Essential role for an isoform of Escherichia coli translation initiation factor IF2 in repair of two-ended DNA double-strand breaks

Initiation Factor ◽

Chromosomal Locus ◽

Strand Breaks ◽

Damage Repair ◽

Replication Restart

In Escherichia coli, three isoforms of the essential translation initiation factor IF2 (IF2-1, IF2-2, and IF2-3) are generated from separate in-frame initiation codons in infB. The isoforms have earlier been suggested to additionally participate in DNA damage repair and replication restart. It is also known that the proteins RecA and RecBCD are needed for repair of DNA double-strand breaks (DSBs) in E. coli. Here we show that strains lacking IF2-1 are profoundly sensitive to two-ended DSBs in DNA generated by radiomimetic agents phleomycin or bleomycin, or by endonuclease I-SceI. However, these strains remained tolerant to other DSB-generating genotoxic agents or perturbations to which recA and recBC mutants remained sensitive, such as to mitomycin C, type-2 DNA topoisomerase inhibitors, or DSB caused by palindrome cleavage behind a replication fork. Data from genome-wide copy number analyses following I-SceI cleavage at a single chromosomal locus suggested that, in a strain lacking IF2-1, the magnitude of break induced replication through replication restart mechanisms is largely preserved but the extent of DNA resection around the DSB site is reduced. We propose that in absence of IF2-1 it is the annealing of a RecA nucleoprotein filament to its homologous target that is weakened, which in turn leads to a specific failure in assembly of Ter-to-oriC directed replisomes needed for consummation of two-ended DSB repair.

Three Isoforms of the Essential Translation Initiation Factor IF2 Differentially Modulate Homologous Recombination in Escherichia coli

10.1101/2021.06.16.448654 ◽

2021 ◽

Author(s):

Jillella Mallikarjun ◽

L SaiSree ◽

P Himabindu ◽

K Anupama ◽

Manjula Reddy ◽

...

Keyword(s):

Escherichia Coli ◽

Homologous Recombination ◽

Translation Initiation ◽

Holliday Junctions ◽

Initiation Factor ◽

Synthetic Lethal ◽

Central Protein ◽

Break Site

In Escherichia coli, three isoforms of the essential translation initiation factor IF2 (IF2-1, IF2-2, and IF2-3) are generated from separate in-frame initiation codons in infB. The isoforms have earlier been suggested to act differentially in DNA replication restart. We report that in synthetic lethal situations associated with trapped Holliday junctions caused by deficiency of enzymes RuvAB or RuvC (that act in the post-synaptic step of homologous recombination [HR]), viability is restored in absence of any of the following: (i) IF2-1, (ii) RecA, which is the central protein for synapsis in HR, or (iii) proteins of the RecFORQ pre-synaptic HR pathway; conversely, loss of IF2-2 and IF2-3 exacerbated the synthetic defect. Strains lacking IF2-1 were also profoundly sensitive to two-ended DNA double-strand breaks (whose repair is mediated by RecA through the RecBCD pre-synaptic HR pathway), which was accompanied by reduction in extent of DNA loss around a break site. In HR assays, recovery of recombinants was diminished in IF2-1's absence. Our results suggest that isoforms IF2-1 and IF2-2/3 exert opposite effects at a step downstream of the two pre-synaptic pathways and of RecA nucleoprotein assembly, so as to increase and decrease, respectively, the efficiency of synapsis during HR

Escherichia coli Induces DNA Double-Strand Breaks in Eukaryotic Cells

Science ◽

10.1126/science.1127059 ◽

2006 ◽

Vol 313 (5788) ◽

pp. 848-851 ◽

Cited By ~ 487

Author(s):

J.-P. Nougayrede

Keyword(s):

Escherichia Coli ◽

Double Strand Breaks ◽

Eukaryotic Cells ◽

Strand Breaks

RecF, UvrD, RecX and RecN proteins suppress DNA degradation at DNA double-strand breaks in Escherichia coli

Biochimie ◽

10.1016/j.biochi.2018.03.005 ◽

2018 ◽

Vol 148 ◽

pp. 116-126 ◽

Cited By ~ 3

Author(s):

Isidoro Feliciello ◽

Davor Zahradka ◽

Ksenija Zahradka ◽

Siniša Ivanković ◽

Nikolina Puc ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Degradation ◽

Double Strand Breaks ◽

Strand Breaks ◽

Recn Proteins

Poly(ADP-ribose) glycohydrolase promotes formation and homology-directed repair of meiotic DNA double-strand breaks independent of its catalytic activity

10.1101/2020.03.12.988840 ◽

2020 ◽

Cited By ~ 2

Author(s):

Eva Janisiw ◽

Marilina Raices ◽

Fabiola Balmir ◽

Luis Paulin Paz ◽

Antoine Baudrimont ◽

...

Keyword(s):

Catalytic Activity ◽

Synaptonemal Complex ◽

Double Strand Breaks ◽

Post Translational Modification ◽

Dna Breaks ◽

Strand Breaks ◽

Homology Directed Repair ◽

Damage Repair ◽

Somatic Tissues

SummaryPoly(ADP-ribosyl)ation is a reversible post-translational modification synthetized by ADP-ribose transferases and removed by poly(ADP-ribose) glycohydrolase (PARG), which plays important roles in DNA damage repair. While well-studied in somatic tissues, much less is known about poly(ADP-ribosyl)ation in the germline, where DNA double-strand breaks are introduced by a regulated program and repaired by crossover recombination to establish a tether between homologous chromosomes. The interaction between the parental chromosomes is facilitated by meiotic specific adaptation of the chromosome axes and cohesins, and reinforced by the synaptonemal complex. Here, we uncover an unexpected role for PARG in promoting the induction of meiotic DNA breaks and their homologous recombination-mediated repair in Caenorhabditis elegans. PARG-1/PARG interacts with both axial and central elements of the synaptonemal complex, REC-8/Rec8 and the MRN/X complex. PARG-1 shapes the recombination landscape and reinforces the tightly regulated control of crossover numbers without requiring its catalytic activity. We unravel roles in regulating meiosis, beyond its enzymatic activity in poly(ADP-ribose) catabolism.

