By their genes ye shall know them: genomic signatures of predatory bacteria

Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the ‘predatome,'' that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. Strikingly, predators and non-predators differ in isoprenoid biosynthesis: predators use the mevalonate pathway, whereas non-predators, like almost all bacteria, use the DOXP pathway. By defining predatory signatures in bacterial genomes, the predatory potential they encode can be uncovered, filling an essential gap for measuring bacterial predation in nature. Moreover, we suggest that full-genome proteomic comparisons are applicable to other ecological interactions between microbes, and provide a convenient and rational tool for the functional classification of bacteria.     

Functional Classification of Immune Regulatory Proteins

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Highlights? An intermediate sequence based clustering algorithm, Brotherhood, is introduced ? The Brotherhood method is used to assign functional families within the human IgSF ? Newly annotated nectin-like family member, CRTAM, structure is solved ? Homophilic transinteraction is observed for CRTAM     

The effect of anthropogenic resources on the space-use patterns of golden jackals

We studied the influence of agricultural villages on space-use patterns of golden jackals (Canis aureus Linnaeus) in the Mediterranean region of Israel. Villages in our research area attract jackals due to poor sanitation conditions in and around villages. As resources in these villages are abundant and predictable, we expected that space-use patterns of jackals near those villages, including home-range characteristics and movement paths, would differ from those of jackals inhabiting more natural areas. Using radio-locations from 16 individuals (8 near villages and 8 from more natural areas), we found that mean home-range size of jackals close to villages was 6.6 ± 4.5 km², smaller than mean home-range size of jackals in more natural areas (21.2 ± 9.3 km², P = 0.001). Similarly, core area size of jackals near villages was 1.2 ± 0.92 km², compared to 3.5 ± 1.6 km² for individuals inhabiting more natural areas (P = 0.004). The core area/home-range ratio was greater for jackals near villages than for those occupying more natural areas (0.122 ± 0.045 vs. 0.095 ± 0.037, respectively, P = 0.004). Jackals moved little during the day, with day ranges smaller for jackals near villages than away from them (1.65 ± 0.67 vs. 7.5 ± 5.6 km², respectively, P = 0.028). However, jackals near villages moved as much at night as did jackals in more natural areas, although movement was in a less directional manner. Changes in distribution and predictability of resources due to anthropogenic activity affect not only the home-range size of jackals, but also how they utilize and move through space. © 2011 The Wildlife Society.     

S6K1 Alternative Splicing Modulates Its Oncogenic Activity and Regulates mTORC1

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Highlights? The long S6K1 isoform functions as a tumor suppressor ? S6K1 short isoforms are upregulated in breast cancer and possess oncogenic properties ? S6K1 short isoforms bind mTORC1 and enhance cap-dependent translation ? Inhibition of mTORC1 can reverse the oncogenic properties of the S6K1 short isoforms     

Cancellous and cortical morselized allograft in revision total hip replacement: A biomechanical study of implant stability

To restore femoral intramedullary bone stock loss in revision surgery of failed total hip arthroplasties, impacted morselized cancellous allograft is recommended. This study investigated the mechanical properties of both impacted cortical (group A) and cancellous (group B) morselized bone graft for reconstruction of femoral bones. Ten matched pairs of fresh frozen human femora were prepared by over-reaming to create a smooth-walled cortical shell. Each pair had one cortical and one cancellous impacted morselized allograft and cement. Stem subsidence was evaluated by a cyclic axial load, which was applied by a servohydraulic test. The stem subsidence was measured for initial subsidence (subsidence at the first 1000 cycles), the total axial subsidence (subsidence at the end of cycles under load) and the final axial subsidence (subsidence after the unloading phase). Torque test was measured by torsional loads through the prosthetic femoral heads. Total axial subsidence was significantly higher in group B (mean: 1.32+/-0.32 mm) compared to group A (mean: 0.94+/-0.26 mm) (P<0.01).There was no significant difference between the two groups in terms of initial subsidence (P=0.09) and final axial subsidence.The mean maximum torque before failure was 39.5+/-22.2 N-m for the cortical morselized allograft and 32.5+/-18.1N-m for cancellous.We concluded that impacted morselized cortical bone graft used for reconstruction of contained femoral bone loss in revision hip arthroplasty, may reduce the stem subsidence. Further animal experimentation for mechanical and histological evaluation of in vivo application is warranted.     

