Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

Abstract

BackgroundZymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. mobilis strains have been completely sequenced and found to contain 2–8 native plasmids. However, systematic verification of predicted Z. mobilis plasmid genes and their contribution to cell fitness has not been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis model strain ZM4 have been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing studies for this model biofuel-producing strain.ResultsIn this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion. Four plasmids were identified in all three strains, with 150 plasmid genes predicted in strain ZM4 and 2032, and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for expanded substrate utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems biology data analyses, and most genes were found to have apparent orthologs in other organisms or identifiable conserved domains. To verify plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene expression under various growth conditions, including anaerobic and aerobic conditions, or growth in different concentrations of biomass hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate concentrations than to oxygen availability. Additionally, our results indicated that although all plasmids were present in low copy number (about 1–2 per cell), the copy number of some plasmids varied under specific growth conditions or due to heterologous gene insertion.ConclusionsThe complete genome of ZM4 and two xylose-utilizing derivatives is reported in this study, with an emphasis on identifying and characterizing plasmid genes. Plasmid gene annotation, validation, expression levels at growth conditions of interest, and contribution to host fitness are reported for the first time.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1116-x) contains supplementary material, which is available to authorized users.

Cell Aggregation and Aerobic Respiration Are Important for Zymomonas mobilis ZM4 Survival in an Aerobic Minimal Medium

“…A cellulose synthase gene cluster and a single diguanylate cyclase are required for flocculation. Because the extracellular matrix of flocs contains cellulose, we examined the ZM4 genome sequence (21)(22)(23) for genes that could be responsible for cellulose synthesis. A gene cluster from ZMO1083 to ZMO1086 (bcsABCZ) was annotated as encoding a cellulose synthase complex ( Fig.…”

Primed acquisition and microhomology-mediated end-joining cooperate to confer specific CRISPR immunity against invasive genetic elements

“…Sequencing was carried out as described previously 46 . Using the BLASTN program against pEZ15Asp plasmid or pEZ15Asp carrying PPS or the Z. mobilis ZM4 genome sequence 47 , the protospacer sequences were identified for new integrated spacers. The 2-bp sequence at the 5’-end of each protospacer was considered as the PAM region.…”

Underlying Mechanism of Uncoupled Cell Growth and Ethanol Fermentation of Zymomonas mobilis using Different Nitrogen Sources

“…Transcriptomics study was followed previous work [16,29,[31][32][33][34][35]. Briefly, cell culture samples were collected during exponential phase with the OD 600 values around 0.6 ~ 0.8.…”