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. 2023 Sep 16;10(9):1090.
doi: 10.3390/bioengineering10091090.

Whole-Genome Sequence and Fermentation Characteristics of Enterobacter hormaechei UW0SKVC1: A Promising Candidate for Detoxification of Lignocellulosic Biomass Hydrolysates and Production of Value-Added Chemicals

Santosh Kumar  1 , Eric Agyeman-Duah  1 , Victor C Ujor  1
Affiliations

Whole-Genome Sequence and Fermentation Characteristics of Enterobacter hormaechei UW0SKVC1: A Promising Candidate for Detoxification of Lignocellulosic Biomass Hydrolysates and Production of Value-Added Chemicals

Santosh Kumar et al. Bioengineering (Basel). .

Abstract

Enterobacter hormaechei is part of the Enterobacter cloacae complex (ECC), which is widespread in nature. It is a facultative Gram-negative bacterium of medical and industrial importance. We assessed the metabolic and genetic repertoires of a new Enterobacter isolate. Here, we report the whole-genome sequence of a furfural- and 5-hydroxymethyl furfural (HMF)-tolerant strain of E. hormaechei (UW0SKVC1), which uses glucose, glycerol, xylose, lactose and arabinose as sole carbon sources. This strain exhibits high tolerance to furfural (IC50 = 34.2 mM; ~3.3 g/L) relative to Escherichia coli DH5α (IC50 = 26.0 mM; ~2.5 g/L). Furfural and HMF are predominantly converted to their less-toxic alcohols. E. hormaechei UW0SKVC1 produces 2,3-butanediol, acetoin, and acetol, among other compounds of industrial importance. E. hormaechei UW0SKVC1 produces as high as ~42 g/L 2,3-butanediol on 60 g/L glucose or lactose. The assembled genome consists of a 4,833,490-bp chromosome, with a GC content of 55.35%. Annotation of the assembled genome revealed 4586 coding sequences and 4516 protein-coding genes (average length 937-bp) involved in central metabolism, energy generation, biodegradation of xenobiotic compounds, production of assorted organic compounds, and drug resistance. E. hormaechei UW0SKVC1 shows considerable promise as a biocatalyst and a genetic repository of genes whose protein products may be harnessed for the efficient bioconversion of lignocellulosic biomass, abundant glycerol and lactose-replete whey permeate to value-added chemicals.

Keywords: 2,3-butanediol; 5-hydroxymethylfurfural; Enterobacter hormaechei; acetol; furfural; lignocellulosic biomass; whole-genome sequence.

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Conflict of interest statement

The authors declare that they have no known competing interests (financial/personal) that could have influenced the work reported in this publication.

Figures

Figure 1
Figure 1
Growth profiles of E. coli DH5α and E. hormaechaei in LB medium supplemented with 1% (w/v) glucose and varying concentrations of furfural/HMF. (A) 0 mM furfural/HMF; (B) 30 mM furfural; (C) 40 mM HMF. Cultures were incubated for 24 h at 37 °C and 200 rpm.
Figure 2
Figure 2
The growth profiles of E. hormaechei on different substrates, with and without furfural and HMF supplementation. (A) Growth on different carbon sources (glucose, xylose, arabinose and glycerol); (B) growth in LB medium supplemented with 1% (w/v) glucose and furfural (10 mM, 30 mM and 50 mM); (C) growth in LB medium supplemented with 1% (w/v) glucose and HMF (10 mM, 30 mM, 50 mM and 70 mM). The data presented here are the mean values ± SD calculated from three independent replicates.
Figure 3
Figure 3
Furfural and furfuryl alcohol concentrations in furfural-supplemented cultures of E. hormaechei. Cells were grown in LB medium supplemented with 1% (w/v) glucose and different concentrations of furfural. (A) 10 mM furfural; (B) 30 mM furfural, and (C) 50 mM furfural. FA—furfuryl alcohol.
Figure 4
Figure 4
HMF and HMF alcohol concentrations in HMF-supplemented cultures of E. hormaechei. (A) 10 mM HMF; (B) 30 mM HMF, and (C) 50 mM HMF. HMFA—HMF alcohol.
Figure 5
Figure 5
The growth profile of E. hormaechei in furoic acid supplemented glucose culture, relative to growth in the glucose control medium.
Figure 6
Figure 6
Circular map of the complete genome of E. hormaechei UW0SKVC1. Map was generated using the Proksee software system for genome assembly, annotation, and visualization (https://proksee.ca/ (accessed on 15 November 2022)). Detailed information on the genome assembly is available under GenBank accession numbers JAPCKH010000001.1 to JAPCKH010000047.1.
Figure 7
Figure 7
Phylogenetic tree constructed based on the whole genome of E. hormaechei UW0SKVC1. Tree was inferred with FastME 2.1.6.1 [50] from GBDP distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above the branches are GBDP pseudo-bootstrap support values > 60% from 100 replications, with an average branch support of 96.5%. The tree was rooted at the midpoint. Color schemes (left to right) indicates the species and subspecies clusters based on similarities among strains. The same box colors indicate strains belonging to the same cluster as defined by each of the listed strains at the top of the boxes.
Figure 8
Figure 8
Availability of enzymes of the 2,3-BD (left light blue panel) and 1,2-PD (right grey panel) pathways in E. hormaechei UW0SKVC1. Enzymes in blue are present in the genome of E. hormaechei, whereas enzymes in green are absent.
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