Acidiphilium cryptum DX1-1 CO2 固定相关基因的克隆及在不同营养 方式下的差异表达研究

目的:研究Acidiphilium cryptum DX1-1 CO2固定相关基因的克隆及在不同营养方式下的差异表达。方法:以Acidiphiliumcryptum DX1-1（CCTCC M 208056）的DNA为模板,基于A.cryptum JF-5同源功能基因序列（JGI,http://genome.ornl.gov/cgi-bin/JGI_microbial/kegg_categories.cgi）设计引物,对菌株DX1-1中的CO2固定相关基因Acry₀824,Acry₀82,Acry₁067,Acry₁272,Acry₀022和Acry₀827进行了克隆和序列比对分析;并对它们在不同营养条件下的基因差异表达进行了分析。结果:从菌株DX1-1成功克隆了所选择的CO2固定相关基因,其序列与菌株JF的同源功能基因序列一致性分别达到了99.8%,99.6%,99.6%,99.5%,99.3%和99.8%;Acry₀824,Acry₁272和Acry₀827三个基因在各种混合养条件下表达均上调,说明它们在DX1-1 CO2固定中起较关键的作用。在加入0.1%的葡萄糖混合养条件下,DX1-1细胞明显利用空气中的CO2来生长和累积PHB。结论:限制性葡萄糖可以促进细胞自养生长和累积PHB。     

Acidiphilium cryptum DX1-1 CO2固定相关基因的克隆及在不同营养方式下的差异表达研究

目的：研究Acidiphilium cryptum DX1-1 CO2固定相关基因的克隆及在不同营养方式下的差异表达。方法：以Acidiphilium cryptum DX1-1（CCTCCM208056）的DNA为模板,基于A．cryptum JF-5同源功能基因序列（JGI,http：／／genome．oml．gov／cgi-bin／JGI_microbial／keggcategories．cgi）设计引物,对菌株DX1-1中的CO2固定相关基因Acry_0824,Acry_082,Acry_1067,Acry_1272,Acry_0022和Acry_0827进行了克隆和序列比对分析;并对它们在不同营养条件下的基因差异表达进行了分析。结果：从菌株DX1—1成功克隆了所选择的CO2固定相关基因,其序列与菌株JF的同源功能基因序列一致性分别达到了99．8％,99．6％,99．6％,99．5％,99．3％和99．8％;Acry_0824,Acry_1272和Acry_0827三个基因在各种混合养条件下表达均上调,说明它们在DX1—1 CO2固定中起较关键的作用。在加入0．1％的葡萄糖混合养条件下,DX1—1细胞明显利用空气中的CO2来生长和累积PHB。结论：限制性葡萄糖可以促进细胞自养生长和累积PHB。     

Production of poly-β-hydroxybutyric acid from carbon dioxide by Alcaligenes eutrophus ATCC 17697T

The characteristics of PHB production from carbon dioxide by autotrophic culture of Alcaligenes eutrophus ATCC 17697^T using a recycled gas closed circuit culture system under the condition of oxygen limitation were investigated. Cell concentration increased to more than 60 g/l after 60 h of cultivation, while the PHB concentration reached 36 g/l. PHB accumulation in the oxygen-limited culture was superior than that in an ammonium-deficient culture. The PHB produced was identified as a homopolymer of d-3-hydroxybutyrate by ¹H and ¹³C NMR analysis. The stoichiometry for PHB production from CO₂ under the oxygen limitation condition was indicated to be as follows: 33H₂ + 12O₂ + 4CO₂ → C₄H₆O₂ + 30H₂O. This stoichiometry shows that the hydrogen consumption per one mole of CO₂ for PHB production is larger than that for cell formation.     

Ilyobacter delafieldii sp. nov., a metabolically restricted anaerobic bacterium fermenting PHB

Enrichments from an estuarine sediment with crotonate as substrate resulted in the isolation of a motile, gram-negative, obligately anaerobic rod with pointed ends, designated strain 10cr1. The organism was asporogenous, did not reduce sulfur, sulfate, thiosulfate, nitrate, oxygen or fumarate, and had a mol %G+C ratio of 29. Strain 10cr1 was able to ferment crotonate, 3-hydroxybutyrate, lactate, pyruvate, and poly--hydroxybutyric acid (PHB). Acetate, propionate, butyrate, CO₂ and H₂ were the fermentation products. When grown on PHB there was accumulation of 3-hydroxybutyrate once growth had ceased, indicating degradation of PHB to the monomer. The 3-hydroxybutyrate formed during growth of the culture was fermented to acetate, butyrate and H₂. Experimental evidence suggested the production of an extracellular PHB depolymerase. The cells were not attached to the PHB granules. This is the first isolation of an anaerobic bacterium capable of degrading exogenous PHB. This strain is described as a new species, Ilyobacter delafieldii sp. nov., and strain 10cr1 (=DSM 5704) is designated as the type (and at present, only) strain.Abbreviations G+C guanine plus cytosine - OD optical density - PHB poly--hydroxybutyric acid - specific growth rate - HPLC high-performance liquid chromatography - YE yeast extract     