Control of pancreatic β cell regeneration by glucose metabolism

Recent studies revealed a surprising regenerative capacity of insulin-producing β cells in mice, suggesting that regenerative therapy for human diabetes could in principle be achieved. Physiologic β cell regeneration under stressed conditions relies on accelerated proliferation of surviving β cells, but the factors that trigger and control this response remain unclear. Using islet transplantation experiments, we show that β cell mass is controlled systemically rather than by local factors such as tissue damage. Chronic changes in β cell glucose metabolism, rather than blood glucose levels per se, are the main positive regulator of basal and compensatory β cell proliferation in vivo. Intracellularly, genetic and pharmacologic manipulations reveal that glucose induces β cell replication via metabolism by glucokinase, the first step of glycolysis, followed by closure of K(ATP) channels and membrane depolarization. Our data provide a molecular mechanism for homeostatic control of β cell mass by metabolic demand.     

Localization of the Drosophila Rad9 protein to the nuclear membrane is regulated by the C-terminal region and is affected in the meiotic checkpoint

Rad9, Rad1, and Hus1 (9-1-1) are part of the DNA integrity checkpoint control system. It was shown previously that the C-terminal end of the human Rad9 protein, which contains a nuclear localization sequence (NLS) nearby, is critical for the nuclear transport of Rad1 and Hus1. In this study, we show that in Drosophila, Hus1 is found in the cytoplasm, Rad1 is found throughout the entire cell and that Rad9 (DmRad9) is a nuclear protein. More specifically, DmRad9 exists in two alternatively spliced forms, DmRad9A and DmRad9B, where DmRad9B is localized at the cell nucleus, and DmRad9A is found on the nuclear membrane both in Drosophila tissues and also when expressed in mammalian cells. Whereas both alternatively spliced forms of DmRad9 contain a common NLS near the C terminus, the 32 C-terminal residues of DmRad9A, specific to this alternative splice form, are required for targeting the protein to the nuclear membrane. We further show that activation of a meiotic checkpoint by a DNA repair gene defect but not defects in the anchoring of meiotic chromosomes to the oocyte nuclear envelope upon ectopic expression of non-phosphorylatable Barrier to Autointegration Factor (BAF) dramatically affects DmRad9A localization. Thus, by studying the localization pattern of DmRad9, our study reveals that the DmRad9A C-terminal region targets the protein to the nuclear membrane, where it might play a role in response to the activation of the meiotic checkpoint.     

Clusters versus affinity-based approaches in F. tularensis whole genome search of CTL epitopes

Deciphering the cellular immunome of a bacterial pathogen is challenging due to the enormous number of putative peptidic determinants. State-of-the-art prediction methods developed in recent years enable to significantly reduce the number of peptides to be screened, yet the number of remaining candidates for experimental evaluation is still in the range of ten-thousands, even for a limited coverage of MHC alleles. We have recently established a resource-efficient approach for down selection of candidates and enrichment of true positives, based on selection of predicted MHC binders located in high density "hotspots" of putative epitopes. This cluster-based approach was applied to an unbiased, whole genome search of Francisella tularensis CTL epitopes and was shown to yield a 17-25 fold higher level of responders as compared to randomly selected predicted epitopes tested in Kb/Db C57BL/6 mice. In the present study, we further evaluate the cluster-based approach (down to a lower density range) and compare this approach to the classical affinity-based approach by testing putative CTL epitopes with predicted IC(50) values of <10 nM. We demonstrate that while the percent of responders achieved by both approaches is similar, the profile of responders is different, and the predicted binding affinity of most responders in the cluster-based approach is relatively low (geometric mean of 170 nM), rendering the two approaches complimentary. The cluster-based approach is further validated in BALB/c F. tularensis immunized mice belonging to another allelic restriction (Kd/Dd) group. To date, the cluster-based approach yielded over 200 novel F. tularensis peptides eliciting a cellular response, all were verified as MHC class I binders, thereby substantially increasing the F. tularensis dataset of known CTL epitopes. The generality and power of the high density cluster-based approach suggest that it can be a valuable tool for identification of novel CTLs in proteomes of other bacterial pathogens.