Structure-function studies of a plant tyrosyl-DNA phosphodiesterase provide novel insights into DNA repair mechanisms of Arabidopsis thaliana.

TDP1 (tyrosyl-DNA phosphodiesterase 1), a member of the PLD (phospholipase D) superfamily, catalyses the hydrolysis of a phosphodiester bond between a tyrosine residue and the 3'-phosphate of DNA. We have previously identified and characterized the AtTDP gene in Arabidopsis thaliana, an orthologue of yeast and human TDP1 genes. Sequence alignment of TDP1 orthologues revealed that AtTDP has both a conserved C-terminal TDP domain and, uniquely, an N-terminal SMAD/FHA (forkhead-associated) domain. To help understand the function of this novel enzyme, we analysed the substrate saturation kinetics of full-length AtTDP compared with a truncated AtTDP mutant lacking the N-terminal FHA domain. The recombinant AtTDP protein hydrolysed a single-stranded DNA substrate with Km and kcat/Km values of 703±137 nM and (1.5±0.04)×10(9) M(-1)·min(-1) respectively. The AtTDP-(Δ1-122) protein (TDP domain) showed kinetic parameters that were equivalent to those of the full-length AtTDP protein. A basic amino acid sequence (RKKVKP) within the AtTDP-(Δ123-605) protein (FHA domain) was necessary for nuclear localization of AtTDP. Analysis of active-site mutations showed that a histidine and a lysine residue in each of the HKD motifs were critical for enzyme activity. Vanadates, inhibitors of phosphoryl transfer reactions, inhibited AtTDP enzymatic activity and retarded the growth of an Arabidopsis tdp mutant. Finally, we showed that expression of the AtTDP gene could complement a yeast tdp1Δrad1Δ mutant, rescuing the growth inhibitory effects of vanadate analogues and CPT (camptothecin). Taken together, the results of the present study demonstrate the structure-based function of AtTDP through which AtTDP can repair DNA strand breaks in plants.

Identification of tyrosyl-DNA phosphodiesterase as a novel DNA damage repair enzyme in Arabidopsis.

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a key enzyme that hydrolyzes the phosphodiester bond between tyrosine of topoisomerase and 3'-phosphate of DNA and repairs topoisomerase-mediated DNA damage during chromosome metabolism. However, functional Tdp1 has only been described in yeast and human to date. In human, mutations of the Tdp1 gene are involved in the disease spinocerebellar ataxia with axonal neuropathy. In plants, we have identified the functional nuclear protein AtTDP, homolog to human Tdp1 from Arabidopsis (Arabidopsis thaliana). The recombinant AtTDP protein certainly hydrolyzes the 3'-phosphotyrosyl DNA substrates related to repairing in vivo topoisomerase I-DNA-induced damage. The loss-of-function AtTDP mutation displays developmental defects and dwarf phenotype in Arabidopsis. This phenotype is substantially caused by decreased cell numbers without any change of individual cell sizes. The tdp plants exhibit hypersensitivities to camptothecin, a potent topoisomerase I inhibitor, and show rigorous cell death in cotyledons and rosette leaves, suggesting the failure of DNA damage repair in tdp mutants. These results indicate that AtTDP plays a clear role in the repair of topoisomerase I-DNA complexes in Arabidopsis.

Quantitative data from six years (2013-2018) of light trap sampling of macromoths (Lepidoptera) in Mt. Hallasan National Park, South Korea.

BACKGROUND: This paper presents the results of long-term monitoring of macromoth communities in Mt. Hallasan National Park, South Korea. This mountain shows an altitudinal gradient of vegetation from evergreen deciduous to boreal trees, harbouring more than 550 species of vascular plants. The goal of this project was to investigate the changes in moth assemblages along the altitudinal gradient in this mountain ecosystem. We monitored macromoth communities at 11 sites in Mt. Hallasan National Park from 2013 to 2018, during which time moths were collected once a month from May to October, using an ultraviolet bucket trap. The generated dataset, which represented 587 species and 13,249 individuals from 14 families, can be adopted to establish a baseline for development of a network-orientated database to assess temporal and spatial changes of moths in temperate and tropical forests. NEW INFORMATION: This is the first long-term sampling-event dataset on macromoth assemblages in changing vegetation from evergreen deciduous to boreal tree zones, conducted in Mt. Hallasan National Park, the national park at the highest elevation and located on the largest volcanic island in South Korea. The aim of this study was to provide a description and a link to published data in the format of a peer-reviewed journal and to provide recognition of the effort in a scholarly article (based on data paper definition published at https://www.gbif.org/en/data-papers).