Reduced Inorganic Carbon Transport in a CO(2)-Requiring Mutant of Chlamydomonas reinhardii

A mendelian mutant of the unicellular green alga Chlamydomonas reinhardii has been isolated that is deficient in inorganic carbon transport. This mutant strain, designated pmp-1-16-5K (gene locus pmp-1), was selected on the basis of a requirement of elevated CO₂ concentration for photoautrophic growth. Inorganic carbon accumulation in the mutant was considerably reduced in comparison to wild type, and the CO₂ response of photosynthesis indicated a reduced affinity for CO₂ in the mutant. At air levels of CO₂ (0.03-0.04%), O₂ inhibited photosynthesis and stimulated the synthesis of photorespiratory intermediates in the mutant but not in wild type. Neither strain was significantly affected by O₂ at saturating CO₂ concentration. Thus, the primary consequence of inorganic carbon transport deficiency in the mutant was a much lower internal CO₂ concentration compared to wild type. From these observations, we conclude that enzyme-mediated transport of inorganic carbon is an essential component of the CO₂ concentrating system in C. reinhardii photosynthesis.     

1H, 13C, and 15N backbone, side-chain, and heme chemical shift assignments for oxidized and reduced forms of the monoheme c-type cytochrome ApcA isolated from the acidophilic metal-reducing bacterium Acidiphilium cryptum

We report the ¹H, ¹³C, and ¹⁵N chemical shift assignments of both oxidized and reduced forms of an abundant periplasmic c-type cytochrome, designated ApcA, isolated from the acidophilic gram-negative facultatively anaerobic metal-reducing alphaproteobacterium Acidiphilium cryptum. These resonance assignments prove that ApcA is a monoheme cytochrome c ₂ and the product of the Acry_2099 gene. An absence of resonance peaks in the NMR spectra for the 21N-terminal residues suggests that a predicted N-terminal signal sequence is cleaved. We also describe the preparation and purification of the protein in labeled form from laboratory cultures of A. cryptum growing on ¹³C- and ¹⁵N- labeled substrates.     

Effect of nitrogen and/or oxygen concentration on poly(3-hydroxybutyrate) accumulation by <Emphasis Type="Italic">Halomonas boliviensis</Emphasis>

The behaviour of Halomonas boliviensis during growth in fed-batch culture under different kind of nutrient restrictions was examined. The metabolic switch between growth and accumulation phase is determined by the limitation in one or more essential nutrient for bacterial growth. The aim of this study was to test the effect of applying limitations of a essential nutrient, such as nitrogen, and the influence of different O₂ concentrations on poly(3-hydroxybutyrate) (PHB) production during the accumulation phase. Single limitations of nitrogen and oxygen provoke PHB accumulations of 45 and 37 % (g g^?1), respectively, while N limitation with low O₂ supply causes the highest PHB accumulation of 73 %. The characterization of the PHB production with the strain H. boliviensis would allow a better optimization of the process and enrich the knowledge about the PHB production from strains different than Cupriavidus necator.     

Increased Bioplastic Production with an RNA Polymerase Sigma Factor SigE during Nitrogen Starvation in Synechocystis sp. PCC 6803

Because cyanobacteria directly harvest CO₂ and light energy, their carbon metabolism is important for both basic and applied sciences. Here, we show that overexpression of the sigma factor sigE in Synechocystis sp. PCC 6803 widely changes sugar catabolism and increases production of the biodegradable polyester polyhydroxybutyrate (PHB) during nitrogen starvation. sigE overexpression elevates the levels of proteins implicated in glycogen catabolism, the oxidative pentose phosphate pathway, and polyhydroxyalkanoate biosynthesis. PHB accumulation is enhanced by sigE overexpression under nitrogen-limited conditions, yet the molecular weights of PHBs synthesized by the parental glucose-tolerant and sigE overexpression strain are similar. Although gene expression induced by nitrogen starvation is changed and other metabolites (such as GDP-mannose and citrate) accumulate under sigE overexpression, genetic engineering of this sigma factor altered the metabolic pathway from glycogen to PHB during nitrogen starvation.     

