Specific roles for the Ccr4-Not complex subunits in expression of the genome

In this work we used micro-array experiments to determine the role of each nonessential subunit of the conserved Ccr4-Not complex in the control of gene expression in the yeast Saccharomyces cerevisiae. The study was performed with cells growing exponentially in high glucose and with cells grown to glucose depletion. Specific patterns of gene deregulation were observed upon deletion of any given subunit, revealing the specificity of each subunit''s function. Consistently, the purification of the Ccr4-Not complex through Caf40p by tandem affinity purification from wild-type cells or cells lacking individual subunits of the Ccr4-Not complex revealed that each subunit had a particular impact on complex integrity. Furthermore, the micro-arrays revealed that the role of each subunit was specific to the growth conditions. From the study of only two different growth conditions, revealing an impact of the Ccr4-Not complex on more than 85% of all studied genes, we can infer that the Ccr4-Not complex is important for expression of most of the yeast genome.     

Effect of glucose analog supplementation on metabolic flux distribution in anaerobic chemostat cultures of Escherichia coli

Previous work in our laboratories investigated the use of methyl alpha-glucoside (alpha-MG), a glucose analog that shares a phosphotransferase system with glucose, to modulate glucose uptake and therefore reduce acetate accumulation. The results of that study showed a significant improvement in batch culture performance and a reduction in acetate excretion without any significant effect on the growth rate in complex medium. The current study investigates the effect of supplementing the culture medium with the glucose analog alpha-MG on the metabolic fluxes of Escherichia coli under anaerobic chemostat conditions at two different dilution rates. Anaerobic chemostat studies utilizing complex media supplemented with glucose or glucose and alpha-MG at dilution rates of 0.1 and 0.4 h(-1), were performed, and the metabolic fluxes were analyzed. It was found that the addition of the glucose analog alpha-MG has an effect on the specific production rate of various extracellular metabolites. This effect is slightly greater at the higher dilution rate of 0.4 h(-1). However, the glucose analog does not cause any major shift in the central metabolic patterns. It was further observed that alpha-MG supplementation does not result in the reduction in specific acetate synthesis rate in anaerobic chemostat cultures. These results emphasize the importance of testing different strategies for metabolic manipulation under the actual operating conditions.     

Impaired growth on glucose of a pyruvate dehydrogenase-negative mutant of Kluyveromyces lactis is due to a limitation in mitochondrial acetyl-coenzyme A uptake

A Kluyveromyces lactis mutant with a disruption in the KlPDA1 gene, encoding the E1 alpha subunit of the pyruvate dehydrogenase complex, exhibited a four-fold reduced specific growth rate on glucose in minimal medium. Growth of the Klpda1 mutant on glucose in complex medium was not affected. Its growth on defined media could be restored by adding amino acids that require mitochondrial acetyl-CoA for their biosynthesis as nitrogen sources. This, together with the observation that low-concentrations of L-carnitine also restored growth on glucose, indicates that the slow-growth phenotype of the Klpda1 mutant is due to a limited capacity of the mitochondria for import of cytosolic acetyl-CoA.     

林肯链霉菌合成林可霉素代谢调节的研究

在摇瓶条件下研究了葡萄糖、铵盐、磷酸盐对林可霉素产生菌林肯链霉菌的生长及林可霉素生物合成的影响。发酵过程中林可霉素的合成主要发生在菌体生长期,逐渐下降。使用6%的葡萄糖未发现通常所说的“葡萄糖效应”。0.2%铵盐有利于细胞生长,但0.8%NH+4对林可霉素的生物合成具有抑制作用。发酵48h后补加0.6% NH^＋_４,对林可霉素的生成没有显著影响。0.05%～0.1%磷酸盐对林可霉素合成具有较强的抑制作用。并就磷酸盐对菌体由初级代谢转向次级代谢的作用作了初步考察。     

Effect of carbon source, growth and temperature on the expression of the sec genes of Streptomyces lividans 1326

