DNA may act as nutritional source for E. coli

By Dr. Liji Thomas, MDReviewed by Aimee MolineuxJul 18 2022

The complex molecule, deoxyribonucleic acid (DNA), is ubiquitous within or outside the living cell. It has been found at concentrations of <0.1-2 mcg/g in soil, at 0.44 mcg/g in ocean water, and in many body fluids within living animals.

A recent study published in Frontiers in Microbiology, however, examines a little-researched aspect of DNA – its nutritional value to bacteria.

The findings of the experiment could help understand how DNA acts as a nutrient for gut bacteria and its impact on the host's health.

Introduction

DNA is found within the nucleus of most living cells that use this molecule as their genetic blueprint. It is also found in the circulation of most animals, in the blood, urine, breastmilk and amniotic fluid, and other body fluids. It is present in contaminated wounds.

The nucleotides found in DNA are added to infant formula, and RNA is used to enrich the feed of infant animals, while both these nucleic acids are considered functional foods.

Bacteria are also ubiquitous, feeding on organic molecules. The question sought to be answered in this study is whether DNA is a valuable nutrient for bacteria.

Contrary to the common belief that DNA comprises a smaller fraction of the cell content than either proteins or complex sugars, nucleic acids make up 7% of wet weight in the bacterium E. coli, compared to the 15% w/w of protein, making them the second most abundant molecules in the cell. DNA by itself comprises 1% of wet weight.

DNA is high in carbon, nitrogen, phosphate and in some cases, sulfur attached to the phosphate groups. In fact, its nitrogen content is higher even than some amino acids.  Therefore, bacteria such as the cholera vibrios and Shewanella, a bacterium that reduces metal, do sometimes use DNA for their supply of these elements.

Yet, apart from such studies, showing DNA to be the source of carbon, phosphorus and nitrogen for several microbes, there is no evidence that it can supply nitrogen by itself when other carbon sources are present.

The current study looked at the ability of E. coli to source nitrogen from DNA in a culture containing glucose as the carbon source (this being the best source of carbon for most organisms), and DNA as the carbon source.

Findings

DNA alone provides C/N

The researchers observed that in this setting, the growth rate of E. coli ws unexpectedly high. In this experiment, the first nitrogen source was ammonium chloride, in M9 medium (which also contains glucose, with other sources of phosphate, calcium chloride, sodium and magnesium).

Later, when salmon sperm DNA was introduced in lieu of ammonium chloride, the growth rate increased significantly, with the logarithmic phase occurring within 3 hours as compared to 12 hours with ammonium chloride. When neither of these nitrogen sources were supplied, no growth occurred. To some extent, the E. coli growth rate was concentration-dependent, with the optimal level being, apparently, 0.2–1.0 g/L of DNA.

Without glucose, however, E. coli growth was slowed, independent of the presence of DNA. Conversely, when both nitrogen sources were present, the rapid growth seen with glucose and DNA alone was not seen. The same was true with the use of nutrient broth, despite its rich content of nutrients of many types, compared to which the M9 medium used at first is nutrient poor.

In further confirmation of the extra-nutritious source represented by DNA, the presence of DNA with nutrient broth showed slower initial growth in the first 3 hours as with DNA and glucose, and no other nitrogen source. However, even without glucose, growth continues, albeit more slowly.

This result demonstrates that DNA can be used as the sole carbon and sole nitrogen source for E. coli growth.”

Despite the slowing of growth compared to the use of DNA alone as a nitrogen source, nutrient broth supplemented with DNA supported dense improved growth. In other words, DNA may be used by the bacterial cell for nutrition, and even as the main source of nitrogen, despite an enriched medium being available.

DNA vs glutamic acid

The second part of the experiment shows that bacteria can assimilate nitrogen using DNA as a source on a level comparable to that when the amino acid glutamic acid was present. Amino acids are to nitrogen as glucose is for carbon. Among them, glutamic acid is central to the metabolic pathways of all three major macronutrients, namely, glucose, protein, and nucleic acids.

When both were present, growth was optimized, but when glutamic acid alone was added, the growth rate fell below that of DNA alone. Glutamic acid is thus synergistic for E. coli growth in the presence of DNA, whereas ammonium chloride reduces growth rate when DNA is present as a nitrogen source.

An initial lag is observable, during which gene expression takes place to allow the use of DNA and/or glutamic acid for nitrogen assimilation. The growth rate speeds up between 2.5 and 3 hours, when digestive proteins are ready for DNA digestion and assimilation.

DNA ‘eating’

Moreover, the uptake of DNA into the bacterial cell and nucleus was rapid and efficient, without any sign that the molecule had to be broken down first. This may be brought about by either of two pathways. The E. coli nuclease may break down DNA to smaller nucleosides, nucleotides and oligonucleotides in the space around the cells, allowing them to be taken up by the cell.

Alternatively, the bacterium may ingest long DNA strands and then digest them. This accounts for the fast growth of E. coli in the presence of DNA.

This model is supported by the results of gel electrophoresis, and by the analysis of messenger ribonucleic acid (mRNA) transcription of two proteins that take up DNA only when long strands are present.

Accordingly, it can be concluded that E. coli can detect the exogenous DNA and be able to “eat” it as food for growth.”

When the DNA concentration is high, DNA uptake genes in E. coli are upregulated, and so are deoxyribonucleases (DNase), as indicated by the expression of the endA gene. However, the latter was mostly observable in the periplasm, rather than outside the cell.

E. coli can directly take up (‘eat’) deoxyribonucleotides (dNMPs) and deoxyribonucleosides when no other nitrogen source is available. When dNMPs are used, the growth rate is similar to when DNA is available. However, when the latter are available without phosphate, the final concentrations were reduced by 40%.

This shows that E. coli preferentially ingests dsDNA directly for periplasmic digestion and that it can also take up and use smaller fragments of DNA. This preference could be because DNA is usually present in the double-stranded form, making this a more efficient method.

The other pathway involves DNase secretion to the culture medium, diluting it. Moreover, the digested DNA will be used by other bacteria, without benefiting E. coli itself. Though this is not the preferred pathway, this does show that DNA is a useful nutrient.

However, this may not be the case with other bacteria, since E. coli is gram-negative and has periplasmic space to digest DNA. Most gram-negative bacteria may show this activity in this space.

For instance, Bifidobacterium bifida, a gram-positive bacterium, can also use DNA, with the highest final concentration being glucose added but no other nitrogen source. Yet, the very rapid initial growth was not seen, and its mode of utilization is probably different.

Conclusions

We believe that the ability of E. coli to assimilate DNA as a nutrient indicates that bacteria utilize DNA very actively as a “delicious” food ingredient of high quality.”

It is also, probably, favorable in terms of energy, and in fact, nucleic acids are likely to be a good source of nutrition for humans, too.

The authors discuss a model whereby E. coli breaks up dsDNA in the periplasm into short fragments. These move into the cytoplasm without further break up. In the cytoplasm, deoxyribonucleotides or deoxyribonucleosides are formed and used to synthesize almost all the molecules that support bacterial growth.

DNA is probably a good source of nutrition for most organisms. The authors continue to study this area and are currently examining RNA use as a nutrient by bacteria.