Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.

RAD51 is the central eukaryotic recombinase required for meiotic recombination and mitotic repair of double-strand DNA breaks (DSBs)1,2. However, the mechanism by which RAD51 functions at DSB sites in chromatin has remained elusive. Here we report the cryo-electron microscopy structures of human RAD51-nucleosome complexes, in which RAD51 forms ring and filament conformations. In the ring forms, the N-terminal lobe domains (NLDs) of RAD51 protomers are aligned on the outside of the RAD51 ring, and directly bind to the nucleosomal DNA. The nucleosomal linker DNA that contains the DSB site is recognized by the L1 and L2 loops-active centres that face the central hole of the RAD51 ring. In the filament form, the nucleosomal DNA is peeled by the RAD51 filament extension, and the NLDs of RAD51 protomers proximal to the nucleosome bind to the remaining nucleosomal DNA and histones. Mutations that affect nucleosome-binding residues of the RAD51 NLD decrease nucleosome binding, but barely affect DNA binding in vitro. Consistently, yeast Rad51 mutants with the corresponding mutations are substantially defective in DNA repair in vivo. These results reveal an unexpected function of the RAD51 NLD, and explain the mechanism by which RAD51 associates with nucleosomes, recognizes DSBs and forms the active filament in chromatin.

Replication fork blocking deficiency leads to a reduction of rDNA copy number in budding yeast.

The ribosomal RNA genes are encoded as hundreds of tandem repeats, known as the rDNA, in eukaryotes. Maintaining these copies seems to be necessary, but copy number changes in an active manner have been reported in only frogs, flies, Neurospora, and yeast. In the best-studied system, yeast, a protein (Fob1) binds to the rDNA and unidirectionally blocks the replication fork. This block stimulates rDNA double-strand breaks (DSBs) leading to recombination and copy number change. To date, copy number maintenance and concerted evolution mediated by rDNA repeat turnover were the proposed benefits of Fob1-dependent replication fork arrest. In this study, we tested whether Fob1 provides these benefits and found that rDNA copy number decreases when FOB1 is deleted, suggesting that Fob1 is important for recovery from low copy number. We suppose that replication fork stalling at rDNA is necessary for recovering from rDNA copy number loss in other species as well.

Efficacy of an oscillating positive expiratory pressure device in patients with Mycobacterium avium complex pulmonary disease.

Patients with Mycobacterium avium complex pulmonary disease (MAC-PD) often suffer from chronic symptoms such as sputum production, which reduces quality of life. Oscillatory positive expiratory pressure (OPEP) devices are used in physiotherapy to promote the clearance of respiratory secretions. We report two cases of improved lung function and improved scores on the Leicester Cough Questionnaire (LCQ) and the Breathlessness, Cough and Sputum Scale (BCSS) after the use of OPEP in patients with MAC-PD where treatment with guideline-based therapy, including amikacin liposome inhalation suspension, had proved ineffective for symptoms. Use of OPEP might maximize the efficacy of therapy and thereby improves outcomes in patients with MAC-PD. It is important to use both guideline-based therapy and OPEP, especially in patients whose health-related quality of life is affected by sputum symptoms. Further prospective studies are warranted to assess the benefit of adding OPEP to guidelines concerning therapy for patients with MAC-PD and sputum symptoms.

Acidic growth conditions stabilize the ribosomal RNA gene cluster and extend lifespan through noncoding transcription repression.

Blackcurrant (Ribes nigrum L.) is a classical fruit that has long been used to make juice, jam, and liqueur. Blackcurrant extract is known to relieve cells from DNA damage caused by hydrogen peroxide (H2 O2 ), methyl methane sulfonate (MMS), and ultraviolet (UV) radiation. We found that blackcurrant extract (BCE) stabilizes the ribosomal RNA gene cluster (rDNA), one of the most unstable regions in the genome, through repression of noncoding transcription in the intergenic spacer (IGS) which extended the lifespan in budding yeast. Reduced formation of extrachromosomal circles (ERCs) after exposure to fractionated BCE suggested that acidity of the growth medium impacted rDNA stability. Indeed, alteration of the acidity of the growth medium to pH ~4.5 by adding HCl increased rDNA stability and extended the lifespan. We identified RPD3 as the gene responsible for this change, which was mediated by the RPD3L histone deacetylase complex. In mammals, as inflammation sites in a tissue are acidic, DNA maintenance may be similarly regulated to prevent genome instability from causing cancer.

4.5SH RNA counteracts deleterious exonization of SINE B1 in mice.

