Reactive oxygen species (ROS) are a group of short-lived, highly reactive, oxygen-containing molecules that can induce DNA damage and affect the DNA damage response (DDR). There is unequivocal pre-clinical and clinical evidence that ROS influence the genotoxic stress caused by chemotherapeutics agents and ionizing radiation. Recent studies have provided mechanistic insight into how ROS can also influence the cellular response to DNA damage caused by genotoxic therapy, especially in the context of Double Strand Breaks (DSBs). This has led to the clinical evaluation of agents modulating ROS in combination with genotoxic therapy for cancer, with mixed success so far. These studies point to context dependent outcomes with ROS modulator combinations with Chemotherapy and radiotherapy, indicating a need for additional pre-clinical research in the field. In this review, we discuss the current knowledge on the effect of ROS in the DNA damage response, and its clinical relevance.

ROS and the DNA damage response in cancer.

R-Loops as Cellular Regulators and Genomic Threats.

К пробиотикам относят «живые микроорганизмы, которые при введении в адекватных количествах оказывают положительное влияние на здоровье хозяина» [1]. В то время как применению некоторых из них (Lactobacillus, Bifidobacterium) было уделено много внимания, другие были изучены позже, и их важное лечебное действие становится ясным только сейчас. Одним из пробиотиков является грамположительная палочка Bacillus subtilis (B.subtilis). Большинство бактерий рода Bacillus (включая B.subtilis) не опасны для человека и широко распространены в окружающей среде. Их обнаруживают в почве, воде, воздухе и пищевых продуктах (пшеница, другие зерновые культуры, хлебобулочные изделия, соевые продукты, цельное мясо, сырое и пастеризованное молоко). Как следствие, они постоянно попадают в желудочно-кишечный тракт и дыхательные пути, засевая эти отделы. Количество бацилл в кишечнике может достигать 10 КОЕ/г, что сравнимо с аналогичным показателем у Lactobacillus. В связи с этим ряд исследователей рассматривают бактерии рода Bacillus как один из доминирующих компонентов нормальной микрофлоры кишечника [2]. В то же время лечебное введение B.subtilis позволяет использовать данный микроорганизм в качестве пробиотика по четырем основным направлениям: 1) для защиты от кишечных патогенов; 2) от дыхательных патогенов; 3) для устранения дисбактериоза при антибиотикотерапии; 4) для усиления переваривания и продвижения пищи. Упрощенная схема пробиотической активности B.subtilis при патологии желудочнокишечного тракта представлена на рис. 1. Таким образом, в научных работах последних десятилетий были сделаны значительные продвижения в выяснении спектра пробиотической активности B.subtilis, что делает данную бактерию одним из наиболее привлекательных пробиотиков для медицинского применения. В настоящем обзоре мы представляем данные соответствующих экспериментальных и клинических исследований, позволяющих составить впечатление о терапевтическом потенциале B.subtilis. УДК 615.331:579.852.1

Bacillus subtilis. (Book Reviews: The Molecular Biology of the Bacilli; Molecular Cloning and Gene Regulation in Bacilli)

RNA splicing, the enzymatic process of removing segments of premature RNA to produce mature RNA, is a key mediator of proteome diversity and regulator of gene expression. Increased systematic sequencing of the genome and transcriptome of cancers has identified a variety of means by which RNA splicing is altered in cancer relative to normal cells. These findings, in combination with the discovery of recurrent change-of-function mutations in splicing factors in a variety of cancers, suggest that alterations in splicing are drivers of tumorigenesis. Greater characterization of altered splicing in cancer parallels increasing efforts to pharmacologically perturb splicing and early-phase clinical development of small molecules that disrupt splicing in patients with cancer. Here we review recent studies of global changes in splicing in cancer, splicing regulation of mitogenic pathways critical in cancer transformation, and efforts to therapeutically target splicing in cancer.

https://www.annualreviews.org/doi/pdf/10.1146/annurev-cancerbio-030617-050407

Aberrant RNA Splicing in Cancer

R-loops are three-stranded structures that harbour an RNA-DNA hybrid and frequently form during transcription. R-loop misregulation is associated with DNA damage, transcription elongation defects, hyper-recombination and genome instability. In contrast to such 'unscheduled' R-loops, evidence is mounting that cells harness the presence of RNA-DNA hybrids in scheduled, 'regulatory' R-loops to promote DNA transactions, including transcription termination and other steps of gene regulation, telomere stability and DNA repair. R-loops formed by cellular RNAs can regulate histone post-translational modification and may be recognized by dedicated reader proteins. The two-faced nature of R-loops implies that their formation, location and timely removal must be tightly regulated. In this Perspective, we discuss the cellular processes that regulatory R-loops modulate, the regulation of R-loops and the potential differences that may exist between regulatory R-loops and unscheduled R-loops.

