Mechanisms of Genome Maintenance in Plants: Playing It Safe With Breaks and Bumps

Abstract

Maintenance of genomic integrity is critical for the perpetuation of all forms of life including humans. Living organisms are constantly exposed to stress from internal metabolic processes and external environmental sources causing damage to the DNA, thereby promoting genomic instability. To counter the deleterious effects of genomic instability, organisms have evolved general and specific DNA damage repair (DDR) pathways that act either independently or mutually to repair the DNA damage. The mechanisms by which various DNA repair pathways are activated have been fairly investigated in model organisms including bacteria, fungi, and mammals; however, very little is known regarding how plants sense and repair DNA damage. Plants being sessile are innately exposed to a wide range of DNA-damaging agents both from biotic and abiotic sources such as ultraviolet rays or metabolic by-products. To escape their harmful effects, plants also harbor highly conserved DDR pathways that share several components with the DDR machinery of other organisms. Maintenance of genomic integrity is key for plant survival due to lack of reserve germline as the derivation of the new plant occurs from the meristem. Untowardly, the accumulation of mutations in the meristem will result in a wide range of genetic abnormalities in new plants affecting plant growth development and crop yield. In this review, we will discuss various DNA repair pathways in plants and describe how the deficiency of each repair pathway affects plant growth and development.

Keywords: DNA damage; DNA repair pathways; DNA replication; genome integrity; mutations.

FIGURE 1

Repair of pyrimidine dimers with photolyase. (1) A blue-light photon is absorbed by the first chromophore MTHFpolyGlu, which functions as a photoantenna. (2) The electron from the excited MTFH* is then transferred to second chromophore FADH^–. (3) The excited electron from *FADH^– is then transferred to pyrimidine dimer and converts it into pyrimidine monomers. (4–5) Electronic rearrangement restores the monomeric pyrimidines, and (6) the electron is transferred back to the flavin radical to regenerate FADH^–. Source: Figure adapted and modified from Bray and West (2005). [MTFH (N5, N10 methenyl-tetrahydro folate); FADH^– (flavin adenine dinucleotide)].

FIGURE 2

Direct reversal of N alkylated DNA bases by alkyltransferase and dioxygenase.

FIGURE 3

(A) Alkyltransferase mediated direct reversal of 6 methyl guanine to guanine. (B) Dioxygenase-mediated direct reversal of 1 methyl adenine to adenine. (C) Dioxygenase-mediated direct reversal of 3 methylcytosine to cytosine. Source: Figure adapted and modified from Yi and He (2013).

FIGURE 4

Mismatch repair. A G-T mismatch is recognized by MutS in association with MutL. MutH cleaves in the vicinity of mismatch. Exonuclease I initiates removal of DNA segment containing the incorrect base DNA. Exonuclease I completes the removal of damaged DNA. DNA polymerase III then synthesizes the new DNA and fills the gap.

FIGURE 5

Uracil bases in DNA, formed by the deamination of cytosine, are excised and replaced by cytosine by the combined action of uracil DNA glycosylase, AP endonuclease, DNA polymerase, and DNA ligase. AP, apurinic/apyrimidinic.

FIGURE 6

Base excision repair. Recognition followed by removal of damaged DNA base by DNA glycosylase resulting in the formation of AP site. An AP endonuclease nicks the phosphodiester backbone near the AP site. DNA polymerase I replaces the damaged portion with a new DNA. Finally, DNA ligase seals the nick. AP, apurinic/apyrimidinic.

FIGURE 7

Nucleotide excision repair. NER eliminates these adducts by making an incision on both sides of adduct by excinucleases followed by the removal of this incised stretch of DNA. DNA polymerase I replaces the damaged portion with a new DNA. The gap is eventually filled by DNA ligase.

FIGURE 8

Homologous recombination repair. The HRR initiates with the recruitment of MRN, and CtIP complex at the repair site activates the kinases such as ATM and ATR. The MRN complex degrades the 3’ end followed by coating with replication protein A and binding of BRCA1/2, which subsequently recruits RAD51 and initiates DNA synthesis. RAD51 displaces the bound RPA and facilitates strand invasion into the homologous template that generates the D-Loop and Holliday junction, which are eventually resolved by resolvase. MRN, Mre11-Rad50-Nbs1; CtIP, carboxy-terminal interacting protein; ATM, ataxia telangiectasia mutated; ATR, ataxia telangiectasia mutated and Rad3 related; BRCA1/2, breast cancer1/2; RAD51, radiation sensitive 51.

FIGURE 9

Non-homologous end-joining recombinational repair. KU70 and KU80 bind at the repair site followed by the processing of DNA ends by DNA-PKcs and Artemis. This is followed by the synthesis of new DNA in association with key proteins such as XLF, ligase 4, and XRCC4 at free DNA ends. KU70 and KU80, heterodimer protein with 70- and 80-kDa molecular weight; DNA-PKcs, DNA-dependent protein kinase, catalytic subunit; XRCC4, X-ray repair cross-complementing protein; XLF, XRCC4-like factor.

FIGURE 10

Genome editing. Site-directed genome editing involves the induction of site-specific double-stranded breaks in the genome followed by the recruitment of endonucleases such as ZFNs, TALENs, CRISPR-Cas9. ZFN recognizes nine nucleotide sites on binding and creates a break when two FokI monomers are in proximity to each other. TALENS also works in a similar manner. In the CRISPR system, a gRNA binds to the target site in the genomic region and forms a complex with Cas 9 nuclease to create a break. These breaks can further be repaired by NHEJ, which inserts indels in the sequence, or by HRR pathways in which homolog donor sequence could be used to modify the target sequence. ZFNs, Zinc-finger nucleases; TALENs, transcription activator–like effector nucleases CRISPR-Cas9, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9; gRNA, guide RNA; FokI, a type IIS restriction endonuclease isolated from Flavobacterium okeanokoites; NHEJ, non-homologous end-joining.