The mRNA level in sec genes of Streptomyces lividans was studied as a function of growth temperature, glucose effect, and growth using two different carbon sources. Glucose and xylan, a complex hemicellulose, were used as carbon sources for the growth of S. lividans. For both substrates, the mRNA levels of secA, secD, secE, secF, and secY genes were almost constant during the early and log phases, but showed a marked decrease at the beginning of the stationary phase followed by a full recovery of mRNA level in the late stationary phase. This indicates that the sec genes are actively transcribed during the differentiation process. The mRNA level in xylan was generally from 1.5- to 2-fold that in glucose. At growth temperatures of 28 degrees C, 34 degrees C, or 40 degrees C, there was no significant difference in the sec gene mRNA levels.     

Reduction of trimethylamine N-oxide by Escherichia coli as anaerobic respiration.

E. coli was found to grow anaerobically on lactate in the presence of trimethylamine N-oxide (TMANO), reducing it to trimethylamine. Anaerobic growth on glucose was promoted in the presence of TMANO. When a culture grown in complex medium was transferred to defined medium, growth on glucose and ammonia took place in the presence of TMANO after consumption of complex nutrients introduced with the preculture, in contrast to growth in nitrate respiration. The amounts of ethanol, succinate, and lactate among the fermentation products were decreased and that of acetate was increased in the presence of TMANO. Formate generation was much reduced at pH 7.4, whereas stoichiometric formation of formate was observed in the absence of TMANO. Cells grown anaerobically in the presence of TMANO had a higher activity of amine N-oxide reductase than cells grown under other conditions. The content of cytochrome-558 was elevated in the presence of TMANO during growth in complex medium. Cytochrome c-552 found in cells grown in diluted complex medium or defined medium in the presence of TMANO was oxidized by TMANO in cell extracts. The molar growth yield on glucose was higher in the presence of TMANO than in its absence and lower than that in the presence of nitrate.     

Effect of vitamins and various amino acids on glucose isomerase biosynthesis by Streptomyces albogriseolus culture

The effect of vitamins (B1, B2, B3, B6, B12, H, PP and folic acid) and amino acids (glutamic and aspartic acids) on glucose isomerase biosynthesis was studied in Streptomyces albogriseolus. These compounds were added either alone or in combinations to different growth media (synthetic and complex). The results were processed using mathematical methods, and the following mixture of vitamins and amino acids was proposed to be added to the complex fermentation medium: B2, 10 micrograms/L; B6, 10 micrograms/L; H, 1 microgram/L; aspartic acid, 0.01 microM. The production of glucose isomerase rose more than 1.5 times after such additions.     

Growth and development kinetics of Bacillus thuringiensis in batch culture

The kinetics of Bacillus thuringiensis growth and its assimilation of nutrient substances were studied under the conditions of batch cultivation in a complex medium containing yeast extract and in a chemically defined medium with amino acids. The growth of B. thuringiensis can be divided into five phases: exponential growth; decelerated growth; stationary phase when protein crystals are formed; stationary phase when spores are formed; lysis of sporangia releasing spores. The first phase may in turn be subdivided into three stages according to changes in the specific growth rate and substrate assimilation: a high specific growth rate and no glucose assimilation; an abrupt drop in mu and the beginning of intensive glucose assimilation from the medium; a new rise in the specific growth rate. As follows from the results of studying the kinetics of B. thuringiensis growth in a chemically defined medium, the above changes in the exponential growth phase are due to the fact that the culture assimilates yeast extract components in the complex medium or amino acids in the chemically defined medium during this phase, and then starts to assimilate glucose and ammonium in the following phases of growth.     

