Stability of a lac operon in Zymomonas mobilis in batch and continuous culture

ZM6100(RP1::Tn951), a strain of Zymomonas mobilis containing the lactose transposon Tn951 on the broad host range plasmid RP1, progressively lost all plasmid markers in batch culture under non-selective conditions. After 120 generations less than 0.1% of the population retained the plasmid markers. ZM6306, derived from ZM6100(RP1::Tn951) by prolonged tetracycline selection, showed 100% stability for all plasmid markers when grown without selection pressure in both batch and continuous culture. In continuous culture, the synthesis of β-galactosidase was induced by the addition of lactose, and low levels of galactose were detected together with a small increase in ethanol concentration.     

Hydrogen sulphide production by Zymomonas and its elimination in a mutant strain

Strains of Zymomonas mobilis grown in media containing either glucose or sucrose were assessed for the production of hydrogen sulphide (H₂S). In a liquid medium with low glucose concentration (20 g l^?1) only a proportion of the strains tested formed H₂S, but in medium containing a higher glucose concentration (100 g l^?1) all the strains tested produced H₂S. Four Z. mobilis strains were assayed quantitatively for H₂S production and strain ZM4 was found to produce the most H₂S in glucose medium. The amount of yeast extract and glucose, and the type of sugar used in the medium affected the amount of H₂S formed by strain ZM4. A mutant, designated ZM4701, of strain ZM4 was isolated which did not produce any detectable H₂S in liquid medium containing yeast extract plus either glucose or sucrose. The nutritional requirements of ZM4701 were investigated.     

A physical map of the genome of ethanol fermentative bacterium Zymomonas mobilis ZM4 and localization of genes on the map

A physical map of the Zymomonas mobilis ZM4 genome has been constructed from the results of reciprocal Southern hybridization with PmeI, PacI, and NotI-digested genomic DNA fragments and linking cosmid clones. Restriction enzyme-digested Z. mobilis ZM4 genome was electrophoresed with phage lambda DNA concatemers as a size standard in a Bio-Rad CHEF-DRII pulsed-field gel electrophoresis (PFGE) system. The restriction enzyme PmeI generated 15 fragments (3–625 kb), and PacI produced 19 fragments (7–525 kb). Each size of restriction fragment was calculated by comparison to the size of phage lambda DNA concatemers, and the genome size of Z. mobilis ZM4 was estimated to be 2085.5 kb. The 19 known genes and three rrn operons were localized on the map.     

Enhanced electrotransformation of the ethanologen Zymomonas mobilis ZM4 with plasmids

The Zymomonas mobilis ZM4 strain with excellent ethanol‐producing capabilities was the first strain of Z. mobilis, which was sequenced. This strain is resistant to transformation, and no previous study has shown a detailed protocol for electrotransfer of ZM4 with foreign DNA. In this work, many electrical and biological parameters were selected and evaluated in order to optimize the electrotransformation of ZM4. First, improved transformation efficiencies of 11 896, 99, 96 and 5989 transformants/μg DNA were separately achieved with shuttle plasmid pZB21‐mini (3082 bp), pZB21 (5930 bp), pZA22 (6994 bp) and broad‐host‐range vector pBBR1MCS‐2 (5144 bp) all prepared from Escherichia coli JM110. The crucial factors affecting the transformation efficiency included the source of the plasmid (the best strain was ZM4), origin and size of the plasmids, growth phase of the cells (the most ideal phase was early log phase with OD₆₀₀ of 0.3–0.4), the electric field strength (generally 11.75 kV/cm–13.25 kV/cm) and the recovery time (3–24 h). Further, based upon the optimal transformation protocol mentioned above for replicative plasmids in ZM4, (i) the electrotransformation by recombinant plasmid pBBR1MCS‐2‐Pgap‐FLP (6880 bp) was an immediate success with the transformation efficiency 10² transformants/μg DNA; (ii) the site‐specific integration efficiencies (expressed in terms of “per μg of DNA”) of 3–6 integrating transformants was obtained using the integrating plasmid pBR328‐ldhR‐cml‐ldhL (7447 bp). This study will assist genetic and biotechnological research of ZM4 and other Z. mobilis strains by providing information about suitable vectors and a more universal and reliable procedure for introducing DNA into this strain.     