Dynamics of RecA-mediated repair of replication-dependent DNA breaks

The Journal of Cell Biology ◽

10.1083/jcb.201803020 ◽

2018 ◽

Vol 217 (7) ◽

pp. 2299-2307 ◽

Cited By ~ 12

Author(s):

Vincent Amarh ◽

Martin A. White ◽

David R.F. Leach

Keyword(s):

Temporal Dynamics ◽

Chromosomal Rearrangements ◽

Double Strand Breaks ◽

Dna Breaks ◽

Chromosomal Locus ◽

Chromosomal Replication ◽

Strand Breaks ◽

Sister Chromosome ◽

Temporal Efficiency

Chromosomal replication is the major source of spontaneous DNA double-strand breaks (DSBs) in living cells. Repair of these DSBs is essential for cell viability, and accuracy of repair is critical to avoid chromosomal rearrangements. Repair of replication-dependent DSBs occurs primarily by homologous recombination with a sister chromosome. However, this reaction has never been visualized at a defined chromosomal locus, so little is known about its spatial or temporal dynamics. Repair of a replication-independent DSB generated in Escherichia coli by a rare-cutting endonuclease leads to the formation of a bundle of RecA filaments. In this study, we show that in contrast, repair of a replication-dependent DSB involves a transient RecA focus localized in the central region of the cell in which the DNA is replicated. The recombining loci remain centrally located with restricted movement before segregating with little extension to the period of postreplicative sister-chromosome cohesion. The spatial and temporal efficiency of this reaction is remarkable.

Messenger RNA secondary structure and translational coupling in the Escherichia coli operon encoding translation initiation factor IF3 and the ribosomal proteins, L35 and L20

Journal of Molecular Biology ◽

10.1016/0022-2836(92)90827-7 ◽

1992 ◽

Vol 228 (2) ◽

pp. 366-386 ◽

Cited By ~ 41

Author(s):

P. Lesage ◽

C. Chiaruttini ◽

M. Graffe ◽

J. Dondon ◽

M. Milet ◽

...

Keyword(s):

Escherichia Coli ◽

Secondary Structure ◽

Translation Initiation ◽

Messenger Rna ◽

Rna Secondary Structure ◽

Ribosomal Proteins ◽

Initiation Factor ◽

Translational Coupling

Organization of the Escherichia coli chromosome around the genes for translation initiation factor IF2 (infB) and a transcription termination factor (nusA)

Journal of Molecular Biology ◽

10.1016/s0022-2836(83)80333-7 ◽

1983 ◽

Vol 167 (2) ◽

pp. 227-243 ◽

Cited By ~ 32

Author(s):

J.A. Plumbridge ◽

M. Springer ◽

M.E. Gottesman

Keyword(s):

Escherichia Coli ◽

Translation Initiation ◽

Transcription Termination ◽

Initiation Factor ◽

Termination Factor ◽

Transcription Termination Factor

Division-induced DNA double strand breaks in the chromosome terminus region of Escherichia coli lacking RecBCD DNA repair enzyme

PLoS Genetics ◽

10.1371/journal.pgen.1006895 ◽

2017 ◽

Vol 13 (10) ◽

pp. e1006895 ◽

Cited By ~ 13

Author(s):

Anurag Kumar Sinha ◽

Adeline Durand ◽

Jean-Michel Desfontaines ◽

Ielyzaveta Iurchenko ◽

Hélène Auger ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Repair ◽

Double Strand Breaks ◽

Repair Enzyme ◽

Strand Breaks

PARP-1 regulation of DNA repair factor availability.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.7_suppl.269 ◽

2019 ◽

Vol 37 (7_suppl) ◽

pp. 269-269

Author(s):

Matthew Joseph Schiewer ◽

Amy C Mandigo ◽

Nicolas Gordon ◽

Christopher McNair ◽

Costas D. Lallas ◽

...

Keyword(s):

Dna Repair ◽

Transcriptional Profiling ◽

Double Strand Breaks ◽

Strand Breaks ◽

Damage Repair ◽

Mechanistic Investigation ◽

Androgen Receptor Activity ◽

Repair Factor ◽

Parp 1

269 Background: PARP-1 holds major functions on chromatin, DNA damage repair and transcriptional regulation, both of which are relevant in the context of cancer. Previously, it was determined that PARP-1 ins involved in regulation of androgen receptor activity. Methods: Here, unbiased transcriptional profiling revealed the downstream transcriptional profile of PARP-1 enzymatic activity.Results: Further investigation of the PARP-1-regulated transcriptome and secondary strategies for assessing PARP-1 activity in patient tissues revealed that PARP-1 activity was unexpectedly enriched as a function of disease progression and was associated with poor outcome independent of DNA double-strand breaks, suggesting that enhanced PARP-1 activity may promote aggressive phenotypes. Mechanistic investigation revealed that active PARP-1 served to enhance E2F1 transcription factor activity, and specifically promoted E2F1-mediated induction of DNA repair factors involved in homologous recombination (HR). Conversely, PARP-1 inhibition reduced HR factor availability and thus acted to induce or enhance “BRCA-ness”. Conclusions: These observations bring new understanding of PARP-1 function in cancer and have significant ramifications on predicting PARP-1 inhibitor function in the clinical setting.