Growth and recombinant protein expression with <Emphasis Type="Italic">Escherichia coli</Emphasis> in different batch cultivation media

Parallel operated milliliter-scale stirred tank bioreactors were applied for recombinant protein expression studies in simple batch experiments without pH titration. An enzymatic glucose release system (EnBase), a complex medium, and the frequently used LB and TB media were compared with regard to growth of Escherichia coli and recombinant protein expression (alcohol dehydrogenase (ADH) from Lactobacillus brevis and formate dehydrogenase (FDH) from Candida boidinii). Dissolved oxygen and pH were recorded online, optical densities were measured at-line, and the activities of ADH and FDH were analyzed offline. Best growth was observed in a complex medium with maximum dry cell weight concentrations of 14 g L⁻¹. EnBase cultivations enabled final dry cell weight concentrations between 6 and 8 g L⁻¹. The pH remained nearly constant in EnBase cultivations due to the continuous glucose release, showing the usefulness of this glucose release system especially for pH-sensitive bioprocesses. Cell-specific enzyme activities varied considerably depending on the different media used. Maximum specific ADH activities were measured with the complex medium, 6 h after induction with IPTG, whereas the highest specific FDH activities were achieved with the EnBase medium at low glucose release profiles 24 h after induction. Hence, depending on the recombinant protein, different medium compositions, times for induction, and times for cell harvest have to be evaluated to achieve efficient expression of recombinant proteins in E. coli. A rapid experimental evaluation can easily be performed with parallel batch operated small-scale stirred tank bioreactors.     

Influence of medium components on growth kinetics of <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis>

Starting with the standard complex medium HL-5C, the influence of different medium components on the growth behavior of Dictyostelium discoideum was investigated. For this purpose, each component was individually deleted from the complex medium HL-5C, and the overall concentration of all components as well as the kinds and concentrations of carbon source were varied. The effects of the supplementation with major components of synthetic medium like vitamins, trace metals, inorganic salts were also investigated. When glucose being the carbon source was deleted from the standard HL-5C medium, the maximal cell density then had a drastic drop. Deletion of yeast extract also caused lower maximal cell density. Of all the carbohydrates investigated only maltose and glucose led to higher final cell concentration. Adding inorganic salts such as CaCl₂ and MgCl₂ to HL-5C medium significantly improved the cell growth, whereas addition of vitamins or trace metals had little effect on cell growth. A semi-empirical model is employed to simulate the cell growth.     

Comparative physiology of two protozoan parasites, Leishmania donovani and Trypanosoma brucei, grown in chemostats.

Cultures of the insect stage of the protozoan parasites Leishmania donovani and Trypanosoma brucei were grown in chemostats with glucose as the growth rate-limiting substrate. L. donovani has a maximum specific growth rate (mu max) of 1.96 day-1 and a Ks for glucose of 0.1 mM; the mu max of T. brucei is 1.06 day-1 and the Ks is 0.06 mM. At each steady state (specific growth rate, mu, equals D, the dilution rate), the following parameters were measured: external glucose concentration (Glcout), cell density, dry weight, protein, internal glucose concentration (Glcin), cellular ATP level, and hexokinase activity. L. donovani shows a relationship between mu and yield that allows an estimation of the maintenance requirement (ms) and the yield per mole of ATP (YATP). Both the ms and the YATP are on the higher margin of the range found for prokaryotes grown on glucose in a complex medium. L. donovani maintains the Glcin at a constant level of about 50 mM as long as it is not energy depleted. T. brucei has a decreasing yield with increasing mu, suggesting that it oxidizes its substrate to a lesser extent at higher growth rates. Glucose is not concentrated internally but is taken up by facilitated diffusion, while phosphorylation by hexokinase is probably the rate-limiting step for glucose metabolism. The Ks is constant as long as glucose is the rate-limiting substrate. The results of this study demonstrate that L. donovani and T. brucei have widely different metabolic strategies for dealing with varying external conditions, which reflect the conditions they are likely to encounter in their respective insect hosts.     

Kinetic modeling of microbial growth,enzyme activity,and gene deletions: An integrated model of β-glucosidase function in Cellvibrio japonicus

Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene-deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacterium Cellvibrio japonicus grown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics of C. japonicus using either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild-type strain as well as in β-glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non-diauxic growth and metabolite consumptions of the wild-type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially-useful strains. Importantly, the model is able to explain the role of the different β-glucosidases and their behavior under genetic perturbations. This integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates.     

