Quantitative Mass Spectrometry Reveals Plasticity of Metabolic Networks in Mycobacterium smegmatis

Mycobacterium tuberculosis has a remarkable ability to persist within the human host as a clinically inapparent or chronically active infection. Fatty acids are thought to be an important carbon source used by the bacteria during long term infection. Catabolism of fatty acids requires reprogramming of metabolic networks, and enzymes central to this reprogramming have been targeted for drug discovery. Mycobacterium smegmatis, a nonpathogenic relative of M. tuberculosis, is often used as a model system because of the similarity of basic cellular processes in these two species. Here, we take a quantitative proteomics-based approach to achieve a global view of how the M. smegmatis metabolic network adjusts to utilization of fatty acids as a carbon source. Two-dimensional liquid chromatography and mass spectrometry of isotopically labeled proteins identified a total of 3,067 proteins with high confidence. This number corresponds to 44% of the predicted M. smegmatis proteome and includes most of the predicted metabolic enzymes. Compared with glucose-grown cells, 162 proteins showed differential abundance in acetate- or propionate-grown cells. Among these, acetate-grown cells showed a higher abundance of proteins that could constitute a functional glycerate pathway. Gene inactivation experiments confirmed that both the glyoxylate shunt and the glycerate pathway are operational in M. smegmatis. In addition to proteins with annotated functions, we demonstrate carbon source-dependent differential abundance of proteins that have not been functionally characterized. These proteins might play as-yet-unidentified roles in mycobacterial carbon metabolism. This study reveals several novel features of carbon assimilation in M. smegmatis, which suggests significant functional plasticity of metabolic networks in this organism.The genus Mycobacterium comprises more than 100 known species of obligate and opportunistic pathogens as well as nonpathogenic saprophytes such as Mycobacterium smegmatis, which shares many characteristics with its pathogenic relatives (1, 2). Because of its similarity in basic cellular processes and the ease and safety in handling nonpathogenic bacteria, M. smegmatis is widely used as a model system for pathogenic Mycobacterium tuberculosis. These organisms share a common framework of carbon metabolism that is complemented with additional reactions and pathways suiting their pathogenic and saprophytic lifestyles. Although the M. smegmatis genome has been sequenced, understanding the many cellular processes is limited by the fact that a large number of genes, many of which are unique to mycobacteria, have not been functionally annotated. Furthermore, genes encoding proteins that mediate specialized functions may be expressed only in response to specific environmental cues. These gaps in our current understanding of mycobacterial metabolism warrant genome-scale studies aimed at delineating the adaptive mechanisms employed under specific growth conditions (3–6).Comparative proteome profiling is a powerful tool for investigating differences in global protein abundance that occur in response to different environmental stimuli (7, 8), and it can provide new insights into the metabolic and regulatory pathways involved in adaptation to the associated stimuli (9–11). Stable isotope dimethyl labeling is a technique that allows precise quantitative mass spectrometry-based analysis of proteome-wide changes within an organism (12, 13). Here, we demonstrate that this technique can also be exploited for deep mining of mycobacterial proteomes and simultaneous comparative analysis of proteomes originating from up to three different experimental conditions. We demonstrate this comparative approach by quantitative analysis of the M. smegmatis proteome in bacterial cells grown with one of three different carbon sources representing glycolytic (glucose) or gluconeogenic (acetate and propionate) substrates. Acetate and propionate are the immediate downstream products of fatty acid β-oxidation, a committed pathway for entry of long-chain fatty acids into the central carbon-metabolizing network.Using this approach, we identified 3,067 proteins in M. smegmatis with high confidence using at least two unique peptides per protein. Among the proteins that we identified, 162 proteins showed differential abundance in cells grown with either acetate or propionate as the carbon source compared with glucose-grown cells. The majority of these proteins clustered within the functional category related to energy metabolism, providing new insights into how these carbon sources are assimilated in M. smegmatis. An interesting feature that emerges from this study is the plasticity of metabolic networks in M. smegmatis, where multiple pathways can be co-utilized for assimilation of the same metabolite. This finding, along with the recent demonstration that mycobacteria can co-catabolize multiple carbon sources (14), underscores the flexibility and metabolic potential of M. smegmatis. In the future, this approach could be used to explore the metabolic adaptations that play a role in growth of M. tuberculosis on fatty acid substrates, which are thought to be an important carbon source for the bacteria in the lungs of the infected host (5, 6, 15, 16).     

Glucose metabolism by isolated fat cells from sloth.

Glucose metabolism by sloth fat cells with and without addition of insulin was investigated. The data were compared to the results obtained with rat fat cells incubated under the same experimental conditions. Sloth fat cells showed a very low glucose oxidation to 14CO2 and incorporation into total lipids. The glucose incorporated into lipids is mainly in the glyceride-glycerol moiety. Addition of insulin did not produce an increase on glucose oxidation and a slight increase in the incorporation into total lipids was observed. Since it has been reported that sloths have a very low rate on thyroxine secretion, the results are discussed in relation to data in the literature on carbohydrate and lipid metabolism in hypothyroid animals.     

Influence of age and sex in serum osteocalcin levels in thoroughbred horses.

