at room temperature. Cells treated under constant (4 and 10 °C) low temperatures expressed a prominent number of induced genes distinct from cells treated to short-term cold-exposure (<60 min), but exhibited an intermediate expression profile when exposed to a prolonged cold exposure (240 min). The most prominent up-regulated genes encode proteins involved in metabolite transport, transcription regulation, protein turnover, oxidoreductase activity, cryoprotection (mannitol, polyamines), fatty acid metabolism, and membrane fluidity. The main categories of genes affected in N33 during cold treatment are sugar transport and protein translocation, lipid biosynthesis, and NADH oxidoreductase (quinone) activity. Some genes were significantly down-regulated and classified in secretion, energy production and conversion, amino acid transport, cell motility, cell envelope and outer membrane biogenesis functions. This might suggest growth cessation or reduction, which is an important strategy to adjust cellular function and save energy under cold stress conditions. Conclusion: Our analysis revealed a complex series of changes associated with cold exposure adaptation and constant growth at low temperatures. Moreover, it highlighted some of the strategies and different physiological states that Mesorhizobium strain N33 has developed to adapt to the cold environment of the Canadian high Arctic and has revealed candidate genes potentially involved in cold adaptati

Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts

Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence and evolutionary dynamics of this phenomenon, 33 cultured cyanophages of known family and host range and viral DNA from field samples were screened for the presence of two core photosystem reaction center genes, psbA and psbD. Combining this expanded dataset with published data for nine other cyanophages, we found that 88% of the phage genomes contain psbA, and 50% contain both psbA and psbD. The psbA gene was found in all myoviruses and Prochlorococcus podoviruses, but could not be amplified from Prochlorococcus siphoviruses or Synechococcus podoviruses. Nearly all of the phages that encoded both psbA and psbD had broad host ranges. We speculate that the presence or absence of psbA in a phage genome may be determined by the length of the latent period of infection. Whether it also carries psbD may reflect constraints on coupling of viral- and host-encoded PsbA–PsbD in the photosynthetic reaction center across divergent hosts. Phylogenetic clustering patterns of these genes from cultured phages suggest that whole genes have been transferred from host to phage in a discrete number of events over the course of evolution (four for psbA, and two for psbD), followed by horizontal and vertical transfer between cyanophages. Clustering patterns of psbA and psbD from Synechococcus cells were inconsistent with other molecular phylogenetic markers, suggesting genetic exchanges involving Synechococcus lineages. Signatures of intragenic recombination, detected within the cyanophage gene pool as well as between hosts and phages in both directions, support this hypothesis. The analysis of cyanophage psbA and psbD genes from field populations revealed significant sequence diversity, much of which is represented in our cultured isolates. Collectively, these findings show that photosynthesis genes are common in cyanophages and that significant genetic exchanges occur from host to phage, phage to host, and within the phage gene pool. This generates genetic diversity among the phage, which serves as a reservoir for their hosts, and in turn influences photosystem evolution

Evolution of hydrogenosomes in anaerobic ciliates

Phd ThesisWithin ciliates (protozoa of the phylum Ciliophora), anaerobic species are widespread and typically possess organelles which produce H2 and ATP, called hydrogenosomes. Hydrogenosomes are mitochondrial homologues and are a product of evolutionary convergence, having been found in wide-ranging and diverse anaerobic eukaryotes. Ciliates seem to have evolved hydrogenosomes on multiple occasions from the mitochondria of their aerobic ancestors. The hydrogenosomes of the ciliate Nyctotherus ovalis were studied in detail previously but little is known about the hydrogenosomes from other ciliate species. In the present study seven species of ciliate, Cyclidium porcatum, Metopus contortus, Metopus es, Metopus striatus, Nyctotherus ovalis, Plagiopyla frontata and Trimyema sp. were cultured and their hydrogenosomes were investigated using genomic and transcriptomic sequencing from whole genome amplifications from single and small numbers of isolated cells. The data were then used to reconstruct putative hydrogenosome metabolic pathways. Components of these pathways are typically encoded by the ciliate nuclear genomes but Nyctotherus ovalis, Metopus contortus, Metopus es, Metopus striatus and Cyclidium porcatum have also retained mitochondrial (now hydrogenosomal) genomes which were sequenced for the first time. The most complete of these genomes were from Nyctotherus ovalis and Metopus contortus. These have both retained genes for proton-pumping subunits of the electron transport chain Complex I and ribosomal subunits needed for their synthesis. The ciliates Plagiopyla frontata and Trimyema sp. appear to have completely lost the organelle genome during the conversion of mitochondria into hydrogenosomes. The ciliate hydrogenosomes for which the most data was obtained appear to have retained some of the enzymes needed to produce energy by substrate-level phosphorylation but some species have also retained a partial electron transport chain and Cyclidium porcatum has retained nuclear encoded subunits of the mitochondrial F1F0 ATP synthase complex. Nuclear genes encoding enzymes that play a key role in H2 production, FeFe-hydrogenase, pyruvate: ferredoxin oxidoreductase and pyruvate: NADPH+ oxidoreductase, were also sequenced from the sampled ciliates and their evolutionary origins were investigated using phylogenies. These suggest that ciliate FeFe-hydrogenases are monophyletic and iii have a separate bacterial origin from FeFe-hydrogenases in other eukaryotes. No evidence was found to support an alpha-proteobacteria or mitochondrial ancestry of these enzymes as predicted by the Hydrogen Hypothesis (Martin and Müller, 1998). Each of the ciliates investigated contained methanogenic Archaea endosymbionts, which can consume the H2 produced by the hydrogenosomes. Some of these endosymbionts were identified to the species-level. The associations they have formed with their hosts appear to be stable over short time-scales but not over longer evolutionary periods, as closely related ciliates like Nyctotherus ovalis and Metopus contortus do not have closely related endosymbionts, providing no evidence for long-term co-speciation

Drosophila Chromosomal Polymorphism: From Population Aspects to Origin Mechanisms of Inversions

High rates of chromosomal rearrangements are remarkably abundant in Drosophila Fallén, 1832 (Insecta, Diptera) genus, highlighting the paracentric inversions. Since different species of this genus are paradigms for genetics, evolutionary, and population studies, polymorphism analyses for chromosomal inversions have provided basic knowledge for beautiful biological questions. Chromosomal inversions suppress meiotic recombination and thus, natural selection can act to preserve favorable gene complexes. Analyses of natural and laboratory populations show that these polymorphisms provide adaptive advantages to their carriers in relation to diverse factors, such as niche exploration and climatic factors. In addition, due to their monophyletic origin, they also serve as genetic markers for the construction of unrooted phylogenies. With the increasing domain of molecular techniques and genome sequencing, factors such as the reuse of breakpoints by different inversions and the mechanisms that give rise to these polymorphisms have been exploited with scientific refinement. These analyses show the presence of regions that are hot spots for breakpoints, fitting the fragile breakage chromosomal evolution model, as well as the involvement of transposition elements at the origin of chromosomal inversions

Investigation of the prevalence and role of mobile genetic elements associated with an aminoglycoside resistance gene, aacC2a, in Acinetobacter baumannii

Includes abstract. Includes bibliographical references (leaves 115-141)