Fermentation of lactose by Zymomonas mobilis carrying a Lac+ recombinant plasmid

Lac⁺ recombinant plasmids encoding a β-galactosidase fused protein and lactose permease of Escherichia coli were introduced Zymomonas mobilis. The fused protein was expressed with 450 to 5,860 Miller units of β-galactosidase activity, and functioned as lactase. Raffinose uptake by Z. mobilis CP4 was enhanced in the plasmid-carrying strain over the plasmid-free strain, suggesting that the lactose permease was functioning in the organism. Z. mobilis carrying the plasmid could produce ethanol from lactose and whey, but could not grow on lactose as the sole carbon source. It was found that the growth of the organism was inhibited by either galactose of the galactose liberated from lactose.     

Kinetic studies on alac-containing strain ofZymomonas mobilis

Summary Batch and continuous culture studies have been carried out on a strain ofZ.mobilis (ZM6306) which can convert lactose directly to ethanol. Previous strain development has established that thelac operon encoded on the transposon Tn951 can be expressed inZ.mobilis. Using a medium containing 80 g/l glucose and 40 g/l lactose, it was found that strain ZM6306 could convert about 13 g/l lactose to 4 g/l ethanol and 6 g/l galactose in continuous culture. Further lactose conversion is likely with increased cell concentration using a cell recycle system.     

Ethanol production from fructose in continuous culture by free and flocculent cells of Zymomonas mobilis

Summary Zymomonas mobilis strain ZM4 was used for ethanol production from fructose (100 g/l) in continuous culture with a mineral (containing Ca pantothenate) or a rich (containing yeast extract) mediium. With both media high conversion yields were observed but the ethanol productivity was limited by the low biomass content of the fermentor. A new flocculent strain of Z.mobilis (ZM4F) was cultivated in a CSTR with an internal settler and showed a maximal productivity of 93 g/l.h (fructose conversion of 80%). When the fructose conversion was 96% an ethanol productivity of 85.6 g/l.h with an ethanol yield of 0.49 g/g (96% of theoretical) was observed.     

High productivity ethanol fermentation on a mineral medium using a flocculent strain ofZymomonas mobilis

Summary A flocculent strain ofZymomonas mobilis (ZM4F JM1) was isolated in continuous culture. The parent strain, ZM4F, had lost its flocculating properties. The isolation was done in a conical fermentor at high dilution rate. Ethanol production by the new strain was then compared on a rich and mineral medium. The mineral medium showed high performance and could be used for industrial production of ethanol since it reduced one hundred fold the vitamin cost of the fermentation.     

Draft Genome Sequence of the Flocculating Zymomonas mobilis Strain ZM401 (ATCC 31822)

Zymomonas mobilis ZM401 is a flocculating strain which can be self-immobilized within fermentors for a high-cell-density culture to improve ethanol productivity, as well as high-gravity fermentation to increase ethanol titer, due to its improved ethanol tolerance associated with the morphological change. Here, we report its draft genome sequence.     

Expression of a Lactose Transposon (Tn951) in Zymomonas mobilis

The potential utility of Zymomonas mobilis as an organism for the commercial production of ethanol would be greatly enhanced by the addition of foreign genes which expand its range of fermentable substrates. We tested various plasmids and mobilizing factors for their ability to act as vectors and introduce foreign genes into Z. mobilis CP4. Plasmid pGC91.14, a derivative of RP1, was found to be transferred from Escherichia coli to Z. mobilis at a higher frequency than previously reported for any other plasmids. Both tetracycline resistance and the lactose operon from this plasmid were expressed in Z. mobilis CP4. Plasmid pGC91.14 was stably maintained in Z. mobilis at 30°C but rapidly lost at 37°C.     

