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

Abstract

The application of systems biology tools holds promise for rational industrial microbial strain development. Here, we characterize a Zymomonas mobilis mutant (AcR) demonstrating sodium acetate tolerance that has potential importance in biofuel development. The genome changes associated with AcR are determined using microarray comparative genome sequencing (CGS) and 454-pyrosequencing. Sanger sequencing analysis is employed to validate genomic differences and to investigate CGS and 454-pyrosequencing limitations. Transcriptomics, genetic data and growth studies indicate that over-expression of the sodium-proton antiporter gene nhaA confers the elevated AcR sodium acetate tolerance phenotype. nhaA over-expression mostly confers enhanced sodium (Na þ ) tolerance and not acetate (Ac − ) tolerance, unless both ions are present in sufficient quantities. NaAc is more inhibitory than potassium and ammonium acetate for Z. mobilis and the combination of elevated Na þ and Ac − ions exerts a synergistic inhibitory effect for strain ZM4. A structural model for the NhaA sodiumproton antiporter is constructed to provide mechanistic insights. We demonstrate that Saccharomyces cerevisiae sodium-proton antiporter genes also contribute to sodium acetate, potassium acetate, and ammonium acetate tolerances. The present combination of classical and systems biology tools is a paradigm for accelerated industrial strain improvement and combines benefits of few a priori assumptions with detailed, rapid, mechanistic studies.ethanol | inhibitor | microarray | sequencing | systems biology

Progress and perspective on lignocellulosic hydrolysate inhibitor tolerance improvement in Zymomonas mobilis

“…For example, a 1.5-kb deletion in acetatetolerant strain AcR was identified through comparative genome sequencing, which likely truncated the majority of gene ZMO0117 and partial of the promoter of the nhaA gene (ZMO0119) encoding a sodium proton antiporter. Further transcriptomics and genetic studies indicated that the acetate tolerance of AcR was attributed to the overexpression of nhaA resulted from the co-transcription of nhaA from ZMO0117 (Yang et al 2010a). Interestingly, a similar result was achieved in another acetate-tolerant mutant ZMA-167 generated through the combination of NTG mutagenesis and ALE .…”

“…In addition, genome-resequencing analysis was also applied to identify the underlying genetic changes responsible for the altered phenotypes in mutants generated through forward genetics approaches as discussed above Mohagheghi et al 2015;Yang et al 2010aYang et al , 2014b. For example, a 1.5-kb deletion in acetatetolerant strain AcR was identified through comparative genome sequencing, which likely truncated the majority of gene ZMO0117 and partial of the promoter of the nhaA gene (ZMO0119) encoding a sodium proton antiporter.…”

Sequential Saccharification and Simultaneous Fermentation (SSSF) of Sago Hampas for the Production of Bioethanol

“…For the broth with 2.5% (w/v) sago hampas, the acetic acid concentrations increased After 72 h, acetic acid concentration started to decrease to 0.95 g/L at 120 h. Although the presence of acetic acid is not as significant as ethanol, it is nevertheless an important indicator to evaluate the efficiency of biomass hydrolysis, as more acetic acid produced indicates constant degradation of lignocellulosic materials during SSSF. In addition, according to Yang et al (2010), the rate of acetic acid generated is related to the production of fermentable sugars.…”

A Transcriptional Regulator Sll0794 Regulates Tolerance to Biofuel Ethanol in Photosynthetic Synechocystis sp. PCC 6803

“…Modification of cell envelope represents an important mechanism against stress in various microbes (62)(63)(64). In the ⌬sll0794 mutant grown under ethanol stress, three proteins involved in cell envelope, Slr0298 of a FraH protein homolog, Sll0016 of a probable membrane-bound lytic transglycosylase A, and Sll0721 of an S-layer-RTX protein-related, were upregulated (Table III).…”