Quantitative analysis of Streptococcus pneumoniae TIGR4 response to in vitro iron restriction by 2-D LC ESI MS/MS

Understanding the growth of bacterial pathogens in a micronutrient restricted host environment can identify potential virulence proteins that help overcome this nutritional barrier to productive infection. In this study, we investigated the pneumococcal protein expression response to iron limitation using an in vitro model. We identified S. pneumoniae TIGR4 proteins by 2-D LC ESI MS/MS and determined significant changes in protein expression in response to iron restriction using computer-intensive random resampling methods. Differential protein expression was studied in the context of a S. pneumoniae TIGR4 protein interaction network using Pathway Studio. Our analysis showed that pneumococcal iron restriction response was marked by increased expression of known virulence factors like PsaA. It involved changes in the expression of stress response, and phase variation and biofilm formation proteins. The net effect of changes in all these biological processes could increase the virulence of S. pneumoniae TIGR4 during in vivo infection.     

酿酒酵母对数生长后期代谢重构的全基因组表达谱芯片分析

为了探讨酵母进入对数生长后期以后酒精生产速度降低的原因,我们利用酵母表达谱芯片技术对酿酒酵母细胞从对数生长中期进入对数生长后期时的全基因组表达谱进行了分析,发现酵母在对数生长中期的表达谱非常稳定,而一旦进入对数生长后期.则出现明显的代谢重构现象.许多氨基酸合成和代谢相关的基因、离子转移以及与能量的生成和储存等功能相关的基因出现了不同程度的上调;而许多涉及酵母转座和DNA重组的基因则表达下调;一些中心代谢途径也发生了代谢重构.包括:琥珀酸和α-酮戊二酸生成途径基因的一致上调,都与氨基酸合成和代谢相关基因表达的结果相吻合.结果表明:由于氨基酸合成的需求量增加,进入对数生长后期酵母的代谢转向TCA循环和乙醛酸循环,导致酒精的生产速率降低.     

The effect of protein expression of Streptococcus pneumoniae by blood

During infection, the common respiratory tract pathogen Streptococcus pneumoniae encounters several environmental conditions, such as upper respiratory tract, lung tissue, and blood stream, etc. In this study, we examined the effects of blood on S. pneumoniae protein expression using a combination of highly sensitive 2-dimensional electrophoresis (DE) and MALDI-TOF MS and/or LC/ESI-MS/MS. A comparison of expression profiles between the growth in THY medium and THY supplemented with blood allowed us to identify 7 spots, which increased or decreased two times or more compared with the control group: tyrosyl-tRNA synthetase, lactate oxidase, glutamyl-aminopeptidase, L-lactate dehydrogenase, cysteine synthase, ribose-phosphate pyrophosphokinase, and orotate phosphoribosyltransferase. This global approach can provide a better understanding of S. pneumoniae adaptation to its human host and a clue for its pathogenicity.     

Feminizing Wolbachia: a transcriptomics approach with insights on the immune response genes in Armadillidium vulgare

Background

Clostridium thermocellum produces H₂ and ethanol, as well as CO₂, acetate, formate, and lactate, directly from cellulosic biomass. It is therefore an attractive model for biofuel production via consolidated bioprocessing. Optimization of end-product yields and titres is crucial for making biofuel production economically feasible. Relative protein expression profiles may provide targets for metabolic engineering, while understanding changes in protein expression and metabolism in response to carbon limitation, pH, and growth phase may aid in reactor optimization. We performed shotgun 2D-HPLC-MS/MS on closed-batch cellobiose-grown exponential phase C. thermocellum cell-free extracts to determine relative protein expression profiles of core metabolic proteins involved carbohydrate utilization, energy conservation, and end-product synthesis. iTRAQ (isobaric tag for relative and absolute quantitation) based protein quantitation was used to determine changes in core metabolic proteins in response to growth phase.

Results

Relative abundance profiles revealed differential levels of putative enzymes capable of catalyzing parallel pathways. The majority of proteins involved in pyruvate catabolism and end-product synthesis were detected with high abundance, with the exception of aldehyde dehydrogenase, ferredoxin-dependent Ech-type [NiFe]-hydrogenase, and RNF-type NADH:ferredoxin oxidoreductase. Using 4-plex 2D-HPLC-MS/MS, 24% of the 144 core metabolism proteins detected demonstrated moderate changes in expression during transition from exponential to stationary phase. Notably, proteins involved in pyruvate synthesis decreased in stationary phase, whereas proteins involved in glycogen metabolism, pyruvate catabolism, and end-product synthesis increased in stationary phase. Several proteins that may directly dictate end-product synthesis patterns, including pyruvate:ferredoxin oxidoreductases, alcohol dehydrogenases, and a putative bifurcating hydrogenase, demonstrated differential expression during transition from exponential to stationary phase.