Fermentation of paddy malt mash to ethanol by mixed cultures of Saccharomyces cerevisiae and Zymomonas mobilis ZM4 with penicillin G

Traditional fermentation of paddy malt mash (containing 18.1% w/v dextrose equivalent) to paddy arrack using paddy husk as source of inoculum yielded very low level of ethanol (4.25% v/v). Use of yeast isolates obtained from paddy husk as well as a potent ethanol producer like Zymomonas mobilis ZM4 and their combinations in the fermentation revealed that a combination of an yeast isolate PH 03 (Saccharomyces cerevisiae) and Z. mobilis ZM4 produced synergistically and statistically more ethanol (10.1% v/v) than the individual and other combination of cultures. In this process, addition of penicillin G at a concentration of 20 U/ml rather than heat sterilization, helped retention of the limited amylase activity in the mash for simultaneous saccharification and fermentation over 7 d at 30°C. About 98.5% of the carbohydrate was accountable in the fermentation which yielded 86.7% of the theoretical yield of ethanol, apart from biomass and acids.     

Stability and expression of a cloned α-glucosidase gene inZymomonas mobilis grown in batch and continuous culture

Summary Strains ofZymomonas mobilis containing an -glucosidase gene cloned fromBacillus brevis strain 27-7 (NRRL B-4389) on the plasmid pNSW358 showed varying degrees of stability in batch culture under non-selective conditions. After 45 generations of growth in continuous culture, pNSW358 was stable inZ.mobilis strain ZM6100 and the specific activity of -glucosidase in these cells was 2.7 nmol/min/mg protein. Lysed cell extracts confirmed the activity of the -glucosidase enzyme in ZM6100(pNSW358) with 21 g/1 ethanol in 50 (82% theoretical conversion of maltose to ethanol). ZM6100(pNSW358) whole cells showed a very slow conversion rate on maltose as a sole carbon source with only 5.3 g/1 ethanol after 30 days on 100 g/l maltose medium.     

Complete Genome Sequence of the Ethanol-Producing Zymomonas mobilis subsp. mobilis Centrotype ATCC 29191

Zymomonas mobilis is an ethanologenic bacterium that has been studied for use in biofuel production. Of the sequenced Zymomonas strains, ATCC 29191 has been described as the phenotypic centrotype of Zymomonas mobilis subsp. mobilis, the taxon that harbors the highest ethanol-producing Z. mobilis strains. ATCC 29191 was isolated in Kinshasa, Congo, from palm wine fermentations. This strain is reported to be a robust levan producer, while in recent years it has been employed in studies addressing Z. mobilis respiration. Here we announce the finishing and annotation of the ATCC 29191 genome, which comprises one chromosome and three plasmids.     

Controlling Morphological Instability of Zymomonas mobilis Strains in Continuous Culture

Growth of Zymomonas mobilis ATCC 29191 and CP4 in a continuous stirred tank fermentor resulted in the selection of stable flocculating variants. Factors responsible for enhancing the system pressures selective for the morphological variants were identified. By incorporating some modifications into the design of the fermentor, it was possible to achieve steady-state operation of the chemostat with both wild-type and flocculating strains. Biochemical and microscopic studies were performed to elucidate the mechanism of flocculation in Z. mobilis.     

