Environmental transcriptome analysis reveals physiological differences between biofilm and planktonic modes of life of the iron oxidizing bacteria Leptospirillum spp. in their natural microbial community

<p>Abstract</p> <p>Background</p> <p>Extreme acidic environments are characterized by their high metal content and lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers). In the Río Tinto (Spain), brown filaments develop under the water stream where the Gram-negative iron-oxidizing bacteria <it>Leptospirillum </it>spp. (<it>L. ferrooxidans </it>and <it>L. ferriphilum</it>) and <it>Acidithiobacillus ferrooxidans </it>are abundant. These microorganisms play a critical role in bioleaching processes for industrial (biominery) and environmental applications (acid mine drainage, bioremediation). The aim of this study was to investigate the physiological differences between the free living (planktonic) and the sessile (biofilm associated) lifestyles of <it>Leptospirillum </it>spp. as part of its natural extremely acidophilic community.</p> <p>Results</p> <p>Total RNA extracted from environmental samples was used to determine the composition of the metabolically active members of the microbial community and then to compare the biofilm and planktonic environmental transcriptomes by hybridizing to a genomic microarray of <it>L. ferrooxidans</it>. Genes up-regulated in the filamentous biofilm are involved in cellular functions related to biofilm formation and maintenance, such as: motility and quorum sensing (<it>mqsR, cheAY, fliA, motAB</it>), synthesis of cell wall structures (<it>lnt, murA, murB</it>), specific proteases (<it>clpX/clpP</it>), stress response chaperons (<it>clpB, clpC, grpE-dnaKJ, groESL</it>), etc. Additionally, genes involved in mixed acid fermentation (<it>poxB</it>, <it>ackA</it>) were up-regulated in the biofilm. This result, together with the presence of small organic acids like acetate and formate (1.36 mM and 0.06 mM respectively) in the acidic (pH 1.8) water stream, suggests that either <it>L. ferrooxidans </it>or other member of the microbial community are producing acetate in the acidophilic biofilm under microaerophilic conditions.</p> <p>Conclusions</p> <p>Our results indicate that the acidophilic filaments are dynamic structures in which different mechanisms for biofilm formation/dispersion are operating. Specific transcriptomic fingerprints can be inferred for both planktonic and sessile cells, having the former a more active TCA cycle, while the mixed acid fermentation process dominate in the latter. The excretion of acetate may play a relevant ecological role as a source of electron donor for heterotrophic Fe³⁺reducers like some Alphaproteobacteria, <it>Acidobacterium </it>spp. and <it>Sulfobacillus </it>spp., also present in the biofilm. Additionally, acetate may have a negative effect on bioleaching by inhibiting the growth of chemolithotrophic bacteria.</p

The evolutionary landscape of the DNA damage response network: a computational approach

The DNA Damage response is a crucial signaling network that preserves genome integrity. This network is an ensemble of distinct but often overlapping sub-networks, where participating components exert different functions according to precise spatiotemporal frameworks. To understand how these sub-networks have been assembled and emerged along evolution, we have screened DDR components in 47 selected species covering the tree of life and analyzed their evolutionary and functional properties according to different gene ages and following a variety of classifications. This is the first time a systematic analysis covers the DDR network’s evolution as a whole. Our results indicate that most of the DDR components are ancestral genes, that all the subnetworks contain at least one representative protein traceable to Prokaryota, and that the ancestral core of the DDR machinery is mainly related to repair and is mostly built upon sensor and effector activities. Along evolution the enlargement of the network has occurred through the addition of new components that have evolved to interact and work together with the ancient ones, which may have increased the complexity of the DDR network in terms of fine-tuning and cross-talk to other pathways.La respuesta al daño en el ADN (DDR) es una red de señalización esencial que mantiene la integridad genética. Esta red es un conjunto de sub-redes distintas, pero a menudo solapantes, donde los componentes que participan desempeñan diversas funciones según marcos espacio-temporales precisos. Para comprender cómo estas sub-redes han surgido a lo largo de la evolución y cómo se han ido ensamblando, hemos buscado componentes de DDR en 47 especies que cubren el árbol de la vida, y hemos analizado sus propiedades evolutivas y funcionales según distintas edades de genes y siguiendo varias clasificaciones. Esta es la primera vez que un análisis sistemático cubre la evolución global de la red de DDR. Nuestros resultados indican que la mayoría de los componentes de la DDR son genes antiguos, que todas las sub-redes contienen al menos un representante trazable hasta procariotas, y que el núcleo ancestral de la maquinaria de DDR está principalmente relacionado con reparación y se construyó sobre actividades de detección y efectores. A lo largo de la evolución, la ampliación de la red ha ocurrido a través de la adición de nuevos componentes que han evolucionado para interaccionar y funcionar junto a los antiguos, lo que puede haber incrementado la complejidad de la red de DDR en términos de precisión y de comunicación con otras redes

DDRprot: a database of DNA damage response-related proteins

The DNA Damage Response (DDR) signalling network is an essential system that protects the genome’s integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches using hidden Markov models can be also used.E.A.-L. was supported by the European Commission grant [FP7-REGPOT-2012-2013-1; A.A. was partially supported by the Spanish Ministry of Science and Innovation grant [PS09/02111].Peer reviewe

Draft Genome Sequence of the Electricigen Acidiphilium sp. Strain PM (DSM 24941)

Acidiphilium sp. strain PM (DSM 24941) was isolated from Rio Tinto's acidic, heavy metal-rich waters. Voltammetry experiments revealed that this strain is capable of electricity production even under aerobic conditions. Here we report the draft genome sequence of Acidiphilium sp. PM and a preliminary genome analysis that reveals a versatile respiratory metabolism

ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins

Abstract Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in this process remains unclear. We show that the ORC1 subunit of the human Origin Recognition Complex interacts with RNAs transcribed from genes with origins in their transcription start sites (TSSs), displaying a positive correlation between RNA binding and origin activity. RNA depletion, or the use of ORC1 RNA-binding mutant, result in inefficient activation of proximal origins, linked to impaired ORC1 chromatin release. ORC1 RNA binding activity resides in its intrinsically disordered region, involved in intra- and inter-molecular interactions, regulation by phosphorylation, and phase-separation. We show that RNA binding favors ORC1 chromatin release, by regulating its phosphorylation and subsequent degradation. Our results unveil a non-coding function of RNA as a dynamic component of the chromatin, orchestrating the activation of replication origins