积累PHB菌种隐藏嗜酸菌DX1-1的诱变改良

采用紫外线照射和放射性元素钴60辐射诱变方法,对分离纯化的一株可积累聚β-羟基丁酸酯(PHB)的Acidiphilium cryptumDX1-1进行了诱变改良,以获得PHB高产菌.结果显示钴60诱变最佳诱变剂量为100 Gy,紫外诱变的最佳剂量为15 W、30 cm、60 s,紫外诱变的效果比钴60诱变的效果好.诱变后筛选得到的一株菌UV60-3,PHB含量达到28.56 g/L,是原菌株的1.45倍,并且可稳定遗传.对菌株UV60-3积累PHB的碳氮比进行了探索,结果显示在碳源浓度60 g/L,氮源浓度30 g/L,C/N为3.76时PHB含量最高,PHB含量达到30.57 g/L.     

Genetic and physiological analysis of the CO2-concentrating system of Chlamydomonas reinhardii

When grown photoautotrophically at air levels of CO₂, Chlamydomonas reinhardii possesses a system involving active transport of inorganic carbon which increases the intracellular CO₂ concentration considerably above ambient, thereby stimulating photosynthetic CO₂ assimilation. In previous investigations, two mutant strains of this unicellular green alga deficient in some component of this CO₂-concentrating system were recovered as strains requiring high levels of CO₂ to support photoautotrophic growth. One of the mutants, ca-1-12-1C, is a leaky (nonstringent) CO₂-requiring strain deficient in carbonic anhydrase (EC 4.2.1.1) activity, while the other, pmp-1-16-5K, is a stringent CO₂-requiring strain deficient in inorganic carbon transport. In the present study a double mutant (ca pmp) was constructed to investigate the physiological and biochemical interaction of the two mutations. The two mutations are unlinked and inherited in a Mendelian fashion. The double mutant was found to have a leaky CO₂-requiring phenotype, indicating that the mutation ca-1 overcomes the stringent CO₂-requirement conferred by the mutation pmp-1. Several physiological characteristics of the double mutant were very similar to the carbonic-anhydrase-deficient mutant, including high CO₂ compensation concentration, photosynthetic CO₂ response curve, and deficiency of carbonic-anhydrase activity. However, the labeling pattern of metabolites during photosynthesis in ¹⁴CO₂ was more like that of the bicarbonatetransport-deficient mutant, and accumulation of internal inorganic carbon was intermediate between that of the two original mutants. These data indicate a previously unsuspected complexity in the Chlamydomonas CO₂-concentrating system.     

Engineering Cupriavidus necator H16 for the autotrophic production of (R)-1,3-butanediol

Butanediols are widely used in the synthesis of polymers, specialty chemicals and important chemical intermediates. Optically pure R-form of 1,3-butanediol (1,3-BDO) is required for the synthesis of several industrial compounds and as a key intermediate of β-lactam antibiotic production. The (R)-1,3-BDO can only be produced by application of a biocatalytic process. Cupriavidus necator H16 is an established production host for biosynthesis of biodegradable polymer poly-3-hydroxybutryate (PHB) via acetyl-CoA intermediate. Therefore, the utilisation of acetyl-CoA or its upstream precursors offers a promising strategy for engineering biosynthesis of value-added products such as (R)-1,3-BDO in this bacterium. Notably, C. necator H16 is known for its natural capacity to fix carbon dioxide (CO₂) using hydrogen as an electron donor. Here, we report engineering of this facultative lithoautotrophic bacterium for heterotrophic and autotrophic production of (R)-1,3-BDO. Implementation of (R)-3-hydroxybutyraldehyde-CoA- and pyruvate-dependent biosynthetic pathways in combination with abolishing PHB biosynthesis and reducing flux through the tricarboxylic acid cycle enabled to engineer strain, which produced 2.97 g/L of (R)-1,3-BDO and achieved production rate of nearly 0.4 Cmol Cmol⁻¹ h⁻¹ autotrophically. This is first report of (R)-1,3-BDO production from CO₂.     

