Complete genome sequence of the bacterium Ketogulonicigenium vulgare Y25

Ketogulonicigenium vulgare is characterized by the efficient production of 2KGA from L-sorbose. Ketogulonicigenium vulgare Y25 is known as a 2-keto-L-gulonic acid-producing strain in the vitamin C industry. Here we report the finished, annotated genome sequence of Ketogulonicigenium vulgare Y25.     

Complete genome sequence of the industrial strain Bacillus megaterium WSH-002

Bacillus megaterium, an industrial strain, has been widely used in protein production and the vitamin C industry. Here we reported a finished, annotated, and compared 4.14-Mbp high-quality genome sequence of B. megaterium WSH-002, which is the companion strain for Ketogulonicigenium vulgare in the vitamin C industry and is stocked in our laboratory.     

Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001

Ketogulonicigenium vulgare WSH001 is an industrial strain commonly used in the vitamin C producing industry. In order to acquire a comprehensive understanding of its physiological characteristics, a genome-scale metabolic model of K. vulgare WSH001, iWZ663, including 830 reactions, 649 metabolites, and 663 genes, was reconstructed by genome annotation and literature mining. This model was capable of predicting quantitatively the growth of K. vulgare under L-sorbose fermentation conditions and the results agreed well with experimental data. Furthermore, phenotypic features, such as the defect in sulfate metabolism hampering the syntheses of L-cysteine, L-methionine, coenzyme A (CoA), and glutathione, were investigated and provided an explanation for the poor growth of K. vulgare in monoculture. The model presented here provides a validated platform that can be used to understand and manipulate the phenotype of K. vulgare to further improve 2-KLG production efficiency.     

Proteomic analysis of Ketogulonicigenium vulgare under glutathione reveals high demand for thiamin transport and antioxidant protection

Ketogulonicigenium vulgare, though grows poorly when mono-cultured, has been widely used in the industrial production of the precursor of vitamin C with the coculture of Bacillus megaterium. Various efforts have been made to clarify the synergic pattern of this artificial microbial community and to improve the growth and production ability of K. vulgare, but there is still no sound explanation. In previous research, we found that the addition of reduced glutathione into K. vulgare monoculture could significantly improve its growth and productivity. By performing SEM and TEM, we observed that after adding GSH into K. vulgare monoculture, cells became about 4-6 folds elongated, and formed intracytoplasmic membranes (ICM). To explore the molecular mechanism and provide insights into the investigation of the synergic pattern of the co-culture system, we conducted a comparative iTRAQ-2-D-LC-MS/MS-based proteomic analysis of K. vulgare grown under reduced glutathione. Principal component analysis of proteomic data showed that after the addition of glutathione, proteins for thiamin/thiamin pyrophosphate (TPP) transport, glutathione transport and the maintenance of membrane integrity, together with several membrane-bound dehydrogenases had significant up-regulation. Besides, several proteins participating in the pentose phosphate pathway and tricarboxylic acid cycle were also up-regulated. Additionally, proteins combating intracellular reactive oxygen species were also up-regulated, which similarly occurred in K. vulgare when the co-cultured B. megaterium cells lysed from our former research results. This study reveals the demand for transmembrane transport of substrates, especially thiamin, and the demand for antioxidant protection of K. vulgare.     

谷胱甘肽对VC一步发酵作用的研究

谷胱甘肽（GSH）能有效促进酮古龙酸杆菌的生长。就GSH对氧化葡萄糖酸杆菌和酮古龙酸杆菌一步混菌发酵的作用进行了探索,为进一步阐明维生素C一步发酵过程中氧化葡萄糖酸杆菌和酮古龙酸杆菌的关系并提供发酵工艺优化的依据。研究发现,在5L的发酵罐中,外加1mg/ml的GSH对混菌的发酵有着显著的促进作用,2-酮-L-古龙酸（2-KGA）产量提高了22.8%。通过16S rDNA荧光定量PCR法测菌数,发现GSH的添加使酮古龙酸杆菌的生长提高到148%,但抑制氧化葡萄糖酸杆菌的生长,使其生物量下降到61%。运用代谢组学方法分析发现,GSH能促进酮古龙酸杆菌的磷酸戊糖、三羧酸循环、硫酸盐等代谢,同时减缓氧化葡萄糖酸杆菌对L-山梨糖的消耗,以促进整个混菌体系的发酵效率。     