Construction of a shuttle vector for Zymomonas mobilis

Summary An Escherichia coli-Zymomonas mobilis shuttle vector was constructed from a 15.5 kb native plasmid of ZM6 00 and the E. coli plasmid, pBR329. Integrative transfer of this shuttle vector from E. coli to Z. mobilis was achieved with the aid of the mobilizing plasmid, pRK2013. The shuttle vector was stable in Z. mobilis for at least 300 generations without antibiotic selection.Offprint requests to: S. F. Delaney     

Growth ofZymomonas on lactose: Gene cloning in combination with mutagenesis

Summary Wild-type strains ofZymomonas mobilis have a limited substrate range of glucose, fructose and sucrose. In order to expand this substrate range, transconjugants ofZ. mobilis containing Lac⁺ plasmids have been constructed. Although -galactosidase is expressed in such strains, they lack the ability to grow on lactose. We now report the development ofZ. mobilis strains capable of growth on lactose. This was achieved in two stages. First, a broad host range plasmid was constructed (pRUT102) which contained the lactose operon under the control of aZ. mobilis promoter plus genes for galactose utilization.Z. mobilis CP4.45 containing pRUT102 was then subjected to mutagenesis combined with continued selection pressure for growth on lactose. One strain,Z. mobilis SB6, produced a turbid culture that yielded 0.25% ethanol from 5% lactose (plus 2% yeast extract) in 15 days.     

DNA restriction-modification systems in the ethanologen, Zymomonas mobilis ZM4

To better understand the DNA restriction-modification (R-M) systems for more amenable strain development of the alternative industrial ethanologen, Zymomonas mobilis, three gene knockout mutants were constructed. The gene knockout mutants were tested for their DNA restriction activities by the determination of transformation efficiency using methylated and unmethylated foreign plasmid DNAs. Inactivation of a putative mrr gene encoded by ZMO0028 (zmrr) resulted in a 60-fold increase in the transformation efficiency when unmethylated plasmid DNA was used. This indicated that the putative mrr gene may serve as a type IV restriction-modification system in Z. mobilis ZM4. To assign the function of a putative type I DNA methyltransferase encoded by ZMO1933 (putative S subunit) and ZMO1934 (putative M subunit), the putative S subunit was inactivated. The gene inactivation of ZMO1933 resulted in a 30-fold increase in the transformation efficiency when methylated plasmid DNA was introduced, indicating that the putative S subunit possibly serves as a part of functional type I R-M system(s). Growth studies performed on the mutant strains indicate inactivation of the type I S subunit resulted in a lower maximum specific glucose consumption rate and biomass yield, while inactivation of the type IV Zmrr had the opposite effect, with an increase in the maximum specific growth rate and biomass yield.     