4.5SH RNA is a highly abundant, small rodent-specific noncoding RNA that localizes to nuclear speckles enriched in pre-mRNA-splicing regulators. To investigate the physiological functions of 4.5SH RNA, we have created mutant mice that lack the expression of 4.5SH RNA. The mutant mice exhibited embryonic lethality, suggesting that 4.5SH RNA is an essential species-specific noncoding RNA in mice. RNA-sequencing analyses revealed that 4.5SH RNA protects the transcriptome from abnormal exonizations of the antisense insertions of the retrotransposon SINE B1 (asB1), which would otherwise introduce deleterious premature stop codons or frameshift mutations. Mechanistically, 4.5SH RNA base pairs with complementary asB1-containing exons via the target recognition region and recruits effector proteins including Hnrnpm via its 5' stem loop region. The modular organization of 4.5SH RNA allows us to engineer a programmable splicing regulator to induce the skipping of target exons of interest. Our results also suggest the general existence of splicing regulatory noncoding RNAs.

COVID-19 in Patients with Pre-Existing Interstitial Lung Disease: Potential Value of a Steroid-Based Treatment Strategy.

The prognosis of patients with coronavirus disease 2019 (COVID-19) and pre-existing interstitial lung disease (preILD) is poor, and no effective treatment strategy has been determined. The aim of this study was to assess the effectiveness of a steroid-based treatment strategy for patients with COVID-19 and preILD. We retrospectively reviewed the medical records of 610 consecutive patients with COVID-19 treated at our institution between 1 March 2020 and 30 October 2021 and identified 7 patients with preILD, all of whom were treated with corticosteroids and remdesivir. All the patients were men with a median age of 63 years. Three of four patients with severe disease required invasive positive-pressure ventilation (n = 2) or nasal high-flow therapy (n = 1). All three patients could be weaned from respiratory support; however, one died in hospital. The remaining patient with severe COVID-19 had a do-not-resuscitate order in place and died while hospitalized. All three patients with moderate COVID-19 were discharged. The 30-day mortality was 0%, and the mortality rate during the entire observation period was 28.5%. The prognosis of our patients with COVID-19 and preILD has been better than in previous reports. Our management strategy using corticosteroids may have improved these patients' prognosis.

Autoimmune Pulmonary Alveolar Proteinosis That Improved after a COVID-19 Episode.

Autoimmune pulmonary alveolar proteinosis (APAP) is caused by macrophage dysfunction owing to the presence of anti-granulocyte-macrophage colony-stimulating factor (GM-CSF) autoantibodies. A 77-year-old man with APAP was referred to our hospital for whole-lung lavage (WLL) due to oxygenation exacerbation and pulmonary shadows. The patient had had coronavirus disease 2019 (COVID-19) during the APAP evaluation before WLL. About three months after COVID-19 resolved, his oxygenation and shadow reflecting APAP had obviously improved, thus avoiding the need for WLL. We suspected that the improvement in APAP was due to various immunological reactions induced by COVID-19.

Cases of severe Mycobacterium avium lung disease occurred in a married couple caused by identical strain.

Bacteria of the Mycobacterium avium complex, which are environmental organisms found in soil and water, have been found to cause human lung diseases. Although infection is reported to occur in cohabiting patients, the incidence of infection from the single clone remains rarely documented. Herein, we report a case of M. avium lung disease caused by specimens with the same clone strains in a married couple. The wife, a 67-year-old female, had severe M. avium lung disease despite receiving multidrug chemotherapy for eleven years. The husband, a 68-year-old male, died of acute lung injury complicated by M. avium pleurisy. The result of the variable-number tandem-repeat analysis of isolates from serial sputum specimens of both patients indicated that the severe M. avium lung disease in a married couple was caused by the isolates with identical pattern. This case were considered to have acquired clarithromycin resistance during each clinical course, revealing the possibility of infection with a strain that may induce severe pulmonary condition.

Changed life course upon defective replication of ribosomal RNA genes.

Genome instability is a major cause of aging. In the budding yeast Saccharomyces cerevisiae, instability of the ribosomal RNA gene repeat (rDNA) is known to shorten replicative lifespan. In yeast, rDNA instability in an aging cell is associated with accumulation of extrachromosomal rDNA circles (ERCs) which titrate factors critical for lifespan maintenance. ERC accumulation is not detected in mammalian cells, where aging is linked to DNA damage. To distinguish effects of DNA damage from those of ERC accumulation on senescence, we re-analyzed a yeast strain with a replication initiation defect in the rDNA, which limits ERC multiplication. In aging cells of this strain (rARS-∆3) rDNA became unstable, as in wild-type cells, whereas significantly fewer ERCs accumulated. Single-cell aging analysis revealed that rARS-∆3 cells follow a linear survival curve and can have a wild-type replicative lifespan, although a fraction of the cells stopped dividing earlier than wild type. The doubling time of rARS-∆3 cells appears to increase in the final cell divisions. Our results suggest that senescence in rARS-∆3 is linked to the accumulation of DNA damage as in mammalian cells, rather than to elevated ERC level. Therefore, this strain should be a good model system to study ERC-independent aging.

Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes.

One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.

Spt4 promotes cellular senescence by activating non-coding RNA transcription in ribosomal RNA gene clusters.

Genome instability can drive aging in many organisms. The ribosomal RNA gene (rDNA) cluster is one of the most unstable regions in the genome and the stability of this region impacts replicative lifespan in budding yeast. To understand the underlying mechanism, we search for yeast mutants with stabler rDNA and longer lifespans than wild-type cells. We show that absence of a transcription elongation factor, Spt4, results in increased rDNA stability, reduced levels of non-coding RNA transcripts from the regulatory E-pro promoter in the rDNA, and extended replicative lifespan in a SIR2-dependent manner. Spt4-dependent lifespan restriction is abolished in the absence of non-coding RNA transcription at the E-pro locus. The amount of Spt4 increases and its function becomes more important as cells age. These findings suggest that Spt4 is a promising aging factor that accelerates cellular senescence through rDNA instability driven by non-coding RNA transcription.

Regulatory processes that maintain or alter ribosomal DNA stability during the repair of programmed DNA double-strand breaks.

Organisms have evolved elaborate mechanisms that maintain genome stability. Deficiencies in these mechanisms result in changes to the nucleotide sequence as well as copy number and structural variations in the genome. Genome instability has been implicated in numerous human diseases. However, genomic alterations can also be beneficial as they are an essential part of the evolutionary process. Organisms sometimes program genomic changes that drive genetic and phenotypic diversity. Therefore, genome alterations can have both positive and negative impacts on cellular growth and functions, which underscores the need to control the processes that restrict or induce such changes to the genome. The ribosomal RNA gene (rDNA) is highly abundant in eukaryotic genomes, forming a cluster where numerous rDNA copies are tandemly arrayed. Budding yeast can alter the stability of its rDNA cluster by changing the rDNA copy number within the cluster or by producing extrachromosomal rDNA circles. Here, we review the mechanisms that regulate the stability of the budding yeast rDNA cluster during repair of DNA double-strand breaks that are formed in response to programmed DNA replication fork arrest.

Mycobacterium avium Pleurisy with Bronchopleural Fistula Resulting in Rapidly Progressive Respiratory Failure Diagnosed by Transbronchial Autopsy.

Nontuberculous mycobacterial lung disease usually manifests as a chronic pulmonary infection. We herein report a fatal case of Mycobacterium avium pleurisy in a man with a refractory bronchopleural fistula that led to rapidly progressive pneumonia. A post-mortem transbronchial biopsy was performed. Histopathology revealed an acute lung injury pattern and epithelioid granulomas. Variable number tandem repeat analyses and drug susceptibility testing revealed Mycobacterium avium had acquired macrolide resistance during chemotherapy with rifampicin, ethambutol, and clarithromycin. Clinicians should be aware that Mycobacterium avium pleurisy with bronchopleural fistula can lead to fatal pneumonia, especially in patients with persistently positive cultures despite multidrug treatment.

Concomitant Recurrent Pneumothorax and Takotsubo Cardiomyopathy in a Chronic Obstructive Pulmonary Disease Patient.

Chest pain is one of the major causes of emergency room visits. Here, we present the case of a patient with chest pain who developed recurrent pneumothorax and Takotsubo cardiomyopathy (TC). An 80-year-old man, receiving supplemental oxygen for chronic obstructive pulmonary disease (COPD), presented to the emergency room with chest pain and dyspnea. On examination, his chest pain was initially assessed to be secondary to recurrent pneumothorax. However, on further evaluation, an electrocardiogram (ECG) showed ST-segment elevation along with elevated troponin levels. Ultimately, he was diagnosed with TC. ECG, if indicated by echocardiography, should be considered to detect concomitant heart disease when dealing with pneumothorax. TC should be recognized as a cardiac disease that can be caused by pneumothorax.

Effect of sputum quality on Mycobacterium avium-intracellulare complex lung disease diagnosis and treatment initiation according to disease type.

We evaluated sputum quality to establish a diagnostic and treatment strategy for Mycobacterium avium-intracellulare complex lung disease (MAC-LD). Of all 905 MAC-LD patients, 564 (62.3%) had nonpurulent sputum. Furthermore, 88 treated patients were associated with purulent sputum. Therefore, sputum quality may be useful for diagnosing MAC-LD and deciding treatment initiation.

RPS12 and UBC4 Are Related to Senescence Signal Production in the Ribosomal RNA Gene Cluster.

