Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea

Background  

Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. It is one of the most radioresistant organisms known amongst the Archaea. We report the determination and annotation of its complete genome sequence, its comparison with other Thermococcales genomes, and a proteomic analysis.     

Mito-nuclear genetic comparison in a Wolbachia infected weevil: insights on reproductive mode, infection age and evolutionary forces shaping genetic variation

Background

The composition and expression of vertebrate gene families is shaped by species specific gene loss in combination with a number of gene and genome duplication events (R1, R2 in all vertebrates, R3 in teleosts) and depends on the ecological and evolutionary context. In this study we analyzed the evolutionary history of the solute carrier 1 (SLC1) gene family. These genes are supposed to be under strong selective pressure (purifying selection) due to their important role in the timely removal of glutamate at the synapse.

Results

In a genomic survey where we manually annotated and analyzing sequences from more than 300 SLC1 genes (from more than 40 vertebrate species), we found evidence for an interesting evolutionary history of this gene family. While human and mouse genomes contain 7 SLC1 genes, in prototheria, sauropsida, and amphibia genomes up to 9 and in actinopterygii up to 13 SLC1 genes are present. While some of the additional slc1 genes in ray-finned fishes originated from R3, the increased number of SLC1 genes in prototheria, sauropsida, and amphibia genomes originates from specific genes retained in these lineages. Phylogenetic comparison and microsynteny analyses of the SLC1 genes indicate, that theria genomes evidently lost several SLC1 genes still present in the other lineage. The genes lost in theria group into two new subfamilies of the slc1 gene family which we named slc1a8/eaat6 and slc1a9/eaat7.

Conclusions

The phylogeny of the SLC1/EAAT gene family demonstrates how multiple genome reorganization and duplication events can influence the number of active genes. Inactivation and preservation of specific SLC1 genes led to the complete loss of two subfamilies in extant theria, while other vertebrates have retained at least one member of two newly identified SLC1 subfamilies.     

NUMB-ing down cancer by more than just a NOTCH

The protein Numb does not live up to its name. This passive-sounding protein is anything but spent. Originally identified as a cell-fate determinant in Drosophila development, Numb received a good deal of attention as an inhibitor of the Notch receptor signaling pathway. It turns out, however, that Numb does a lot more than simply regulate Notch. It has been implicated in a variety of biochemical pathways connected with signaling (it regulates Notch-, Hedgehog- and TP53-activated pathways), endocytosis (it is involved in cargo internalization and recycling), determination of polarity (it interacts with the PAR complex, and regulates adherens and tight junctions), and ubiquitination (it exploits this mechanism to regulate protein function and stability). This complex biochemical network lies at the heart of Numb's involvement in diverse cellular phenotypes, including cell fate developmental decisions, maintenance of stem cell compartments, regulation of cell polarity and adhesion, and migration. Considering its multifaceted role in cellular homeostasis, it is not surprising that Numb has been implicated in cancer as a tumor suppressor. Our major goal here is to explain the cancer-related role of Numb based on our understanding of its role in cell physiology. We will attempt to do this by reviewing the present knowledge of Numb at the biochemical and functional level, and by integrating its apparently heterogeneous functions into a unifying scenario, based on our recently proposed concept of the "endocytic matrix". Finally, we will discuss the role of Numb in the maintenance of the normal stem cell compartment, as a starting point to interpret the tumor suppressor function of Numb in the context of the cancer stem cell hypothesis.     

Copper-mediated genotoxic stress is attenuated by the overexpression of the DNA repair gene MtTdp2α (tyrosyl-DNA phosphodiesterase 2) in Medicago truncatula plants

Key message

Our study highlights the use of the DNA repair gene MtTdp2α as a tool for improving the plant response to heavy metal stress.

Abstract

Tyrosyl-DNA phosphodiesterase 2 (Tdp2), involved in the removal of DNA topoisomerase II-mediated DNA damage and cell proliferation/differentiation signalling in animal cells, is still poorly characterised in plants. The Medicago truncatula lines Tdp2α-13c and Tdp2α-28 overexpressing the MtTdp2α gene and control (CTRL) line were exposed to 0.2 mM CuCl₂. The DNA diffusion assay revealed a significant reduction in the percentage of necrosis caused by copper in the aerial parts of the Tdp2α-13c and Tdp2α-28 plants while neutral single cell gel electrophoresis highlighted a significant decrease in double strand breaks (DSBs), compared to CTRL. In the copper-treated Tdp2α-13c and Tdp2α-28 lines there was up-regulation (up to 4.0-fold) of genes encoding the α and β isoforms of Tyrosyl-DNA phosphodiesterase 1, indicating the requirement for Tdp1 function in the response to heavy metals. As for DSB sensing, the MtMRE11, MtRAD50 and MtNBS1 genes were also significantly up-regulated (up to 2.3-fold) in the MtTdp2α-overexpressing plants grown under physiological conditions, compared to CTRL line, and then further stimulated in response to copper. The basal antioxidant machinery was always activated in all the tested lines, as indicated by the concomitant up-regulation of MtcytSOD and MtcpSOD genes (cytosolic and chloroplastic Superoxide Dismutase), and MtMT2 (type 2 metallothionein) gene. The role of MtTdp2α gene in enhancing the plant response to genotoxic injury under heavy metal stress is discussed.     

