Draft Genome Sequence of the Strict Anaerobe Clostridium homopropionicum LuHBu1 (DSM 5847)

Abstract

Here, we report the draft genome sequence of Clostridium homopropionicum LuHBu1 (DSM 5847^T), a strictly anaerobic bacterium, which performs propionate fermentation and is capable of growing with 2-, 3-, or 4-hydroxybutyrate as its sole substrate. The genome consists of a single chromosome of 3.65 Mb.

GENOME ANNOUNCEMENT

The endospore-forming obligately anaerobic organism Clostridium homopropionicum is able to ferment various hydroxy- and chlorobutyrates to acetate and butyrate, lactate to acetate and propionate, and fructose to acetate, butyrate, and butanol. The dismutation of 3-hydroxybutyrate to C₂ and C₄ compounds obviously plays a central role in its metabolism (1). Despite using the energetically less favorable acrylyl-coenzyme A (CoA) pathway for lactate fermentation, C. homopropionicum compensates the lower ATP yield, compared to the methylmalonyl-CoA pathway, by far higher maximal substrate turnover rates (2). C. homopropionicum differs from Clostridium propionicum (3) in its ability to ferment 2- and 4-hydroxybutyrate (1).

Chromosomal DNA was isolated with the MasterPure complete DNA purification kit (Epicentre, Madison, WI, USA) and used to generate Illumina shotgun sequencing libraries. Sequencing was performed with a MiSeq using MiSeq reagent kit version 3 (600 cycles), as recommended by the manufacturer (Illumina, San Diego, CA, United States), resulting in 2,883,306 paired-end reads (300 bp) that were trimmed using Trimmomatic 0.32 (4). The de novo assembly performed with the SPAdes genome assembler software version 3.5.0 (5) resulted in 48 contigs (>500 bp) and an average coverage of 180-fold. The genome of C. homopropionicum probably consists of a circular chromosome (3.65 Mb), with an overall G+C content of 31.09%.

Automatic gene prediction was performed with Prokka version 1.9.2 (6). Genes coding for rRNA and tRNA were identified using RNAmmer (7) and tRNAscan (8), respectively.

The genome harbored 10 rRNA genes, 67 tRNA genes, 2,688 protein-coding genes with predicted functions, and 896 genes coding for hypothetical proteins.

With respect to butanol production, the genome analysis revealed that no sol operon according to the Clostridium acetobutylicum (9) or Clostridium beijerinckii type (10) is present. Several copies of coenzyme A transferase genes (ctfAB) are present in different locations of the genome. 4-Hydroxybutyrate is most probably metabolized by a CoA transferase and a bifunctional 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA Δ³-Δ²-isomerase. Such enzymes and genes (abfT and abfD) have been purified and identified from Clostridium aminobutyricum and Clostridium kluyveri (11–15). Homologs of abfD and abfT are present in C. homopropionicum. Genes homologous to those encoding the key enzymes of the acrylyl-CoA pathway in C. propionicum (propionate CoA transferase [Pct] and lactoyl-CoA dehydratase [Lcd]) (16) were identified. C. homopropionicum can fix molecular nitrogen (1). The respective nif genes were found to be organized in a cluster, remarkably similar to C. acetobutylicum ATCC 824.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LHUR00000000. The version described in this paper is version LHUR01000000.