Isolation and characterization of a new strain of Methanothermobacter marburgensis DX01 from hot springs in China

Strain DX01, a thermophilic methanogen, was isolated from a hot spring in China. Strain DX01 grew only on H₂/CO₂. The DNA G + C content is 52 mol% and optimal growth temperature is 65 °C. The cell pellet is brick red. By analyzing 16S rRNA sequence, methyl-coenzyme M reductase I, gamma subunit protein sequences, we determined the DX01 strain to be closely related to the species of Methanothermobacter marburgensis. In addition, Methanothermobacter thermautotrophicus delta H^T and strain DX01 had clear differences in their biochemical composition and protein expression profiles. Based on the above analysis, we propose that strain DX01 is a novel strain within thermoautotrophicus the species of M. marburgensis, namely M. marburgensis DX01. The isolation and characterization of the new M. marburgensis DX01 strain expands the known range of the Methanothermobacter genus.     

Glyphosate inhibits photosynthesis and allocation of carbon to starch in sugar beet leaves

Application of glyphosate (N-[phosphonomethyl] glycine) to exporting leaves of sugar beet (Beta vulgaris, L.) during the day lowered stomatal conductance and carbon fixation. Allocation of newly fixed carbon to foliar starch accumulation was nearly completely inhibited, being decreased by the same amount as net carbon fixation. In contrast, decreasing net carbon fixation in untreated leaves by lowering CO₂ concentration caused starch accumulation to decrease, but only in the same proportion as net carbon fixation. Shikimate level increased 50-fold in treated leaves but the elevated rate of carbon accumulation in shikimate was only 4% of the decrease in the rate of starch accumulation. Application of steady state labeling with ¹⁴CO₂ to exporting leaves confirmed the above changes in carbon metabolism, but revealed no other major daytime differences in the ¹⁴C-content of amino acids or other compounds between treated and control leaves. Less ¹⁴C accumulated in treated leaves because of decreased fixation, not increased export. The proportion of newly fixed carbon allocated to sucrose increased, maintaining export at the level in control leaves. Returning net carbon exchange to the rate before treatment restored starch accumulation fully and prevented a decrease in export during the subsequent dark period.     

Enhancement of photohydrogen production using phbC deficient mutant Rhodopseudomonas palustris strain M23

This study used a DNA recombination method to knock out the poly-β-hydroxybutyrate (PHB) synthesis gene phbC in the photosynthetic bacterium Rhodopseudomonas palustris WP3-5. The experimental results indicated that the mutant strain Rps. palustris M23 could be successfully screened. Fluorescent observation with Nile blue staining showed no significant PHB granule accumulation in the mutant cells. Batch mode experiments using acetic acid as a carbon source revealed a 29.1% and 25.9% hydrogen gas content from M23 and WP3-5, respectively. However, this trend did not appear when using propionic acid as carbon source. Under continuous operation, the hydrogen gas content from M23 could be maintained above 72%. The average hydrogen production rates of the WP3-5 and M23 strains were 264 mL-H₂/L/day and 457 mL-H₂/L/day, respectively. The total biogas volume collected from M23 was 1.7 times higher than that from the wild type.     

On the ATP generation by Chromatium in darkness

Summary In Chromatium strain 6412 storage carbohydrate synthesized in the light, gradually disappeared in the dark. Simultaneously, poly--hydroxybutyric acid (PHB) was produced, CO₂ was released and intracellular elemental sulfur was reduced to sulfide. Expressed on a molar base, the ratio between storage carbohydrate monomer (as glucose) consumed, sulfur reduced, PHB monomer produced, and sulfide released was approximately 1 : 3 : 1 : 3. This indicates that sulfur acts electron acceptor in the conversion of storage carbohydrate to PHB. Assuming that in the dark storage carbohydrate is broken down to pyruvate via the Embden-Meyerhoff pathway, whereafter PHB is synthesized from pyruvate via acetyl-CoA and acetoacetyl-CoA, the conversion of storage carbohydrate to PHB results in a net gain of 3 ATP per glycosyl unit converted. Since Thiorhodaceae are photolithotrophs, these processes would provide the organisms with maintenance energy during dark periods. They also explain motility of Chromatium in the dark.     

PHB accumulation in Nostoc muscorum under different carbon stress situations

Use of algae for intracellular poly-β-hydroxybutyrate (PHB) accumulation for bioplastic production offers an opportunity in economic efficiency by reduced costs. The cyanobacterium Nostoc muscorum is a PHB accumulator which presents a great potential as raw material supplier because of short generation cycles. Here, we examined a range of experimental conditions including different growth conditions of phosphate-starved cells with the addition of external carbon sources. The highest, absolute PHB accumulation was measured in a phosphate-starved medium with 1% (w/w) glucose and 1% (w/w) acetate. PHB accumulated inside algae cells. After 23 days of growth in phosphate-starved medium, 1 L of culture contained up to 145.1 mg PHB. The highest PHB accumulation based on the cell dry weight was in an experiment with aeration and CO₂ addition. The intracellular level of PHB was up to 21.5% cell dry weight after 8 days.     