Conclusions

Relative expression profiles demonstrate which proteins are likely utilized in carbohydrate utilization and end-product synthesis and suggest that H₂ synthesis occurs via bifurcating hydrogenases while ethanol synthesis is predominantly catalyzed by a bifunctional aldehyde/alcohol dehydrogenase. Differences in expression profiles of core metabolic proteins in response to growth phase may dictate carbon and electron flux towards energy storage compounds and end-products. Combined knowledge of relative protein expression levels and their changes in response to physiological conditions may aid in targeted metabolic engineering strategies and optimization of fermentation conditions for improvement of biofuels production.     

Proteomic analysis of protein expression in Streptococcus pneumoniae in response to temperature shift

From its initial colonization to causation of disease, Streptococcus pneumoniae has evolved strategies to cope with a number of stressful in vivo environmental conditions. In order to analyze a global view of this organism's response to heat shock, we established a 2-D electrophoresis proteome map of the S. pneumoniae D39 soluble proteins under in vitro culture conditions and performed the comparative proteome analysis to a 37 to 42 degrees temperature up-shift in S. pneumoniae. When the temperature of an exponentially growing S. pneumoniae D39 culture was raised to 42 degrees , the expression level of 25 proteins showed changes when compared to the control. Among these 25 proteins, 12 were identified by MALDI-TOF and LC-coupled ESI MS/MS. The identified proteins were shown to be involved in the general stress response, energy metabolism, nucleotide biosynthesis pathways, and purine metabolism. These results provide clues for understanding the mechanism of adaptation to heat shock by S. pneumoniae and may facilitate the assessment of a possible role for these proteins in the physiology and pathogenesis of this pathogen.     

Temporal quantitative proteomics of Saccharomyces cerevisiae in response to a nonlethal concentration of furfural

Furfural, one of the main inhibitory compounds in lignocellulosic hydrolytes, inhibits the growth and ethanol production rate of yeast. To get a global view of the dynamic expression pattern of proteins in Saccharomyces cerevisiae during the fermentation with the introduction of 8 g/L furfural, the protein samples were taken before the addition of furfural, during the initial phase of furfural conversion and immediately after the conversion of furfural for comparative proteomic analysis with iTRAQ on a LC‐ESI‐MS/MS instrument. A comparison of the temporal expression pattern of 107 proteins related to protein synthesis between the reference cultures and the furfural‐treated cultures showed that a temporal downregulation of these proteins was retarded after the addition of furfural. The expression levels of 20 enzymes in glucose fermentation and 5 enzymes in the tricarboxylic acid cycle were reduced by furfural, with notably delayed temporal downregulations of Glk1p, Tdh1p, Eno1p and Aco1p, which is correlated to the reduced ethanol formation rate and glucose consumption rate by 66.7 and 60.4%, respectively. In the presence of furfural, proteins catalyzing the upper part of the super pathway of sulfur amino acid biosynthesis were repressed at all time points, which is related to the inhibited growth of furfural‐treated yeast. The expressions of 18 proteins related to stress response showed increased trends, including several highly induced heat shock proteins and proteins related to cellular signaling pathways.     

Proteomic analysis of membrane proteins from Streptococcus pneumoniae with multiple separation methods plus high accuracy mass spectrometry

Abstract Streptococcus pneumoniae is a Gram-positive human pathogen that causes a variety of serious mucosal and invasive diseases in human. Bacterial membrane proteins play crucial roles in host-pathogen interactions and bacterial pathogenesis, and thus are potential drug targets or vaccine candidates. In this study, membranes from Streptococcus pneumoniae D39 were enriched by mechanical grinding and ultracentrifugation, and then the membrane proteins were extracted with trifluroethanol and chloroform. Around 60% of the extracted proteins were identified to be membrane proteins with 2-DE coupled with MALDI-MS/MS and 2D-LC-ESI-MS/MS. These identified membrane proteins can be functionally categorized into various groups involved in nutriment transport, signal transduction, protein folding or secretion, oxidation, carbohydrate metabolism, and other physiological processes. A protein interaction network was constructed for understanding the regulation relationship of the membrane proteins. This study represents the first global characterization of membrane proteome from Gram-positive streptococcus species of bacteria, providing valuable clues for further investigation aiming at identifying drug/vaccine targets for the bacterial infection.     

