Detecting dipicolinic acid production and biosynthesis pathways in Bacilli and Clostridia

Abstract

Bacterial endospores are highly resistant structures and dipicolinic acid is a key component of their resilience and stability. Due to the difficulty in controlling endospore contaminants, they are of interest in clean rooms, food processing, and production industries, while benefical endospore-formers are sought for potential utility. Dipicolinic acid production has traditionally been recognized in Bacilli, Clostridia, and Paenibacilli. Here, sixty-seven strains of aerobic and anaerobic endospore-forming bacteria belonging to the genera Bacillus, Brevibacillus, Clostridium, Fontibacillus, Lysinibacillus, Paenibacillus, Rummeliibacillus, and Terribacillus were grown axenically and sporulated biomasses were assayed for dipicolinic acid production using fluorimetric detection. Strains testing positive were sequenced and the genomes analyzed to identify dipicolinic acid biosynthesis genes. The well-characterized biosynthesis pathway was conserved in 59 strains of Bacilli and Paenibacilli as well as two strains of Clostridia; six strains of Clostridia lacked homologs to genes recognized as involved in dipicolinic acid biosynthesis. Our results confirm dipicolinic acid production across different classes and families of Firmicutes. We find that members of Clostridium (cluster I) lack recognized dipicolinic acid biosynthesis genes and propose an alternate genetic pathway in these strains. Finally, we explore why the extent and mechanism of dipicolinic acid production in endospore-forming bacteria should be fully understood. We believe that understanding the mechanism by which dipicolinic acid is produced can expand the methods to utilize endospore-forming bacteria, such as novel bacterial strains added to products, for genes to create inputs for the polymer industry and to be better equipped to control contaminating spores in industrial processes.

Role of the Dihydrodipicolinate Synthase DapA1 on Iron Homeostasis During Cyanide Assimilation by the Alkaliphilic Bacterium Pseudomonas pseudoalcaligenes CECT5344

“…However, the ferrous iron needs to be trafficked through the cell as a chelate, bound to a metabolite or a protein, to minimize oxidative stress and adverse reactions (Djaman et al, 2004). In this regard, dipicolinates are dicarboxylic compounds that show an excellent ability to chelate metals, both in vivo and in vitro (Fernández-Pol, 1978;Maringanti and Imlay, 1999;Pearce et al, 2017;Gordon et al, 2019). Additionally, crosstalk between metals has been described in bacteria.…”

“…However, genome analysis reveals that P. pseudoalcaligenes CECT5344 is not able to produce siderophores, and therefore, other iron homeostasis mechanisms like the synthesis of chelators that facilitate the recycling of ferrous iron released from damaged iron-sulfur centers may be present this strain. In this regard, the DapA1 protein catalyzes the condensation of L-aspartate-4-semialdehyde with pyruvate to form 4-hydroxy-2,3,4,5-tetrahydrodipicolinate, an intermediate that is either converted into 2,3-dihydrodipicolinate in the lysine biosynthesis pathway or used to synthesize dipicolinic acid (McClintock et al, 2018;Gordon et al, 2019), a multi-functional compound that has been described as a highly effective metal chelator (Fernández-Pol, 1978;Maringanti and Imlay, 1999;Djaman et al, 2004;Pearce et al, 2017).…”

Engineering Pseudomonas putida KT2440 for Dipicolinate Production via the Entner–Doudoroff Pathway

“…DPA production has traditionally been recognized in Bacilli, Clostridia, and Paenibacilli . Natural DPA is only produced in the sporulation phase of bacillus or rare entomogenous fungi with rather low levels .…”