scholarly journals Little or No Repair of Cyclobutyl Pyrimidine Dimers Is Observed in the Organellar Genomes of the Young Arabidopsis Seedling

1996 ◽  
Vol 111 (1) ◽  
pp. 19-25 ◽  
Author(s):  
J. J. Chen ◽  
C. Z. Jiang ◽  
A. B. Britt
Keyword(s):  
Arabidopsis Seedling ◽  
Organellar Genomes ◽  
Pyrimidine Dimers

Thymine Dimerization Induced by Oxidative DNA Lesions and Epigenetic Intermediates via Triplet-Triplet Energy Transfer

2020 ◽  
Author(s):  
Mauricio Lineros-Rosa ◽  
Antonio Francés-Monerris ◽  
Antonio Monari ◽  
Miguel Angél Miranda ◽  
Virginie Lhiaubet-Vallet
Keyword(s):  
Energy Transfer ◽  
Excitation Energy ◽  
Transient Absorption ◽  
Theoretical Calculations ◽  
Dna Lesions ◽  
Transient Absorption Spectroscopy ◽  
Triplet Energy ◽  
Pyrimidine Dimers ◽  
Triplet Energy Transfer ◽  
Dna Nucleobases

Interaction of nucleic acids with light is a scientific question of paramount relevance not only in the understanding of life functioning and evolution, but also in the insurgence of diseases such as malignant skin cancer and in the development of biomarkers and novel light-assisted therapeutic tools. This work shows that the UVA portion of sunlight, not absorbed by canonical DNA nucleobases, can be absorbed by 5-formyluracil (ForU) and 5-formylcytosine (ForC), two ubiquitous oxidative lesions and epigenetic intermediates present in living beings in natural conditions. We measure the strong propensity of these molecules to populate triplet excited states able to transfer the excitation energy to thymine-thymine dyads, inducing the formation of the highly toxic and mutagenic cyclobutane pyrimidine dimers (CPDs). By using steady-state and transient absorption spectroscopy, NMR, HPLC, and theoretical calculations, we quantify the differences in the triplet-triplet energy transfer mediated by ForU and ForC, revealing that the former is much more efficient in delivering the excitation energy and producing the CPD photoproduct. Although significantly slower than ForU, ForC is also able to harm DNA nucleobases and therefore this process has to be taken into account as a viable photosensitization mechanism. The present findings evidence a rich photochemistry crucial to understand DNA photodamage and of potential use in the development of biomarkers and non-conventional photodynamic therapy agents.

Determination of Luciferase Activity in Arabidopsis seedling

BIO-PROTOCOL ◽  
2014 ◽  
Vol 4 (12) ◽  
Author(s):  
Mohan TC ◽  
Gabriel Castrillo ◽  
Antonio Leyva
Keyword(s):  
Luciferase Activity ◽  
Arabidopsis Seedling

scholarly journals Sequencing of Organellar Genomes of Nowellia curvifolia (Cephaloziaceae Jungermanniales) Revealed the Smallest Plastome with Complete Gene Set and High Intraspecific Variation Suggesting Cryptic Speciation

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 81
Author(s):  
Jakub Sawicki ◽  
Katarzyna Krawczyk ◽  
Monika Ślipiko ◽  
Monika Szczecińska
Keyword(s):  
Cryptic Speciation ◽  
Editing Event ◽  
Protein Coding ◽  
Gene Set ◽  
Protein Coding Genes ◽  
Organellar Genomes ◽  
The Family ◽  
Leafy Liverwort ◽  
Aneura Mirabilis ◽  
First Time

The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time.

scholarly journals A Role for Histone H2B During Repair of UV-Induced DNA Damage in Saccharomyces cerevisiae

Genetics ◽  
2002 ◽  
Vol 160 (4) ◽  
pp. 1375-1387
Author(s):  
Emmanuelle M D Martini ◽  
Scott Keeney ◽  
Mary Ann Osley
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Chromatin Structure ◽  
Specific Effect ◽  
Cell Killing ◽  
Cyclobutane Pyrimidine Dimers ◽  
Histone H2b ◽  
Uv Sensitivity ◽  
Pyrimidine Dimers

Abstract To investigate the role of the nucleosome during repair of DNA damage in yeast, we screened for histone H2B mutants that were sensitive to UV irradiation. We have isolated a new mutant, htb1-3, that shows preferential sensitivity to UV-C. There is no detectable difference in bulk chromatin structure or in the number of UV-induced cis-syn cyclobutane pyrimidine dimers (CPD) between HTB1 and htb1-3 strains. These results suggest a specific effect of this histone H2B mutation in UV-induced DNA repair processes rather than a global effect on chromatin structure. We analyzed the UV sensitivity of double mutants that contained the htb1-3 mutation and mutations in genes from each of the three epistasis groups of RAD genes. The htb1-3 mutation enhanced UV-induced cell killing in rad1Δ and rad52Δ mutants but not in rad6Δ or rad18Δ mutants, which are defective in postreplicational DNA repair (PRR). When combined with other mutations that affect PRR, the histone mutation increased the UV sensitivity of strains with defects in either the error-prone (rev1Δ) or error-free (rad30Δ) branches of PRR, but did not enhance the UV sensitivity of a strain with a rad5Δ mutation. When combined with a ubc13Δ mutation, which is also epistatic with rad5Δ, the htb1-3 mutation enhanced UV-induced cell killing. These results suggest that histone H2B acts in a novel RAD5-dependent branch of PRR.

scholarly journals Organellar Introns in Fungi, Algae, and Plants

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 2001
Author(s):  
Jigeesha Mukhopadhyay ◽  
Georg Hausner
Keyword(s):  
Gene Expression ◽  
Ribosomal Proteins ◽  
Heterologous Gene Expression ◽  
Group I Introns ◽  
Group Ii Introns ◽  
Homing Endonucleases ◽  
Organellar Genomes ◽  
Chloroplast Genomes ◽  
Group I ◽  
Group Ii

Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.

scholarly journals OGDA: a comprehensive organelle genome database for algae

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Tao Liu ◽  
Yutong Cui ◽  
Xuli Jia ◽  
Jing Zhang ◽  
Ruoran Li ◽  
...  
Keyword(s):  
Marine Organism ◽  
Structural Characteristics ◽  
Genome Structure ◽  
Evolutionary Relationship ◽  
Uniparental Inheritance ◽  
Genome Database ◽  
Organelle Genome ◽  
Organellar Genomes ◽  
Genome Data ◽  
Plastid Genomes

Abstract Algae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provide an organelle genome platform for algae, we have developed a user-friendly database named Organelle Genome Database for Algae (OGDA, http://ogda.ytu.edu.cn/). OGDA contains organelle genome data either retrieved from several public databases or sequenced in our laboratory (Laboratory of Genetics and Breeding of Marine Organism [MOGBL]), which are continuously updated. The first release of OGDA contains 1055 plastid genomes and 755 mitochondrial genomes. Additionally, a variety of applications have been integrated into this platform to analyze the structural characteristics, collinearity and phylogeny of organellar genomes for algae. This database represents a useful tool for users, enabling the rapid retrieval and analysis of information related to organellar genomes for biological discovery.

scholarly journals Discordant evolution of organellar genomes in peas (Pisum L.)

2021 ◽  
pp. 107136
Author(s):  
Vera S. Bogdanova ◽  
Natalia V. Shatskaya ◽  
Anatoliy V. Mglinets ◽  
Oleg E. Kosterin ◽  
Gennadiy V. Vasiliev
Keyword(s):  
Organellar Genomes
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