Comparison of growth-phase-dependent cytosolic proteomes of two Lactobacillus plantarum strains used in food and feed fermentations

Lactobacillus plantarum is a facultative heterofermentative lactic acid bacterium highly adapted to a wide variety of environments and widely used in food and feed fermentations. Proteomes of two strains of L. plantarum, one isolated from spontaneously fermented cereal-based feed (strain REB1), and the other from white cabbage (strain MLBPL1), were studied to elucidate the strain-specific variation and the physiological changes occurring between the growth (lag, early-exponential, late-exponential and early-stationary) phases of this bacterium when cultivated in a standard rich medium. A total of 231 protein spots were identified by LC-MS/MS. These proteins showed that strain MLBPL1 had more proteins with growth phase-dependent expression than REB1, which possesses a more constant expression profile. The proteins with growth phase-dependent expression in REB1 and MLBPL1 were mainly associated with energy metabolism (glycolysis, phosphoketolase pathway and ribose metabolism), all having preferential expression in the early-exponential phase, confirming the use of different carbohydrates simultaneously. Indication of energy production was also seen in lag and early-stationary phases.     

Inhibition of ubiquitin ligase F-box and WD repeat domain-containing 7α (Fbw7α) causes hepatosteatosis through Krüppel-like factor 5 (KLF5)/peroxisome proliferator-activated receptor γ2 (PPARγ2) pathway but not SREBP-1c protein in mice

F-box and WD repeat domain-containing 7α (Fbw7α) is the substrate recognition component of a ubiquitin ligase that controls the degradation of factors involved in cellular growth, including c-Myc, cyclin E, and c-Jun. In addition, Fbw7α degrades the nuclear form of sterol regulatory element-binding protein (SREBP)-1a, a global regulator of lipid synthesis, particularly during mitosis in cultured cells. This study investigated the in vivo role of Fbw7α in hepatic lipid metabolism. siRNA knockdown of Fbw7α in mice caused marked hepatosteatosis with the accumulation of triglycerides. However, inhibition of Fbw7α did not change the level of nuclear SREBP-1 protein or the expression of genes involved in fatty acid synthesis and oxidation. In vivo experiments on the gain and loss of Fbw7α function indicated that Fbw7α regulated the expression of peroxisome proliferator-activated receptor (PPAR) γ2 and its target genes involved in fatty acid uptake and triglyceride synthesis. These genes included fatty acid transporter Cd36, diacylglycerol acyltransferase 1 (Dgat1), and fat-specific protein 27 (Cidec). The regulation of PPARγ2 by Fbw7α was mediated, at least in part, by the direct degradation of the Krüppel-like factor 5 (KLF5) protein, upstream of PPARγ2 expression. Hepatic Fbw7α contributes to normal fatty acid and triglyceride metabolism, functions that represent novel aspects of this cell growth regulator.     

Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein

Microbial production of many commercially important secondary metabolites occurs during stationary phase, and methods to measure metabolic flux during this growth phase would be valuable. Metabolic flux analysis is often based on isotopomer information from proteinogenic amino acids. As such, flux analysis primarily reflects the metabolism pertinent to the growth phase during which most proteins are synthesized. To investigate central metabolism and amino acids synthesis activity during stationary phase, addition of fully ¹³C‐labeled glucose followed by induction of green fluorescent protein (GFP) expression during stationary phase was used. Our results indicate that Escherichia coli was able to produce new proteins (i.e., GFP) in the stationary phase, and the amino acids in GFP were mostly from degraded proteins synthesized during the exponential growth phase. Among amino acid biosynthetic pathways, only those for serine, alanine, glutamate/glutamine, and aspartate/asparagine had significant activity during the stationary phase. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Quantification of proteome dynamics in Corynebacterium glutamicum by (15)N-labeling and selected reaction monitoring

Selected reaction monitoring allows quantitative measurements of proteins over several orders of magnitude in complex biological samples. Here we present a targeted approach for quantification of 19 enzymes from Corynebacterium glutamicum applying isotope dilution mass spectrometry coupled to high performance liquid chromatography (IDMS-LC-MS/MS). Investigations of protein dynamics upon growth on acetate and glucose as sole carbon source shows highly stable peptide amounts for enzymes of the central carbon metabolism during the transition phase and after substrate depletion. However significant adaptations of protein amounts are observed between both growth conditions well agreeing with known changes in metabolic fluxes. Time-resolved measurements of protein expression after metabolic switch from glycolytic to gluconeogenetic conditions reveal fast responses in protein synthesis rates for glyoxylate shunt enzymes.     