Biocalorimetric studies of the metabolic activity of Pseudomonas aeruginosa aerobically grown in a glucose-limited complex growth medium

Biocalorimetric experiments were performed to investigate the aerobic growth of Pseudomonas aeruginosa, isolated from tannery saline wastewater. Growth factors (pH, Inoculum size, carbon source, temperature, aeration rate, and agitation rate) were optimized in shaker and calorimeter based on the growth of P. aeruginosa and heat generation rates. A limiting value of 0.2% glucose concentration was found to be optimum for the growth of P. aeruginosa in a complex growth medium, and the heat flux (q(r)) profiles resulting from the metabolic activity of P. aeruginosa further confirmed this observation. The bacterial growth profile was found to correlate well with the metabolic heat generated. Heat-yield values were calculated for both glucose consumption and the growth of P. aeruginosa from the calorimetric results. Metabolic shifts in substrate uptake from glucose to peptone present in growth medium was observed by the variations in heat-flux profile. The calorimetric data presented in this study should be useful in understanding the behavior of the isolated bacterial strain in degrading complex and mixed substrates commonly observed in tannery saline waste stream, and further to extend the results for scale-up studies.     

普甜玉米种子萌发期糖代谢和水解酶活性动态变化

种子萌发是一个较复杂的生理生化过程,是种子贮藏物质在酶的作用下经过一系列反应生成蔗糖、葡萄糖、果糖等各种糖类化合物,为种子萌发提供碳源和能量。该研究利用两个不同来源、籽粒营养成分具有差异的普甜玉米种子动态分析了种子萌发期蔗糖、果糖和葡萄糖代谢及关键水解酶活性的变化。结果表明:在种子萌发过程中,E22和T26两个普甜玉米种子的物质动员量、物质利用率、蔗糖、葡萄糖和果糖含量均存在遗传差异,其中淀粉含量较高的T26种子具有较突出的物质利用率,表明淀粉是影响普通甜玉米种子萌发的关键因子;在种子萌发4~8 d、6~10 d时,E22分别具有较高的蔗糖和葡萄糖含量,而T26是在萌发10 d时具有较高的果糖含量。随着种子发芽进程,蔗糖合成酶活性、淀粉酶活性都呈逐渐上升的趋势,但淀粉酶活性变幅较明显;进一步关联分析8个种子萌发物质利用性状间关系,结果表明种子萌发期间,种子物质动员量主要受淀粉酶活性影响,而种子物质利用率则主要受糖含量多少制约。因此,提高甜玉米种子萌发期物质利用率对其种子发芽和幼苗生长,增强其与杂草生长的竞争力,提高甜玉米产量均具有重要意义。     

葡萄糖对表皮葡萄球菌生物被膜形成的影响及调节机制的研究

生物被膜(Biofilm)是条件致病菌表皮葡萄球菌(Staphylococcusepidermidis)的主要致病因素,生物被膜的形成依赖多糖PIA合成,合成PIA的糖基转移酶由icaADBC基因编码。以生物被膜形成能力不同的菌株为对象,通过研究不同环境对生物被膜形成、细菌总糖量及相关基因表达的变化,探索外界环境对生物被膜形成的影响及葡萄糖对生物被膜诱导的分子机制。有利于生物被膜形成培养条件促进生物被膜形成及多糖的表达,葡萄糖能诱导ica基因的表达和生物被膜形成,ica基因的反义寡核苷酸(ODN)能对抗葡萄糖的作用;葡萄糖作用下不同生长周期生物被膜形成相关基因ica、icaR、AtlE表达不同。表皮葡萄球菌生物被膜的形成与细菌糖代谢有关,葡萄糖通过上调ica表达诱导生物膜形成,但不需要ica基因的持续表达;葡萄糖的诱导作用不是直接通过调节AtlE和icaR基因来实现的     

