Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms.

BACKGROUND: Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. RESULTS: We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. CONCLUSIONS: We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.

Characterization of homologs of the small RNA SgrS reveals diversity in function.

SgrS is a small RNA (sRNA) that requires the RNA chaperone Hfq for its function. SgrS is a unique dual-function sRNA with a base pairing function that regulates mRNA targets and an mRNA function that allows production of the 43-amino-acid protein SgrT. SgrS is expressed when non-metabolizable sugars accumulate intracellularly (glucose-phosphate stress) and is required to allow Escherichia coli cells to recover from stress. In this study, homologs of SgrS were used to complement an E. coli sgrS mutant in order elucidate the physiological relevance of differences among homologs. These analyses revealed that the base pairing function of E. coli and Yersinia pestis SgrS homologs is critical for rescue from glucose-phosphate stress. In contrast, base pairing-deficient SgrS homologs from Salmonella typhimurium, Erwinia carotovora and Klebsiella pneumoniae rescue E. coli cells from stress despite their failure to regulate target mRNAs. Compared with E. coli SgrS, S. typhimurium SgrS produces more SgrT and this rescues cell growth even when the base pairing function is inactivated. Genetic evidence suggests that a secondary structure in the E. coli SgrS 5' region inhibits sgrT translation. This structure is not present in S. typhimurium SgrS, which explains its higher level of SgrT production.

A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide.

SgrS is a 227-nt small RNA that is expressed in Escherichia coli during glucose-phosphate stress, a condition associated with intracellular accumulation of glucose-6-phosphate caused by disruption of glycolytic flux. Under stress conditions, SgrS negatively regulates translation and stability of the ptsG mRNA, encoding the major glucose transporter, by means of a base pairing-dependent mechanism requiring the RNA chaperone Hfq. SgrS activity mitigates the effects of glucose-phosphate stress, and the present study has elucidated a function of SgrS that is proposed to contribute to the stress response. The 5' end of SgrS, upstream of the nucleotides involved in base pairing with the ptsG mRNA, contains a 43-aa ORF, sgrT, that is conserved in most species that contain SgrS-like small RNAs. The sgrT gene is translated in E. coli under conditions of glucose-phosphate stress. Analysis of alleles that separate the base pairing function of SgrS from the sgrT coding sequence revealed that either of these functions alone are sufficient for previously characterized SgrS phenotypes. SgrS-dependent down-regulation of ptsG mRNA stability does not require SgrT and SgrT by itself has no effect on ptsG mRNA stability. Cells expressing sgrT alone had a defect in glucose uptake even though they had nearly wild-type levels of PtsG (IICB(Glc)). Together, these data suggest that SgrS represents a previously unrecognized paradigm for small RNA (sRNA) regulators as a bifunctional RNA that encodes physiologically redundant but mechanistically distinct functions contributing to the same stress response.