In this study, we assessed the potential value of free serum osteocalcin or bone gla protein (BGP), the most abundant non collagenous matrix protein found in bone and dentin, to reflect changes of bone turnover in thoroughbred horses. Levels of osteocalcin were analyzed in serum samples of 54 clinically normal animals divided into three groups (A, B, C) according to age: 8, 16-18 and 24-36 months, in order to determine the standard for young horses of different age and sex. Serum BGP was measured by an in-house developed double antibody radioimmunoassay using bovine antigen. The mean BGP levels (ng/ml) were 45.65 +/- 11.69; 33.65 +/- 16.65; 15.08 +/- 6.70 respectively for groups A, B and C; statistically significant differences were found between groups (A vs B and C; Bvs C). Difference between males and females was found significant in group C with higher values in the females: 18.75 +/- 5.00 against 14.43 +/- 10.47 i n the males. This can be considered a sex related effect on BGP serum levels after the onset of puberty. Correlation coefficient between age and serum BGP for females and males were r 5 20.598 ( P < 0.001) and r 5 200.807 (P < 0.001) respectively. A significant negative linear relationship could be established between these two parameters in males during the growth period. The regression equation between serum BGP and age for males was (month of age = 65.14-1.68. BGP). In the female group the gestation and lactation are variables that lower the correlation coefficient between age and serum BGP levels. These results suggest that serum BGP decreases in thoroughbred horses during the growth period, and significant differences between sexes were found only after the onset of puberty.     

Haploinsufficient Bmp4 ocular phenotypes include anterior segment dysgenesis with elevated intraocular pressure

Background  

Glaucoma is a common disease but its molecular etiology is poorly understood. It involves retinal ganglion cell death and optic nerve damage that is often associated with elevated intraocular pressure. Identifying genes that modify glaucoma associated phenotypes is likely to provide insights to mechanisms of glaucoma. We previously reported glaucoma in DBA/2J mice caused by recessive alleles at two loci, isa and ipd, that cause iris stromal atrophy and iris pigment dispersion, respectively. A approach for identifying modifier genes is to study the effects of specific mutations in different mouse strains. When the phenotypic effect of a mutation is modified upon its introduction into a new strain, crosses between the parental strains can be used to identify modifier genes. The purpose of this study was to determine if the effects of the DBA/2J derived isa and ipd loci are modified in strain AKXD-28/Ty.     

Enantioselective hydrolysis of epoxides: the employment of the soluble fraction from Vicia sativa seedlings

Biocatalytic hydrolysis of meso and racemic aryl- and alkyl-oxiranes was accomplished by employing the epoxide hydrolase activity of the soluble fraction of Vicia sativa seedlings. Whereas meso epoxides were not hydrolyzed by this fraction, racemic compounds were transformed into the corresponding diols by formal anti-stereoselective water attack. Both substrate and product enantioselectivity were strongly influenced by the chains length and the presence of a hydroxyl group.     

Enantioselectivity in the Rabbit Liver Microsomal Biotransformation of Styrene and Phenylpropenes

The rabbit liver microsomal P-450 catalyzed oxidation of styrene (1a) and isomeric phenylpropenes, trans-1-phenylpropene (1b), cis-1-phenylpropene (1c) and 3-phenylpropene (1d), was investigated and the enantioselectivity of the epoxidation of the olefinic double bond was determined by checking the enantiomeric excesses of the corresponding first formed epoxides (2). These enantiomeric excesses were always modest, ranging between 7% of (1S,2S)-(2b) and 22% of (1R,2R)-(2c). In the case of (1d) a nonenantioselective hydroxylation at the benzylic-allylic C(3) was also oberved. The ratio between this hydroxylation and olefin epoxidation of (Id) was 1:2.     

The rabbit liver microsomal biotransformation of 1,1-dialkylethylenes: Enantioface selection of epoxidation and enantioselectivity of epoxide hydrolysis

The rabbit liver microsomal biotransformation of α-methylstyrene ( 1a ), 2-methyl-1-hexene ( 1b ), 2,4,4-trimethyl-1-pentene ( 1c ), and 2,3,3-trimethyl-1-butene ( 1d ) has been investigated with the aim at establishing the enantioface selection of the cytochrome P-450-promoted epoxidation of the double bond and the enantioselectivity of microsomal epoxide hydrolase (mEH)-catalyzed hydrolysis of the resulting epoxides. GLC on a Chiraldex G-TA (ASTEC) column was used to determine the enantiomeric composition of the products. The epoxides 2 first produced in incubations carried out in the presence of an NADPH regenerating system were not detected, being rapidly hydrolyzed by mEH to diols 3 . The enantiomeric composition of the latter showed that no enantioface selection occurred in the epoxidation of 1c and 1d , and a very low (8%) ee of the (R)-epoxide was formed from 1b . Incubation of racemic epoxides 2b–d with the microsomal fraction showed that the mEH-catalyzed hydrolysis of 2c and 2d was practically nonenantioselective, while that of 2b exhibited a selectivity E = 4.9 favoring the hydrolysis of the (S)-enantiomer. A comparison of these results with those previously obtained for linear and branched chain alkyl monosubstituted oxiranes shows that the introduction of the second alkyl substituent suppresses the selectivity of the mEH reaction of the latter and reverses that of the former substrates. © 1994 Wiley-Liss, Inc.