Microbial production of L-ascorbic acid from D-sorbitol, L-sorbose, L-gulose, and L-sorbosone by Ketogulonicigenium vulgare DSM 4025

Ketogulonicigenium vulgare DSM 4025, known as a 2-keto-L-gulonic acid producing strain from L-sorbose via L-sorbosone, surprisingly produced L-ascorbic acid from D-sorbitol, L-sorbose, L-gulose, and L-sorbosone as the substrate under a growing or resting condition. As the best result, K. vulgare DSM 4025 produced 1.37 g per liter of L-AA from 5.00 g per liter of L-sorbosone during 4 h incubation time at 30 degrees C under the resting cell condition having 5.70 g per liter of wet cells. The precursor of L-AA formation from D-sorbitol and L-sorbose, except for L-gulose, was thought to be the putative furanose form of L-sorbosone. This is the first time it is reported that bacteria can produce vitamin C via L-sorbosone.     

Metabolome profiling reveals metabolic cooperation between Bacillus megaterium and Ketogulonicigenium vulgare during induced swarm motility

The metabolic cooperation in the ecosystem of Bacillus megaterium and Ketogulonicigenium vulgare was investigated by cultivating them spatially on a soft agar plate. We found that B. megaterium swarmed in a direction along the trace of K. vulgare on the agar plate. Metabolomics based on gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF-MS) was employed to analyze the interaction mechanism between the two microorganisms. We found that the microorganisms interact by exchanging a number of metabolites. Both intracellular metabolism and cell-cell communication via metabolic cooperation were essential in determining the population dynamics of the ecosystem. The contents of amino acids and other nutritional compounds in K. vulgare were rather low in comparison to those in B. megaterium, but the levels of these compounds in the medium surrounding K. vulgare were fairly high, even higher than in fresh medium. Erythrose, erythritol, guanine, and inositol accumulated around B. megaterium were consumed by K. vulgare upon its migration. The oxidization products of K. vulgare, including 2-keto-gulonic acids (2KGA), were sharply increased. Upon coculturing of B. megaterium and K. vulgare, 2,6-dipicolinic acid (the biomarker of sporulation of B. megaterium), was remarkably increased compared with those in the monocultures. Therefore, the interactions between B. megaterium and K. vulgare were a synergistic combination of mutualism and antagonism. This paper is the first to systematically identify a symbiotic interaction mechanism via metabolites in the ecosystem established by two isolated colonies of B. megaterium and K. vulgare.     

分阶段pH调控提高2-酮基-L-古龙酸生产

为了提高酮古龙酸菌Ketogulonicigenium vulgare和巨大芽胞杆菌Bacillus megaterium生产2-酮基-L-古龙酸(2-KLG)的生产效率,分析了pH对K.vulgare和B.megaterium生长和产酸的影响,发现K.vulgare和B.megaterium的最适生长pH值分别为6.0和8.0,但是K.vulgare的糖酸转化活力在pH7.0时达到最大值,因此提出了三阶段pH控制策略(第一阶段:0～8h,pH8.0;第二阶段:8～20h,pH6.0;第三阶段:20h至发酵结束,pH7.0)以促进K.vulgare生长和2-KLG生产。结果表明,三阶段pH控制策略的实施进一步提高了2-KLG的产量(77.3g/L)、生产强度(1.38g/(L·h))和L-山梨糖消耗速率(1.42g/(L·h)),分别比恒定pH7.0时提高了9.7%、33.2%和25.7%。     

Integrated proteomic and metabolomic analysis of an artificial microbial community for two-step production of vitamin C