Plant Water Use Efficiency over Geological Time – Evolution of Leaf Stomata Configurations Affecting Plant Gas Exchange

Plant gas exchange is a key process shaping global hydrological and carbon cycles and is often characterized by plant water use efficiency (WUE - the ratio of CO₂ gain to water vapor loss). Plant fossil record suggests that plant adaptation to changing atmospheric CO₂ involved correlated evolution of stomata density (d) and size (s), and related maximal aperture, a_max. We interpreted the fossil record of s and d correlated evolution during the Phanerozoic to quantify impacts on gas conductance affecting plant transpiration, E, and CO₂ uptake, A, independently, and consequently, on plant WUE. A shift in stomata configuration from large s-low d to small s-high d in response to decreasing atmospheric CO₂ resulted in large changes in plant gas exchange characteristics. The relationships between gas conductance, g_ws, A and E and maximal relative transpiring leaf area, (a_max⋅d), exhibited hysteretic-like behavior. The new WUE trend derived from independent estimates of A and E differs from established WUE-CO₂ trends for atmospheric CO₂ concentrations exceeding 1,200 ppm. In contrast with a nearly-linear decrease in WUE with decreasing CO₂ obtained by standard methods, the newly estimated WUE trend exhibits remarkably stable values for an extended geologic period during which atmospheric CO₂ dropped from 3,500 to 1,200 ppm. Pending additional tests, the findings may affect projected impacts of increased atmospheric CO₂ on components of the global hydrological cycle.     

Kinetic Studies and Biochemical Pathway Analysis of Anaerobic Poly-(R)-3-Hydroxybutyric Acid Synthesis in Escherichia coli

Poly-(R)-3-hydroxybutyric acid (PHB) was synthesized anaerobically in recombinant Escherichia coli. The host anaerobically accumulated PHB to more than 50% of its cell dry weight during cultivation in either growth or nongrowth medium. The maximum specific PHB production rate during growth-associated synthesis was approximately 2.3 ± 0.2 mmol of PHB/g of residual cell dry weight/h. The by-product secretion profiles differed significantly between the PHB-synthesizing strain and the control strain. PHB production decreased acetate accumulation for both growth and nongrowth-associated PHB synthesis. For instance under nongrowth cultivation, the PHB-synthesizing culture produced approximately 66% less acetate on a glucose yield basis as compared to a control culture. A theoretical biochemical network model was used to provide a rational basis to interpret the experimental results like the fermentation product secretion profiles and to study E. coli network capabilities under anaerobic conditions. For example, the maximum theoretical carbon yield for anaerobic PHB synthesis in E. coli is 0.8. The presented study is expected to be generally useful for analyzing, interpreting, and engineering cellular metabolisms.     

Transport and Partitioning of CO(2) Fixed by Root Nodules of Ureide and Amide Producing Legumes

Nodulated and denodulated roots of adzuki bean (Vigna angularis), soybean (Glycine max), and alfalfa (Medicago sativa) were exposed to ¹⁴CO₂ to investigate the contribution of nodule CO₂ fixation to assimilation and transport of fixed nitrogen. The distribution of radioactivity in xylem sap and partitioning of carbon fixed by nodules to the whole plant were measured. Radioactivity in the xylem sap of nodulated soybean and adzuki bean was located primarily (70 to 87%) in the acid fraction while the basic (amino acid) fraction contained 10 to 22%. In contrast, radioactivity in the xylem sap of nodulated alfalfa was primarily in amino acids with about 20% in organic acids. Total ureide concentration was 8.1, 4.7, and 0.0 micromoles per milliliter xylem sap for soybean, adzuki bean, and alfalfa, respectively. While the major nitrogen transport products in soybeans and adzuki beans are ureides, this class of metabolites contained less than 20% of the total radioactivity. When nodules of plants were removed, radioactivity in xylem sap decreased by 90% or more. Pulse-chase experiments indicated that CO₂ fixed by nodules was rapidly transported to shoots and incorporated into acid stable constituents. The data are consistent with a role for nodule CO₂ fixation providing carbon for the assimilation and transport of fixed nitrogen in amide-based legumes. In contrast, CO₂ fixation by nodules of ureide transporting legumes appears to contribute little to assimilation and transport of fixed nitrogen.