An approach for genome analysis based on assembly of fragments of DNA from the whole genome can be applied to obtain the complete nucleotide sequence of the genome of Zymomonas mobilis. However, the problem of fragment assembly raise thorny computational issues. Computer simulation studies of sequence assembly usually show some abnormal assemblage of artificial sequences containing repetitive or duplicated regions, and suggest methods to correct those abnormalities. In this paper, we describe five simulation studies which had been performed previous to the actual genome assembly process of Zymomonas mobilis ZM4.
Base Sequence ; Computer Simulation* ; DNA ; Genome ; Zymomonas*

Co-fermentation of glucose and xylose is critical for cellulosic ethanol, as xylose is the second most abundant sugar in lignocellulosic hydrolysate. In this study, a xylose-utilizing recombinant Zymomonas mobilis TSH01 was constructed by gene cloning, and ethanol fermentation of the recombinant was evaluated under batch fermentation conditions with a fermentation time of 72 h. When the medium containing 8% glucose or xylose, was tested, all glucose and 98.9% xylose were consumed, with 87.8% and 78.3% ethanol yield, respectively. Furthermore, the medium containing glucose and xylose, each at a concentration of 8%, was tested, and 98.5% and 97.4% of glucose and xylose was fermented, with an ethanol yield of 94.9%. As for the hydrolysate of corn stover containing 3.2% glucose and 3.5% xylose, all glucose and 92.3% xylose were consumed, with an ethanol yield of 91.5%. In addition, monopotassium phosphate can facilitate the consumption of xylose and enhance ethanol yield.
Ethanol ; metabolism ; Fermentation ; Glucose ; metabolism ; Recombination, Genetic ; Xylose ; metabolism ; Zymomonas ; genetics ; metabolism

The nucleotide sequence of pZMO1, a small cryptic plasmid of Zymomonas mobilis ATCC10988 was determined. Analysis of 1,680 bp of sequence revealed 69% identity with Shigella sonnei plasmid, pKYM and 61% identity with Nostoc sp. ss DNA replicating plasmid. Analysis of a deduced amino acid sequence of an orf of pZMO1 revealed 75% identity and 90% similarity with the repA gene of Synechocystis sp. plasmid pCA2.4. The upstream region of the repA gene of pZMO1 possesses six directed repeat sequences and two inverted repeat sequences at downstream of the IR consensus sequence of nick region of rolling circle replication (RCR) plasmid. A typical terminator hairpin structure was found at the downstream region of repA gene. Degradation of single-stranded plasmid DNA by S1 nuclease was detected by Southern hybridization. It suggests that pZMO1 replicates by a rolling circle mechanism in Z. mobilis ATCC10988 cells.
Amino Acid Sequence ; Animals ; Base Sequence ; Consensus Sequence ; DNA ; Ecthyma, Contagious ; Inverted Repeat Sequences ; Nostoc ; Plasmids* ; Shigella sonnei ; Synechocystis ; Zymomonas*

Dye-decolorizing peroxidase (DyP-type peroxidase) represents a group of heme-containing peroxidases able to decolour various organic dyes, most of which are xenobiotics. To identify and characterize a new DyP-type peroxidase (ZmDyP) from Zymomonas mobilis ZM4 (ATCC 31821), ZmDyP was amplified from the genomic DNA of Z. mobilis by PCR, and cloned into the Escherichia coli expression vector pET-21b(+). Alignment of the amino acid sequence of ZmDyP with other members of the DyP-type peroxidases revealed the presence of the active site conserved residues D149, R239, T254, F256 as well as the typical GXXDG motif, indicating that ZmDyP is a new member of the Dyp-type peroxidase family. pET-21b(+) containing ZmDyP gene was expressed in E. coli by IPTG induction. The expressed enzyme was purified by Ni-Chelating chromatography. SDS-PAGE analysis of the purified enzyme revealed a molecular weight of 36 kDa, whereas activity staining gave a molecular weight of 108 kDa, suggesting that the enzyme could be a trimer. In addition, ZmDyP is a heme-containing enzyme as shown by a typical heme absorption peak of Soret band. Moreover, ZmDyP showed high catalytic efficiency with 2, 2'-Azinobis-(3-ethylbenzthiazoline-6-sulphonate) as a substrate. These results enrich the pool of DyP-type peroxidases and lay a foundation for further studies.
Amino Acid Sequence ; Catalysis ; Coloring Agents ; metabolism ; Escherichia coli ; genetics ; metabolism ; Molecular Sequence Data ; Peroxidases ; biosynthesis ; genetics ; isolation & purification ; Recombinant Proteins ; biosynthesis ; genetics ; isolation & purification ; Zymomonas ; enzymology

We constructed several recombinant Escherichia coli strains to transform phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS system) and compared the characteristics of growth and metabolism of the mutants. We knocked-out the key genes ptsI and ptsG in PTS system by using Red homologous recombination in E. coli and meanwhile we also knocked-in the glucose facilitator gene glf from Zymomonas mobilis in the E. coli chromosome. Recombinant E. coli strains were constructed and the effects of cell growth, glucose consumption and acetic acid accumulation were also evaluated in all recombinant strains. The deletion of gene ptsG and ptsI inactivated some PTS system functions and inhibited the growth ability of the cell. Expressing the gene glf can help recombinant E. coli strains re-absorb the glucose through Glf-Glk (glucose facilitator-glucokinase) pathway as it can use ATP to phosphorylate glucose and transport into cell. This pathway can improve the availability of glucose and also reduce the accumulation of acetic acid; it can also broaden the carbon flux in the metabolism pathway.
Biological Transport ; Escherichia coli ; enzymology ; genetics ; Gene Deletion ; Gene Knock-In Techniques ; Gene Knockout Techniques ; Glucose ; metabolism ; Phosphoenolpyruvate Sugar Phosphotransferase System ; genetics ; Zymomonas ; genetics

Coenzyme Q10 (CoQ10) is a lipophilic antioxidant that improves human immunity, delays senility and enhances the vitality of the human body and has wide applications in pharmaceutical and cosmetic industries. Microbial fermentation is a sustainable way to produce CoQ10, and attracts increased interest. In this work, the native CoQ8 synthetic pathway of Escherichia coli was replaced by the CoQ10 synthetic pathway through integrating decaprenyl diphosphate synthase gene (dps) from Rhodobacter sphaeroides into chromosome of E. coli ATCC 8739, followed by deletion of the native octaprenyl diphosphate synthase gene (ispB). The resulting strain GD-14 produced 0.68 mg/L CoQ10 with a yield of 0.54 mg/g DCW. Modulation of dxs and idi genes of the MEP pathway and ubiCA genes in combination led to 2.46-fold increase of CoQ10 production (from 0.54 to 1.87 mg/g DCW). Recruiting glucose facilitator protein of Zymomonas mobilis to replace the native phosphoenolpyruvate: carbohydrate phosphotransferase systems (PTS) further led to a 16% increase of CoQ10 yield. Finally, fed-batch fermentation of the best strain GD-51 was performed, which produced 433 mg/L CoQ10 with a yield of 11.7 mg/g DCW. To the best of our knowledge, this was the highest CoQ10 titer and yield obtained for engineered E. coli.
Alkyl and Aryl Transferases ; genetics ; Bacterial Proteins ; genetics ; Batch Cell Culture Techniques ; Escherichia coli ; genetics ; metabolism ; Fermentation ; Gene Deletion ; Industrial Microbiology ; Metabolic Engineering ; Rhodobacter sphaeroides ; enzymology ; genetics ; Ubiquinone ; analogs & derivatives ; biosynthesis ; Zymomonas ; genetics