Microcompartments for B ₁₂ -Dependent 1,2-Propanediol Degradation Provide Protection from DNA and Cellular Damage by a Reactive Metabolic Intermediate

Abstract

Salmonella enterica grows on 1,2-propanediol (1,2-PD) in a coenzyme B 12 -dependent fashion. Prior studies showed that a bacterial microcompartment (MCP) is involved in this process and that an MCP-minus mutant undergoes a 20-h period of growth arrest during 1,2-PD degradation. It was previously proposed that growth arrest resulted from propionaldehyde toxicity, but no direct evidence was presented. Here, high-pressure liquid chromatography analyses of culture medium were used to show that the major products of aerobic 1,2-PD degradation are propionaldehyde, propionate, and 1-propanol. A MCP-minus mutant accumulated a level of propionaldehyde 10-fold higher than that of the wild type (1.6 mM compared to 15.7 mM), associating this compound with growth arrest. The addition of propionaldehyde to cultures of S. enterica caused growth arrest from 8 to 20 mM, but not at 4 mM, providing direct evidence for propionaldehyde toxicity. Studies also indicated that propionaldehyde was toxic due to the inhibition of respiratory processes, and the growth arrest ended when propionaldehyde was depleted primarily by conversion to propionate and 1-propanol and secondarily due to volatility. The Ames test was used to show that propionaldehyde is a mutagen and that mutation frequencies are increased in MCP-minus mutants during 1,2-PD degradation. We propose that a primary function of the MCPs involved in 1,2-PD degradation is the mitigation of toxicity and DNA damage by propionaldehyde.

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

“…(Sampson et al, 2005;Parsons et al, 2010). The presence of PduPL suggests that the putative 'Atribacteria' BMC may sequester metabolically generated, toxic aldehydes as has been proposed for catabolic BMCs in other organisms (Sampson and Bobik, 2008). However, the lack of several other key Pdu genes required for 1,2-propanediol catabolism suggest that this specific substrate is not utilized by 'Atribacteria ' (Parsons et al, 2010).…”

“…The only obvious alternative NADH sink encoded by the putative propionate-oxidizing JS1-1 and JS1-2 lineages involves acetyl-CoA reduction to acetaldehyde by BMC-associated PduPL (Figure 4a), suggesting that the BMC has a critical role in propionate catabolism. As BMC are thought to allow aldehyde concentration and storage (Sampson and Bobik, 2008), this could serve as both a NADH sink and carbon storage mechanism analogous to polyhydroxyalkanoate synthesis (Nobu et al, 2014c). The association of aldehyde-condensing DERA and sugar isomerase with the BMC locus suggests potential conversion of aldehydes to sugar.…”

Localization of Proteins to the 1,2-Propanediol Utilization Microcompartment by Non-native Signal Sequences Is Mediated by a Common Hydrophobic Motif

“…To observe Eut MCP formation, we used a fluorescent reporter of encapsulation in which EutC 1-20 is fused to GFP followed by a C-terminal ssrA tag, which mediates degradation of the fluorophore by the ClpXP protease in the cytosol (encapsulation in an MCP thus rescues the reporter from proteolysis). When expression of the encapsulation reporter construct pBADeutC [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20] -gfp-ssrA was induced by the addition of 0.02% arabinose, fluorescent puncta were not observed in a ⌬eutR::FRT strain upon the addition of 30 mM ethanolamine and 150 nM vitamin B 12 , but puncta were observed in the ⌬pocR::FRT strain under the same conditions (Figs. 2 and 3).…”

“…Bacterial microcompartments (MCPs) 2 are proteinaceous bacterial organelles that function to localize metabolic pathways to sequester toxic intermediates and contain private pools of cofactors (1,2). There is increasing interest in applying these organelles to the encapsulation of engineered enzymatic pathways to enhance pathway flux (3).…”

Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

“…This represents a potentially important ecological function as L. ivannovii and S. termitidis have been associated with the ruminant and the termite guts, respectively, and propanediol is thought to be important in these anoxic environments (Obradors et al, 1988). Propanediol is a major product of the anaerobic degradation of common plant sugars (for example, rhamnose and fucose); however, its degradation is highly toxic, and bacteria need microcompartments (carboxysomes) to enclose the highly reactive intermediates of the degradation (Sampson and Bobik, 2008). Consistent with this, several carboxysome structural proteins were also exchanged between these genomes (for example, GI numbers 347548556 and 269119660) relatively recently, as reflected by the high amino-acid identities, ranging from 57% to 85%.…”