The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4

Abstract

We report the complete genome sequence of Zymomonas mobilis ZM4 (ATCC31821), an ethanologenic microorganism of interest for the production of fuel ethanol. The genome consists of 2,056,416 base pairs forming a circular chromosome with 1,998 open reading frames (ORFs) and three ribosomal RNA transcription units. The genome lacks recognizable genes for 6-phosphofructokinase, an essential enzyme in the Embden-Meyerhof-Parnas pathway, and for two enzymes in the tricarboxylic acid cycle, the 2-oxoglutarate dehydrogenase complex and malate dehydrogenase, so glucose can be metabolized only by the Entner-Doudoroff pathway. Whole genome microarrays were used for genomic comparisons with the Z. mobilis type strain ZM1 (ATCC10988) revealing that 54 ORFs predicted to encode for transport and secretory proteins, transcriptional regulators and oxidoreductase in the ZM4 strain were absent from ZM1. Most of these ORFs were also found to be actively transcribed in association with ethanol production by ZM4.Growing environmental concerns over the use and depletion of nonrenewable energy resources, together with the recent price increases and instabilities in the international oil markets have stimulated an increasing interest in the use of fermentation processes for the large-scale production of alternative fuels such as ethanol. As such, ethanol-producing microorganisms, such as the Gram-negative bacterium Z. mobilis, have potential for the production of fuel ethanol.Z. mobilis, which is used in the tropics to produce pulque and alcoholic palm wines, uses the Entner-Doudoroff (ED) pathway to metabolize glucose, which results in only 1 mole of ATP being produced per mole of glucose 1 . The potential advantages of using Z. mobilis for ethanol production include: (i) its high and specific rates of sugar uptake and ethanol production, (ii) its production of ethanol at yields close to the theoretical maximum with relatively low biomass formation, (iii) its high ethanol tolerance of up to 16% (vol/vol) and (iv) its facility for genetic manipulation 2-6 . However, wild strains of Z. mobilis can use only glucose, fructose and sucrose as carbon substrates, so recent research has focused on the development of recombinant strains capable of using pentose sugars 7,8 for the conversion of cheaper lignocellulosic hydrolysates to ethanol. Improved mutants 9-11 as well as the application of metabolic flux analysis, sitedirected mutagenesis, specific gene deletion/insertion and metabolic engineering for strain developlment 12,13 have also been reported. A physical map of Z. mobilis ZM4 genome and the ribosomal transcriptional unit have been previously reported 14,15 . In the current paper, the features of the complete sequence of the Z. mobilis ZM4 genome are presented and genomic characters are compared with those of another Z. mobilis strain, ZM1.

Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae

“…The GSMapper application in the 454 GS FLX software package 1.1.03 (454 Life Sciences) was used to map the pyrosequencing reads onto the Z. mobilis ZM4 reference genome (GenBank accession: AE008692) (13). This identified 200 and 219 high confidence differences (HCDiffs) for strains ZM4 and AcR respectively (Table S3).…”

“…Pyrosequencing using the Roche 454 GS FLX System (454 Life Sciences) was carried out using both shotgun and paired-end DNA library preparation methods. The GSMapper application in the 454 GS FLX software package 1.1.03 (454 Life Sciences) was used to map the reads generated from GS FLX onto the ZM4 reference genome (GenBank accession: AE008692) and the GSAssembler application was used to assemble the sequence reads into contigs, which were then compared with ZM4 genome sequence (13).…”

Biofuel alternatives to ethanol: pumping the microbial well

“…phytoene [C40]) serve as inter-mediates in the production of large isoprenoid compounds, and they might be suitable as biocrude. Both E. coli and S. cerevisiae have been successfully engineered for the pro-duction of the phytoene-based carotenoids [51,[57][58][59]; unfortunately, the current yields of these compounds fall far short of what is required if they are to produce viable fuel alternatives [47,50,60]. However, if sufficient titers of phytoene are reached, it could be refined into motor and jet fuel through the infrastructure currently used to process petroleum.…”

Evaluation of Cellulase Production by Zymomonas mobilis

“…Hence, Z. mobilis cellulase is an endoglucanase, as its highest enzyme activity was against CMC substrates (Adsul et al 2007). Several Z. mobilis strains (ATCC 39676 and CP4) natively produce endoglucanase activity against CMC (He et al bioresources.com Todhanakasem & Jittjang (2017 (Table 7) (Seo et al 2005;Kouvelis et al 2009;Kouvelis et al 2011;Pappas et al 2011;Desiniotis et al 2012;Kouvelis et al 2014). ZMO 1086 from Z. mobilis has been cloned and successfully expressed in Escherichia coli (Rajnish et al 2008).…”