Regulatory R-loops as facilitators of gene expression and genome stability.

Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1

Alternative Lengthening of Telomeres through Two Distinct Break-Induced Replication Pathways.

In all living organisms, the response to double-strand breaks (DSBs) is critical for the maintenance of chromosome integrity. Homologous recombination (HR), which utilizes a homologous template to prime DNA synthesis and to restore genetic information lost at the DNA break site, is a complex multistep response. In Bacillus subtilis, this response can be subdivided into five general acts: (1) recognition of the break site(s) and formation of a repair center (RC), which enables cells to commit to HR; (2) end-processing of the broken end(s) by different avenues to generate a 3'-tailed duplex and RecN-mediated DSB 'coordination'; (3) loading of RecA onto single-strand DNA at the RecN-induced RC and concomitant DNA strand exchange; (4) branch migration and resolution, or dissolution, of the recombination intermediates, and replication restart, followed by (5) disassembly of the recombination apparatus formed at the dynamic RC and segregation of sister chromosomes. When HR is impaired or an intact homologous template is not available, error-prone nonhomologous end-joining directly rejoins the two broken ends by ligation. In this review, we examine the functions that are known to contribute to DNA DSB repair in B. subtilis, and compare their properties with those of other bacterial phyla.

Double-strand break repair in bacteria: a view from Bacillus subtilis.

Actively transcribed regions of the genome are protected by transcription-coupled DNA repair mechanisms, including transcription-coupled homologous recombination (TC-HR). Here we used reactive oxygen species (ROS) to induce and characterize TC-HR at a transcribed locus in human cells. As canonical HR, TC-HR requires RAD51. However, the localization of RAD51 to damage sites during TC-HR does not require BRCA1 and BRCA2, but relies on RAD52 and Cockayne Syndrome Protein B (CSB). During TC-HR, RAD52 is recruited by CSB through an acidic domain. CSB in turn is recruited by R loops, which are strongly induced by ROS in transcribed regions. Notably, CSB displays a strong affinity for DNA:RNA hybrids in vitro, suggesting that it is a sensor of ROS-induced R loops. Thus, TC-HR is triggered by R loops, initiated by CSB, and carried out by the CSB-RAD52-RAD51 axis, establishing a BRCA1/2-independent alternative HR pathway protecting the transcribed genome.

/pdf/ros-induced-r-loops-trigger-a-transcription-coupled-but-4x4gs7a2gx.pdf

ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB

We have investigated the structural, biochemical and cellular roles of the two single-stranded (ss) DNA-binding proteins from Bacillus subtilis, SsbA and SsbB. During transformation, SsbB localizes at the DNA entry pole where it binds and protects internalized ssDNA. The 2.8-A resolution structure of SsbB bound to ssDNA reveals a similar overall protein architecture and ssDNA-binding surface to that of Escherichia coli SSB. SsbA, which binds ssDNA with higher affinity than SsbB, co-assembles onto SsbB-coated ssDNA and the two proteins inhibit ssDNA binding by the recombinase RecA. During chromosomal transformation, the RecA mediators RecO and DprA provide RecA access to ssDNA. Interestingly, RecO interaction with ssDNA-bound SsbA helps to dislodge both SsbA and SsbB from the DNA more efficiently than if the DNA is coated only with SsbA. Once RecA is nucleated onto the ssDNA, RecA filament elongation displaces SsbA and SsbB and enables RecA-mediated DNA strand exchange. During plasmid transformation, RecO localizes to the entry pole and catalyzes annealing of SsbA- or SsbA/SsbB-coated complementary ssDNAs to form duplex DNA with ssDNA tails. Our results provide a mechanistic framework for rationalizing the coordinated events modulated by SsbA, SsbB and RecO that are crucial for RecA-dependent chromosomal transformation and RecA-independent plasmid transformation.

/pdf/genetic-recombination-in-bacillus-subtilis-a-division-of-1qm1iaxl3z.pdf

Tribhuwan Yadav

Papers

Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1

Alternative Lengthening of Telomeres through Two Distinct Break-Induced Replication Pathways.

Double-strand break repair in bacteria: a view from Bacillus subtilis.

ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB

Genetic recombination in Bacillus subtilis : a division of labor between two single-strand DNA-binding proteins