An artificial microbial community consisted of Ketogulonicigenium vulgare and Bacillus megaterium has been used in industry to produce 2-keto-gulonic acid (2-KGA), the precursor of vitamin C. During the mix culture fermentation process, sporulation and cell lysis of B. megaterium can be observed. In order to investigate how these phenomena correlate with 2-KGA production, and to explore how two species interact with each other during the fermentation process, an integrated time-series proteomic and metabolomic analysis was applied to the system. The study quantitatively identified approximate 100 metabolites and 258 proteins. Principal Component Analysis of all the metabolites identified showed that glutamic acid, 5-oxo-proline, L-sorbose, 2-KGA, 2, 6-dipicolinic acid and tyrosine were potential biomarkers to distinguish the different time-series samples. Interestingly, most of these metabolites were closely correlated with the sporulation process of B. megaterium. Together with several sporulation-relevant proteins identified, the results pointed to the possibility that Bacillus sporulation process might be important part of the microbial interaction. After sporulation, cell lysis of B. megaterium was observed in the co-culture system. The proteomic results showed that proteins combating against intracellular reactive oxygen stress (ROS), and proteins involved in pentose phosphate pathway, L-sorbose pathway, tricarboxylic acid cycle and amino acids metabolism were up-regulated when the cell lysis of B. megaterium occurred. The cell lysis might supply purine substrates needed for K. vulgare growth. These discoveries showed B. megaterium provided key elements necessary for K. vulgare to grow better and produce more 2-KGA. The study represents the first attempt to decipher 2-KGA-producing microbial communities using quantitative systems biology analysis.     

Pyrroloquinoline quinone-dependent dehydrogenases from Ketogulonicigenium vulgare catalyze the direct conversion of L-sorbosone to L-ascorbic acid

A novel enzyme, L-sorbosone dehydrogenase 1 (SNDH1), which directly converts L-sorbosone to L-ascorbic acid (L-AA), was isolated from Ketogulonicigenium vulgare DSM 4025 and characterized. This enzyme was a homooligomer of 75-kDa subunits containing pyrroloquinoline quinone (PQQ) and heme c as the prosthetic groups. Two isozymes of SNDH, SNDH2 consisting of 75-kDa and 55-kDa subunits and SNDH3 consisting of 55-kDa subunits, were also purified from the bacterium. All of the SNDHs produced L-AA, as well as 2-keto-L-gulonic acid (2KGA), from L-sorbosone, suggesting that tautomerization of L-sorbosone causes the dual conversion by SNDHs. The sndH gene coding for SNDH1 was isolated and analyzed. The N-terminal four-fifths of the SNDH amino acid sequence exhibited 40% identity to the sequence of a soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus. The C-terminal one-fifth of the sequence exhibited similarity to a c-type cytochrome with a heme-binding motif. A lysate of Escherichia coli cells expressing sndH exhibited SNDH activity in the presence of PQQ and CaCl2. Gene disruption analysis of K. vulgare indicated that all of the SNDH proteins are encoded by the sndH gene. The 55-kDa subunit was derived from the 75-kDa subunit, as indicated by cleavage of the C-terminal domain in the bacterial cells.     

山梨酮脱氢酶模块与酮古龙酸杆菌底盘细胞的适配分析

酮古龙酸杆菌Ketogulonigenium vulgare是维生素C二步混菌发酵过程中的产酸菌。山梨酮脱氢酶(L-sorbosone dehydrogenase,缩写为SNDH)作为维生素C直接前体2-酮基-L-古龙酸(2-KGA)合成的关键酶,其作用机制并不十分清楚。借助全基因组测序抽提2个山梨酮脱氢酶基因,分别位于基因组(缩写为sndhg)和质粒(缩写为sndhp)上。通过工程化改造技术在工业产酸菌中构建山梨酮脱氢酶功能模块,比较其对2-KGA产量的影响。研究发现sndhg过表达对菌株产酸影响不明显,sndhp过表达使菌株明显产生副产物。将sndhg和sndhp分别配合辅因子PQQ合成基因pqq A,分别构建sndhg-pqq A和sndhp-pqq A模块,得到的工程菌株产酸情况与之前的结果大致相同。将4株K.vulgare工程菌株分别与内生芽孢杆菌Bacillus endophyticus混合培养传代50 d后,分离菌株进行混菌发酵,其2-KGA的转化率分别提高了15.4%、179%、0.65%和125%。表明混菌适应性进化策略是一种增加功能模块与底盘细胞适配性,进而快速获得优良性状菌种的有效方法。     

