Exonuclease characteristics, structure and functions

The exonucleases They are a type of nucleases that digest nucleic acids at one of their free ends - either the 3 'or the 5'. The result is a progressive digestion of the genetic material, releasing the nucleotides one by one. The counterpart to these enzymes are endonucleases, which hydrolyze nucleic acids in internal sections of the chain..

These enzymes work by hydrolysis of the phosphodiester bonds of the nucleotide chain. They participate in the maintenance of the stability of the genome and in various aspects of cellular metabolism.

Specifically, both in prokaryotic and eukaryotic lineages we find different types of exonucleases that participate in DNA replication and repair and in RNA maturation and degradation..

Article index

• 1 Features
• 2 Functions
  • 2.1 Exonuclease activity in bacteria
  • 2.2 Exonuclease activity in eukaryotes
  • 2.3 Degradation
• 3 Examples
• 4 Applications
• 5 Structure
• 6 References

Characteristics

Exonucleases are a type of nucleases that hydrolyze the phosphodiester bonds of nucleic acid chains progressively at one of their ends, either 3 'or 5'.

A phosphodiester bond is formed by the covalent bond between a hydroxyl group located at the 3 'carbon and a phosphate group located at the 5' carbon. The union between both chemical groups results in a double bond of the ester type. The function of exonucleases - and nucleases in general - is to break these chemical bonds.

There is a great variety of exonucleases. These enzymes can use DNA or RNA as a substrate, depending on the type of nuclease. In the same way, the molecule can be in single or double band.

Features

One of the critical aspects for maintaining the life of an organism in optimal conditions is the stability of the genome. Fortunately, the genetic material has a series of very effective mechanisms that allow its repair, in case of being affected..

These mechanisms require the controlled breaking of phosphodiester bonds, and, as mentioned, nucleases are the enzymes that fulfill this vital function..

Polymerases are enzymes present in both eukaryotes and prokaryotes that participate in the synthesis of nucleic acids. In bacteria, three types have been characterized and in eukaryotes five. In these enzymes, exonuclease activity is necessary to fulfill their functions. Next we will see how they do it.

Exonuclease activity in bacteria

In bacteria, all three polymerases have exonuclease activity. Polymerase I has activity in two directions: 5'-3 'and 3'-5', while II and III only show activity in the 3'-5 'direction.

The 5'-3 'activity allows the enzyme to remove the first of RNA, added by an enzyme called primase. Subsequently, the gap created will be filled with newly synthesized nucleotides..

The first It is a molecule made up of a few nucleotides that allows DNA polymerase activity to begin. So it will always be present at the replication event.

In case the DNA polymerase adds a nucleotide that does not correspond, it can correct it thanks to the activity of the exonuclease.

Exonuclease activity in eukaryotes

The five polymerases in these organisms are denoted using Greek letters. Only gamma, delta and epsilon show exonuclease activity, all in the 3'-5 'direction.

Gamma DNA polymerase is related to the replication of mitochondrial DNA, while the remaining two participate in the replication of the genetic material located in the nucleus and in its repair..

Degradation

Exonucleases are key enzymes in eliminating certain nucleic acid molecules that are no longer needed by the body..

In some cases, the cell must prevent the action of these enzymes from affecting the nucleic acids that must be conserved.

For example, a "cap" is added to the messenger RNA. This consists of the methylation of a terminal guanine and two ribose units. The function of the cap is believed to be the protection of DNA against the action of 5 'exonuclease.

Examples

One of the essential exonucleases for the maintenance of genetic stability is human exonuclease I, abbreviated as hExo1. This enzyme is found in different DNA repair pathways. It is relevant for the maintenance of telomeres.

This exonuclease allows the repair of the gaps in both chains, which, if not repaired, can lead to chromosomal rearrangements or deletions that result in a patient with cancer or premature aging.

Applications

Some exonucleases are in commercial use. For example exonuclease I that allows the degradation of primers in single-band (cannot degrade double-band substrates), exonuclease III is used for site-directed mutagenesis and lambda exonuclease can be used for the removal of a nucleotide located at the 5 'end of a double-band DNA.

Historically, exonucleases were determining elements in the process of elucidating the nature of the bonds that held together the building blocks of nucleic acids: nucleotides..

Furthermore, in some old sequencing techniques the action of exonucleases was coupled with the use of mass spectrometry..

As the product of the exonuclease is the progressive release of oligonucleotides, it represented a convenient tool for sequence analysis. Although the method did not work very well, it was useful for short sequences.

In this way, exonucleases are considered as very flexible and invaluable tools in the laboratory for the manipulation of nucleic acids..

Structure

Exonucleases have an extremely varied structure, so it is not possible to generalize their characteristics. The same can be extrapolated for the different types of nucleases that we find in living organisms. Therefore, we will describe the structure of a specific enzyme.

Exonuclease I (ExoI) taken from the model organism Escherichia coli It is a monomeric enzyme, involved in the recombination and repair of genetic material. Thanks to the application of crystallographic techniques, its structure was illustrated.

In addition to the exonuclease domain of the polymerase, the enzyme includes other domains called SH3. The three regions combine to form a kind of C, although some segments make the enzyme look similar to one O.

References

1. Breyer, W. A., & Matthews, B. W. (2000). Structure of Escherichia coli exonuclease I suggests how processivity is achieved. Nature Structural & Molecular Biology, 7(12), 1125.
2. Brown, T. (2011). Introduction to genetics: A molecular approach. Garland science.
3. Davidson, J., & Adams, R. L. P. (1980). Biochemistry of Davidson Nucleic Acids. I reversed.
4. Hsiao, Y. Y., Duh, Y., Chen, Y. P., Wang, Y. T., & Yuan, H. S. (2012). How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes. Nucleic acids research, 40(16), 8144-8154.
5. Khare, V., & Eckert, K. A. (2002). The proofreading 3 '→ 5' exonuclease activity of DNA polymerases: a kinetic barrier to translesion DNA synthesis. Mutation Research / Fundamental and Molecular Mechanisms of Mutagenesis, 510(1-2), 45-54.
6. Kolodner, R. D., & Marsischky, G. T. (1999). Eukaryotic DNA mismatch repair. Current opinion in genetics & development, 9(1), 89-96.
7. Nishino, T., & Morikawa, K. (2002). Structure and function of nucleases in DNA repair: shape, grip, and blade of the DNA scissors. Oncogene, twenty-one(58), 9022.
8. Orans, J., McSweeney, E. A., Iyer, R. R., Hast, M. A., Hellinga, H. W., Modrich, P., & Beese, L. S. (2011). Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family. Cell, 145(2), 212-223.
9. Yang, W. (2011). Nucleases: diversity of structure, function, and mechanism. Quarterly reviews of Biophysics, 44(1), 1-93.