Complete Genome Sequence of the Ethanol Producer Zymomonas mobilis NCIMB 11163

Zymomonas mobilis is an ethanol-producing alphaproteobacterium currently considered a major candidate organism for bioethanol production. Here we report the finished and annotated genome sequence of Z. mobilis subsp. mobilis strain NCIMB 11163, a British ale-infecting isolate. This is the first Z. mobilis strain whose genome, chromosomal and plasmid, is presented in its entirety.Zymomonas mobilis is a bacterium vigorously studied as a platform organism for bioethanol production in North America and other parts of the world. Z. mobilis converts sugars such as glucose or sucrose into ethanol and carbon dioxide to almost theoretical yields and to rates higher than those of yeasts (17). Genetically engineered strains that ferment pentoses in addition to naturally utilized hexoses also hold great promise for use in lignocellulosic biomass degradations (5, 22). Besides ethanol, Z. mobilis can produce other high-value chemicals such as sorbitol, levan, or phenylacetylcarbinol and has attracted interest for its unusual membrane steroid content (11). Lastly, Zymomonas is regarded as a safe organism and is even used for medicinal purposes (12, 20), which further facilitates its employment in large-scale biotechnological endeavors.The chromosomal sequence of the Z. mobilis subsp. mobilis industrial strain ATCC 31821 (ZM4) was recently published (19). Here we announce the first entire genome sequence of a Z. mobilis subsp. mobilis strain, that of the United Kingdom-originating strain NCIMB 11163 (B70) (20). Total DNA from NCIMB 11163 (16) was used for whole-genome shotgun sequencing at the U.S. DOE Joint Genome Institute. For this, an 8.7-kb DNA library and 454 and Solexa reads were used (http://www.jgi.doe.gov). Draft assemblies were based on 8,551 Sanger reads and 454 pyrosequencing to 20× coverage, whereas the Phred/Phrap/Consed software package was used for sequence assembly and quality assessment (6, 7, 9; http://www.phrap.com). After the shotgun stage, reads were assembled with parallel Phrap (High Performance Software, LLC), and misassemblies were corrected with Dupfinisher (10) or transposon bombing of bridging clones (Epicentre Biotechnologies, Madison, WI). A total of 144 primer walk reactions, five transposon bomb libraries, 53 PCR end reads, and two PCR shatter libraries were necessary to close gaps, resolve repetitive regions, and raise the quality of the finished sequence. The completed genome sequence of NCIMB 11163 was based on 11,048 reads, with an error rate of less than 6 bp out of 100,000 bp.Open reading frame prediction and annotation were performed using Prodigal (http://compbio.ornl.gov/prodigal/) and BLAST (1); tRNAscan-SE and RNAmmer (14, 15) were used for tRNA and rRNA recognition, respectively. Functional assignment of genes was performed by searching translated open reading frames against sequences in the SPTR (TrEMBL) (2), Pfam (8), TIGRFAMs (18), COG (21), and KEGG (13) databases.Z. mobilis NCIMB 11163 contains a single, circular chromosome of 2,124,771 bp and three plasmids, p11163_1, p11163_2, and p11163_3 of 53,380 bp, 40,818 bp, and 4,551 bp, respectively. The overall GC content of the chromosome is 46.83%, whereas those of the plasmids are 42.32%, 43.80%, and 36.37%, respectively. The entire genome of NCIMB 11163 contains 1,884 protein-encoding genes and 51 tRNA and nine rRNA genes, which are chromosomally located.The chromosome of NCIMB 11163 is 68,355 bp larger than that of ZM4 (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"NC_006526","term_id":"283856168","term_text":"NC_006526"}}NC_006526) (19) and colinear at its largest part with that of ZM4 (genome structure comparisons were performed using ACT) (3). It bears several unique regions, among which are two genomic islands of ca. 25 and 79 kb, with no detectable nucleotide homology to same-species sequences and high regional similarity to chromosomal stretches of Paracoccus denitrificans PD1222 (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"CP000489.1","term_id":"119372524","term_text":"CP000489.1"}}CP000489.1), Xanthobacter autotrophicus Py2 (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"CP000781.1","term_id":"154158043","term_text":"CP000781.1"}}CP000781.1), and Gluconacetobacter diazotrophicus PAl 5 (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"CP001189.1","term_id":"209529865","term_text":"CP001189.1"}}CP001189.1). Genome plasticity in NCIMB 11163 is further indicated by the presence of a type IV secretion system on the 79-kb island, syntenous to the Agrobacterium tumefaciens Ti (IncRh1) conjugal trb system (4), and also by multiple transposase and phage-related genes.In plasmids, housekeeping genes implicated in replication, active partitioning, and plasmid addiction are recognized, as well as genes involved in metabolism, transport, regulation, transposition, and DNA modification. Most notably, p11163_1 bears an arsenical resistance operon inserted in a type II secretion locus, whereas p11163_2, otherwise homologous to the 41-kb ZM4 plasmid (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"AY057845","term_id":"26983909","term_text":"AY057845"}}AY057845), harbors a unique ca. 12-kb CRISPR insertion that interrupts nucleotide colinearity with the aforementioned replicon.     

An improved synthetic medium for continuous cultivation of Zymomonas mobilis

Summary A synthetic medium for continuous cultivation of Zymomonas mobilis was developed using the chemostat pulse technique in appropriate experimental designs. Yeast extract could be replaced by a mixture of six mineral salts, Ca-pantothenate, l-as-partate, and l-serine. Kinetic data from continuous cultivations of strains ATCC 10988 and ZM4 are presented and compared with published data.