Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry

The genome sequencing of H37Rv strain of Mycobacterium tuberculosis was completed in 1998 followed by the whole genome sequencing of a clinical isolate, CDC1551 in 2002. Since then, the genomic sequences of a number of other strains have become available making it one of the better studied pathogenic bacterial species at the genomic level. However, annotation of its genome remains challenging because of high GC content and dissimilarity to other model prokaryotes. To this end, we carried out an in-depth proteogenomic analysis of the M. tuberculosis H37Rv strain using Fourier transform mass spectrometry with high resolution at both MS and tandem MS levels. In all, we identified 3176 proteins from Mycobacterium tuberculosis representing ~80% of its total predicted gene count. In addition to protein database search, we carried out a genome database search, which led to identification of ~250 novel peptides. Based on these novel genome search-specific peptides, we discovered 41 novel protein coding genes in the H37Rv genome. Using peptide evidence and alternative gene prediction tools, we also corrected 79 gene models. Finally, mass spectrometric data from N terminus-derived peptides confirmed 727 existing annotations for translational start sites while correcting those for 33 proteins. We report creation of a high confidence set of protein coding regions in Mycobacterium tuberculosis genome obtained by high resolution tandem mass-spectrometry at both precursor and fragment detection steps for the first time. This proteogenomic approach should be generally applicable to other organisms whose genomes have already been sequenced for obtaining a more accurate catalogue of protein-coding genes.     

Mechanisms of Araucaria (Atlantic) Forest Expansion into Southern Brazilian Grasslands

Recent studies have shown that tropical and subtropical forests expanded during the late Holocene, but rates and mechanisms of expansion are still unknown. Here, we investigate how a forest–grassland mosaic changed over the past 10,000 years at the southernmost limit of the Brazilian Atlantic forest. We used soil organic matter carbon isotopes (δ¹³C and ¹⁴C) to quantify and date changes in vegetation, examining soil properties and leaf traits of tree species (nutrient content, δ¹³C, δ¹⁵N, and specific leaf area—SLA) to describe potential mechanisms of expansion. Our results show that after several millennia of stability, forests have been expanding over grasslands through continuous, but very slow, border dynamics and patch formation (<100 m since ~4,000 YBP). This process of expansion coincided with past changes in climate, but biotic feedback mechanisms also appear to be important for the long-term persistence and expansion of forests. Soil fertility and microbial biomass match current rather than past vegetation distribution, increasing progressively across the gradient: grasslands < isolated trees < forest patches < forests. Foliar δ¹⁵N values of trees that are able to colonize the grassland are consistently lower across this vegetation gradient, suggesting an increasingly greater reliance on symbiotic nutrient uptake from grasslands to forests. No significant relationships were found between soil and leaf nutrients, but SLA explained variation in leaf N, P, and K (positive relationships) and in leaf δ¹³C (negative relationship). These findings suggest that a tradeoff between tree growth and water use efficiency is an important regulator of forest–grassland dynamics in the study region.     

Assessing the Use of Functional Diversity as a Measure of Ecological Resilience in Arid Rangelands

It is becoming more apparent that species richness alone many not be sufficient to fully understand ecosystem resilience but that functional diversity (diversity of species having similar effects on an ecosystem process) may be more relevant. In particular, response diversity (diversity of species that respond differently to disturbance) within functional groups (FG) is suggested to be critical for resilience. We assess for the first time the use of response diversity as a measure of resilience in an empirical study. Our experimental design consisted of sites with three disturbance intensities during a grazing exclosure period and the same sites, 1 year later, after grazing. Plant FGs were identified based on effect traits related to nutrient cycling and soil retention, and species richness within groups was assessed during exclosure and after grazing. To assess if response diversity could predict loss of species richness (resilience analysis), response diversity was calculated only during the exclosure period, based on traits related to grazing tolerance. We also assessed the contribution of richness to response diversity during exclosure (redundancy analysis). Response diversity was significantly and highly correlated with species richness within FGs during disturbance. That is, FGs with the lowest response diversity were the most affected, disappearing when disturbance appeared. Richness within FGs during exclosure was not significantly correlated with response diversity, showing that higher richness does not ensure resilience. We conclude that response diversity can be used to predict which FGs are more resilient, and hence, less vulnerable to future disturbance.     