Modeling and parameters identification of 2-keto-<Emphasis Type="SmallCaps">l</Emphasis>-gulonic acid fed-batch fermentation

This article presents a modeling approach for industrial 2-keto-l-gulonic acid (2-KGA) fed-batch fermentation by the mixed culture of Ketogulonicigenium vulgare (K. vulgare) and Bacillus megaterium (B. megaterium). A macrokinetic model of K. vulgare is constructed based on the simplified metabolic pathways. The reaction rates obtained from the macrokinetic model are then coupled into a bioreactor model such that the relationship between substrate feeding rates and the main state variables, e.g., the concentrations of the biomass, substrate and product, is constructed. A differential evolution algorithm using the Lozi map as the random number generator is utilized to perform the model parameters identification, with the industrial data of 2-KGA fed-batch fermentation. Validation results demonstrate that the model simulations of substrate and product concentrations are well in coincidence with the measurements. Furthermore, the model simulations of biomass concentrations reflect principally the growth kinetics of the two microbes in the mixed culture.     

Identification of intergenomic translocations involving wheat,Hordeum vulgare and Hordeum chilense chromosomes by FISH

Intergenomic translocations between wheat, Hordeum chilense and Hordeum vulgare have been obtained in tritordeum background. Advanced lines from the crosses between three disomic chromosome addition lines for chromosome 2Hv, 3Hv, and 4Hv of barley (Hordeum vulgare) in Triticum aestivum cv. Chinese Spring (CS) and hexaploid tritordeum (2n = 6x = 42, AABBHchHch) were analyzed. Multicolor FISH using both genomic DNA from H. chilense and H. vulgare were used to establish the presence and numbers of H. vulgare introgressions into tritordeum. Interspecific H. vulgare/H. chilense and intergeneric wheat/H. vulgare and wheat/H. chilense translocations were identified. Frequencies of plants containing different kinds of intergenomic translocations between chromosome arms are presented. These lines can be useful for introgressing into tritordeum characters of interest from H. vulgare.     

Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum

In this study we report the development of primers to amplify polymorphic chloroplast simple sequence repeats in the genus Hordeum , which includes cultivated barley ( H. vulgare ssp. vulgare ) and its wild progenitor H. vulgare ssp. spontaneum . Polymorphic products were amplified in a wide range of Hordeum spp. and intraspecific variation was detected in both cultivated and wild barley. A decrease in cytoplasmic diversity was observed between sspp. spontaneum and vulgare as well as between ssp. vulgare landraces and cultivars, which is characteristic of domestication processes in many crop species. We also observed possible evidence for reticulate evolution of H. brachyantherum polyploids, with apparent multiple cytoplasmic introgressions during successive polyploidization events.     

Rapid verification of wheat-Hordeum introgressions by direct staining of SCAR, STS, and SSR amplicons.

A range of single tagged site (STS), simple sequence repeat (SSR), and sequence-characterized amplified region (SCAR) markers were screened for their utility in detecting Hordeum vulgare and H. chilense chromosomes in a wheat background. PCR conditions were optimized for specific amplification of the targeted sequences and to avoid cross-species amplification. Two H. vulgare derived STSs, six H. vulgare derived SSRs, and nine H. chilense derived SCARs were usable for the detection of five H. vulgare and three H. chilense chromosomes by direct ethidium bromide staining of the PCR products in test tubes, avoiding the more costly and time-consuming DNA electrophoresis step. The practical application of the method is illustrated by the identification of a monotelosomic substitution of H. vulgare chromosome 6HS in tritordeum and a monosomic addition of H. chilense chromosome 6Hch in durum wheat.     