Organization and expression of the COX6 genetic locus in Saccharomyces cerevisiae: multiple mRNAs with different 3' termini are transcribed from COX6 and regulated differentially

COX6 and its surrounding genetic locus have been characterized for the yeast Saccharomyces cerevisiae. Flanking genes are found closely spaced upstream and downstream of COX6. The upstream gene and COX6 are transcribed from opposite strands and are separated by no more than 300 bp. COX6 is transcribed into three different size classes of mRNA (1000b, 830b, and 700b) differing in length in their 3' untranslated regions. All three classes of mRNAs are found on polysomes and, hence, are most likely translated. The different COX6 mRNAs vary in abundance during growth in rich media and are affected differentially as cells are shifted into media containing high or low glucose concentrations. The largest mRNA is much more susceptible to glucose repression/derepression than are the two smaller mRNAs, whereas the smallest RNA is preferentially accumulated during growth in rich media. These findings demonstrate that COX6 mRNAs with different 3'-termini are either synthesized differentially or differ in stability and suggest the existence of a complex system regulating COX6 expression.     

Unveiling the role of Dps in the organization of mycobacterial nucleoid

In order to preserve genetic information in stress conditions, bacterial DNA is organized into higher order nucleoid structure. In this paper, with the help of Atomic Force Microscopy, we show the different structural changes in mycobacterial nucleoid at different points of growth in the presence of different concentrations of glucose in the medium. We also observe that in Mycobacterium smegmatis, two different Dps proteins (Dps1 and Dps2) promote two types of nucleoid organizations. At the late stationary phase, under low glucose availability, Dps1 binds to DNA to form a very stable toroid structure. On the other hand, under the same condition, Dps2-DNA complex forms an incompletely condensed toroid and finally forms a further stable coral reef structure in the presence of RNA. This coral reef structure is stable in high concentration of bivalent ion like Mg(2+).     

Differential activation of the JNK signal pathway by UV irradiation and glucose deprivation

Exposure of mammalian cells to ultraviolet (UV) light or glucose deprivation activates c-Jun NH2-terminal protein kinase (JNK). However, the exact mechanism by which UV induces JNK activation is not yet understood completely. Previously, we have observed that glucose deprivation activates the ASK1-SEK1-JNK signal transduction pathway. In the present study, we reveal that UVC irradiation-induced JNK activation has a different signal transduction pathway from glucose deprivation. UVC irradiation increases the interaction between JIP3 and MEKK1, SEK1, while glucose deprivation increases the interaction between JIP3 and ASK1, SEK1, and JNK. UVC irradiation activates MEKK1 rather than ASK1. We also observed that MEKK1 interacted with Grb2 and Grb2-MEKK1 complex was recruited to epidermal growth factor receptor (EGFR) after UVC irradiation. Taken together, our data demonstrate that UVC-induced JNK activation adopts a different signaling cascade (EGFR-Grb2-MEKK1-SEK1-JNK) from glucose deprivation (ASK1-SEK1-JNK).     

Biosynthesis of Bacillus intermedius glutamyl endopeptidase in recombinant Bacillus subtilis cells during the stationary growth phase

We studied the biosynthesis of Bacillus intermedius glutamyl endopeptidase in the recombinant Bacillus subtilis strain AJ73 delta58.21 during the stationary growth phase. We optimized the composition of the culture medium to favor effective enzyme production during the stationary growth phase, and found that the nutritional requirements for glutamyl endopeptidase synthesis were different in the stationary phase and growth retardation phase. Proteinase accumulation was activated by complex organic substrates (casein and gelatin). During final stages of the culture growth, the enzyme production was stimulated by Ca2+, Mn2+, and Co2+ and inhibited by Zn2+, Fe2+, and Cu2+. The synthesis of glutamyl endopeptidase in the late stationary phase was not inhibited by glucose, unlike that in the trophophase during proliferation. We conclude that the regulatory mechanisms of proteinase synthesis during vegetative growth and sporulation are different.