Is Munida gregaria (Crustacea: Decapoda: Munididae) a truly transpacific species?

The “East Pacific Barrier” has been recognized as the World’s largest marine biogeographic barrier. Munida gregaria is the only species of its family with transpacific populations; however, it still remains to be elucidated whether these two distantly located populations belong to the same species. In this study, we investigated the genetic cohesion of M. gregaria across the East Pacific Barrier by analyzing mitochondrial markers. Cytochrome oxidase subunit I and NADH dehydrogenase subunit 1 genes were sequenced for individuals from different areas, i.e., the southeast Pacific, the southern tip of South America, the southwest Atlantic, and the southwest Pacific. A median-joining network, pairwise F _STs, genetic diversity statistics, and neutrality tests were computed. Our results, i.e., the absence of different haplogroups on both sides of the East Pacific Barrier and existence of shared haplotypes, showed that populations on both sides of this barrier belong to the same species. At a population genetic level, our results suggest that individuals from both regions have been connected, since although some differentiation was found between the southern tip of South America and the southwest Pacific, the southeast Pacific and southwest Atlantic showed no signs of differentiation from the southwest Pacific. In addition, our results provided evidence of a population expansion in southern South America during the Pleistocene. The role of Pleistocene glaciations and the Antarctic Circumpolar Current in shaping the distribution of sub-Antarctic marine invertebrates is discussed.     

A RAB5/RAB4 recycling circuitry induces a proteolytic invasive program and promotes tumor dissemination

The mechanisms by which tumor cells metastasize and the role of endocytic proteins in this process are not well understood. We report that overexpression of the GTPase RAB5A, a master regulator of endocytosis, is predictive of aggressive behavior and metastatic ability in human breast cancers. RAB5A is necessary and sufficient to promote local invasion and distant dissemination of various mammary and nonmammary tumor cell lines, and this prometastatic behavior is associated with increased intratumoral cell motility. Specifically, RAB5A is necessary for the formation of invadosomes, membrane protrusions specialized in extracellular matrix (ECM) degradation. RAB5A promotes RAB4- and RABENOSYN-5–dependent endo/exocytic cycles (EECs) of critical cargos (membrane-type 1 matrix metalloprotease [MT1-MMP] and β3 integrin) required for invadosome formation in response to motogenic stimuli. This trafficking circuitry is necessary for spatially localized hepatocyte growth factor (HGF)/MET signaling that drives invasive, proteolysis-dependent chemotaxis in vitro and for conversion of ductal carcinoma in situ to invasive ductal carcinoma in vivo. Thus, RAB5A/RAB4 EECs promote tumor dissemination by controlling a proteolytic, mesenchymal invasive program.     

Surfing parameter hyperspaces under climate change scenarios to design future rice ideotypes

Growing food crops to meet global demand and the search for more sustainable cropping systems are increasing the need for new cultivars in key production areas. This study presents the identification of rice traits putatively producing the largest yield benefits in five areas that markedly differ in terms of environmental conditions in the Philippines, India, China, Japan and Italy. The ecophysiological model WARM and sensitivity analysis techniques were used to evaluate phenotypic traits involved with light interception, photosynthetic efficiency, tolerance to abiotic stressors, resistance to fungal pathogens and grain quality. The analysis involved only model parameters that have a close relationship with phenotypic traits breeders are working on, to increase the in vivo feasibility of selected ideotypes. Current climate and future projections were considered, in the light of the resources required by breeding programs and of the role of weather variables in the identification of promising traits. Results suggest that breeding for traits involved with disease resistance, and tolerance to cold‐ and heat‐induced spikelet sterility could provide benefits similar to those obtained from the improvement of traits involved with canopy structure and photosynthetic efficiency. In contrast, potential benefits deriving from improved grain quality traits are restricted by weather variability and markedly affected by G × E interactions. For this reason, district‐specific ideotypes were identified using a new index accounting for both their productivity and feasibility.     

An adaptive explanation for geographically structured allozyme variation inDichroplus elongatus (Orthoptera: Acrididae)

Previous studies on allozyme variation in five populations of the grasshopperDichroplus elongatus along a geographical gradient in Argentina revealed a significant degree of population structuring and a significant association between one of the loci (Aat-1) and latitude. As this could not be entirely explained by historical factors, the possible adaptive significance of this locus or loci in linkage disequilibrium was investigated in the present study, with an emphasis on the role of environmental variables correlated with latitude. The present paper reports a study of the geographical organization of allozyme diversity over a wider range of the distribution ofD. elongatus. The relation of allelic frequencies with geographic climatic variables was analysed. We have found (i) that different loci (Aat-1 andPep-1) covary significantly with different variables, (ii) discordance between genetic and geographical distances, (iii) copious gene flow that would mask allelic frequency differences due solely to genetic drift, (iv) and temporal stability of the gradient found. The results suggest that causes other than drift and migration may explain the observed directional patterns of variation inD. elongatus.