Changes in the major cell envelope components of Mycobacterium tuberculosis during in vitro growth.

One-third of the world's population is infected with Mycobacterium tuberculosis (M.tb), which causes tuberculosis. Mycobacterium tuberculosis cell envelope components such as glycolipids, lipoglycans and polysaccharides play important roles in bacteria-host cell interactions that dictate the host immune response. However, little is known about the changes in the amounts and types of these cell envelope components as the bacillus divides during in vitro culture. To shed light on these phenomena, we examined growth-dependent changes over time in major cell envelope components of virulent M.tb by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, thin-layer chromatography, mass spectrometry, immunoblotting and flow cytometry. Our studies provide evidence that major mannosylated glycoconjugates on the M.tb cell envelope change as M.tb grows in vitro on the widely used Middlebrook 7H11 agar. In particular, our compositional analyses show that from Day 9 to 28 the amounts of mannose-containing molecules, such as mannose-capped lipoarabinomannan, lipomannan and phosphatidyl-myo-inositol mannosides, change continuously in both the cell envelope and outer cell surface. Along with these changes, mannan levels on the outer cell surface also increase significantly over time. The implications of these differences in terms of how M.tb is grown for studies performed in vitro and in vivo for assessing M.tb-host recognition and establishment of infection are discussed.

Unambiguous determination of isobaric histone modifications by reversed-phase retention time and high-mass accuracy.

Methylation and acetylation of lysines are crucial posttranslational modifications that regulate gene transcription and have been shown to be misregulated in many forms of cancers. Western blot, immunoprecipitation, and immunofluorescence are commonly used to characterize histone acetylation and methylation. However, these approaches are limited by the availability, site specificity, and cross-reactivity of antibodies. Mass spectrometry is emerging as an additional powerful tool for histone characterization. The isobaric nature of trimethylation and acetylation (42.0470 and 42.0106 Da, respectively) confounds histone characterization by means other than high-resolution/high-mass accuracy mass spectrometry. In this study, we adapted methodology that exploits difference in the relative retention time of acetylated and methylated peptides to unequivocally distinguish between these two modifications even with low-mass accuracy mass spectrometers. The approach was tested on tryptic digest of Saccharomyces cerevisiae histones. We found that acetylation resulted in increased retention in reversed-phase chromatography, whereas methylation, including trimethylation, showed little change in retention. For example, the acetylated forms of peptide (27)KSAPSTGGVKKPHR(40) eluted at 15.63 min, whereas the methylated forms eluted at 13.89 min. In addition, the effect of acetylation was cumulative as observed in the case of peptide (9)KSTGGKAPR(17), whose unmodified, monoacetylated, and diacetylated isoforms eluted at 7.43, 10.47, and 16.49 min, respectively. The modification patterns of the peptides in question were subsequently verified by high-mass accuracy tandem mass spectrometry.

A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time.

BACKGROUND: Rejection of false positive peptide matches in database searches of shotgun proteomic experimental data is highly desirable. Several methods have been developed to use the peptide retention time as to refine and improve peptide identifications from database search algorithms. This report describes the implementation of an automated approach to reduce false positives and validate peptide matches. RESULTS: A robust linear regression based algorithm was developed to automate the evaluation of peptide identifications obtained from shotgun proteomic experiments. The algorithm scores peptides based on their predicted and observed reversed-phase liquid chromatography retention times. The robust algorithm does not require internal or external peptide standards to train or calibrate the linear regression model used for peptide retention time prediction. The algorithm is generic and can be incorporated into any database search program to perform automated evaluation of the candidate peptide matches based on their retention times. It provides a statistical score for each peptide match based on its retention time. CONCLUSION: Analysis of peptide matches where the retention time score was included resulted in a significant reduction of false positive matches with little effect on the number of true positives. Overall higher sensitivities and specificities were achieved for database searches carried out with MassMatrix, Mascot and X!Tandem after implementation of the retention time based score algorithm.

Identification of histone demethylases in Saccharomyces cerevisiae.

Based on the prediction that histone lysine demethylases may contain the JmjC domain, we examined the methylation patterns of five knock-out strains (ecm5Delta, gis1Delta, rph1Delta, jhd1Delta, and jhd2Delta (yjr119cDelta)) of Saccharomyces cerevisiae. Mass spectrometry (MS) analyses of histone H3 showed increased modifications in all mutants except ecm5Delta. High-resolution MS was used to unequivocally differentiate trimethylation from acetylation in various tryptic fragments. The relative abundance of specific fragments indicated that histones K36me3 and K4me3 accumulate in rph1Delta and jhd2Delta strains, respectively, whereas both histone K36me2 and K36me accumulate in gis1Delta and jhd1Delta strains. Analyses performed with strains overexpressing the JmjC proteins yielded changes in methylation patterns that were the reverse of those obtained in the complementary knock-out strains. In vitro enzymatic assays confirmed that the JmjC domain of Rph1 specifically demethylates K36me3 primarily and K36me2 secondarily. Overexpression of RPH1 generated a growth defect in response to UV irradiation. The demethylase activity of Rph1 is responsible for the phenotype. Collectively, in addition to Jhd1, our results identified three novel JmjC domain-containing histone demethylases and their sites of action in budding yeast S. cerevisiae. Furthermore, the methodology described here will be useful for identifying histone demethylases and their target sites in other organisms.

Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes.

Acetylation of histone H3 on lysine 56 occurs during mitotic and meiotic S phase in fungal species. This acetylation blocks a direct electrostatic interaction between histone H3 and nucleosomal DNA, and the absence of this modification is associated with extreme sensitivity to genotoxic agents. We show here that H3-K56 acetylation is catalyzed when Rtt109, a protein that lacks significant homology to known acetyltransferases, forms an active complex with either of two histone binding proteins, Asf1 or Vps75. Rtt109 binds to both these cofactors, but not to histones alone, forming enzyme complexes with kinetic parameters similar to those of known histone acetyltransferase (HAT) enzymes. Therefore, H3-K56 acetylation is catalyzed by a previously unknown mechanism that requires a complex of two proteins: Rtt109 and a histone chaperone. Additionally, these complexes are functionally distinct, with the Rtt109/Asf1 complex, but not the Rtt109/Vps75 complex, being critical for resistance to genotoxic agents.

ICP-AES detection of ultratrace aluminum(III) and chromium(III) ions with a microcolumn preconcentration system using dynamically immobilized 8-hydroxyquinoline on TiO2 nanoparticles.

Titanium dioxide nanoparticle dynamically loaded with 8-hydroxyquinoline (nanometer TiO2-Oxine) was used as a solid-phase extractant for the preconcentration of trace amounts of aluminum(III) and chromium(III) prior to their determination by inductively coupled plasma atomic emission spectrometry (ICP-AES). The optimal conditions for preparing nanometer TiO2-Oxine were obtained. Also, the separation/preconcentration conditions of analytes, including the effects of the pH, the sample flow rate and the volume, the elution solution and the interfering ions on the recovery of the analytes were investigated. At pH 6.0, the adsorption capacity of nanometer TiO2-Oxine was found to be 5.23 mg g(-1) and 9.58 mg g(-1) for Al(III) and Cr(III), respectively. An enrichment factor of 50 was achieved by this method, and the detection limits (3sigma) for Al(III) and Cr(III) were 1.96 and 0.32 microg L(-1) respectively. The proposed method was applied for the determination of trace Al(III) and Cr(III) in biological samples and lake water with satisfactory results.