金属蛋白质组学研究锌离子匮乏对肺炎链球菌的影响

【目的】研究锌离子缺乏对肺炎链球菌的影响,找到其适应性生长机制。【方法】以肺炎链球菌为模型,利用加锌和不加锌的培养基对细菌进行培养,收集细胞蛋白,采用双向凝胶电泳,结合金属亲和层析和质谱技术鉴定差异表达蛋白,进而通过生物信息学分析蛋白质相互关系,从中找到细菌适应锌离子匮乏条件的关键代谢通路和蛋白。【结果】测定了在限制培养条件下肺炎链球菌的最适生长浓度,建立了锌离子调控蛋白双向凝胶电泳图谱,鉴定到了96个差异表达蛋白斑点,共67个差异蛋白,其中32个表达下调,35个表达上调,锌离子调控蛋白的作用可能主要体现在糖代谢、核酸代谢、氧化还原作用、辅助蛋白质翻译、合成及折叠等方面。建立了锌结合蛋白的差异表达图谱,鉴定到了10个差异表达蛋白斑点,共7个差异蛋白,其中1个表达下调,6个表达上调。锌离子结合蛋白的作用可能主要体现在应对压力、蛋白质折叠和转运、氨基酸代谢等方面。【结论】肺炎链球菌主要通过调控碳水化合物代谢和核酸代谢等多个代谢通路来应对宿主锌金属离子匮乏的环境,从而使自身能够存活并对宿主形成感染。本研究为揭示细菌在宿主环境,特别是金属离子匮乏条件下的适应性生长机制提供理论基础。     

Temporal and spatial profiling of internode elongation-associated protein expression in rapidly growing culms of bamboo

In natural conditions, culms of developing Moso bamboo, Phyllostachys heterocycla var. pubescens, reach their final height of more than ten meters within a short period of two to four months. To study this phenomenon, bamboo culm material collected from different developmental stages and internodes was analyzed. Histological observations indicated that the development of culm was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. Development, maturation, and aging in different regions of the culm were studied systematically from the basal to the top internode. The four major endogenous hormones, indole acetic acid, gibberellic acid, zeatin riboside, and abscisic acid appeared to strongly influence the cell elongation phase. A total of 258 spots were differentially expressed in culm development. Of these, 213 spots were identified by MALDI-TOF/TOF MS and were involved in many physiological and metabolic processes including carbohydrate metabolism, cell division, cell expansion, protein synthesis, amino acid metabolism and redox homeostasis. These proteins with different expression patterns constructed an ingenious network to regulate the culm development. Developmental stage-specific and internode-specific protein expression patterns were identified. Protein abundance was regulated temporally and to some extent spatially, and the sequential development from base to apex of bamboo culm was implemented by temporal and spatial expression of enzymes. Results indicate that during development energy was mainly derived from sucrose degradation, as photosynthetic capacity was poor. The regulation of anaerobic and aerobic modes of respiration appeared to play an important role in energy generation. This is the first report on proteomic profiling in bamboo and helps in understanding the regulatory processes in developing culms.     

Plasma proteome dynamics: analysis of lipoproteins and acute phase response proteins with 2H2O metabolic labeling

Understanding the pathologies related to the regulation of protein metabolism requires methods for studying the kinetics of individual proteins. We developed a (2)H(2)O metabolic labeling technique and software for protein kinetic studies in free living organisms. This approach for proteome dynamic studies requires the measurement of total body water enrichments by GC-MS, isotopic distribution of the tryptic peptide by LC-MS/MS, and estimation of the asymptotical number of deuterium incorporated into a peptide by software. We applied this technique to measure the synthesis rates of several plasma lipoproteins and acute phase response proteins in rats. Samples were collected at different time points, and proteins were separated by a gradient gel electrophoresis. (2)H labeling of tryptic peptides was analyzed by ion trap tandem mass spectrometry (LTQ MS/MS) for measurement of the fractional synthesis rates of plasma proteins. The high sensitivity of LTQ MS in zoom scan mode in combination with (2)H label amplification in proteolytic peptides allows detection of the changes in plasma protein synthesis related to animal nutritional status. Our results demonstrate that fasting has divergent effects on the rate of synthesis of plasma proteins, increasing synthesis of ApoB 100 but decreasing formation of albumin and fibrinogen. We conclude that this technique can effectively measure the synthesis of plasma proteins and can be used to study the regulation of protein homeostasis under physiological and pathological conditions.