高渗条件下利用蔗糖提升2-酮基-L-古龙酸生产效率

旨在进一步提升维生素C前体2-酮基-L-古龙酸(2-KLG)的生产效率。在详细考察了2-KLG工业化生产过程中渗透压变化规律的基础上,研究了高渗对混合菌系细胞生长和2-KLG合成的影响,提出蔗糖促进伴生菌巨大芽胞杆菌Bacillus megaterium生长,进而促进普通生酮古龙酸菌Ketogulonigenium vulgare生长和产酸的策略。结果表明,2-KLG的积累和碱性物质的流加使渗透压上升了832mOsmol/kg;高渗抑制了巨大芽胞杆菌的生长(15.4%),从而抑制普通生酮古龙酸菌(31.7%)的生长,导致2-KLG产量和生产强度分别下降67.5%和69.3%(以1250mOsmol/kg为例);蔗糖的添加则显著促进巨大芽胞杆菌的生长,使高渗条件下(摇瓶,1250 mOsmol/kg)2-KLG产量(40.6g/L)提高87%;在3L发酵罐中,补加10mmol/L蔗糖使2-KLG发酵周期缩短10.8%,2-KLG生产强度提高10.4%。研究成果为在环境胁迫下提高混菌生产目标代谢产物的产量提供了潜在的策略。     

Identification and characterization of simple sequence repeat markers from a glandular Origanum vulgare expressed sequence tag

Oregano (Origanum vulgare) and marjoram (Origanum majorana) are two sensorial distinct spices within the genus Origanum (Lamiaceae). Simple sequence repeat (SSR) markers were developed from expressed sequence tags (ESTs) of essential oil glands of O. vulgare. Thirteen EST-SSR loci were evaluated using 20 individual plants of O. vulgare and 19 plants of Origanum majorana. The number of alleles per locus ranged from one to four. All loci developed from O. vulgare successfully cross-amplified in O. majorana.     

Intraspecific plant chemical diversity and its relation to herbivory

Several aromatic plant species are well known for their high intraspecific variation in terpene composition. Within these species, different chemotypes can be distinguished, which are characterised by one major metabolite and distinct satellite compounds in lower abundance. Such intraspecific differences in plant quality should have major effects on herbivorous insects but may also be partly shaped by their feeding activities. In the present study, the effects of selected Tanacetum vulgare L. chemotypes on herbivore presence and preferences were investigated, and the naturally occurring diversity of T. vulgare was explored at a small spatial scale. A distinct distribution pattern of aphids and miners was found on different chemotypes of different origin of T. vulgare, with species-specific preferences of different herbivorous species. Larvae of two generalist noctuid species performed worse on most chemotypes of T. vulgare than on other plant species. Furthermore, the specific terpene composition of T. vulgare influenced larval development of these two generalist species. The naturally occurring chemical diversity of T. vulgare plants in an area smaller than 3 km(2) was extremely high, exhibiting 14 different chemotypes. Several individual patches of T. vulgare consisted of more than one chemotype. In conclusion, the existing chemotypical pattern of T. vulgare plants leads to a species-specific distribution of herbivores but may in turn be the result of contrasting selection pressures of various specialist and generalist herbivores.     

Evidence for a new feminizing Wolbachia strain in the isopod Armadillidium vulgare: evolutionary implications

Wolbachia are intracellular maternally inherited alpha-Proteobacteria infecting a wide range of arthropods. In the common pill bug Armadillidium vulgare, the known Wolbachia strain is responsible for feminization of genetic males. We have investigated Wolbachia diversity in 20 populations of A. vulgare from west and east Europe, north Africa and north America. A new Wolbachia strain (wVulM) was identified through the variability of the wsp gene, distantly related to that previously known (wVulC) in this host species. No individual with multiple infections was detected. Inoculation experiments indicated that the new wVulM bacterial strain also induces feminization in A. vulgare. However, the wVulC strain showed a higher transmission rate than the wVulM strain and was the most geographically widespread Wolbachia in A. vulgare populations. Mitochondrial 16SrDNA gene sequencing was conducted in Wolbachia-infected individuals, revealing the occurrence of four host lineages. The comparison of bacterial strains and their respective host mitochondrial phylogenies failed to show concordance, indicating horizontal transmission of the Wolbachia strains within populations of A. vulgare.