Reconstruction of Acetogenesis Pathway Using Short-Read Sequencing of Clostridium aceticum Genome

Abstract

Clostridium aceticum is an anaerobic homoacetogen, able to reduce CO2 to multi-carbon productsusing the reductive acetyl-CoA pathway. This unique ability to use CO2 or CO makes the microbea potential platform for the biotech industry. However, the development of genetically engineeredhomoacetogen for the large-scale production of commodity chemicals is hampered by the limitedamount of their genetic and metabolic information. Here we exploited next-generation sequencingto reveal C. aceticum genome. The short-read sequencing produced 44,871,196 high quality readswith an average length of 248 bases. Following sequence trimming step, 30,256,976 reads wereassembled into 12,563 contigs with 168-fold coverage and 1,971 bases in length using de Bruijngraph algorithm. Since the k-mer hash length in the algorithm is an important factor for the qualityof output contigs, a window of k-mers (k-51 to k-201) was tested to obtain high quality contigs.In addition to the assembly metrics, the functional annotation of the contigs was investigated toselect the k-mer optimum. Metabolic pathway mapping using the functional annotation identifiedthe majority of central metabolic pathways, such as the glycolysis and TCA cycle. Further, theseanalyses elucidated the enzymes consisting of Wood–Ljungdahl pathway, in which CO2 is fixed intoacetyl-CoA. Thus, the metabolic reconstruction based on the draft genome assembly provides afoundation for the functional genomics required to engineer C. aceticum