Hydrodynamic regulation of monocyte inflammatory response to an intracellular pathogen

Systemic bacterial infections elicit inflammatory response that promotes acute or chronic complications such as sepsis, arthritis or atherosclerosis. Of interest, cells in circulation experience hydrodynamic shear forces, which have been shown to be a potent regulator of cellular function in the vasculature and play an important role in maintaining tissue homeostasis. In this study, we have examined the effect of shear forces due to blood flow in modulating the inflammatory response of cells to infection. Using an in vitro model, we analyzed the effects of physiological levels of shear stress on the inflammatory response of monocytes infected with chlamydia, an intracellular pathogen which causes bronchitis and is implicated in the development of atherosclerosis. We found that chlamydial infection alters the morphology of monocytes and trigger the release of pro-inflammatory cytokines TNF-α, IL-8, IL-1β and IL-6. We also found that the exposure of chlamydia-infected monocytes to short durations of arterial shear stress significantly enhances the secretion of cytokines in a time-dependent manner and the expression of surface adhesion molecule ICAM-1. As a functional consequence, infection and shear stress increased monocyte adhesion to endothelial cells under flow and in the activation and aggregation of platelets. Overall, our study demonstrates that shear stress enhances the inflammatory response of monocytes to infection, suggesting that mechanical forces may contribute to disease pathophysiology. These results provide a novel perspective on our understanding of systemic infection and inflammation.     

A three-hybrid system to probe in vivo protein-protein interactions: application to the essential proteins of the RD1 complex of M. tuberculosis

Background

Protein-protein interactions play a crucial role in enabling a pathogen to survive within a host. In many cases the interactions involve a complex of proteins rather than just two given proteins. This is especially true for pathogens like M. tuberculosis that are able to successfully survive the inhospitable environment of the macrophage. Studying such interactions in detail may help in developing small molecules that either disrupt or augment the interactions. Here, we describe the development of an E. coli based bacterial three-hybrid system that can be used effectively to study ternary protein complexes.

Methodology/Principal Findings

The protein-protein interactions involved in M. tuberculosis pathogenesis have been used as a model for the validation of the three-hybrid system. Using the M. tuberculosis RD1 encoded proteins CFP10, ESAT6 and Rv3871 for our proof-of-concept studies, we show that the interaction between the proteins CFP10 and Rv3871 is strengthened and stabilized in the presence of ESAT6, the known heterodimeric partner of CFP10. Isolating peptide candidates that can disrupt crucial protein-protein interactions is another application that the system offers. We demonstrate this by using CFP10 protein as a disruptor of a previously established interaction between ESAT6 and a small peptide HCL1; at the same time we also show that CFP10 is not able to disrupt the strong interaction between ESAT6 and another peptide SL3.

Conclusions/Significance

The validation of the three-hybrid system paves the way for finding new peptides that are stronger binders of ESAT6 compared even to its natural partner CFP10. Additionally, we believe that the system offers an opportunity to study tri-protein complexes and also perform a screening of protein/peptide binders to known interacting proteins so as to elucidate novel tri-protein complexes.     

Protozoan parasite Toxoplasma gondii manipulates mate choice in rats by enhancing attractiveness of males

Females in various species typically avoid males infected with parasites, while parasite-free males advertise their status through conspicuous phenotypic traits. This process selects for heritable resistance and reduces direct exposure of the female to parasites. Coevolving parasites are likely to attempt to circumvent this obstacle. In this paper, we demonstrate a case of parasitic manipulation of host mate choice. We report that Toxoplasma gondii, a sexually transmitted infection of brown rats, enhances sexual attractiveness of infected males. Thus under some evolutionary niches, parasites can indeed manipulate host sexual signaling to their own advantage.     

Rab11 is required during Drosophila eye development

In an effort to identify the role of Rab11, a small GTP binding protein, during Drosophila differentiation, phenotypic manifestations associated with different alleles of Rab11 were studied. The phenotypes ranged from eye-defects, bristle abnormalities and sterility to lethality during various developmental stages. In this paper, our focus is targeted on eye defects caused by Rab11 mutations. A novel P-element insertion in the Rab11 locus, Rab11mo, displayed characteristic retinal anomalies, which could be reverted by P-element excision and expression of Rab11+ transgenes. During larval development, Rab11 is widely synthesized in photoreceptor cells and localizes to the rhabdomeres and lamina neuropil in adult eyes. Photoreceptors and associated bristles failed to be formed in homozygous clones generated in Rab11EP(3)3017 eyes. Decreased levels of Rab11 protein and increased cell death in Rab11mo third-instar larval eye-antennal discs suggest that the retinal defects originate during larval development. Our data indicate a requirement for Rab11 in ommatidial differentiation during Drosophila eye development.