Escherichia coli Can Eat DNA as an Excellent Nitrogen Source to Grow Quickly

Abstract

Is DNA or RNA a good nutrient? Although scientists have raised this question for dozens of years, few textbooks mention the nutritional role of nucleic acids. Paradoxically, mononucleotides are widely added to infant formula milk and animal feed. Interestingly, competent bacteria can bind and ingest extracellular DNA and even integrate it into their genome. These results prompt us to clarify whether bacteria can “eat” DNA as food. We found that Escherichia coli can grow well in the medium with DNA as carbon and nitrogen sources. More interestingly, in the presence of glucose and DNA, bacteria grew more rapidly, showing that bacteria can use DNA as an excellent nitrogen source. Surprisingly, the amount of DNA in the culture media decreased but its length remained unchanged, demonstrating that E. coli ingested long DNA directly. The gene expression study shows that E. coli mainly ingests DNA before digestion and digests it in the periplasm. Bifidobacterium bifidum can also use DNA as the nitrogen source for growth, but not efficiently as E. coli. This study is of great significance to study DNA metabolism and utilization in organisms. It also lays a foundation to understand the nutritional function of DNA in intestinal flora and human health.

Effect of DNA Origami Nanostructures on Bacterial Growth

“…Previously, dsDNA acting as nutrient has been reported to improve both growth rate and bacterial density of E. coli in nutrient broth [16,28,29] . This is consistent with the data reported in the present work and suggests that the DNA origami triangle and the 24HB can be taken up by E. coli as a source of nutrients, resulting in an increase in the population.…”

“…[26,27] Previously, dsDNA acting as nutrient has been reported to improve both growth rate and bacterial density of E. coli in nutrient broth. [16,28,29] This is consistent with the data reported in the present work and suggests that the DNA origami triangle and the 24HB can be taken up by E. coli as a source of nutrients, resulting in an increase in the population. These DNA origami nanostructures have lateral dimensions of more than 100 nm and widths up to 12 nm (see Figures 1 and 2), whereas E. coli is about 2 μm long and 0.25-1.0 μm in diameter [30] with a periplasmic space of only about 15 nm.…”

“…It was shown conclusively by Huang et al that even though dsDNA is taken up predominantly by the route discussed above and processed within the periplasmic space, E. coli does nevertheless secrete nucleases that can degrade extracellular dsDNA, albeit to a much lower extent than other bacteria such as S. aureus. [28] The fact that this route is less efficient than the classical competence mechanism provides an explanation for the greatly reduced growth-promoting effect of DNA origami nanostructures compared to genomic ssDNA and dsDNA. Furthermore, several studies have shown that the efficiency and rate at which a given nuclease digests DNA origami nanostructures depends on a variety of intrinsic design parameters, such as the overall shape, the lattice type, the density and arrangement of crossovers, and the local and global mechanical properties.…”

“…It was shown conclusively by Huang et al. that even though dsDNA is taken up predominantly by the route discussed above and processed within the periplasmic space, E. coli does nevertheless secrete nucleases that can degrade extracellular dsDNA, albeit to a much lower extent than other bacteria such as S. aureus [28] . The fact that this route is less efficient than the classical competence mechanism provides an explanation for the greatly reduced growth‐promoting effect of DNA origami nanostructures compared to genomic ssDNA and dsDNA.…”

A nitrifier‐enriched microbial community contributes to the degradation of environmental DNA

“…These processes contribute to biogeochemical cycling of elements, such as carbon and nitrogen, into usable forms required by higher tropic level organisms (Maier, 2015). Microorganisms can metabolize and transform elements from a variety of sources including nucleic acids (Finkel & Kolter, 2001; Jorgensen & Jacobsen, 1996), and laboratory studies using Escherichia coli strains provide evidence that DNA can serve as the sole source of carbon, nitrogen, and/or phosphorus for some bacteria (Finkel & Kolter, 2001; Huang et al, 2022; Wang et al, 2016). This functional capability may help explain why the presence of microorganisms results in faster degradation of eDNA in experimental freshwater studies (Lance et al, 2017; Zulkefli et al, 2019).…”