Genome instability causes cellular senescence in many organisms. The rRNA gene cluster (rDNA) is one of the most unstable regions in the genome and this instability might convey a signal that induces senescence in the budding yeast. The instability of rDNA mostly depends on replication fork blocking (RFB) activity which induces recombination and gene amplification. By overexpression of Fob1, responsible for the RFB activity, we found that unstable rDNA induces cell cycle arrest and restricts replicative life span. We isolated yeast mutants that grew normally while Fob1 was overexpressed, expecting that some of the mutated genes would be related to the production of a "senescence signal" that elongates cell cycle, stops cell division and finally restricts replicative life span. Our screen identified three suppressor genes, RPS12, UBC4, and CCR4. Replicative life spans of the rps12 and ubc4 mutants were longer than that of wild-type cells. An increase in the levels of extrachromosomal rDNA circles and noncoding transcripts, known to shorten replicative life span, was observed in ubc4 and rps12 respectively, while DNA double strand-breaks at the RFB that are triggers of rDNA instability were reduced in the rps12 mutant. Overall, our observations indicate that Rps12 and Ubc4 contribute to the connection between rDNA instability and replicative life span.

Pleuroparenchymal Fibroelastosis with a Predominantly Airway-centered Distribution: A Late Complication of Chemotherapy.

Airway-centered fibroelastosis is a distinct entity characterized by prominent airway-centered elastosis of the upper lobe with little or no pleural involvement. Little is known regarding its etiology; however, it was reported to have an idiopathic or asthma-associated etiology. We document, for the first time, 2 women (19 and 60 years old) who developed pleuroparenchymal fibroelastosis with a predominantly airway-centered distribution as a late complication (6 and 9 years later, respectively) of chemotherapy. The disease rapidly progressed following the manifestation of symptoms, and they subsequently died (3 and 2 years later, respectively). Therefore, post-chemotherapy long-term monitoring for this disease is warranted.

The feasibility of rifampicin Re-administration in patients with tuberculosis and Clostridioides difficile infection.

BACKGROUND: The effects of a rifampicin (RIF) on the evolution of Clostridioides difficile infection (CDI) have not previously been investigated and there is currently no consensus on whether RIF re-administration is feasible. METHODS: This retrospective observational study included consecutive tuberculosis (TB) patients diagnosed with comorbid RIF-associated CDI (RA-CDI) using strict diagnostic criteria. We investigated the association between RA-CDI and clinical outcomes, and also examined the feasibility of re-administering RIF. RESULTS: Out of the 11,230 patients were admitted to TB ward at our hospital, 156 TB patients (1.4%) were diagnosed with CDI and the overall incidence of CDI was calculated as 2.1 cases per 10,000 patient-days. Of 156 patients with CDI, 86 were diagnosed with RA-CDI, of whom 28 (32.6%) were re-administered with RIF. In the re-administration group, time to initial sputum smear conversion was significantly shorter than for patients who were not re-administered with RIF (42 days [interquartile range, IQR: 35-65] vs. 55 days [IQR: 44-70], p = 0.041). Further, RIF re-administration significantly reduced length of hospital stay (69 days [IQR: 66-82] vs. 81 days [IQR: 72-89], p = 0.014). Ten patients (35.7%) had recurrent CDI after RIF re-administration. On the other hand, 15 patients (53.6%) were able to continue their TB treatment, including the RIF regimen. CONCLUSIONS: The present study strengthens the argument for including RIF in the list of antibiotics that can induce CDI, particularly in elderly men suffering from underlying conditions. Although careful attention must be paid to the possibility of CDI recurrence, a strategy of re-administration of RIF is feasible.

Secreted acid phosphatases maintain replicative lifespan via inositol polyphosphate metabolism in budding yeast.

Secreted acid phosphatases (APases) dephosphorylate extracellular organic phosphate compounds to supply inorganic phosphate (Pi) to maintain cellular functions. Here, we show that APases are necessary to maintain a normal replicative lifespan in Saccharomyces cerevisiae. Deletion of all four APase genes shortened the lifespan in yeast strains on synthetic media (irrespective of the concentrations of Pi in the media), but it did not affect the intracellular ortho- and polyphosphate levels. Deletion of inositol-pentakisphosphate 2-kinase (IPK1), which encodes inositol-pentakisphosphate 2-kinase, restored the lifespan in APase-null mutants, and IPK1 overexpression shortened the lifespan in wild-type strains. Overexpression of inositol hexakisphosphate (IP6 ) and heptakisphosphate kinases, KCS1 and VIP1, recovered the lifespan in APase-null mutants. Thus, yeast APases modulate the replicative lifespan, probably through dephosphorylation of intracellular IP6 .