Transcriptional analysis of degenerate strain Clostridium beijerinckii DG-8052 reveals a pleiotropic response to CaCO3-associated recovery of solvent production

Abstract

Degenerate Clostridium beijerinckii strain (DG-8052) can be partially recovered by supplementing CaCO3 to fermentation media. Genome resequencing of DG-8052 showed no general regulator mutated. This study focused on transcriptional analysis of DG-8052 and its response to CaCO3 treatment via microarray. The expressions of 5168 genes capturing 98.6% of C. beijerinckii NCIMB 8052 genome were examed. The results revealed that with addition of CaCO3 565 and 916 genes were significantly up-regulated, and 704 and 1044 genes significantly down-regulated at acidogenic and solventogenic phase of DG-8052, respectively. These genes are primarily responsible for glycolysis to solvent/acid production (poR, pfo), solventogensis (buk, ctf, aldh, adh, bcd) and sporulation (spo0A, sigE, sigma-70, bofA), cell motility and division (ftsA, ftsK, ftsY, ftsH, ftsE, mreB, mreC, mreD, rodA), and molecular chaperones (grpE, dnaK, dnaJ, hsp20, hsp90), etc. The functions of some altered genes in DG-8052, totalling 5.7% at acidogenisis and 8.0% at sovlentogenisis, remain unknown. The response of the degenerate strain to CaCO3 was suggested significantly pleiotropic. This study reveals the multitude of regulatory function that CaCO3 has in clostridia and provides detailed insights into degeneration mechanisms at gene regulation level. It also enables us to develop effective strategies to prevent strain degeneration in future.

Sigma Factor Regulated Cellular Response in a Non-solvent Producing Clostridium beijerinckii Degenerated Strain: A Comparative Transcriptome Analysis

“…Compared with WT-8052, genome resequencing of DG-8052 (SRP082285) showed no general regulator mutated. As we reported recently ( Jiao et al, 2016 ), a total of 20 SNPs (17 non-synonymous, two premature stop, and one intergenic) and 16 InDels (10 coding and six non-coding) were found in the DG-8052 genome; among them, eight SNPs were effected by strain degeneration (Supplementary Table S2 ), and no transcription change was observed in the remaining 12 DG-8052 mutations. The transcriptional analysis suggested there’s little doubt that C. beijerinckii 8052 degeneration drastically altered gene regulation, resulting in corresponding morphological and physiological changes.…”

Genome-wide transcriptomic analysis of n-caproic acid production in Ruminococcaceae bacterium CPB6 with lactate supplementation

“…6 and Table 3. Generally, in clostridia, glucose is converted into pyruvate via glycolysis, and the produced pyruvate is further converted into acetyl-CoA for the production of acetate and butyrate at acidogenic phase [23][24][25]. In the present study, the expression of genes for glycolysis was detected in the CPB6 transcriptome, which reinforced its genome annotation [17].…”

Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives

“…Continuous bioprocessing with solventogenic clostridia is challenging due to strain degeneration and because steady-state conditions can be difficult to establish [ 16 , 18 , 131 , 141 , 319 , 343 ]. In the past, the degeneration of different Clostridium acetobutylicum strains (ATCC 824, DSM I73, NCIB 8052 and P262) in chemostat cultivations was investigated in multiple studies [ 9 , 272 , 319 ].…”

“…In C. acetobutylicum ATCC 824, degeneration is caused by the loss of the mega plasmid pSol carrying the genes for solvent formation [ 45 ]. In case of the degenerated strain C. beijerinckii DG 8052, the ability to form solvents was lost without a genetic change and could be restored by addition of CaCO 3 [ 131 ]. Even phage infection caused strain degeneration during the industrial cultivation of C. madisonii [ 132 ].…”

“…Naturally, studies aimed to understand phenomena that impair the industrial application and continuous cultivation of solventogenic and acetogenic clostridia. Regarding solventogenic clostridia, such phenomena include strain degeneration [ 131 ], solvent tolerance [ 110 ] and the response to inhibitors found in hydrolyzed lignocellulose [ 160 , 176 , 337 ]. A review about systems biology studies of C. acetobutylicum has been published recently and is highly recommended to the reader [ 333 ].…”